SfePy Documentation

Release version: 2022.1+git.f9873484

Robert Cimrman and Contributors

May 03, 2022

 CONTENTS

1 Documentation 3
1.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2.1 Supported Platforms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2.2 Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.2.3 Installing SfePy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.2.4 Using SfePy Docker Images . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.2.5 Installing SfePy from Sources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.2.6 Testing Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.2.7 Debugging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.2.8 Using IPython . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.2.9 Notes on Multi-platform Python Distributions . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.2.10 Notes on Installing SfePy Dependencies on Various Platforms . . . . . . . . . . . . . . . . 9
1.3 Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
1.3.1 Basic SfePy Usage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
1.3.2 Basic Notions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
1.3.3 Running a Simulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
1.3.4 Example Problem Description File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
1.3.5 Interactive Example: Linear Elasticity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
1.4 User’s Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
1.4.1 Running a Simulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
1.4.2 Visualization of Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
1.4.3 Problem Description File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
1.4.4 Building Equations in SfePy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
1.4.5 Term Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
1.4.6 Solution Postprocessing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
1.4.7 Probing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
1.4.8 Postprocessing filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
1.4.9 Solvers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
1.4.10 Solving Problems in Parallel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
1.4.11 Isogeometric Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
1.5 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
1.5.1 Primer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
1.5.2 Using Salome with SfePy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
1.5.3 Preprocessing: FreeCAD/OpenSCAD + Gmsh . . . . . . . . . . . . . . . . . . . . . . . . . 85
1.5.4 Material Identification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
1.5.5 Mesh parametrization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
1.5.6 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
1.5.7 Example Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 586
1.6 Useful Code Snippets and FAQ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 586

i
 1.6.1 Miscellaneous . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 586
1.6.2 Mesh-Related Tasks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 588
1.6.3 Regions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 589
1.6.4 Material Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 590
1.7 Theoretical Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 591
1.7.1 Notes on solving PDEs by the Finite Element Method . . . . . . . . . . . . . . . . . . . . . 591
1.7.2 Implementation of Essential Boundary Conditions . . . . . . . . . . . . . . . . . . . . . . . 593
1.8 Term Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 595
1.8.1 Term Syntax . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 595
1.8.2 Term Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 596

2 Development 621
2.1 General Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 621
2.2 Possible Topics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 621
2.3 Developer Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 622
2.3.1 Retrieving the Latest Code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 622
2.3.2 SfePy Directory Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 623
2.3.3 Exploring the Code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 624
2.3.4 How to Contribute . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 624
2.3.5 How to Regenerate Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 629
2.3.6 How to Implement a New Term . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 630
2.3.7 Multi-linear Terms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 636
2.3.8 How To Make a Release . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 638
2.3.9 Module Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 640

Bibliography 1033

Python Module Index 1035

Index 1039

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• genindex
• modindex
• search

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2 CONTENTS
 CHAPTER

ONE

DOCUMENTATION

1.1 Introduction

SfePy (http://sfepy.org) is a software for solving systems of coupled partial differential equations (PDEs) by the finite
element method in 1D, 2D and 3D. It can be viewed both as black-box PDE solver, and as a Python package which can
be used for building custom applications. The word “simple” means that complex FEM problems can be coded very
easily and rapidly.
There is also a preliminary support for the isogeometric analysis, outlined in Isogeometric Analysis.
The code is written almost entirely in Python, with exception of the most time demanding routines - those are written
in C and wrapped by Cython or written directly in Cython.
SfePy is a free software released under the New BSD License. It relies on NumPy and SciPy (an excellent collection
of tools for scientific computations in Python). It is a multi-platform software that should work on Linux, Mac OS X
and Windows.
SfePy was originally developed as a flexible framework to quickly implement and test the mathematical models devel-
oped during our various research projects. It has evolved, however, to a rather full-featured (yet small) finite element
code. Many terms have been implemented that can be used to build the PDEs, see Term Overview. SfePy comes also
with a number of examples that can get you started, check Examples, Gallery and Tutorial. Some more advanced
features are discussed in Primer.

1.2 Installation

1.2.1 Supported Platforms

SfePy is known to work on various flavors of recent Linux, Intel-based MacOS and Windows. SfePy requires Python
3. The release 2019.4 was the last with Python 2.7 support.
Note: Depending on Python installation and OS used, replacing python by python3 might be required in all the
commands below (e.g. in Compilation of C Extension Modules) in order to use Python 3.

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1.2.2 Requirements

Installation prerequisites, required to build SfePy:

• a C compiler suite,
• Python 3.x,
• NumPy,
• Cython.
Python packages required for using SfePy:
• Pyparsing,
• SciPy,
• meshio for reading and writing mesh files,
• scikit-umfpack for enabling UMFPACK solver for SciPy >= 0.14.0,
• Matplotlib for various plots, GTKAgg for live plotting via log.py,
• PyTables for storing results in HDF5 files,
• SymPy for some tests and functions,
• Mayavi for postproc.py,
• igakit for script/gen_iga_patch.py - simple IGA domain generator,
• petsc4py and mpi4py for running parallel examples and using parallel solvers from PETSc,
• slepc4py for eigenvalue problem solvers from SLEPc
• pymetis for mesh partitioning using Metis,
• wxPython for better IPython integration.
• Read the Docs Sphinx theme for building documentation
• psutil for memory requirements checking
• PyVista for post-processing via resview.py
Make sure the dependencies of those packages are also installed (e.g igakit reguires FORTRAN compiler, scikit-
umfpack does not work without UMFPACK, petsc4py without PETSc etc.). All dependencies of meshio need to be
installed for full mesh file format support (when using pip: pip install meshio[all]).
SfePy should work both with bleeding edge (Git) and last released versions of NumPy and SciPy. Please, submit an
issue at Issues page in case this does not hold.
Other dependencies/suggestions:
• To be able to (re)generate the documentation Sphinx, numpydoc and LaTeX are needed (see How to Regenerate
Documentation).
• If doxygen is installed, the documentation of data structures and functions can be automatically generated by
running:

python setup.py doxygendocs

• Mesh generation tools use pexpect and gmsh or tetgen.

• IPython is recommended over the regular Python shell to fluently follow some parts of primer/tutorial (see Using
IPython).

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• MUMPS library for using MUMPS linear direct solver (real and complex arithmetic, parallel factorization)

Notes on selecting Python Distribution

SfePy should work with any recent Python 3.x (in long-term view Python 3.6+ is recommended). It is only matter of
taste to use either native OS Python installation or any other suitable distribution. We could recommend the following
distributions to use:
• Linux: OS native installation (See Notes on Installing SfePy Dependencies on Various Platforms for further
details.)
• macOS: multi-platform scientific Python distributions Anaconda (See Notes on Multi-platform Python Distri-
butions for further details.)
• Windows: use free versions of commercial multi-platform scientific Python distributions Anaconda or Enthought
Canopy (see Notes on Multi-platform Python Distributions for further details). In addition a completely free
open-source portable distribution WinPython can be used.
On any supported platform we could recommend Anaconda distribution as easy-to-use, stable and up-to-date Python
distribution with all the required dependencies (including pre-built sfepy package).
Note: all SfePy releases are regularly tested on recent Linux distributions (Debian and (K)Ubuntu) using OS Python
installation and Anaconda, macOS 10.12+ using Anaconda and Windows 8.1+ using Anaconda.

1.2.3 Installing SfePy

For Anaconda and .deb based Linux distributions (Debian, (K)Ubuntu), pre-built SfePy packages are available. You
may directly install them with:
• Anaconda distribution: install sfepy from conda-forge channel:

conda install -c conda-forge sfepy

• Debian/(K)Ubuntu: install python-sfepy:

sudo apt-get install python-sfepy

There are no further steps required to install/configure SfePy (see Notes on Multi-platform Python Distributions for
additional notes).

1.2.4 Using SfePy Docker Images

Besides the classical installation we also provide experimental Docker images with ready-to-run Anaconda and Sfepy
installation.
Before you start using SfePy images, you need to first install and configure Docker on your computer. To do this follow
official Docker documentation.
Currently available images are:
• sfepy/sfepy-notebook - basic command line interface and web browser access to Jupyter notebook/JupyterLab
interface,
• sfepy/sfepy-x11vnc-desktop - optimized Ubuntu desktop environment accessible via standard web browser or
VNC client.

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For available runtime options and further information see sfepy-docker project on Github.
As a convenience, use the following Docker compose file, which will start the SfePy image, run Jupyter Lab, and map
the contents of the local directory to the SfePy home directory within the image. Just create an empty folder and add
the following to a file named docker-compose.yml. Then, run docker-compose up in the same directory.

1.2.5 Installing SfePy from Sources

The latest stable release can be obtained from the download page. Otherwise, download the development version of
the code from SfePy git repository:

git clone git://github.com/sfepy/sfepy.git

In case you wish to use a specific release instead of the latest master version, use:

git tag -l

to see the available releases - the release tags have form release_<year>.<int>.
See the download page for additional download options.

Compilation of C Extension Modules

In the SfePy top-level directory:

1. Look at site_cfg_template.py and follow the instructions therein. Usually no changes are necessary.
2. Compile the extension modules
• for in-place use:

python setup.py build_ext --inplace

• for installation:

python setup.py build

We recommend starting with the in-place build.

Installation

SfePy can be used without any installation by running its main scripts and examples from the top-level directory of the
distribution or can be installed locally or system-wide:
• system-wide (may require root privileges):

python setup.py install

• local (requires write access to <installation prefix>):

python setup.py install --root=<installation prefix>

If all went well, proceed with Testing Installation.

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1.2.6 Testing Installation

After building and/or installing SfePy you should check if all the functions are working properly by running the auto-
mated tests.

Running Automated Test Suite

The tests can be run using:

python -c "import sfepy; sfepy.test()"

in the SfePy top-level directory in case of the in-place build and anywhere else when testing the installed package.
The testing function is based on pytest. Additional pytest options can be passed as arguments to sfepy.test(), for
example:

python -c "import sfepy; sfepy.test('-v', '--durations=0', '-m not slow')"

The tests output directory can be specified using:

python -c "import sfepy; sfepy.test('--output-dir=output-tests')"

1.2.7 Debugging

If something goes wrong, edit the site_cfg.py config file and set debug_flags = '-DDEBUG_FMF' to turn on
bound checks in the low level C functions, and recompile the code:

python setup.py clean

python setup.py build_ext --inplace

Then re-run your code and report the output to the SfePy mailing list.

1.2.8 Using IPython

We generally recommend to use (a customized) IPython interactive shell over the regular Python interpreter when
following Tutorial or Primer (or even for any regular interactive work with SfePy).
Install IPython (as a generic part of your selected distribution) and then customize it to your choice.
Depending on your IPython usage, you can customize your default profile or create a SfePy specific new one as follows:
1. Create a new SfePy profile:

ipython profile create sfepy

2. Open the ~/.ipython/profile_sfepy/ipython_config.py file in a text editor and add/edit after the c =
get_config() line:

exec_lines = [
'import numpy as nm',
'import matplotlib as mpl',
'mpl.use("WXAgg")',
#
# Add your preferred SfePy customization here...
(continues on next page)

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(continued from previous page)

#
]

c.InteractiveShellApp.exec_lines = exec_lines
c.TerminalIPythonApp.gui = 'wx'
c.TerminalInteractiveShell.colors = 'Linux' # NoColor, Linux, or LightBG

Please note, that generally it is not recommended to use star (*) imports here.
3. Run the customized IPython shell:

ipython --profile=sfepy

1.2.9 Notes on Multi-platform Python Distributions

Anaconda

We highly recommend this scientific-oriented Python distribution.

(Currently regularly tested by developers on SfePy releases with Python 3.6 64-bit on Ubuntu 16.04 LTS, Windows
8.1+ and macOS 10.12+.)
Download appropriate Anaconda Python 3.x installer package and follow install instructions. We recommend to choose
user-level install option (no admin privileges required).
Anaconda can be used for:
1. installing the latest release of SfePy directly from the conda-forge channel (see sfepy-feedstock). In this case,
follow the instructions in Installing SfePy.
Installing/upgrading SfePy from the conda-forge channel can also be achieved by adding conda-forge to your
channels with:

conda config --add channels conda-forge

Once the conda-forge channel has been enabled, SfePy can be installed with:

conda install sfepy

It is possible to list all of the versions of SfePy available on your platform with:

conda search sfepy --channel conda-forge

2. installing the SfePy dependencies only - then proceed with the Installing SfePy from Sources instructions.
In this case, install the missing/required packages using built-in conda package manager:

conda install mayavi wxpython

See conda help for further information.

Occasionally, you should check for distribution and/or installed packages updates (there is no built-in automatic update
mechanism available):

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conda update conda

conda update anaconda
conda update <package>

or try:

conda update --all

Compilation of C Extension Modules on Windows

To build SfePy extension modules, included mingw-w32/64 compiler tools should work fine. If you encounter any
problems, we recommend to install and use Microsoft Visual C++ Build Tools instead (see Anaconda FAQ).

1.2.10 Notes on Installing SfePy Dependencies on Various Platforms

The following information has been provided by users of the listed platforms and may become obsolete over time. The
generic installation instructions above should work in any case, provided the required dependencies are installed.

Gentoo

emerge -va pytables pyparsing numpy scipy matplotlib ipython mayavi

Archlinux

pacman -S python2-numpy python2-scipy python2-matplotlib ipython2 python2-sympy

yaourt -S python-pytables python2-mayavi

Instructions

Edit Makefile and change all references from python to python2. Edit scripts and change shebangs to point to python2.

Debian

(Old instructions, check also (K)Ubuntu below.)

First, you have to install the dependencies packages:

apt-get install python-tables python-pyparsing python-matplotlib python-scipy

Than SfePy can be installed with:

apt-get install python-sfepy

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(K)Ubuntu

(Tested on Kubuntu 16.04 LTS.)

First, you have to install the dependencies packages (if apt-get is not installed, install it or try apt-get install instead):

sudo apt-get install python-scipy python-matplotlib python-tables python-pyparsing␣

˓→libsuitesparse-dev python-setuptools mayavi2 python-dev ipython python-sympy cython␣

˓→python-sparse

Than SfePy can be installed with:

apt-get install python-sfepy

1.3 Tutorial

1.3.1 Basic SfePy Usage

SfePy package can be used in two basic ways as a:

1. Black-box Partial Differential Equation (PDE) solver,
2. Python package to build custom applications involving solving PDEs by the Finite Element Method (FEM).
This tutorial focuses on the first way and introduces the basic concepts and nomenclature used in the following parts
of the documentation. Check also the Primer which focuses on a particular problem in detail.
Users not familiar with the finite element method should start with the Notes on solving PDEs by the Finite Element
Method.

Invoking SfePy from the Command Line

This section introduces the basics of running SfePy from the command line.
The script simple.py is the most basic starting point in SfePy. It can be invoked in many (similar) ways which de-
pends on used OS, Python distribution and SfePy build method (see Installing SfePy for further info). All (working)
alternatives described below are interchangeable, so don’t panic and feel free to pick your preferred choice (see Basic
Usage for further explanation and more usage examples).
Depending on selected build method and OS used we recommend for:
• In-place build
Use the top-level directory of SfePy source tree as your working directory and use:

./simple.py <problem_description_file>

or (particularly on Windows based systems)

python ./simple.py <problem_description_file>

• Installed (local or system-wide) build

Use any working directory including your problem description file and use:

python <path/to/installed/simple.py> <problem_description_file>

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or simply (on Unix based systems)

<path/to/installed/simple.py> <problem_description_file>

You can also use the simple SfePy command-wrapper (ensure that SfePy installation executable directory is
included in your PATH):

sfepy-run simple <problem_description_file>

Please note, that improper mixing of in-place and install builds on single command line may result in strange runtime
errors.

Using SfePy Interactively

All functions of SfePy package can be also used interactively (see Interactive Example: Linear Elasticity for instance).
We recommend to use the IPython interactive shell for the best fluent user experience. You can customize your IPython
startup profile as described in Using IPython.

1.3.2 Basic Notions

The simplest way of using SfePy is to solve a system of PDEs defined in a problem description file, also referred to
as input file. In such a file, the problem is described using several keywords that allow one to define the equations,
variables, finite element approximations, solvers and solution domain and subdomains (see Problem Description File
for a full list of those keywords).
The syntax of the problem description file is very simple yet powerful, as the file itself is just a regular Python module
that can be normally imported – no special parsing is necessary. The keywords mentioned above are regular Python
variables (usually of the dict type) with special names.
Below we show:
• how to solve a problem given by a problem description file, and
• explain the elements of the file on several examples.
But let us begin with a slight detour. . .

Sneak Peek: What is Going on Under the Hood

1. A top-level script (usually simple.py as in this tutorial) reads in an input file.

2. Following the contents of the input file, a Problem instance is created – this is the input file coming to life. Let
us call the instance problem.
• The Problem instance sets up its domain, regions (various sub-domains), fields (the FE approximations),
the equations and the solvers. The equations determine the materials and variables in use – only those are
fully instantiated, so the input file can safely contain definitions of items that are not used actually.
3. The solution is then obtained by calling problem.solve() function, which in turn calls a top-level time-stepping
solver. In each step, problem.time_update() is called to setup boundary conditions, material parameters and
other potentially time-dependent data. The problem.save_state() is called at the end of each time step to save the
results. This holds also for stationary problems with a single “time step”.
So that is it – using the code a black-box PDE solver shields the user from having to create the Problem instance by
hand. But note that this is possible, and often necessary when the flexibility of the default solvers is not enough. At the

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end of the tutorial an example demonstrating the interactive creation of the Problem instance is shown, see Interactive
Example: Linear Elasticity.
Now let us continue with running a simulation.

1.3.3 Running a Simulation

The following commands should be run in the top-level directory of the SfePy source tree after compiling the C extension
files. See Installation for full installation instructions.
• Download sfepy/examples/diffusion/poisson_short_syntax.py. It represents our sample SfePy Prob-
lem Description File, which defines the problem to be solved in terms SfePy can understand.
• Use the downloaded file in place of <problem_description_file.py> and run simple.py as described above. The
successful execution of the command creates output file cylinder.vtk in the SfePy top-level directory.

Postprocessing the Results

• The postproc.py script can be used for quick postprocessing and visualization of the SfePy output files. It requires
mayavi installed on your system.
• As a simple example, try:

./postproc.py cylinder.vtk

• The following interactive 3D window should display:

• You can manipulate displayed image using:

– the left mouse button by itself orbits the 3D view,

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– holding shift and the left mouse button pans the view,
– holding control and the left mouse button rotates about the screen normal axis,
– the right mouse button controls the zoom.

1.3.4 Example Problem Description File

Here we discuss the contents of the sfepy/examples/diffusion/poisson_short_syntax.py problem descrip-

tion file. For additional examples, see the problem description files in the sfepy/examples/ directory of SfePy.
The problem at hand is the following:

𝑐∆𝑇 = 𝑓 in Ω, 𝑇 (𝑡) = 𝑇¯(𝑡) on Γ , (1.1)

where Γ ⊆ Ω is a subset of the domain Ω boundary. For simplicity, we set 𝑓 ≡ 0, but we still work with the material
constant 𝑐 even though it has no influence on the solution in this case. We also assume zero fluxes over 𝜕Ω ∖ Γ, i.e.
𝜕𝑛 = 0 there. The particular boundary conditions used below are 𝑇 = 2 on the left side of the cylindrical domain
𝜕𝑇

depicted in the previous section and 𝑇 = −2 on the right side.

The first step to do is to write (1.1) in weak formulation (1.15). The 𝑓 = 0, 𝑔 = 𝜕𝑇
𝜕𝑛 = 0. So only one term in weak
form (1.15) remains:
∫︁
𝑐 ∇𝑇 · ∇𝑠 = 0, ∀𝑠 ∈ 𝑉0 . (1.2)
Ω

Comparing the above integral term with the long table in Term Overview, we can see that SfePy contains this term
under name dw_laplace. We are now ready to proceed to the actual problem definition.
Open the sfepy/examples/diffusion/poisson_short_syntax.py file in your favorite text editor. Note that the
file is a regular Python source code.

from sfepy import data_dir

filename_mesh = data_dir + '/meshes/3d/cylinder.mesh'

The filename_mesh variable points to the file containing the mesh for the particular problem. SfePy supports a variety
of mesh formats.

materials = {
'coef': ({'val' : 1.0},),
}

Here we define just a constant coefficient 𝑐 of the Poisson equation, using the ‘values’ attribute. Other possible attribute
is ‘function’ for material coefficients computed/obtained at runtime.
Many finite element problems require the definition of material parameters. These can be handled in SfePy with material
variables which associate the material parameters with the corresponding region of the mesh.

regions = {
'Omega' : 'all', # or 'cells of group 6'
'Gamma_Left' : ('vertices in (x < 0.00001)', 'facet'),
'Gamma_Right' : ('vertices in (x > 0.099999)', 'facet'),
}

Regions assign names to various parts of the finite element mesh. The region names can later be referred to, for
example when specifying portions of the mesh to apply boundary conditions to. Regions can be specified in a variety
of ways, including by element or by node. Here, ‘Omega’ is the elemental domain over which the PDE is solved and
‘Gamma_Left’ and ‘Gamma_Right’ define surfaces upon which the boundary conditions will be applied.

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fields = {
'temperature': ('real', 1, 'Omega', 1)
}

A field is used mainly to define the approximation on a (sub)domain, i.e. to define the discrete spaces 𝑉ℎ , where we
seek the solution.
The Poisson equation can be used to compute e.g. a temperature distribution, so let us call our field ‘temperature’. On
the region ‘Omega’ it will be approximated using linear finite elements.
A field in a given region defines the finite element approximation. Several variables can use the same field, see below.
variables = {
't': ('unknown field', 'temperature', 0),
's': ('test field', 'temperature', 't'),
}

One field can be used to generate discrete degrees of freedom (DOFs) of several variables. Here the unknown variable
(the temperature) is called ‘t’, it’s associated DOF name is ‘t.0’ – this will be referred to in the Dirichlet boundary
section (ebc). The corresponding test variable of the weak formulation is called ‘s’. Notice that the ‘dual’ item of a
test variable must specify the unknown it corresponds to.
For each unknown (or state) variable there has to be a test (or virtual) variable defined, as usual in weak formulation of
PDEs.
ebcs = {
't1': ('Gamma_Left', {'t.0' : 2.0}),
't2', ('Gamma_Right', {'t.0' : -2.0}),
}

Essential (Dirichlet) boundary conditions can be specified as above.

Boundary conditions place restrictions on the finite element formulation and create a unique solution to the problem.
Here, we specify that a temperature of +2 is applied to the left surface of the mesh and a temperature of -2 is applied
to the right surface.
integrals = {
'i': 2,
}

Integrals specify which numerical scheme to use. Here we are using a 2nd order quadrature over a 3 dimensional space.
equations = {
'Temperature' : """dw_laplace.i.Omega( coef.val, s, t ) = 0"""
}

The equation above directly corresponds to the discrete version of (1.2), namely: Find 𝑡 ∈ 𝑉ℎ , such that
∫︁
𝑇
𝑠 ( 𝑐 𝐺𝑇 𝐺)𝑡 = 0, ∀𝑠 ∈ 𝑉ℎ0 ,
Ωℎ

where ∇𝑢 ≈ 𝐺𝑢.
The equations block is the heart of the SfePy problem description file. Here, we are specifying that the Laplacian of the
temperature (in the weak formulation) is 0, where coef.val is a material constant. We are using the ‘i’ integral defined
previously, over the domain specified by the region ‘Omega’.
The above syntax is useful for defining custom integrals with user-defined quadrature points and weights, see Integrals.
The above uniform integration can be more easily achieved by:

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equations = {
'Temperature' : """dw_laplace.2.Omega( coef.val, s, t ) = 0"""
}

The integration order is specified directly in place of the integral name. The integral definition is superfluous in this
case.

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton',
{'i_max' : 1,
'eps_a' : 1e-10,
}),
}

Here, we specify the linear and nonlinear solver kinds and options. See sfepy.solvers.ls, sfepy.solvers.nls
and sfepy.solvers.ts_solvers for available solvers and their parameters.. Even linear problems are solved by a
nonlinear solver (KISS rule) – only one iteration is needed and the final residual is obtained for free. Note that we do
not need to define a time-stepping solver here - the problem is stationary and the default 'ts.stationary' solver is
created automatically.

options = {
'nls' : 'newton',
'ls' : 'ls',
}

The solvers to use are specified in the options block. We can define multiple solvers with different convergence param-
eters.
That’s it! Now it is possible to proceed as described in Invoking SfePy from the Command Line.

1.3.5 Interactive Example: Linear Elasticity

This example shows how to use SfePy interactively, but also how to make a custom simulation script. We will use
IPython interactive shell which allows more flexible and intuitive work (but you can use standard Python shell as well).
We wish to solve the following linear elasticity problem:
𝜕𝜎𝑖𝑗 (𝑢)
− + 𝑓𝑖 = 0 in Ω, 𝑢 = 0 on Γ1 , ¯1 on Γ2 ,
𝑢1 = 𝑢 (1.3)
𝜕𝑥𝑗
𝜕𝑢
where the stress is defined as 𝜎𝑖𝑗 = 2𝜇𝑒𝑖𝑗 +𝜆𝑒𝑘𝑘 𝛿𝑖𝑗 , 𝜆, 𝜇 are the Lamé’s constants, the strain is 𝑒𝑖𝑗 (𝑢) = 21 ( 𝜕𝑥
𝜕𝑢𝑖
𝑗
+ 𝜕𝑥𝑗𝑖 )
and 𝑓 are volume forces. This can be written in general form as 𝜎𝑖𝑗 (𝑢) = 𝐷𝑖𝑗𝑘𝑙 𝑒𝑘𝑙 (𝑢), where in our case 𝐷𝑖𝑗𝑘𝑙 =
𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .
In the weak form the equation (1.3) is
∫︁ ∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑘𝑙 (𝑢)𝑒𝑖𝑗 (𝑣) + 𝑓 𝑖 𝑣𝑖 = 0 , (1.4)
Ω Ω

where 𝑣 is the test function, and both 𝑢, 𝑣 belong to a suitable function space.
Hint: Whenever you create a new object (e.g. a Mesh instance, see below), try to print it using the print statement – it
will give you insight about the object internals.
The whole example summarized in a script is available below in Complete Example as a Script.
In the SfePy top-level directory run

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ipython

In [1]: import numpy as nm

In [2]: from sfepy.discrete.fem import Mesh, FEDomain, Field

Read a finite element mesh, that defines the domain Ω.

In [3]: mesh = Mesh.from_file('meshes/2d/rectangle_tri.mesh')

Create a domain. The domain allows defining regions or subdomains.

In [4]: domain = FEDomain('domain', mesh)

Define the regions – the whole domain Ω, where the solution is sought, and Γ1 , Γ2 , where the boundary conditions will
be applied. As the domain is rectangular, we first get a bounding box to get correct bounds for selecting the boundary
edges.

In [5]: min_x, max_x = domain.get_mesh_bounding_box()[:, 0]

In [6]: eps = 1e-8 * (max_x - min_x)
In [7]: omega = domain.create_region('Omega', 'all')
In [8]: gamma1 = domain.create_region('Gamma1',
...: 'vertices in x < %.10f ' % (min_x + eps),
...: 'facet')
In [9]: gamma2 = domain.create_region('Gamma2',
...: 'vertices in x > %.10f ' % (max_x - eps),
...: 'facet')

Next we define the actual finite element approximation using the Field class.

In [10]: field = Field.from_args('fu', nm.float64, 'vector', omega,

....: approx_order=2)

Using the field fu, we can define both the unknown variable 𝑢 and the test variable 𝑣.

In [11]: from sfepy.discrete import (FieldVariable, Material, Integral, Function,

....: Equation, Equations, Problem)

In [12]: u = FieldVariable('u', 'unknown', field)

In [13]: v = FieldVariable('v', 'test', field, primary_var_name='u')

Before we can define the terms to build the equation of linear elasticity, we have to create also the materials, i.e. define
the (constitutive) parameters. The linear elastic material m will be defined using the two Lamé constants 𝜆 = 1, 𝜇 = 1.
The volume forces will be defined also as a material as a constant (column) vector [0.02, 0.01]𝑇 .

In [14]: from sfepy.mechanics.matcoefs import stiffness_from_lame

In [15]: m = Material('m', D=stiffness_from_lame(dim=2, lam=1.0, mu=1.0))

In [16]: f = Material('f', val=[[0.02], [0.01]])

One more thing needs to be defined – the numerical quadrature that will be used to integrate each term over its domain.

In [17]: integral = Integral('i', order=3)

Now we are ready to define the two terms and build the equations.

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In [18]: from sfepy.terms import Term

In [19]: t1 = Term.new('dw_lin_elastic(m.D, v, u)',

....: integral, omega, m=m, v=v, u=u)

In [20]: t2 = Term.new('dw_volume_lvf(f.val, v)',

....: integral, omega, f=f, v=v)
In [21]: eq = Equation('balance', t1 + t2)
In [22]: eqs = Equations([eq])

The equations have to be completed by boundary conditions. Let us clamp the left edge Γ1 , and shift the right edge Γ2
in the 𝑥 direction a bit, depending on the 𝑦 coordinate.

In [23]: from sfepy.discrete.conditions import Conditions, EssentialBC

In [24]: fix_u = EssentialBC('fix_u', gamma1, {'u.all' : 0.0})

In [25]: def shift_u_fun(ts, coors, bc=None, problem=None, shift=0.0):
....: val = shift * coors[:,1]**2
....: return val
In [26]: bc_fun = Function('shift_u_fun', shift_u_fun,
....: extra_args={'shift' : 0.01})
In [27]: shift_u = EssentialBC('shift_u', gamma2, {'u.0' : bc_fun})

The last thing to define before building the problem are the solvers. Here we just use a sparse direct SciPy solver and
the SfePy Newton solver with default parameters. We also wish to store the convergence statistics of the Newton solver.
As the problem is linear it should converge in one iteration.

In [28]: from sfepy.base.base import IndexedStruct

In [29]: from sfepy.solvers.ls import ScipyDirect
In [30]: from sfepy.solvers.nls import Newton

In [31]: ls = ScipyDirect({})
In [32]: nls_status = IndexedStruct()
In [33]: nls = Newton({}, lin_solver=ls, status=nls_status)

Now we are ready to create a Problem instance.

In [34]: pb = Problem('elasticity', equations=eqs)

The Problem has several handy methods for debugging. Let us try saving the regions into a VTK file.

In [35]: pb.save_regions_as_groups('regions')

And view them.

In [36]: from sfepy.postprocess.viewer import Viewer

In [37]: view = Viewer('regions.vtk')

In [38]: view()

You should see this:

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Finally, we set the boundary conditions and the top-level solver , solve the problem, save and view the results. For
stationary problems, the top-level solver needs not to be a time-stepping solver - when a nonlinear solver is set instead,
the default 'ts.stationary' time-stepping solver is created automatically.

In [39]: pb.set_bcs(ebcs=Conditions([fix_u, shift_u]))

In [40]: pb.set_solver(nls)

In [41]: status = IndexedStruct()

In [42]: variables = pb.solve(status=status)

In [43]: print('Nonlinear solver status:\n', nls_status)

In [44]: print('Stationary solver status:\n', status)

In [45]: pb.save_state('linear_elasticity.vtk', variables)

In [46]: view = Viewer('linear_elasticity.vtk')
In [47]: view()

This is the resulting image:

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The default view is not very fancy. Let us show the displacements by shifting the mesh. Close the previous window
and do:

In [48]: view(vector_mode='warp_norm', rel_scaling=2,

...: is_scalar_bar=True, is_wireframe=True)

And the result is:

See the docstring of view() and play with its options.

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Complete Example as a Script

The source code: linear_elastic_interactive.py.

This file should be run from the top-level SfePy source directory so it can find the mesh file correctly. Please note that
the provided example script may differ from above tutorial in some minor details.
1 #!/usr/bin/env python
2 from argparse import ArgumentParser
3 import numpy as nm
4

5 import sys
6 sys.path.append('.')
7

8 from sfepy.base.base import IndexedStruct

9 from sfepy.discrete import (FieldVariable, Material, Integral, Function,
10 Equation, Equations, Problem)
11 from sfepy.discrete.fem import Mesh, FEDomain, Field
12 from sfepy.terms import Term
13 from sfepy.discrete.conditions import Conditions, EssentialBC
14 from sfepy.solvers.ls import ScipyDirect
15 from sfepy.solvers.nls import Newton
16 from sfepy.postprocess.viewer import Viewer
17 from sfepy.mechanics.matcoefs import stiffness_from_lame
18

19

20 def shift_u_fun(ts, coors, bc=None, problem=None, shift=0.0):

21 """
22 Define a displacement depending on the y coordinate.
23 """
24 val = shift * coors[:,1]**2
25

26 return val
27

28 helps = {
29 'show' : 'show the results figure',
30 }
31

32 def main():
33 from sfepy import data_dir
34

35 parser = ArgumentParser()
36 parser.add_argument('--version', action='version', version='%(prog)s')
37 parser.add_argument('-s', '--show',
38 action="store_true", dest='show',
39 default=False, help=helps['show'])
40 options = parser.parse_args()
41

42 mesh = Mesh.from_file(data_dir + '/meshes/2d/rectangle_tri.mesh')

43 domain = FEDomain('domain', mesh)
44

45 min_x, max_x = domain.get_mesh_bounding_box()[:,0]

46 eps = 1e-8 * (max_x - min_x)
47 omega = domain.create_region('Omega', 'all')
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48 gamma1 = domain.create_region('Gamma1',
49 'vertices in x < %.10f ' % (min_x + eps),
50 'facet')
51 gamma2 = domain.create_region('Gamma2',
52 'vertices in x > %.10f ' % (max_x - eps),
53 'facet')
54

55 field = Field.from_args('fu', nm.float64, 'vector', omega,

56 approx_order=2)
57

58 u = FieldVariable('u', 'unknown', field)

59 v = FieldVariable('v', 'test', field, primary_var_name='u')
60

61 m = Material('m', D=stiffness_from_lame(dim=2, lam=1.0, mu=1.0))

62 f = Material('f', val=[[0.02], [0.01]])
63

64 integral = Integral('i', order=3)

65

66 t1 = Term.new('dw_lin_elastic(m.D, v, u)',
67 integral, omega, m=m, v=v, u=u)
68 t2 = Term.new('dw_volume_lvf(f.val, v)', integral, omega, f=f, v=v)
69 eq = Equation('balance', t1 + t2)
70 eqs = Equations([eq])
71

72 fix_u = EssentialBC('fix_u', gamma1, {'u.all' : 0.0})

73

74 bc_fun = Function('shift_u_fun', shift_u_fun,

75 extra_args={'shift' : 0.01})
76 shift_u = EssentialBC('shift_u', gamma2, {'u.0' : bc_fun})
77

78 ls = ScipyDirect({})
79

80 nls_status = IndexedStruct()
81 nls = Newton({}, lin_solver=ls, status=nls_status)
82

83 pb = Problem('elasticity', equations=eqs)
84 pb.save_regions_as_groups('regions')
85

86 pb.set_bcs(ebcs=Conditions([fix_u, shift_u]))
87

88 pb.set_solver(nls)
89

90 status = IndexedStruct()
91 variables = pb.solve(status=status)
92

93 print('Nonlinear solver status:\n', nls_status)

94 print('Stationary solver status:\n', status)
95

96 pb.save_state('linear_elasticity.vtk', variables)
97

98 if options.show:
99 view = Viewer('linear_elasticity.vtk')
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100 view(vector_mode='warp_norm', rel_scaling=2,
101 is_scalar_bar=True, is_wireframe=True)
102

103 if __name__ == '__main__':

104 main()

1.4 User’s Guide

This manual provides reference documentation to SfePy from a user’s perspective.

1.4.1 Running a Simulation

The following should be run in the top-level directory of the SfePy source tree after compiling the C extension files.
See Installation for full installation instructions info. The $ indicates the command prompt of your terminal.

Basic Usage

• $ ./simple.py sfepy/examples/diffusion/poisson_short_syntax.py

– Creates cylinder.vtk

• $ ./simple.py sfepy/examples/navier_stokes/stokes.py

– Creates channels_symm944t.vtk

Applications

• Phononic Materials

– $ ./phonon.py -p sfepy/examples/phononic/band_gaps.py

∗ see sfepy/examples/phononic/output/

Using Command Wrapper

All top-level SfePy scripts (applications) can be run via single sfepy-run wrapper:

$ ./sfepy-run
usage: sfepy-run [command] [options]

Simple wrapper for main SfePy commands.

positional arguments:
{extractor,phonon,postproc,probe,simple}
Available SfePy command(s).
options Additional options passed directly to selected
[command].
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optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
-w, --window use alternative (pythonw) interpreter

Notes

• This is a “new” supported method. Any SfePy script can be still run as stand-alone (as mentioned above).
• Both “inplace” and “system-wide” installations are supported.

Running Tests

The tests are based on pytest and can be run using:

python -c "import sfepy; sfepy.test()"

See Testing Installation for additional information.

Computations and Examples

The example problems in the examples directory can be computed by the script simple.py which is in the top-level
directory of the SfePy distribution. If it is run without arguments, a help message is printed:

$ ./simple.py
Usage: simple.py [options] filename_in

Solve partial differential equations given in a SfePy problem definition file.

Example problem definition files can be found in ``sfepy/examples/`` directory

of the SfePy top-level directory.

Both normal and parametric study runs are supported. A parametric study
allows repeated runs for varying some of the simulation parameters - see
``sfepy/examples/diffusion/poisson_parametric_study.py`` file.

Options:
--version show program's version number and exit
-h, --help show this help message and exit
-c "key : value, ...", --conf="key : value, ..."
override problem description file items, written as
python dictionary without surrounding braces
-O "key : value, ...", --options="key : value, ..."
override options item of problem description, written
as python dictionary without surrounding braces
-d "key : value, ...", --define="key : value, ..."
pass given arguments written as python dictionary
without surrounding braces to define() function of
problem description file
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-o filename basename of output file(s) [default: <basename of
input file>]
--format=format output file format, one of: {vtk, h5} [default: vtk]
--save-restart=mode if given, save restart files according to the given
mode.
--load-restart=filename
if given, load the given restart file
--log=file log all messages to specified file (existing file will
be overwritten!)
-q, --quiet do not print any messages to screen
--save-ebc save a zero solution with applied EBCs (Dirichlet
boundary conditions)
--save-ebc-nodes save a zero solution with added non-zeros in EBC
(Dirichlet boundary conditions) nodes - scalar
variables are shown using colors, vector variables
using arrows with non-zero components corresponding to
constrained components
--save-regions save problem regions as meshes
--save-regions-as-groups
save problem regions in a single mesh but mark them by
using different element/node group numbers
--save-field-meshes save meshes of problem fields (with extra DOF nodes)
--solve-not do not solve (use in connection with --save-*)
--list=what list data, what can be one of: {terms, solvers}

Additional (stand-alone) examples are in the sfepy/examples/ directory, e.g.:

$ python sfepy/examples/large_deformation/compare_elastic_materials.py

Parametric study example:

$ ./simple.py sfepy/examples/diffusion/poisson_parametric_study.py

Common Tasks

• Run a simulation:

./simple.py sfepy/examples/diffusion/poisson_short_syntax.py
./simple.py sfepy/examples/diffusion/poisson_short_syntax.py -o some_results # ->␣
˓→produces some_results.vtk

• Print available terms:

./simple.py --list=terms

• Run a simulation and also save Dirichlet boundary conditions:

./simple.py --save-ebc sfepy/examples/diffusion/poisson_short_syntax.py # ->␣

˓→produces an additional .vtk file with BC visualization

• Use a restart file to continue an interrupted simulation:

– Warning: This feature is preliminary and does not support terms with internal state.

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– Run:

./simple.py sfepy/examples/large_deformation/balloon.py --save-restart=-1

and break the computation after a while (hit Ctrl-C). The mode --save-restart=-1 is currently the only
supported mode. It saves a restart file for each time step, and only the last computed time step restart file is
kept.
– A file named 'unit_ball.restart-??.h5' should be created, where '??' indicates the last stored time
step. Let us assume it is 'unit_ball.restart-04.h5', i.e. the fifth step.
– Restart the simulation by:

./simple.py sfepy/examples/large_deformation/balloon.py --load-restart=unit_

˓→ball.restart-04.h5

The simulation should continue from the next time step. Verify that by running:

./simple.py sfepy/examples/large_deformation/balloon.py

and compare the residuals printed in the corresponding time steps.

1.4.2 Visualization of Results

resview.py – PyVista

Quick visualisation of the SfePy results can be done by resview.py script, which uses PyVista visualisation toolkit
(need to be installed).
The help message of the script is:

usage: resview.py [-h] [-f field_spec [field_spec ...]]

[--fields-map map [map ...]] [-s step] [-l] [-e] [-w field]
[--factor factor] [--opacity opacity] [--color-map cmap]
[--axes-options options [options ...]] [--no-axes]
[--position-vector position_vector] [--no-labels]
[--label-position position] [--no-scalar-bars]
[--scalar-bar-size size] [--scalar-bar-position position]
[-v position] [-a output_file] [-r rate] [-o output_file]
[--off-screen] [-2]
filenames [filenames ...]

This is a script for quick VTK-based visualizations of finite element

computations results.

Examples
--------
The examples assume that
``python -c "import sfepy; sfepy.test('--output-dir=output-tests')"``
has been run successfully and the resulting data files are present.

- View data in output-tests/test_navier_stokes.vtk.

$ python resview.py output-tests/navier_stokes-navier_stokes.vtk

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- Customize the above output:

plot0: field "p", switch on edges,
plot1: field "u", surface with opacity 0.4, glyphs scaled by factor 2e-2.

$ python resview.py output-tests/navier_stokes-navier_stokes.vtk -f p:e:p0 u:o.4:p1␣

˓→u:g:f2e-2:p1

- As above, but glyphs are scaled by the factor determined automatically as

20% of the minimum bounding box size.

$ python resview.py output-tests/navier_stokes-navier_stokes.vtk -f p:e:p0 u:o.4:p1␣

˓→u:g:f10%:p1

- View data and take a screenshot.

$ python resview.py output-tests/diffusion-poisson.vtk -o image.png

- Take a screenshot without a window popping up.

$ python resview.py output-tests/diffusion-poisson.vtk -o image.png --off-screen

- Create animation from output-tests/diffusion-time_poisson.*.vtk.

$ python resview.py output-tests/diffusion-time_poisson.*.vtk -a mov.mp4

- Create animation from output-tests/test_hyperelastic.*.vtk,

set frame rate to 3, plot displacements and mooney_rivlin_stress.

$ python resview.py output-tests/test_hyperelastic_TL.*.vtk -f u:wu:e:p0 mooney_rivlin_

˓→stress:p1 -a mov.mp4 -r 3

positional arguments:
filenames

optional arguments:
-h, --help show this help message and exit
-f field_spec [field_spec ...], --fields field_spec [field_spec ...]
fields to plot, options separated by ":" are possible:
"cX" - plot only Xth field component; "e" - print
edges; "fX" - scale factor for warp/glyphs, see
--factor option; "g - glyphs (for vector fields only),
scale by factor; "tX" - plot X streamlines, gradient
employed for scalar fields; "mX" - plot cells with
mat_id=X; "oX" - set opacity to X; "pX" - plot in slot
X; "r" - recalculate cell data to point data; "sX" -
plot data in step X; "vX" - plotting style: s=surface,
w=wireframe, p=points; "wX" - warp mesh by vector
field X, scale by factor
--fields-map map [map ...]
map fields and cell groups, e.g. 1:u1,p1 2:u2,p2
-s step, --step step select data in a given time step
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-l, --outline plot mesh outline
-e, --edges plot cell edges
-w field, --warp field
warp mesh by vector field
--factor factor scaling factor for mesh warp and glyphs. Append "%" to
scale relatively to the minimum bounding box size.
--opacity opacity set opacity [default: 1.0]
--color-map cmap set color_map, e.g. hot, cool, bone, etc. [default:
viridis]
--axes-options options [options ...]
options for directional axes, e.g. xlabel="z1"
ylabel="z2", zlabel="z3"
--no-axes hide orientation axes
--position-vector position_vector
define positions of plots [default: "0, 0, 1.6"]
--no-labels hide plot labels
--label-position position
define position of plot labels [default: "-1, -1, 0,
0.2"]
--no-scalar-bars hide scalar bars
--scalar-bar-size size
define size of scalar bars [default: "0.15, 0.05"]
--scalar-bar-position position
define position of scalar bars [default: "0.8, 0.02,
0, 1.5"]
-v position, --view position
camera azimuth, elevation angles, and optionally zoom
factor [default: "225,75,0.9"]
-a output_file, --animation output_file
create animation, mp4 file type supported
-r rate, --frame-rate rate
set framerate for animation
-o output_file, --screenshot output_file
save screenshot to file
--off-screen off screen plots, e.g. when screenshotting
-2, --2d-view 2d view of XY plane

The first example in the above help:

./resview.py output-tests/test_navier_stokes.vtk

produces:

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Using -f p:e:p0 u:o.4:p1 u:g:f2e-2:p1 arguments:

./resview.py output-tests/test_navier_stokes.vtk -f p:e:p0 u:o.4:p1 u:g:f2e-2:p1

the output is split into plots plot:0 and plot:1, where these plots contain:
• plot:0: field p, mesh edges are switched on
• plot:1: magnitude of vector field u displayed as the surface with opacity set to 0.4; glyphs related to field u and
scaled by factor 2e-2

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The argument -o filename.png takes the screenshot of the produced view:

./resview.py output-tests/test_poisson.vtk -o image.png

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postproc.py – Mayavi2

The postproc.py script can be used for quick postprocessing and visualization of the SfePy results. It requires mayavi2
installed on your system.
The help message of the script is:
usage: postproc.py [-h] [--version] [--debug] [-o filename]
[--output-dir directory] [-n] [--no-offscreen]
[-a <ffmpeg-supported format>]
[--ffmpeg-options <ffmpeg options>] [--step step]
[--time time] [-w] [--all] [--only-names list of names]
[-l] [--ranges name1,min1,max1:name2,min2,max2:...]
[-r resolution] [--layout layout] [--3d]
[--view angle,angle[,distance[,focal_point]]]
[--roll angle] [--parallel-projection] [--fgcolor R,G,B]
[--bgcolor R,G,B] [--colormap colormap]
[--anti-aliasing value] [-b] [--wireframe]
[--group-names name1,...,nameN:...]
[--subdomains mat_id_name,threshold_limits,single_color]
[-d "var_name0,function_name0,par0=val0,par1=val1,...:var_name1,..."]
[--scalar-mode mode] [--vector-mode mode] [-s scale]
[--clamping] [--opacity opacity] [--rel-text-width width]
filenames [filenames ...]

This is a script for quick Mayavi-based visualizations of finite element

computations results.

Examples
--------
The examples assume that
``python -c "import sfepy; sfepy.test('--output-dir=output-tests')"``
has been run successfully and the resulting data files are present.

- view data in output-tests/navier_stokes-navier_stokes.vtk

$ python postproc.py output-tests/navier_stokes-navier_stokes.vtk

$ python postproc.py output-tests/navier_stokes-navier_stokes.vtk --3d

- save a snapshot image and exit

$ python postproc.py output-tests/diffusion-poisson.vtk -o image.png -n

- save a snapshot image without off-screen rendering and exit

$ python postproc.py output-tests/diffusion-poisson.vtk -o image.png -n --no-offscreen

- create animation (forces offscreen rendering) from

output-tests/diffusion-time_poisson.*.vtk

$ python postproc.py output-tests/diffusion-time_poisson.*.vtk -a mov

- create animation (forces offscreen rendering) from

output-tests/test_hyperelastic_TL.*.vtk
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The range specification for the displacements 'u' is required, as

output-tests/test_hyperelastic_TL.00.vtk contains only zero
displacements which leads to invisible glyph size.

$ python postproc.py output-tests/test_hyperelastic_TL.*.vtk --ranges=u,0,0.02 -a mov

- same as above, but slower frame rate

$ python postproc.py output-tests/test_hyperelastic_TL.*.vtk --ranges=u,0,0.02 -a mov -

˓→-ffmpeg-options="-framerate 2"

positional arguments:
filenames

optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
--debug automatically start debugger when an exception is
raised

Output Options:
-o filename, --output filename
view image file name [default: "view.png"]
--output-dir directory
output directory for saving view images; ignored when
-o option is given, as the directory part of the
filename is taken instead [default: "."]
-n, --no-show do not call mlab.show()
--no-offscreen force no offscreen rendering for --no-show
-a <ffmpeg-supported format>, --animation <ffmpeg-supported format>
if set to a ffmpeg-supported format (e.g. mov, avi,
mpg), ffmpeg is installed and results of multiple time
steps are given, an animation is created in the same
directory as the view images
--ffmpeg-options <ffmpeg options>
ffmpeg animation encoding options (enclose in
"")[default: "-framerate 10"]

Data Options:
--step step set the time step. Negative indices are allowed, -1
means the last step. The closest higher step is used
if the desired one is not available. Has precedence
over --time. [default: the first step]
--time time set the time. The closest higher time is used if the
desired one is not available. [default: None]
-w, --watch watch the results file for changes (single file mode
only)
--all draw all data (normally, node_groups and mat_id are
omitted)
--only-names list of names
draw only named data
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-l, --list-ranges do not plot, only list names and ranges of all data
--ranges name1,min1,max1:name2,min2,max2:...
force data ranges [default: automatic from data]

View Options:
-r resolution, --resolution resolution
image resolution in NxN format [default: shorter axis:
600; depends on layout: for rowcol it is 800x600]
--layout layout layout for multi-field plots, one of: rowcol, colrow,
row, col, row#n,col#n, where #n is the number of plots
in the specified direction [default: rowcol]
--3d 3d plot mode
--view angle,angle[,distance[,focal_point]]
camera azimuth, elevation angles, and optionally also
distance and focal point coordinates (without []) as
in `mlab.view()` [default: if --3d is True: "45,45",
else: "0,0"]
--roll angle camera roll angle [default: 0.0]
--parallel-projection
use parallel projection
--fgcolor R,G,B foreground color, that is the color of all text
annotation labels (axes, orientation axes, scalar bar
labels) [default: 0.0,0.0,0.0]
--bgcolor R,G,B background color [default: 1.0,1.0,1.0]
--colormap colormap mayavi2 colormap name [default: blue-red]
--anti-aliasing value
value of anti-aliasing [default: mayavi2 default]

Custom Plots Options:

-b, --scalar-bar show scalar bar for each data
--wireframe show wireframe of mesh surface for each data
--group-names name1,...,nameN:...
superimpose plots of data in each group
--subdomains mat_id_name,threshold_limits,single_color
superimpose surfaces of subdomains over each data;
example value: mat_id,0,None,True
-d "var_name0,function_name0,par0=val0,par1=val1,...:var_name1,...", --domain-specific
˓→"var_name0,function_name0,par0=val0,par1=val1,...:var_name1,..."

domain specific drawing functions and configurations

Mayavi Options:
--scalar-mode mode mode for plotting scalars with --3d, one of:
cut_plane, iso_surface, both [default: iso_surface]
--vector-mode mode mode for plotting vectors, one of: arrows, norm,
arrows_norm, warp_norm [default: arrows_norm]
-s scale, --scale-glyphs scale
relative scaling of glyphs (vector field
visualization) [default: 0.05]
--clamping glyph clamping mode
--opacity opacity opacity in [0.0, 1.0]. Can be given either globally as
a single float, or per module, e.g.
"wireframe=0.1,scalar_cut_plane=0.5". Possible
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keywords are: wireframe, scalar_cut_plane,
vector_cut_plane, surface, iso_surface,
arrows_surface, glyphs. [default: 1.0]
--rel-text-width width
relative text annotation width [default: 0.02]

As a simple example, try:

$ ./simple.py sfepy/examples/diffusion/poisson_short_syntax.py
$ ./postproc.py cylinder.vtk

The following window should display:

The -l switch lists information contained in a results file, e.g.:

$ ./postproc.py -l cylinder.vtk
sfepy: 0: cylinder.vtk
point scalars
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"node_groups" (354,) range: 0 0 l2_norm_range: 0.0 0.0
"t" (354,) range: -2.0 2.0 l2_norm_range: 0.0106091 2.0
cell scalars
"mat_id" (1348,) range: 6 6 l2_norm_range: 6.0 6.0

1.4.3 Problem Description File

Here we discuss the basic items that users have to specify in their input files. For complete examples, see the problem
description files in the sfepy/examples/ directory of SfePy.

Long Syntax

Besides the short syntax described below there is (due to history) also a long syntax which is explained in prob-
lem_desc_file_long. The short and long syntax can be mixed together in one description file.

FE Mesh

A FE mesh defining a domain geometry can be stored in several formats:

• legacy VTK (.vtk)
• custom HDF5 file (.h5)
• medit mesh file (.mesh)
• tetgen mesh files (.node, .ele)
• comsol text mesh file (.txt)
• abaqus text mesh file (.inp)
• avs-ucd text mesh file (.inp)
• hypermesh text mesh file (.hmascii)
• hermes3d mesh file (.mesh3d)
• nastran text mesh file (.bdf)
• gambit neutral text mesh file (.neu)
• salome/pythonocc med binary mesh file (.med)
Example:

filename_mesh = 'meshes/3d/cylinder.vtk'

The VTK and HDF5 formats can be used for storing the results. The format can be selected in options, see Miscella-
neous.
The following geometry elements are supported:

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Note the orientation of the vertices matters, the figure displays the correct orientation when interpreted in a right-handed
coordinate system.

Regions

Regions serve to select a certain part of the computational domain using topological entities of the FE mesh. They are
used to define the boundary conditions, the domains of terms and materials etc.
Let us denote D the maximal dimension of topological entities. For volume meshes it is also the dimension of space
the domain is embedded in. Then the following topological entities can be defined on the mesh (notation follows
[Logg2012]):

topological entity dimension co-dimension

vertex 0 D
edge 1 D-1
face 2 D-2
facet D-1 1
cell D 0

If D = 2, faces are not defined and facets are edges. If D = 3, facets are faces.
Following the above definitions, a region can be of different kind:
• cell, facet, face, edge, vertex - entities of higher dimension are not included.
• cell_only, facet_only, face_only, edge_only, vertex_only - only the specified entities are included,
other entities are empty sets, so that set-like operators still work, see below.

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• The cell kind is the most general and should be used with volume terms. It is also the default if the kind is not
specified in region definition.
• The facet kind (same as edge in 2D and face in 3D) is to be used with boundary (surface integral) terms.
• The vertex (same as vertex_only) kind can be used with point-wise defined terms (e.g. point loads).
The kinds allow a clear distinction between regions of different purpose (volume integration domains, surface domains,
etc.) and could be uses to lower memory usage.
A region definition involves topological entity selections combined with set-like operators. The set-like operators can
result in intermediate regions that have the cell kind. The desired kind is set to the final region, removing unneeded
entities. Most entity selectors are defined in terms of vertices and cells - the other entities are computed as needed.

Topological Entity Selection

topological entity selection explanation

all all entities of the mesh
vertices of surface surface of the mesh
vertices of group <integer> vertices of given group
vertices of set <str> vertices of a given named vertex set2
vertices in <expr> vertices given by an expression3
vertices by <function> vertices given by a function of coordinates4
vertex <id>[, <id>, ...] vertices given by their ids
vertex in r.<name of another region> any single vertex in the given region
cells of group <integer> cells of given group
cells by <efunction> cells given by a function of coordinates5
cell <id>[, <id>, ...], cells given by their ids
copy r.<name of another region> a copy of the given region
r.<name of another region> a reference to the given region

2 Only if mesh format supports reading boundary condition vertices as vertex sets.
3 <expr> is a logical expression like (y <= 0.1) & (x < 0.2). In 2D use x, y, in 3D use x, y and z. & stands for logical and, | stands for
logical or.
4 <function> is a function with signature fun(coors, domain=None), where coors are coordinates of mesh vertices.
5 <efunction> is a function with signature fun(coors, domain=None), where coors are coordinates of mesh cell centroids.

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topological entity selection footnotes

set-like operator explanation

+v vertex union
+e edge union
+f face union
+s facet union
+c cell union
-v vertex difference
-e edge difference
-f face difference
-s facet difference
-c cell difference
*v vertex intersection
*e edge intersection
*f face intersection
*s facet intersection
*c cell intersection

Region Definition Syntax

Regions are defined by the following Python dictionary:

regions = {
<name> : (<selection>, [<kind>], [<parent>], [{<misc. options>}]),
}

or:

regions = {
<name> : <selection>,
}

Example definitions:

regions = {
'Omega' : 'all',
'Right' : ('vertices in (x > 0.99)', 'facet'),
'Gamma1' : ("""(cells of group 1 *v cells of group 2)
+v r.Right""", 'facet', 'Omega'),
'Omega_B' : 'vertices by get_ball',
}

The Omega_B region illustrates the selection by a function (see Topological Entity Selection). In this example, the
function is:

import numpy as nm

def get_ball(coors, domain=None):

x, y, z = coors[:, 0], coors[:, 1], coors[:, 2]

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r = nm.sqrt(x**2 + y**2 + z**2)
flag = nm.where((r < 0.1))[0]

return flag

The function needs to be registered in Functions:

functions = {
'get_ball' : (get_ball,),
}

The mirror region can be defined explicitly as:

regions = {
'Top': ('r.Y *v r.Surf1', 'facet', 'Y', {'mirror_region': 'Bottom'}),
'Bottom': ('r.Y *v r.Surf2', 'facet', 'Y', {'mirror_region': 'Top'}),
}

Fields

Fields correspond to FE spaces:

fields = {
<name> : (<data_type>, <shape>, <region_name>, <approx_order>)
}

where
• <data_type> is a numpy type (float64 or complex128) or ‘real’ or ‘complex’
• <shape> is the number of DOFs per node: 1 or (1,) or ‘scalar’, space dimension (2, or (2,) or 3 or (3,)) or
‘vector’; it can be other positive integer than just 1, 2, or 3
• <region_name> is the name of region where the field is defined
• <approx_order> is the FE approximation order, e.g. 0, 1, 2, ‘1B’ (1 with bubble)
Example: scalar P1 elements in 2D on a region Omega:

fields = {
'temperature' : ('real', 1, 'Omega', 1),
}

The following approximation orders can be used:

• simplex elements: 1, 2, ‘1B’, ‘2B’
• tensor product elements: 0, 1, ‘1B’
Optional bubble function enrichment is marked by ‘B’.

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Variables

Variables use the FE approximation given by the specified field:

variables = {
<name> : (<kind>, <field_name>, <spec>, [<history>])
}

where
• <kind> - ‘unknown field’, ‘test field’ or ‘parameter field’
• <spec> - in case of: primary variable - order in the global vector of unknowns, dual variable - name of
primary variable
• <history> - number of time steps to remember prior to current step
Example:

variables = {
't' : ('unknown field', 'temperature', 0, 1),
's' : ('test field', 'temperature', 't'),
}

Integrals

Define the integral type and quadrature rule. This keyword is optional, as the integration orders can be specified directly
in equations (see below):

integrals = {
<name> : <order>
}

where
• <name> - the integral name - it has to begin with ‘i’!
• <order> - the order of polynomials to integrate, or ‘custom’ for integrals with explicitly given values and
weights
Example:

import numpy as nm
N = 2
integrals = {
'i1' : 2,
'i2' : ('custom', zip(nm.linspace( 1e-10, 0.5, N ),
nm.linspace( 1e-10, 0.5, N )),
[1./N] * N),
}

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Essential Boundary Conditions and Constraints

The essential boundary conditions set values of DOFs in some regions, while the constraints constrain or transform
values of DOFs in some regions.

Dirichlet Boundary Conditions

The Dirichlet, or essential, boundary conditions apply in a given region given by its name, and, optionally, in selected
times. The times can be given either using a list of tuples (t0, t1) making the condition active for t0 <= t < t1, or by a
name of a function taking the time argument and returning True or False depending on whether the condition is active
at the given time or not.
Dirichlet (essential) boundary conditions:

ebcs = {
<name> : (<region_name>, [<times_specification>,]
{<dof_specification> : <value>[,
<dof_specification> : <value>, ...]})
}

Example:

ebcs = {
'u1' : ('Left', {'u.all' : 0.0}),
'u2' : ('Right', [(0.0, 1.0)], {'u.0' : 0.1}),
'phi' : ('Surface', {'phi.all' : 0.0}),
'u_yz' : ('Gamma', {'u.[1,2]' : 'rotate_yz'}),
}

The u_yz condition illustrates calculating the condition value by a function. In this example, it is a function of coordi-
nates coors of region nodes:

import numpy as nm

def rotate_yz(ts, coor, **kwargs):

from sfepy.linalg import rotation_matrix2d

vec = coor[:,1:3] - centre

angle = 10.0 * ts.step

mtx = rotation_matrix2d(angle)
vec_rotated = nm.dot(vec, mtx)

displacement = vec_rotated - vec

return displacement

The function needs to be registered in Functions:

functions = {
'rotate_yz' : (rotate_yz,),
}

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Periodic Boundary Conditions

The periodic boundary conditions tie DOFs of a single variable in two regions that have matching nodes. Can be used
with functions in sfepy.discrete.fem.periodic.
Periodic boundary conditions:

epbcs = {
<name> : ((<region1_name>, <region2_name>), [<times_specification>,]
{<dof_specification> : <dof_specification>[,
<dof_specification> : <dof_specification>, ...]},
<match_function_name>)
}

Example:

epbcs = {
'up1' : (('Left', 'Right'), {'u.all' : 'u.all', 'p.0' : 'p.0'},
'match_y_line'),
}

Linear Combination Boundary Conditions

The linear combination boundary conditions (LCBCs) are more general than the Dirichlet BCs or periodic BCs. They
can be used to substitute one set of DOFs in a region by another set of DOFs, possibly in another region and of another
variable. The LCBCs can be used only in FEM with nodal (Lagrange) basis.
Available LCBC kinds:
• 'rigid' - in linear elasticity problems, a region moves as a rigid body;
• 'no_penetration' - in flow problems, the velocity vector is constrained to the plane tangent to the surface;
• 'normal_direction' - the velocity vector is constrained to the normal direction;
• 'edge_direction' - the velocity vector is constrained to the mesh edge direction;
• 'integral_mean_value' - all DOFs in a region are summed to a single new DOF;
• 'shifted_periodic' - generalized periodic BCs that work with two different variables and can have a non-zero
mutual shift.
Only the 'shifted_periodic' LCBC needs the second region and the DOF mapping function, see below.
Linear combination boundary conditions:

lcbcs = {
'shifted' : (('Left', 'Right'),
{'u1.all' : 'u2.all'},
'match_y_line', 'shifted_periodic',
'get_shift'),
'mean' : ('Middle', {'u1.all' : None}, None, 'integral_mean_value'),
}

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Initial Conditions

Initial conditions are applied prior to the boundary conditions - no special care must be used for the boundary dofs:

ics = {
<name> : (<region_name>, {<dof_specification> : <value>[,
<dof_specification> : <value>, ...]},...)
}

Example:

ics = {
'ic' : ('Omega', {'T.0' : 5.0}),
}

Materials

Materials are used to define constitutive parameters (e.g. stiffness, permeability, or viscosity), and other non-field
arguments of terms (e.g. known traction or volume forces). Depending on a particular term, the parameters can be
constants, functions defined over FE mesh nodes, functions defined in the elements, etc.
Example:

material = {
'm' : ({'val' : [0.0, -1.0, 0.0]},),
'm2' : 'get_pars',
'm3' : (None, 'get_pars'), # Same as the above line.
}

Example: different material parameters in regions ‘Yc’, ‘Ym’:

from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson

dim = 3
materials = {
'mat' : ({'D' : {
'Ym': stiffness_from_youngpoisson(dim, 7.0e9, 0.4),
'Yc': stiffness_from_youngpoisson(dim, 70.0e9, 0.2)}
},),
}

Defining Material Parameters by Functions

The functions for defining material parameters can work in two modes, distinguished by the mode argument. The two
modes are ‘qp’ and ‘special’. The first mode is used for usual functions that define parameters in quadrature points
(hence ‘qp’), while the second one can be used for special values like various flags.
The shape and type of data returned in the ‘special’ mode can be arbitrary (depending on the term used). On the other
hand, in the ‘qp’ mode all the data have to be numpy float64 arrays with shape (n_coor, n_row, n_col), where n_coor
is the number of quadrature points given by the coors argument, n_coor = coors.shape[0], and (n_row, n_col) is the
shape of a material parameter in each quadrature point. For example, for scalar parameters, the shape is (n_coor, 1, 1).
The shape is determined by each term.
Example:

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def get_pars(ts, coors, mode=None, **kwargs):

if mode == 'qp':
val = coors[:,0]
val.shape = (coors.shape[0], 1, 1)

return {'x_coor' : val}

The function needs to be registered in Functions:

functions = {
'get_pars' : (get_pars,),
}

If a material parameter has the same value in all quadrature points, than it is not necessary to repeat the constant and
the array can be with shape (1, n_row, n_col).

Equations and Terms

Equations can be built by combining terms listed in Term Table.

Examples

• Laplace equation, named integral:

equations = {
'Temperature' : """dw_laplace.i.Omega( coef.val, s, t ) = 0"""
}

• Laplace equation, simplified integral given by order:

equations = {
'Temperature' : """dw_laplace.2.Omega( coef.val, s, t ) = 0"""
}

• Laplace equation, automatic integration order (not implemented yet!):

equations = {
'Temperature' : """dw_laplace.a.Omega( coef.val, s, t ) = 0"""
}

• Navier-Stokes equations:

equations = {
'balance' :
"""+ dw_div_grad.i2.Omega( fluid.viscosity, v, u )
+ dw_convect.i2.Omega( v, u )
- dw_stokes.i1.Omega( v, p ) = 0""",
'incompressibility' :
"""dw_stokes.i1.Omega( u, q ) = 0""",
}

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Configuring Solvers

In SfePy, a non-linear solver has to be specified even when solving a linear problem. The linear problem is/should be
then solved in one iteration of the nonlinear solver.
Linear and nonlinear solver:

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton',
{'i_max' : 1}),
}

Solver selection:

options = {
'nls' : 'newton',
'ls' : 'ls',
}

For the case that a chosen linear solver is not available, it is possible to define the fallback option of the chosen solver
which specifies a possible alternative:

solvers = {
'ls': ('ls.mumps', {'fallback': 'ls2'}),
'ls2': ('ls.scipy_umfpack', {}),
'newton': ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
}),
}

Another possibility is to use a “virtual” solver that ensures an automatic selection of an available solver, see Virtual
Linear Solvers with Automatic Selection.

Functions

Functions are a way of customizing SfePy behavior. They make it possible to define material properties, boundary
conditions, parametric sweeps, and other items in an arbitrary manner. Functions are normal Python functions declared
in the Problem Definition file, so they can invoke the full power of Python. In order for SfePy to make use of the
functions, they must be declared using the function keyword. See the examples below, and also the corresponding
sections above.

Examples

See sfepy/examples/diffusion/poisson_functions.py for a complete problem description file demonstrating

how to use different kinds of functions.
• functions for defining regions:

def get_circle(coors, domain=None):

r = nm.sqrt(coors[:,0]**2.0 + coors[:,1]**2.0)
return nm.where(r < 0.2)[0]
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(continued from previous page)

functions = {
'get_circle' : (get_circle,),
}

• functions for defining boundary conditions:

def get_p_edge(ts, coors, bc=None, problem=None):

if bc.name == 'p_left':
return nm.sin(nm.pi * coors[:,1])
else:
return nm.cos(nm.pi * coors[:,1])

functions = {
'get_p_edge' : (get_p_edge,),
}

ebcs = {
'p' : ('Gamma', {'p.0' : 'get_p_edge'}),
}

The values can be given by a function of time, coordinates and possibly other data, for example:

ebcs = {
'f1' : ('Gamma1', {'u.0' : 'get_ebc_x'}),
'f2' : ('Gamma2', {'u.all' : 'get_ebc_all'}),
}

def get_ebc_x(coors, amplitude):

z = coors[:, 2]
val = amplitude * nm.sin(z * 2.0 * nm.pi)
return val

def get_ebc_all(ts, coors):

val = ts.step * coors
return val

functions = {
'get_ebc_x' : (lambda ts, coors, bc, problem, **kwargs:
get_ebc_x(coors, 5.0),),
'get_ebc_all' : (lambda ts, coors, bc, problem, **kwargs:
get_ebc_all(ts, coors),),
}

Note that when setting more than one component as in get_ebc_all() above, the function should return either
an array of shape (coors.shape[0], n_components), or the same array flattened to 1D row-by-row (i.e. node-by-
node), where n_components corresponds to the number of components in the boundary condition definition. For
example, with ‘u.[0, 1]’, n_components is 2.
• function for defining usual material parameters:

def get_pars(ts, coors, mode=None, **kwargs):

if mode == 'qp':
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(continued from previous page)

val = coors[:,0]
val.shape = (coors.shape[0], 1, 1)

return {'x_coor' : val}

functions = {
'get_pars' : (get_pars,),
}

The keyword arguments contain both additional use-specified arguments, if any, and the following: equations,
term, problem, for cases when the function needs access to the equations, problem, or term instances that
requested the parameters that are being evaluated. The full signature of the function is:
def get_pars(ts, coors, mode=None,
equations=None, term=None, problem=None, **kwargs)

• function for defining special material parameters, with an extra argument:

def get_pars_special(ts, coors, mode=None, extra_arg=None):
if mode == 'special':
if extra_arg == 'hello!':
ic = 0
else:
ic = 1
return {('x_%s' % ic) : coors[:,ic]}

functions = {
'get_pars1' : (lambda ts, coors, mode=None, **kwargs:
get_pars_special(ts, coors, mode,
extra_arg='hello!'),),
}

# Just another way of adding a function, besides 'functions' keyword.

function_1 = {
'name' : 'get_pars2',
'function' : lambda ts, coors, mode=None, **kwargs:
get_pars_special(ts, coors, mode, extra_arg='hi!'),
}

• function combining both kinds of material parameters:

def get_pars_both(ts, coors, mode=None, **kwargs):
out = {}

if mode == 'special':

out['flag'] = coors.max() > 1.0

elif mode == 'qp':

val = coors[:,1]
val.shape = (coors.shape[0], 1, 1)

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(continued from previous page)

out['y_coor'] = val

return out

functions = {
'get_pars_both' : (get_pars_both,),
}

• function for setting values of a parameter variable:

variable_1 = {
'name' : 'p',
'kind' : 'parameter field',
'field' : 'temperature',
'like' : None,
'special' : {'setter' : 'get_load_variable'},
}

def get_load_variable(ts, coors, region=None):

y = coors[:,1]
val = 5e5 * y
return val

functions = {
'get_load_variable' : (get_load_variable,)
}

Miscellaneous

The options can be used to select solvers, output file format, output directory, to register functions to be called at various
phases of the solution (the hooks), and for other settings.
Additional options (including solver selection):
options = {
# int >= 0, uniform mesh refinement level
'refinement_level : 0',

# bool, default: False, if True, allow selecting empty regions with no

# entities
'allow_empty_regions' : True,

# string, output directory

'output_dir' : 'output/<output_dir>',

# 'vtk' or 'h5', output file (results) format

'output_format' : 'h5',

# string, nonlinear solver name

'nls' : 'newton',

# string, linear solver name

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(continued from previous page)

'ls' : 'ls',

# string, time stepping solver name

'ts' : 'ts',

# The times at which results should be saved:

# - a sequence of times
# - or 'all' for all time steps (the default value)
# - or an int, number of time steps, spaced regularly from t0 to t1
# - or a function `is_save(ts)`
'save_times' : 'all',

# save a restart file for each time step, only the last computed time
# step restart file is kept.
'save_restart' : -1,

# string, a function to be called after each time step

'step_hook' : '<step_hook_function>',

# string, a function to be called after each time step, used to

# update the results to be saved
'post_process_hook' : '<post_process_hook_function>',

# string, as above, at the end of simulation

'post_process_hook_final' : '<post_process_hook_final_function>',

# string, a function to generate probe instances

'gen_probes' : '<gen_probes_function>',

# string, a function to probe data

'probe_hook' : '<probe_hook_function>',

# string, a function to modify problem definition parameters

'parametric_hook' : '<parametric_hook_function>',

# float, default: 1e-9. If the distance between two mesh vertices

# is less than this value, they are considered identical.
# This affects:
# - periodic regions matching
# - mirror regions matching
# - fixing of mesh doubled vertices
'mesh_eps': 1e-7,

# bool, default: True. If True, the (tangent) matrices and residual

# vectors (right-hand sides) contain only active DOFs, otherwise all
# DOFs (including the ones fixed by the Dirichlet or periodic boundary
# conditions) are included. Note that the rows/columns corresponding to
# fixed DOFs are modified w.r.t. a problem without the boundary
# conditions.
'active_only' : False,
}

• post_process_hook enables computing derived quantities, like stress or strain, from the primary unknown

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variables. See the examples in sfepy/examples/large_deformation/ directory.

• parametric_hook makes it possible to run parametric studies by modifying the problem description program-
matically. See sfepy/examples/diffusion/poisson_parametric_study.py for an example.
• output_dir redirects output files to specified directory

1.4.4 Building Equations in SfePy

Equations in SfePy are built using terms, which correspond directly to the integral forms of weak formulation of a
problem to be solved. As an example, let us consider the Laplace equation in time interval 𝑡 ∈ [0, 𝑡final ]:
𝜕𝑇
+ 𝑐∆𝑇 = 0 in Ω, 𝑇 (𝑡) = 𝑇¯(𝑡) on Γ . (1.5)
𝜕𝑡
The weak formulation of (1.5) is: Find 𝑇 ∈ 𝑉 , such that
∫︁ ∫︁
𝜕𝑇
𝑠 + 𝑐 ∇𝑇 : ∇𝑠 = 0, ∀𝑠 ∈ 𝑉0 , (1.6)
Ω 𝜕𝑡 Ω

where we assume no fluxes over 𝜕Ω ∖ Γ. In the syntax used in SfePy input files, this can be written as:

dw_dot.i.Omega( s, dT/dt ) + dw_laplace.i.Omega( coef, s, T) = 0

which directly corresponds to the discrete version of (1.6): Find 𝑇 ∈ 𝑉ℎ , such that
∫︁ ∫︁
𝜕𝑇
𝑠𝑇 ( 𝜑𝑇 𝜑) + 𝑠𝑇 ( 𝑐 𝐺𝑇 𝐺)𝑇 = 0, ∀𝑠 ∈ 𝑉ℎ0 ,
Ωℎ 𝜕𝑡 Ωℎ

where 𝑢 ≈ 𝜑𝑢, ∇𝑢 ≈ 𝐺𝑢 for 𝑢 ∈ {𝑠, 𝑇 }. The integrals over the discrete domain Ωℎ are approximated by a numerical
quadrature, that is named i in our case.

Syntax of Terms in Equations

The terms in equations are written in form:

<term_name>.<i>.<r>( <arg1>, <arg2>, ... )

where <i> denotes an integral name (i.e. a name of numerical quadrature to use) and <r> marks a region (domain
of the integral). In the following, <virtual> corresponds to a test function, <state> to a unknown function and
<parameter> to a known function arguments.
When solving, the individual terms in equations are evaluated in the ‘weak’ mode. The evaluation modes are described
in the next section.

1.4.5 Term Evaluation

Terms can be evaluated in two ways:

1. implicitly by using them in equations;
2. explicitly using Problem.evaluate(). This way is mostly used in the postprocessing.
Each term supports one or more evaluation modes:
• ‘weak’ : Assemble (in the finite element sense) either the vector or matrix depending on diff_var argument (the
name of variable to differentiate with respect to) of Term.evaluate(). This mode is usually used implicitly
when building the linear system corresponding to given equations.

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• ‘eval’ : The evaluation mode integrates the term (= integral) over a region. The result has the same dimension
as the quantity being integrated. This mode can be used, for example, to compute some global quantities during
postprocessing such as fluxes or total values of extensive quantities (mass, volume, energy, . . . ).
• ‘el_eval’ : The element evaluation mode results in an array of a quantity integrated over each element of a region.
• ‘el_avg’ : The element average mode results in an array of a quantity averaged in each element of a region. This
is the mode for postprocessing.
• ‘qp’ : The quadrature points mode results in an array of a quantity interpolated into quadrature points of each
element in a region. This mode is used when further point-wise calculations with the result are needed. The
same element type and number of quadrature points in each element are assumed.
Not all terms support all the modes - consult the documentation of the individual terms. There are, however, certain
naming conventions:
• ‘dw_*’ terms support ‘weak’ mode
• ‘dq_*’ terms support ‘qp’ mode
• ‘d_*’, ‘di_*’ terms support ‘eval’ and ‘el_eval’ modes
• ‘ev_*’ terms support ‘eval’, ‘el_eval’, ‘el_avg’ and ‘qp’ modes
Note that the naming prefixes are due to history when the mode argument to Problem.evaluate() and Term.
evaluate() was not available. Now they are often redundant, but are kept around to indicate the evaluation purpose
of each term.
Several examples of using the Problem.evaluate() function are shown below.

1.4.6 Solution Postprocessing

A solution to equations given in a problem description file is given by the variables of the ‘unknown field’ kind, that
are set in the solution procedure. By default, those are the only values that are stored into a results file. The solution
postprocessing allows computing additional, derived, quantities, based on the primary variables values, as well as any
other quantities to be stored in the results.
Let us illustrate this using several typical examples. Let us assume that the postprocessing function is
called ‘post_process()’, and is added to options as discussed in Miscellaneous, see ‘post_process_hook’ and
‘post_process_hook_final’. Then:
• compute stress and strain given the displacements (variable u):

def post_process(out, problem, variables, extend=False):

"""
This will be called after the problem is solved.

Parameters
----------
out : dict
The output dictionary, where this function will store additional
data.
problem : Problem instance
The current Problem instance.
variables : Variables instance
The computed state, containing FE coefficients of all the unknown
variables.
extend : bool
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The flag indicating whether to extend the output data to the whole
domain. It can be ignored if the problem is solved on the whole
domain already.

Returns
-------
out : dict
The updated output dictionary.
"""
from sfepy.base.base import Struct

# Cauchy strain averaged in elements.

strain = problem.evaluate('ev_cauchy_strain.i.Omega(u)',
mode='el_avg')
out['cauchy_strain'] = Struct(name='output_data',
mode='cell', data=strain,
dofs=None)
# Cauchy stress averaged in elements.
stress = problem.evaluate('ev_cauchy_stress.i.Omega(solid.D, u)',
mode='el_avg')
out['cauchy_stress'] = Struct(name='output_data',
mode='cell', data=stress,
dofs=None)

return out

The full example is linear_elasticity-linear_elastic_probes.

• compute diffusion velocity given the pressure:

def post_process(out, pb, state, extend=False):

from sfepy.base.base import Struct

dvel = pb.evaluate('ev_diffusion_velocity.i.Omega(m.K, p)',

mode='el_avg')
out['dvel'] = Struct(name='output_data',
mode='cell', data=dvel, dofs=None)

return out

The full example is biot-biot_npbc.

• store values of a non-homogeneous material parameter:

def post_process(out, pb, state, extend=False):

from sfepy.base.base import Struct

mu = pb.evaluate('ev_integrate_mat.2.Omega(nonlinear.mu, u)',
mode='el_avg', copy_materials=False, verbose=False)
out['mu'] = Struct(name='mu', mode='cell', data=mu, dofs=None)

return out

The full example is linear_elasticity/material_nonlinearity.py.

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• compute volume of a region (u is any variable defined in the region Omega):

volume = problem.evaluate('ev_volume.2.Omega(u)')

1.4.7 Probing

Probing applies interpolation to output the solution along specified paths. There are two ways of probing:
• VTK probes: It is the simple way of probing using the ‘post_process_hook’. It generates matplotlib figures
with the probing results and previews of the mesh with the probe paths. See Primer or linear_elasticity-its2D_5
example.
• SfePy probes: As mentioned in Miscellaneous, it relies on defining two additional functions, namely the
‘gen_probes’ function, that should create the required probes (see sfepy.discrete.probes), and the
‘probe_hook’ function that performs the actual probing of the results for each of the probes. This function can re-
turn the probing results, as well as a handle to a corresponding matplotlib figure. See linear_elasticity/its2D_4.py
for additional explanation.
Using sfepy.discrete.probes allows correct probing of fields with the approximation order greater than one,
see Interactive Example in Primer or linear_elasticity/its2D_interactive.py for an example of interactive use.

1.4.8 Postprocessing filters

The following postprocessing functions based on the VTK filters are available:
• ‘get_vtk_surface’: extract mesh surface
• ‘get_vtk_edges’: extract mesh edges
• ‘get_vtk_by_group’: extract domain by a material ID
• ‘tetrahedralize_vtk_mesh’: 3D cells are converted to tetrahedral meshes, 2D cells to triangles
The following code demonstrates the use of the postprocessing filters:

mesh = problem.domain.mesh
mesh_name = mesh.name[mesh.name.rfind(osp.sep) + 1:]

vtkdata = get_vtk_from_mesh(mesh, out, 'postproc_')

matrix = get_vtk_by_group(vtkdata, 1, 1)

matrix_surf = get_vtk_surface(matrix)
matrix_surf_tri = tetrahedralize_vtk_mesh(matrix_surf)
write_vtk_to_file('%s_mat1_surface.vtk' % mesh_name, matrix_surf_tri)

matrix_edges = get_vtk_edges(matrix)
write_vtk_to_file('%s_mat1_edges.vtk' % mesh_name, matrix_edges)

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1.4.9 Solvers

This section describes the time-stepping, nonlinear, linear, eigenvalue and optimization solvers available in SfePy.
There are many internal and external solvers in the sfepy.solvers package that can be called using a uniform interface.

Time-stepping solvers

All PDEs that can be described in a problem description file are solved internally by a time-stepping solver. This holds
even for stationary problems, where the default single-step solver ('ts.stationary') is created automatically. In this
way, all problems are treated in a uniform way. The same holds when building a problem interactively, or when writing
a script, whenever the Problem.solve() function is used for a problem solution.
The following solvers are available:
• ts.adaptive: Implicit time stepping solver with an adaptive time step.
• ts.bathe: Solve elastodynamics problems by the Bathe method.
• ts.euler: Simple forward euler method
• ts.generalized_alpha: Solve elastodynamics problems by the generalized 𝛼 method.
• ts.multistaged: Explicit time stepping solver with multistage solve_step method
• ts.newmark: Solve elastodynamics problems by the Newmark method.
• ts.runge_kutta_4: Classical 4th order Runge-Kutta method,
• ts.simple: Implicit time stepping solver with a fixed time step.
• ts.stationary: Solver for stationary problems without time stepping.
• ts.tvd_runge_kutta_3: 3rd order Total Variation Diminishing Runge-Kutta method
• ts.velocity_verlet: Solve elastodynamics problems by the velocity-Verlet method.
See sfepy.solvers.ts_solvers for available time-stepping solvers and their options.

Nonlinear Solvers

Almost every problem, even linear, is solved in SfePy using a nonlinear solver that calls a linear solver in each iteration.
This approach unifies treatment of linear and non-linear problems, and simplifies application of Dirichlet (essential)
boundary conditions, as the linear system computes not a solution, but a solution increment, i.e., it always has zero
boundary conditions.
The following solvers are available:
• nls.newton: Solves a nonlinear system 𝑓 (𝑥) = 0 using the Newton method.
• nls.oseen: The Oseen solver for Navier-Stokes equations.
• nls.petsc: Interface to PETSc SNES (Scalable Nonlinear Equations Solvers).
• nls.scipy_broyden_like: Interface to Broyden and Anderson solvers from scipy.optimize.
• nls.semismooth_newton: The semi-smooth Newton method.
See sfepy.solvers.nls, sfepy.solvers.oseen and sfepy.solvers.semismooth_newton for all available
nonlinear solvers and their options.

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Linear Solvers

Choosing a suitable linear solver is key to solving efficiently stationary as well as transient PDEs. SfePy allows using
a number of external solvers with a unified interface.
The following solvers are available:
• ls.cm_pb: Conjugate multiple problems.
• ls.mumps: Interface to MUMPS solver.
• ls.mumps_par: Interface to MUMPS parallel solver.
• ls.petsc: PETSc Krylov subspace solver.
• ls.pyamg: Interface to PyAMG solvers.
• ls.pyamg_krylov: Interface to PyAMG Krylov solvers.
• ls.schur_mumps: Mumps Schur complement solver.
• ls.scipy_direct: Direct sparse solver from SciPy.
• ls.scipy_iterative: Interface to SciPy iterative solvers.
• ls.scipy_superlu: SuperLU - direct sparse solver from SciPy.
• ls.scipy_umfpack: UMFPACK - direct sparse solver from SciPy.
See sfepy.solvers.ls for all available linear solvers and their options.

Virtual Linear Solvers with Automatic Selection

A “virtual” solver can be used in case it is not clear which external linear solvers are available. Each “virtual” solver
selects the first available solver from a pre-defined list.
The following solvers are available:
• ls.auto_direct: The automatically selected linear direct solver.
• ls.auto_iterative: The automatically selected linear iterative solver.
See sfepy.solvers.auto_fallback for all available virtual solvers.

Eigenvalue Problem Solvers

The following eigenvalue problem solvers are available:

• eig.matlab: Matlab eigenvalue problem solver.
• eig.scipy: SciPy-based solver for both dense and sparse problems.
• eig.scipy_lobpcg: SciPy-based LOBPCG solver for sparse symmetric problems.
• eig.sgscipy: SciPy-based solver for dense symmetric problems.
• eig.slepc: General SLEPc eigenvalue problem solver.
See sfepy.solvers.eigen for available eigenvalue problem solvers and their options.

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Quadratic Eigenvalue Problem Solvers

The following quadratic eigenvalue problem solvers are available:

• eig.qevp: Quadratic eigenvalue problem solver based on the problem linearization.
See sfepy.solvers.qeigen for available quadratic eigenvalue problem solvers and their options.

Optimization Solvers

The following optimization solvers are available:

• nls.scipy_fmin_like: Interface to SciPy optimization solvers scipy.optimize.fmin_*.
• opt.fmin_sd: Steepest descent optimization solver.
See sfepy.solvers.optimize for available optimization solvers and their options.

1.4.10 Solving Problems in Parallel

The PETSc-based nonlinear equations solver 'nls.petsc' and linear system solver 'ls.petsc' can be used for
parallel computations, together with the modules in sfepy.parallel package. This feature is very preliminary, and can
be used only with the commands for interactive use - problem description files are not supported (yet). The key module
is sfepy.parallel.parallel that takes care of the domain and field DOFs distribution among parallel tasks, as well
as parallel assembling to PETSc vectors and matrices.

Current Implementation Drawbacks

• The partitioning of the domain and fields DOFs is not done in parallel and all tasks need to load the whole mesh
and define the global fields - those must fit into memory available to each task.
• While all KSP and SNES solver are supported, in principle, most of their options have to be passed using the
command-line parameters of PETSc - they are not supported yet in the SfePy solver parameters.
• There are no performance statistics yet. The code was tested on a single multi-cpu machine only.
• The global solution is gathered to task 0 and saved to disk serially.
• The vertices of surface region selector does not work in parallel, because the region definition is applied
to a task-local domain.

Examples

The examples demonstrating the use parallel problem solving in SfePy are:
• diffusion/poisson_parallel_interactive.py
• multi_physics/biot_parallel_interactive.py
See their help messages for further information.

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1.4.11 Isogeometric Analysis

Isogeometric analysis (IGA) is a recently developed computational approach that allows using the NURBS-based do-
main description from CAD design tools also for approximation purposes similar to the finite element method.
The implementation is SfePy is based on Bezier extraction of NURBS as developed in1 . This approach allows reusing
the existing finite element assembling routines, as still the evaluation of weak forms occurs locally in “elements” and
the local contributions are then assembled to the global system.

Current Implementation

The IGA code is still very preliminary and some crucial components are missing. The current implementation is also
very slow, as it is in pure Python.
The following already works:
• single patch tensor product domain support in 2D and 3D
• region selection based on topological Bezier mesh, see below
• Dirichlet boundary conditions using projections for non-constant values
• evaluation in arbitrary point in the physical domain
• both scalar and vector volume terms work
• term integration over the whole domain as well as a volume subdomain
• simple linearization (output file generation) based on sampling the results with uniform parametric vectors
• basic domain generation with script/gen_iga_patch.py based on igakit
The following is not implemented yet:
• tests
• theoretical convergence rate verification
• surface terms
• other boundary conditions
• proper (adaptive) linearization for post-processing
• support for multiple NURBS patches

Domain Description

The domain description is in custom HDF5-based files with .iga extension. Such a file contains:
• NURBS patch data (knots, degrees, control points and weights). Those can either be generated using igakit,
created manually or imported from other tools.
• Bezier extraction operators and corresponding DOF connectivity (computed by SfePy).
• Bezier mesh control points, weights and connectivity (computed by SfePy).
The Bezier mesh is used to create a topological Bezier mesh - a subset of the Bezier mesh containing the Bezier
element corner vertices only. Those vertices are interpolatory (are on the exact geometry) and so can be used for region
selections.
1 Michael J. Borden, Michael A. Scott, John A. Evans, Thomas J. R. Hughes: Isogeometric finite element data structures based on Bezier

extraction of NURBS, Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, Texas, March 2010.

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Region Selection

The domain description files contain vertex sets for regions corresponding to the patch sides, named 'xiIJ', where I
is the parametric axis (0, 1, or 2) and J is 0 or 1 for the beginning and end of the axis knot span. Other regions can be
defined in the usual way, using the topological Bezier mesh entities.

Examples

The examples demonstrating the use of IGA in SfePy are:

• diffusion/poisson_iga.py
• linear_elasticity/linear_elastic_iga.py
• navier_stokes/navier_stokes2d_iga.py
Their problem description files are almost the same as their FEM equivalents, with the following differences:
• There is filename_domain instead of filename_mesh.
• Fields are defined as follows:

fields = {
't1' : ('real', 1, 'Omega', None, 'H1', 'iga'),
't2' : ('real', 1, 'Omega', 'iga', 'H1', 'iga'),
't3' : ('real', 1, 'Omega', 'iga+%d', 'H1', 'iga'),
}

The approximation order in the first definition is None as it is given by the NURBS degrees in the domain
description. The second definition is equivalent to the first one. The third definition, where %d should be a non-
negative integer, illustrates how to increase the field’s NURBS degrees (while keeping the continuity) w.r.t. the
domain NURBS description. It is applied in the navier_stokes/navier_stokes2d_iga.py example to the velocity
field.

1.5 Examples

This section contains domain-specific tutorials as well as the automatically generated list of the standard examples that
come with SfePy.

1.5.1 Primer

A beginner’s tutorial highlighting the basics of SfePy.

Introduction

This primer presents a step-by-step walk-through of the process to solve a simple mechanics problem. The typical
process to solve a problem using SfePy is followed: a model is meshed, a problem definition file is drafted, SfePy is run
to solve the problem and finally the results of the analysis are visualised.

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Problem statement

A popular test to measure the tensile strength of concrete or asphalt materials is the indirect tensile strength (ITS) test
pictured below. In this test a cylindrical specimen is loaded across its diameter to failure. The test is usually run by
loading the specimen at a constant deformation rate of 50 mm/minute (say) and measuring the load response. When
the tensile stress that develops in the specimen under loading exceeds its tensile strength then the specimen will fail.
To model this problem using finite elements the indirect tensile test can be simplified to represent a diametrically point
loaded disk as shown in the schematic.

The tensile and compressive stresses that develop in the specimen as a result of the point loads P are a function of the
diameter 𝐷 and thickness 𝑡 of the cylindrical specimen. At the centre of the specimen, the compressive stress is 3 times
the tensile stress and the analytical formulation for these are, respectively:

2𝑃
𝜎𝑡 = (1.7)
𝜋𝑡𝐷
6𝑃
𝜎𝑐 = (1.8)
𝜋𝑡𝐷
These solutions may be approximated using finite element methods. To solve this problem using SfePy the first step is
meshing a suitable model.

Meshing

Assuming plane strain conditions, the indirect tensile test may be modelled using a 2D finite element mesh. Further-
more, the geometry of the model is symmetrical about the x- and y-axes passing through the centre of the circle. To
take advantage of this symmetry only one quarter of the 2D model will be meshed and boundary conditions will be
established to indicate this symmetry. The meshing program Gmsh is used here to very quickly mesh the model. Follow
these steps to model the ITS:
1. The ITS specimen has a diameter of 150 mm. Using Gmsh add three new points (geometry elementary entities)
at the following coordinates: (0.00.0), (75.0, 0.0) and (0.0, 75.0).
2. Next add two straight lines connecting the points.

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3. Next add a Circle arc connecting two of the points to form the quarter circle segment.
4. Still under Geometry add a ruled surface.
5. With the geometry of the model defined, add a mesh by clicking on the 2D button under the Mesh functions.
The figures that follow show the various stages in the model process.

That’s the meshing done. Save the mesh in a format that SfePy recognizes. For now use the medit .mesh format e.g.
its2D.mesh.
Hint: Check the drop down in the Save As dialog for the different formats that Gmsh can save to.

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If you open the its2D.mesh file using a text editor you’ll notice that Gmsh saves the mesh in a 3D format and includes
some extra geometry items that should be deleted. Reformatted the mesh file to a 2D format and delete the Edges block.
Note that when you do this the file cannot be reopened by Gmsh so it is always a good idea to also save your meshes in
Gmsh’s native format as well (Shift-Ctrl-S). Click here to download the reformatted mesh file that will be used in the
tutorial.

You’ll notice that the mesh contains 55 vertices (nodes) and 83 triangle elements. The mesh file provides the coordinates
of the nodes and the element connectivity. It is important to note that node and element numbering in SfePy start at 0
and not 1 as is the case in Gmsh and some other meshing programs.
To view .mesh files you can use a demo of medit. After loading your mesh file with medit you can see the node and
element numbering by pressing P and F respectively. The numbering in medit starts at 1 as shown. Thus the node
at the center of the model in SfePy numbering is 0, and elements 76 and 77 are connected to this node. Node and
element numbers can also be viewed in Gmsh – under the mesh option under the Visibility tab enable the node and
surface labels. Note that the surface labels as numbered in Gmsh follow on from the line numbering. So to get the
corresponding element number in SfePy you’ll need to subtract the number of lines in the Gmsh file + 1. Confused yet?
Luckily, SfePy provides some useful mesh functions to indicate which elements are connected to which nodes. Nodes
and elements can also be identified by defining regions, which is addressed later.
Another open source python option to view .mesh files is the appropriately named Python Mesh Viewer.
The next step in the process is coding the SfePy problem definition file.

Problem description

The programming of the problem description file is well documented in the SfePy User’s Guide. The problem descrip-
tion file used in the tutorial follows:

r"""
Diametrically point loaded 2-D disk. See :ref:`sec-primer`.

Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
= 0
\;, \quad \forall \ul{v} \;,

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where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.
"""
from __future__ import absolute_import
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
from sfepy.discrete.fem.utils import refine_mesh
from sfepy import data_dir

# Fix the mesh file name if you run this file outside the SfePy directory.
filename_mesh = data_dir + '/meshes/2d/its2D.mesh'

refinement_level = 0
filename_mesh = refine_mesh(filename_mesh, refinement_level)

output_dir = '.' # set this to a valid directory you have write access to

young = 2000.0 # Young's modulus [MPa]

poisson = 0.4 # Poisson's ratio

options = {
'output_dir' : output_dir,
}

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < 0.001)', 'facet'),
'Bottom' : ('vertices in (y < 0.001)', 'facet'),
'Top' : ('vertex 2', 'vertex'),
}

materials = {
'Asphalt' : ({'D': stiffness_from_youngpoisson(2, young, poisson)},),
'Load' : ({'.val' : [0.0, -1000.0]},),
}

fields = {
'displacement': ('real', 'vector', 'Omega', 1),
}

equations = {
'balance_of_forces' :
"""dw_lin_elastic.2.Omega(Asphalt.D, v, u)
= dw_point_load.0.Top(Load.val, v)""",
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
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}

ebcs = {
'XSym' : ('Bottom', {'u.1' : 0.0}),
'YSym' : ('Left', {'u.0' : 0.0}),
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-6,
}),
}

Download the Problem description file and open it in your favourite Python editor. Note that you may wish to
change the location of the output directory to somewhere on your drive. You may also need to edit the mesh file name.
For the analysis we will assume that the material of the test specimen is linear elastic and isotropic. We define two
material constants i.e. Young’s modulus and Poisson’s ratio. The material is assumed to be asphalt concrete having a
Young’s modulus of 2,000 MPa and a Poisson’s ration of 0.4.
Note: Be consistent in your choice and use of units. In the tutorial we are using Newton (N), millimeters (mm) and
megaPascal (MPa). The sfepy.mechanics.units module might help you in determining which derived units correspond
to given basic units.
The following block of code defines regions on your mesh:

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < 0.001)', 'facet'),
'Bottom' : ('vertices in (y < 0.001)', 'facet'),
'Top' : ('vertex 2', 'vertex'),
}

Four regions are defined:

1. ‘Omega’: all the elements in the mesh,
2. ‘Left’: the y-axis,
3. ‘Bottom’: the x-axis,
4. ‘Top’: the topmost node. This is where the load is applied.
Having defined the regions these can be used in other parts of your code. For example, in the definition of the boundary
conditions:

ebcs = {
'XSym' : ('Bottom', {'u.1' : 0.0}),
'YSym' : ('Left', {'u.0' : 0.0}),
}

Now the power of the regions entity becomes apparent. To ensure symmetry about the x-axis, the vertical or y-
displacement of the nodes in the ‘Bottom’ region are prevented or set to zero. Similarly, for symmetry about the
y-axis, any horizontal or displacement in the x-direction of the nodes in the ‘Left’ region or y-axis is prevented.
The load is specified in terms of the ‘Load’ material as follows:

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materials = {
'Asphalt' : ({
'lam' : lame_from_youngpoisson(young, poisson)[0],
'mu' : lame_from_youngpoisson(young, poisson)[1],
},),
'Load' : ({'.val' : [0.0, -1000.0]},),
}

Note the dot in ‘.val’ – this denotes a special material value, i.e., a value that is not to be evaluated in quadrature points.
The load is then applied in equations using the ‘dw_point_load.0.Top(Load.val, v)’ term in the topmost node (region
‘Top’).
We provided the material constants in terms of Young’s modulus and Poisson’s ratio, but the linear elastic isotropic
equation used requires as input Lamé’s parameters. The lame_from_youngpoisson() function is thus used for conver-
sion. Note that to use this function it was necessary to import the function into the code, which was done up front:

from sfepy.mechanics.matcoefs import lame_from_youngpoisson

Hint: Check out the sfepy.mechanics.matcoefs module for other useful material related functions.
That’s it – we are now ready to solve the problem.

Running SfePy

One option to solve the problem is to run the SfePy simple.py script from the command line:

./simple.py its2D_1.py

Note: For the purpose of this tutorial it is assumed that the problem description file (its2D_1.py) is in the same
directory as the simple.py script. If you have the its2D_1.py file in another directory then make sure you include the
path to this file as well.
SfePy solves the problem and outputs the solution to the output path (output_dir) provided in the script. The output file
will be in the VTK format by default if this is not explicitly specified and the name of the output file will be the same
as that used for the mesh file except with the ‘.vtk’ extension i.e. its2D.vtk.
The VTK format is an ASCII format. Open the file using a text editor. You’ll notice that the output file includes separate
sections:
• POINTS (these are the model nodes),
• CELLS (the model element connectivity),
• VECTORS (the node displacements in the x-, y- and z- directions).
SfePy provides a script (postproc.py) to quickly view the solution. To run this script you need to have Mayavi installed.
From the command line issue the following (assuming the correct paths):

./postproc.py its2D.vtk

The postproc.py script generates the image shown below, which shows by default the displacements in the model as
arrows and their magnitude as color scale. Cool, but we are more interested in the stresses. To get these we need to
modify the problem description file and do some post-processing.

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Post-processing

SfePy provides functions to calculate stresses and strains. We’ll include a function to calculate these and update the
problem material definition and options to call this function as a post_process_hook(). Save this file as its2D_2.py.

r"""
Diametrically point loaded 2-D disk with postprocessing. See
:ref:`sec-primer`.

Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
= 0
\;, \quad \forall \ul{v} \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.
"""

from __future__ import absolute_import

from sfepy.examples.linear_elasticity.its2D_1 import *

from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson

def stress_strain(out, pb, state, extend=False):

"""
Calculate and output strain and stress for given displacements.
"""
from sfepy.base.base import Struct

ev = pb.evaluate
strain = ev('ev_cauchy_strain.2.Omega(u)', mode='el_avg')
stress = ev('ev_cauchy_stress.2.Omega(Asphalt.D, u)', mode='el_avg',
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copy_materials=False)

out['cauchy_strain'] = Struct(name='output_data', mode='cell',

data=strain, dofs=None)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)

return out

asphalt = materials['Asphalt'][0]
asphalt.update({'D' : stiffness_from_youngpoisson(2, young, poisson)})
options.update({'post_process_hook' : 'stress_strain',})

The updated file imports all of the previous definitions in its2D_1.py. The stress function (de_cauchy_stress())
requires as input the stiffness tensor – thus it was necessary to update the materials accordingly. The problem options
were also updated to call the stress_strain() function as a post_process_hook().
Run SfePy to solve the updated problem and view the solution (assuming the correct paths):

./simple.py its2D_2.py
./postproc.py its2D.vtk -b

In addition to the node displacements, the VTK output shown below now also includes the stresses and strains averaged
in the elements:

Remember the objective was to determine the stresses at the centre of the specimen under a load 𝑃 . The solution as
currently derived is expressed in terms of a global displacement vector 𝑢. The global (residual) force vector 𝑓 is a
function of the global displacement vector and the global stiffness matrix 𝐾 as: 𝑓 = 𝐾𝑢. Let’s determine the force
vector interactively.

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Running SfePy in interactive mode

In addition to solving problems using the simple.py script you can also run SfePy interactively (we will use IPython
interactive shell in following examples).
In the SfePy top-level directory run

ipython

issue the following commands:

In [1]: from sfepy.applications import solve_pde

In [2]: pb, variables = solve_pde('its2D_2.py')

The problem is solved and the problem definition and solution are provided in the pb and variables variables respec-
tively. The solution, or in this case, the global displacement vector 𝑢, contains the x- and y-displacements at the nodes
in the 2D model:

In [3]: u = variables()

In [4]: u
Out[4]:
array([ 0. , 0. , 0.37376671, ..., -0.19923848,
0.08820237, -0.11201528])

In [5]: u.shape
Out[5]: (110,)

In [6]: u.shape = (55, 2)

In [7]: u
Out[7]:
array([[ 0. , 0. ],
[ 0.37376671, 0. ],
[ 0. , -1.65318152],
...,
[ 0.08716448, -0.23069047],
[ 0.27741356, -0.19923848],
[ 0.08820237, -0.11201528]])

Note: We have used the fact, that the state vector contains only one variable (u). In general, the following can be used:

In [8]: u = variables.get_state_parts()['u']

In [9]: u
Out[9]:
array([[ 0. , 0. ],
[ 0.37376671, 0. ],
[ 0. , -1.65318152],
...,
[ 0.08716448, -0.23069047],
[ 0.27741356, -0.19923848],
[ 0.08820237, -0.11201528]])

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Both variables() and variables.get_state_parts() return a view of the DOF vector, that is why in Out[8] the vector is
reshaped according to Out[6]. It is thus possible to set the values of state variables by manipulating the state vector,
but shape changes such as the one above are not advised (see In [15] below) - work on a copy instead.
From the above it can be seen that u holds the displacements at the 55 nodes in the model and that the displacement
at node 2 (on which the load is applied) is (0, −1.65318152). The global stiffness matrix is saved in pb as a sparse
matrix:

In [10]: K = pb.mtx_a

In [11]: K
Out[11]:
<94x94 sparse matrix of type '<type 'numpy.float64'>'
with 1070 stored elements in Compressed Sparse Row format>

In [12]: print(K)
(0, 0) 2443.95959851
(0, 7) -2110.99917491
(0, 14) -332.960423597
(0, 15) 1428.57142857
(1, 1) 2443.95959852
(1, 13) -2110.99917492
(1, 32) 1428.57142857
(1, 33) -332.960423596
(2, 2) 4048.78343529
(2, 3) -1354.87004384
(2, 52) -609.367453538
(2, 53) -1869.0018791
(2, 92) -357.41672785
(2, 93) 1510.24654193
(3, 2) -1354.87004384
(3, 3) 4121.03202907
(3, 4) -1696.54911732
(3, 48) 76.2400806561
(3, 49) -1669.59247304
(3, 52) -1145.85294856
(3, 53) 2062.13955556
(4, 3) -1696.54911732
(4, 4) 4410.17902905
(4, 5) -1872.87344838
(4, 42) -130.515009576
: :
(91, 81) -1610.0550578
(91, 86) -199.343680224
(91, 87) -2330.41406097
(91, 90) -575.80373408
(91, 91) 7853.23899229
(92, 2) -357.41672785
(92, 8) 1735.59411191
(92, 50) -464.976034459
(92, 51) -1761.31189004
(92, 52) -3300.45367361
(92, 53) 1574.59387937
(92, 88) -250.325600254
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(92, 89) 1334.11823335
(92, 92) 9219.18643706
(92, 93) -2607.52659081
(93, 2) 1510.24654193
(93, 8) -657.361661955
(93, 50) -1761.31189004
(93, 51) 54.1134516246
(93, 52) 1574.59387937
(93, 53) -315.793227627
(93, 88) 1334.11823335
(93, 89) -4348.13351285
(93, 92) -2607.52659081
(93, 93) 9821.16012014

In [13]: K.shape
Out[13]: (94, 94)

One would expect the shape of the global stiffness matrix 𝐾 to be (110, 110) i.e. to have the same number of rows and
columns as u. This matrix has been reduced by the fixed degrees of freedom imposed by the boundary conditions set
at the nodes on symmetry axes. To restore the matrix, temporarily remove the imposed boundary conditions:

In [14]: pb.remove_bcs()

Now we can calculate the force vector 𝑓 :

In [15]: f = pb.evaluator.eval_residual(u)

This leads to:

ValueError: shape mismatch: value array of shape (55,2) could not be broadcast to␣
˓→indexing result of shape (110,)

• the original shape of the DOF vector needs to be restored:

In [16]: variables.vec.shape = (110,)

In [17]: f = pb.evaluator.eval_residual(u)

In [18]: f.shape
Out[18]: (110,)

In [19]: f
Out[19]:
array([ -4.73618436e+01, 1.42752386e+02, 1.56921124e-13, ...,
-2.06057393e-13, 2.13162821e-14, -2.84217094e-14])

Remember to restore the original boundary conditions previously removed in step [14]:

In [20]: pb.time_update()

To view the residual force vector, we can save it to a VTK file. This requires setting f to (a copy of) the variables as
follows:

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In [21]: fvars = variables.copy()

In [22]: fvars.set_state(f, reduced=False)
In [23]: out = variables.create_output()
In [24]: pb.save_state('file.vtk', out=out)

Running the postproc.py script on file.vtk displays the average nodal forces as shown below:

The forces in the x- and y-directions at node 2 are:

In [25]: f.shape = (55, 2)

In [26]: f[2]
Out[26]: array([ 6.20373272e+02, -1.13686838e-13])

Great, we have an almost zero residual vertical load or force apparent at node 2 i.e. -1.13686838e-13 Newton. Let us
now check the stress at node 0, the centre of the specimen.

Generating output at element nodes

Previously we had calculated the stresses in the model but these were averaged from those calculated at Gauss quadrature
points within the elements. It is possible to provide custom integrals to allow the calculation of stresses with the Gauss
quadrature points at the element nodes. This will provide us a more accurate estimate of the stress at the centre of the
specimen located at node 0. The code below outlines one way to achieve this.

r"""
Diametrically point loaded 2-D disk with nodal stress calculation. See
:ref:`sec-primer`.

Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
= 0
\;, \quad \forall \ul{v} \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
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\lambda \ \delta_{ij} \delta_{kl}
\;.
"""
from __future__ import print_function
from __future__ import absolute_import
from sfepy.examples.linear_elasticity.its2D_1 import *

from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson

from sfepy.discrete.fem.geometry_element import geometry_data
from sfepy.discrete import FieldVariable
from sfepy.discrete.fem import Field
import numpy as nm

gdata = geometry_data['2_3']
nc = len(gdata.coors)

def nodal_stress(out, pb, state, extend=False, integrals=None):

'''
Calculate stresses at nodal points.
'''

# Point load.
mat = pb.get_materials()['Load']
P = 2.0 * mat.get_data('special', 'val')[1]

# Calculate nodal stress.

pb.time_update()

if integrals is None: integrals = pb.get_integrals()

stress = pb.evaluate('ev_cauchy_stress.ivn.Omega(Asphalt.D, u)', mode='qp',

integrals=integrals, copy_materials=False)
sfield = Field.from_args('stress', nm.float64, (3,),
pb.domain.regions['Omega'])
svar = FieldVariable('sigma', 'parameter', sfield,
primary_var_name='(set-to-None)')
svar.set_from_qp(stress, integrals['ivn'])

print('\n==================================================================')
print('Given load = %.2f N' % -P)
print('\nAnalytical solution')
print('===================')
print('Horizontal tensile stress = %.5e MPa/mm' % (-2.*P/(nm.pi*150.)))
print('Vertical compressive stress = %.5e MPa/mm' % (-6.*P/(nm.pi*150.)))
print('\nFEM solution')
print('============')
print('Horizontal tensile stress = %.5e MPa/mm' % (svar()[0]))
print('Vertical compressive stress = %.5e MPa/mm' % (-svar()[1]))
print('==================================================================')
return out

asphalt = materials['Asphalt'][0]
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asphalt.update({'D' : stiffness_from_youngpoisson(2, young, poisson)})
options.update({'post_process_hook' : 'nodal_stress',})

integrals = {
'ivn' : ('custom', gdata.coors, [gdata.volume / nc] * nc),
}

The output:

==================================================================
Given load = 2000.00 N

Analytical solution
===================
Horizontal tensile stress = 8.48826e+00 MPa/mm
Vertical compressive stress = 2.54648e+01 MPa/mm

FEM solution
============
Horizontal tensile stress = 7.57220e+00 MPa/mm
Vertical compressive stress = 2.58660e+01 MPa/mm
==================================================================

Not bad for such a coarse mesh! Re-running the problem using a finer mesh provides a more accurate solution:

==================================================================
Given load = 2000.00 N

Analytical solution
===================
Horizontal tensile stress = 8.48826e+00 MPa/mm
Vertical compressive stress = 2.54648e+01 MPa/mm

FEM solution
============
Horizontal tensile stress = 8.50042e+00 MPa/mm
Vertical compressive stress = 2.54300e+01 MPa/mm

To see how the FEM solution approaches the analytical one, try to play with the uniform mesh refinement level in the
Problem description file, namely lines 25, 26:

refinement_level = 0
filename_mesh = refine_mesh(filename_mesh, refinement_level)

The above computation could also be done in the IPython shell:

In [23]: from sfepy.applications import solve_pde

In [24]: from sfepy.discrete import (Field, FieldVariable, Material,
Integral, Integrals)
In [25]: from sfepy.discrete.fem.geometry_element import geometry_data

In [26]: gdata = geometry_data['2_3']

In [27]: nc = len(gdata.coors)
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In [28]: ivn = Integral('ivn', order=-1,
....: coors=gdata.coors, weights=[gdata.volume / nc] * nc)

In [29]: pb, variables = solve_pde('sfepy/examples/linear_elasticity/its2D_2.py')

In [30]: stress = pb.evaluate('ev_cauchy_stress.ivn.Omega(Asphalt.D,u)',

....: mode='qp', integrals=Integrals([ivn]))
In [31]: sfield = Field.from_args('stress', nm.float64, (3,), pb.domain.regions['Omega'])
In [32]: svar = FieldVariable('sigma', 'parameter', sfield,
....: primary_var_name='(set-to-None)')
In [33]: svar.set_from_qp(stress, ivn)

In [34]: print('Horizontal tensile stress = %.5e MPa/mm' % (svar()[0]))

Horizontal tensile stress = 7.57220e+00 MPa/mm
In [35]: print('Vertical compressive stress = %.5e MPa/mm' % (-svar()[1]))
Vertical compressive stress = 2.58660e+01 MPa/mm

In [36]: mat = pb.get_materials()['Load']

In [37]: P = 2.0 * mat.get_data('special', 'val')[1]
In [38]: P
Out[38]: -2000.0

In [39]: print('Horizontal tensile stress = %.5e MPa/mm' % (-2.*P/(nm.pi*150.)))

Horizontal tensile stress = 8.48826e+00 MPa/mm
In [40]: print('Vertical compressive stress = %.5e MPa/mm' % (-6.*P/(nm.pi*150.)))
Vertical compressive stress = 2.54648e+01 MPa/mm

To wrap this tutorial up let’s explore SfePy’s probing functions.

Probing

As a bonus for sticking to the end of this tutorial see the following Problem description file that provides SfePy
functions to quickly and neatly probe the solution.

r"""
Diametrically point loaded 2-D disk with postprocessing and probes. See
:ref:`sec-primer`.

Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
= 0
\;, \quad \forall \ul{v} \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.
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"""
from __future__ import absolute_import
from sfepy.examples.linear_elasticity.its2D_1 import *

from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson

from sfepy.postprocess.probes_vtk import Probe

import os
from six.moves import range

def stress_strain(out, pb, state, extend=False):

"""
Calculate and output strain and stress for given displacements.
"""
from sfepy.base.base import Struct
import matplotlib.pyplot as plt
import matplotlib.font_manager as fm

ev = pb.evaluate
strain = ev('ev_cauchy_strain.2.Omega(u)', mode='el_avg')
stress = ev('ev_cauchy_stress.2.Omega(Asphalt.D, u)', mode='el_avg')

out['cauchy_strain'] = Struct(name='output_data', mode='cell',

data=strain, dofs=None)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)

probe = Probe(out, pb.domain.mesh, probe_view=True)

ps0 = [[0.0, 0.0, 0.0], [ 0.0, 0.0, 0.0]]

ps1 = [[75.0, 0.0, 0.0], [ 0.0, 75.0, 0.0]]
n_point = 10

labels = ['%s -> %s' % (p0, p1) for p0, p1 in zip(ps0, ps1)]
probes = []
for ip in range(len(ps0)):
p0, p1 = ps0[ip], ps1[ip]
probes.append('line%d' % ip)
probe.add_line_probe('line%d' % ip, p0, p1, n_point)

for ip, label in zip(probes, labels):

fig = plt.figure()
plt.clf()
fig.subplots_adjust(hspace=0.4)
plt.subplot(311)
pars, vals = probe(ip, 'u')
for ic in range(vals.shape[1] - 1):
plt.plot(pars, vals[:,ic], label=r'$u_{%d}$' % (ic + 1),
lw=1, ls='-', marker='+', ms=3)
plt.ylabel('displacements')
plt.xlabel('probe %s' % label, fontsize=8)
plt.legend(loc='best', prop=fm.FontProperties(size=10))
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sym_labels = ['11', '22', '12']

plt.subplot(312)
pars, vals = probe(ip, 'cauchy_strain')
for ii in range(vals.shape[1]):
plt.plot(pars, vals[:, ii], label=r'$e_{%s}$' % sym_labels[ii],
lw=1, ls='-', marker='+', ms=3)
plt.ylabel('Cauchy strain')
plt.xlabel('probe %s' % label, fontsize=8)
plt.legend(loc='best', prop=fm.FontProperties(size=8))

plt.subplot(313)
pars, vals = probe(ip, 'cauchy_stress')
for ii in range(vals.shape[1]):
plt.plot(pars, vals[:, ii], label=r'$\sigma_{%s}$' % sym_labels[ii],
lw=1, ls='-', marker='+', ms=3)
plt.ylabel('Cauchy stress')
plt.xlabel('probe %s' % label, fontsize=8)
plt.legend(loc='best', prop=fm.FontProperties(size=8))

opts = pb.conf.options
filename_results = os.path.join(opts.get('output_dir'),
'its2D_probe_%s.png' % ip)

fig.savefig(filename_results)

return out

materials['Asphalt'][0].update({'D' : stiffness_from_youngpoisson(2, young, poisson)})

options.update({
'post_process_hook' : 'stress_strain',
})

Probing applies interpolation to output the solution along specified paths. For the tutorial, line probing is done along
the x- and y-axes of the model.
Run SfePy to solve the problem and apply the probes:

./simple.py its2D_5.py

The probing function will generate the following figures that show the displacements, normal stresses and strains as
well as shear stresses and strains along the probe paths. Note that you need matplotlib installed to run this example.

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The probing function also generates previews of the mesh with the probe paths.

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Interactive Example

SfePy can be used also interactively by constructing directly the classes that corresponds to the keywords in the problem
description files. The following listing shows a script with the same (and more) functionality as the above examples:
#!/usr/bin/env python
"""
Diametrically point loaded 2-D disk, using commands for interactive use. See
:ref:`sec-primer`.

The script combines the functionality of all the ``its2D_?.py`` examples and
allows setting various simulation parameters, namely:

- material parameters
- displacement field approximation order
- uniform mesh refinement level

The example shows also how to probe the results as in

:ref:`linear_elasticity-its2D_4`, and how to display the results using Mayavi.
Using :mod:`sfepy.discrete.probes` allows correct probing of fields with the
approximation order greater than one.

In the SfePy top-level directory the following command can be used to get usage
information::

python sfepy/examples/linear_elasticity/its2D_interactive.py -h

Notes
-----

The ``--probe`` and ``--show`` options work simultaneously only if Mayavi and
Matplotlib use the same backend type (for example wx).
"""
from __future__ import absolute_import
import sys
from six.moves import range
sys.path.append('.')
from argparse import ArgumentParser, RawDescriptionHelpFormatter

import numpy as nm
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import matplotlib.pyplot as plt

from sfepy.base.base import assert_, output, ordered_iteritems, IndexedStruct

from sfepy.discrete import (FieldVariable, Material, Integral, Integrals,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
from sfepy.solvers.auto_fallback import AutoDirect
from sfepy.solvers.nls import Newton
from sfepy.discrete.fem.geometry_element import geometry_data
from sfepy.discrete.probes import LineProbe
from sfepy.discrete.projections import project_by_component

from sfepy.examples.linear_elasticity.its2D_2 import stress_strain

from sfepy.examples.linear_elasticity.its2D_3 import nodal_stress

def gen_lines(problem):
"""
Define two line probes.

Additional probes can be added by appending to `ps0` (start points) and

`ps1` (end points) lists.
"""
ps0 = [[0.0, 0.0], [0.0, 0.0]]
ps1 = [[75.0, 0.0], [0.0, 75.0]]

# Use enough points for higher order approximations.

n_point = 1000

labels = ['%s -> %s' % (p0, p1) for p0, p1 in zip(ps0, ps1)]
probes = []
for ip in range(len(ps0)):
p0, p1 = ps0[ip], ps1[ip]
probes.append(LineProbe(p0, p1, n_point))

return probes, labels

def probe_results(u, strain, stress, probe, label):

"""
Probe the results using the given probe and plot the probed values.
"""
results = {}

pars, vals = probe(u)

results['u'] = (pars, vals)
pars, vals = probe(strain)
results['cauchy_strain'] = (pars, vals)
pars, vals = probe(stress)
results['cauchy_stress'] = (pars, vals)

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fig = plt.figure()
plt.clf()
fig.subplots_adjust(hspace=0.4)
plt.subplot(311)
pars, vals = results['u']
for ic in range(vals.shape[1]):
plt.plot(pars, vals[:,ic], label=r'$u_{%d}$' % (ic + 1),
lw=1, ls='-', marker='+', ms=3)
plt.ylabel('displacements')
plt.xlabel('probe %s' % label, fontsize=8)
plt.legend(loc='best', fontsize=10)

sym_indices = ['11', '22', '12']

plt.subplot(312)
pars, vals = results['cauchy_strain']
for ic in range(vals.shape[1]):
plt.plot(pars, vals[:,ic], label=r'$e_{%s}$' % sym_indices[ic],
lw=1, ls='-', marker='+', ms=3)
plt.ylabel('Cauchy strain')
plt.xlabel('probe %s' % label, fontsize=8)
plt.legend(loc='best', fontsize=10)

plt.subplot(313)
pars, vals = results['cauchy_stress']
for ic in range(vals.shape[1]):
plt.plot(pars, vals[:,ic], label=r'$\sigma_{%s}$' % sym_indices[ic],
lw=1, ls='-', marker='+', ms=3)
plt.ylabel('Cauchy stress')
plt.xlabel('probe %s' % label, fontsize=8)
plt.legend(loc='best', fontsize=10)

return fig, results

helps = {
'young' : "the Young's modulus [default: %(default)s]",
'poisson' : "the Poisson's ratio [default: %(default)s]",
'load' : "the vertical load value (negative means compression)"
" [default: %(default)s]",
'order' : 'displacement field approximation order [default: %(default)s]',
'refine' : 'uniform mesh refinement level [default: %(default)s]',
'probe' : 'probe the results',
'show' : 'show the results figure',
}

def main():
from sfepy import data_dir

parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('--young', metavar='float', type=float,
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action='store', dest='young',
default=2000.0, help=helps['young'])
parser.add_argument('--poisson', metavar='float', type=float,
action='store', dest='poisson',
default=0.4, help=helps['poisson'])
parser.add_argument('--load', metavar='float', type=float,
action='store', dest='load',
default=-1000.0, help=helps['load'])
parser.add_argument('--order', metavar='int', type=int,
action='store', dest='order',
default=1, help=helps['order'])
parser.add_argument('-r', '--refine', metavar='int', type=int,
action='store', dest='refine',
default=0, help=helps['refine'])
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
parser.add_argument('-p', '--probe',
action="store_true", dest='probe',
default=False, help=helps['probe'])
options = parser.parse_args()

assert_((0.0 < options.poisson < 0.5),

"Poisson's ratio must be in ]0, 0.5[!")
assert_((0 < options.order),
'displacement approximation order must be at least 1!')

output('using values:')
output(" Young's modulus:", options.young)
output(" Poisson's ratio:", options.poisson)
output(' vertical load:', options.load)
output('uniform mesh refinement level:', options.refine)

# Build the problem definition.

mesh = Mesh.from_file(data_dir + '/meshes/2d/its2D.mesh')
domain = FEDomain('domain', mesh)

if options.refine > 0:
for ii in range(options.refine):
output('refine %d...' % ii)
domain = domain.refine()
output('... %d nodes %d elements'
% (domain.shape.n_nod, domain.shape.n_el))

omega = domain.create_region('Omega', 'all')

left = domain.create_region('Left',
'vertices in x < 0.001', 'facet')
bottom = domain.create_region('Bottom',
'vertices in y < 0.001', 'facet')
top = domain.create_region('Top', 'vertex 2', 'vertex')

field = Field.from_args('fu', nm.float64, 'vector', omega,

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approx_order=options.order)

u = FieldVariable('u', 'unknown', field)

v = FieldVariable('v', 'test', field, primary_var_name='u')

D = stiffness_from_youngpoisson(2, options.young, options.poisson)

asphalt = Material('Asphalt', D=D)

load = Material('Load', values={'.val' : [0.0, options.load]})

integral = Integral('i', order=2*options.order)

integral0 = Integral('i', order=0)

t1 = Term.new('dw_lin_elastic(Asphalt.D, v, u)',
integral, omega, Asphalt=asphalt, v=v, u=u)
t2 = Term.new('dw_point_load(Load.val, v)',
integral0, top, Load=load, v=v)
eq = Equation('balance', t1 - t2)
eqs = Equations([eq])

xsym = EssentialBC('XSym', bottom, {'u.1' : 0.0})

ysym = EssentialBC('YSym', left, {'u.0' : 0.0})

ls = AutoDirect({})

nls_status = IndexedStruct()
nls = Newton({}, lin_solver=ls, status=nls_status)

pb = Problem('elasticity', equations=eqs)

pb.set_bcs(ebcs=Conditions([xsym, ysym]))

pb.set_solver(nls)

# Solve the problem.

variables = pb.solve()
output(nls_status)

# Postprocess the solution.

out = variables.create_output()
out = stress_strain(out, pb, variables, extend=True)
pb.save_state('its2D_interactive.vtk', out=out)

gdata = geometry_data['2_3']
nc = len(gdata.coors)

integral_vn = Integral('ivn', coors=gdata.coors,

weights=[gdata.volume / nc] * nc)

nodal_stress(out, pb, variables, integrals=Integrals([integral_vn]))

if options.probe:
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# Probe the solution.
probes, labels = gen_lines(pb)

sfield = Field.from_args('sym_tensor', nm.float64, 3, omega,

approx_order=options.order - 1)
stress = FieldVariable('stress', 'parameter', sfield,
primary_var_name='(set-to-None)')
strain = FieldVariable('strain', 'parameter', sfield,
primary_var_name='(set-to-None)')

cfield = Field.from_args('component', nm.float64, 1, omega,

approx_order=options.order - 1)
component = FieldVariable('component', 'parameter', cfield,
primary_var_name='(set-to-None)')

ev = pb.evaluate
order = 2 * (options.order - 1)
strain_qp = ev('ev_cauchy_strain.%d.Omega(u)' % order, mode='qp')
stress_qp = ev('ev_cauchy_stress.%d.Omega(Asphalt.D, u)' % order,
mode='qp', copy_materials=False)

project_by_component(strain, strain_qp, component, order)

project_by_component(stress, stress_qp, component, order)

all_results = []
for ii, probe in enumerate(probes):
fig, results = probe_results(u, strain, stress, probe, labels[ii])

fig.savefig('its2D_interactive_probe_%d.png' % ii)
all_results.append(results)

for ii, results in enumerate(all_results):

output('probe %d:' % ii)
output.level += 2
for key, res in ordered_iteritems(results):
output(key + ':')
val = res[1]
output(' min: %+.2e, mean: %+.2e, max: %+.2e'
% (val.min(), val.mean(), val.max()))
output.level -= 2

if options.show:
# Show the solution. If the approximation order is greater than 1, the
# extra DOFs are simply thrown away.
from sfepy.postprocess.viewer import Viewer

view = Viewer('its2D_interactive.vtk')
view(vector_mode='warp_norm', rel_scaling=1,
is_scalar_bar=True, is_wireframe=True)

if __name__ == '__main__':
main()

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The script can be run from the SfePy top-level directory, assuming the in-place build, as follows:

python sfepy/examples/linear_elasticity/its2D_interactive.py

The script allows setting several parameters that influence the solution, see:

python sfepy/examples/linear_elasticity/its2D_interactive.py -h

for the complete list. Besides the material parameters, a uniform mesh refinement level and the displacement field
approximation order can be specified. The script demonstrates how to
• project a derived quantity, that is evaluated in quadrature points (e.g. a strain or stress), into a field variable;
• probe the solution defined in the field variables.
Using sfepy.discrete.probes allows correct probing of fields with the approximation order greater than one.
The end.

1.5.2 Using Salome with SfePy

Introduction

Salome is a powerful open-source tool for generating meshes for numerical simulation and post processing the results.
This is a short tutorial on using Salome as a preprocessor for preparing meshes for use with SfePy.

Tutorial prerequisites

This tutorial assumes that you have a working copy of Salome. It is possible to build Salome from source code.
Fortunately, for the less brave, many pre-compiled binaries for different platforms are available at the Salome download
page. Registration for a free account may be required to download from the preceding site.
In addition, this tutorial assumes you have a working copy of SfePy with MED read support. See the Installation for
help. Note that it is not actually necessary to “install” SfePy; one may run the code from the source directory (see
notation below) after compilation of the C extension modules (again, see the installation notes if you are confused).

Note on notation used in this tutorial

We are using the following notations:

• <sfepy_root>: the root directory of the SfePy source code
• <work_dir>: the working directory where you plan to save your files

Step 1: Using Salome

Salome has its own set of tutorials and community resources. It is suggested you look around on Salome web site to
familiarize yourself with the available resources.
This tutorial follows the EDF Exercise 1 available from the Salome Tutorial Site. Go ahead and complete this tutorial
now. We will use the result from there in the following.
This is the mesh you should end up with:

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Step 2: Exporting mesh from Salome

In the Salome MESH module, right click on the mesh object Mesh_Partition_Hexa you created in the Salome EDF
Exercise 1 Tutorial and click Export to MED file. Save the file as Mesh_Partition_Hexa.med in your working
directory <work_dir>.

Step 3: Copy SfePy project description files

In this tutorial, we will assume that we need to solve a linear elasticity problem on the mesh generated by Salome. Since
the Salome mesh looks a bit like a fish, we will try to simulate the fish waving its tail.
Copy the file <sfepy_root>/sfepy/examples/linear_elasticity/linear_elastic.py to <work_dir>. Use
your favorite python editor to load this file. We will customize this file for our purposes.

Step 4: Modify linear_elastic.py

Mesh specification

The first thing we have to do is tell SfePy to use our new mesh. Change the line

filename_mesh = data_dir + '/meshes/3d/cylinder.mesh'

to

filename_mesh = 'Mesh_Partition_Hexa.med'

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Region specification

Next, we have to define sensible Regions for the mesh. We will apply a displacement to the Tail and keep the Top and
Bottom of the fish fixed. Change the lines

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < 0.001)', 'facet'),
'Right' : ('vertices in (x > 0.099)', 'facet'),
'SomewhereTop' : ('vertices in (z > 0.017) & (x > 0.03) & (x < 0.07)', 'vertex'),
}

to

regions = {
'Omega' : 'all',
'Tail' : ('vertices in (x < -94)', 'facet'),
'TopFixed' : ('vertices in (z > 9.999) & (x > 54)', 'facet'),
'BotFixed' : ('vertices in (z < 0.001) & (x > 54)', 'facet'),
}

Field specification

The Salome mesh uses hexahedral linear order elements; in SfePy notation these are called 3_8, see User’s Guide.
Just keep the lines

fields = {
'displacement': ('real', 'vector', 'Omega', 1),
}

Boundary condition specifications

In this section, we tell SfePy to fix the top and bottom parts of the “head” of the fish and move the tail 10 units to the
side (z direction).
Change the lines

ebcs = {
'Fixed' : ('Left', {'u.all' : 0.0}),
'Displaced' : ('Right', {'u.0' : 0.01, 'u.[1,2]' : 0.0}),
'PerturbedSurface' : ('SomewhereTop', {'u.2' : 0.005}),
}

to

ebcs = {
'TopFixed' : ('TopFixed', {'u.all' : 0.0}),
'BotFixed' : ('BotFixed', {'u.all' : 0.0}),
'Displaced' : ('Tail', {'u.2' : 10, 'u.[0,1]' : 0.0}),
}

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Step 5: Run SfePy

Save your changes to linear_elastic.py. Now it’s time to run the SfePy calculation. In your <work_dir> in your
terminal type:

./simple.py linear_elastic.py

This will run the SfePy calculation. Some progress information is printed to your screen and the residual (a measure
of the convergence of the solution) is printed for each iteration of the solver. The solver terminates when this residual
is less than a certain value. It should only take 1 iteration since we are solving a linear problem. The results will be
saved to Mesh_Partition_Hexa.vtk.
Now we can view the results of our work. In your terminal, type:

./postproc.py --wireframe --vector-mode=warp_norm -s 2 Mesh_Partition_Hexa.vtk

You should get the following plot. The undeformed mesh is displayed with a wireframe for comparison. Notice how
the fish is bending its tail in response to the applied displacement.
Now you should be able to use meshes created in Salome with SfePy!

1.5.3 Preprocessing: FreeCAD/OpenSCAD + Gmsh

Introduction

There are several open source tools for preparing 2D and 3D finite element meshes like Salome, FreeCAD, Gmsh,
Netgen, etc. Most of them are GUI based geometrical modeling and meshing environments/tools but they also usually
allow using their libraries in user scripts. Some of the above mentioned tools are handy for solid modeling, some
of them are great for meshing. This tutorial shows how to combine solid geometry modeling functions provided by
FreeCAD or OpenSCAD with meshing functions of Gmsh.
The collaboration of modeling, meshing and conversion tools and the workflow are illustrated in the following scheme.

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Creating geometry using FreeCAD

Functionalities of FreeCAD are accessible to Python and can be used to define geometrical models in simple Python
scripts. There is a tutorial related to Python scripting in FreeCAD.
The first step in creating a Python script is to set up a path to the FreeCAD libraries and import all required modules:

1 import sys
2 FREECADPATH = '/usr/lib/freecad/lib/'
3 sys.path.append(FREECADPATH)
4

5 from FreeCAD import Base, newDocument

6 import Part
7 import Draft
8 import ProfileLib.RegularPolygon as Poly

Now, a new empty FreeCAD document can be defined as:

doc = newDocument()

All new objects describing the geometry will be added to this document.
In the following lines a geometrical model of a screwdriver handle will be created. Let’s start by defining a sphere and
a cylinder and join these objects into the one called uni:

1 radius = 0.01
2 height = 0.1
3

4 cyl = doc.addObject("Part::Cylinder", "cyl")

5 cyl.Radius = radius
6 cyl.Height = height
7

8 sph = doc.addObject("Part::Sphere", "sph")

9 sph.Radius = radius
10

11 uni = doc.addObject("Part::MultiFuse", "uni")

12 uni.Shapes = [cyl, sph]

Create a polygon, revolve it around the z-axis to create a solid and use the result as the cutting tool applied to uni
object:

1 ske = doc.addObject('Sketcher::SketchObject', 'Sketch')

2 ske.Placement = Base.Placement(Base.Vector(0, 0, 0),
3 Base.Rotation(-0.707107, 0, 0, -0.707107))
4 Poly.makeRegularPolygon('Sketch', 5,
5 Base.Vector(-1.2 * radius, 0.9 * height, 0),
6 Base.Vector(-0.8 * radius, 0.9 * height, 0))
7

8 cut = doc.addObject("PartDesign::Revolution", "Revolution")

9 cut.Sketch = ske
10 cut.ReferenceAxis = (ske, ['V_Axis'])
11 cut.Angle = 360.0
12

13 dif = doc.addObject("Part::Cut", "dif")

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14 dif.Base = uni
15 dif.Tool = cut

Create a cylinder, make a polar array of the cylinder objects and subtract it from the previous result:

1 cyl1 = doc.addObject("Part::Cylinder", "cyl1")

2 cyl1.Radius = 0.2 * radius
3 cyl1.Height = 1.1 * height
4 cyl1.Placement = Base.Placement(Base.Vector(-1.1 * radius, 0, -0.2 * height),
5 Base.Rotation(0, 0, 0, 1))
6

7 arr = Draft.makeArray(cyl1, Base.Vector(1, 0, 0), Base.Vector(0, 1, 0), 2, 2)

8 arr.ArrayType = "polar"
9 arr.NumberPolar = 6
10

11 dif2 = doc.addObject("Part::Cut", "dif2")

12 dif2.Base = dif
13 dif2.Tool = arr

Create a middle hole for the screwdriver metal part:

1 cyl2 = doc.addObject("Part::Cylinder", "cyl2")

2 cyl2.Radius = 0.3 * radius
3 cyl2.Height = height
4

5 dif3 = doc.addObject("Part::Cut", "dif3")

6 dif3.Base = dif2
7 dif3.Tool = cyl2

Finally, recompute the geometry, export the part to the STEP file and save the document in FreeCAD format (not really
needed for subsequent mesh generation, but may be useful for visualization and geometry check):

1 doc.recompute()
2

3 Part.export([dif3], 'screwdriver_handle.step')
4

5 doc.saveAs('screwdriver_handle.FCStd')

A finite element mesh can be generated directly in FreeCAD using MeshPart module:

1 import MeshPart
2

3 mesh = doc.addObject("Mesh::Feature", "Mesh")

4 mesh.Mesh = MeshPart.meshFromShape(Shape=dif3.Shape, MaxLength=0.002)
5 mesh.Mesh.write("./screwdriver_handle.bdf", "NAS", "mesh")

The meshing function of MeshPart module is limited to triangular grids so it is better to use Gmsh mesh generator
which can provide triangular and quadrilateral meshes in 2D or tetrahedral and hexahedral meshes in 3D. Gmsh allows
to control the meshing process through a wide range of parameters. Meshing by Gmsh will be described in section
Gmsh - generating finite element mesh.

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The example of screwdriver handle: screwdriver_handle.py.

There are two simple ways how to discover Python calls of FreeCAD functions. You can enable “show script
commands in python console” in Edit->Preferences->General->Macro and the Python console by selecting
View->Views->Python Console and all subsequent operations will be printed in the console as the Python code.
The second way is to switch on the macro recording function (Macro->Macro recording ...) which generates a
Python script (FCMacro file) containing all the code related to actions in the FreeCAD graphical interface.

Creating geometry using OpenSCAD

The alternative tool for solid geometrical modeling is OpenSCAD - “The Programmers Solid 3D CAD Modeller”.
It has its own description language based on functional programming that is used to construct solid models using
geometrical primitives similar to FreeCAD. Solid geometries can be exported to several file formats including STL and
CSG. OpenSCAD allows solid modeling based on Constructive Solid Geometry (CSG) principles and extrusion of 2D
objects into 3D. The model of a screwdriver handle presented in the previous section can be defined in OpenSCAD by
the following code (screwdriver_handle.scad):

1 radius = 0.01;
2 height = 0.1;
3 $fn = 50;
4

5 difference() {
6 difference() {
7 difference() {
8 union() {
9 cylinder(center=false, h=height, r=radius);
10 sphere(radius);
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11 };
12 translate([0, 0, 0.9*height])
13 rotate_extrude()
14 polygon([[0.8*radius, 0], [1.8*radius, -0.577*radius], [1.8*radius, 0.
˓→577*radius]]);

15 }
16 cylinder(center=false, h=1.1*height, r=0.3*radius);
17 }
18 for (i = [1:6]) {
19 rotate([0, 0, 360/6*i])
20 translate([-1.1*radius, 0.0, -0.2*height])
21 cylinder(center=false, h=1.1*height, r=0.2*radius);
22 }
23 }

To generate a finite element mesh of the solid geometry the model must be exported to a suitable file format. OpenSCAD
has limited export options, but by using FreeCAD import/export functions, it is possible to find a workaround. The
OpenSCAD model can be exported to the CSG file format and FreeCAD can be used as a mesh converter to the STEP
format:

1 import sys
2 sys.path.append('/usr/lib/freecad/lib/')
3 sys.path.append('/usr/lib/freecad/Mod/OpenSCAD/')
4

5 import FreeCAD
6 import Part
7 import importCSG
8

9 importCSG.open('screwdriver_handle.csg')
10 Part.export([FreeCAD.ActiveDocument.Objects[-1]], 'screwdriver_handle.step')

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Gmsh - generating finite element mesh

Gmsh can create finite element meshes using geometrical models imported from STEP, IGES and BRep files (has to
be compiled with OpenCASCADE support).
The following GEO file imports screwdriver_handle.step file and defines a field controlling the mesh size
(screwdriver_handle.geo):

1 Merge "screwdriver_handle.step";
2

3 Field[1] = MathEval;
4 Field[1].F = "0.002";
5 Background Field = 1;

Now, run Gmsh generator and export the mesh into the MSH format in which all surface and volumetric elements are
stored:

gmsh -3 -format msh -o screwdriver_handle.msh screwdriver_handle.geo

By converting the MSH file into the VTK format using script/convert_mesh.py:

script/convert_mesh.py -d 3 screwdriver_handle.msh screwdriver_handle.vtk

the surface elements are discarded and only the volumetric mesh is preserved.

Note: planar 2D meshes

To create a planar 2D mesh, such as

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that can be described by this Gmsh code, the mesh generator can be called as follows:

gmsh -2 -format msh -o circle_in_square.msh circle_in_square.geo

This, however is not enough to create a truly 2D mesh - the created mesh vertices still have the third, 𝑧, component
which is equal to zero. In order to remove the third component, use:

script/convert_mesh.py --2d circle_in_square.msh circle_in_square.h5

Now, in the resulting circle_in_square.h5, each vertex has only two coordinates. Another way of generating the
2D mesh is to use the legacy VTK format as follows:

gmsh -2 -format vtk -o circle_in_square.vtk circle_in_square.geo

script/convert_mesh.py circle_in_square.vtk circle_in_square.h5

This is due to the fact that the legacy VTK does not support 2D vertices and so the VTKMeshIO reader tries to detect
the planar geometry by comparing the 𝑧 components to zero - the --2d option of script/convert_mesh.py is not
needed in this case.

Multipart models

Meshing models composed of parts with different material groups is a little bit tricky task. But there are some more or
less general ways of doing that. Here, the method using functions of Gmsh for periodic meshes will be shown.
The screwdriver handle example is extended by adding a screwdriver shank. The new part is composed of a cylinder
trimmed at one end:

1 cyl3 = doc.addObject("Part::Cylinder", "cyl3")

2 cyl3.Radius = 0.3 * radius
3 cyl3.Height = height
4 cyl3.Placement = Base.Placement(Base.Vector(0, 0, height),
5 Base.Rotation(0, 0, 0, 1))
6

7 tip1 = doc.addObject("Part::Box", "tip1")

8 tip1.Length = radius
9 tip1.Width = 2 * radius
10 tip1.Height = 3 * radius
11 tip1.Placement = Base.Placement(Base.Vector(0, -radius, 1.71 * height),
12 Base.Rotation(Base.Vector(0, 1, 0), -10),
13 Base.Vector(0, 0, 3 * radius))
14

15 tip2 = doc.addObject("Part::Mirroring", "tip2")

16 tip2.Source = tip1
17 tip2.Normal = (1, 0, 0)
18

19 tip3 = doc.addObject("Part::MultiFuse", "tip3")

20 tip3.Shapes = [tip1, tip2]
21

22 dif4 = doc.addObject("Part::Cut", "dif4")

23 dif4.Base = cyl3
24 dif4.Tool = tip3
25

26 uni2 = doc.addObject("Part::MultiFuse", "uni2")

27 uni2.Shapes = [cyl2, dif4]

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The handle and shank are exported to the STEP file as two separated parts:

1 doc.recompute()
2

3 Part.export([dif3, uni2], 'screwdriver_full.step')

4 doc.saveAs('screwdriver_full.FCStd')

The full screwdriver example (handle + shank): screwdriver_full.py.

To create a coincidence mesh on the handle and shank interface, it is necessary to identify the interface surfaces and
declare them to be periodic in the GEO file. The identification has to be done manually in the Gmsh graphical interface.

The input file for Gmsh is than as follows (screwdriver_full.geo):

1 Merge "screwdriver_full.step";
2

3 Periodic Surface 5 {7} = 26 {67};

4 Periodic Surface 3 {6, 2, -6, 7} = 27 {68, 69, -68, 67};
5

6 Physical Volume(1) = {1};

7 Physical Volume(2) = {2};
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8

9 Field[1] = MathEval;
10 Field[1].F = "0.0015";
11 Background Field = 1;

where the first pair of periodic surfaces corresponds to the common circle faces (bottom of the shank) and the second
pair to the common cylindrical surfaces. See Gmsh Reference manual for details on periodic meshing.
Using the above stated GEO file, Gmsh creates a mesh containing duplicate vertices on the handle/shank interface.
These duplicate vertices can be removed during the conversion to the VTK format by giving --merge (or just -m)
argument to convert_mesh.py script:

script/convert_mesh.py -m screwdriver_full.msh screwdriver_full.vtk

In order to extract the cells by the physical groups use the conversion script with --save-per-mat argument:

script/convert_mesh.py --save-per-mat screwdriver_full.vtk screwdriver.vtk

It produces screwdriver.vtk contaning the original mesh and screwdriver_matid_1.vtk, screwdriver_matid_2.vtk files
containing only the cells of a given physical group and all vertices of the original mesh.

When using OpenSCAD, define the full screwdriver geometry as (screwdriver_full.scad):

1 radius = 0.01;
2 height = 0.1;
3 $fn = 50;
4

5 module tip() {
6 rotate([0, -10, 0])
7 translate([0, -radius, -3*radius])
8 cube([radius, 2*radius, 3*radius], center=false);
9 }
10

11 difference() {
12 difference() {
13 difference() {
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(continued from previous page)

14 union() {
15 cylinder(center=false, h=height, r=radius);
16 sphere(radius);
17 };
18 translate([0, 0, 0.9*height])
19 rotate_extrude()
20 polygon([[0.8*radius, 0], [1.8*radius, -0.577*radius], [1.8*radius, 0.
˓→577*radius]]);

21 }
22 cylinder(center=false, h=height, r=0.3*radius);
23 }
24 for (i = [1:6]) {
25 rotate([0, 0, 360/6*i])
26 translate([-1.1*radius, 0.0, -0.2*height])
27 cylinder(center=false, h=1.1*height, r=0.2*radius);
28 }
29 }
30

31 union() {
32 difference() {
33 translate([0, 0, height])
34 cylinder(center=false, h=height, r=0.3*radius);
35 translate([0, 0, 1.71*height + 3*radius])
36 union() {
37 tip();
38 mirror ([1, 0, 0]) tip();
39 }
40 }
41 cylinder(center=false, h=height, r=0.3*radius);
42 }

and convert the CSG file to the STEP file by:

1 importCSG.open('screwdriver_full.csg')
2 top_group = FreeCAD.ActiveDocument.Objects[-1]
3 Part.export(top_group.OutList, 'screwdriver_full.step')

Since the different tools for geometry definition have been used, the numbering of geometric objects may differ and the
surface and edge numbers have to be changed in the GEO file:

Periodic Surface 5 {6} = 26 {66};

Periodic Surface 3 {5, 2, -5, 6} = 27 {67, 68, -67, 66};

Note: The numbering of objects may vary between FreeCAD, OpenSCAD and Gmsh versions.

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1.5.4 Material Identification

Introduction

This tutorial shows identification of material parameters of a composite structure using data (force-displacement curves)
obtained by a standard tensile test.

Composite structure

The unidirectional long fiber carbon-epoxy composite is considered. Its microstructure was analysed by the scanning
electron microscopy and the data, volume fractions and fibers cross-sections, were used to generate a periodic finite
element mesh (representative volume element - RVE) representing the random composite structure at the microscopic
level (the random structure generation algorithm is described in1 ):

This RVE is used in the micromechanical FE analysis which is based on the two-scale homogenization method.

Material testing

Several carbon-expoxy specimens with different fiber orientations (0, 30, 60 and 90 degrees) were subjected to the
tensile test in order to obtain force-elongation dependencies, see2 . The slopes of the linearized dependencies were used
in an objective function of the identification process.
1 Lubachevsky B. D., How to Simulate Billiards and Similar Systems, Journal of Computational Physics, 94(2), 1991. http://arxiv.org/PS_cache/

cond-mat/pdf/0503/0503627v2.pdf
2 Srbová H., Kroupa T., Zemčík R., Identification of the Material Parameters of a Unidirectional Fiber Composite Using a Micromodel, Materiali

in Tehnologije, 46(5), 2012, 431-434.

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Numerical simulation

The linear isotropic material model is used for both components (fiber and matrix) of the composite so only four material
parameters (Young’s modulus and Poisson’s ratio for each component) are necessary to fully describe the mechanical
behavior of the structure.
The numerical simulations of the tensile tests are based on the homogenization method applied to the linear elastic prob-
lem3 . The homogenization procedure results in the microscopic problem solved within the RVE and the macroscopic
problem that involves the homogenized elastic coefficients.

3 Pinho-da-Cruz L., Oliveira J. A. and Teixeira-Dias F., Asymptotic homogenization in linear elasticity. Part I: Mathematical formulation and

finite element modeling, Computational Materials Science, 45(4), 2009, 1073–1080.

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Homogenized coefficients

The problem at the microscopic level is formulated in terms of characteristic response functions and its solution is used
to evaluate the homogenized elasticity tensor. The microscopic problem has to be solved with the periodic boundary
conditions.
The following SfePy description file is used for definition of the microscopic problem: homogenization_opt_src.
In the case of the identification process function get_mat() obtains the material parameters (Young’s modules, Poisson’s
ratios) from the outer identification loop. Otherwise these parameters are given by values.
Notice the use of parametric_hook (Miscellaneous) to pass around the optimization parameters.

Macroscopic simulation

The homogenized elasticity problem is solved for the unknown macroscopic displacements and the elongation of the
composite specimen is evaluated for a given loading. These values are used to determine the slopes of the calculated
force-elongation dependencies which are required by the objective function.
The SfePy description file for the macroscopic analysis: linear_elasticity_opt_src.

Identification procedure

The identification of material parameters, i.e. the Young’s modulus and Poisson’s ratio, of the epoxy matrix (𝐸𝑚 , 𝜈𝑚 )
and carbon fibers (𝐸𝑓 , 𝜈𝑓 ) can be formulated as a minimization of the following objective function:
(︃ )︃2
𝑖
∑︁ 𝑘𝑐𝑜𝑚𝑝 (x)
Φ(x) = 1− 𝑖
, (1.9)
𝑘𝑒𝑥𝑝
𝑖∈{0,30,60,90}

where 𝑘𝑐𝑜𝑚𝑝
𝑖
and 𝑘𝑒𝑥𝑝
𝑖
are the computed and measured slopes of the force-elongation tangent lines for a given fiber ori-
entation. This function is minimized using scipy.optimize.fmin_tnc(), considering bounds of the identified parameters.
Tho following steps are performed in each iteration of the optimization loop:
1. Solution of the microscopic problem, evaluation of the homogenized elasticity tensor.
2. Solution of the macroscopic problems for different fiber orientations (0, 30, 60, 90), this is incorporated by
appropriate rotation of the elasticity tensor.
3. Evaluation of the objective function.
Python script for material identification: material_opt_src.

Running identification script

Run the script from the command shell as (from the top-level directory of SfePy):

$ python sfepy/examples/homogenization/material_opt.py

The iteration process is monitored using graphs where the values of the objective function and material parameters are
plotted.

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The resulting values of 𝐸𝑓 , 𝜈𝑓 , 𝐸𝑚 , 𝜈𝑚 can be found at the end of the script output:

>>> material optimization FINISHED <<<

material_opt_micro: terminated
optimized parameters: [1.71129526e+11 3.20844131e-01 2.33507829e+09 2.00000000e-01]

So that:
𝐸𝑓 = 171.13 GPa
𝜈𝑓 = 3.21
𝐸𝑚 = 2.34 GPa
𝜈𝑚 = 0.20
Note: The results may vary across SciPy versions and related libraries.

1.5.5 Mesh parametrization

Introduction

When dealing with shape optimization we usually need to modify a FE mesh using a few optimization parameters
describing the mesh geometry. The B-spline parametrization offers an efficient way to do that. A mesh region (2D or
3D) that is to be parametrized is enclosed in the so called spline-box and the positions of all vertices inside the box can
be changed by moving the control points of the B-spline curves.
There are two different classes for the B-spline parametrization implemented in SfePy (module sfepy.mesh.
splinebox): SplineBox and SplineRegion2D. The first one defines a rectangular parametrization box in 2D or
3D while the second one allows to set up an arbitrary shaped region of parametrization in 2D.

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SplineBox

The rectangular B-spline parametrization is created as follows:

1 from sfepy.mesh.splinebox import SplineBox

2

3 spb = SplineBox(<bbox>, <coors>, <nsg>)

the first parameter defines the range of the box in each dimension, the second parameter is the array of coordinates
(vertices) to be parametrized and the last one (optional) determines the number of control points in each dimension.
The number of the control points (𝑛𝑐𝑝) is calculated as:

𝑛𝑐𝑝𝑖 = 𝑛𝑠𝑔𝑖 + 𝑑𝑒𝑔𝑟𝑒𝑒, 𝑖 = 1, 2(, 3) (1.10)

where 𝑑𝑒𝑔𝑟𝑒𝑒 is the degree of the B-spline curve (default value: 3 = cubic spline) and 𝑛𝑠𝑔 is the number of the spline
segments (default value: [1,1(,1)] = 4 control points for all dimensions).
The position of the vertices can be modified by moving the control points:

spb.move_control_point(<cpoint>, <val>)

where <cpoint> is the index or position of the control point, for explanation see the following figure.

The displacement is given by <val>. The modified coordinates of the vertices are evaluated by:

new_coors = spb.evaluate()

Example

• Create a new 2D SplineBox with the left bottom corner at [-1,-1] and the right top corner at [1, 0.6] which has
5 control points in x-direction and 4 control points in y-direction:

1 from sfepy.mesh.splinebox import SplineBox

2 from sfepy.discrete.fem import Mesh
3

4 mesh = Mesh.from_file('meshes/2d/square_tri1.mesh')
5 spb = SplineBox([[-1, 1], [-1, 0.6]], mesh.coors, nsg=[2,1])

• Modify the position of mesh coordinates by moving three control points (with indices 1,2 and 3):

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1 spb.move_control_point(1, [0.1, -0.2])

2 spb.move_control_point(2, [0.2, -0.3])
3 spb.move_control_point(3, [0.0, -0.1])

• Evaluate the new coordinates:

mesh.cmesh.coors[:] = spb.evaluate()

• Write the deformed mesh and the spline control net (the net of control points) into vtk files:

spb.write_control_net('square_tri1_spbox.vtk')
mesh.write('square_tri1_deform.vtk')

The following figures show the undeformed (left) and deformed (right) mesh and the control net.

SplineRegion2D

In this case, the region (only in 2D) of parametrization is defined by four B-spline curves:

1 from sfepy.mesh.splinebox import SplineRegion2D

2

3 spb = SplineRegion2D([<bspl1>, <bspl2>, <bspl3>, <bspl4>], <coors>)

The curves must form a closed loop, must be oriented counterclockwise and the opposite curves (<bspl1>, <bspl3>
and <bspl2>, <bspl4>) must have the same number of control points and the same knot vectors, see the figure below,
on the left.

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The position of the selected vertices, depicted in the figure on the right, are driven by the control points in the same
way as explained above for SplineBox.
Note: Initializing SplineRegion2D may be time consuming due to the fact that for all vertex coordinates the spline
parameters have to be found using an optimization method in which the B-spline basis is repeatedly evaluated.

Example

• First of all, define four B-spline curves (the default degree of the spline curve is 3) representing the boundary of
a parametrization area:

1 from sfepy.mesh.bspline import BSpline

2

3 # left / right boundary

4 line_l = nm.array([[-1, 1], [-1, .5], [-1, 0], [-1, -.5]])
5 line_r = nm.array([[0, -.2], [.1, .2], [.3, .6], [.4, 1]])
6

7 sp_l = BSpline()
8 sp_l.approximate(line_l, ncp=4)
9 kn_lr = sp_l.get_knot_vector()
10

11 sp_r = BSpline()
12 sp_r.approximate(line_r, knots=kn_lr)
13

14 # bottom / top boundary

15 line_b = nm.array([[-1, -.5], [-.8, -.6], [-.5, -.4], [-.2, -.2], [0, -.2]])
16 line_t = nm.array([[.4, 1], [0, 1], [-.2, 1], [-.6, 1], [-1, 1]])
17

18 sp_b = BSpline()
19 sp_b.approximate(line_b, ncp=5)
20 kn_bt = sp_b.get_knot_vector()
21

22 sp_t = BSpline()
23 sp_t.approximate(line_t, knots=kn_bt)

• Create a new 2D SplineRegion2D object:

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1 from sfepy.mesh.splinebox import SplineRegion2D

2

3 spb = SplineRegion2D([sp_b, sp_r, sp_t, sp_l], mesh.coors)

• Move the control points:

1 spb.move_control_point(5, [-.2, .1])

2 spb.move_control_point(10, [-.3, .2])
3 spb.move_control_point(15, [-.1, .2])

• Evaluate the new coordinates:

mesh.cmesh.coors[:] = spb.evaluate()

The figures below show the undeformed (left) and deformed (right) mesh and the control net.

1.5.6 Examples

acoustics

acoustics/acoustics.py

Description
Acoustic pressure distribution.
This example shows how to solve a problem in complex numbers, note the ‘accoustic_pressure’ field definition.
Find 𝑝 such that:
∫︁ ∫︁ ∫︁ ∫︁
𝑐2 ∇𝑞 · ∇𝑝 − 𝑤2 𝑞𝑝 − 𝑖𝑤𝑐 𝑞𝑝 = 𝑖𝑤𝑐2 𝜌𝑣𝑛 𝑞, ∀𝑞 .
Ω Ω Γ𝑜𝑢𝑡 Γ𝑖𝑛

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r"""
Acoustic pressure distribution.

This example shows how to solve a problem in complex numbers, note the
'accoustic_pressure' field definition.

Find :math:`p` such that:

.. math::
c^2 \int_{\Omega} \nabla q \cdot \nabla p
- w^2 \int_{\Omega} q p
- i w c \int_{\Gamma_{out}} q p
= i w c^2 \rho v_n \int_{\Gamma_{in}} q
\;, \quad \forall q \;.
"""
from __future__ import absolute_import
from sfepy import data_dir

filename_mesh = data_dir + '/meshes/2d/special/two_rectangles.mesh'

v_n = 1.0 # m/s

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w = 1000.0
c = 343.0 # m/s
rho = 1.55 # kg/m^3

options = {
'nls' : 'newton',
'ls' : 'ls',
}

materials = {
'one' : ({'one' : 1.0},),
}

regions = {
'Omega' : 'all',
'Gamma_in' : ('vertices in (x < 0.01)', 'facet'),
'Gamma_out' : ('vertices in (x > 0.99)', 'facet'),
}

fields = {
'accoustic_pressure' : ('complex', 1, 'Omega', 1),
}

variables = {
'p' : ('unknown field', 'accoustic_pressure', 0),
'q' : ('test field', 'accoustic_pressure', 'p'),
}

ebcs = {
}

integrals = {
'i' : 2,
}

equations = {
'Acoustic pressure' :
"""%s * dw_laplace.i.Omega( one.one, q, p )
- %s * dw_dot.i.Omega( q, p )
- %s * dw_dot.i.Gamma_out( q, p )
= %s * dw_integrate.i.Gamma_in( q )"""
% (c*c, w*w, 1j*w*c, 1j*w*c*c*rho*v_n)
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-1,
'eps_r' : 1.0,
'macheps' : 1e-16,
'lin_red' : 1e-1, # Linear system error < (eps_a * lin_red).
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'ls_red' : 0.1,
'ls_red_warp' : 0.001,
'ls_on' : 1.1,
'ls_min' : 1e-5,
'check' : 0,
'delta' : 1e-6,
})
}

acoustics/acoustics3d.py

Description
Acoustic pressure distribution in 3D.
Two Laplace equations, one in Ω1 , other in Ω2 , connected on the interface region Γ12 using traces of variables.
Find two complex acoustic pressures 𝑝1 , 𝑝2 such that:
∫︁ ∫︁
𝑘 2 𝑞𝑝 − ∇𝑞 · ∇𝑝
Ω
∫︁ ∫︁ ∫︁ Ω
−𝑖𝑤/𝑐 𝑞𝑝 + 𝑖𝑤𝜌/𝑍 𝑞(𝑝2 − 𝑝1 ) + 𝑖𝑤𝜌/𝑍 𝑞(𝑝1 − 𝑝2 )
Γ𝑜𝑢𝑡 Γ2
∫︁ Γ1
= 𝑖𝑤𝜌 𝑣𝑛 𝑞 , ∀𝑞 .
Γ𝑖𝑛

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r"""
Acoustic pressure distribution in 3D.

Two Laplace equations, one in :math:`\Omega_1`, other in

:math:`\Omega_2`, connected on the interface region :math:`\Gamma_{12}`
using traces of variables.

Find two complex acoustic pressures :math:`p_1`, :math:`p_2` such that:

.. math::
\int_{\Omega} k^2 q p - \int_{\Omega} \nabla q \cdot \nabla p \\
- i w/c \int_{\Gamma_{out}} q p
+ i w \rho/Z \int_{\Gamma_2} q (p_2 - p_1)
+ i w \rho/Z \int_{\Gamma_1} q (p_1 - p_2) \\
= i w \rho \int_{\Gamma_{in}} v_n q
\;, \quad \forall q \;.
"""

from __future__ import absolute_import

from sfepy import data_dir

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filename_mesh = data_dir + '/meshes/3d/acoustics_mesh3d.mesh'

freq = 1200
v_n = 1.0 # m/s
c = 343.0 # m/s
rho = 1.55 # kg/m^3
R = 1000
w = 2.0 * freq

k1 = w / c
rhoc1 = rho * c

coef_k = ((1.0 + 0.1472 * (freq / R)**(-0.577))

+ 1j * (-0.1734 * (freq / R)**(-0.595)))
coef_r = ((1.0 + 0.0855 * (freq / R)**(-0.754))
+ 1j * (-0.0765 * (freq / R)**(-0.732)))

k2 = k1 * coef_k
rhoc2 = rhoc1 * coef_r

# perforation geometry parameters

tw = 0.9e-3
dh = 2.49e-3
por = 0.08

# acoustic impedance
Z = rho * c / por * (0.006 + 1j * k1 * (tw + 0.375 * dh
* (1 + rhoc2/rhoc1 * k2/k1)))

regions = {
'Omega' : 'all',
'Omega_1' : 'cells of group 1',
'Omega_2' : 'cells of group 2',
'Gamma_12' : ('r.Omega_1 *v r.Omega_2', 'facet'),
'Gamma_12_1' : ('copy r.Gamma_12', 'facet', 'Omega_1'),
'Gamma_12_2' : ('copy r.Gamma_12', 'facet', 'Omega_2'),
'Gamma_in' : ('vertices in (z < 0.001)', 'facet'),
'Gamma_out' : ('vertices in (z > 0.157)', 'facet'),
}

materials = {
}

fields = {
'accoustic_pressure_1' : ('complex', 'scalar', 'Omega_1', 1),
'accoustic_pressure_2' : ('complex', 'scalar', 'Omega_2', 1),
}

variables = {
'p_1' : ('unknown field', 'accoustic_pressure_1'),
'q_1' : ('test field', 'accoustic_pressure_1', 'p_1'),
'p_2' : ('unknown field', 'accoustic_pressure_2'),
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'q_2' : ('test field', 'accoustic_pressure_2', 'p_2'),
}

ebcs = {
}

integrals = {
'i' : 2,
}

equations = {
'Acoustic pressure' :
"""%s * dw_dot.i.Omega_1(q_1, p_1)
+ %s * dw_dot.i.Omega_2(q_2, p_2)
- dw_laplace.i.Omega_1(q_1, p_1)
- dw_laplace.i.Omega_2(q_2, p_2)
- %s * dw_dot.i.Gamma_out(q_1, p_1)
+ %s * dw_jump.i.Gamma_12_1(q_1, p_1, tr(p_2))
+ %s * dw_jump.i.Gamma_12_2(q_2, p_2, tr(p_1))
= %s * dw_integrate.i.Gamma_in(q_1)"""
% (k1*k1, k2*k2,
1j*k1,
1j*k1*rhoc1 / Z, 1j*k2*rhoc2 / Z,
1j*k1*rhoc1 * v_n)
}

options = {
'nls': 'newton',
'ls': 'ls',
'file_per_var': True,
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
'eps_r' : 1.0,
'macheps' : 1e-16,
'lin_red' : 1e-1,
'ls_red' : 0.1,
'ls_red_warp' : 0.001,
'ls_on' : 1.1,
'ls_min' : 1e-5,
'check' : 0,
'delta' : 1e-6,
})
}

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acoustics/vibro_acoustic3d.py

Description
Vibro-acoustic problem
3D acoustic domain with 2D perforated deforming interface.
Master problem: defined in 3D acoustic domain (vibro_acoustic3d.py)
Slave subproblem: 2D perforated interface (vibro_acoustic3d_mid.py)
Master 3D problem - find 𝑝 (acoustic pressure) and 𝑔 (transversal acoustic velocity) such that:
∫︁ ∫︁ ∫︁ ∫︁ ∫︁ ∫︁
𝑐2 ∇𝑞 · ∇𝑝 − 𝜔 2 𝑞𝑝 + 𝑖𝜔𝑐 𝑞𝑝 + 𝑖𝜔𝑐 𝑞𝑝 − 𝑖𝜔𝑐2 (𝑞 + − 𝑞 − )𝑔 = 2𝑖𝜔𝑐 𝑞 𝑝¯ , ∀𝑞 ,
Ω Ω Γ𝑖𝑛 Γ𝑜𝑢𝑡 Γ0 Γ𝑖𝑛
∫︁ ∫︁ ∫︁
−𝑖𝜔 𝑓 (𝑝+ − 𝑝− ) − 𝜔 2 𝐹 𝑓 𝑔 + 𝜔2 𝐶𝑓 𝑤 = 0 , ∀𝑓 ,
Γ0 Γ0 Γ0

Slave 2D subproblem - find 𝑤 (plate deflection) and 𝜃 (rotation) such that:

∫︁ ∫︁ ∫︁ ∫︁
2 2
𝜔 𝐶𝑧𝑔 − 𝜔 𝑆𝑧𝑤 + ∇𝑧 · 𝐺 · ∇𝑤 − 𝜃 · 𝐺 · ∇𝑧 = 0 , ∀𝑧 ,
Γ0 Γ0 Γ0 Γ0
∫︁ ∫︁ ∫︁ ∫︁
−𝜔 2 𝑅𝜈 ·𝜃 + 𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝜈)𝑒𝑘𝑙 (𝜃) − 𝜈 · 𝐺 · ∇𝑤 + 𝜈·𝐺·𝜃 =0, ∀𝜈 ,
Γ0 Γ0 Γ0 Γ0

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r"""
Vibro-acoustic problem

3D acoustic domain with 2D perforated deforming interface.

*Master problem*: defined in 3D acoustic domain (``vibro_acoustic3d.py``)

*Slave subproblem*: 2D perforated interface (``vibro_acoustic3d_mid.py``)

Master 3D problem - find :math:`p` (acoustic pressure)

and :math:`g` (transversal acoustic velocity) such that:

.. math::
c^2 \int_{\Omega} \nabla q \cdot \nabla p
- \omega^2 \int_{\Omega} q p
+ i \omega c \int_{\Gamma_{in}} q p
+ i \omega c \int_{\Gamma_{out}} q p
- i \omega c^2 \int_{\Gamma_0} (q^+ - q^-) g
= 2i \omega c \int_{\Gamma_{in}} q \bar{p}
\;, \quad \forall q \;,

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- i \omega \int_{\Gamma_0} f (p^+ - p^-)
- \omega^2 \int_{\Gamma_0} F f g
+ \omega^2 \int_{\Gamma_0} C f w
= 0
\;, \quad \forall f \;,

Slave 2D subproblem - find :math:`w` (plate deflection)

and :math:`\ul{\theta}` (rotation) such that:

.. math::
\omega^2 \int_{\Gamma_0} C z g
- \omega^2 \int_{\Gamma_0} S z w
+ \int_{\Gamma_0} \nabla z \cdot \ull{G} \cdot \nabla w
- \int_{\Gamma_0} \ul{\theta} \cdot \ull{G} \cdot \nabla z
= 0
\;, \quad \forall z \;,

- \omega^2 \int_{\Gamma_0} R\, \ul{\nu} \cdot \ul{\theta}

+ \int_{\Gamma_0} D_{ijkl} e_{ij}(\ul{\nu}) e_{kl}(\ul{\theta})
- \int_{\Gamma_0} \ul{\nu} \cdot \ull{G} \cdot \nabla w
+ \int_{\Gamma_0} \ul{\nu} \cdot \ull{G} \cdot \ul{\theta}
= 0
\;, \quad \forall \ul{\nu}
\;,
"""
from __future__ import absolute_import
from sfepy import data_dir, base_dir
filename_mesh = data_dir + '/meshes/3d/acoustic_wg.vtk'

sound_speed = 343.0
wave_num = 5.5
p_inc = 300

c = sound_speed
c2 = c**2
w = wave_num * c
w2 = w**2
wc = w * c
wc2 = w * c2

regions = {
'Omega1': 'cells of group 1',
'Omega2': 'cells of group 2',
'GammaIn': ('vertices of group 1', 'face'),
'GammaOut': ('vertices of group 2', 'face'),
'Gamma_aux': ('r.Omega1 *v r.Omega2', 'face'),
'Gamma0_1': ('copy r.Gamma_aux', 'face', 'Omega1'),
'Gamma0_2': ('copy r.Gamma_aux', 'face', 'Omega2'),
'aux_Left': ('vertices in (x < 0.001)', 'face'),
'aux_Right': ('vertices in (x > 0.299)', 'face'),
'Gamma0_1_Left': ('r.Gamma0_1 *v r.aux_Left', 'edge'),
'Gamma0_1_Right': ('r.Gamma0_1 *v r.aux_Right', 'edge'),
}
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fields = {
'pressure1': ('complex', 'scalar', 'Omega1', 1),
'pressure2': ('complex', 'scalar', 'Omega2', 1),
'tvelocity': ('complex', 'scalar', 'Gamma0_1', 1),
'deflection': ('complex', 'scalar', 'Gamma0_1', 1),
}

variables = {
'p1': ('unknown field', 'pressure1', 0),
'q1': ('test field', 'pressure1', 'p1'),
'p2': ('unknown field', 'pressure2', 1),
'q2': ('test field', 'pressure2', 'p2'),
'g0': ('unknown field', 'tvelocity', 2),
'f0': ('test field', 'tvelocity', 'g0'),
'w': ('unknown field', 'deflection', 3),
'z': ('test field', 'deflection', 'w'),
}

ebcs = {
'fixed_l': ('Gamma0_1_Left', {'w.0': 0.0}),
'fixed_r': ('Gamma0_1_Right', {'w.0': 0.0}),
}

options = {
'file_per_var': True,
}

functions = {
}

materials = {
'ac' : ({'F': -2.064e+00, 'c': -1.064e+00}, ),
}

equations = {
'eq_1' : """
%e * dw_laplace.5.Omega1(q1, p1)
+ %e * dw_laplace.5.Omega2(q2, p2)
- %e * dw_dot.5.Omega1(q1, p1)
- %e * dw_dot.5.Omega2(q2, p2)
+ %s * dw_dot.5.GammaIn(q1, p1)
+ %s * dw_dot.5.GammaOut(q2, p2)
- %s * dw_dot.5.Gamma0_1(q1, g0)
+ %s * dw_dot.5.Gamma0_2(q2, tr(g0))
= %s * dw_integrate.5.GammaIn(q1)"""\
% (c2, c2, w2, w2,
1j * wc, 1j * wc,
1j * wc2, 1j * wc2,
2j * wc * p_inc),
'eq_2' : """
- %s * dw_dot.5.Gamma0_1(f0, p1)
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+ %s * dw_dot.5.Gamma0_1(f0, tr(p2))
- %e * dw_dot.5.Gamma0_1(ac.F, f0, g0)
+ %e * dw_dot.5.Gamma0_1(ac.c, f0, w)
= 0"""\
% (1j * w, 1j * w, w2, w2),
}

solvers = {
'ls': ('ls.cm_pb',
{'others': [base_dir
+ '/examples/acoustics/vibro_acoustic3d_mid.py'],
'coupling_variables': ['g0', 'w'],
}),
'nls': ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-6,
'eps_r' : 1e-6,
})
}

dg

dg/advection_1D.py

Description
Transient advection equation in 1D solved using discontinous galerkin method.

𝑑𝑝
+ 𝑎 · 𝑑𝑝/𝑑𝑥 = 0
𝑑𝑡
𝑝(𝑡, 0) = 𝑝(𝑡, 1)

Usage Examples

Run with simple.py script:

python simple.py sfepy/examples/dg/advection_1D.py

To view animated results use script/dg_plot_1D.py specifing name of the output in output/ folder, default is
dg/advection_1D:

python simple.py script/dg_plot_1D.py dg/advection_1D

script/dg_plot_1D.py also accepts full and relative paths:

python ./script/dg_plot_1D.py output/dg/advection_1D

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r"""
Transient advection equation in 1D solved using discontinous galerkin method.

.. math:: \frac{dp}{dt} + a \cdot dp/dx = 0

p(t,0) = p(t,1)

Usage Examples
--------------
Run with simple.py script::

python simple.py sfepy/examples/dg/advection_1D.py

To view animated results use ``script/dg_plot_1D.py`` specifing name of the

output in ``output/`` folder, default is ``dg/advection_1D``::

python simple.py script/dg_plot_1D.py dg/advection_1D

``script/dg_plot_1D.py`` also accepts full and relative paths::

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python ./script/dg_plot_1D.py output/dg/advection_1D

"""
from sfepy.examples.dg.example_dg_common import *
from sfepy.discrete.dg.limiters import MomentLimiter1D

dim = 1

def define(filename_mesh=None,
approx_order=2,

adflux=0.0,
limit=True,

cw=None,
diffcoef=None,
diffscheme="symmetric",

cfl=0.4,
dt=None,
t1=0.1
):

t0 = 0
transient = True

mstart = 0
mend = 1

diffcoef = None
cw = None

example_name = "advection_1D"
dim = 1

if filename_mesh is None:
filename_mesh = get_gen_1D_mesh_hook(0, 1, 100)

materials = {
'a': ({'val': [1.0], '.flux': adflux},),

regions = {
'Omega': 'all',
'Gamma': ('vertices of surface', 'facet'),
'left': ('vertices in x == 0', 'vertex'),
'right': ('vertices in x == 1', 'vertex')
}

fields = {
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'f': ('real', 'scalar', 'Omega', str(approx_order) + 'd', 'DG', 'legendre')
}

variables = {
'p': ('unknown field', 'f', 0, 1),
'v': ('test field', 'f', 'p'),
}

dgebcs = {
'u_left': ('left', {'p.all': 0}),
'u_righ': ('right', {'p.all': 0}),
}

dgepbc_1 = {
'name' : 'u_rl',
'region': ['right', 'left'],
'dofs': {'p.all': 'p.all'},
'match': 'match_y_line',
}

integrals = {
'i': 2 * approx_order,
}

equations = {
'Advection': """
dw_dot.i.Omega(v, p)
- dw_s_dot_mgrad_s.i.Omega(a.val, p[-1], v)
+ dw_dg_advect_laxfrie_flux.i.Omega(a.flux, a.val, v, p[-1]) = 0
"""
}

solvers = {
"tss": ('ts.tvd_runge_kutta_3',
{"t0" : t0,
"t1" : t1,
'limiters': {"f": MomentLimiter1D} if limit else {}
}),
'nls': ('nls.newton', {}),
'ls' : ('ls.scipy_direct', {})
}

options = {
'ts' : 'tss',
'nls' : 'newton',
'ls' : 'ls',
'save_times' : 100,
'active_only' : False,
'pre_process_hook': get_cfl_setup(cfl)
if dt is None else
get_cfl_setup(dt=dt),
'output_dir' : 'output/dg/' + example_name,
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'output_format' : "vtk",
}

functions = {}

def local_register_function(fun):
try:
functions.update({fun.__name__: (fun,)})

except AttributeError: # Already a sfepy Function.

fun = fun.function
functions.update({fun.__name__: (fun,)})

return fun

def four_step_p(x):
"""
piecewise constant (-inf, 1.8],(1.8, a + 4](a+4, a + 5](a + 5, inf)
"""
return nm.piecewise(x,
[x <= mstart,
x <= mstart + .4,
mstart + .4 < x,
mstart + .5 <= x],
[0, 0, .5, 0])

@local_register_function
def get_ic(x, ic=None):
return four_step_p(x)

def analytic_sol(coors, t=None, uset=False):

x = coors[..., 0]
if uset:
res = get_ic(x[..., None] - t[None, ...])
return res # for animating transient problem

res = get_ic(x[..., None])

return res[..., 0]

@local_register_function
def sol_fun(ts, coors, mode="qp", **kwargs):
t = ts.time
if mode == "qp":
return {"p": analytic_sol(coors, t)[..., None, None]}

ics = {
'ic': ('Omega', {'p.0': 'get_ic'}),
}

return locals()

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globals().update(define())

dg/advection_2D.py

Description
Transient advection equation in 2D solved by discontinous Galerkin method.
𝑑𝑝
+ 𝑎 · 𝑔𝑟𝑎𝑑 𝑝 = 0
𝑑𝑡

Usage Examples

Run with simple.py script:

python simple.py examples/dg/advection_2D.py

Results are saved to output/dg/advection_2D folder by default as .msh files, the best way to view them is through GMSH
(http://gmsh.info/) version 4.6 or newer. Start GMSH and use File | Open menu or Crtl + O shortcut, navigate to the
output folder, select all .msh files and hit Open, all files should load as one item in Post-processing named p_cell_nodes.
GMSH is capable of rendering high order approximations in individual elements, to modify fidelity of rendering, double
click the displayed mesh, quick options menu should pop up, click on All view options.... This brings up the
Options window with View [0] selected in left column. Under the tab General ensure that Adapt visualization
grid is ticked, then you can adjust Maximum recursion depth and `Target visualization error to tune the
visualization. To see visualization elements (as opposed to mesh elements) go to Visibility tab and tick Draw
element outlines, this option is also available from quick options menu as View element outlines or under
shortcut Alt+E. In the quick options menu, you can also modify normal raise by clicking View Normal Raise to see
solution rendered as surface above the mesh. Note that for triangular meshes normal raise -1 produces expected raise
above the mesh. This is due to the opposite orientation of the reference elements in GMSH and Sfepy and might get
patched in the future.
source code

r"""
Transient advection equation in 2D solved by discontinous Galerkin method.

.. math:: \frac{dp}{dt} + a\cdot grad\,p = 0

Usage Examples
--------------

Run with simple.py script::

python simple.py sfepy/examples/dg/advection_2D.py

Results are saved to output/dg/advection_2D folder by default as ``.msh`` files,

the best way to view them is through GMSH (http://gmsh.info/) version 4.6 or
newer. Start GMSH and use ``File | Open`` menu or Crtl + O shortcut, navigate to
the output folder, select all ``.msh`` files and hit Open, all files should load
as one item in Post-processing named p_cell_nodes.
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GMSH is capable of rendering high order approximations in individual elements,

to modify fidelity of rendering, double click the displayed mesh, quick options
menu should pop up, click on ``All view options...``. This brings up the Options
window with ``View [0]`` selected in left column. Under the tab ``General``
ensure that ``Adapt visualization grid`` is ticked, then you can adjust
``Maximum recursion depth`` and ```Target visualization error`` to tune
the visualization. To see visualization elements (as opposed to mesh elements)
go to ``Visibility`` tab and tick ``Draw element outlines``, this option is also
available from quick options menu as ``View element outlines`` or under shortcut
``Alt+E``. In the quick options menu, you can also modify normal raise by
clicking ``View Normal Raise`` to see solution rendered as surface above the
mesh. Note that for triangular meshes normal raise -1 produces expected raise
above the mesh. This is due to the opposite orientation of the reference
elements in GMSH and Sfepy and might get patched in the future.
"""
from sfepy.examples.dg.example_dg_common import *
from sfepy.discrete.dg.limiters import MomentLimiter2D

mesh_center = (0.5, 0.25)

mesh_size = (1.0, 0.5)

def define(filename_mesh=None,
approx_order=2,

adflux=0,
limit=True,

cw=None,
diffcoef=None,
diffscheme="symmetric",

cfl=0.4,
dt=None,
t1=0.01

):

example_name = "advection_2D"
dim = 2

diffcoef = None
cw = None

if filename_mesh is None:
filename_mesh = get_gen_block_mesh_hook((1., 1.), (20, 20), (.5, .5))

t0 = 0.

angle = 0
# get_common(approx_order, cfl, t0, t1, None, get_ic)
rotm = nm.array([[nm.cos(angle), -nm.sin(angle)],
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[nm.sin(angle), nm.cos(angle)]])
velo = nm.sum(rotm.T * nm.array([1., 0.]), axis=-1)[:, None]
materials = {
'a': ({'val': [velo], '.flux': adflux},),
}

regions = {
'Omega' : 'all',
'left': ('vertices in x == 0', 'edge'),
'right': ('vertices in x == 1', 'edge'),
'top': ('vertices in y == 1', 'edge'),
'bottom': ('vertices in y == 0', 'edge')
}

fields = {
'f': ('real', 'scalar', 'Omega', str(approx_order) + 'd', 'DG', 'legendre') #
}

variables = {
'p': ('unknown field', 'f', 0, 1),
'v': ('test field', 'f', 'p'),
}

def gsmooth(x):
"""
.. :math: C_0^{\inf}
"""
return .3 * nm.piecewise(x, [x <= 0.1, x >= 0.1, .3 < x],
[0, lambda x:
nm.exp(1 / ((10 * (x - .2)) ** 2 - 1) + 1),
0])

def analytic_sol(coors, t):

x_1 = coors[..., 0]
x_2 = coors[..., 1]
sin = nm.sin
pi = nm.pi
exp = nm.exp
# res = four_step_u(x_1) * four_step_u(x_2)
res = gsmooth(x_1) * gsmooth(x_2)
return res

@local_register_function
def sol_fun(ts, coors, mode="qp", **kwargs):
t = ts.time
if mode == "qp":
return {"p": analytic_sol(coors, t)[..., None, None]}

def get_ic(x, ic=None):

return gsmooth(x[..., 0:1]) * gsmooth(x[..., 1:])

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functions = {
'get_ic': (get_ic,)
}

ics = {
'ic': ('Omega', {'p.0': 'get_ic'}),
}

dgepbc_1 = {
'name': 'u_rl',
'region': ['right', 'left'],
'dofs': {'p.all': 'p.all'},
'match': 'match_y_line',
}

integrals = {
'i': 3 * approx_order,
}

equations = {
'Advection': """
dw_dot.i.Omega(v, p)
- dw_s_dot_mgrad_s.i.Omega(a.val, p[-1], v)
+ dw_dg_advect_laxfrie_flux.i.Omega(a.flux, a.val, v, p[-1]) = 0
"""
}

solvers = {
"tss": ('ts.tvd_runge_kutta_3',
{"t0" : t0,
"t1" : t1,
'limiters': {"f": MomentLimiter2D} if limit else {}}),
'nls': ('nls.newton',{}),
'ls' : ('ls.scipy_direct', {})
}

options = {
'ts' : 'tss',
'nls' : 'newton',
'ls' : 'ls',
'save_times' : 100,
'active_only' : False,
'output_dir' : 'output/dg/' + example_name,
'output_format' : 'msh',
'file_format' : 'gmsh-dg',
'pre_process_hook': get_cfl_setup(cfl) if dt is None else get_cfl_setup(dt=dt)
}

return locals()

globals().update(define())

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dg/advection_diffusion_2D.py

Description
Static advection-diffusion equation in 2D solved by discontinous Galerkin method.

𝑎 · 𝑔𝑟𝑎𝑑 𝑝 − 𝑑𝑖𝑣(𝑔𝑟𝑎𝑑 𝑝) = 0

Based on
Antonietti, P., & Quarteroni, A. (2013). Numerical performance of discontinuous and stabilized continuous
Galerkin methods for convection-diffusion problems.

Usage Examples

Run with simple.py script:

python simple.py examples/dg/advection_diffusion_2D.py

Results are saved to output/dg/advection_diffusion_2D folder by default as ` .msh` files, the best way to view them is
through GMSH (http://gmsh.info/) version 4.6 or newer. Start GMSH and use File | Open menu or Crtl + O shortcut,
navigate to the output folder, select all .msh files and hit Open, all files should load as one item in Post-processing named
p_cell_nodes.
GMSH is capable of rendering high order approximations in individual elements, to modify fidelity of rendering, double
click the displayed mesh, quick options menu should pop up, click on All view options.... This brings up the
Options window with View [0] selected in left column. Under the tab General ensure that Adapt visualization
grid is ticked, then you can adjust Maximum recursion depth and `Target visualization error to tune the
visualization. To see visualization elements (as opposed to mesh elements) go to Visibility tab and tick Draw
element outlines, this option is also available from quick options menu as View element outlines or under
shortcut Alt+E. In the quick options menu, you can also modify normal raise by clicking View Normal Raise to see
solution rendered as surface above the mesh. Note that for triangular meshes normal raise -1 produces expected raise
above the mesh. This is due to the opposite orientation of the reference elements in GMSH and Sfepy and might get
patched in the future.
source code

r"""
Static advection-diffusion equation in 2D solved by discontinous Galerkin method.

.. math:: a \cdot grad\, p - div(grad\,p) = 0

Based on

Antonietti, P., & Quarteroni, A. (2013). Numerical performance of discontinuous

and stabilized continuous Galerkin methods for convection-diffusion problems.

Usage Examples
--------------

Run with simple.py script::

python simple.py sfepy/examples/dg/advection_diffusion_2D.py

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Results are saved to output/dg/advection_diffusion_2D folder by default as `

`.msh`` files, the best way to view them is through GMSH (http://gmsh.info/)
version 4.6 or newer. Start GMSH and use ``File | Open`` menu or Crtl + O
shortcut, navigate to the output folder, select all ``.msh`` files and hit Open,
all files should load as one item in Post-processing named p_cell_nodes.

GMSH is capable of rendering high order approximations in individual elements,

to modify fidelity of rendering, double click the displayed mesh, quick options
menu should pop up, click on ``All view options...``. This brings up the Options
window with ``View [0]`` selected in left column. Under the tab ``General``
ensure that ``Adapt visualization grid`` is ticked, then you can adjust
``Maximum recursion depth`` and ```Target visualization error`` to tune
the visualization. To see visualization elements (as opposed to mesh elements)
go to ``Visibility`` tab and tick ``Draw element outlines``, this option is also
available from quick options menu as ``View element outlines`` or under shortcut
``Alt+E``. In the quick options menu, you can also modify normal raise by
clicking ``View Normal Raise`` to see solution rendered as surface above the
mesh. Note that for triangular meshes normal raise -1 produces expected raise
above the mesh. This is due to the opposite orientation of the reference
elements in GMSH and Sfepy and might get patched in the future.
"""

from sfepy.examples.dg.example_dg_common import *

def define(filename_mesh=None,
approx_order=3,

adflux=0,
limit=False,

cw=1000,
diffcoef=1,
diffscheme="symmetric",

cfl=None,
dt=None,
):

cfl = None
dt = None

functions = {}
def local_register_function(fun):
try:
functions.update({fun.__name__: (fun,)})

except AttributeError: # Already a sfepy Function.

fun = fun.function
functions.update({fun.__name__: (fun,)})

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return fun

example_name = "advection_diffusion_2D"
dim = 2

if filename_mesh is None:
filename_mesh = get_gen_block_mesh_hook((1., 1.), (20, 20), (.5, .5))

velo = [1., 1.]

angle = 0.0 # - nm.pi / 5

rotm = nm.array([[nm.cos(angle), -nm.sin(angle)],
[nm.sin(angle), nm.cos(angle)]])
velo = nm.sum(rotm.T * nm.array(velo), axis=-1)[:, None]

regions = {
'Omega' : 'all',
'left' : ('vertices in x == 0', 'edge'),
'right': ('vertices in x == 1', 'edge'),
'top' : ('vertices in y == 1', 'edge'),
'bottom': ('vertices in y == 0', 'edge')
}

fields = {
'f': ('real', 'scalar', 'Omega', str(approx_order) + 'd', 'DG', 'legendre')
}

variables = {
'p': ('unknown field', 'f', 0),
'v': ('test field', 'f', 'p'),
}

integrals = {
'i': 2 * approx_order,
}

@local_register_function
def bc_funs(ts, coors, bc, problem):
# return 2*coors[..., 1]
t = ts.dt*ts.step
x_1 = coors[..., 0]
x_2 = coors[..., 1]
res = nm.zeros(nm.shape(x_1))

sin = nm.sin
cos = nm.cos
exp = nm.exp
pi = nm.pi

if bc.diff == 0:
if "left" in bc.name:
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res[:] = 0
elif "right" in bc.name:
res[:] = 0
elif "bottom" in bc.name:
res[:] = 0 #-2*sin(2*pi*x_1)
elif "top" in bc.name:
res[:] = 0

elif bc.diff == 1:
if "left" in bc.name:
res = nm.stack((-2*pi*(x_2**2 - x_2),
res),
axis=-2)
elif "right" in bc.name:
res = nm.stack((-2*pi*(x_2**2 - x_2), res,),
axis=-2)
elif "bot" in bc.name:
res = nm.stack((res,
sin(2*pi*x_1)),
axis=-2)
elif "top" in bc.name:
res = nm.stack((res,
-sin(2*pi*x_1)),
axis=-2)

return res

@local_register_function
def source_fun(ts, coors, mode="qp", **kwargs):
# t = ts.dt * ts.step
eps = diffcoef
sin = nm.sin
cos = nm.cos
exp = nm.exp
sqrt = nm.sqrt
pi = nm.pi
if mode == "qp":
x_1 = coors[..., 0]
x_2 = coors[..., 1]
res = -2*pi*(x_2**2 - x_2)*cos(2*pi*x_1)\
- 2*(2*pi**2*(x_2**2 - x_2)*sin(2*pi*x_1) - sin(2*pi*x_1))*eps\
- (2*x_2 - 1)*sin(2*pi*x_1)
return {"val": res[..., None, None]}

def analytic_sol(coors, t):

x_1 = coors[..., 0]
x_2 = coors[..., 1]
sin = nm.sin
pi = nm.pi
res = -(x_2 ** 2 - x_2) * sin(2 * pi * x_1)
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return res

@local_register_function
def sol_fun(ts, coors, mode="qp", **kwargs):
t = ts.time
if mode == "qp":
return {"p": analytic_sol(coors, t)[..., None, None]}

dgebcs = {
'u_left' : ('left', {'p.all': "bc_funs", 'grad.p.all' : "bc_funs"}),
'u_top' : ('top', {'p.all': "bc_funs", 'grad.p.all' : "bc_funs"}),
'u_bot' : ('bottom', {'p.all': "bc_funs", 'grad.p.all' : "bc_funs"}),
'u_right': ('right', {'p.all': "bc_funs", 'grad.p.all' : "bc_funs"}),
}

materials = {
'a' : ({'val': [velo], '.flux': adflux},),
'D' : ({'val': [diffcoef], '.cw': cw},),
'g' : 'source_fun'
}

equations = {
'balance': """
- dw_s_dot_mgrad_s.i.Omega(a.val, p, v)
+ dw_dg_advect_laxfrie_flux.i.Omega(a.flux, a.val, v, p)
"""
+
" + dw_laplace.i.Omega(D.val, v, p) " +
diffusion_schemes_implicit[diffscheme] +
" + dw_dg_interior_penalty.i.Omega(D.val, D.cw, v, p)" +
" - dw_volume_lvf.i.Omega(g.val, v)" +
"= 0"
}

solver_0 = {
'name' : 'ls',
'kind' : 'ls.scipy_direct',
}

solver_1 = {
'name' : 'newton',
'kind' : 'nls.newton',

'i_max' : 5,
'eps_a' : 1e-8,
'eps_r' : 1.0,
'macheps' : 1e-16,
'lin_red' : 1e-2, # Linear system error < (eps_a * lin_red).
'ls_red' : 0.1,
'ls_red_warp' : 0.001,
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'ls_on' : 0.99999,
'ls_min' : 1e-5,
'check' : 0,
'delta' : 1e-6,
}

options = {
'nls' : 'newton',
'ls' : 'ls',
'output_dir' : 'output/dg/' + example_name,
'output_format' : 'msh',
'file_format' : 'gmsh-dg'
}
return locals()

globals().update(define())
pass

dg/burgers_2D.py

Description
Burgers equation in 2D solved using discontinous Galerkin method

𝑑𝑝
+ 𝑑𝑖𝑣 𝑓 (𝑝) − 𝑑𝑖𝑣(𝑔𝑟𝑎𝑑 𝑝) = 0
𝑑𝑡
Based on
Kučera, V. (n.d.). Higher order methods for the solution of compressible flows. Charles University. p. 21 eq. (1.39)

Usage Examples

Run with simple.py script:

python simple.py examples/dg/burgers_2D.py

Results are saved to output/dg/burgers_2D folder by default as .msh files, the best way to view them is through GMSH
(http://gmsh.info/) version 4.6 or newer. Start GMSH and use File | Open menu or Crtl + O shortcut, navigate to the
output folder, select all .msh files and hit Open, all files should load as one item in Post-processing named p_cell_nodes.
GMSH is capable of rendering high order approximations in individual elements, to modify fidelity of rendering, double
click the displayed mesh, quick options menu should pop up, click on All view options.... This brings up the
Options window with View [0] selected in left column. Under the tab General ensure that Adapt visualization
grid is ticked, then you can adjust Maximum recursion depth and `Target visualization error to tune the
visualization. To see visualization elements (as opposed to mesh elements) go to Visibility tab and tick Draw
element outlines, this option is also available from quick options menu as View element outlines or under
shortcut Alt+E. In the quick options menu, you can also modify normal raise by clicking View Normal Raise to see
solution rendered as surface above the mesh. Note that for triangular meshes normal raise -1 produces expected raise
above the mesh. This is due to the opposite orientation of the reference elements in GMSH and Sfepy and might get
patched in the future.

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source code

r"""
Burgers equation in 2D solved using discontinous Galerkin method

.. math:: \frac{dp}{dt} + div\,f(p) - div(grad\,p) = 0

Based on

Kučera, V. (n.d.). Higher order methods for the solution of compressible flows.
Charles University. p. 21 eq. (1.39)

Usage Examples
--------------

Run with simple.py script::

python simple.py sfepy/examples/dg/burgers_2D.py

Results are saved to output/dg/burgers_2D folder by default as ``.msh`` files,

the best way to view them is through GMSH (http://gmsh.info/) version 4.6 or
newer. Start GMSH and use ``File | Open`` menu or Crtl + O shortcut, navigate to
the output folder, select all ``.msh`` files and hit Open, all files should load
as one item in Post-processing named p_cell_nodes.

GMSH is capable of rendering high order approximations in individual elements,

to modify fidelity of rendering, double click the displayed mesh, quick options
menu should pop up, click on ``All view options...``. This brings up the Options
window with ``View [0]`` selected in left column. Under the tab ``General``
ensure that ``Adapt visualization grid`` is ticked, then you can adjust
``Maximum recursion depth`` and ```Target visualization error`` to tune
the visualization. To see visualization elements (as opposed to mesh elements)
go to ``Visibility`` tab and tick ``Draw element outlines``, this option is also
available from quick options menu as ``View element outlines`` or under shortcut
``Alt+E``. In the quick options menu, you can also modify normal raise by
clicking ``View Normal Raise`` to see solution rendered as surface above the
mesh. Note that for triangular meshes normal raise -1 produces expected raise
above the mesh. This is due to the opposite orientation of the reference
elements in GMSH and Sfepy and might get patched in the future.
"""

from sfepy.examples.dg.example_dg_common import *

from sfepy import data_dir

from sfepy.discrete.dg.limiters import MomentLimiter2D, IdentityLimiter

mesh_center = (0, 0)
mesh_size = (2, 2)

def define(filename_mesh=None,
approx_order=2,
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adflux=0,
limit=False,

cw=10,
diffcoef=0.002,
diffscheme="symmetric",

cfl=None,
dt=1e-5,
t1=0.01
):

functions = {}
def local_register_function(fun):
try:
functions.update({fun.__name__: (fun,)})

except AttributeError: # Already a sfepy Function.

fun = fun.function
functions.update({fun.__name__: (fun,)})

return fun

example_name = "burgers_2D"
dim = 2

if filename_mesh is None:
filename_mesh = data_dir + "/meshes/2d/square_tri2.mesh"

t0 = 0.
if dt is None and cfl is None:
dt = 1e-5

velo = [1., 1.]

angle = 0 # - nm.pi / 5
rotm = nm.array([[nm.cos(angle), -nm.sin(angle)],
[nm.sin(angle), nm.cos(angle)]])
velo = nm.sum(rotm.T * nm.array(velo), axis=-1)[:, None]
burg_velo = velo.T / nm.linalg.norm(velo)

regions = {
'Omega': 'all',
'left' : ('vertices in x == -1', 'edge'),
'right': ('vertices in x == 1', 'edge'),
'top' : ('vertices in y == 1', 'edge'),
'bottom': ('vertices in y == -1', 'edge')
}

fields = {
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'f': ('real', 'scalar', 'Omega',
str(approx_order) + 'd', 'DG', 'legendre')
}

variables = {
'p': ('unknown field', 'f', 0, 1),
'v': ('test field', 'f', 'p'),
}

integrals = {
'i': 5,
}

def analytic_sol(coors, t):

x_1 = coors[..., 0]
x_2 = coors[..., 1]
sin = nm.sin
pi = nm.pi
exp = nm.exp
res = -(exp(-t) - 1)*(sin(5*x_1*x_2) + sin(-4*x_1*x_2 + 4*x_1 + 4*x_2))
return res

@local_register_function
def sol_fun(ts, coors, mode="qp", **kwargs):
t = ts.time
if mode == "qp":
return {"p": analytic_sol(coors, t)[..., None, None]}

@local_register_function
def bc_funs(ts, coors, bc, problem):
# return 2*coors[..., 1]
t = ts.dt*ts.step
x_1 = coors[..., 0]
x_2 = coors[..., 1]
sin = nm.sin
cos = nm.cos
exp = nm.exp
if bc.diff == 0:
if "left" in bc.name:
res = -(exp(-t) - 1)*(sin(-5*x_2) + sin(8*x_2 - 4))
elif "bottom" in bc.name:
res = -(exp(-t) - 1) * (sin(-5 * x_1) + sin(8 * x_1 - 4))
elif "right" in bc.name:
res = -(exp(-t) - 1)*(sin(4) + sin(5*x_2))
elif "top" in bc.name:
res = -(exp(-t) - 1)*(sin(4) + sin(5*x_1))

elif bc.diff == 1:
if "left" in bc.name:
res = nm.stack(((4*(x_2 - 1)*cos(4) - 5*x_2*cos(5*x_2))*
(exp(-t) - 1),
-5*(exp(-t) - 1)*cos(5*x_2)),
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axis=-2)
elif "bottom" in bc.name:
res = nm.stack(((5*cos(-5*x_1) - 8*cos(8*x_1 - 4))*(exp(-t) - 1),
-(5*x_1*cos(-5*x_1) - 4*(x_1 - 1)*cos(8*x_1 - 4))*
(exp(-t) - 1)),
axis=-2)

elif "right" in bc.name:

res = nm.stack(((4*(x_2 - 1)*cos(4) - 5*x_2*cos(5*x_2))*
(exp(-t) - 1),
-5*(exp(-t) - 1)*cos(5*x_2)),
axis=-2)
elif "top" in bc.name:
res = nm.stack((-5*(exp(-t) - 1)*cos(5*x_1),
(4*(x_1 - 1)*cos(4) - 5*x_1*cos(5*x_1))*
(exp(-t) - 1)),
axis=-2)

return res

@local_register_function
def source_fun(ts, coors, mode="qp", **kwargs):
if mode == "qp":
t = ts.dt * ts.step
x_1 = coors[..., 0]
x_2 = coors[..., 1]
sin = nm.sin
cos = nm.cos
exp = nm.exp
res = (
+ (5 * x_1 * cos(5 * x_1 * x_2)
- 4 * (x_1 - 1) * cos(4 * x_1 * x_2 - 4 * x_1 - 4 * x_2)) *
(exp(-t) - 1) ** 2 * (sin(5 * x_1 * x_2)
- sin(4 * x_1 * x_2 - 4 * x_1 - 4 * x_2))
+ (5 * x_2 * cos(5 * x_1 * x_2)
- 4 * (x_2 - 1) * cos(4 * x_1 * x_2 - 4 * x_1 - 4 * x_2)) *
(exp(-t) - 1) ** 2 * (sin(5 * x_1 * x_2)
- sin(4 * x_1 * x_2 - 4 * x_1 - 4 * x_2))
- diffcoef *
((25 * x_1 ** 2 * sin(5 * x_1 * x_2) - 16 * (x_1 - 1) ** 2 *
sin(4 * x_1 * x_2 - 4 * x_1 - 4 * x_2)) * (exp(-t) - 1)
+ (25 * x_2 ** 2 * sin(5 * x_1 * x_2) - 16 * (x_2 - 1) ** 2 *
sin(4 * x_1 * x_2 - 4 * x_1 - 4 * x_2)) * (exp(-t) - 1))
+ (sin(5 * x_1 * x_2) - sin(4 * x_1 * x_2 - 4 * x_1 - 4 * x_2))*
exp(-t)
)
return {"val": res[..., None, None]}

def adv_fun(p):
vu = velo.T * p[..., None]
return vu

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def adv_fun_d(p):
v1 = velo.T * nm.ones(p.shape + (1,))
return v1

def burg_fun(p):
vu = .5*burg_velo * p[..., None] ** 2
return vu

def burg_fun_d(p):
v1 = burg_velo * p[..., None]
return v1

materials = {
'a' : ({'val': [velo], '.flux':adflux},),
'D' : ({'val': [diffcoef], '.Cw': cw},),
'g' : 'source_fun'
}

ics = {
'ic': ('Omega', {'p.0': 0}),
}

dgebcs = {
'u_left' : ('left', {'p.all': 'bc_funs', 'grad.p.all': 'bc_funs'}),
'u_right' : ('right', {'p.all': 'bc_funs', 'grad.p.all': 'bc_funs'}),
'u_bottom' : ('bottom', {'p.all': 'bc_funs', 'grad.p.all': 'bc_funs'}),
'u_top' : ('top', {'p.all': 'bc_funs', 'grad.p.all': 'bc_funs'}),
}

equations = {
'balance':
"dw_dot.i.Omega(v, p)" +
# non-linear hyperbolic terms
" - dw_ns_dot_grad_s.i.Omega(burg_fun, burg_fun_d, p[-1], v)" +
" + dw_dg_nonlinear_laxfrie_flux.i.Omega(a.flux, burg_fun, burg_fun_d, v, p[-1])
˓→" +

# diffusion
" + dw_laplace.i.Omega(D.val, v, p[-1])" +
diffusion_schemes_explicit[diffscheme] +
" - dw_dg_interior_penalty.i.Omega(D.val, D.Cw, v, p[-1])"
# source
+ " - dw_volume_lvf.i.Omega(g.val, v)"
" = 0"
}

solvers = {
"tss.tvd_runge_kutta_3": ('ts.tvd_runge_kutta_3',
{"t0": t0,
"t1": t1,
'limiters': {
"f": MomentLimiter2D} if limit else {}}),
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"tss.euler": ('ts.euler',
{"t0" : t0,
"t1" : t1,
'limiters': {"f": MomentLimiter2D} if limit else {}}),
'nls': ('nls.newton', {}),
'ls' : ('ls.scipy_direct', {})
}

options = {
'ts' : 'tss.euler',
'nls' : 'nls.newton',
'ls' : 'ls.mumps',
'save_times' : 100,
'output_dir' : 'output/dg/' + example_name,
'output_format' : 'msh',
'file_format' : 'gmsh-dg',
'pre_process_hook': get_cfl_setup(CFL=cfl, dt=dt)
}

return locals()

globals().update(define())

dg/example_dg_common.py

Description
Functions common to DG examples
source code

"""
Functions common to DG examples
"""
import os
from glob import glob

import numpy as nm

from sfepy.base.base import output

from sfepy.discrete.fem import Mesh
from sfepy.discrete.fem.meshio import UserMeshIO
from sfepy.mesh.mesh_generators import gen_block_mesh

diffusion_schemes_implicit = {
"symmetric":
" + dw_dg_diffusion_flux.i.Omega(D.val, p, v)"
+ " + dw_dg_diffusion_flux.i.Omega(D.val, v, p)",
"non-symmetric":
" + dw_dg_diffusion_flux.i.Omega(D.val, p, v)"
+ " - dw_dg_diffusion_flux.i.Omega(D.val, v, p)",
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"incomplete":
" + dw_dg_diffusion_flux.i.Omega(D.val, p, v)"}

diffusion_schemes_explicit = {
"symmetric":
" - dw_dg_diffusion_flux.i.Omega(D.val, p[-1], v)"
+ " - dw_dg_diffusion_flux.i.Omega(D.val, v, p[-1])",
"non-symmetric":
" - dw_dg_diffusion_flux.i.Omega(D.val, p[-1], v)"
+ " + dw_dg_diffusion_flux.i.Omega(D.val, v, p[-1])",
"incomplete":
" - dw_dg_diffusion_flux.i.Omega(D.val, p[-1], v)"}

functions = {}
def local_register_function(fun):
try:
functions.update({fun.__name__: (fun,)})

except AttributeError: # Already a sfepy Function.

fun = fun.function
functions.update({fun.__name__: (fun,)})

return fun

def get_cfl_setup(CFL=None, dt=None):

"""
Provide either CFL or dt to create preprocess hook that sets up
Courant-Friedrichs-Levi stability condition for either advection or
diffusion.

Parameters
----------
CFL : float, optional
dt: float, optional

Returns
-------
setup_cfl_condition : callable
expects sfepy.discrete.problem as argument

"""

if CFL is None and dt is None:

raise ValueError("Specifiy either CFL or dt in CFL setup")

def setup_cfl_condition(problem):
"""
Sets up CFL condition for problem ts_conf in problem

Parameters
----------
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problem : discrete.problem.Problem
"""
ts_conf = problem.ts_conf
mesh = problem.domain.mesh
dim = mesh.dim
first_field = list(problem.fields.values())[0]
first_field_name = list(problem.fields.keys())[0]
approx_order = first_field.approx_order
mats = problem.create_materials(['a', 'D'])
try:
# make this more general?
# maybe require material name in parameter
velo = problem.conf_materials['material_a__0'].values["val"]
max_velo = nm.max(nm.linalg.norm(velo))
except KeyError:
max_velo = 1

try:
# make this more general?
# maybe require material name in parameter
diffusion = problem.conf_materials['material_D__0'].values["val"]
max_diffusion = nm.max(nm.linalg.norm(diffusion))
except KeyError:
max_diffusion = None

dx = nm.min(problem.domain.mesh.cmesh.get_volumes(dim))

output("Preprocess hook - setup_cfl_condition:...")

output("Approximation order of field {}({}) is {}"
.format(first_field_name, first_field.family_name, approx_order))
output("Space divided into {0} cells, {1} steps, step size {2}"
.format(mesh.n_el, len(mesh.coors), dx))

if dt is None:
adv_dt = get_cfl_advection(max_velo, dx, approx_order, CFL)
diff_dt = get_cfl_diffusion(max_diffusion, dx, approx_order, CFL)
_dt = min(adv_dt, diff_dt)
else:
output("CFL coefficient {0} ignored, dt specified directly"
.format(CFL))
_dt = dt

tn = int(nm.ceil((ts_conf.t1 - ts_conf.t0) / _dt))

dtdx = _dt / dx

ts_conf.dt = _dt
ts_conf.n_step = tn
ts_conf.cour = max_velo * dtdx

output("Time divided into {0} nodes, {1} steps, step size is {2}"
.format(tn - 1, tn, _dt))
output("Courant number c = max(norm(a)) * dt/dx = {0}"
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.format(ts_conf.cour))
output("Time stepping solver is {}".format(ts_conf.kind))
output("... CFL setup done.")

return setup_cfl_condition

def get_cfl_advection(max_velo, dx, approx_order, CFL):

"""

Parameters
----------
max_velo : float
dx : float
approx_order : int
CFL : CFL

Returns
-------
dt : float
"""
order_corr = 1. / (2 * approx_order + 1)

dt = dx / max_velo * CFL * order_corr

if not (nm.isfinite(dt)):
dt = 1
output(("CFL advection: CFL coefficient was {0} " +
"and order correction 1/{1} = {2}")
.format(CFL, (2 * approx_order + 1), order_corr))
output("CFL advection: resulting dt={}".format((dt)))
return dt

def get_cfl_diffusion(max_diffusion, dx, approx_order, CFL,

do_order_corr=False):
"""

Parameters
----------
max_diffusion : float
dx : float
approx_order : int
CFL : float
do_order_corr : bool

Returns
-------
dt : float
"""
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if max_diffusion is None:
return 1

if do_order_corr:
order_corr = 1. / (2 * approx_order + 1)
else:
order_corr = 1

dt = dx**2 / max_diffusion * CFL * order_corr

if not (nm.isfinite(dt)):
dt = 1
output(("CFL diffusion: CFL coefficient was {0} " +
"and order correction 1/{1} = {2}")
.format(CFL, (2 * approx_order + 1), order_corr))
output("CFL diffusion: resulting dt={}".format(dt))
return dt

def get_gen_1D_mesh_hook(XS, XE, n_nod):

"""

Parameters
----------
XS : float
leftmost coordinate
XE : float
rightmost coordinate
n_nod : int
number of nodes, number of cells is then n_nod - 1

Returns
-------
mio : UserMeshIO instance
"""
def mesh_hook(mesh, mode):
"""
Generate the 1D mesh.
"""
if mode == 'read':

coors = nm.linspace(XS, XE, n_nod).reshape((n_nod, 1))

conn = nm.arange(n_nod, dtype=nm.int32) \
.repeat(2)[1:-1].reshape((-1, 2))
mat_ids = nm.zeros(n_nod - 1, dtype=nm.int32)
descs = ['1_2']

mesh = Mesh.from_data('uniform_1D{}'.format(n_nod), coors, None,

[conn], [mat_ids], descs)
return mesh

elif mode == 'write':

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pass

mio = UserMeshIO(mesh_hook)
return mio

def get_gen_block_mesh_hook(dims, shape, centre, mat_id=0, name='block',

coors=None, verbose=True):
"""

Parameters
----------
dims : array of 2 or 3 floats
Dimensions of the block.
shape : array of 2 or 3 ints
Shape (counts of nodes in x, y, z) of the block mesh.
centre : array of 2 or 3 floats
Centre of the block.
mat_id : int, optional
The material id of all elements.
name : string
Mesh name.
verbose : bool
If True, show progress of the mesh generation.

Returns
-------
mio : UserMeshIO instance
"""
def mesh_hook(mesh, mode):
"""
Generate the 1D mesh.
"""
if mode == 'read':

mesh = gen_block_mesh(dims, shape, centre, mat_id=mat_id, name=name,

coors=coors, verbose=verbose)
return mesh

elif mode == 'write':

pass

mio = UserMeshIO(mesh_hook)
return mio

def clear_folder(clear_format, confirm=False, doit=True):

"""
Deletes files matching the format

Parameters
----------
clear_format : str
confirm : bool
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doit : bool
if False do not delete anything no matter the confirmation

Returns
-------
deleted_anything :
True if there was something to delete
"""
files = glob(clear_format)
if confirm:
for file in files:
output("Will delete file {}".format(file))
doit = input("--------------\nDelete files [Y/n]? ").strip() == "Y"

if doit:
for file in files:
os.remove(file)
return bool(files)

dg/imperative_burgers_1D.py

Description
Burgers equation in 1D solved using discontinous Galerkin method
source code
#!/usr/bin/env python
"""
Burgers equation in 1D solved using discontinous Galerkin method
"""
import argparse
import sys
sys.path.append('.')
from os.path import join as pjoin

import numpy as nm

from sfepy.examples.dg.example_dg_common import \

clear_folder, get_gen_1D_mesh_hook
from script.dg_plot_1D import load_and_plot_fun

# sfepy imports
from sfepy.base.base import IndexedStruct
from sfepy.base.base import Struct, configure_output, output
from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.conditions import InitialCondition, EssentialBC, Conditions
from sfepy.discrete.dg.fields import DGField
from sfepy.discrete.dg.limiters import MomentLimiter1D
from sfepy.discrete.fem import FEDomain
from sfepy.solvers.ls import ScipyDirect
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from sfepy.solvers.nls import Newton
from sfepy.solvers.ts_dg_solvers import TVDRK3StepSolver
from sfepy.terms.terms_dg import Term

def parse_args(argv=None):
if argv is None:
argv = sys.argv

parser = argparse.ArgumentParser(
description='Solve Burgers equation and display animated results, '
'change script code to modify the problem.',
epilog='(c) 2019 T. Zitka , Man-machine Interaction at NTC UWB')
parser.add_argument('-o', '--output-dir', default='.',
help='output directory')
parser.add_argument('-p', '--plot',
action='store_true', dest='plot',
default=False, help='plot animated results')
options = parser.parse_args(argv[1:])
return options

def main(argv=None):
options = parse_args(argv=argv)

# vvvvvvvvvvvvvvvv #
approx_order = 2
# ^^^^^^^^^^^^^^^^ #

# Setup output names

outputs_folder = options.output_dir

domain_name = "domain_1D"
problem_name = "iburgers_1D"
output_folder = pjoin(outputs_folder, problem_name, str(approx_order))
output_format = "vtk"
save_timestn = 100
clear_folder(pjoin(output_folder, "*." + output_format))
configure_output({'output_screen': True,
'output_log_name':
pjoin(output_folder,
f"last_run_{problem_name}_{approx_order}.txt")})

# ------------
# | Get mesh |
# ------------
X1 = 0.
XN = 1.
n_nod = 100
n_el = n_nod - 1
mesh = get_gen_1D_mesh_hook(X1, XN, n_nod).read(None)

# -----------------------------
# | Create problem components |
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# -----------------------------

integral = Integral('i', order=approx_order * 2)

domain = FEDomain(domain_name, mesh)
omega = domain.create_region('Omega', 'all')
left = domain.create_region('Gamma1',
'vertices in x == %.10f ' % X1,
'vertex')
right = domain.create_region('Gamma2',
'vertices in x == %.10f ' % XN,
'vertex')
field = DGField('dgfu', nm.float64, 'scalar', omega,
approx_order=approx_order)

u = FieldVariable('u', 'unknown', field, history=1)

v = FieldVariable('v', 'test', field, primary_var_name='u')

MassT = Term.new('dw_dot(v, u)', integral, omega, u=u, v=v)

velo = nm.array(1.0)

def adv_fun(u):
vu = velo.T * u[..., None]
return vu

def adv_fun_d(u):
v1 = velo.T * nm.ones(u.shape + (1,))
return v1

burg_velo = velo.T / nm.linalg.norm(velo)

def burg_fun(u):
vu = burg_velo * u[..., None] ** 2
return vu

def burg_fun_d(u):
v1 = 2 * burg_velo * u[..., None]
return v1

StiffT = Term.new('dw_ns_dot_grad_s(fun, fun_d, u[-1], v)',

integral, omega,
u=u, v=v,
fun=burg_fun, fun_d=burg_fun_d)

# alpha = Material('alpha', val=[.0])

# FluxT = AdvectDGFluxTerm("adv_lf_flux(a.val, v, u)", "a.val, v, u[-1]",
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# integral, omega, u=u, v=v, a=a, alpha=alpha)

FluxT = Term.new('dw_dg_nonlinear_laxfrie_flux(fun, fun_d, v, u[-1])',

integral, omega,
u=u, v=v,
fun=burg_fun, fun_d=burg_fun_d)

eq = Equation('balance', MassT - StiffT + FluxT)

eqs = Equations([eq])

# ------------------------------
# | Create boundary conditions |
# ------------------------------
left_fix_u = EssentialBC('left_fix_u', left, {'u.all': 1.0})
right_fix_u = EssentialBC('right_fix_u', right, {'u.all': 0.0})

# ----------------------------
# | Create initial condition |
# ----------------------------
def ghump(x):
"""
Nice gaussian.
"""
return nm.exp(-200 * x ** 2)

def ic_wrap(x, ic=None):

return ghump(x - .3)

ic_fun = Function('ic_fun', ic_wrap)

ics = InitialCondition('ic', omega, {'u.0': ic_fun})

# ------------------
# | Create problem |
# ------------------
pb = Problem(problem_name,
equations=eqs,
conf=Struct(options={"save_times": save_timestn},
ics={}, ebcs={}, epbcs={}, lcbcs={},
materials={}),
active_only=False)
pb.setup_output(output_dir=output_folder, output_format=output_format)
pb.set_ics(Conditions([ics]))

# ------------------
# | Create limiter |
# ------------------
limiter = MomentLimiter1D

# ---------------------------
# | Set time discretization |
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# ---------------------------
CFL = .2
max_velo = nm.max(nm.abs(velo))
t0 = 0
t1 = .2
dx = nm.min(mesh.cmesh.get_volumes(1))
dt = dx / max_velo * CFL / (2 * approx_order + 1)
tn = int(nm.ceil((t1 - t0) / dt))
dtdx = dt / dx

# ------------------
# | Create solver |
# ------------------
ls = ScipyDirect({})
nls_status = IndexedStruct()
nls = Newton({'is_linear': True}, lin_solver=ls, status=nls_status)

tss_conf = {'t0' : t0,

't1' : t1,
'n_step' : tn,
'limiters': {"dgfu": limiter}}

tss = TVDRK3StepSolver(tss_conf,
nls=nls, context=pb, verbose=True)

# ---------
# | Solve |
# ---------
pb.set_solver(tss)
state_end = pb.solve()

output("Solved equation \n\n\t\t u_t - div(f(u))) = 0\n")

output(f"With IC: {ic_fun.name}")
# output("and EBCs: {}".format(pb.ebcs.names))
# output("and EPBCS: {}".format(pb.epbcs.names))
output("-------------------------------------")
output(f"Approximation order is {approx_order}")
output(f"Space divided into {mesh.n_el} cells, " +
f"{len(mesh.coors)} steps, step size is {dx}")
output(f"Time divided into {tn - 1} nodes, {tn} steps, step size is {dt}")
output(f"CFL coefficient was {CFL} and " +
f"order correction {1 / (2 * approx_order + 1)}")
output(f"Courant number c = max(abs(u)) * dt/dx = {max_velo * dtdx}")
output("------------------------------------------")
output(f"Time stepping solver is {tss.name}")
output(f"Limiter used: {limiter.name}")
output("======================================")

# ----------
# | Plot 1D|
# ----------
if options.plot:
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load_and_plot_fun(output_folder, domain_name,
t0, t1, min(tn, save_timestn),
ic_fun)

if __name__ == '__main__':
main()

dg/laplace_2D.py

Description
Laplace equation solved in 2d by discontinous Galerkin method

−𝑑𝑖𝑣(𝑔𝑟𝑎𝑑 𝑝) = 0

on rectangle
p = 0 p_y = 0
[0,b]—————————–[a, b]
|
|
p_x = -a | p(x,y) | p_x = 0 p = 0 | | p = 0
|
[0,0]—————————–[a, 0] p_y = b p = 0
solution to this is

𝑝(𝑥, 𝑦) = 1/2 * 𝑥 * *2 − 1/2 * 𝑦 * *2 − 𝑎 * 𝑥 + 𝑏 * 𝑦

Usage Examples

Run with simple.py script:

python simple.py examples/dg/laplace_2D.py

Results are saved to output/dg/laplace_2D folder by default as .msh files, the best way to view them is through GMSH
(http://gmsh.info/) version 4.6 or newer. Start GMSH and use File | Open menu or Crtl + O shortcut, navigate to the
output folder, select all .msh files and hit Open, all files should load as one item in Post-processing named p_cell_nodes.
GMSH is capable of rendering high order approximations in individual elements, to modify fidelity of rendering, double
click the displayed mesh, quick options menu should pop up, click on All view options.... This brings up the
Options window with View [0] selected in left column. Under the tab General ensure that Adapt visualization
grid is ticked, then you can adjust Maximum recursion depth and `Target visualization error to tune the
visualization. To see visualization elements (as opposed to mesh elements) go to Visibility tab and tick Draw
element outlines, this option is also available from quick options menu as View element outlines or under
shortcut Alt+E. In the quick options menu, you can also modify normal raise by clicking View Normal Raise to see
solution rendered as surface above the mesh. Note that for triangular meshes normal raise -1 produces expected raise
above the mesh. This is due to the opposite orientation of the reference elements in GMSH and Sfepy and might get
patched in the future.

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source code

r"""
Laplace equation solved in 2d by discontinous Galerkin method

.. math:: - div(grad\,p) = 0

on rectangle
p = 0
p_y = 0
[0,b]-----------------------------[a, b]
| |
| |
p_x = -a | p(x,y) | p_x = 0
p = 0 | | p = 0
| |
[0,0]-----------------------------[a, 0]
p_y = b
p = 0

solution to this is
.. math:: p(x,y) = 1/2*x**2 - 1/2*y**2 - a*x + b*y

Usage Examples
--------------

Run with simple.py script::

python simple.py sfepy/examples/dg/laplace_2D.py

Results are saved to output/dg/laplace_2D folder by default as ``.msh`` files,

the best way to view them is through GMSH (http://gmsh.info/) version 4.6 or
newer. Start GMSH and use ``File | Open`` menu or Crtl + O shortcut, navigate to
the output folder, select all ``.msh`` files and hit Open, all files should load
as one item in Post-processing named p_cell_nodes.

GMSH is capable of rendering high order approximations in individual elements,

to modify fidelity of rendering, double click the displayed mesh, quick options
menu should pop up, click on ``All view options...``. This brings up the Options
window with ``View [0]`` selected in left column. Under the tab ``General``
ensure that ``Adapt visualization grid`` is ticked, then you can adjust
``Maximum recursion depth`` and ```Target visualization error`` to tune
the visualization. To see visualization elements (as opposed to mesh elements)
go to ``Visibility`` tab and tick ``Draw element outlines``, this option is also
available from quick options menu as ``View element outlines`` or under shortcut
``Alt+E``. In the quick options menu, you can also modify normal raise by
clicking ``View Normal Raise`` to see solution rendered as surface above the
mesh. Note that for triangular meshes normal raise -1 produces expected raise
above the mesh. This is due to the opposite orientation of the reference
elements in GMSH and Sfepy and might get patched in the future.
"""

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from sfepy.examples.dg.example_dg_common import *

def define(filename_mesh=None,
approx_order=2,

adflux=None,
limit=False,

cw=100,
diffcoef=1,
diffscheme="symmetric",

cfl=None,
dt=None,
):

cfl = None
dt = None

functions = {}
def local_register_function(fun):
try:
functions.update({fun.__name__: (fun,)})

except AttributeError: # Already a sfepy Function.

fun = fun.function
functions.update({fun.__name__: (fun,)})

return fun

example_name = "laplace_2D"
dim = 2

if filename_mesh is None:
filename_mesh = get_gen_block_mesh_hook((1., 1.), (16, 16), (.5, .5))

a = 1
b = 1
c = 0

regions = {
'Omega' : 'all',
'left' : ('vertices in x == 0', 'edge'),
'right': ('vertices in x == 1', 'edge'),
'top' : ('vertices in y == 1', 'edge'),
'bottom': ('vertices in y == 0', 'edge')
}
fields = {
'f': ('real', 'scalar', 'Omega', str(approx_order) + 'd', 'DG', 'legendre') #
}

variables = {
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'p': ('unknown field', 'f', 0, 1),
'v': ('test field', 'f', 'p'),
}

def analytic_sol(coors, t):

x_1, x_2 = coors[..., 0], coors[..., 1]
res = 1/2*x_1**2 - 1/2*x_2**2 - a*x_1 + b*x_2 + c
return res

@local_register_function
def sol_fun(ts, coors, mode="qp", **kwargs):
t = ts.time
if mode == "qp":
return {"p": analytic_sol(coors, t)[..., None, None]}

@local_register_function
def bc_funs(ts, coors, bc, problem):
t = ts.time
x_1, x_2 = coors[..., 0], coors[..., 1]
res = nm.zeros(x_1.shape)
if bc.diff == 0:
res[:] = analytic_sol(coors, t)

elif bc.diff == 1:
res = nm.stack((x_1 - a, -x_2 + b),
axis=-2)
return res

materials = {
'D' : ({'val': [diffcoef], '.Cw': cw},),
}

dgebcs = {
'u_left' : ('left', {'p.all': "bc_funs", 'grad.p.all': "bc_funs"}),
'u_right' : ('right', {'p.all': "bc_funs", 'grad.p.all': "bc_funs"}),
'u_bottom' : ('bottom', {'p.all': "bc_funs", 'grad.p.all': "bc_funs"}),
'u_top' : ('top', {'p.all': "bc_funs", 'grad.p.all': "bc_funs"}),

integrals = {
'i': 2 * approx_order,
}

equations = {
'laplace': " dw_laplace.i.Omega(D.val, v, p) " +
diffusion_schemes_implicit[diffscheme] +
" + dw_dg_interior_penalty.i.Omega(D.val, D.Cw, v, p)" +
" = 0"
}

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solver_0 = {
'name' : 'ls',
'kind' : 'ls.scipy_direct',
}

solver_1 = {
'name' : 'newton',
'kind' : 'nls.newton',

# 'i_max' : 5,
# 'eps_a' : 1e-8,
# 'eps_r' : 1.0,
# 'macheps' : 1e-16,
# 'lin_red' : 1e-2, # Linear system error < (eps_a * lin_red).
# 'ls_red' : 0.1,
# 'ls_red_warp' : 0.001,
# 'ls_on' : 0.99999,
# 'ls_min' : 1e-5,
# 'check' : 0,
# 'delta' : 1e-6,
}

options = {
'nls' : 'newton',
'ls' : 'ls',
'output_dir' : 'output/dg/' + example_name,
'output_format' : 'msh',
'file_format' : 'gmsh-dg',
# 'pre_process_hook': get_cfl_setup(cfl)
}
return locals()

globals().update(define())

diffusion

diffusion/cube.py

Description
Laplace equation (e.g. temperature distribution) on a cube geometry with different boundary condition values on the
cube sides. This example was used to create the SfePy logo.
Find 𝑇 such that:
∫︁
𝑐∇𝑠 · ∇𝑇 = 0 , ∀𝑠 .
Ω

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source code

r"""
Laplace equation (e.g. temperature distribution) on a cube geometry with
different boundary condition values on the cube sides. This example was
used to create the SfePy logo.

Find :math:`T` such that:

.. math::
\int_{\Omega} c \nabla s \cdot \nabla T
= 0
\;, \quad \forall s \;.
"""
from __future__ import absolute_import
from sfepy import data_dir

#filename_mesh = data_dir + '/meshes/3d/cube_big_tetra.mesh'

filename_mesh = data_dir + '/meshes/3d/cube_medium_hexa.mesh'

############# Laplace.

material_1 = {
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'name' : 'coef',
'values' : {'val' : 1.0},
}

field_1 = {
'name' : 'temperature',
'dtype' : 'real',
'shape' : (1,),
'region' : 'Omega',
'approx_order' : 1,
}

if filename_mesh.find('cube_medium_hexa.mesh') >= 0:
region_1000 = {
'name' : 'Omega',
'select' : 'cells of group 0',
}
integral_1 = {
'name' : 'i',
'order' : 1,
}
solver_0 = {
'name' : 'ls',
'kind' : 'ls.scipy_direct',
}

elif filename_mesh.find('cube_big_tetra.mesh') >= 0:

region_1000 = {
'name' : 'Omega',
'select' : 'cells of group 6',
}
integral_1 = {
'name' : 'i',
'quadrature' : 'custom',
'vals' : [[1./3., 1./3., 1./3.]],
'weights' : [0.5]
}
solver_0 = {
'name' : 'ls',
'kind' : 'ls.scipy_iterative',

'method' : 'cg',
'i_max' : 1000,
'eps_r' : 1e-12,
}

variable_1 = {
'name' : 'T',
'kind' : 'unknown field',
'field' : 'temperature',
'order' : 0, # order in the global vector of unknowns
}
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variable_2 = {
'name' : 's',
'kind' : 'test field',
'field' : 'temperature',
'dual' : 'T',
}

region_0 = {
'name' : 'Surface',
'select' : 'vertices of surface',
'kind' : 'facet',
}
region_1 = {
'name' : 'Bottom',
'select' : 'vertices in (z < -0.4999999)',
'kind' : 'facet',
}
region_2 = {
'name' : 'Top',
'select' : 'vertices in (z > 0.4999999)',
'kind' : 'facet',
}
region_03 = {
'name' : 'Left',
'select' : 'vertices in (x < -0.4999999)',
'kind' : 'facet',
}

ebc_1 = {
'name' : 'T0',
'region' : 'Surface',
'dofs' : {'T.0' : -3.0},
}
ebc_4 = {
'name' : 'T1',
'region' : 'Top',
'dofs' : {'T.0' : 1.0},
}
ebc_3 = {
'name' : 'T2',
'region' : 'Bottom',
'dofs' : {'T.0' : -1.0},
}
ebc_2 = {
'name' : 'T3',
'region' : 'Left',
'dofs' : {'T.0' : 2.0},
}

equations = {
'nice_equation' : """dw_laplace.i.Omega( coef.val, s, T ) = 0""",
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}

solver_1 = {
'name' : 'newton',
'kind' : 'nls.newton',

'i_max' : 1,
'eps_a' : 1e-10,
'eps_r' : 1.0,
'macheps' : 1e-16,
'lin_red' : 1e-2, # Linear system error < (eps_a * lin_red).
'ls_red' : 0.1,
'ls_red_warp' : 0.001,
'ls_on' : 1.1,
'ls_min' : 1e-5,
'check' : 0,
'delta' : 1e-6,
}

diffusion/darcy_flow_multicomp.py

Description
Each of the two equations describes a flow in one compartment of a porous medium. The equations are based on the
Darcy flow and the i-th compartment is defined in Ω𝑖 .
∫︁ ∫︁ ∑︁ ∫︁
𝐾 𝑖 ∇𝑝𝑖 · ∇𝑞 𝑖 + ¯ 𝑘 𝑝𝑖 − 𝑝𝑗 𝑞 𝑖 = 𝑓 𝑖 𝑞𝑖 ,
(︀ )︀
𝐺𝛼
Ω𝑖 Ω𝑖 𝑗 Ω𝑖

∀𝑞 𝑖 ∈ 𝑄𝑖 , 𝑖, 𝑗 = 1, 2 and 𝑖 ̸= 𝑗,
where 𝐾 is the local permeability of the i-th compartment, 𝐺𝛼
𝑖 ¯ 𝑘 = 𝐺𝑖 is the perfusion coefficient related to the
𝑗
compartments 𝑖 and 𝑗, 𝑓 𝑖 are sources or sinks which represent the external flow into the i-th compartment and 𝑝𝑖 is the
pressure in the i-th compartment.

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source code

r"""
Each of the two equations describes a flow in one compartment of a porous
medium. The equations are based on the Darcy flow and the i-th compartment is
defined in :math:`\Omega_{i}`.

.. math::
\int_{\Omega_{i}} K^{i} \nabla p^{i} \cdot \nabla q^{i}+\int_{\Omega_{i}}
\sum_{j} \bar{G}\alpha_{k} \left( p^{i}-p^{j} \right)q^{i}
= \int_{\Omega_{i}} f^{i} q^{i},
.. math::
\forall q^{i} \in Q^{i}, \quad i,j=1,2 \quad \mbox{and} \quad i\neq j,

where :math:`K^{i}` is the local permeability of the i-th compartment,

:math:`\bar{G}\alpha_{k} = G^{i}_{j}` is the perfusion coefficient
related to the compartments :math:`i` and :math:`j`, :math:`f^i` are
sources or sinks which represent the external flow into the i-th
compartment and :math:`p^{i}` is the pressure in the i-th compartment.
"""

from __future__ import absolute_import

from sfepy.base.base import Struct
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import numpy as nm
from sfepy import data_dir

filename_mesh = data_dir + '/meshes/3d/cube_medium_hexa.mesh'

G_bar = 2.0
alpha1 = 1.3
alpha2 = 1.0

materials = {
'mat': ('mat_fun')
}

regions = {
'Omega': 'cells of group 0',
'Sigma_1': ('vertex 0', 'vertex'),
'Omega1': ('copy r.Omega', 'cell', 'Omega'),
'Omega2': ('copy r.Omega', 'cell', 'Omega'),
'Source': 'cell 24',
'Sink': 'cell 1',
}

fields = {
'pressure':('real', 1, 'Omega', 1)
}

variables = {
'p1': ('unknown field', 'pressure'),
'q1': ('test field', 'pressure', 'p1'),
'p2': ('unknown field', 'pressure'),
'q2': ('test field', 'pressure', 'p2'),
}

ebcs = {
'P1': ('Sigma_1', {'p1.0' : 0.0}),
}

equations = {
'komp1': """dw_diffusion.5.Omega1(mat.K, q1, p1)
+ dw_dot.5.Omega1(mat.G_alfa, q1, p1)
- dw_dot.5.Omega1(mat.G_alfa, q1, p2)
= dw_integrate.5.Source(mat.f_1, q1)""",

'komp2': """dw_diffusion.5.Omega2(mat.K, q2, p2)

+ dw_dot.5.Omega2(mat.G_alfa, q2, p2)
- dw_dot.5.Omega2(mat.G_alfa, q2, p1)
= dw_integrate.5.Sink(mat.f_2, q2)"""
}

solvers = {
'ls': ('ls.scipy_direct', {}),
'newton': ('nls.newton',
{'i_max' : 1,
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'eps_a' : 1e-6,
'eps_r' : 1.0,
})
}

def mat_fun(ts, coors, mode=None, **kwargs):

if mode == 'qp':
nqp, dim = coors.shape
alpha = nm.zeros((nqp,1,1), dtype=nm.float64)
alpha[0:nqp // 2,...] = alpha1
alpha[nqp // 2:,...] = alpha2
K = nm.eye(dim, dtype=nm.float64)
K2 = nm.tile(K, (nqp,1,1))
out = {
'K' : K2,
'f_1': 20.0 * nm.ones((nqp,1,1), dtype=nm.float64),
'f_2': -20.0 * nm.ones((nqp,1,1), dtype=nm.float64),
'G_alfa': G_bar * alpha,
}

return out

functions = {
'mat_fun': (mat_fun,),
}

options = {
'post_process_hook': 'postproc',
}

def postproc(out, pb, state, extend=False):

alpha = pb.evaluate('ev_integrate_mat.5.Omega(mat.G_alfa, p1)',
mode='el_avg')
out['alpha'] = Struct(name='output_data',
mode='cell',
data=alpha.reshape(alpha.shape[0], 1, 1, 1),
dofs=None)
return out

diffusion/laplace_1d.py

Description
Laplace equation in 1D with a variable coefficient.
Because the mesh is trivial in 1D, it is generated by mesh_hook(), and registered using UserMeshIO.
Find 𝑡 such that:
∫︁
d𝑠 d𝑡
𝑐(𝑥) =0, ∀𝑠 ,
Ω d𝑥 d𝑥

where the coefficient 𝑐(𝑥) = 0.1 + sin(2𝜋𝑥)2 is computed in get_coef().

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View the results using:

$ ./postproc.py -b -d't,plot_warp_scalar,rel_scaling=1' --wireframe --view=-90,90,1.5,0,
˓→0,0 --roll=0 laplace_1d.vtk

source code
r"""
Laplace equation in 1D with a variable coefficient.

Because the mesh is trivial in 1D, it is generated by :func:`mesh_hook()`, and

registered using :class:`UserMeshIO <sfepy.discrete.fem.meshio.UserMeshIO>`.

Find :math:`t` such that:

.. math::
\int_{\Omega} c(x) \tdiff{s}{x} \tdiff{t}{x}
= 0
\;, \quad \forall s \;,

where the coefficient :math:`c(x) = 0.1 + \sin(2 \pi x)^2` is computed in

:func:`get_coef()`.

View the results using::

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$ ./postproc.py -b -d't,plot_warp_scalar,rel_scaling=1' --wireframe --view=-90,90,1.5,0,

˓→0,0 --roll=0 laplace_1d.vtk
"""
from __future__ import absolute_import
import numpy as nm
from sfepy.discrete.fem import Mesh
from sfepy.discrete.fem.meshio import UserMeshIO

def mesh_hook(mesh, mode):

"""
Generate the 1D mesh.
"""
if mode == 'read':
n_nod = 101

coors = nm.linspace(0.0, 1.0, n_nod).reshape((n_nod, 1))

conn = nm.arange(n_nod, dtype=nm.int32).repeat(2)[1:-1].reshape((-1, 2))
mat_ids = nm.zeros(n_nod - 1, dtype=nm.int32)
descs = ['1_2']

mesh = Mesh.from_data('laplace_1d', coors, None,

[conn], [mat_ids], descs)
return mesh

elif mode == 'write':

pass

def get_coef(ts, coors, mode=None, **kwargs):

if mode == 'qp':
x = coors[:, 0]

val = 0.1 + nm.sin(2 * nm.pi * x)**2

val.shape = (coors.shape[0], 1, 1)

return {'val' : val}

filename_mesh = UserMeshIO(mesh_hook)

materials = {
'coef' : 'get_coef',
}

functions = {
'get_coef' : (get_coef,),
}

regions = {
'Omega' : 'all',
'Gamma_Left' : ('vertices in (x < 0.00001)', 'facet'),
'Gamma_Right' : ('vertices in (x > 0.99999)', 'facet'),
}
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fields = {
'temperature' : ('real', 1, 'Omega', 1),
}

variables = {
't' : ('unknown field', 'temperature', 0),
's' : ('test field', 'temperature', 't'),
}

ebcs = {
't1' : ('Gamma_Left', {'t.0' : 0.3}),
't2' : ('Gamma_Right', {'t.0' : -0.3}),
}

integrals = {
'i' : 2,
}

equations = {
'Temperature' : """dw_laplace.i.Omega(coef.val, s, t) = 0"""
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
}),
}

options = {
'nls' : 'newton',
'ls' : 'ls',
}

diffusion/laplace_coupling_lcbcs.py

Description
Two Laplace equations with multiple linear combination constraints.
The two equations are coupled by a periodic-like boundary condition constraint with a shift, given as a non-
homogeneous linear combination boundary condition.

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Find 𝑢 such that:

∫︁
∇𝑣1 · ∇𝑢1 = 0 , ∀𝑣1 ,
Ω1
∫︁
∇𝑣2 · ∇𝑢2 = 0 , ∀𝑣2 ,
Ω2
𝑢1 = 0 on Γ𝑏𝑜𝑡𝑡𝑜𝑚 ,
𝑢2 = 1 on Γ𝑡𝑜𝑝 ,
𝑢1 (𝑥) = 𝑢2 (𝑥) + 𝑎(𝑥) for 𝑥 ∈ Γ = Ω̄1 ∩ Ω̄2
𝑢1 (𝑥) = 𝑢1 (𝑦) + 𝑏(𝑦) for 𝑥 ∈ Γ𝑙𝑒𝑓 𝑡 , 𝑦 ∈ Γ𝑟𝑖𝑔ℎ𝑡 , 𝑦 = 𝑃 (𝑥) ,
𝑢1 = 𝑐11 in Ω𝑚11 ⊂ Ω1 ,
𝑢1 = 𝑐12 in Ω𝑚12 ⊂ Ω1 ,
𝑢2 = 𝑐2 in Ω𝑚2 ⊂ Ω2 ,

where 𝑎(𝑥), 𝑏(𝑦) are given functions (shifts), 𝑃 is the periodic coordinate mapping and 𝑐11 , 𝑐12 and 𝑐2 are unknown
constant values - the unknown DOFs in Ω𝑚11 , Ω𝑚12 and Ω𝑚2 are replaced by the integral mean values.
View the results using:

$ ./postproc.py square_quad.vtk -b --wireframe -d'u1,plot_warp_scalar,rel_scaling=1:u2,

˓→plot_warp_scalar,rel_scaling=1'

source code

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r"""
Two Laplace equations with multiple linear combination constraints.

The two equations are coupled by a periodic-like boundary condition constraint

with a shift, given as a non-homogeneous linear combination boundary condition.

Find :math:`u` such that:

.. math::
\int_{\Omega_1} \nabla v_1 \cdot \nabla u_1
= 0
\;, \quad \forall v_1 \;,

\int_{\Omega_2} \nabla v_2 \cdot \nabla u_2

= 0
\;, \quad \forall v_2 \;,

u_1 = 0 \mbox{ on } \Gamma_{bottom} \;,

u_2 = 1 \mbox{ on } \Gamma_{top} \;,

u_1(\ul{x}) = u_2(\ul{x}) + a(\ul{x}) \mbox{ for }

\ul{x} \in \Gamma = \bar\Omega_1 \cap \bar\Omega_2

u_1(\ul{x}) = u_1(\ul{y}) + b(\ul{y}) \mbox{ for }

\ul{x} \in \Gamma_{left}, \ul{y} \in \Gamma_{right}, \ul{y} = P(\ul{x}) \;,

u_1 = c_{11} \mbox{ in } \Omega_{m11} \subset \Omega_1 \;,

u_1 = c_{12} \mbox{ in } \Omega_{m12} \subset \Omega_1 \;,

u_2 = c_2 \mbox{ in } \Omega_{m2} \subset \Omega_2 \;,

where :math:`a(\ul{x})`, :math:`b(\ul{y})` are given functions (shifts),

:math:`P` is the periodic coordinate mapping and :math:`c_{11}`, :math:`c_{12}`
and :math:`c_2` are unknown constant values - the unknown DOFs in
:math:`\Omega_{m11}`, :math:`\Omega_{m12}` and :math:`\Omega_{m2}` are replaced
by the integral mean values.

View the results using::

$ ./postproc.py square_quad.vtk -b --wireframe -d'u1,plot_warp_scalar,rel_scaling=1:u2,

˓→plot_warp_scalar,rel_scaling=1'
"""
from __future__ import absolute_import
import numpy as nm

import sfepy.discrete.fem.periodic as per

from sfepy import data_dir

filename_mesh = data_dir + '/meshes/2d/square_quad.mesh'

options = {
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'nls' : 'newton',
'ls' : 'ls',
}

def get_shift1(ts, coors, region):

val = 0.1 * coors[:, 0]

return val

def get_shift2(ts, coors, region):

val = nm.empty_like(coors[:, 1])
val.fill(0.3)

return val

functions = {
'get_shift1' : (get_shift1,),
'get_shift2' : (get_shift2,),
'match_y_line' : (per.match_y_line,),
'match_x_line' : (per.match_x_line,),
}

fields = {
'scalar1': ('real', 1, 'Omega1', 1),
'scalar2': ('real', 1, 'Omega2', 1),
}

materials = {
}

variables = {
'u1' : ('unknown field', 'scalar1', 0),
'v1' : ('test field', 'scalar1', 'u1'),
'u2' : ('unknown field', 'scalar2', 1),
'v2' : ('test field', 'scalar2', 'u2'),
}

regions = {
'Omega1' : 'cells of group 1',
'Omega2' : 'cells of group 2',
'Omega_m1' : 'r.Omega1 -v (r.Gamma +s vertices of surface)',
'Omega_m11' : 'r.Omega_m1 *v vertices in (x < 0)',
'Omega_m12' : 'r.Omega_m1 *v vertices in (x > 0)',
'Omega_m2' : 'r.Omega2 -v (r.Gamma +s vertices of surface)',
'Left' : ('vertices in (x < -0.499)', 'facet'),
'Right' : ('vertices in (x > 0.499)', 'facet'),
'Bottom' : ('vertices in ((y < -0.499))', 'facet'),
'Top' : ('vertices in ((y > 0.499))', 'facet'),
'Gamma' : ('r.Omega1 *v r.Omega2 -v vertices of surface', 'facet'),
'Gamma1' : ('copy r.Gamma', 'facet', 'Omega1'),
'Gamma2' : ('copy r.Gamma', 'facet', 'Omega2'),
}
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ebcs = {
'fix1' : ('Top', {'u2.all' : 1.0}),
'fix2' : ('Bottom', {'u1.all' : 0.0}),
}

lcbcs = {
'shifted1' : (('Gamma1', 'Gamma2'),
{'u1.all' : 'u2.all'},
'match_x_line', 'shifted_periodic',
'get_shift1'),
'shifted2' : (('Left', 'Right'),
{'u1.all' : 'u1.all'},
'match_y_line', 'shifted_periodic',
'get_shift2'),
'mean11' : ('Omega_m11', {'u1.all' : None}, None, 'integral_mean_value'),
'mean12' : ('Omega_m12', {'u1.all' : None}, None, 'integral_mean_value'),
'mean2' : ('Omega_m2', {'u2.all' : None}, None, 'integral_mean_value'),
}

integrals = {
'i1' : 2,
}

equations = {
'eq1' : """
dw_laplace.i1.Omega1(v1, u1) = 0
""",
'eq2' : """
dw_laplace.i1.Omega2(v2, u2) = 0
""",
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
}),
}

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diffusion/laplace_fluid_2d.py

Description
A Laplace equation that models the flow of “dry water” around an obstacle shaped like a Citroen CX.

Description

As discussed e.g. in the Feynman lectures Section 12-5 of Volume 2 (https://www.feynmanlectures.caltech.edu/II_12.

html#Ch12-S5), the flow of an irrotational and incompressible fluid can be modelled with a potential 𝑣 = 𝑔𝑟𝑎𝑑(𝜑)
that obeys

∇ · ∇𝜑 = ∆𝜑 = 0

The weak formulation for this problem is to find 𝜑 such that:

∫︁ ∫︁ ∫︁ ∫︁ ∫︁
∇𝜓 · ∇𝜑 = 𝑣0 · 𝑛 𝜓 + 𝑣0 · 𝑛 𝜓 + 𝑣0 · 𝑛 𝜓 + 𝑣0 · 𝑛 𝜓 , ∀𝜓 ,
Ω Γ𝑙𝑒𝑓 𝑡 Γ𝑟𝑖𝑔ℎ𝑡 Γ𝑡𝑜𝑝 Γ𝑏𝑜𝑡𝑡𝑜𝑚

where 𝑣 0 is the 2D vector defining the far field velocity that generates the incompressible flow.
Since the value of the potential is defined up to a constant value, a Dirichlet boundary condition is set at a single vertex
to avoid having a singular matrix.

Usage examples

This example can be run with the simple.py script with the following:

python3 simple.py examples/diffusion/laplace_fluid_2d.py

python3 resview.py citroen.vtk -f phi:p0 phi:t50:p0 --2d-view

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Generating the mesh

The mesh can be generated with:

gmsh -2 -f msh22 meshes/2d/citroen.geo -o meshes/2d/citroen.msh

python3 script/convert_mesh.py --2d meshes/2d/citroen.msh meshes/2d/citroen.h5

source code

r"""
A Laplace equation that models the flow of "dry water" around an obstacle
shaped like a Citroen CX.

Description
-----------

As discussed e.g. in the Feynman lectures Section 12-5 of Volume 2

(https://www.feynmanlectures.caltech.edu/II_12.html#Ch12-S5),
the flow of an irrotational and incompressible fluid can be modelled with a
potential :math:`\ul{v} = \ul{grad}(\phi)` that obeys

.. math::
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\nabla \cdot \ul{\nabla}\,\phi = \Delta\,\phi = 0

The weak formulation for this problem is to find :math:`\phi` such that:

.. math::
\int_{\Omega} \nabla \psi \cdot \nabla \phi
= \int_{\Gamma_{left}} \ul{v}_0 \cdot n \, \psi
+ \int_{\Gamma_{right}} \ul{v}_0 \cdot n \, \psi
+ \int_{\Gamma_{top}} \ul{v}_0 \cdot n \,\psi
+ \int_{\Gamma_{bottom}} \ul{v}_0 \cdot n \, \psi
\;, \quad \forall \psi \;,

where :math:`\ul{v}_0` is the 2D vector defining the far field velocity that
generates the incompressible flow.

Since the value of the potential is defined up to a constant value, a Dirichlet

boundary condition is set at a single vertex to avoid having a singular matrix.

Usage examples
--------------

This example can be run with the ``simple.py`` script with the following::

python3 simple.py sfepy/examples/diffusion/laplace_fluid_2d.py

python3 resview.py citroen.vtk -f phi:p0 phi:t50:p0 --2d-view

Generating the mesh

-------------------

The mesh can be generated with::

gmsh -2 -f msh22 meshes/2d/citroen.geo -o meshes/2d/citroen.msh

python3 script/convert_mesh.py --2d meshes/2d/citroen.msh meshes/2d/citroen.h5

"""
import numpy as nm
from sfepy import data_dir

filename_mesh = data_dir + '/meshes/2d/citroen.h5'

v0 = nm.array([1, 0.25])

materials = {
'm': ({'v0': v0.reshape(-1, 1)},),
}

regions = {
'Omega': 'all',
'Gamma_Left': ('vertices in (x < 0.1)', 'facet'),
'Gamma_Right': ('vertices in (x > 1919.9)', 'facet'),
'Gamma_Top': ('vertices in (y > 917.9)', 'facet'),
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'Gamma_Bottom': ('vertices in (y < 0.1)', 'facet'),
'Vertex': ('vertex in r.Gamma_Left', 'vertex'),
}

fields = {
'u': ('real', 1, 'Omega', 1),
}

variables = {
'phi': ('unknown field', 'u', 0),
'psi': ('test field', 'u', 'phi'),
}

# these EBCS prevent the matrix from being singular, see description
ebcs = {
'fix': ('Vertex', {'phi.0': 0.0}),
}

integrals = {
'i': 2,
}

equations = {
'Laplace equation':
"""dw_laplace.i.Omega( psi, phi )
= dw_surface_ndot.i.Gamma_Left( m.v0, psi )
+ dw_surface_ndot.i.Gamma_Right( m.v0, psi )
+ dw_surface_ndot.i.Gamma_Top( m.v0, psi )
+ dw_surface_ndot.i.Gamma_Bottom( m.v0, psi )"""
}

solvers = {
'ls': ('ls.scipy_direct', {}),
'newton': ('nls.newton', {
'i_max': 1,
'eps_a': 1e-10,
}),
}

diffusion/laplace_iga_interactive.py

Description
Laplace equation with Dirichlet boundary conditions solved in a single patch NURBS domain using the isogeometric
analysis (IGA) approach, using commands for interactive use.
This script allows the creation of a customisable NURBS surface using igakit built-in CAD routines, which is then
saved in custom HDF5-based files with .iga extension.

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Notes

The create_patch function creates a NURBS-patch of the area between two coplanar nested circles using igakit
CAD built-in routines. The created patch is not connected in the orthoradial direction. This is a problem when the
disconnected boundary is not perpendicular to the line connecting the two centres of the circles, as the solution then
exhibits a discontinuity along this line. A workaround for this issue is to enforce perpendicularity by changing the start
angle in function igakit.cad.circle (see the code down below for the actual trick). The discontinuity disappears.

Usage Examples

Default options, storing results in this file’s parent directory:

$ python3 examples/diffusion/laplace_iga_interactive.py

Command line options for tweaking the geometry of the NURBS-patch & more:
$ python3 examples/diffusion/laplace_iga_interactive.py --R1=0.7 --C2=0.1,0.1 --viewpatch

View the results using:

$ python3 postproc.py concentric_circles.vtk

source code
#!/usr/bin/env python
r"""
Laplace equation with Dirichlet boundary conditions solved in a single patch
NURBS domain using the isogeometric analysis (IGA) approach, using commands
for interactive use.

This script allows the creation of a customisable NURBS surface using igakit
built-in CAD routines, which is then saved in custom HDF5-based files with
.iga extension.

Notes
-----

The ``create_patch`` function creates a NURBS-patch of the area between two

coplanar nested circles using igakit CAD built-in routines. The created patch
is not connected in the orthoradial direction. This is a problem when the
disconnected boundary is not perpendicular to the line connecting the two
centres of the circles, as the solution then exhibits a discontinuity along
this line. A workaround for this issue is to enforce perpendicularity by
changing the start angle in function ``igakit.cad.circle`` (see the code down
below for the actual trick). The discontinuity disappears.

Usage Examples
--------------

Default options, storing results in this file's parent directory::

$ python3 sfepy/examples/diffusion/laplace_iga_interactive.py

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Command line options for tweaking the geometry of the NURBS-patch & more::

$ python3 sfepy/examples/diffusion/laplace_iga_interactive.py --R1=0.7 --C2=0.1,0.1 --

˓→viewpatch

View the results using::

$ python3 postproc.py concentric_circles.vtk

"""

from argparse import RawDescriptionHelpFormatter, ArgumentParser

import os
import sys
sys.path.append('.')

import numpy as nm
from sfepy import data_dir
from sfepy.base.ioutils import ensure_path
from sfepy.base.base import IndexedStruct
from sfepy.discrete import (FieldVariable, Integral, Equation,Equations,
Problem)
from sfepy.discrete.iga.domain import IGDomain
from sfepy.discrete.common.fields import Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton

def create_patch(R1, R2, C1, C2, order=2, viewpatch=False):

"""
Create a single 2d NURBS-patch of the area between two coplanar nested
circles using igakit.

Parameters
----------
R1 : float
Radius of the inner circle.
R2 : float
Radius of the outer circle.
C1 : list of two floats
Coordinates of the center of the inner circle given as [x1, y1].
C2 : list of two floats
Coordinates of the center of the outer circle given as [x2, y2].
order : int, optional
Degree of the NURBS basis functions. The default is 2.
viewpatch : bool, optional
When set to True, display the NURBS patch. The default is False.

Returns
-------
None.
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"""

from sfepy.discrete.iga.domain_generators import create_from_igakit

import sfepy.discrete.iga.io as io
from igakit.cad import circle, ruled
from igakit.plot import plt as iplt
from numpy import pi

# Assert the inner circle is inside the outer one

inter_centers = nm.sqrt((C2[0]-C1[0])**2 + (C2[1]-C1[1])**2)
assert R2>R1, "Outer circle should have a larger radius than the inner one"
assert inter_centers<R2-R1, "Circles are not nested"

# Geometry Creation
centers_direction = [C2[0]-C1[0], C2[1]-C1[1]]
if centers_direction[0]==0 and centers_direction[1]==0:
start_angle = 0.0
else:
start_angle = nm.arctan2(centers_direction[1], centers_direction[0])
c1 = circle(radius=R1, center=C1, angle=(start_angle, start_angle + 2*pi))
c2 = circle(radius=R2, center=C2, angle=(start_angle, start_angle + 2*pi))
srf = ruled(c1,c2).transpose() # make the radial direction first

# Refinement
insert_U = insert_uniformly(srf.knots[0], 6)
insert_V = insert_uniformly(srf.knots[1], 6)
srf.refine(0, insert_U).refine(1, insert_V)

# Setting the NURBS-surface degree

srf.elevate(0, order-srf.degree[0] if order-srf.degree[0] > 0 else 0)
srf.elevate(1, order-srf.degree[1] if order-srf.degree[1] > 0 else 0)

# Sfepy .iga file creation

nurbs, bmesh, regions = create_from_igakit(srf, verbose=True)

# Save .iga file in sfepy/meshes/iga

filename_domain = data_dir + '/meshes/iga/concentric_circles.iga'
io.write_iga_data(filename_domain, None, nurbs.knots, nurbs.degrees,
nurbs.cps, nurbs.weights, nurbs.cs, nurbs.conn,
bmesh.cps, bmesh.weights, bmesh.conn, regions)

if viewpatch:
try:
iplt.use('mayavi')
iplt.figure()
iplt.plot(srf)
iplt.show()
except ImportError:
iplt.use('matplotlib')
iplt.figure()
iplt.plot(srf)
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iplt.show()

def insert_uniformly(U, n):

"""
Find knots to uniformly add to U.
[Code from igakit/demo/venturi.py file]

Given a knot vector U and the number of uniform spans desired,

find the knots which need to be inserted.

Parameters
----------
U : numpy.ndarray
Original knot vector for a C^p-1 space.
n : int
Target number of uniformly-spaced knot spans.

Returns
-------
Knots to be inserted into U
"""
U0 = U
dU=(U.max()-U.min())/float(n) # target dU in knot vector
idone=0
while idone == 0:
# Add knots in middle of spans which are too large
Uadd=[]
for i in range(len(U)-1):
if U[i+1]-U[i] > dU:
Uadd.append(0.5*(U[i+1]+U[i]))
# Now we add these knots (once only, assumes C^(p-1))
if len(Uadd) > 0:
U = nm.sort(nm.concatenate([U,nm.asarray(Uadd)]))
else:
idone=1
# And now a little Laplacian smoothing
for num_iterations in range(5):
for i in range(len(U)-2):
if abs(U0[U0.searchsorted(U[i+1])]-U[i+1]) > 1.0e-14:
U[i+1] = 0.5*(U[i]+U[i+2])
return nm.setdiff1d(U,U0)

helps = {
'output_dir' :
'output directory',
'R1' :
'Inner circle radius [default: %(default)s]',
'R2' :
'Outer circle radius [default: %(default)s]',
'C1' :
'centre of the inner circle [default: %(default)s]',
'C2' :
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'centre of the outer circle [default: %(default)s]',
'order' :
'field approximation order [default: %(default)s]',
'viewpatch' :
'generate a plot of the NURBS-patch',
}

def main():
parser = ArgumentParser(description=__doc__.rstrip(),
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('-o', '--output-dir', default='.',
help=helps['output_dir'])
parser.add_argument('--R1', metavar='R1',
action='store', dest='R1',
default='0.5', help=helps['R1'])
parser.add_argument('--R2', metavar='R2',
action='store', dest='R2',
default='1.0', help=helps['R2'])
parser.add_argument('--C1', metavar='C1',
action='store', dest='C1',
default='0.0,0.0', help=helps['C1'])
parser.add_argument('--C2', metavar='C2',
action='store', dest='C2',
default='0.0,0.0', help=helps['C2'])
parser.add_argument('--order', metavar='int', type=int,
action='store', dest='order',
default=2, help=helps['order'])
parser.add_argument('-v', '--viewpatch',
action='store_true', dest='viewpatch',
default=False, help=helps['viewpatch'])
options = parser.parse_args()

# Creation of the NURBS-patch with igakit

R1 = eval(options.R1)
R2 = eval(options.R2)
C1 = list(eval(options.C1))
C2 = list(eval(options.C2))
order = options.order
viewpatch = options.viewpatch
create_patch(R1, R2, C1, C2, order=order, viewpatch=viewpatch)

# Setting a Domain instance

filename_domain = data_dir + '/meshes/iga/concentric_circles.iga'
domain = IGDomain.from_file(filename_domain)

# Sub-domains
omega = domain.create_region('Omega', 'all')
Gamma_out = domain.create_region('Gamma_out', 'vertices of set xi01',
kind='facet')
Gamma_in = domain.create_region('Gamma_in', 'vertices of set xi00',
kind='facet')

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# Field (featuring order elevation)
order_increase = order - domain.nurbs.degrees[0]
order_increase *= int(order_increase>0)
field = Field.from_args('fu', nm.float64, 'scalar', omega,
approx_order='iga', space='H1',
poly_space_base='iga')

# Variables
u = FieldVariable('u', 'unknown', field) # unknown function
v = FieldVariable('v', 'test', field, primary_var_name='u') # test function

# Integral
integral = Integral('i', order=2*field.approx_order)

# Term
t = Term.new('dw_laplace( v, u )', integral, omega, v=v, u=u)

# Equation
eq = Equation('laplace', t)
eqs = Equations([eq])

# Boundary Conditions
u_in = EssentialBC('u_in', Gamma_in, {'u.all' : 7.0})
u_out = EssentialBC('u_out', Gamma_out, {'u.all' : 3.0})

# solvers
ls = ScipyDirect({})
nls_status = IndexedStruct()
nls = Newton({}, lin_solver=ls, status=nls_status)

# problem instance
pb = Problem('potential', equations=eqs, active_only=True)

# Set boundary conditions

pb.set_bcs(ebcs=Conditions([u_in, u_out]))

# solving
pb.set_solver(nls)
status = IndexedStruct()
state = pb.solve(status=status, save_results=True, verbose=True)

# Saving the results to a classic VTK file

filename = os.path.join(options.output_dir, 'concentric_circles.vtk')
ensure_path(filename)
pb.save_state(filename, state)

if __name__ == '__main__':
main()

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diffusion/laplace_refine_interactive.py

Description
Example of solving Laplace’s equation on a block domain refined with level 1 hanging nodes.
The domain is progressively refined towards the edge/face of the block, where Dirichlet boundary conditions are pre-
scribed by an oscillating function.
Find 𝑢 such that:
∫︁
∇𝑣 · ∇𝑢 = 0 , ∀𝑠 .
Ω

Notes

The implementation of the mesh refinement with level 1 hanging nodes is a proof-of-concept code with many unresolved
issues. The main problem is the fact that a user needs to input the cells to refine at each level, while taking care of the
following constraints:
• the level 1 hanging nodes constraint: a cell that has a less-refined neighbour cannot be refined;
• the implementation constraint: a cell with a refined neighbour cannot be refined.
The hanging nodes are treated by a basis transformation/DOF substitution, which has to be applied explicitly by the
user:
• call field.substitute_dofs(subs) before assembling and solving;
• then call field.restore_dofs() before saving results.

Usage Examples

Default options, 2D, storing results in ‘output’ directory:

$ python examples/diffusion/laplace_refine_interactive.py output

$ python postproc.py output/hanging.vtk --wireframe -b -d'u,plot_warp_scalar'

Default options, 3D, storing results in ‘output’ directory:

$ python examples/diffusion/laplace_refine_interactive.py -3 output

$ python postproc.py output/hanging.vtk --wireframe -b --3d

Finer initial domain, 2D, storing results in ‘output’ directory:

$ python examples/diffusion/laplace_refine_interactive.py --shape=11,11 output

$ python postproc.py output/hanging.vtk --wireframe -b -d'u,plot_warp_scalar'

Bi-quadratic approximation, 2D, storing results in ‘output’ directory:

$ python examples/diffusion/laplace_refine_interactive.py --order=2 output

# View solution with higher order DOFs removed.

$ python postproc.py output/hanging.vtk --wireframe -b -d'u,plot_warp_scalar'

# View full solution on a mesh adapted for visualization.

$ python postproc.py output/hanging_u.vtk --wireframe -b -d'u,plot_warp_scalar'

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source code

#!/usr/bin/env python
r"""
Example of solving Laplace's equation on a block domain refined with level 1
hanging nodes.

The domain is progressively refined towards the edge/face of the block, where
Dirichlet boundary conditions are prescribed by an oscillating function.

Find :math:`u` such that:

.. math::
\int_{\Omega} \nabla v \cdot \nabla u = 0
\;, \quad \forall s \;.

Notes
-----
The implementation of the mesh refinement with level 1 hanging nodes is a
proof-of-concept code with many unresolved issues. The main problem is the fact
that a user needs to input the cells to refine at each level, while taking care
of the following constraints:

- the level 1 hanging nodes constraint: a cell that has a less-refined

neighbour cannot be refined;
- the implementation constraint: a cell with a refined neighbour cannot be
refined.

The hanging nodes are treated by a basis transformation/DOF substitution, which

has to be applied explicitly by the user:

- call ``field.substitute_dofs(subs)`` before assembling and solving;

- then call ``field.restore_dofs()`` before saving results.

Usage Examples
--------------

Default options, 2D, storing results in 'output' directory::

$ python sfepy/examples/diffusion/laplace_refine_interactive.py output

$ python postproc.py output/hanging.vtk --wireframe -b -d'u,plot_warp_scalar'

Default options, 3D, storing results in 'output' directory::

$ python sfepy/examples/diffusion/laplace_refine_interactive.py -3 output

$ python postproc.py output/hanging.vtk --wireframe -b --3d

Finer initial domain, 2D, storing results in 'output' directory::

$ python sfepy/examples/diffusion/laplace_refine_interactive.py --shape=11,11 output

$ python postproc.py output/hanging.vtk --wireframe -b -d'u,plot_warp_scalar'

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Bi-quadratic approximation, 2D, storing results in 'output' directory::

$ python sfepy/examples/diffusion/laplace_refine_interactive.py --order=2 output

# View solution with higher order DOFs removed.

$ python postproc.py output/hanging.vtk --wireframe -b -d'u,plot_warp_scalar'

# View full solution on a mesh adapted for visualization.

$ python postproc.py output/hanging_u.vtk --wireframe -b -d'u,plot_warp_scalar'
"""
from __future__ import absolute_import
from argparse import RawDescriptionHelpFormatter, ArgumentParser

import os
import sys
sys.path.append('.')
import numpy as nm

from sfepy.base.base import output, Struct

from sfepy.base.ioutils import ensure_path
from sfepy.mesh.mesh_generators import gen_block_mesh
from sfepy.discrete import (FieldVariable, Integral, Equation, Equations,
Function, Problem)
from sfepy.discrete.fem import FEDomain, Field
from sfepy.discrete.conditions import (Conditions, EssentialBC)
import sfepy.discrete.fem.refine_hanging as rh
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.terms import Term

def refine_towards_facet(domain0, grading, axis):

subs = None
domain = domain0
for level, coor in enumerate(grading):
refine = nm.zeros(domain.mesh.n_el, dtype=nm.uint8)

region = domain.create_region('aux',
'vertices in (%s %.10f )' % (axis, coor),
add_to_regions=False)
refine[region.cells] = 1

domain, subs = rh.refine(domain, refine, subs=subs)

return domain, subs

helps = {
'output_dir' :
'output directory',
'dims' :
'dimensions of the block [default: %(default)s]',
'shape' :
'shape (counts of nodes in x, y[, z]) of the block [default: %(default)s]',
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'centre' :
'centre of the block [default: %(default)s]',
'3d' :
'generate a 3D block',
'order' :
'field approximation order',
}

def main():
parser = ArgumentParser(description=__doc__.rstrip(),
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('output_dir', help=helps['output_dir'])
parser.add_argument('--dims', metavar='dims',
action='store', dest='dims',
default='1.0,1.0,1.0', help=helps['dims'])
parser.add_argument('--shape', metavar='shape',
action='store', dest='shape',
default='7,7,7', help=helps['shape'])
parser.add_argument('--centre', metavar='centre',
action='store', dest='centre',
default='0.0,0.0,0.0', help=helps['centre'])
parser.add_argument('-3', '--3d',
action='store_true', dest='is_3d',
default=False, help=helps['3d'])
parser.add_argument('--order', metavar='int', type=int,
action='store', dest='order',
default=1, help=helps['order'])
options = parser.parse_args()

dim = 3 if options.is_3d else 2

dims = nm.array(eval(options.dims), dtype=nm.float64)[:dim]
shape = nm.array(eval(options.shape), dtype=nm.int32)[:dim]
centre = nm.array(eval(options.centre), dtype=nm.float64)[:dim]

output('dimensions:', dims)
output('shape: ', shape)
output('centre: ', centre)

mesh0 = gen_block_mesh(dims, shape, centre, name='block-fem',

verbose=True)
domain0 = FEDomain('d', mesh0)

bbox = domain0.get_mesh_bounding_box()
min_x, max_x = bbox[:, 0]
eps = 1e-8 * (max_x - min_x)

cnt = (shape[0] - 1) // 2
g0 = 0.5 * dims[0]
grading = nm.array([g0 / 2**ii for ii in range(cnt)]) + eps + centre[0] - g0

domain, subs = refine_towards_facet(domain0, grading, 'x <')

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omega = domain.create_region('Omega', 'all')

gamma1 = domain.create_region('Gamma1',
'vertices in (x < %.10f )' % (min_x + eps),
'facet')
gamma2 = domain.create_region('Gamma2',
'vertices in (x > %.10f )' % (max_x - eps),
'facet')

field = Field.from_args('fu', nm.float64, 1, omega,

approx_order=options.order)

if subs is not None:

field.substitute_dofs(subs)

u = FieldVariable('u', 'unknown', field)

v = FieldVariable('v', 'test', field, primary_var_name='u')

integral = Integral('i', order=2*options.order)

t1 = Term.new('dw_laplace(v, u)',
integral, omega, v=v, u=u)
eq = Equation('eq', t1)
eqs = Equations([eq])

def u_fun(ts, coors, bc=None, problem=None):

"""
Define a displacement depending on the y coordinate.
"""
if coors.shape[1] == 2:
min_y, max_y = bbox[:, 1]
y = (coors[:, 1] - min_y) / (max_y - min_y)

val = (max_y - min_y) * nm.cos(3 * nm.pi * y)

else:
min_y, max_y = bbox[:, 1]
min_z, max_z = bbox[:, 2]
y = (coors[:, 1] - min_y) / (max_y - min_y)
z = (coors[:, 2] - min_z) / (max_z - min_z)

val = ((max_y - min_y) * (max_z - min_z)

* nm.cos(3 * nm.pi * y) * (1.0 + 3.0 * (z - 0.5)**2))

return val

bc_fun = Function('u_fun', u_fun)

fix1 = EssentialBC('shift_u', gamma1, {'u.0' : bc_fun})
fix2 = EssentialBC('fix2', gamma2, {'u.all' : 0.0})

ls = ScipyDirect({})

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nls = Newton({}, lin_solver=ls)

pb = Problem('heat', equations=eqs)

pb.set_bcs(ebcs=Conditions([fix1, fix2]))

pb.set_solver(nls)

state = pb.solve(save_results=False)

if subs is not None:

field.restore_dofs()

filename = os.path.join(options.output_dir, 'hanging.vtk')

ensure_path(filename)

pb.save_state(filename, state)
if options.order > 1:
pb.save_state(filename, state, linearization=Struct(kind='adaptive',
min_level=0,
max_level=8,
eps=1e-3))

if __name__ == '__main__':
main()

diffusion/laplace_shifted_periodic.py

Description
Laplace equation with shifted periodic BCs.
Display using:

./postproc.py laplace_shifted_periodic.vtk --wireframe -b -d'u,plot_warp_scalar,rel_

˓→scaling=1'

or use the –show option.

source code

#!/usr/bin/env python
"""
Laplace equation with shifted periodic BCs.

Display using::

./postproc.py laplace_shifted_periodic.vtk --wireframe -b -d'u,plot_warp_scalar,rel_

˓→scaling=1'

or use the --show option.

"""
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from __future__ import absolute_import
import sys
sys.path.append('.')
from argparse import ArgumentParser, RawDescriptionHelpFormatter
import numpy as nm

from sfepy.base.base import output

from sfepy.discrete import (FieldVariable, Integral, Equation, Equations,
Function, Problem)
from sfepy.discrete.fem import FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import (Conditions, EssentialBC,
LinearCombinationBC)
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.mesh.mesh_generators import gen_block_mesh
import sfepy.discrete.fem.periodic as per

def run(domain, order, output_dir=''):

omega = domain.create_region('Omega', 'all')
bbox = domain.get_mesh_bounding_box()
min_x, max_x = bbox[:, 0]
min_y, max_y = bbox[:, 1]
eps = 1e-8 * (max_x - min_x)
gamma1 = domain.create_region('Gamma1',
'vertices in (x < %.10f )' % (min_x + eps),
'facet')
gamma2 = domain.create_region('Gamma2',
'vertices in (x > %.10f )' % (max_x - eps),
'facet')
gamma3 = domain.create_region('Gamma3',
'vertices in y < %.10f ' % (min_y + eps),
'facet')
gamma4 = domain.create_region('Gamma4',
'vertices in y > %.10f ' % (max_y - eps),
'facet')

field = Field.from_args('fu', nm.float64, 1, omega, approx_order=order)

u = FieldVariable('u', 'unknown', field)

v = FieldVariable('v', 'test', field, primary_var_name='u')

integral = Integral('i', order=2*order)

t1 = Term.new('dw_laplace(v, u)',
integral, omega, v=v, u=u)
eq = Equation('eq', t1)
eqs = Equations([eq])

fix1 = EssentialBC('fix1', gamma1, {'u.0' : 0.4})

fix2 = EssentialBC('fix2', gamma2, {'u.0' : 0.0})

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def get_shift(ts, coors, region):
return nm.ones_like(coors[:, 0])

dof_map_fun = Function('dof_map_fun', per.match_x_line)

shift_fun = Function('shift_fun', get_shift)

sper = LinearCombinationBC('sper', [gamma3, gamma4], {'u.0' : 'u.0'},

dof_map_fun, 'shifted_periodic',
arguments=(shift_fun,))

ls = ScipyDirect({})
nls = Newton({}, lin_solver=ls)

pb = Problem('laplace', equations=eqs)
pb.set_output_dir(output_dir)

pb.set_bcs(ebcs=Conditions([fix1, fix2]), lcbcs=Conditions([sper]))

pb.set_solver(nls)

state = pb.solve()

return pb, state

helps = {
'dims' :
'dimensions of the block [default: %(default)s]',
'centre' :
'centre of the block [default: %(default)s]',
'shape' :
'numbers of vertices along each axis [default: %(default)s]',
'show' : 'show the results figure',
}

def main():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-d', '--dims', metavar='dims',
action='store', dest='dims',
default='[1.0, 1.0]', help=helps['dims'])
parser.add_argument('-c', '--centre', metavar='centre',
action='store', dest='centre',
default='[0.0, 0.0]', help=helps['centre'])
parser.add_argument('-s', '--shape', metavar='shape',
action='store', dest='shape',
default='[11, 11]', help=helps['shape'])
parser.add_argument('--show',
action="store_true", dest='show',
default=False, help=helps['show'])
options = parser.parse_args()

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dims = nm.array(eval(options.dims), dtype=nm.float64)
centre = nm.array(eval(options.centre), dtype=nm.float64)
shape = nm.array(eval(options.shape), dtype=nm.int32)

output('dimensions:', dims)
output('centre: ', centre)
output('shape: ', shape)

mesh = gen_block_mesh(dims, shape, centre, name='block-fem')

fe_domain = FEDomain('domain', mesh)

pb, state = run(fe_domain, 1)

pb.save_state('laplace_shifted_periodic.vtk', state)

if options.show:
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.domain_specific import DomainSpecificPlot

view = Viewer('laplace_shifted_periodic.vtk')
view(rel_scaling=1,
domain_specific={'u' : DomainSpecificPlot('plot_warp_scalar',
['rel_scaling=1'])},
is_scalar_bar=True, is_wireframe=True,
opacity=0.3)

if __name__ == '__main__':
main()

diffusion/laplace_time_ebcs.py

Description
Example explaining how to change Dirichlet boundary conditions depending on time. It is shown on the stationary
Laplace equation for temperature, so there is no dynamics, only the conditions change with time.
Five time steps are solved on a cube domain, with the temperature fixed to zero on the bottom face, and set to other
values on the left, right and top faces in different time steps.
Find 𝑡 such that:
∫︁
𝑐∇𝑠 · ∇𝑡 = 0 , ∀𝑠 .
Ω

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source code

r"""
Example explaining how to change Dirichlet boundary conditions depending
on time. It is shown on the stationary Laplace equation for temperature,
so there is no dynamics, only the conditions change with time.

Five time steps are solved on a cube domain, with the temperature fixed
to zero on the bottom face, and set to other values on the left, right
and top faces in different time steps.

Find :math:`t` such that:

.. math::
\int_{\Omega} c \nabla s \cdot \nabla t
= 0
\;, \quad \forall s \;.
"""
from __future__ import absolute_import
from sfepy import data_dir

filename_mesh = data_dir + '/meshes/3d/cube_medium_tetra.mesh'

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options = {
'nls' : 'newton',
'ls' : 'ls',
'ts' : 'ts',

'active_only' : False,
}

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < -0.499)', 'facet'),
'Right' : ('vertices in (x > 0.499)', 'facet'),
'Bottom' : ('vertices in (z < -0.499)', 'facet'),
'Top' : ('vertices in (z > 0.499)', 'facet'),
}

materials = {
'one' : ({'val' : 1.0},),
}

fields = {
'temperature' : ('real', 1, 'Omega', 1),
}

variables = {
't' : ('unknown field', 'temperature', 0),
's' : ('test field', 'temperature', 't'),
}

ebcs = {
'fixed' : ('Bottom', {'t.all' : 0}),
't_t02' : ('Left', [(-0.5, 0.5), (2.5, 3.5)], {'t.all' : 1.0}),
't_t1' : ('Right', [(0.5, 1.5)], {'t.all' : 2.0}),
't_t4' : ('Top', 'is_ebc', {'t.all' : 3.0}),
}

def is_ebc(ts):
if ts.step in (2, 4):
return True

else:
return False

functions = {
'is_ebc' : (is_ebc,),
}

equations = {
'eq' : """dw_laplace.2.Omega( one.val, s, t ) = 0""",
}

solvers = {
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'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
}),
'ts' : ('ts.simple', {
't0' : 0.0,
't1' : 4.0,
'dt' : None,
'n_step' : 5, # has precedence over dt!

'quasistatic' : True,
'verbose' : 1,
}),
}

diffusion/poisson.py

Description
Laplace equation using the long syntax of keywords.
See the tutorial section Example Problem Description File for a detailed explanation. See diffu-
sion/poisson_short_syntax.py for the short syntax version.
Find 𝑡 such that:
∫︁
𝑐∇𝑠 · ∇𝑡 = 0 , ∀𝑠 .
Ω

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source code

r"""
Laplace equation using the long syntax of keywords.

See the tutorial section :ref:`poisson-example-tutorial` for a detailed

explanation. See :ref:`diffusion-poisson_short_syntax` for the short syntax
version.

Find :math:`t` such that:

.. math::
\int_{\Omega} c \nabla s \cdot \nabla t
= 0
\;, \quad \forall s \;.
"""
from __future__ import absolute_import
from sfepy import data_dir

filename_mesh = data_dir + '/meshes/3d/cylinder.mesh'

material_2 = {
'name' : 'coef',
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'values' : {'val' : 1.0},
}

region_1000 = {
'name' : 'Omega',
'select' : 'cells of group 6',
}

region_03 = {
'name' : 'Gamma_Left',
'select' : 'vertices in (x < 0.00001)',
'kind' : 'facet',
}

region_4 = {
'name' : 'Gamma_Right',
'select' : 'vertices in (x > 0.099999)',
'kind' : 'facet',
}

field_1 = {
'name' : 'temperature',
'dtype' : 'real',
'shape' : (1,),
'region' : 'Omega',
'approx_order' : 1,
}

variable_1 = {
'name' : 't',
'kind' : 'unknown field',
'field' : 'temperature',
'order' : 0, # order in the global vector of unknowns
}

variable_2 = {
'name' : 's',
'kind' : 'test field',
'field' : 'temperature',
'dual' : 't',
}

ebc_1 = {
'name' : 't1',
'region' : 'Gamma_Left',
'dofs' : {'t.0' : 2.0},
}

ebc_2 = {
'name' : 't2',
'region' : 'Gamma_Right',
'dofs' : {'t.0' : -2.0},
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}

integral_1 = {
'name' : 'i',
'order' : 2,
}

equations = {
'Temperature' : """dw_laplace.i.Omega( coef.val, s, t ) = 0"""
}

solver_0 = {
'name' : 'ls',
'kind' : 'ls.scipy_direct',
'method' : 'auto',
}

solver_1 = {
'name' : 'newton',
'kind' : 'nls.newton',

'i_max' : 1,
'eps_a' : 1e-10,
'eps_r' : 1.0,
'macheps' : 1e-16,
'lin_red' : 1e-2, # Linear system error < (eps_a * lin_red).
'ls_red' : 0.1,
'ls_red_warp' : 0.001,
'ls_on' : 1.1,
'ls_min' : 1e-5,
'check' : 0,
'delta' : 1e-6,
}

options = {
'nls' : 'newton',
'ls' : 'ls',
}

diffusion/poisson_field_dependent_material.py

Description
Laplace equation with a field-dependent material parameter.
Find 𝑇 (𝑡) for 𝑡 ∈ [0, 𝑡final ] such that:
∫︁
𝑐(𝑇 )∇𝑠 · ∇𝑇 = 0 , ∀𝑠 .
Ω

where 𝑐(𝑇 ) is the 𝑇 dependent diffusion coefficient. Each iteration calculates 𝑇 and adjusts 𝑐(𝑇 ).

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source code

r"""
Laplace equation with a field-dependent material parameter.

Find :math:`T(t)` for :math:`t \in [0, t_{\rm final}]` such that:

.. math::
\int_{\Omega} c(T) \nabla s \cdot \nabla T
= 0
\;, \quad \forall s \;.

where :math:`c(T)` is the :math:`T` dependent diffusion coefficient.

Each iteration calculates :math:`T` and adjusts :math:`c(T)`.
"""
from __future__ import absolute_import
from sfepy import data_dir
from sfepy.base.base import output

filename_mesh = data_dir + '/meshes/3d/cylinder.mesh'

t0 = 0.0
t1 = 0.1
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n_step = 11

def get_conductivity(ts, coors, problem, equations=None, mode=None, **kwargs):

"""
Calculates the conductivity as 2+10*T and returns it.
This relation results in larger T gradients where T is small.
"""
if mode == 'qp':
# T-field values in quadrature points coordinates given by integral i
# - they are the same as in `coors` argument.
T_values = problem.evaluate('ev_integrate.i.Omega(T)',
mode='qp', verbose=False)
val = 2 + 10 * (T_values + 2)

output('conductivity: min:', val.min(), 'max:', val.max())

val.shape = (val.shape[0] * val.shape[1], 1, 1)

return {'val' : val}

materials = {
'coef' : 'get_conductivity',
}

fields = {
'temperature' : ('real', 1, 'Omega', 1),
}

variables = {
'T' : ('unknown field', 'temperature', 0),
's' : ('test field', 'temperature', 'T'),
}

regions = {
'Omega' : 'all',
'Gamma_Left' : ('vertices in (x < 0.00001)', 'facet'),
'Gamma_Right' : ('vertices in (x > 0.099999)', 'facet'),
}

ebcs = {
'T1' : ('Gamma_Left', {'T.0' : 2.0}),
'T2' : ('Gamma_Right', {'T.0' : -2.0}),
}

functions = {
'get_conductivity' : (get_conductivity,),
}

ics = {
'ic' : ('Omega', {'T.0' : 0.0}),
}

integrals = {
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'i' : 1,
}

equations = {
'Temperature' : """dw_laplace.i.Omega( coef.val, s, T ) = 0"""
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
'eps_r' : 1.0,
}),
'ts' : ('ts.simple', {
't0' : t0,
't1' : t1,
'dt' : None,
'n_step' : n_step, # has precedence over dt!
'quasistatic' : True,
'verbose' : 1,
}),
}

options = {
'nls' : 'newton',
'ls' : 'ls',
'ts' : 'ts',
'save_times' : 'all',
}

diffusion/poisson_functions.py

Description
Poisson equation with source term.
Find 𝑢 such that:
∫︁ ∫︁ ∫︁
𝑐∇𝑣 · ∇𝑢 = − 𝑏𝑣 = − 𝑓 𝑣𝑝 , ∀𝑣 ,
Ω Ω𝐿 Ω𝐿

where 𝑏(𝑥) = 𝑓 (𝑥)𝑝(𝑥), 𝑝 is a given FE field and 𝑓 is a given general function of space.
This example demonstrates use of functions for defining material parameters, regions, parameter variables or boundary
conditions. Notably, it demonstrates the following:
1. How to define a material parameter by an arbitrary function - see the function get_pars() that evaluates 𝑓 (𝑥)
in quadrature points.
2. How to define a known function that belongs to a given FE space (field) - this function, 𝑝(𝑥), is defined in a FE
sense by its nodal values only - see the function get_load_variable().
In order to define the load 𝑏(𝑥) directly, the term dw_dot should be replaced by dw_integrate.

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source code

r"""
Poisson equation with source term.

Find :math:`u` such that:

.. math::
\int_{\Omega} c \nabla v \cdot \nabla u
= - \int_{\Omega_L} b v = - \int_{\Omega_L} f v p
\;, \quad \forall v \;,

where :math:`b(x) = f(x) p(x)`, :math:`p` is a given FE field and :math:`f` is

a given general function of space.

This example demonstrates use of functions for defining material parameters,

regions, parameter variables or boundary conditions. Notably, it demonstrates
the following:

1. How to define a material parameter by an arbitrary function - see the

function :func:`get_pars()` that evaluates :math:`f(x)` in quadrature
points.
2. How to define a known function that belongs to a given FE space (field) -
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this function, :math:`p(x)`, is defined in a FE sense by its nodal values
only - see the function :func:`get_load_variable()`.

In order to define the load :math:`b(x)` directly, the term ``dw_dot``

should be replaced by ``dw_integrate``.
"""
from __future__ import absolute_import
import numpy as nm
from sfepy import data_dir

filename_mesh = data_dir + '/meshes/3d/cylinder.mesh'

options = {
'nls' : 'newton',
'ls' : 'ls',
}

materials = {
'm' : ({'c' : 1.0},),
'load' : 'get_pars',
}

regions = {
'Omega' : 'all',
'Omega_L' : 'vertices by get_middle_ball',
'Gamma_Left' : ('vertices in (x < 0.00001)', 'facet'),
'Gamma_Right' : ('vertices in (x > 0.099999)', 'facet'),
}

fields = {
'temperature' : ('real', 1, 'Omega', 1),
'velocity' : ('real', 'vector', 'Omega', 1),
}

variables = {
'u' : ('unknown field', 'temperature', 0),
'v' : ('test field', 'temperature', 'u'),
'p' : ('parameter field', 'temperature',
{'setter' : 'get_load_variable'}),
'w' : ('parameter field', 'velocity',
{'setter' : 'get_convective_velocity'}),
}

ebcs = {
'u1' : ('Gamma_Left', {'u.0' : 'get_ebc'}),
'u2' : ('Gamma_Right', {'u.0' : -2.0}),
}

integrals = {
'i' : 1,
}

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equations = {
'Laplace equation' :
"""dw_laplace.i.Omega( m.c, v, u )
- dw_convect_v_grad_s.i.Omega( v, w, u )
= - dw_dot.i.Omega_L( load.f, v, p )"""
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
}),
}

def get_pars(ts, coors, mode=None, **kwargs):

"""
Evaluate the coefficient `load.f` in quadrature points `coors` using a
function of space.

For scalar parameters, the shape has to be set to `(coors.shape[0], 1, 1)`.

"""
if mode == 'qp':
x = coors[:, 0]

val = 55.0 * (x - 0.05)

val.shape = (coors.shape[0], 1, 1)
return {'f' : val}

def get_middle_ball(coors, domain=None):

"""
Get the :math:`\Omega_L` region as a function of mesh coordinates.
"""
x, y, z = coors[:, 0], coors[:, 1], coors[:, 2]

r1 = nm.sqrt((x - 0.025)**2.0 + y**2.0 + z**2)

r2 = nm.sqrt((x - 0.075)**2.0 + y**2.0 + z**2)
flag = nm.where((r1 < 2.3e-2) | (r2 < 2.3e-2))[0]

return flag

def get_load_variable(ts, coors, region=None):

"""
Define nodal values of 'p' in the nodal coordinates `coors`.
"""
y = coors[:,1]

val = 5e5 * y
return val

def get_convective_velocity(ts, coors, region=None):

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"""
Define nodal values of 'w' in the nodal coordinates `coors`.
"""
val = 100.0 * nm.ones_like(coors)

return val

def get_ebc(coors, amplitude):

"""
Define the essential boundary conditions as a function of coordinates
`coors` of region nodes.
"""
z = coors[:, 2]
val = amplitude * nm.sin(z * 2.0 * nm.pi)
return val

functions = {
'get_pars' : (get_pars,),
'get_load_variable' : (get_load_variable,),
'get_convective_velocity' : (get_convective_velocity,),
'get_middle_ball' : (get_middle_ball,),
'get_ebc' : (lambda ts, coor, bc, problem, **kwargs: get_ebc(coor, 5.0),),
}

diffusion/poisson_iga.py

Description
Poisson equation solved in a single patch NURBS domain using the isogeometric analysis (IGA) approach.
Find 𝑡 such that:
∫︁ ∫︁
𝑐∇𝑠 · ∇𝑡 = 𝑓𝑠 , ∀𝑠 .
Ω Ω0

Try setting the Dirichlet boundary condition (ebcs) on various sides of the domain ('Gamma1', . . . , 'Gamma4').
View the results using:

$ ./postproc.py patch2d.vtk --wireframe -b

$ ./postproc.py patch2d.vtk --wireframe -b -d't,plot_warp_scalar,rel_scaling=1'

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source code

r"""
Poisson equation solved in a single patch NURBS domain using the isogeometric
analysis (IGA) approach.

Find :math:`t` such that:

.. math::
\int_{\Omega} c \nabla s \cdot \nabla t
= \int_{\Omega_0} f s
\;, \quad \forall s \;.

Try setting the Dirichlet boundary condition (ebcs) on various sides of the
domain (``'Gamma1'``, ..., ``'Gamma4'``).

View the results using::

$ ./postproc.py patch2d.vtk --wireframe -b

$ ./postproc.py patch2d.vtk --wireframe -b -d't,plot_warp_scalar,rel_scaling=1'
"""
from __future__ import absolute_import
from sfepy import data_dir
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filename_domain = data_dir + '/meshes/iga/patch2d.iga'

materials = {
'm' : ({'c' : 1.0, 'f' : -10.0},),
}

regions = {
'Omega' : 'all',
'Omega_0' : 'vertices in (x > 1.5)',
'Gamma1' : ('vertices of set xi00', 'facet'),
'Gamma2' : ('vertices of set xi01', 'facet'),
'Gamma3' : ('vertices of set xi10', 'facet'),
'Gamma4' : ('vertices of set xi11', 'facet'),
}

fields = {
'temperature' : ('real', 1, 'Omega', None, 'H1', 'iga'),
}

variables = {
't' : ('unknown field', 'temperature', 0),
's' : ('test field', 'temperature', 't'),
}

ebcs = {
't1' : ('Gamma3', {'t.0' : 2.0}),
't2' : ('Gamma4', {'t.0' : -2.0}),
}

integrals = {
'i' : 3,
}

equations = {
'Temperature' : """dw_laplace.i.Omega(m.c, s, t)
= dw_volume_lvf.i.Omega_0(m.f, s)"""
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
}),
}

options = {
'nls' : 'newton',
'ls' : 'ls',
}

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diffusion/poisson_neumann.py

Description
The Poisson equation with Neumann boundary conditions on a part of the boundary.
Find 𝑇 such that:
∫︁ ∫︁
𝐾𝑖𝑗 ∇𝑖 𝑠∇𝑗 𝑝𝑇 = 𝑠𝑔 , ∀𝑠 ,
Ω Γ𝑁

where 𝑔 is the given flux, 𝑔 = 𝑛 · 𝐾𝑖𝑗 ∇𝑗 𝑇¯, and 𝐾𝑖𝑗 = 𝑐𝛿𝑖𝑗 (an isotropic medium). See the tutorial section Strong form
of Poisson’s equation and its integration for a detailed explanation.
The diffusion velocity and fluxes through various parts of the boundary are computed in the post_process() function.
On ‘Gamma_N’ (the Neumann condition boundary part), the flux/length should correspond to the given value 𝑔 = −50,
while on ‘Gamma_N0’ the flux should be zero. Use the ‘refinement_level’ option (see the usage examples below) to
check the convergence of the numerical solution to those values. The total flux and the flux through ‘Gamma_D’ (the
Dirichlet condition boundary part) are shown as well.

Usage Examples

Run with the default settings (no refinement):

python simple.py examples/diffusion/poisson_neumann.py

Refine the mesh twice:

python simple.py examples/diffusion/poisson_neumann.py -O "'refinement_level' : 2"

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r"""
The Poisson equation with Neumann boundary conditions on a part of the
boundary.

Find :math:`T` such that:

.. math::
\int_{\Omega} K_{ij} \nabla_i s \nabla_j p T
= \int_{\Gamma_N} s g
\;, \quad \forall s \;,

where :math:`g` is the given flux, :math:`g = \ul{n} \cdot K_{ij} \nabla_j
\bar{T}`, and :math:`K_{ij} = c \delta_{ij}` (an isotropic medium). See the
tutorial section :ref:`poisson-weak-form-tutorial` for a detailed explanation.

The diffusion velocity and fluxes through various parts of the boundary are
computed in the :func:`post_process()` function. On 'Gamma_N' (the Neumann
condition boundary part), the flux/length should correspond to the given value
:math:`g = -50`, while on 'Gamma_N0' the flux should be zero. Use the
'refinement_level' option (see the usage examples below) to check the
convergence of the numerical solution to those values. The total flux and the
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flux through 'Gamma_D' (the Dirichlet condition boundary part) are shown as
well.

Usage Examples
--------------

Run with the default settings (no refinement)::

python simple.py sfepy/examples/diffusion/poisson_neumann.py

Refine the mesh twice::

python simple.py sfepy/examples/diffusion/poisson_neumann.py -O "'refinement_level' : 2"

"""
from __future__ import absolute_import
import numpy as nm

from sfepy.base.base import output, Struct

from sfepy import data_dir

def post_process(out, pb, state, extend=False):

"""
Calculate :math:`\nabla t` and compute boundary fluxes.
"""
dv = pb.evaluate('ev_diffusion_velocity.i.Omega(m.K, t)', mode='el_avg',
verbose=False)
out['dv'] = Struct(name='output_data', mode='cell',
data=dv, dofs=None)

totals = nm.zeros(3)
for gamma in ['Gamma_N', 'Gamma_N0', 'Gamma_D']:

flux = pb.evaluate('ev_surface_flux.i.%s(m.K, t)' % gamma,

verbose=False)
area = pb.evaluate('ev_volume.i.%s(t)' % gamma, verbose=False)

flux_data = (gamma, flux, area, flux / area)

totals += flux_data[1:]

output('%8s flux: % 8.3f length: % 8.3f flux/length: % 8.3f '

% flux_data)

totals[2] = totals[0] / totals[1]

output(' total flux: % 8.3f length: % 8.3f flux/length: % 8.3f '
% tuple(totals))

return out

filename_mesh = data_dir + '/meshes/2d/cross-51-0.34.mesh'

materials = {
'flux' : ({'val' : -50.0},),
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'm' : ({'K' : 2.7 * nm.eye(2)},),
}

regions = {
'Omega' : 'all',
'Gamma_D' : ('vertices in (x < -0.4999)', 'facet'),
'Gamma_N0' : ('vertices in (y > 0.4999)', 'facet'),
'Gamma_N' : ('vertices of surface -s (r.Gamma_D +v r.Gamma_N0)',
'facet'),
}

fields = {
'temperature' : ('real', 1, 'Omega', 1),
}

variables = {
't' : ('unknown field', 'temperature', 0),
's' : ('test field', 'temperature', 't'),
}

ebcs = {
't1' : ('Gamma_D', {'t.0' : 5.3}),
}

integrals = {
'i' : 2
}

equations = {
'Temperature' : """
dw_diffusion.i.Omega(m.K, s, t)
= dw_integrate.i.Gamma_N(flux.val, s)
"""
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
}),
}

options = {
'nls' : 'newton',
'ls' : 'ls',

'refinement_level' : 0,
'post_process_hook' : 'post_process',
}

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diffusion/poisson_parallel_interactive.py

Description
Parallel assembling and solving of a Poisson’s equation, using commands for interactive use.
Find 𝑢 such that:
∫︁ ∫︁
∇𝑣 · ∇𝑢 = 𝑣𝑓 , ∀𝑠 .
Ω Ω

Important Notes

• This example requires petsc4py, mpi4py and (optionally) pymetis with their dependencies installed!
• This example generates a number of files - do not use an existing non-empty directory for the output_dir
argument.
• Use the --clear option with care!

Notes

• Each task is responsible for a subdomain consisting of a set of cells (a cell region).
• Each subdomain owns PETSc DOFs within a consecutive range.
• When both global and task-local variables exist, the task-local variables have _i suffix.
• This example does not use a nonlinear solver.
• This example can serve as a template for solving a linear single-field scalar problem - just replace the equations
in create_local_problem().
• The command line options are saved into <output_dir>/options.txt file.

Usage Examples

See all options:

$ python examples/diffusion/poisson_parallel_interactive.py -h

See PETSc options:

$ python examples/diffusion/poisson_parallel_interactive.py -help

Single process run useful for debugging with debug():

$ python examples/diffusion/poisson_parallel_interactive.py output-parallel

Parallel runs:

$ mpiexec -n 3 python examples/diffusion/poisson_parallel_interactive.py output-parallel␣

˓→-2 --shape=101,101

$ mpiexec -n 3 python examples/diffusion/poisson_parallel_interactive.py output-parallel␣

˓→-2 --shape=101,101 --metis

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$ mpiexec -n 5 python examples/diffusion/poisson_parallel_interactive.py output-parallel␣

˓→-2 --shape=101,101 --verify --metis -ksp_monitor -ksp_converged_reason

View the results using:

$ python postproc.py output-parallel/sol.h5 --wireframe -b -d'u,plot_warp_scalar'

source code

#!/usr/bin/env python
r"""
Parallel assembling and solving of a Poisson's equation, using commands for
interactive use.

Find :math:`u` such that:

.. math::
\int_{\Omega} \nabla v \cdot \nabla u
= \int_{\Omega} v f
\;, \quad \forall s \;.

Important Notes
---------------

- This example requires petsc4py, mpi4py and (optionally) pymetis with their
dependencies installed!
- This example generates a number of files - do not use an existing non-empty
directory for the ``output_dir`` argument.
- Use the ``--clear`` option with care!

Notes
-----

- Each task is responsible for a subdomain consisting of a set of cells (a cell

region).
- Each subdomain owns PETSc DOFs within a consecutive range.
- When both global and task-local variables exist, the task-local
variables have ``_i`` suffix.
- This example does not use a nonlinear solver.
- This example can serve as a template for solving a linear single-field scalar
problem - just replace the equations in :func:`create_local_problem()`.
- The command line options are saved into <output_dir>/options.txt file.

Usage Examples
--------------

See all options::

$ python sfepy/examples/diffusion/poisson_parallel_interactive.py -h

See PETSc options::

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$ python sfepy/examples/diffusion/poisson_parallel_interactive.py -help

Single process run useful for debugging with :func:`debug()

<sfepy.base.base.debug>`::

$ python sfepy/examples/diffusion/poisson_parallel_interactive.py output-parallel

Parallel runs::

$ mpiexec -n 3 python sfepy/examples/diffusion/poisson_parallel_interactive.py output-

˓→parallel -2 --shape=101,101

$ mpiexec -n 3 python sfepy/examples/diffusion/poisson_parallel_interactive.py output-

˓→parallel -2 --shape=101,101 --metis

$ mpiexec -n 5 python sfepy/examples/diffusion/poisson_parallel_interactive.py output-

˓→parallel -2 --shape=101,101 --verify --metis -ksp_monitor -ksp_converged_reason

View the results using::

$ python postproc.py output-parallel/sol.h5 --wireframe -b -d'u,plot_warp_scalar'

"""
from __future__ import absolute_import
from argparse import RawDescriptionHelpFormatter, ArgumentParser
import os
import sys
sys.path.append('.')
import csv

import numpy as nm
import matplotlib.pyplot as plt

from sfepy.base.base import output, Struct

from sfepy.base.ioutils import ensure_path, remove_files_patterns, save_options
from sfepy.base.timing import Timer
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.discrete.common.region import Region
from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.discrete.evaluate import apply_ebc_to_matrix
from sfepy.terms import Term
from sfepy.solvers.ls import PETScKrylovSolver

import sfepy.parallel.parallel as pl
import sfepy.parallel.plot_parallel_dofs as ppd

def create_local_problem(omega_gi, order):

"""
Local problem definition using a domain corresponding to the global region
`omega_gi`.
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"""
mesh = omega_gi.domain.mesh

# All tasks have the whole mesh.

bbox = mesh.get_bounding_box()
min_x, max_x = bbox[:, 0]
eps_x = 1e-8 * (max_x - min_x)

mesh_i = Mesh.from_region(omega_gi, mesh, localize=True)

domain_i = FEDomain('domain_i', mesh_i)
omega_i = domain_i.create_region('Omega', 'all')

gamma1_i = domain_i.create_region('Gamma1',
'vertices in (x < %.10f )'
% (min_x + eps_x),
'facet', allow_empty=True)
gamma2_i = domain_i.create_region('Gamma2',
'vertices in (x > %.10f )'
% (max_x - eps_x),
'facet', allow_empty=True)

field_i = Field.from_args('fu', nm.float64, 1, omega_i,

approx_order=order)

output('number of local field DOFs:', field_i.n_nod)

u_i = FieldVariable('u_i', 'unknown', field_i)

v_i = FieldVariable('v_i', 'test', field_i, primary_var_name='u_i')

integral = Integral('i', order=2*order)

mat = Material('m', lam=10, mu=5)

t1 = Term.new('dw_laplace(m.lam, v_i, u_i)',
integral, omega_i, m=mat, v_i=v_i, u_i=u_i)

def _get_load(coors):
val = nm.ones_like(coors[:, 0])
for coor in coors.T:
val *= nm.sin(4 * nm.pi * coor)
return val

def get_load(ts, coors, mode=None, **kwargs):

if mode == 'qp':
return {'val' : _get_load(coors).reshape(coors.shape[0], 1, 1)}

load = Material('load', function=Function('get_load', get_load))

t2 = Term.new('dw_volume_lvf(load.val, v_i)',
integral, omega_i, load=load, v_i=v_i)

eq = Equation('balance', t1 - 100 * t2)

eqs = Equations([eq])
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ebc1 = EssentialBC('ebc1', gamma1_i, {'u_i.all' : 0.0})

ebc2 = EssentialBC('ebc2', gamma2_i, {'u_i.all' : 0.1})

pb = Problem('problem_i', equations=eqs, active_only=False)

pb.time_update(ebcs=Conditions([ebc1, ebc2]))
pb.update_materials()

return pb

def verify_save_dof_maps(field, cell_tasks, dof_maps, id_map, options,

verbose=False):
vec = pl.verify_task_dof_maps(dof_maps, id_map, field, verbose=verbose)

order = options.order
mesh = field.domain.mesh

sfield = Field.from_args('aux', nm.float64, 'scalar', field.region,

approx_order=order)
aux = FieldVariable('aux', 'parameter', sfield,
primary_var_name='(set-to-None)')
out = aux.create_output(vec,
linearization=Struct(kind='adaptive',
min_level=order-1,
max_level=order-1,
eps=1e-8))

filename = os.path.join(options.output_dir,
'para-domains-dofs.h5')
if field.is_higher_order():
out['aux'].mesh.write(filename, out=out)

else:
mesh.write(filename, out=out)

out = Struct(name='cells', mode='cell',

data=cell_tasks[:, None, None, None])
filename = os.path.join(options.output_dir,
'para-domains-cells.h5')
mesh.write(filename, out={'cells' : out})

def solve_problem(mesh_filename, options, comm):

order = options.order

rank, size = comm.Get_rank(), comm.Get_size()

output('rank', rank, 'of', size)

stats = Struct()
timer = Timer('solve_timer')

timer.start()
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mesh = Mesh.from_file(mesh_filename)
stats.t_read_mesh = timer.stop()

timer.start()
if rank == 0:
cell_tasks = pl.partition_mesh(mesh, size, use_metis=options.metis,
verbose=True)

else:
cell_tasks = None

stats.t_partition_mesh = timer.stop()

output('creating global domain and field...')

timer.start()

domain = FEDomain('domain', mesh)

omega = domain.create_region('Omega', 'all')
field = Field.from_args('fu', nm.float64, 1, omega, approx_order=order)

stats.t_create_global_fields = timer.stop()
output('...done in', timer.dt)

output('distributing field %s...' % field.name)

timer.start()

distribute = pl.distribute_fields_dofs
lfds, gfds = distribute([field], cell_tasks,
is_overlap=True,
save_inter_regions=options.save_inter_regions,
output_dir=options.output_dir,
comm=comm, verbose=True)
lfd = lfds[0]

stats.t_distribute_fields_dofs = timer.stop()
output('...done in', timer.dt)

if rank == 0:
dof_maps = gfds[0].dof_maps
id_map = gfds[0].id_map

if options.verify:
verify_save_dof_maps(field, cell_tasks,
dof_maps, id_map, options, verbose=True)

if options.plot:
ppd.plot_partitioning([None, None], field, cell_tasks, gfds[0],
options.output_dir, size)

output('creating local problem...')

timer.start()

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omega_gi = Region.from_cells(lfd.cells, field.domain)
omega_gi.finalize()
omega_gi.update_shape()

pb = create_local_problem(omega_gi, order)

variables = pb.get_initial_state()
eqs = pb.equations

u_i = variables['u_i']
field_i = u_i.field

stats.t_create_local_problem = timer.stop()
output('...done in', timer.dt)

if options.plot:
ppd.plot_local_dofs([None, None], field, field_i, omega_gi,
options.output_dir, rank)

output('allocating global system...')

timer.start()

sizes, drange = pl.get_sizes(lfd.petsc_dofs_range, field.n_nod, 1)

output('sizes:', sizes)
output('drange:', drange)

pdofs = pl.get_local_ordering(field_i, lfd.petsc_dofs_conn)

output('pdofs:', pdofs)

pmtx, psol, prhs = pl.create_petsc_system(pb.mtx_a, sizes, pdofs, drange,

is_overlap=True, comm=comm,
verbose=True)

stats.t_allocate_global_system = timer.stop()
output('...done in', timer.dt)

output('evaluating local problem...')

timer.start()

variables.fill_state(0.0)
variables.apply_ebc()

rhs_i = eqs.eval_residuals(variables())
# This must be after pl.create_petsc_system() call!
mtx_i = eqs.eval_tangent_matrices(variables(), pb.mtx_a)

stats.t_evaluate_local_problem = timer.stop()
output('...done in', timer.dt)

output('assembling global system...')

timer.start()
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apply_ebc_to_matrix(mtx_i, u_i.eq_map.eq_ebc)
pl.assemble_rhs_to_petsc(prhs, rhs_i, pdofs, drange, is_overlap=True,
comm=comm, verbose=True)
pl.assemble_mtx_to_petsc(pmtx, mtx_i, pdofs, drange, is_overlap=True,
comm=comm, verbose=True)

stats.t_assemble_global_system = timer.stop()
output('...done in', timer.dt)

output('creating solver...')
timer.start()

conf = Struct(method='cg', precond='gamg', sub_precond='none',

i_max=10000, eps_a=1e-50, eps_r=1e-5, eps_d=1e4, verbose=True)
status = {}
ls = PETScKrylovSolver(conf, comm=comm, mtx=pmtx, status=status)

stats.t_create_solver = timer.stop()
output('...done in', timer.dt)

output('solving...')
timer.start()

psol = ls(prhs, psol)

psol_i = pl.create_local_petsc_vector(pdofs)
gather, scatter = pl.create_gather_scatter(pdofs, psol_i, psol, comm=comm)

scatter(psol_i, psol)

sol0_i = variables() - psol_i[...]

psol_i[...] = sol0_i

gather(psol, psol_i)

stats.t_solve = timer.stop()
output('...done in', timer.dt)

output('saving solution...')
timer.start()

variables.set_state(sol0_i)
out = u_i.create_output()

filename = os.path.join(options.output_dir, 'sol_%02d.h5' % comm.rank)

pb.domain.mesh.write(filename, io='auto', out=out)

gather_to_zero = pl.create_gather_to_zero(psol)

psol_full = gather_to_zero(psol)

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if comm.rank == 0:
sol = psol_full[...].copy()[id_map]

u = FieldVariable('u', 'parameter', field,

primary_var_name='(set-to-None)')

filename = os.path.join(options.output_dir, 'sol.h5')

if (order == 1) or (options.linearization == 'strip'):
out = u.create_output(sol)
mesh.write(filename, io='auto', out=out)

else:
out = u.create_output(sol, linearization=Struct(kind='adaptive',
min_level=0,
max_level=order,
eps=1e-3))

out['u'].mesh.write(filename, io='auto', out=out)

stats.t_save_solution = timer.stop()
output('...done in', timer.dt)

stats.t_total = timer.total

stats.n_dof = sizes[1]
stats.n_dof_local = sizes[0]
stats.n_cell = omega.shape.n_cell
stats.n_cell_local = omega_gi.shape.n_cell

if options.show:
plt.show()

return stats

def save_stats(filename, pars, stats, overwrite, rank, comm=None):

out = stats.to_dict()
names = sorted(out.keys())
shape_dict = {'n%d' % ii : pars.shape[ii] for ii in range(pars.dim)}
keys = ['size', 'rank', 'dim'] + list(shape_dict.keys()) + ['order'] + names

out['size'] = comm.size
out['rank'] = rank
out['dim'] = pars.dim
out.update(shape_dict)
out['order'] = pars.order

if rank == 0 and overwrite:

with open(filename, 'w') as fd:
writer = csv.DictWriter(fd, fieldnames=keys)
writer.writeheader()
writer.writerow(out)

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else:
with open(filename, 'a') as fd:
writer = csv.DictWriter(fd, fieldnames=keys)
writer.writerow(out)

helps = {
'output_dir' :
'output directory',
'dims' :
'dimensions of the block [default: %(default)s]',
'shape' :
'shape (counts of nodes in x, y, z) of the block [default: %(default)s]',
'centre' :
'centre of the block [default: %(default)s]',
'2d' :
'generate a 2D rectangle, the third components of the above'
' options are ignored',
'order' :
'field approximation order',
'linearization' :
'linearization used for storing the results with approximation order > 1'
' [default: %(default)s]',
'metis' :
'use metis for domain partitioning',
'verify' :
'verify domain partitioning, save cells and DOFs of tasks'
' for visualization',
'plot' :
'make partitioning plots',
'save_inter_regions' :
'save inter-task regions for debugging partitioning problems',
'show' :
'show partitioning plots (implies --plot)',
'stats_filename' :
'name of the stats file for storing elapsed time statistics',
'new_stats' :
'create a new stats file with a header line (overwrites existing!)',
'silent' : 'do not print messages to screen',
'clear' :
'clear old solution files from output directory'
' (DANGEROUS - use with care!)',
}

def main():
parser = ArgumentParser(description=__doc__.rstrip(),
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('output_dir', help=helps['output_dir'])
parser.add_argument('--dims', metavar='dims',
action='store', dest='dims',
default='1.0,1.0,1.0', help=helps['dims'])
parser.add_argument('--shape', metavar='shape',
action='store', dest='shape',
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default='11,11,11', help=helps['shape'])
parser.add_argument('--centre', metavar='centre',
action='store', dest='centre',
default='0.0,0.0,0.0', help=helps['centre'])
parser.add_argument('-2', '--2d',
action='store_true', dest='is_2d',
default=False, help=helps['2d'])
parser.add_argument('--order', metavar='int', type=int,
action='store', dest='order',
default=1, help=helps['order'])
parser.add_argument('--linearization', choices=['strip', 'adaptive'],
action='store', dest='linearization',
default='strip', help=helps['linearization'])
parser.add_argument('--metis',
action='store_true', dest='metis',
default=False, help=helps['metis'])
parser.add_argument('--verify',
action='store_true', dest='verify',
default=False, help=helps['verify'])
parser.add_argument('--plot',
action='store_true', dest='plot',
default=False, help=helps['plot'])
parser.add_argument('--show',
action='store_true', dest='show',
default=False, help=helps['show'])
parser.add_argument('--save-inter-regions',
action='store_true', dest='save_inter_regions',
default=False, help=helps['save_inter_regions'])
parser.add_argument('--stats', metavar='filename',
action='store', dest='stats_filename',
default=None, help=helps['stats_filename'])
parser.add_argument('--new-stats',
action='store_true', dest='new_stats',
default=False, help=helps['new_stats'])
parser.add_argument('--silent',
action='store_true', dest='silent',
default=False, help=helps['silent'])
parser.add_argument('--clear',
action='store_true', dest='clear',
default=False, help=helps['clear'])
options, petsc_opts = parser.parse_known_args()

if options.show:
options.plot = True

comm = pl.PETSc.COMM_WORLD

output_dir = options.output_dir

filename = os.path.join(output_dir, 'output_log_%02d.txt' % comm.rank)

if comm.rank == 0:
ensure_path(filename)
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comm.barrier()

output.prefix = 'sfepy_%02d:' % comm.rank

output.set_output(filename=filename, combined=options.silent == False)

output('petsc options:', petsc_opts)

mesh_filename = os.path.join(options.output_dir, 'para.h5')

dim = 2 if options.is_2d else 3

dims = nm.array(eval(options.dims), dtype=nm.float64)[:dim]
shape = nm.array(eval(options.shape), dtype=nm.int32)[:dim]
centre = nm.array(eval(options.centre), dtype=nm.float64)[:dim]
output('dimensions:', dims)
output('shape: ', shape)
output('centre: ', centre)

if comm.rank == 0:
from sfepy.mesh.mesh_generators import gen_block_mesh

if options.clear:
remove_files_patterns(output_dir,
['*.h5', '*.mesh', '*.txt', '*.png'],
ignores=['output_log_%02d.txt' % ii
for ii in range(comm.size)],
verbose=True)

save_options(os.path.join(output_dir, 'options.txt'),
[('options', vars(options))])

mesh = gen_block_mesh(dims, shape, centre, name='block-fem',

verbose=True)
mesh.write(mesh_filename, io='auto')

comm.barrier()

output('field order:', options.order)

stats = solve_problem(mesh_filename, options, comm)

output(stats)

if options.stats_filename:
if comm.rank == 0:
ensure_path(options.stats_filename)
comm.barrier()

pars = Struct(dim=dim, shape=shape, order=options.order)

pl.call_in_rank_order(
lambda rank, comm:
save_stats(options.stats_filename, pars, stats, options.new_stats,
rank, comm),
comm
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)

if __name__ == '__main__':
main()

diffusion/poisson_parametric_study.py

Description
Poisson equation.
This example demonstrates parametric study capabilities of Application classes. In particular (written in the strong
form):

𝑐∆𝑡 = 𝑓 in Ω,
𝑡 = 2 on Γ1 , 𝑡 = −2 on Γ2 , 𝑓 = 1 in Ω1 , 𝑓 = 0 otherwise,

where Ω is a square domain, Ω1 ∈ Ω is a circular domain.

Now let’s see what happens if Ω1 diameter changes.
Run:

$ ./simple.py <this file>

and then look in ‘output/r_omega1’ directory, try for example:

$ ./postproc.py output/r_omega1/circles_in_square*.vtk

Remark: this simple case could be achieved also by defining Ω1 by a time-dependent function and solve the static
problem as a time-dependent problem. However, the approach below is much more general.
Find 𝑡 such that:
∫︁
𝑐∇𝑠 · ∇𝑡 = 0 , ∀𝑠 .
Ω

source code

r"""
Poisson equation.

This example demonstrates parametric study capabilities of Application

classes. In particular (written in the strong form):

.. math::
c \Delta t = f \mbox{ in } \Omega,

t = 2 \mbox{ on } \Gamma_1 \;,

t = -2 \mbox{ on } \Gamma_2 \;,
f = 1 \mbox{ in } \Omega_1 \;,
f = 0 \mbox{ otherwise,}

where :math:`\Omega` is a square domain, :math:`\Omega_1 \in \Omega` is

a circular domain.
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Now let's see what happens if :math:`\Omega_1` diameter changes.

Run::

$ ./simple.py <this file>

and then look in 'output/r_omega1' directory, try for example::

$ ./postproc.py output/r_omega1/circles_in_square*.vtk

Remark: this simple case could be achieved also by defining

:math:`\Omega_1` by a time-dependent function and solve the static
problem as a time-dependent problem. However, the approach below is much
more general.

Find :math:`t` such that:

.. math::
\int_{\Omega} c \nabla s \cdot \nabla t
= 0
\;, \quad \forall s \;.
"""
from __future__ import absolute_import
import os
import numpy as nm

from sfepy import data_dir

from sfepy.base.base import output

# Mesh.
filename_mesh = data_dir + '/meshes/2d/special/circles_in_square.vtk'

# Options. The value of 'parametric_hook' is the function that does the

# parametric study.
options = {
'nls' : 'newton', # Nonlinear solver
'ls' : 'ls', # Linear solver

'parametric_hook' : 'vary_omega1_size',
'output_dir' : 'output/r_omega1',
}

# Domain and subdomains.

default_diameter = 0.25
regions = {
'Omega' : 'all',
'Gamma_1' : ('vertices in (x < -0.999)', 'facet'),
'Gamma_2' : ('vertices in (x > 0.999)', 'facet'),
'Omega_1' : 'vertices by select_circ',
}

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# FE field defines the FE approximation: 2_3_P1 = 2D, P1 on triangles.
field_1 = {
'name' : 'temperature',
'dtype' : 'real',
'shape' : (1,),
'region' : 'Omega',
'approx_order' : 1,
}

# Unknown and test functions (FE sense).

variables = {
't' : ('unknown field', 'temperature', 0),
's' : ('test field', 'temperature', 't'),
}

# Dirichlet boundary conditions.

ebcs = {
't1' : ('Gamma_1', {'t.0' : 2.0}),
't2' : ('Gamma_2', {'t.0' : -2.0}),
}

# Material coefficient c and source term value f.

material_1 = {
'name' : 'coef',
'values' : {
'val' : 1.0,
}
}
material_2 = {
'name' : 'source',
'values' : {
'val' : 10.0,
}
}

# Numerical quadrature and the equation.

integral_1 = {
'name' : 'i',
'order' : 2,
}

equations = {
'Poisson' : """dw_laplace.i.Omega( coef.val, s, t )
= dw_volume_lvf.i.Omega_1( source.val, s )"""
}

# Solvers.
solver_0 = {
'name' : 'ls',
'kind' : 'ls.scipy_direct',
}

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solver_1 = {
'name' : 'newton',
'kind' : 'nls.newton',

'i_max' : 1,
'eps_a' : 1e-10,
'eps_r' : 1.0,
'macheps' : 1e-16,
'lin_red' : 1e-2, # Linear system error < (eps_a * lin_red).
'ls_red' : 0.1,
'ls_red_warp' : 0.001,
'ls_on' : 1.1,
'ls_min' : 1e-5,
'check' : 0,
'delta' : 1e-6,
}

functions = {
'select_circ': (lambda coors, domain=None:
select_circ(coors[:,0], coors[:,1], 0, default_diameter),),
}

# Functions.
def select_circ( x, y, z, diameter ):
"""Select circular subdomain of a given diameter."""
r = nm.sqrt( x**2 + y**2 )

out = nm.where(r < diameter)[0]

n = out.shape[0]
if n <= 3:
raise ValueError( 'too few vertices selected! (%d)' % n )

return out

def vary_omega1_size( problem ):

"""Vary size of \Omega1. Saves also the regions into options['output_dir'].

Input:
problem: Problem instance
Return:
a generator object:
1. creates new (modified) problem
2. yields the new (modified) problem and output container
3. use the output container for some logging
4. yields None (to signal next iteration to Application)
"""
from sfepy.discrete import Problem
from sfepy.solvers.ts import get_print_info

output.prefix = 'vary_omega1_size:'

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diameters = nm.linspace( 0.1, 0.6, 7 ) + 0.001
ofn_trunk, output_format = problem.ofn_trunk, problem.output_format
output_dir = problem.output_dir
join = os.path.join

conf = problem.conf
cf = conf.get_raw( 'functions' )
n_digit, aux, d_format = get_print_info( len( diameters ) + 1 )
for ii, diameter in enumerate( diameters ):
output( 'iteration %d: diameter %3.2f ' % (ii, diameter) )

cf['select_circ'] = (lambda coors, domain=None:

select_circ(coors[:,0], coors[:,1], 0, diameter),)
conf.edit('functions', cf)
problem = Problem.from_conf(conf)

problem.save_regions( join( output_dir, ('regions_' + d_format) % ii ),

['Omega_1'] )
region = problem.domain.regions['Omega_1']
if not region.has_cells():
raise ValueError('region %s has no cells!' % region.name)

ofn_trunk = ofn_trunk + '_' + (d_format % ii)

problem.setup_output(output_filename_trunk=ofn_trunk,
output_dir=output_dir,
output_format=output_format)

out = []
yield problem, out

out_problem, state = out[-1]

filename = join( output_dir,

('log_%s.txt' % d_format) % ii )
fd = open( filename, 'w' )
log_item = '$r(\Omega_1)$: %f \n' % diameter
fd.write( log_item )
fd.write( 'solution:\n' )
nm.savetxt(fd, state())
fd.close()

yield None

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diffusion/poisson_periodic_boundary_condition.py

Description
Transient Laplace equation with a localized power source and periodic boundary conditions.
This example is using a mesh generated by gmsh. Both the .geo script used by gmsh to generate the file and the .mesh
file can be found in meshes.
The mesh is suitable for periodic boundary conditions. It consists of a cylinder enclosed by a box in the x and y
directions.
The cylinder will act as a power source.
The transient Laplace equation will be solved in time interval 𝑡 ∈ [0, 𝑡final ].
Find 𝑇 (𝑡) for 𝑡 ∈ [0, 𝑡final ] such that:
∫︁ ∫︁ ∫︁
𝜕𝑇
𝑐𝑠 + 𝜎2 ∇𝑠 · ∇𝑇 = 𝑃3 𝑇 , ∀𝑠 .
Ω 𝜕𝑡 Ω Ω2

source code

r"""
Transient Laplace equation with a localized power source and
periodic boundary conditions.
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This example is using a mesh generated by gmsh. Both the

.geo script used by gmsh to generate the file and the .mesh
file can be found in meshes.

The mesh is suitable for periodic boundary conditions. It consists

of a cylinder enclosed by a box in the x and y directions.

The cylinder will act as a power source.

The transient Laplace equation will be solved in time interval

:math:`t \in [0, t_{\rm final}]`.

Find :math:`T(t)` for :math:`t \in [0, t_{\rm final}]` such that:

.. math::
\int_{\Omega}c s \pdiff{T}{t}
+ \int_{\Omega} \sigma_2 \nabla s \cdot \nabla T
= \int_{\Omega_2} P_3 T
\;, \quad \forall s \;.
"""

from __future__ import absolute_import

from sfepy import data_dir
import numpy as nm
import sfepy.discrete.fem.periodic as per

filename_mesh = data_dir + '/meshes/3d/cylinder_in_box.mesh'

t0 = 0.0
t1 = 1.
n_step = 11
power_per_volume =1.e2 # Heating power per volume of the cylinder
capacity_cylinder = 1. # Heat capacity of cylinder
capacity_fill = 1. # Heat capacity of filling material
conductivity_cylinder = 1. # Heat conductivity of cylinder
conductivity_fill = 1. # Heat conductivity of filling material

def cylinder_material_func(ts, coors, problem, mode=None, **kwargs):

"""
Returns the thermal conductivity, the thermal mass, and the power of the
material in the cylinder.
"""
if mode == 'qp':
shape = (coors.shape[0], 1, 1)

power = nm.empty(shape, dtype=nm.float64)

if ts.step < 5:
# The power is turned on in the first 5 steps only.
power.fill(power_per_volume)

else:
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power.fill(0.0)

conductivity = nm.ones(shape) * conductivity_cylinder

capacity = nm.ones(shape) * capacity_cylinder

return {'power' : power, 'capacity' : capacity,

'conductivity' : conductivity}

materials = {
'cylinder' : 'cylinder_material_func',
'fill' : ({'capacity' : capacity_fill,
'conductivity' : conductivity_fill,},),
}

fields = {
'temperature' : ('real', 1, 'Omega', 1),
}

variables = {
'T' : ('unknown field', 'temperature', 1, 1),
's' : ('test field', 'temperature', 'T'),
}

regions = {
'Omega' : 'all',
'cylinder' : 'cells of group 444',
'fill' : 'cells of group 555',
'Gamma_Left' : ('vertices in (x < -2.4999)', 'facet'),
'y+' : ('vertices in (y >2.4999)', 'facet'),
'y-' : ('vertices in (y <-2.4999)', 'facet'),
'z+' : ('vertices in (z >0.4999)', 'facet'),
'z-' : ('vertices in (z <-0.4999)', 'facet'),
}

ebcs = {
'T1' : ('Gamma_Left', {'T.0' : 0.0}),
}

# The matching functions link the elements on each side with that on the
# opposing side.
functions = {
'cylinder_material_func' : (cylinder_material_func,),
"match_y_plane" : (per.match_y_plane,),
"match_z_plane" : (per.match_z_plane,),
}

epbcs = {
# In the y-direction
'periodic_y' : (['y+', 'y-'], {'T.0' : 'T.0'}, 'match_y_plane'),
# and in the z-direction. Due to the symmetry of the problem, this periodic
# boundary condition is actually not necessary, but we include it anyway.
'periodic_z' : (['z+', 'z-'], {'T.0' : 'T.0'}, 'match_z_plane'),
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}

ics = {
'ic' : ('Omega', {'T.0' : 0.0}),
}

integrals = {
'i' : 1,
}

equations = {
'Temperature' :
"""dw_dot.i.cylinder( cylinder.capacity, s, dT/dt )
dw_dot.i.fill( fill.capacity, s, dT/dt )
dw_laplace.i.cylinder( cylinder.conductivity, s, T )
dw_laplace.i.fill( fill.conductivity, s, T )
= dw_integrate.i.cylinder( cylinder.power, s )"""
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
'eps_r' : 1.0,
}),
'ts' : ('ts.simple', {
't0' : t0,
't1' : t1,
'dt' : None,
'n_step' : n_step, # has precedence over dt!
'quasistatic' : False,
'verbose' : 1,
}),
}

options = {
'nls' : 'newton',
'ls' : 'ls',
'ts' : 'ts',
'output_dir' : 'output',
'save_times' : 'all',
'active_only' : False,
}

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diffusion/poisson_short_syntax.py

Description
Laplace equation using the short syntax of keywords.
See diffusion/poisson.py for the long syntax version.
Find 𝑡 such that:
∫︁
𝑐∇𝑠 · ∇𝑡 = 0 , ∀𝑠 .
Ω

source code

r"""
Laplace equation using the short syntax of keywords.

See :ref:`diffusion-poisson` for the long syntax version.

Find :math:`t` such that:

.. math::
\int_{\Omega} c \nabla s \cdot \nabla t
= 0
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\;, \quad \forall s \;.
"""
from __future__ import absolute_import
from sfepy import data_dir

filename_mesh = data_dir + '/meshes/3d/cylinder.mesh'

materials = {
'coef' : ({'val' : 1.0},),
}

regions = {
'Omega' : 'all', # or 'cells of group 6'
'Gamma_Left' : ('vertices in (x < 0.00001)', 'facet'),
'Gamma_Right' : ('vertices in (x > 0.099999)', 'facet'),
}

fields = {
'temperature' : ('real', 1, 'Omega', 1),
}

variables = {
't' : ('unknown field', 'temperature', 0),
's' : ('test field', 'temperature', 't'),
}

ebcs = {
't1' : ('Gamma_Left', {'t.0' : 2.0}),
't2' : ('Gamma_Right', {'t.0' : -2.0}),
}

integrals = {
'i' : 2,
}

equations = {
'Temperature' : """dw_laplace.i.Omega( coef.val, s, t ) = 0"""
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton',
{'i_max' : 1,
'eps_a' : 1e-10,
}),
}

options = {
'nls' : 'newton',
'ls' : 'ls',
}

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diffusion/sinbc.py

Description
Laplace equation with Dirichlet boundary conditions given by a sine function and constants.
Find 𝑡 such that:
∫︁
𝑐∇𝑠 · ∇𝑡 = 0 , ∀𝑠 .
Ω

The sfepy.discrete.fem.meshio.UserMeshIO class is used to refine the original two-element mesh before the
actual solution.
The FE polynomial basis and the approximation order can be chosen on the command-line. By default, the fifth order
Lagrange polynomial space is used, see define() arguments.
This example demonstrates how to visualize higher order approximations of the continuous solution. The adaptive
linearization is applied in order to save viewable results, see both the options keyword and the post_process()
function that computes the solution gradient. The linearization parameters can also be specified on the command line.
The Lagrange or Bernstein polynomial bases support higher order DOFs in the Dirichlet boundary conditions, unlike
the hierarchical Lobatto basis implementation, compare the results of:

python simple.py examples/diffusion/sinbc.py -d basis=lagrange

python simple.py examples/diffusion/sinbc.py -d basis=bernstein
python simple.py examples/diffusion/sinbc.py -d basis=lobatto

Use the following commands to view each of the results of the above commands (assuming default output directory
and names):

python postproc.py -b -d't,plot_warp_scalar,rel_scaling=1' 2_4_2_refined_t.vtk --

˓→wireframe

python postproc.py -b 2_4_2_refined_grad.vtk

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source code

r"""
Laplace equation with Dirichlet boundary conditions given by a sine function
and constants.

Find :math:`t` such that:

.. math::
\int_{\Omega} c \nabla s \cdot \nabla t
= 0
\;, \quad \forall s \;.

The :class:`sfepy.discrete.fem.meshio.UserMeshIO` class is used to refine the

original two-element mesh before the actual solution.

The FE polynomial basis and the approximation order can be chosen on the
command-line. By default, the fifth order Lagrange polynomial space is used,
see ``define()`` arguments.

This example demonstrates how to visualize higher order approximations of the

continuous solution. The adaptive linearization is applied in order to save
viewable results, see both the options keyword and the ``post_process()``
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function that computes the solution gradient. The linearization parameters can
also be specified on the command line.

The Lagrange or Bernstein polynomial bases support higher order

DOFs in the Dirichlet boundary conditions, unlike the hierarchical Lobatto
basis implementation, compare the results of::

python simple.py sfepy/examples/diffusion/sinbc.py -d basis=lagrange

python simple.py sfepy/examples/diffusion/sinbc.py -d basis=bernstein
python simple.py sfepy/examples/diffusion/sinbc.py -d basis=lobatto

Use the following commands to view each of the results of the above commands
(assuming default output directory and names)::

python postproc.py -b -d't,plot_warp_scalar,rel_scaling=1' 2_4_2_refined_t.vtk --

˓→wireframe
python postproc.py -b 2_4_2_refined_grad.vtk
"""
from __future__ import absolute_import
import numpy as nm

from sfepy import data_dir

from sfepy.base.base import output

from sfepy.discrete.fem import Mesh, FEDomain
from sfepy.discrete.fem.meshio import UserMeshIO, MeshIO
from sfepy.homogenization.utils import define_box_regions
from six.moves import range

base_mesh = data_dir + '/meshes/elements/2_4_2.mesh'

def mesh_hook(mesh, mode):

"""
Load and refine a mesh here.
"""
if mode == 'read':
mesh = Mesh.from_file(base_mesh)
domain = FEDomain(mesh.name, mesh)
for ii in range(3):
output('refine %d...' % ii)
domain = domain.refine()
output('... %d nodes %d elements'
% (domain.shape.n_nod, domain.shape.n_el))

domain.mesh.name = '2_4_2_refined'

return domain.mesh

elif mode == 'write':

pass

def post_process(out, pb, state, extend=False):

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"""
Calculate gradient of the solution.
"""
from sfepy.discrete.fem.fields_base import create_expression_output

aux = create_expression_output('ev_grad.ie.Elements( t )',

'grad', 'temperature',
pb.fields, pb.get_materials(),
pb.get_variables(), functions=pb.functions,
mode='qp', verbose=False,
min_level=0, max_level=5, eps=1e-3)
out.update(aux)

return out

def define(order=5, basis='lagrange', min_level=0, max_level=5, eps=1e-3):

filename_mesh = UserMeshIO(mesh_hook)

# Get the mesh bounding box.

io = MeshIO.any_from_filename(base_mesh)
bbox, dim = io.read_bounding_box(ret_dim=True)

options = {
'nls' : 'newton',
'ls' : 'ls',
'post_process_hook' : 'post_process',
'linearization' : {
'kind' : 'adaptive',
'min_level' : min_level, # Min. refinement level applied everywhere.
'max_level' : max_level, # Max. refinement level.
'eps' : eps, # Relative error tolerance.
},
}

materials = {
'coef' : ({'val' : 1.0},),
}

regions = {
'Omega' : 'all',
}
regions.update(define_box_regions(dim, bbox[0], bbox[1], 1e-5))

fields = {
'temperature' : ('real', 1, 'Omega', order, 'H1', basis),
}

variables = {
't' : ('unknown field', 'temperature', 0),
's' : ('test field', 'temperature', 't'),
}
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amplitude = 1.0
def ebc_sin(ts, coor, **kwargs):
x0 = 0.5 * (coor[:, 1].min() + coor[:, 1].max())
val = amplitude * nm.sin( (coor[:, 1] - x0) * 2. * nm.pi )
return val

ebcs = {
't1' : ('Left', {'t.0' : 'ebc_sin'}),
't2' : ('Right', {'t.0' : -0.5}),
't3' : ('Top', {'t.0' : 1.0}),
}

functions = {
'ebc_sin' : (ebc_sin,),
}

equations = {
'Temperature' : """dw_laplace.10.Omega(coef.val, s, t) = 0"""
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
}),
}

return locals()

diffusion/time_advection_diffusion.py

Description
The transient advection-diffusion equation with a given divergence-free advection velocity.
Find 𝑢 such that:
∫︁ ∫︁ ∫︁
𝜕𝑢
𝑠 + 𝑠∇ · (𝑣𝑢) + 𝐷∇𝑠 · ∇𝑢 = 0 , ∀𝑠 .
Ω 𝜕𝑡 Ω Ω

View the results using:

python postproc.py square_tri2.*.vtk -b --wireframe

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source code

r"""
The transient advection-diffusion equation with a given divergence-free
advection velocity.

Find :math:`u` such that:

.. math::
\int_{\Omega} s \pdiff{u}{t}
+ \int_{\Omega} s \nabla \cdot \left(\ul{v} u \right)
+ \int_{\Omega} D \nabla s \cdot \nabla u
= 0
\;, \quad \forall s \;.

View the results using::

python postproc.py square_tri2.*.vtk -b --wireframe

"""
from __future__ import absolute_import
from sfepy import data_dir

filename_mesh = data_dir + '/meshes/2d/square_tri2.mesh'

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regions = {
'Omega' : 'all', # or 'cells of group 6'
'Gamma_Left' : ('vertices in (x < -0.99999)', 'facet'),
'Gamma_Right' : ('vertices in (x > 0.99999)', 'facet'),
}

fields = {
'concentration' : ('real', 1, 'Omega', 1),
}

variables = {
'u' : ('unknown field', 'concentration', 0, 1),
's' : ('test field', 'concentration', 'u'),
}

ebcs = {
'u1' : ('Gamma_Left', {'u.0' : 2.0}),
'u2' : ('Gamma_Right', {'u.0' : 0.0}),
}

# Units: D: 0.0001 m^2 / day, v: [0.1, 0] m / day -> time in days.

materials = {
'm' : ({'D' : 0.0001, 'v' : [[0.1], [0.0]]},),
}

integrals = {
'i' : 2,
}

equations = {
'advection-diffusion' :
"""
dw_dot.i.Omega(s, du/dt)
+ dw_advect_div_free.i.Omega(m.v, s, u)
+ dw_laplace.i.Omega(m.D, s, u)
= 0
"""
}

solvers = {
'ts' : ('ts.simple', {
't0' : 0.0,
't1' : 10.0,
'dt' : None,
'n_step' : 11, # Has precedence over dt.
'verbose' : 1,
}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
}),
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'ls' : ('ls.scipy_direct', {}),
}

options = {
'ts' : 'ts',
'nls' : 'newton',
'ls' : 'ls',
'save_times' : 'all',
}

diffusion/time_poisson.py

Description
Transient Laplace equation with non-constant initial conditions given by a function.
Find 𝑇 (𝑡) for 𝑡 ∈ [0, 𝑡final ] such that:
∫︁ ∫︁
𝜕𝑇
𝑠 + 𝑐∇𝑠 · ∇𝑇 = 0 , ∀𝑠 .
Ω 𝜕𝑡 Ω

source code

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r"""
Transient Laplace equation with non-constant initial conditions given by a
function.

Find :math:`T(t)` for :math:`t \in [0, t_{\rm final}]` such that:

.. math::
\int_{\Omega} s \pdiff{T}{t}
+ \int_{\Omega} c \nabla s \cdot \nabla T
= 0
\;, \quad \forall s \;.
"""
from __future__ import absolute_import
from sfepy import data_dir

filename_mesh = data_dir + '/meshes/3d/cylinder.mesh'

t0 = 0.0
t1 = 0.1
n_step = 11

material_2 = {
'name' : 'coef',
'values' : {'val' : 0.01},
'kind' : 'stationary', # 'stationary' or 'time-dependent'
}

field_1 = {
'name' : 'temperature',
'dtype' : 'real',
'shape' : (1,),
'region' : 'Omega',
'approx_order' : 1,
}

variable_1 = {
'name' : 'T',
'kind' : 'unknown field',
'field' : 'temperature',
'order' : 0,
'history' : 1,
}
variable_2 = {
'name' : 's',
'kind' : 'test field',
'field' : 'temperature',
'dual' : 'T',
}

regions = {
'Omega' : 'all',
'Gamma_Left' : ('vertices in (x < 0.00001)', 'facet'),
'Gamma_Right' : ('vertices in (x > 0.099999)', 'facet'),
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}

ebcs = {
'T1': ('Gamma_Left', {'T.0' : 2.0}),
'T2': ('Gamma_Right', {'T.0' : -2.0}),
}

def get_ic(coor, ic):

"""Non-constant initial condition."""
import numpy as nm
# Normalize x coordinate.
mi, ma = coor[:,0].min(), coor[:,0].max()
nx = (coor[:,0] - mi) / (ma - mi)
return nm.where( (nx > 0.25) & (nx < 0.75 ), 8.0 * (nx - 0.5), 0.0 )

functions = {
'get_ic' : (get_ic,),
}

ics = {
'ic' : ('Omega', {'T.0' : 'get_ic'}),
}

integral_1 = {
'name' : 'i',
'order' : 1,
}

equations = {
'Temperature' :
"""dw_dot.i.Omega( s, dT/dt )
+ dw_laplace.i.Omega( coef.val, s, T ) = 0"""
}

solver_0 = {
'name' : 'ls',
'kind' : 'ls.scipy_direct',
'use_presolve' : True,
}

solver_1 = {
'name' : 'newton',
'kind' : 'nls.newton',

'i_max' : 1,
'eps_a' : 1e-10,
'eps_r' : 1.0,
'macheps' : 1e-16,
'lin_red' : 1e-2, # Linear system error < (eps_a * lin_red).
'ls_red' : 0.1,
'ls_red_warp' : 0.001,
'ls_on' : 1.1,
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'ls_min' : 1e-5,
'check' : 0,
'delta' : 1e-6,
'is_linear' : True,
}

solver_2 = {
'name' : 'ts',
'kind' : 'ts.simple',

't0' : t0,
't1' : t1,
'dt' : None,
'n_step' : n_step, # has precedence over dt!
'verbose' : 1,
}

options = {
'nls' : 'newton',
'ls' : 'ls',
'ts' : 'ts',
'save_times' : 'all',
}

diffusion/time_poisson_explicit.py

Description
Transient Laplace equation.
The same example as time_poisson.py, but using the short syntax of keywords, and explicit time-stepping.
Find 𝑇 (𝑡) for 𝑡 ∈ [0, 𝑡final ] such that:
∫︁ ∫︁
𝜕𝑇
𝑠 + 𝑐∇𝑠 · ∇𝑇 = 0 , ∀𝑠 .
Ω 𝜕𝑡 Ω

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r"""
Transient Laplace equation.

The same example as time_poisson.py, but using the short syntax of keywords,
and explicit time-stepping.

Find :math:`T(t)` for :math:`t \in [0, t_{\rm final}]` such that:

.. math::
\int_{\Omega} s \pdiff{T}{t}
+ \int_{\Omega} c \nabla s \cdot \nabla T
= 0
\;, \quad \forall s \;.
"""
from __future__ import absolute_import
from sfepy import data_dir

from sfepy.examples.diffusion.time_poisson import get_ic

filename_mesh = data_dir + '/meshes/3d/cylinder.mesh'

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materials = {
'coef' : ({'val' : 0.01},),
}

regions = {
'Omega' : 'all',
'Gamma_Left' : ('vertices in (x < 0.00001)', 'facet'),
'Gamma_Right' : ('vertices in (x > 0.099999)', 'facet'),
}

fields = {
'temperature' : ('real', 1, 'Omega', 1),
}

variables = {
'T' : ('unknown field', 'temperature', 0, 1),
's' : ('test field', 'temperature', 'T'),
}

ebcs = {
't1' : ('Gamma_Left', {'T.0' : 2.0}),
't2' : ('Gamma_Right', {'T.0' : -2.0}),
}

ics = {
'ic' : ('Omega', {'T.0' : 'get_ic'}),
}

functions = {
'get_ic' : (get_ic,),
}

integrals = {
'i' : 1,
}

equations = {
'Temperature' :
"""dw_dot.i.Omega( s, dT/dt )
+ dw_laplace.i.Omega( coef.val, s, T[-1] ) = 0"""
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'is_linear' : True,
}),
'ts' : ('ts.simple', {
't0' : 0.0,
't1' : 0.07,
'dt' : 0.00002,
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'n_step' : None,
'verbose' : 1,
}),
}

options = {
'ls' : 'ls',
'ts' : 'ts',
'save_times' : 100,
'output_format' : 'h5',
}

diffusion/time_poisson_interactive.py

Description
Transient Laplace equation (heat equation) with non-constant initial conditions given by a function, using commands
for interactive use.
The script allows setting various simulation parameters, namely:
• the diffusivity coefficient
• the max. initial condition value
• temperature field approximation order
• uniform mesh refinement
The example shows also how to probe the results.
In the SfePy top-level directory the following command can be used to get usage information:

python examples/diffusion/time_poisson_interactive.py -h

source code

#!/usr/bin/env python
"""
Transient Laplace equation (heat equation) with non-constant initial conditions
given by a function, using commands for interactive use.

The script allows setting various simulation parameters, namely:

- the diffusivity coefficient

- the max. initial condition value
- temperature field approximation order
- uniform mesh refinement

The example shows also how to probe the results.

In the SfePy top-level directory the following command can be used to get usage
information::

python sfepy/examples/diffusion/time_poisson_interactive.py -h
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"""
from __future__ import absolute_import
import sys
from six.moves import range
sys.path.append('.')
from argparse import ArgumentParser, RawDescriptionHelpFormatter

import numpy as nm
import matplotlib.pyplot as plt

from sfepy.base.base import assert_, output, ordered_iteritems, IndexedStruct

from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.problem import prepare_matrix
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC, InitialCondition
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.solvers.ts_solvers import SimpleTimeSteppingSolver
from sfepy.discrete.probes import LineProbe, CircleProbe
from sfepy.discrete.projections import project_by_component

def gen_probes(problem):
"""
Define a line probe and a circle probe.
"""
# Use enough points for higher order approximations.
n_point = 1000

p0, p1 = nm.array([0.0, 0.0, 0.0]), nm.array([0.1, 0.0, 0.0])

line = LineProbe(p0, p1, n_point, share_geometry=True)
# Workaround current probe code shortcoming.
line.set_options(close_limit=0.5)

centre = 0.5 * (p0 + p1)

normal = [0.0, 1.0, 0.0]
r = 0.019
circle = CircleProbe(centre, normal, r, n_point, share_geometry=True)
circle.set_options(close_limit=0.0)

probes = [line, circle]

labels = ['%s -> %s' % (p0, p1),
'circle(%s, %s, %s' % (centre, normal, r)]

return probes, labels

def probe_results(ax_num, T, dvel, probe, label):

"""
Probe the results using the given probe and plot the probed values.
"""
results = {}
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pars, vals = probe(T)

results['T'] = (pars, vals)

pars, vals = probe(dvel)

results['dvel'] = (pars, vals)

fig = plt.figure(1)

ax = plt.subplot(2, 2, 2 * ax_num + 1)
ax.cla()
pars, vals = results['T']
ax.plot(pars, vals, label=r'$T$', lw=1, ls='-', marker='+', ms=3)
dx = 0.05 * (pars[-1] - pars[0])
ax.set_xlim(pars[0] - dx, pars[-1] + dx)
ax.set_ylabel('temperature')
ax.set_xlabel('probe %s' % label, fontsize=8)
ax.legend(loc='best', fontsize=10)

ax = plt.subplot(2, 2, 2 * ax_num + 2)
ax.cla()
pars, vals = results['dvel']
for ic in range(vals.shape[1]):
ax.plot(pars, vals[:, ic], label=r'$w_{%d}$' % (ic + 1),
lw=1, ls='-', marker='+', ms=3)
dx = 0.05 * (pars[-1] - pars[0])
ax.set_xlim(pars[0] - dx, pars[-1] + dx)
ax.set_ylabel('diffusion velocity')
ax.set_xlabel('probe %s' % label, fontsize=8)
ax.legend(loc='best', fontsize=10)

return fig, results

helps = {
'diffusivity' : 'the diffusivity coefficient [default: %(default)s]',
'ic_max' : 'the max. initial condition value [default: %(default)s]',
'order' : 'temperature field approximation order [default: %(default)s]',
'refine' : 'uniform mesh refinement level [default: %(default)s]',
'probe' : 'probe the results',
'show' : 'show the probing results figure, if --probe is used',
}

def main():
from sfepy import data_dir

parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('--diffusivity', metavar='float', type=float,
action='store', dest='diffusivity',
default=1e-5, help=helps['diffusivity'])
parser.add_argument('--ic-max', metavar='float', type=float,
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action='store', dest='ic_max',
default=2.0, help=helps['ic_max'])
parser.add_argument('--order', metavar='int', type=int,
action='store', dest='order',
default=2, help=helps['order'])
parser.add_argument('-r', '--refine', metavar='int', type=int,
action='store', dest='refine',
default=0, help=helps['refine'])
parser.add_argument('-p', '--probe',
action="store_true", dest='probe',
default=False, help=helps['probe'])
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
options = parser.parse_args()

assert_((0 < options.order),

'temperature approximation order must be at least 1!')

output('using values:')
output(' diffusivity:', options.diffusivity)
output(' max. IC value:', options.ic_max)
output('uniform mesh refinement level:', options.refine)

mesh = Mesh.from_file(data_dir + '/meshes/3d/cylinder.mesh')

domain = FEDomain('domain', mesh)

if options.refine > 0:
for ii in range(options.refine):
output('refine %d...' % ii)
domain = domain.refine()
output('... %d nodes %d elements'
% (domain.shape.n_nod, domain.shape.n_el))

omega = domain.create_region('Omega', 'all')

left = domain.create_region('Left',
'vertices in x < 0.00001', 'facet')
right = domain.create_region('Right',
'vertices in x > 0.099999', 'facet')

field = Field.from_args('fu', nm.float64, 'scalar', omega,

approx_order=options.order)

T = FieldVariable('T', 'unknown', field, history=1)

s = FieldVariable('s', 'test', field, primary_var_name='T')

m = Material('m', diffusivity=options.diffusivity * nm.eye(3))

integral = Integral('i', order=2*options.order)

t1 = Term.new('dw_diffusion(m.diffusivity, s, T)',
integral, omega, m=m, s=s, T=T)
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t2 = Term.new('dw_dot(s, dT/dt)',
integral, omega, s=s, T=T)
eq = Equation('balance', t1 + t2)
eqs = Equations([eq])

# Boundary conditions.
ebc1 = EssentialBC('T1', left, {'T.0' : 2.0})
ebc2 = EssentialBC('T2', right, {'T.0' : -2.0})

# Initial conditions.
def get_ic(coors, ic):
x, y, z = coors.T
return 2 - 40.0 * x + options.ic_max * nm.sin(4 * nm.pi * x / 0.1)
ic_fun = Function('ic_fun', get_ic)
ic = InitialCondition('ic', omega, {'T.0' : ic_fun})

pb = Problem('heat', equations=eqs)
pb.set_bcs(ebcs=Conditions([ebc1, ebc2]))
pb.set_ics(Conditions([ic]))

variables = pb.get_initial_state()
init_fun, prestep_fun, _poststep_fun = pb.get_tss_functions()

ls = ScipyDirect({})
nls_status = IndexedStruct()
nls = Newton({'is_linear' : True}, lin_solver=ls, status=nls_status)
tss = SimpleTimeSteppingSolver({'t0' : 0.0, 't1' : 100.0, 'n_step' : 11},
nls=nls, context=pb, verbose=True)
pb.set_solver(tss)

if options.probe:
# Prepare probe data.
probes, labels = gen_probes(pb)

ev = pb.evaluate
order = 2 * (options.order - 1)

gfield = Field.from_args('gu', nm.float64, 'vector', omega,

approx_order=options.order - 1)
dvel = FieldVariable('dvel', 'parameter', gfield,
primary_var_name='(set-to-None)')
cfield = Field.from_args('gu', nm.float64, 'scalar', omega,
approx_order=options.order - 1)
component = FieldVariable('component', 'parameter', cfield,
primary_var_name='(set-to-None)')

nls_options = {'eps_a' : 1e-16, 'i_max' : 1}

suffix = tss.ts.suffix
def poststep_fun(ts, vec):
_poststep_fun(ts, vec)

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# Probe the solution.
dvel_qp = ev('ev_diffusion_velocity.%d.Omega(m.diffusivity, T)'
% order, copy_materials=False, mode='qp')
project_by_component(dvel, dvel_qp, component, order,
nls_options=nls_options)

all_results = []
for ii, probe in enumerate(probes):
fig, results = probe_results(ii, T, dvel, probe, labels[ii])

all_results.append(results)

plt.tight_layout()
fig.savefig('time_poisson_interactive_probe_%s.png'
% (suffix % ts.step), bbox_inches='tight')

for ii, results in enumerate(all_results):

output('probe %d (%s):' % (ii, probes[ii].name))
output.level += 2
for key, res in ordered_iteritems(results):
output(key + ':')
val = res[1]
output(' min: %+.2e, mean: %+.2e, max: %+.2e'
% (val.min(), val.mean(), val.max()))
output.level -= 2

else:
poststep_fun = _poststep_fun

pb.time_update(tss.ts)
variables.apply_ebc()

# This is required if {'is_linear' : True} is passed to Newton.

mtx = prepare_matrix(pb, variables)
pb.try_presolve(mtx)

tss_status = IndexedStruct()
tss(variables.get_state(pb.active_only, force=True),
init_fun=init_fun, prestep_fun=prestep_fun, poststep_fun=poststep_fun,
status=tss_status)

output(tss_status)

if options.show:
plt.show()

if __name__ == '__main__':
main()

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homogenization

homogenization/homogenization_opt.py

Description
missing description!
source code

from __future__ import absolute_import

import numpy as nm

import sfepy.discrete.fem.periodic as per

from sfepy.discrete.fem.mesh import Mesh
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
from sfepy.homogenization.utils import define_box_regions
import sfepy.homogenization.coefs_base as cb
from sfepy import data_dir

# material function
def get_mat(coors, mode, pb):
if mode == 'qp':
cnf = pb.conf
# get material coefficients
if hasattr(cnf, 'opt_data'):
# from optim.
E_f, nu_f, E_m, nu_m = cnf.opt_data['mat_params']
else:
# given values
E_f, nu_f, E_m, nu_m = 160.e9, 0.28, 5.e9, 0.45

nqp = coors.shape[0]
nel = pb.domain.mesh.n_el
nqpe = nqp // nel
out = nm.zeros((nqp, 6, 6), dtype=nm.float64)

# set values - matrix

D_m = stiffness_from_youngpoisson(3, E_m, nu_m)
Ym = pb.domain.regions['Ym'].get_cells()
idx0 = (nm.arange(nqpe)[:,nm.newaxis] * nm.ones((1, Ym.shape[0]),
dtype=nm.int32)).T.flatten()
idxs = (Ym[:,nm.newaxis] * nm.ones((1, nqpe),
dtype=nm.int32)).flatten() * nqpe
out[idxs + idx0,...] = D_m

# set values - fiber

D_f = stiffness_from_youngpoisson(3, E_f, nu_f)
Yf = pb.domain.regions['Yf'].get_cells()
idx0 = (nm.arange(nqpe)[:,nm.newaxis] * nm.ones((1, Yf.shape[0]),
dtype=nm.int32)).T.flatten()
idxs = (Yf[:,nm.newaxis] * nm.ones((1, nqpe),
dtype=nm.int32)).flatten() * nqpe
out[idxs + idx0,...] = D_f
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return {'D': out}

def optimization_hook(pb):
cnf = pb.conf
out = []
yield pb, out

if hasattr(cnf, 'opt_data'):
# store homogenized tensor
pb.conf.opt_data['D_homog'] = out[-1].D.copy()

yield None

def define(is_opt=False):
filename_mesh = data_dir + '/meshes/3d/matrix_fiber_rand.vtk'

mesh = Mesh.from_file(filename_mesh)
bbox = mesh.get_bounding_box()

regions = {
'Y' : 'all',
'Ym' : ('cells of group 7', 'cell'),
'Yf' : ('r.Y -c r.Ym', 'cell'),
}

regions.update(define_box_regions(3, bbox[0], bbox[1]))

functions = {
'get_mat': (lambda ts, coors, mode=None, problem=None, **kwargs:
get_mat(coors, mode, problem),),
'match_x_plane' : (per.match_x_plane,),
'match_y_plane' : (per.match_y_plane,),
'match_z_plane' : (per.match_z_plane,),
}

materials = {
'mat': 'get_mat',
}

fields = {
'corrector' : ('real', 3, 'Y', 1),
}

variables = {
'u': ('unknown field', 'corrector'),
'v': ('test field', 'corrector', 'u'),
'Pi': ('parameter field', 'corrector', 'u'),
'Pi1': ('parameter field', 'corrector', '(set-to-None)'),
'Pi2': ('parameter field', 'corrector', '(set-to-None)'),
}

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ebcs = {
'fixed_u' : ('Corners', {'u.all' : 0.0}),
}

epbcs = {
'periodic_x' : (['Left', 'Right'], {'u.all' : 'u.all'}, 'match_x_plane'),
'periodic_y' : (['Near', 'Far'], {'u.all' : 'u.all'}, 'match_y_plane'),
'periodic_z' : (['Top', 'Bottom'], {'u.all' : 'u.all'}, 'match_z_plane'),
}

all_periodic = ['periodic_%s' % ii for ii in ['x', 'y', 'z'][:3]]

options = {
'coefs': 'coefs',
'requirements': 'requirements',
'volume': { 'variables' : ['u'], 'expression' : 'ev_volume.5.Y( u )' },
'output_dir': 'output',
'coefs_filename': 'coefs_le',
}

equation_corrs = {
'balance_of_forces':
"""dw_lin_elastic.5.Y(mat.D, v, u)
= - dw_lin_elastic.5.Y(mat.D, v, Pi)"""
}

coefs = {
'D' : {
'requires' : ['pis', 'corrs_rs'],
'expression' : 'dw_lin_elastic.5.Y(mat.D, Pi1, Pi2 )',
'set_variables': [('Pi1', ('pis', 'corrs_rs'), 'u'),
('Pi2', ('pis', 'corrs_rs'), 'u')],
'class' : cb.CoefSymSym,
},
'vol': {
'regions': ['Ym', 'Yf'],
'expression': 'ev_volume.5.%s(u)',
'class': cb.VolumeFractions,
},
'filenames' : {},
}

requirements = {
'pis' : {
'variables' : ['u'],
'class' : cb.ShapeDimDim,
},
'corrs_rs' : {
'requires' : ['pis'],
'ebcs' : ['fixed_u'],
'epbcs' : all_periodic,
'equations' : equation_corrs,
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'set_variables' : [('Pi', 'pis', 'u')],
'class' : cb.CorrDimDim,
'save_name' : 'corrs_le',
},
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-4,
'problem': 'linear',
})
}

if is_opt:
options.update({
'parametric_hook': 'optimization_hook',
'float_format': '%.16e',
})

return locals()

homogenization/linear_elastic_mM.py

Description
missing description!

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source code

from __future__ import absolute_import

import os
from sfepy import data_dir, base_dir
from sfepy.base.base import nm
from sfepy.homogenization.micmac import get_homog_coefs_linear
from sfepy.homogenization.recovery import save_recovery_region,\
recover_micro_hook

def post_process(out, pb, state, extend=False):

from sfepy.base.base import Struct

if isinstance(state, dict):
pass
else:
stress = pb.evaluate('ev_cauchy_stress.i.Omega(solid.D, u)',
mode='el_avg')
strain = pb.evaluate('ev_cauchy_strain.i.Omega(u)',
mode='el_avg')
out['cauchy_strain'] = Struct(name='output_data',
mode='cell', data=strain,
dofs=None)
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out['cauchy_stress'] = Struct(name='output_data',
mode='cell', data=stress,
dofs=None)

if pb.conf.options.get('recover_micro', False):
rname = pb.conf.options.recovery_region
region = pb.domain.regions[rname]

filename = os.path.join(os.path.dirname(pb.get_output_name()),
'recovery_region.vtk')
save_recovery_region(pb, rname, filename=filename);

rstrain = pb.evaluate('ev_cauchy_strain.i.%s(u)' % rname,

mode='el_avg')

recover_micro_hook(pb.conf.options.micro_filename,
region, {'strain' : rstrain},
output_dir=pb.conf.options.output_dir)

return out

def get_elements(coors, domain=None):

return nm.arange(50, domain.shape.n_el, 100)

regenerate = True

def get_homog(ts, coors, mode=None,

equations=None, term=None, problem=None, **kwargs):
global regenerate

out = get_homog_coefs_linear(ts, coors, mode, regenerate=regenerate,

micro_filename=options['micro_filename'],
output_dir=problem.conf.options.output_dir)
regenerate = False

return out

functions = {
'get_elements' : (get_elements,),
'get_homog' : (get_homog,),
}

filename_mesh = data_dir + '/meshes/3d/cylinder.mesh'

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < 0.001)', 'facet'),
'Right' : ('vertices in (x > 0.099)', 'facet'),
'Recovery' : 'cells by get_elements',
}

materials = {
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'solid' : 'get_homog',
}

fields = {
'3_displacement' : ('real', 3, 'Omega', 1),
}

integrals = {
'i' : 1,
}

variables = {
'u' : ('unknown field', '3_displacement', 0),
'v' : ('test field', '3_displacement', 'u'),
}

ebcs = {
'Fixed' : ('Left', {'u.all' : 0.0}),
'PerturbedSurface' : ('Right', {'u.0' : 0.02, 'u.1' : 0.0, 'u.2' : 0.0}),
}

equations = {
'balance_of_forces' :
"""dw_lin_elastic.i.Omega(solid.D, v, u) = 0""",
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-6,
}),
}

micro_filename = base_dir \
+ '/examples/homogenization/linear_homogenization_up.py'

options = {
'nls' : 'newton',
'ls' : 'ls',
'output_dir' : 'output',
'post_process_hook' : 'post_process',
'output_prefix' : 'macro:',
'recover_micro': True,
'recovery_region' : 'Recovery',
'micro_filename' : micro_filename,
}

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homogenization/linear_elasticity_opt.py

Description
missing description!
source code

from __future__ import absolute_import

import numpy as nm

from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson

from sfepy.discrete.fem.meshio import UserMeshIO
from sfepy.mesh.mesh_generators import gen_block_mesh
from sfepy import data_dir

def mesh_hook(mesh, mode):

if mode == 'read':
mesh = gen_block_mesh([0.0098, 0.0011, 0.1], [5, 3, 17],
[0, 0, 0.05], name='specimen',
verbose=False)
return mesh

elif mode == 'write':

pass

def optimization_hook(pb):
cnf = pb.conf
out = []
yield pb, out

state = out[-1][1].get_state_parts()
coors = pb.domain.cmesh.coors
displ = state['u'].reshape((coors.shape[0],3))
# elongation
mcoors = coors[cnf.mnodes, 2]
mdispl = displ[cnf.mnodes, 2]
dl = (mdispl[1] - mdispl[0]) / (mcoors[1] - mcoors[0])

if hasattr(cnf, 'opt_data'):
# compute slope of the force-elongation curve
cnf.opt_data['k'] = cnf.F / dl

yield None

def get_mat(coors, mode, pb):

if mode == 'qp':
# get material data
if hasattr(pb.conf, 'opt_data'):
# from homogenization
D = pb.conf.opt_data['D_homog']
else:
# given values
D = stiffness_from_youngpoisson(3, 150.0e9, 0.3)
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nqp = coors.shape[0]
return {'D': nm.tile(D, (nqp, 1, 1))}

def define(is_opt=False):
filename_mesh = UserMeshIO(mesh_hook)
mnodes = (107, 113) # nodes for elongation eval.

regions = {
'Omega': 'all',
'Bottom': ('vertices in (z < 0.001)', 'facet'),
'Top': ('vertices in (z > 0.099)', 'facet'),
}

functions = {
'get_mat': (lambda ts, coors, mode=None, problem=None, **kwargs:
get_mat(coors, mode, problem),),
}

S = 1.083500e-05 # specimen cross-section

F = 5.0e3 # force
materials = {
'solid': 'get_mat',
'load': ({'val': F / S},),
}

fields = {
'displacement': ('real', 'vector', 'Omega', 1),
}

variables = {
'u': ('unknown field', 'displacement', 0),
'v': ('test field', 'displacement', 'u'),
}

ebcs = {
'FixedBottom': ('Bottom', {'u.all': 0.0}),
'FixedTop': ('Top', {'u.0': 0.0, 'u.1': 0.0}),
}

equations = {
'balance_of_forces' :
"""dw_lin_elastic.5.Omega(solid.D, v, u)
= dw_surface_ltr.5.Top(load.val, v)""",
}

solvers = {
'ls': ('ls.scipy_direct', {}),
'newton': ('nls.newton', {'eps_a': 1e-6, 'eps_r': 1.e-6,
'check': 0, 'problem': 'nonlinear'}),
}

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options = {
'parametric_hook': 'optimization_hook',
'output_dir' : 'output',
}

return locals()

homogenization/linear_homogenization.py

Description
Compute homogenized elastic coefficients for a given heterogeneous linear elastic microstructure, see [1] for details or
[2] and [3] for a quick explanation.
[1] D. Cioranescu, J.S.J. Paulin: Homogenization in open sets with holes. Journal of Mathematical Analysis and
Applications 71(2), 1979, pages 590-607. https://doi.org/10.1016/0022-247X(79)90211-7
[2] J. Pinho-da-Cruz, J.A. Oliveira, F. Teixeira-Dias: Asymptotic homogenisation in linear elasticity. Part I: Mathe-
matical formulation and finite element modelling. Computational Materials Science 45(4), 2009, pages 1073-1080.
http://dx.doi.org/10.1016/j.commatsci.2009.02.025
[3] J. Pinho-da-Cruz, J.A. Oliveira, F. Teixeira-Dias: Asymptotic homogenisation in linear elasticity. Part II: Finite
element procedures and multiscale applications. Computational Materials Science 45(4), 2009, pages 1081-1096.
http://dx.doi.org/10.1016/j.commatsci.2009.01.027
source code

r"""
Compute homogenized elastic coefficients for a given heterogeneous linear
elastic microstructure, see [1] for details or [2] and [3] for a quick
explanation.

[1] D. Cioranescu, J.S.J. Paulin: Homogenization in open sets with holes.

Journal of Mathematical Analysis and Applications 71(2), 1979, pages 590-607.
https://doi.org/10.1016/0022-247X(79)90211-7

[2] J. Pinho-da-Cruz, J.A. Oliveira, F. Teixeira-Dias:

Asymptotic homogenisation in linear elasticity.
Part I: Mathematical formulation and finite element modelling.
Computational Materials Science 45(4), 2009, pages 1073-1080.
http://dx.doi.org/10.1016/j.commatsci.2009.02.025

[3] J. Pinho-da-Cruz, J.A. Oliveira, F. Teixeira-Dias:

Asymptotic homogenisation in linear elasticity.
Part II: Finite element procedures and multiscale applications.
Computational Materials Science 45(4), 2009, pages 1081-1096.
http://dx.doi.org/10.1016/j.commatsci.2009.01.027
"""

from __future__ import absolute_import

import sfepy.discrete.fem.periodic as per
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
from sfepy.homogenization.utils import define_box_regions
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import sfepy.homogenization.coefs_base as cb
from sfepy import data_dir
from sfepy.base.base import Struct
from sfepy.homogenization.recovery import compute_micro_u,\
compute_stress_strain_u, compute_mac_stress_part

def recovery_le(pb, corrs, macro):

out = {}

dim = corrs['corrs_le']['u_00'].shape[1]
mic_u = - compute_micro_u(corrs['corrs_le'], macro['strain'], 'u', dim)

out['u_mic'] = Struct(name='output_data',
mode='vertex', data=mic_u,
var_name='u', dofs=None)

stress_Y, strain_Y = \
compute_stress_strain_u(pb, 'i', 'Y', 'mat.D', 'u', mic_u)
stress_Y += \
compute_mac_stress_part(pb, 'i', 'Y', 'mat.D', 'u', macro['strain'])

strain = macro['strain'] + strain_Y

out['cauchy_strain'] = Struct(name='output_data',
mode='cell', data=strain,
dofs=None)
out['cauchy_stress'] = Struct(name='output_data',
mode='cell', data=stress_Y,
dofs=None)
return out

filename_mesh = data_dir + '/meshes/3d/matrix_fiber.mesh'

dim = 3
region_lbn = (0, 0, 0)
region_rtf = (1, 1, 1)

regions = {
'Y': 'all',
'Ym': 'cells of group 1',
'Yc': 'cells of group 2',
}
regions.update(define_box_regions(dim, region_lbn, region_rtf))

materials = {
'mat': ({'D': {'Ym': stiffness_from_youngpoisson(dim, 7.0e9, 0.4),
'Yc': stiffness_from_youngpoisson(dim, 70.0e9, 0.2)}},),
}

fields = {
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'corrector': ('real', dim, 'Y', 1),
}

variables = {
'u': ('unknown field', 'corrector', 0),
'v': ('test field', 'corrector', 'u'),
'Pi': ('parameter field', 'corrector', 'u'),
'Pi1': ('parameter field', 'corrector', '(set-to-None)'),
'Pi2': ('parameter field', 'corrector', '(set-to-None)'),
}

functions = {
'match_x_plane': (per.match_x_plane,),
'match_y_plane': (per.match_y_plane,),
'match_z_plane': (per.match_z_plane,),
}

ebcs = {
'fixed_u': ('Corners', {'u.all': 0.0}),
}

if dim == 3:
epbcs = {
'periodic_x': (['Left', 'Right'], {'u.all': 'u.all'},
'match_x_plane'),
'periodic_y': (['Near', 'Far'], {'u.all': 'u.all'},
'match_y_plane'),
'periodic_z': (['Top', 'Bottom'], {'u.all': 'u.all'},
'match_z_plane'),
}
else:
epbcs = {
'periodic_x': (['Left', 'Right'], {'u.all': 'u.all'},
'match_x_plane'),
'periodic_y': (['Bottom', 'Top'], {'u.all': 'u.all'},
'match_y_plane'),
}

all_periodic = ['periodic_%s' % ii for ii in ['x', 'y', 'z'][:dim]]

integrals = {
'i': 2,
}

options = {
'coefs': 'coefs',
'requirements': 'requirements',
'ls': 'ls', # linear solver to use
'volume': {'expression': 'ev_volume.i.Y(u)'},
'output_dir': 'output',
'coefs_filename': 'coefs_le',
'recovery_hook': 'recovery_le',
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}

equation_corrs = {
'balance_of_forces':
"""dw_lin_elastic.i.Y(mat.D, v, u) =
- dw_lin_elastic.i.Y(mat.D, v, Pi)"""
}

expr_coefs = """dw_lin_elastic.i.Y(mat.D, Pi1, Pi2)"""

coefs = {
'D': {
'requires': ['pis', 'corrs_rs'],
'expression': expr_coefs,
'set_variables': [('Pi1', ('pis', 'corrs_rs'), 'u'),
('Pi2', ('pis', 'corrs_rs'), 'u')],
'class': cb.CoefSymSym,
},
'filenames': {},
}

requirements = {
'pis': {
'variables': ['u'],
'class': cb.ShapeDimDim,
'save_name': 'corrs_pis',
},
'corrs_rs': {
'requires': ['pis'],
'ebcs': ['fixed_u'],
'epbcs': all_periodic,
'equations': equation_corrs,
'set_variables': [('Pi', 'pis', 'u')],
'class': cb.CorrDimDim,
'save_name': 'corrs_le',
'is_linear': True,
},
}

solvers = {
'ls': ('ls.scipy_direct', {}),
'newton': ('nls.newton', {
'i_max': 1,
'eps_a': 1e-4,
})
}

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homogenization/linear_homogenization_postproc.py

Description
This example shows how to use the VTK postprocessing functions.
source code

"""
This example shows how to use the VTK postprocessing functions.
"""

from __future__ import absolute_import

import os.path as osp
from .linear_homogenization import *
from sfepy.postprocess.utils_vtk import get_vtk_from_mesh,\
get_vtk_by_group, get_vtk_surface, get_vtk_edges, write_vtk_to_file,\
tetrahedralize_vtk_mesh

options.update({
'post_process_hook' : 'post_process',
})

def post_process(out, problem, state, extend=False):

mesh = problem.domain.mesh
mesh_name = mesh.name[mesh.name.rfind(osp.sep) + 1:]

vtkdata = get_vtk_from_mesh(mesh, out, 'postproc_')

matrix = get_vtk_by_group(vtkdata, 1, 1)

matrix_surf = get_vtk_surface(matrix)
matrix_surf_tri = tetrahedralize_vtk_mesh(matrix_surf)
write_vtk_to_file('%s_mat1_surface.vtk' % mesh_name, matrix_surf_tri)

matrix_edges = get_vtk_edges(matrix)
write_vtk_to_file('%s_mat1_edges.vtk' % mesh_name, matrix_edges)

return out

homogenization/linear_homogenization_up.py

Description
Compute homogenized elastic coefficients for a given heterogeneous linear elastic microstructure, see [1] for details or
[2] and [3] for a quick explanation. The mixed formulation, where displacements and pressures are as unknowns, is
used in this example.
[1] D. Cioranescu, J.S.J. Paulin: Homogenization in open sets with holes. Journal of Mathematical Analysis and
Applications 71(2), 1979, pages 590-607. https://doi.org/10.1016/0022-247X(79)90211-7
[2] J. Pinho-da-Cruz, J.A. Oliveira, F. Teixeira-Dias: Asymptotic homogenisation in linear elasticity. Part I: Mathe-
matical formulation and finite element modelling. Computational Materials Science 45(4), 2009, pages 1073-1080.
http://dx.doi.org/10.1016/j.commatsci.2009.02.025

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[3] J. Pinho-da-Cruz, J.A. Oliveira, F. Teixeira-Dias: Asymptotic homogenisation in linear elasticity. Part II: Finite
element procedures and multiscale applications. Computational Materials Science 45(4), 2009, pages 1081-1096.
http://dx.doi.org/10.1016/j.commatsci.2009.01.027
source code

r"""
Compute homogenized elastic coefficients for a given heterogeneous linear
elastic microstructure, see [1] for details or [2] and [3] for a quick
explanation. The mixed formulation, where displacements and pressures are
as unknowns, is used in this example.

[1] D. Cioranescu, J.S.J. Paulin: Homogenization in open sets with holes.

Journal of Mathematical Analysis and Applications 71(2), 1979, pages 590-607.
https://doi.org/10.1016/0022-247X(79)90211-7

[2] J. Pinho-da-Cruz, J.A. Oliveira, F. Teixeira-Dias:

Asymptotic homogenisation in linear elasticity.
Part I: Mathematical formulation and finite element modelling.
Computational Materials Science 45(4), 2009, pages 1073-1080.
http://dx.doi.org/10.1016/j.commatsci.2009.02.025

[3] J. Pinho-da-Cruz, J.A. Oliveira, F. Teixeira-Dias:

Asymptotic homogenisation in linear elasticity.
Part II: Finite element procedures and multiscale applications.
Computational Materials Science 45(4), 2009, pages 1081-1096.
http://dx.doi.org/10.1016/j.commatsci.2009.01.027
"""

from __future__ import absolute_import

import numpy as nm

import sfepy.discrete.fem.periodic as per

from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson_mixed,\
bulk_from_youngpoisson
from sfepy.homogenization.utils import define_box_regions, get_box_volume
import sfepy.homogenization.coefs_base as cb

from sfepy import data_dir

from sfepy.base.base import Struct
from sfepy.homogenization.recovery import compute_micro_u,\
compute_stress_strain_u, compute_mac_stress_part, add_stress_p

def recovery_le(pb, corrs, macro):

out = {}
dim = corrs['corrs_le']['u_00'].shape[1]
mic_u = - compute_micro_u(corrs['corrs_le'], macro['strain'], 'u', dim)
mic_p = - compute_micro_u(corrs['corrs_le'], macro['strain'], 'p', dim)

out['u_mic'] = Struct(name='output_data',
mode='vertex', data=mic_u,
var_name='u', dofs=None)
out['p_mic'] = Struct(name='output_data',
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mode='cell', data=mic_p[:, nm.newaxis,
:, nm.newaxis],
var_name='p', dofs=None)

stress_Y, strain_Y = \
compute_stress_strain_u(pb, 'i', 'Y', 'mat.D', 'u', mic_u)
stress_Y += \
compute_mac_stress_part(pb, 'i', 'Y', 'mat.D', 'u', macro['strain'])
add_stress_p(stress_Y, pb, 'i', 'Y', 'p', mic_p)

strain = macro['strain'] + strain_Y

out['cauchy_strain'] = Struct(name='output_data',
mode='cell', data=strain,
dofs=None)
out['cauchy_stress'] = Struct(name='output_data',
mode='cell', data=stress_Y,
dofs=None)
return out

dim = 3
filename_mesh = data_dir + '/meshes/3d/matrix_fiber.mesh'
region_lbn = (0, 0, 0)
region_rtf = (1, 1, 1)

regions = {
'Y': 'all',
'Ym': 'cells of group 1',
'Yc': 'cells of group 2',
}
regions.update(define_box_regions(dim, region_lbn, region_rtf))

materials = {
'mat': ({'D': {'Ym': stiffness_from_youngpoisson_mixed(dim, 7.0e9, 0.4),
'Yc': stiffness_from_youngpoisson_mixed(dim, 70.0e9, 0.2)},
'gamma': {'Ym': 1.0/bulk_from_youngpoisson(7.0e9, 0.4),
'Yc': 1.0/bulk_from_youngpoisson(70.0e9, 0.2)}},),
}

fields = {
'corrector_u': ('real', dim, 'Y', 1),
'corrector_p': ('real', 1, 'Y', 0),
}

variables = {
'u': ('unknown field', 'corrector_u'),
'v': ('test field', 'corrector_u', 'u'),
'p': ('unknown field', 'corrector_p'),
'q': ('test field', 'corrector_p', 'p'),
'Pi': ('parameter field', 'corrector_u', 'u'),
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'Pi1u': ('parameter field', 'corrector_u', '(set-to-None)'),
'Pi2u': ('parameter field', 'corrector_u', '(set-to-None)'),
'Pi1p': ('parameter field', 'corrector_p', '(set-to-None)'),
'Pi2p': ('parameter field', 'corrector_p', '(set-to-None)'),
}

functions = {
'match_x_plane': (per.match_x_plane,),
'match_y_plane': (per.match_y_plane,),
'match_z_plane': (per.match_z_plane,),
}

ebcs = {
'fixed_u': ('Corners', {'u.all': 0.0}),
}

if dim == 3:
epbcs = {
'periodic_x': (['Left', 'Right'], {'u.all': 'u.all'},
'match_x_plane'),
'periodic_y': (['Near', 'Far'], {'u.all': 'u.all'},
'match_y_plane'),
'periodic_z': (['Top', 'Bottom'], {'u.all': 'u.all'},
'match_z_plane'),
}
else:
epbcs = {
'periodic_x': (['Left', 'Right'], {'u.all': 'u.all'},
'match_x_plane'),
'periodic_y': (['Bottom', 'Top'], {'u.all': 'u.all'},
'match_y_plane'),
}

all_periodic = ['periodic_%s' % ii for ii in ['x', 'y', 'z'][:dim]]

integrals = {
'i': 2,
}

options = {
'coefs': 'coefs',
'requirements': 'requirements',
'ls': 'ls', # linear solver to use
'volume': {'value': get_box_volume(dim, region_lbn, region_rtf), },
'output_dir': 'output',
'coefs_filename': 'coefs_le_up',
'recovery_hook': 'recovery_le',
'multiprocessing': False,
}

equation_corrs = {
'balance_of_forces':
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""" dw_lin_elastic.i.Y(mat.D, v, u)
- dw_stokes.i.Y(v, p) =
- dw_lin_elastic.i.Y(mat.D, v, Pi)""",
'pressure constraint':
"""- dw_stokes.i.Y(u, q)
- dw_dot.i.Y(mat.gamma, q, p) =
+ dw_stokes.i.Y(Pi, q)""",
}

coefs = {
'elastic_u': {
'requires': ['pis', 'corrs_rs'],
'expression': 'dw_lin_elastic.i.Y(mat.D, Pi1u, Pi2u)',
'set_variables': [('Pi1u', ('pis', 'corrs_rs'), 'u'),
('Pi2u', ('pis', 'corrs_rs'), 'u')],
'class': cb.CoefSymSym,
},
'elastic_p': {
'requires': ['corrs_rs'],
'expression': 'dw_dot.i.Y(mat.gamma, Pi1p, Pi2p)',
'set_variables': [('Pi1p', 'corrs_rs', 'p'),
('Pi2p', 'corrs_rs', 'p')],
'class': cb.CoefSymSym,
},
'D': {
'requires': ['c.elastic_u', 'c.elastic_p'],
'class': cb.CoefSum,
},
'filenames': {},
}

requirements = {
'pis': {
'variables': ['u'],
'class': cb.ShapeDimDim,
},
'corrs_rs': {
'requires': ['pis'],
'ebcs': ['fixed_u'],
'epbcs': all_periodic,
'equations': equation_corrs,
'set_variables': [('Pi', 'pis', 'u')],
'class': cb.CorrDimDim,
'save_name': 'corrs_le',
'is_linear': True,
},
}

solvers = {
'ls': ('ls.auto_iterative', {}),
'newton': ('nls.newton', {
'i_max': 1,
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'eps_a': 1e2,
})
}

homogenization/material_opt.py

Description
See the Material Identification tutorial for a comprehensive description of this example.
source code
#!/usr/bin/env python
"""
See the :ref:`sec-mat_optim` tutorial for a comprehensive description of this
example.
"""
from __future__ import print_function
from __future__ import absolute_import
import sys
sys.path.append('.')

import numpy as nm
from scipy.optimize import fmin_tnc

import sfepy
from sfepy.base.base import Struct
from sfepy.base.log import Log

class MaterialOptimizer(object):

@staticmethod
def create_app(filename, is_homog=False, **kwargs):
from sfepy.base.conf import ProblemConf, get_standard_keywords
from sfepy.homogenization.homogen_app import HomogenizationApp
from sfepy.applications import PDESolverApp

required, other = get_standard_keywords()

if is_homog:
required.remove('equations')

conf = ProblemConf.from_file(filename, required, other,

define_args=kwargs)
options = Struct(output_filename_trunk=None,
save_ebc=False,
save_ebc_nodes=False,
save_regions=False,
save_regions_as_groups=False,
save_field_meshes=False,
solve_not=False)

if is_homog:
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app = HomogenizationApp(conf, options, 'material_opt_micro:')

else:
app = PDESolverApp(conf, options, 'material_opt_macro:')

app.conf.opt_data = {}
opts = conf.options
if hasattr(opts, 'parametric_hook'): # Parametric study.
parametric_hook = conf.get_function(opts.parametric_hook)
app.parametrize(parametric_hook)

return app

def x_norm2real(self, x):

return x * (self.x_U - self.x_L) + self.x_L

def x_real2norm(self, x):

return (x - self.x_L) / (self.x_U - self.x_L)

def __init__(self, macro_fn, micro_fn, x0, x_L, x_U, exp_data):

self.macro_app = self.create_app(macro_fn, is_homog=False, is_opt=True)
self.micro_app = self.create_app(micro_fn, is_homog=True, is_opt=True)
self.x_L = nm.array(x_L)
self.x_U = nm.array(x_U)
self.x0 = self.x_real2norm(nm.array(x0))
self.x = []
self.eval_f = []
self.exp_data = exp_data

@staticmethod
def rotate_mat(D, angle):
s = nm.sin(angle)
c = nm.cos(angle)
s2 = s**2
c2 = c**2
sc = s * c
T = nm.array([[c2, 0, s2, 0, 2*sc,0],
[0, 1, 0, 0, 0, 0],
[s2, 0, c2, 0, -2*sc, 0],
[0, 0, 0, c, 0, -s],
[-sc, 0, sc, 0, c2 - s2, 0],
[0, 0, 0, s, 0, c]])

return nm.dot(nm.dot(T, D), T.T)

def matopt_eval(self, x):

mic_od = self.micro_app.conf.opt_data
mac_od = self.macro_app.conf.opt_data

mic_od['coefs'] = {}
mic_od['mat_params'] = x
self.micro_app()
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D = mic_od['D_homog']
val = 0.0
aux = []
for phi, exp_k in self.exp_data:
print('phi = %d' % phi)

mac_od['D_homog'] = self.rotate_mat(D, nm.deg2rad(phi))

self.macro_app()

comp_k = mac_od['k']
val += (1.0 - comp_k / exp_k)**2
aux.append((comp_k, exp_k))

val = nm.sqrt(val)
self.x.append(x)
self.eval_f.append(val)

return val

def iter_step(self, x, first_step=False):

if first_step:
self.log = Log([['O'], ['E_f', 'E_m'], ['v_f', 'v_m']],
ylabels=['Obj. fun.', "Young's modulus", "Poisson's ratio"],
xlabels=['iter', 'iter', 'iter'],
aggregate=0)
self.istep = 0
self.log(0.5, x[0], x[2], x[1], x[3],
x=[0, 0, 0, 0])
else:
self.istep += 1
self.log(self.eval_f[-1], x[0], x[2], x[1], x[3],
x=(self.istep,)*4)

def material_optimize(self):
x0 = self.x0
bnds = zip(self.x_real2norm(self.x_L), self.x_real2norm(self.x_U))
feval = lambda x: self.matopt_eval(self.x_norm2real(x))
istep = lambda x: self.iter_step(self.x_norm2real(x))
self.iter_step(self.x_norm2real(x0), first_step=True)

print('>>> material optimization START <<<')

xopt = fmin_tnc(feval, x0, approx_grad=True, bounds=list(bnds),
xtol=1e-3, callback=istep)
print('>>> material optimization FINISHED <<<')

self.log(finished=True)
return self.x_norm2real(xopt[0])

def main():
srcdir = sfepy.base_dir + '/examples/homogenization/'
micro_filename = srcdir + 'homogenization_opt.py'
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macro_filename = srcdir + 'linear_elasticity_opt.py'

exp_data = zip([0, 30, 60, 90], [1051140., 197330., 101226., 95474.])

mo = MaterialOptimizer(macro_filename, micro_filename,
[160.e9, 0.25, 5.e9, 0.45],
[120e9, 0.2, 2e9, 0.2],
[200e9, 0.45, 8e9, 0.45],
list(exp_data))

optim_par = mo.material_optimize()
print('optimized parameters: ', optim_par)

if __name__ == '__main__':
main()

homogenization/nonlinear_homogenization.py

Description
missing description!
source code
# -*- coding: utf-8 -*-
import numpy as nm
from sfepy.homogenization.utils import define_box_regions
import sfepy.homogenization.coefs_base as cb
import sfepy.discrete.fem.periodic as per
from sfepy.base.base import Struct
from sfepy.terms.terms_hyperelastic_ul import\
HyperElasticULFamilyData, NeoHookeanULTerm, BulkPenaltyULTerm
from sfepy.terms.extmods.terms import sym2nonsym
from sfepy.discrete.functions import ConstantFunctionByRegion
from sfepy import data_dir
import sfepy.linalg as la

def recovery_hook(pb, ncoors, region, ts,

naming_scheme='step_iel', recovery_file_tag=''):
from sfepy.base.ioutils import get_print_info
from sfepy.homogenization.recovery import get_output_suffix
import os.path as op

for ii, icell in enumerate(region.cells):

out = {}
pb.set_mesh_coors(ncoors[ii], update_fields=True,
clear_all=False, actual=True)
stress = pb.evaluate('ev_integrate_mat.3.Y(mat_he.S, u)',
mode='el_avg')

out['cauchy_stress'] = Struct(name='output_data',
mode='cell',
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data=stress,
dofs=None)

strain = pb.evaluate('ev_integrate_mat.3.Y(mat_he.E, u)',

mode='el_avg')

out['green_strain'] = Struct(name='output_data',
mode='cell',
data=strain,
dofs=None)

out['displacement'] = Struct(name='output_data',
mode='vertex',
data=ncoors[ii] - pb.get_mesh_coors(),
dofs=None)

output_dir = pb.conf.options.get('output_dir', '.')

format = get_print_info(pb.domain.mesh.n_el, fill='0')[1]
suffix = get_output_suffix(icell, ts, naming_scheme, format,
pb.output_format)

micro_name = pb.get_output_name(extra='recovered_'
+ recovery_file_tag + suffix)
filename = op.join(output_dir, op.basename(micro_name))
fpv = pb.conf.options.get('file_per_var', False)
pb.save_state(filename, out=out, file_per_var=fpv)

def def_mat(ts, mode, coors, term, pb):

if not (mode == 'qp'):
return

if not hasattr(pb, 'family_data'):

pb.family_data = HyperElasticULFamilyData()

update_var = pb.conf.options.mesh_update_variable
if pb.equations is None:
state_u = pb.create_variables([update_var])[update_var]
else:
state_u = pb.get_variables()[update_var]

if state_u.data[0] is None:
state_u.init_data()

state_u.set_data(
pb.domain.get_mesh_coors(actual=True) - pb.domain.get_mesh_coors())
state_u.field.clear_mappings()
family_data = pb.family_data(state_u, term.region,
term.integral, term.integration)

if len(state_u.field.mappings0) == 0:
state_u.field.save_mappings()
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n_el, n_qp, dim, n_en, n_c = state_u.get_data_shape(term.integral,

term.integration,
term.region.name)

conf_mat = pb.conf.materials
solid_key = [key for key in conf_mat.keys() if 'solid' in key][0]
solid_mat = conf_mat[solid_key].values
mat = {}
for mat_key in ['mu', 'K']:
if isinstance(solid_mat[mat_key], dict):
mat_fun = ConstantFunctionByRegion({mat_key: solid_mat[mat_key]})
mat[mat_key] = mat_fun.function(ts=ts, coors=coors, mode='qp',
term=term, problem=pb)[mat_key].reshape((n_el, n_qp, 1, 1))
else:
mat[mat_key] = nm.ones((n_el, n_qp, 1, 1)) * solid_mat[mat_key]

shape = family_data.green_strain.shape[:2]
sym = family_data.green_strain.shape[-2]
dim2 = dim**2

fargs = [family_data.get(name)
for name in NeoHookeanULTerm.family_data_names]
stress = nm.empty(shape + (sym, 1), dtype=nm.float64)
tanmod = nm.empty(shape + (sym, sym), dtype=nm.float64)
NeoHookeanULTerm.stress_function(stress, mat['mu'], *fargs)
NeoHookeanULTerm.tan_mod_function(tanmod, mat['mu'], *fargs)

fargs = [family_data.get(name)
for name in BulkPenaltyULTerm.family_data_names]
stress_p = nm.empty(shape + (sym, 1), dtype=nm.float64)
tanmod_p = nm.empty(shape + (sym, sym), dtype=nm.float64)
BulkPenaltyULTerm.stress_function(stress_p, mat['K'], *fargs)
BulkPenaltyULTerm.tan_mod_function(tanmod_p, mat['K'], *fargs)

stress_ns = nm.zeros(shape + (dim2, dim2), dtype=nm.float64)

tanmod_ns = nm.zeros(shape + (dim2, dim2), dtype=nm.float64)
sym2nonsym(stress_ns, stress + stress_p)
sym2nonsym(tanmod_ns, tanmod + tanmod_p)

npts = nm.prod(shape)
J = family_data.det_f
mtx_f = family_data.mtx_f.reshape((npts, dim, dim))

out = {
'E': 0.5 * (la.dot_sequences(mtx_f, mtx_f, 'ATB') - nm.eye(dim)),
'A': ((tanmod_ns + stress_ns) / J).reshape((npts, dim2, dim2)),
'S': ((stress + stress_p) / J).reshape((npts, sym, 1)),
}

return out

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filename_mesh = data_dir + '/meshes/2d/special/circle_in_square_small.mesh'

dim = 2

options = {
'coefs': 'coefs',
'requirements': 'requirements',
'volume': {'expression': 'ev_volume.5.Y(u)'},
'output_dir': './output',
'coefs_filename': 'coefs_hyper_homog',
'multiprocessing': True,
'chunks_per_worker': 2,
'micro_update': {'coors': [('corrs_rs', 'u', 'mtx_e')]},
'mesh_update_variable': 'u',
'recovery_hook': 'recovery_hook',
'store_micro_idxs': [49, 81],
}

fields = {
'displacement': ('real', 'vector', 'Y', 1),
}

functions = {
'match_x_plane': (per.match_x_plane,),
'match_y_plane': (per.match_y_plane,),
'mat_fce': (lambda ts, coors, mode=None, term=None, problem=None, **kwargs:
def_mat(ts, mode, coors, term, problem),),
}

materials = {
'mat_he': 'mat_fce',
'solid': ({'K': 1000,
'mu': {'Ym': 100, 'Yc': 10},
},),
}

variables = {
'u': ('unknown field', 'displacement'),
'v': ('test field', 'displacement', 'u'),
'Pi': ('parameter field', 'displacement', 'u'),
'Pi1u': ('parameter field', 'displacement', '(set-to-None)'),
'Pi2u': ('parameter field', 'displacement', '(set-to-None)'),
}

regions = {
'Y': 'all',
'Ym': 'cells of group 1',
'Yc': 'cells of group 2',
}

regions.update(define_box_regions(dim, (0., 0.), (1., 1.)))

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ebcs = {
'fixed_u': ('Corners', {'u.all': 0.0}),
}

epbcs = {
'periodic_ux': (['Left', 'Right'], {'u.all': 'u.all'}, 'match_x_plane'),
'periodic_uy': (['Bottom', 'Top'], {'u.all': 'u.all'}, 'match_y_plane'),
}

coefs = {
'A': {
'requires': ['pis', 'corrs_rs'],
'expression': 'dw_nonsym_elastic.3.Y(mat_he.A, Pi1u, Pi2u)',
'set_variables': [('Pi1u', ('pis', 'corrs_rs'), 'u'),
('Pi2u', ('pis', 'corrs_rs'), 'u')],
'class': cb.CoefNonSymNonSym,
},
'S': {
'expression': 'ev_integrate_mat.3.Y(mat_he.S, u)',
'class': cb.CoefOne,
}
}

requirements = {
'pis': {
'variables': ['u'],
'class': cb.ShapeDimDim,
},
'corrs_rs': {
'requires': ['pis'],
'ebcs': ['fixed_u'],
'epbcs': ['periodic_ux', 'periodic_uy'],
'equations': {
'balance_of_forces':
"""dw_nonsym_elastic.3.Y(mat_he.A, v, u)
= - dw_nonsym_elastic.3.Y(mat_he.A, v, Pi)"""
},
'set_variables': [('Pi', 'pis', 'u')],
'class': cb.CorrDimDim,
'save_name': 'corrs_hyper_homog',
},
}

solvers = {
'ls': ('ls.scipy_direct', {}),
'newton': ('nls.newton', {
'i_max': 1,
'eps_a': 1e-4,
'problem': 'nonlinear',
}),
}

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homogenization/nonlinear_hyperelastic_mM.py

Description
missing description!

source code

import numpy as nm
import six

from sfepy import data_dir

from sfepy.base.base import Struct, output
from sfepy.terms.terms_hyperelastic_ul import HyperElasticULFamilyData
from sfepy.homogenization.micmac import get_homog_coefs_nonlinear
import sfepy.linalg as la
from sfepy.discrete.evaluate import Evaluator

hyperelastic_data = {}

def post_process(out, pb, state, extend=False):

if isinstance(state, dict):
pass
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else:
pb.update_materials_flag = 2
stress = pb.evaluate('ev_integrate_mat.1.Omega(solid.S, u)',
mode='el_avg')

out['cauchy_stress'] = Struct(name='output_data',
mode='cell',
data=stress,
dofs=None)

strain = pb.evaluate('ev_integrate_mat.1.Omega(solid.E, u)',

mode='el_avg')

out['green_strain'] = Struct(name='output_data',
mode='cell',
data=strain,
dofs=None)

pb.update_materials_flag = 0

if pb.conf.options.get('recover_micro', False):
happ = pb.homogen_app
if pb.ts.step == 0:
rname = pb.conf.options.recovery_region
rcells = pb.domain.regions[rname].get_cells()
sh = hyperelastic_data['homog_mat_shape']

happ.app_options.store_micro_idxs = sh[1] * rcells

else:
hpb = happ.problem
recovery_hook = hpb.conf.options.get('recovery_hook', None)
if recovery_hook is not None:
recovery_hook = hpb.conf.get_function(recovery_hook)
rname = pb.conf.options.recovery_region
rcoors = []
for ii in happ.app_options.store_micro_idxs:
key = happ.get_micro_cache_key('coors', ii, pb.ts.step)
if key in happ.micro_state_cache:
rcoors.append(happ.micro_state_cache[key])

recovery_hook(hpb, rcoors, pb.domain.regions[rname], pb.ts)

return out

def get_homog_mat(ts, coors, mode, term=None, problem=None, **kwargs):

if problem.update_materials_flag == 2 and mode == 'qp':
out = hyperelastic_data['homog_mat']
return {k: nm.array(v) for k, v in six.iteritems(out)}
elif problem.update_materials_flag == 0 or not mode == 'qp':
return

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output('get_homog_mat')
dim = problem.domain.mesh.dim

update_var = problem.conf.options.mesh_update_variables[0]
state_u = problem.equations.variables[update_var]
state_u.field.clear_mappings()
family_data = problem.family_data(state_u, term.region,
term.integral, term.integration)

mtx_f = family_data.mtx_f.reshape((coors.shape[0],)
+ family_data.mtx_f.shape[-2:])

if hasattr(problem, 'mtx_f_prev'):
rel_mtx_f = la.dot_sequences(mtx_f, nm.linalg.inv(problem.mtx_f_prev),
'AB')
else:
rel_mtx_f = mtx_f

problem.mtx_f_prev = mtx_f.copy()

macro_data = {'mtx_e': rel_mtx_f - nm.eye(dim)} # '*' - macro strain

out = get_homog_coefs_nonlinear(ts, coors, mode, macro_data,
term=term, problem=problem,
iteration=problem.iiter, **kwargs)

out['E'] = 0.5 * (la.dot_sequences(mtx_f, mtx_f, 'ATB') - nm.eye(dim))

hyperelastic_data['time'] = ts.step
hyperelastic_data['homog_mat_shape'] = family_data.det_f.shape[:2]
hyperelastic_data['homog_mat'] = \
{k: nm.array(v) for k, v in six.iteritems(out)}

return out

def ulf_iteration_hook(pb, nls, vec, it, err, err0):

Evaluator.new_ulf_iteration(pb, nls, vec, it, err, err0)

pb.iiter = it
pb.update_materials_flag = True
pb.update_materials()
pb.update_materials_flag = False

class MyEvaluator(Evaluator):
def eval_residual(self, vec, is_full=False):
if not is_full:
vec = self.problem.equations.make_full_vec(vec)
vec_r = self.problem.equations.eval_residuals(vec * 0)

return vec_r

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def ulf_init(pb):
pb.family_data = HyperElasticULFamilyData()
pb_vars = pb.get_variables()
pb_vars['u'].init_data()

pb.update_materials_flag = True
pb.iiter = 0

options = {
'output_dir': 'output',
'mesh_update_variables': ['u'],
'nls_iter_hook': ulf_iteration_hook,
'pre_process_hook': ulf_init,
'micro_filename': 'examples/homogenization/nonlinear_homogenization.py',
'recover_micro': True,
'recovery_region': 'Recovery',
'post_process_hook': post_process,
'user_evaluator': MyEvaluator,
}

materials = {
'solid': 'get_homog',
}

fields = {
'displacement': ('real', 'vector', 'Omega', 1),
}

variables = {
'u': ('unknown field', 'displacement'),
'v': ('test field', 'displacement', 'u'),
}

filename_mesh = data_dir + '/meshes/2d/its2D.mesh'

regions = {
'Omega': 'all',
'Left': ('vertices in (x < 0.001)', 'facet'),
'Bottom': ('vertices in (y < 0.001 )', 'facet'),
'Recovery': ('cell 49, 81', 'cell'),
}

ebcs = {
'l': ('Left', {'u.all': 0.0}),
'b': ('Bottom', {'u.all': 'move_bottom'}),
}

centre = nm.array([0, 0], dtype=nm.float64)

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def move_bottom(ts, coor, **kwargs):

from sfepy.linalg import rotation_matrix2d

vec = coor[:, 0:2] - centre

angle = 3 * ts.step
print('angle:', angle)
mtx = rotation_matrix2d(angle)
out = nm.dot(vec, mtx) - vec

return out

functions = {
'move_bottom': (move_bottom,),
'get_homog': (get_homog_mat,),
}

equations = {
'balance_of_forces':
"""dw_nonsym_elastic.1.Omega(solid.A, v, u)
= - dw_lin_prestress.1.Omega(solid.S, v)""",
}

solvers = {
'ls': ('ls.scipy_direct', {}),
'newton': ('nls.newton', {
'eps_a': 1e-3,
'eps_r': 1e-3,
'i_max': 20,
}),
'ts': ('ts.simple', {
't0': 0,
't1': 1,
'n_step': 3 + 1,
'verbose': 1,
})
}

homogenization/perfusion_micro.py

Description
Homogenization of the Darcy flow in a thin porous layer. The reference cell is composed of the matrix representing
the dual porosity and of two disconnected channels representing the primary porosity, see paper [1].
[1] E. Rohan, V. Lukeš: Modeling Tissue Perfusion Using a Homogenized Model with Layer-wise Decomposition.
IFAC Proceedings Volumes 45(2), 2012, pages 1029-1034. https://doi.org/10.3182/20120215-3-AT-3016.00182
source code

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# -*- coding: utf-8

r"""
Homogenization of the Darcy flow in a thin porous layer.
The reference cell is composed of the matrix representing the dual porosity
and of two disconnected channels representing the primary porosity,
see paper [1].

[1] E. Rohan, V. Lukeš: Modeling Tissue Perfusion Using a Homogenized

Model with Layer-wise Decomposition. IFAC Proceedings Volumes 45(2), 2012,
pages 1029-1034.
https://doi.org/10.3182/20120215-3-AT-3016.00182
"""

from __future__ import absolute_import

from sfepy.discrete.fem.periodic import match_x_plane, match_y_plane
import sfepy.homogenization.coefs_base as cb
import numpy as nm
from sfepy import data_dir
import six
from six.moves import range

def get_mats(pk, ph, pe, dim):

m1 = nm.eye(dim, dtype=nm.float64) * pk
m1[-1, -1] = pk / ph
m2 = nm.eye(dim, dtype=nm.float64) * pk
m2[-1, -1] = pk / ph ** 2

return m1, m2

def recovery_perf(pb, corrs, macro):

from sfepy.homogenization.recovery import compute_p_from_macro
from sfepy.base.base import Struct

slev = ''

micro_nnod = pb.domain.mesh.n_nod

centre_Y = nm.sum(pb.domain.mesh.coors, axis=0) / micro_nnod

nodes_Y = {}

channels = {}
for k in six.iterkeys(macro):
if 'press' in k:
channels[k[-1]] = 1

channels = list(channels.keys())

varnames = ['pM']
for ch in channels:
nodes_Y[ch] = pb.domain.regions['Y' + ch].vertices
varnames.append('p' + ch)

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pvars = pb.create_variables(varnames)

press = {}

# matrix
press['M'] = \
corrs['corrs_%s_gamma_p' % pb_def['name']]['pM'] * macro['g_p'] + \
corrs['corrs_%s_gamma_m' % pb_def['name']]['pM'] * macro['g_m']

out = {}
# channels
for ch in channels:
press_mac = macro['press' + ch][0, 0]
press_mac_grad = macro['pressg' + ch]
nnod = corrs['corrs_%s_pi%s' % (pb_def['name'], ch)]\
['p%s_0' % ch].shape[0]

press_mic = nm.zeros((nnod, 1))

for key, val in \
six.iteritems(corrs['corrs_%s_pi%s' % (pb_def['name'], ch)]):
kk = int(key[-1])
press_mic += val * press_mac_grad[kk, 0]

for key in six.iterkeys(corrs):

if ('_gamma_' + ch in key):
kk = int(key[-1]) - 1
press_mic += corrs[key]['p' + ch] * macro['g' + ch][kk]

press_mic += \
compute_p_from_macro(press_mac_grad[nm.newaxis,nm.newaxis, :, :],
micro_coors[nodes_Y[ch]], 0,
centre=centre_Y, extdim=-1).reshape((nnod, 1))

press[ch] = press_mac + eps0 * press_mic

out[slev + 'p' + ch] = Struct(name='output_data',

mode='vertex',
data=press[ch],
var_name='p' + ch,
dofs=None)

pvars['p' + ch].set_data(press_mic)
dvel = pb.evaluate('ev_diffusion_velocity.iV.Y%s(mat1%s.k, p%s)'
% (ch, ch, ch),
var_dict={'p' + ch: pvars['p' + ch]},
mode='el_avg')

out[slev + 'w' + ch] = Struct(name='output_data',

mode='cell',
data=dvel,
var_name='w' + ch,
dofs=None)
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press['M'] += corrs['corrs_%s_eta%s' % (pb_def['name'], ch)]['pM']\

* press_mac

pvars['pM'].set_data(press['M'])
dvel = pb.evaluate('%e * ev_diffusion_velocity.iV.YM(mat1M.k, pM)' % eps0,
var_dict={'pM': pvars['pM']}, mode='el_avg')

out[slev + 'pM'] = Struct(name='output_data',

mode='vertex',
dat=press['M'],
var_name='pM',
dofs=None)

out[slev + 'wM'] = Struct(name='output_data',

mode='cell',
data=dvel,
var_name='wM',
dofs=None)

return out

geoms = {
'2_4': ['2_4_Q1', '2', 5],
'3_8': ['3_8_Q1', '4', 5],
'3_4': ['3_4_P1', '3', 3],
}

pb_def = {
'name': '3d_2ch',
'mesh_filename': data_dir + '/meshes/3d/perfusion_micro3d.mesh',
'dim': 3,
'geom': geoms['3_4'],
'eps0': 1.0e-2,
'param_h': 1.0,
'param_kappa_m': 0.1,
'matrix_mat_el_grp': 3,
'channels': {
'A': {
'mat_el_grp': 1,
'fix_nd_grp': (4, 1),
'io_nd_grp': [1, 2, 3],
'param_kappa_ch': 1.0,
},
'B': {
'mat_el_grp': 2,
'fix_nd_grp': (14, 11),
'io_nd_grp': [11, 12, 13],
'param_kappa_ch': 2.0,
},
},
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}

filename_mesh = pb_def['mesh_filename']
eps0 = pb_def['eps0']
param_h = pb_def['param_h']

# integrals
integrals = {
'iV': 2,
'iS': 2,
}

functions = {
'match_x_plane': (match_x_plane,),
'match_y_plane': (match_y_plane,),
}

aux = []
for ch, val in six.iteritems(pb_def['channels']):
aux.append('r.bYM' + ch)

# basic regions
regions = {
'Y': 'all',
'YM': 'cells of group %d' % pb_def['matrix_mat_el_grp'],
# periodic boundaries
'Pl': ('vertices in (x < 0.001)', 'facet'),
'Pr': ('vertices in (x > 0.999)', 'facet'),
'PlYM': ('r.Pl *v r.YM', 'facet'),
'PrYM': ('r.Pr *v r.YM', 'facet'),
'bYMp': ('r.bYp *v r.YM', 'facet', 'YM'),
'bYMm': ('r.bYm *v r.YM', 'facet', 'YM'),
'bYMpm': ('r.bYMp +v r.bYMm', 'facet', 'YM'),
}

# matrix/channel boundaries
regions.update({
'bYMchs': (' +v '.join(aux), 'facet', 'YM'),
'YMmchs': 'r.YM -v r.bYMchs',
})

# boundary conditions Gamma+/-

ebcs = {
'gamma_pm_bYMchs': ('bYMchs', {'pM.0': 0.0}),
'gamma_pm_YMmchs': ('YMmchs', {'pM.0': 1.0}),
}

# periodic boundary conditions - matrix, X-direction

epbcs = {'periodic_xYM': (['PlYM', 'PrYM'], {'pM.0': 'pM.0'}, 'match_x_plane')}
lcbcs = {}

all_periodicYM = ['periodic_%sYM' % ii for ii in ['x', 'y'][:pb_def['dim']-1]]

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all_periodicY = {}

if pb_def['dim'] == 2:
regions.update({
'bYm': ('vertices in (y < 0.001)', 'facet'),
'bYp': ('vertices in (y > 0.999)', 'facet'),
})
if pb_def['dim'] == 3:
regions.update({
'Pn': ('vertices in (y < 0.001)', 'facet'),
'Pf': ('vertices in (y > 0.999)', 'facet'),
'PnYM': ('r.Pn *v r.YM', 'facet'),
'PfYM': ('r.Pf *v r.YM', 'facet'),
'bYm': ('vertices in (z < 0.001)', 'facet'),
'bYp': ('vertices in (z > 0.999)', 'facet'),
})
# periodic boundary conditions - matrix, Y-direction
epbcs.update({
'periodic_yYM': (['PnYM', 'PfYM'], {'pM.0': 'pM.0'}, 'match_y_plane'),
})

reg_io = {}
ebcs_eta = {}
ebcs_gamma = {}

# generate regions, ebcs, epbcs

for ch, val in six.iteritems(pb_def['channels']):

all_periodicY[ch] = ['periodic_%sY%s' % (ii, ch)

for ii in ['x', 'y'][:pb_def['dim']-1]]

# channels: YA, fixedYA, bYMA (matrix/channel boundaries)

regions.update({
'Y' + ch: 'cells of group %d' % val['mat_el_grp'],
'bYM' + ch: ('r.YM *v r.Y' + ch, 'facet', 'YM'),
'PlY' + ch: ('r.Pl *v r.Y' + ch, 'facet'),
'PrY' + ch: ('r.Pr *v r.Y' + ch, 'facet'),
})

if 'fix_nd_grp' in val:
regions.update({
'fixedY' + ch: ('vertices of group %d' % val['fix_nd_grp'][0],
'vertex'),
})

ebcs_eta[ch] = []
for ch2, val2 in six.iteritems(pb_def['channels']):
aux = 'eta%s_bYM%s' % (ch, ch2)
if ch2 == ch:
ebcs.update({aux: ('bYM' + ch2, {'pM.0': 1.0})})
else:
ebcs.update({aux: ('bYM' + ch2, {'pM.0': 0.0})})
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ebcs_eta[ch].append(aux)

# boundary conditions
# periodic boundary conditions - channels, X-direction
epbcs.update({
'periodic_xY' + ch: (['PlY' + ch, 'PrY' + ch],
{'p%s.0' % ch: 'p%s.0' % ch},
'match_x_plane'),
})

if pb_def['dim'] == 3:
regions.update({
'PnY' + ch: ('r.Pn *v r.Y' + ch, 'facet'),
'PfY' + ch: ('r.Pf *v r.Y' + ch, 'facet'),
})
# periodic boundary conditions - channels, Y-direction
epbcs.update({
'periodic_yY' + ch: (['PnY' + ch, 'PfY' + ch],
{'p%s.0' % ch: 'p%s.0' % ch},
'match_y_plane'),
})

reg_io[ch] = []
aux_bY = []
# channel: inputs/outputs
for i_io in range(len(val['io_nd_grp'])):
io = '%s_%d' % (ch, i_io+1)

# regions
aux = val['io_nd_grp'][i_io]
if 'fix_nd_grp' in val and val['fix_nd_grp'][1] == aux:
regions.update({
'bY%s' % io: ('vertices of group %d +v r.fixedY%s' % (aux, ch),
'facet', 'Y%s' % ch),
})
else:
regions.update({
'bY%s' % io: ('vertices of group %d' % aux,
'facet', 'Y%s' % ch),
})

aux_bY.append('r.bY%s' % io)
reg_io[ch].append('bY%s' % io)

regions.update({
'bY' + ch: (' +v '.join(aux_bY), 'facet', 'Y' + ch),
})

# channel: inputs/outputs
for i_io in range(len(val['io_nd_grp'])):
io = '%s_%d' % (ch, i_io + 1)
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ion = '%s_n%d' % (ch, i_io + 1)
regions.update({
'bY%s' % ion: ('r.bY%s -v r.bY%s' % (ch, io), 'facet', 'Y%s' % ch),
})

# boundary conditions
aux = 'fix_p%s_bY%s' % (ch, ion)
ebcs.update({
aux: ('bY%s' % ion, {'p%s.0' % ch: 0.0}),
})

lcbcs.update({
'imv' + ch: ('Y' + ch, {'ls%s.all' % ch: None}, None,
'integral_mean_value')
})

matk1, matk2 = get_mats(pb_def['param_kappa_m'], param_h, eps0, pb_def['dim'])

materials = {
'mat1M': ({'k': matk1},),
'mat2M': ({'k': matk2},),
}

fields = {
'corrector_M': ('real', 'scalar', 'YM', 1),
'vel_M': ('real', 'vector', 'YM', 1),
'vol_all': ('real', 'scalar', 'Y', 1),
}

variables = {
'pM': ('unknown field', 'corrector_M'),
'qM': ('test field', 'corrector_M', 'pM'),
'Pi_M': ('parameter field', 'corrector_M', '(set-to-None)'),
'corr_M': ('parameter field', 'corrector_M', '(set-to-None)'),
'corr1_M': ('parameter field', 'corrector_M', '(set-to-None)'),
'corr2_M': ('parameter field', 'corrector_M', '(set-to-None)'),
'wM': ('parameter field', 'vel_M', '(set-to-None)'),
'vol_all': ('parameter field', 'vol_all', '(set-to-None)'),
}

# generate regions for channel inputs/outputs

for ch, val in six.iteritems(pb_def['channels']):

matk1, matk2 = get_mats(val['param_kappa_ch'], param_h,

eps0, pb_def['dim'])
materials.update({
'mat1' + ch: ({'k': matk1},),
'mat2' + ch: ({'k': matk2},),
})

fields.update({
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'corrector_' + ch: ('real', 'scalar', 'Y' + ch, 1),
'vel_' + ch: ('real', 'vector', 'Y' + ch, 1),
})

variables.update({
'p' + ch: ('unknown field', 'corrector_' + ch),
'q' + ch: ('test field', 'corrector_' + ch, 'p' + ch),
'Pi_' + ch: ('parameter field', 'corrector_' + ch, '(set-to-None)'),
'corr1_' + ch: ('parameter field', 'corrector_' + ch, '(set-to-None)'),
'corr2_' + ch: ('parameter field', 'corrector_' + ch, '(set-to-None)'),
'w' + ch: ('unknown field', 'vel_' + ch),
# lagrange mutltipliers - integral mean value
'ls' + ch: ('unknown field', 'corrector_' + ch),
'lv' + ch: ('test field', 'corrector_' + ch, 'ls' + ch),
})

options = {
'coefs': 'coefs',
'requirements': 'requirements',
'ls': 'ls', # linear solver to use
'volumes': {
'total': {
'variables': ['vol_all'],
'expression': """ev_volume.iV.Y(vol_all)""",
},
'one': {
'value': 1.0,
}
},
'output_dir': './output',
'file_per_var': True,
'coefs_filename': 'coefs_perf_' + pb_def['name'],
'coefs_info': {'eps0': eps0},
'recovery_hook': 'recovery_perf',
'multiprocessing': False,
}

for ipm in ['p', 'm']:

options['volumes'].update({
'bYM' + ipm: {
'variables': ['pM'],
'expression': "ev_volume.iS.bYM%s(pM)" % ipm,
},
'bY' + ipm: {
'variables': ['vol_all'],
'expression': "ev_volume.iS.bY%s(vol_all)" % ipm,
}
})

for ch in six.iterkeys(reg_io):
for ireg in reg_io[ch]:
options['volumes'].update({
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ireg: {
'variables': ['p' + ch],
'expression': "ev_volume.iS.%s(p%s)" % (ireg, ch),
}
})

coefs = {
'vol_bYMpm': {
'regions': ['bYMp', 'bYMm'],
'expression': 'ev_volume.iS.%s(pM)',
'class': cb.VolumeFractions,
},
'filenames': {},
}

requirements = {
'corrs_one_YM': {
'variable': ['pM'],
'ebcs': ['gamma_pm_YMmchs', 'gamma_pm_bYMchs'],
'epbcs': [],
'save_name': 'corrs_one_YM',
'class': cb.CorrSetBCS,
},
}

for ipm in ['p', 'm']:

requirements.update({
'corrs_gamma_' + ipm: {
'requires': [],
'ebcs': ['gamma_pm_bYMchs'],
'epbcs': all_periodicYM,
'equations': {
'eq_gamma_pm': """dw_diffusion.iV.YM(mat2M.k, qM, pM) =
%e * dw_integrate.iS.bYM%s(qM)"""
% (1.0/param_h, ipm),
},
'class': cb.CorrOne,
'save_name': 'corrs_%s_gamma_%s' % (pb_def['name'], ipm),
},
})

for ipm2 in ['p', 'm']:

coefs.update({
'H' + ipm + ipm2: { # test+
'requires': ['corrs_gamma_' + ipm],
'set_variables': [('corr_M', 'corrs_gamma_' + ipm, 'pM')],
'expression': 'ev_integrate.iS.bYM%s(corr_M)' % ipm2,
'set_volume': 'bYp',
'class': cb.CoefOne,
},
})

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def get_channel(keys, bn):

for ii in keys:
if bn in ii:
return ii[(ii.rfind(bn) + len(bn)):]

return None

def set_corrpis(variables, ir, ic, mode, **kwargs):

ch = get_channel(list(kwargs.keys()), 'pis_')
pis = kwargs['pis_' + ch]
corrs_pi = kwargs['corrs_pi' + ch]

if mode == 'row':
val = pis.states[ir]['p' + ch] + corrs_pi.states[ir]['p' + ch]
variables['corr1_' + ch].set_data(val)
elif mode == 'col':
val = pis.states[ic]['p' + ch] + corrs_pi.states[ic]['p' + ch]
variables['corr2_' + ch].set_data(val)

def set_corr_S(variables, ir, *args, **kwargs):

ch = get_channel(list(kwargs.keys()), 'pis_')
io = get_channel(list(kwargs.keys()), 'corrs_gamma_')

pis = kwargs['pis_' + ch]

corrs_gamma = kwargs['corrs_gamma_' + io]

pi = pis.states[ir]['p' + ch]
val = corrs_gamma.state['p' + ch]
variables['corr1_' + ch].set_data(pi)
variables['corr2_' + ch].set_data(val)

def set_corr_cc(variables, ir, *args, **kwargs):

ch = get_channel(list(kwargs.keys()), 'pis_')
pis = kwargs['pis_' + ch]
corrs_pi = kwargs['corrs_pi' + ch]

pi = pis.states[ir]['p' + ch]
pi = pi - nm.mean(pi)
val = pi + corrs_pi.states[ir]['p' + ch]
variables['corr1_' + ch].set_data(val)

for ch, val in six.iteritems(pb_def['channels']):

coefs.update({
'G' + ch: { # test+
'requires': ['corrs_one' + ch, 'corrs_eta' + ch],
'set_variables': [('corr1_M', 'corrs_one' + ch, 'pM'),
('corr2_M', 'corrs_eta' + ch, 'pM')],
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'expression': 'dw_diffusion.iV.YM(mat2M.k, corr1_M, corr2_M)',
'class': cb.CoefOne,
},
'K' + ch: { # test+
'requires': ['pis_' + ch, 'corrs_pi' + ch],
'set_variables': set_corrpis,
'expression': 'dw_diffusion.iV.Y%s(mat2%s.k, corr1_%s, corr2_%s)'\
% ((ch,) * 4),
'dim': pb_def['dim'] - 1,
'class': cb.CoefDimDim,
},
})

requirements.update({
'pis_' + ch: {
'variables': ['p' + ch],
'class': cb.ShapeDim,
},
'corrs_one' + ch: {
'variable': ['pM'],
'ebcs': ebcs_eta[ch],
'epbcs': [],
'save_name': 'corrs_%s_one%s' % (pb_def['name'], ch),
'class': cb.CorrSetBCS,
},
'corrs_eta' + ch: {
'ebcs': ebcs_eta[ch],
'epbcs': all_periodicYM,
'equations': {
'eq_eta': 'dw_diffusion.iV.YM(mat2M.k, qM, pM) = 0',
},
'class': cb.CorrOne,
'save_name': 'corrs_%s_eta%s' % (pb_def['name'], ch),
},
'corrs_pi' + ch: {
'requires': ['pis_' + ch],
'set_variables': [('Pi_' + ch, 'pis_' + ch, 'p' + ch)],
'ebcs': [],
'epbcs': all_periodicY[ch],
'lcbcs': ['imv' + ch],
'equations': {
'eq_pi': """dw_diffusion.iV.Y%s(mat2%s.k, q%s, p%s)
+ dw_dot.iV.Y%s(q%s, ls%s)
= - dw_diffusion.iV.Y%s(mat2%s.k, q%s, Pi_%s)"""
% ((ch,) * 11),
'eq_imv': 'dw_dot.iV.Y%s(lv%s, p%s) = 0' % ((ch,) * 3),
},
'dim': pb_def['dim'] - 1,
'class': cb.CorrDim,
'save_name': 'corrs_%s_pi%s' % (pb_def['name'], ch),
},
})
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for ipm in ['p', 'm']:

coefs.update({
'E' + ipm + ch: { # test+
'requires': ['corrs_eta' + ch],
'set_variables': [('corr_M', 'corrs_eta' + ch, 'pM')],
'expression': 'ev_integrate.iS.bYM%s(corr_M)' % ipm,
'set_volume': 'bYp',
'class': cb.CoefOne,
},
'F' + ipm + ch: { # test+
'requires': ['corrs_one' + ch, 'corrs_gamma_' + ipm],
'set_variables': [('corr1_M', 'corrs_one' + ch, 'pM'),
('corr2_M', 'corrs_gamma_' + ipm, 'pM')],
'expression': """dw_diffusion.iV.YM(mat2M.k, corr1_M, corr2_M)
- %e * ev_integrate.iS.bYM%s(corr1_M)"""\
% (1.0/param_h, ipm),
'class': cb.CoefOne,
},
})

for i_io in range(len(val['io_nd_grp'])):

io = '%s_%d' % (ch, i_io + 1)

coefs.update({
'S' + io: { # [Rohan1] (4.28), test+
'requires': ['corrs_gamma_' + io, 'pis_' + ch],
'set_variables': set_corr_S,
'expression': 'dw_diffusion.iV.Y%s(mat2%s.k,corr1_%s,corr2_%s)'
% ((ch,) * 4),
'dim': pb_def['dim'] - 1,
'class': cb.CoefDim,
},
'P' + io: { # test+
'requires': ['pis_' + ch, 'corrs_pi' + ch],
'set_variables': set_corr_cc,
'expression': 'ev_integrate.iS.bY%s(corr1_%s)'\
% (io, ch),
'set_volume': 'bYp',
'dim': pb_def['dim'] - 1,
'class': cb.CoefDim,
},
'S_test' + io: {
'requires': ['corrs_pi' + ch],
'set_variables': [('corr1_' + ch, 'corrs_pi' + ch, 'p' + ch)],
'expression': '%e * ev_integrate.iS.bY%s(corr1_%s)'\
% (1.0 / param_h, io, ch),
'dim': pb_def['dim'] - 1,
'class': cb.CoefDim,
},
})

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requirements.update({
'corrs_gamma_' + io: {
'requires': [],
'variables': ['p' + ch, 'q' + ch],
'ebcs': [],
'epbcs': all_periodicY[ch],
'lcbcs': ['imv' + ch],
'equations': {
'eq_gamma': """dw_diffusion.iV.Y%s(mat2%s.k, q%s, p%s)
+ dw_dot.iV.Y%s(q%s, ls%s)
= %e * dw_integrate.iS.bY%s(q%s)"""
% ((ch,) * 7 + (1.0/param_h, io, ch)),
'eq_imv': 'dw_dot.iV.Y%s(lv%s, p%s) = 0'
% ((ch,) * 3),
},
'class': cb.CorrOne,
'save_name': 'corrs_%s_gamma_%s' % (pb_def['name'], io),
},
})

for i_io2 in range(len(val['io_nd_grp'])):

io2 = '%s_%d' % (ch, i_io2 + 1)
io12 = '%s_%d' % (io, i_io2 + 1)
coefs.update({
'R' + io12: { # test+
'requires': ['corrs_gamma_' + io2],
'set_variables': [('corr1_' + ch, 'corrs_gamma_' + io2,
'p' + ch)],
'expression': 'ev_integrate.iS.bY%s(corr1_%s)'\
% (io, ch),
'set_volume': 'bYp',
'class': cb.CoefOne,
},
})

solvers = {
'ls': ('ls.scipy_direct', {}),
'newton': ('nls.newton', {
'i_max': 1,
})
}

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homogenization/rs_correctors.py

Description
Compute homogenized elastic coefficients for a given microstructure.
source code

#!/usr/bin/env python
"""
Compute homogenized elastic coefficients for a given microstructure.
"""
from __future__ import print_function
from __future__ import absolute_import
from argparse import ArgumentParser
import sys
import six
sys.path.append('.')

import numpy as nm

from sfepy import data_dir

import sfepy.discrete.fem.periodic as per
from sfepy.homogenization.utils import define_box_regions

def define_regions(filename):
"""
Define various subdomains for a given mesh file.
"""
regions = {}
dim = 2

regions['Y'] = 'all'

eog = 'cells of group %d'

if filename.find('osteonT1') >= 0:
mat_ids = [11, 39, 6, 8, 27, 28, 9, 2, 4, 14, 12, 17, 45, 28, 15]
regions['Ym'] = ' +c '.join((eog % im) for im in mat_ids)
wx = 0.865
wy = 0.499

regions['Yc'] = 'r.Y -c r.Ym'

# Sides and corners.

regions.update(define_box_regions(2, (wx, wy)))

return dim, regions

def get_pars(ts, coor, mode=None, term=None, **kwargs):

"""
Define material parameters: :math:`D_ijkl` (elasticity), in a given region.
"""
if mode == 'qp':
dim = coor.shape[1]
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sym = (dim + 1) * dim // 2

out = {}

# in 1e+10 [Pa]
lam = 1.7
mu = 0.3
o = nm.array([1.] * dim + [0.] * (sym - dim), dtype = nm.float64)
oot = nm.outer(o, o)
out['D'] = lam * oot + mu * nm.diag(o + 1.0)

for key, val in six.iteritems(out):

out[key] = nm.tile(val, (coor.shape[0], 1, 1))

channels_cells = term.region.domain.regions['Yc'].cells
n_cell = term.region.get_n_cells()
val = out['D'].reshape((n_cell, -1, 3, 3))
val[channels_cells] *= 1e-1

return out

##
# Mesh file.
filename_mesh = data_dir + '/meshes/2d/special/osteonT1_11.mesh'

##
# Define regions (subdomains, boundaries) - $Y$, $Y_i$, ...
# depending on a mesh used.
dim, regions = define_regions(filename_mesh)

functions = {
'get_pars' : (lambda ts, coors, **kwargs:
get_pars(ts, coors, **kwargs),),
'match_x_plane' : (per.match_x_plane,),
'match_y_plane' : (per.match_y_plane,),
'match_z_plane' : (per.match_z_plane,),
'match_x_line' : (per.match_x_line,),
'match_y_line' : (per.match_y_line,),
}

##
# Define fields: 'displacement' in $Y$,
# 'pressure_m' in $Y_m$.
fields = {
'displacement' : ('real', dim, 'Y', 1),
}

##
# Define corrector variables: unknown displaements: uc, test: vc
# displacement-like variables: Pi, Pi1, Pi2
variables = {
'uc' : ('unknown field', 'displacement', 0),
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'vc' : ('test field', 'displacement', 'uc'),
'Pi' : ('parameter field', 'displacement', 'uc'),
'Pi1' : ('parameter field', 'displacement', None),
'Pi2' : ('parameter field', 'displacement', None),
}

##
# Periodic boundary conditions.
if dim == 3:
epbcs = {
'periodic_x' : (['Left', 'Right'], {'uc.all' : 'uc.all'},
'match_x_plane'),
'periodic_y' : (['Near', 'Far'], {'uc.all' : 'uc.all'},
'match_y_plane'),
'periodic_z' : (['Top', 'Bottom'], {'uc.all' : 'uc.all'},
'match_z_plane'),
}
else:
epbcs = {
'periodic_x' : (['Left', 'Right'], {'uc.all' : 'uc.all'},
'match_y_line'),
'periodic_y' : (['Bottom', 'Top'], {'uc.all' : 'uc.all'},
'match_x_line'),
}

##
# Dirichlet boundary conditions.
ebcs = {
'fixed_u' : ('Corners', {'uc.all' : 0.0}),
}

##
# Material defining constitutive parameters of the microproblem.
materials = {
'm' : 'get_pars',
}

##
# Numerical quadratures for volume (i3 - order 3) integral terms.
integrals = {
'i3' : 3,
}

##
# Homogenized coefficients to compute.
def set_elastic(variables, ir, ic, mode, pis, corrs_rs):
mode2var = {'row' : 'Pi1', 'col' : 'Pi2'}

val = pis.states[ir, ic]['uc'] + corrs_rs.states[ir, ic]['uc']

variables[mode2var[mode]].set_data(val)

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coefs = {
'E' : {
'requires' : ['pis', 'corrs_rs'],
'expression' : 'dw_lin_elastic.i3.Y(m.D, Pi1, Pi2)',
'set_variables' : set_elastic,
},
}

all_periodic = ['periodic_%s' % ii for ii in ['x', 'y', 'z'][:dim] ]

requirements = {
'pis' : {
'variables' : ['uc'],
},
##
# Steady state correctors $\bar{\omega}^{rs}$.
'corrs_rs' : {
'requires' : ['pis'],
'save_variables' : ['uc'],
'ebcs' : ['fixed_u'],
'epbcs' : all_periodic,
'equations' : {'eq' : """dw_lin_elastic.i3.Y(m.D, vc, uc)
= - dw_lin_elastic.i3.Y(m.D, vc, Pi)"""},
'set_variables' : [('Pi', 'pis', 'uc')],
'save_name' : 'corrs_elastic',
'is_linear' : True,
},
}

##
# Solvers.
solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-8,
'eps_r' : 1e-2,
})
}

############################################
# Mini-application below, computing the homogenized elastic coefficients.
helps = {
'no_pauses' : 'do not make pauses',
}

def main():
import os
from sfepy.base.base import spause, output
from sfepy.base.conf import ProblemConf, get_standard_keywords
from sfepy.discrete import Problem
import sfepy.homogenization.coefs_base as cb

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parser = ArgumentParser(description=__doc__)
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-n', '--no-pauses',
action="store_true", dest='no_pauses',
default=False, help=helps['no_pauses'])
options = parser.parse_args()

if options.no_pauses:
def spause(*args):
output(*args)

nm.set_printoptions(precision=3)

spause(r""">>>
First, this file will be read in place of an input
(problem description) file.
Press 'q' to quit the example, press any other key to continue...""")
required, other = get_standard_keywords()
required.remove('equations')
# Use this file as the input file.
conf = ProblemConf.from_file(__file__, required, other)
print(list(conf.to_dict().keys()))
spause(r""">>>
...the read input as a dict (keys only for brevity).
['q'/other key to quit/continue...]""")

spause(r""">>>
Now the input will be used to create a Problem instance.
['q'/other key to quit/continue...]""")
problem = Problem.from_conf(conf, init_equations=False)
# The homogenization mini-apps need the output_dir.
output_dir = ''
problem.output_dir = output_dir
print(problem)
spause(r""">>>
...the Problem instance.
['q'/other key to quit/continue...]""")

spause(r""">>>
The homogenized elastic coefficient $E_{ijkl}$ is expressed
using $\Pi$ operators, computed now. In fact, those operators are permuted
coordinates of the mesh nodes.
['q'/other key to quit/continue...]""")
req = conf.requirements['pis']
mini_app = cb.ShapeDimDim('pis', problem, req)
mini_app.setup_output(save_formats=['vtk'],
file_per_var=False)
pis = mini_app()
print(pis)
spause(r""">>>
...the $\Pi$ operators.
['q'/other key to quit/continue...]""")
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spause(r""">>>
Next, $E_{ijkl}$ needs so called steady state correctors $\bar{\omega}^{rs}$,
computed now.
['q'/other key to quit/continue...]""")
req = conf.requirements['corrs_rs']

save_name = req.get('save_name', '')

name = os.path.join(output_dir, save_name)

mini_app = cb.CorrDimDim('steady rs correctors', problem, req)

mini_app.setup_output(save_formats=['vtk'],
file_per_var=False)
corrs_rs = mini_app(data={'pis': pis})
print(corrs_rs)
spause(r""">>>
...the $\bar{\omega}^{rs}$ correctors.
The results are saved in: %s.%s

Try to display them with:

python postproc.py %s.%s

['q'/other key to quit/continue...]""" % (2 * (name, problem.output_format)))

spause(r""">>>
Then the volume of the domain is needed.
['q'/other key to quit/continue...]""")
volume = problem.evaluate('ev_volume.i3.Y(uc)')
print(volume)

spause(r""">>>
...the volume.
['q'/other key to quit/continue...]""")

spause(r""">>>
Finally, $E_{ijkl}$ can be computed.
['q'/other key to quit/continue...]""")
mini_app = cb.CoefSymSym('homogenized elastic tensor',
problem, conf.coefs['E'])
c_e = mini_app(volume, data={'pis': pis, 'corrs_rs' : corrs_rs})
print(r""">>>
The homogenized elastic coefficient $E_{ijkl}$, symmetric storage
with rows, columns in 11, 22, 12 ordering:""")
print(c_e)

if __name__ == '__main__':
main()

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large_deformation

large_deformation/active_fibres.py

Description
Nearly incompressible hyperelastic material model with active fibres.
Large deformation is described using the total Lagrangian formulation. Models of this kind can be used in biomechanics
to model biological tissues, e.g. muscles.
Find 𝑢 such that:
∫︁ (︁ )︁
𝑆 eff (𝑢) + 𝐾(𝐽 − 1) 𝐽𝐶 −1 : 𝛿𝐸(𝑣) d𝑉 = 0 , ∀𝑣 ,
Ω(0)

where

𝐹 deformation gradient 𝐹𝑖𝑗 = 𝜕𝑋 𝜕𝑥𝑖

𝑗
𝐽 det(𝐹 )
𝐶 right Cauchy-Green deformation tensor 𝐶 = 𝐹 𝑇 𝐹
𝜕𝑢
𝐸(𝑢) Green strain tensor 𝐸𝑖𝑗 = 21 ( 𝜕𝑋
𝜕𝑢𝑖
𝑗
+ 𝜕𝑋𝑗𝑖 + 𝜕𝑢 𝑚 𝜕𝑢𝑚
𝜕𝑋𝑖 𝜕𝑋𝑗 )
𝑆 eff (𝑢) effective second Piola-Kirchhoff stress tensor

The effective stress 𝑆 eff (𝑢) incorporates also the effects of the active fibres in two preferential directions:

2
2 1 ∑︁
𝑆 eff (𝑢) = 𝜇𝐽 − 3 (𝐼 − tr(𝐶)𝐶 −1 ) + 𝜏 𝑘 𝜔𝑘 .
3
𝑘=1

The first term is the neo-Hookean term and the sum add contributions of the two fibre systems. The tensors 𝜔 𝑘 = 𝑑𝑘 𝑑𝑘
are defined by the fibre system direction vectors 𝑑𝑘 (unit).
For the one-dimensional tensions 𝜏 𝑘 holds simply (𝑘 omitted):
{︂ }︂
𝜖 − 𝜀opt 2
𝜏 = 𝐴𝑓max exp −( ) ,𝜖=𝐸 :𝜔.
𝑠

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source code

# -*- coding: utf-8 -*-

r"""
Nearly incompressible hyperelastic material model with active fibres.

Large deformation is described using the total Lagrangian formulation.

Models of this kind can be used in biomechanics to model biological
tissues, e.g. muscles.

Find :math:`\ul{u}` such that:

.. math::
\intl{\Omega\suz}{} \left( \ull{S}\eff(\ul{u})
+ K(J-1)\; J \ull{C}^{-1} \right) : \delta \ull{E}(\ul{v}) \difd{V}
= 0
\;, \quad \forall \ul{v} \;,

where

.. list-table::
:widths: 20 80

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* - :math:`\ull{F}`
- deformation gradient :math:`F_{ij} = \pdiff{x_i}{X_j}`
* - :math:`J`
- :math:`\det(F)`
* - :math:`\ull{C}`
- right Cauchy-Green deformation tensor :math:`C = F^T F`
* - :math:`\ull{E}(\ul{u})`
- Green strain tensor :math:`E_{ij} = \frac{1}{2}(\pdiff{u_i}{X_j} +
\pdiff{u_j}{X_i} + \pdiff{u_m}{X_i}\pdiff{u_m}{X_j})`
* - :math:`\ull{S}\eff(\ul{u})`
- effective second Piola-Kirchhoff stress tensor

The effective stress :math:`\ull{S}\eff(\ul{u})` incorporates also the

effects of the active fibres in two preferential directions:

.. math::
\ull{S}\eff(\ul{u}) = \mu J^{-\frac{2}{3}}(\ull{I}
- \frac{1}{3}\tr(\ull{C}) \ull{C}^{-1})
+ \sum_{k=1}^2 \tau^k \ull{\omega}^k
\;.

The first term is the neo-Hookean term and the sum add contributions of
the two fibre systems. The tensors :math:`\ull{\omega}^k =
\ul{d}^k\ul{d}^k` are defined by the fibre system direction vectors
:math:`\ul{d}^k` (unit).

For the one-dimensional tensions :math:`\tau^k` holds simply (:math:`^k`

omitted):

.. math::
\tau = A f_{\rm max} \exp{\left\{-(\frac{\epsilon - \varepsilon_{\rm
opt}}{s})^2\right\}} \mbox{ , } \epsilon = \ull{E} : \ull{\omega}
\;.
"""
from __future__ import print_function
from __future__ import absolute_import
import numpy as nm

from sfepy import data_dir

filename_mesh = data_dir + '/meshes/3d/cylinder.mesh'

vf_matrix = 0.5
vf_fibres1 = 0.2
vf_fibres2 = 0.3

options = {
'nls' : 'newton',
'ls' : 'ls',
'ts' : 'ts',
'save_times' : 'all',
'post_process_hook' : 'stress_strain',
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}

fields = {
'displacement': (nm.float64, 3, 'Omega', 1),
}

materials = {
'solid' : ({
'K' : vf_matrix * 1e3, # bulk modulus
'mu' : vf_matrix * 20e0, # shear modulus of neoHookean term
},),
'f1' : 'get_pars_fibres1',
'f2' : 'get_pars_fibres2',
}

def get_pars_fibres(ts, coors, mode=None, which=0, vf=1.0, **kwargs):

"""
Parameters
----------
ts : TimeStepper
Time stepping info.
coors : array_like
The physical domain coordinates where the parameters shound be defined.
mode : 'qp' or 'special'
Call mode.
which : int
Fibre system id.
vf : float
Fibre system volume fraction.
"""
if mode != 'qp': return

fmax = 10.0
eps_opt = 0.01
s = 1.0

tt = ts.nt * 2.0 * nm.pi

if which == 0: # system 1
fdir = nm.array([1.0, 0.0, 0.0], dtype=nm.float64)
act = 0.5 * (1.0 + nm.sin(tt - (0.5 * nm.pi)))

elif which == 1: # system 2

fdir = nm.array([0.0, 1.0, 0.0], dtype=nm.float64)
act = 0.5 * (1.0 + nm.sin(tt + (0.5 * nm.pi)))

else:
raise ValueError('unknown fibre system! (%d)' % which)

fdir.shape = (3, 1)
fdir /= nm.linalg.norm(fdir)
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print(act)

shape = (coors.shape[0], 1, 1)
out = {
'fmax' : vf * nm.tile(fmax, shape),
'eps_opt' : nm.tile(eps_opt, shape),
's' : nm.tile(s, shape),
'fdir' : nm.tile(fdir, shape),
'act' : nm.tile(act, shape),
}

return out

functions = {
'get_pars_fibres1' : (lambda ts, coors, mode=None, **kwargs:
get_pars_fibres(ts, coors, mode=mode, which=0,
vf=vf_fibres1, **kwargs),),
'get_pars_fibres2' : (lambda ts, coors, mode=None, **kwargs:
get_pars_fibres(ts, coors, mode=mode, which=1,
vf=vf_fibres2, **kwargs),),
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
}

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < 0.001)', 'facet'),
'Right' : ('vertices in (x > 0.099)', 'facet'),
}

##
# Dirichlet BC.
ebcs = {
'l' : ('Left', {'u.all' : 0.0}),
}

##
# Balance of forces.
integral_1 = {
'name' : 'i',
'order' : 1,
}
equations = {
'balance'
: """dw_tl_he_neohook.i.Omega( solid.mu, v, u )
+ dw_tl_bulk_penalty.i.Omega( solid.K, v, u )
+ dw_tl_fib_a.i.Omega( f1.fmax, f1.eps_opt, f1.s, f1.fdir, f1.act,
v, u )
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+ dw_tl_fib_a.i.Omega( f2.fmax, f2.eps_opt, f2.s, f2.fdir, f2.act,
v, u )
= 0""",
}

def stress_strain(out, problem, state, extend=False):

from sfepy.base.base import Struct, debug

ev = problem.evaluate
strain = ev('dw_tl_he_neohook.i.Omega( solid.mu, v, u )',
mode='el_avg', term_mode='strain')
out['green_strain'] = Struct(name='output_data',
mode='cell', data=strain, dofs=None)

stress = ev('dw_tl_he_neohook.i.Omega( solid.mu, v, u )',

mode='el_avg', term_mode='stress')
out['neohook_stress'] = Struct(name='output_data',
mode='cell', data=stress, dofs=None )

stress = ev('dw_tl_bulk_penalty.i.Omega( solid.K, v, u )',

mode='el_avg', term_mode= 'stress')
out['bulk_stress'] = Struct(name='output_data',
mode='cell', data=stress, dofs=None)

return out

##
# Solvers etc.
solver_0 = {
'name' : 'ls',
'kind' : 'ls.scipy_direct',
}

solver_1 = {
'name' : 'newton',
'kind' : 'nls.newton',

'i_max' : 7,
'eps_a' : 1e-10,
'eps_r' : 1.0,
'macheps' : 1e-16,
'lin_red' : 1e-2, # Linear system error < (eps_a * lin_red).
'ls_red' : 0.1,
'ls_red_warp': 0.001,
'ls_on' : 1.1,
'ls_min' : 1e-5,
'check' : 0,
'delta' : 1e-6,
}

solver_2 = {
'name' : 'ts',
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'kind' : 'ts.simple',

't0' : 0,
't1' : 1,
'dt' : None,
'n_step' : 21, # has precedence over dt!
'verbose' : 1,
}

large_deformation/balloon.py

Description
Inflation of a Mooney-Rivlin hyperelastic balloon.
This example serves as a verification of the membrane term (dw_tl_membrane, TLMembraneTerm) implementation.
Following Rivlin 1952 and Dumais, the analytical relation between a relative stretch 𝐿 = 𝑟/𝑟0 of a thin (membrane)
sphere made of the Mooney-Rivlin material of the undeformed radius 𝑟0 , membrane thickness ℎ0 and the inner pressure
𝑝 is
ℎ0 1 1
𝑝=4 ( − 7 )(𝑐1 + 𝑐2 𝐿2 ) ,
𝑟0 𝐿 𝐿
where 𝑐1 , 𝑐2 are the Mooney-Rivlin material parameters.
In the equations below, only the surface of the domain is mechanically important - a stiff 2D membrane is embedded
in the 3D space and coincides with the balloon surface. The volume is very soft, to simulate a fluid-filled cavity. A
similar model could be used to model e.g. plant cells. The balloon surface is loaded by prescribing the inner volume
change 𝜔(𝑡). The fluid pressure in the cavity is a single scalar value, enforced by the 'integral_mean_value' linear
combination condition.
Find 𝑢(𝑋) and a constant 𝑝 such that:
• balance of forces:
∫︁ (︁ )︁ ∫︁
𝑆 eff (𝑢) − 𝑝 𝐽𝐶 −1 : 𝛿𝐸(𝑣; 𝑣) d𝑉 + 𝑆 eff (˜
𝑢)𝛿𝐸(˜
𝑢; 𝑣˜)ℎ0 d𝑆 = 0 , ∀𝑣 ∈ [𝐻01 (Ω)]3 ,
Ω(0) Γ(0)

• volume conservation:
∫︁
[𝜔(𝑡) − 𝐽(𝑢)] 𝑞 𝑑𝑥 = 0 ∀𝑞 ∈ 𝐿2 (Ω) ,
Ω0

where

𝐹 deformation gradient 𝐹𝑖𝑗 = 𝜕𝑋 𝜕𝑥𝑖

𝑗
𝐽 det(𝐹 )
𝐶 right Cauchy-Green deformation tensor 𝐶 = 𝐹 𝑇 𝐹
𝜕𝑢
𝐸(𝑢) Green strain tensor 𝐸𝑖𝑗 = 21 ( 𝜕𝑋
𝜕𝑢𝑖
𝑗
+ 𝜕𝑋𝑗𝑖 + 𝜕𝑢 𝑚 𝜕𝑢𝑚
𝜕𝑋𝑖 𝜕𝑋𝑗 )
𝑆 eff (𝑢) effective second Piola-Kirchhoff stress tensor

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The effective stress 𝑆 eff (𝑢) is given by:

2 1 4 2
𝑆 eff (𝑢) = 𝜇𝐽 − 3 (𝐼 − tr(𝐶)𝐶 −1 ) + 𝜅𝐽 − 3 (tr(𝐶𝐼 − 𝐶 − ((tr 𝐶)2 − tr (𝐶 2 ))𝐶 −1 ) .
3 6
The 𝑢
˜ and 𝑣˜ variables correspond to 𝑢, 𝑣, respectively, transformed to the membrane coordinate frame.
Use the following command to show a comparison of the FEM solution with the above analytical relation (notice the
nonlinearity of the dependence):

python simple.py examples/large_deformation/balloon.py -d 'plot: True'

The agreement should be very good, even though the mesh is coarse.
View the results using:

python postproc.py unit_ball.h5 --wireframe -b -d'u,plot_displacements,rel_scaling=1' --

˓→step=-1

This example uses the adaptive time-stepping solver ('ts.adaptive') with the default adaptivity function
adapt_time_step(). Plot the used time steps by:

python script/plot_times.py unit_ball.h5

source code

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r"""
Inflation of a Mooney-Rivlin hyperelastic balloon.

This example serves as a verification of the membrane term (``dw_tl_membrane``,

:class:`TLMembraneTerm <sfepy.terms.terms_membrane.TLMembraneTerm>`)
implementation.

Following Rivlin 1952 and Dumais, the analytical relation between a

relative stretch :math:`L = r / r_0` of a thin (membrane) sphere made of the
Mooney-Rivlin material of the undeformed radius :math:`r_0`, membrane
thickness :math:`h_0` and the inner pressure :math:`p` is

.. math::

p = 4 \frac{h_0}{r_0} (\frac{1}{L} - \frac{1}{L^7}) (c_1 + c_2 L^2) \;,

where :math:`c_1`, :math:`c_2` are the Mooney-Rivlin material parameters.

In the equations below, only the surface of the domain is mechanically

important - a stiff 2D membrane is embedded in the 3D space and coincides with
the balloon surface. The volume is very soft, to simulate a fluid-filled
cavity. A similar model could be used to model e.g. plant cells. The balloon
surface is loaded by prescribing the inner volume change :math:`\omega(t)`.
The fluid pressure in the cavity is a single scalar value, enforced by the
``'integral_mean_value'`` linear combination condition.

Find :math:`\ul{u}(\ul{X})` and a constant :math:`p` such that:

- balance of forces:

.. math::
\intl{\Omega\suz}{} \left( \ull{S}\eff(\ul{u})
- p\; J \ull{C}^{-1} \right) : \delta \ull{E}(\ul{v}; \ul{v}) \difd{V}
+ \intl{\Gamma\suz}{} \ull{S}\eff(\tilde{\ul{u}}) \delta
\ull{E}(\tilde{\ul{u}}; \tilde{\ul{v}}) h_0 \difd{S}
= 0 \;, \quad \forall \ul{v} \in [H^1_0(\Omega)]^3 \;,

- volume conservation:

.. math::
\int\limits_{\Omega_0} \left[\omega(t)-J(u)\right] q\, dx = 0
\qquad \forall q \in L^2(\Omega) \;,

where

.. list-table::
:widths: 20 80

* - :math:`\ull{F}`
- deformation gradient :math:`F_{ij} = \pdiff{x_i}{X_j}`
* - :math:`J`
- :math:`\det(F)`
* - :math:`\ull{C}`
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- right Cauchy-Green deformation tensor :math:`C = F^T F`
* - :math:`\ull{E}(\ul{u})`
- Green strain tensor :math:`E_{ij} = \frac{1}{2}(\pdiff{u_i}{X_j} +
\pdiff{u_j}{X_i} + \pdiff{u_m}{X_i}\pdiff{u_m}{X_j})`
* - :math:`\ull{S}\eff(\ul{u})`
- effective second Piola-Kirchhoff stress tensor

The effective stress :math:`\ull{S}\eff(\ul{u})` is given by:

.. math::
\ull{S}\eff(\ul{u}) = \mu J^{-\frac{2}{3}}(\ull{I}
- \frac{1}{3}\tr(\ull{C}) \ull{C}^{-1})
+ \kappa J^{-\frac{4}{3}} (\tr(\ull{C}\ull{I} - \ull{C}
- \frac{2}{6}((\tr{\ull{C}})^2 - \tr{(\ull{C}^2)})\ull{C}^{-1})
\;.

The :math:`\tilde{\ul{u}}` and :math:`\tilde{\ul{v}}` variables correspond to

:math:`\ul{u}`, :math:`\ul{v}`, respectively, transformed to the membrane
coordinate frame.

Use the following command to show a comparison of the FEM solution with the
above analytical relation (notice the nonlinearity of the dependence)::

python simple.py sfepy/examples/large_deformation/balloon.py -d 'plot: True'

The agreement should be very good, even though the mesh is coarse.

View the results using::

python postproc.py unit_ball.h5 --wireframe -b -d'u,plot_displacements,rel_scaling=1' --

˓→step=-1

This example uses the adaptive time-stepping solver (``'ts.adaptive'``) with

the default adaptivity function :func:`adapt_time_step()
<sfepy.solvers.ts_solvers.adapt_time_step>`. Plot the used time steps by::

python script/plot_times.py unit_ball.h5

"""
import os
import numpy as nm

from sfepy.base.base import Output

from sfepy.discrete.fem import MeshIO
from sfepy.linalg import get_coors_in_ball
from sfepy import data_dir

output = Output('balloon:')

def get_nodes(coors, radius, eps, mode):

if mode == 'ax1':
centre = nm.array([0.0, 0.0, -radius], dtype=nm.float64)

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elif mode == 'ax2':
centre = nm.array([0.0, 0.0, radius], dtype=nm.float64)

elif mode == 'equator':

centre = nm.array([radius, 0.0, 0.0], dtype=nm.float64)

else:
raise ValueError('unknown mode %s!' % mode)

return get_coors_in_ball(coors, centre, eps)

def get_volume(ts, coors, region=None):

rs = 1.0 + 1.0 * ts.time

rv = get_rel_volume(rs)
output('relative stretch:', rs)
output('relative volume:', rv)

out = nm.empty((coors.shape[0],), dtype=nm.float64)

out.fill(rv)

return out

def get_rel_volume(rel_stretch):
"""
Get relative volume V/V0 from relative stretch r/r0 of a ball.
"""
return nm.power(rel_stretch, 3.0)

def get_rel_stretch(rel_volume):
"""
Get relative stretch r/r0 from relative volume V/V0 of a ball.
"""
return nm.power(rel_volume, 1.0/3.0)

def get_balloon_pressure(rel_stretch, h0, r0, c1, c2):

"""
Rivlin 1952 + Dumais:

P = 4*h0/r0 * (1/L-1/L^7).*(C1+L^2*C2)
"""
L = rel_stretch
p = 4.0 * h0 / r0 * (1.0/L - 1.0/L**7) * (c1 + c2 * L**2)

return p

def plot_radius(problem, state):

import matplotlib.pyplot as plt

from sfepy.postprocess.time_history import extract_time_history

ths, ts = extract_time_history('unit_ball.h5', 'p e 0')

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p = ths['p'][0]
L = 1.0 + ts.times[:p.shape[0]]

L2 = 1.0 + nm.linspace(ts.times[0], ts.times[-1], 1000)

p2 = get_balloon_pressure(L2, 1e-2, 1, 3e5, 3e4)

plt.rcParams['lines.linewidth'] = 3
plt.rcParams['font.size'] = 16

plt.plot(L2, p2, 'r', label='theory')

plt.plot(L, p, 'b*', ms=12, label='FEM')

plt.title('Mooney-Rivlin hyperelastic balloon inflation')

plt.xlabel(r'relative stretch $r/r_0$')
plt.ylabel(r'pressure $p$')

plt.legend(loc='best')

fig = plt.gcf()
fig.savefig('balloon_pressure_stretch.pdf')

plt.show()

def define(plot=False):
filename_mesh = data_dir + '/meshes/3d/unit_ball.mesh'

conf_dir = os.path.dirname(__file__)
io = MeshIO.any_from_filename(filename_mesh, prefix_dir=conf_dir)
bbox = io.read_bounding_box()
dd = bbox[1] - bbox[0]

radius = bbox[1, 0]
eps = 1e-8 * dd[0]

options = {
'nls' : 'newton',
'ls' : 'ls',
'ts' : 'ts',
'save_times' : 'all',
'output_dir' : '.',
'output_format' : 'h5',
}

if plot:
options['post_process_hook_final'] = plot_radius

fields = {
'displacement': (nm.float64, 3, 'Omega', 1),
'pressure': (nm.float64, 1, 'Omega', 0),
}

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materials = {
'solid' : ({
'mu' : 50, # shear modulus of neoHookean term
'kappa' : 0.0, # shear modulus of Mooney-Rivlin term
},),
'walls' : ({
'mu' : 3e5, # shear modulus of neoHookean term
'kappa' : 3e4, # shear modulus of Mooney-Rivlin term
'h0' : 1e-2, # initial thickness of wall membrane
},),
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
'p' : ('unknown field', 'pressure', 1),
'q' : ('test field', 'pressure', 'p'),
'omega' : ('parameter field', 'pressure', {'setter' : 'get_volume'}),
}

regions = {
'Omega' : 'all',
'Ax1' : ('vertices by get_ax1', 'vertex'),
'Ax2' : ('vertices by get_ax2', 'vertex'),
'Equator' : ('vertices by get_equator', 'vertex'),
'Surface' : ('vertices of surface', 'facet'),
}

ebcs = {
'fix1' : ('Ax1', {'u.all' : 0.0}),
'fix2' : ('Ax2', {'u.[0, 1]' : 0.0}),
'fix3' : ('Equator', {'u.1' : 0.0}),
}

lcbcs = {
'pressure' : ('Omega', {'p.all' : None}, None, 'integral_mean_value'),
}

equations = {
'balance'
: """dw_tl_he_neohook.2.Omega(solid.mu, v, u)
+ dw_tl_he_mooney_rivlin.2.Omega(solid.kappa, v, u)
+ dw_tl_membrane.2.Surface(walls.mu, walls.kappa, walls.h0, v, u)
+ dw_tl_bulk_pressure.2.Omega(v, u, p)
= 0""",
'volume'
: """dw_tl_volume.2.Omega(q, u)
= dw_dot.2.Omega(q, omega)""",
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
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'newton' : ('nls.newton', {
'i_max' : 6,
'eps_a' : 1e-4,
'eps_r' : 1e-8,
'macheps' : 1e-16,
'lin_red' : 1e-2,
'ls_red' : 0.5,
'ls_red_warp': 0.1,
'ls_on' : 100.0,
'ls_min' : 1e-5,
'check' : 0,
'delta' : 1e-6,
'is_plot' : False,
'problem' : 'nonlinear',
}),
'ts' : ('ts.adaptive', {
't0' : 0.0,
't1' : 5.0,
'dt' : None,
'n_step' : 11,

'dt_red_factor' : 0.8,
'dt_red_max' : 1e-3,
'dt_inc_factor' : 1.25,
'dt_inc_on_iter' : 4,
'dt_inc_wait' : 3,

'verbose' : 1,
'quasistatic' : True,
}),
}

functions = {
'get_ax1' : (lambda coors, domain:
get_nodes(coors, radius, eps, 'ax1'),),
'get_ax2' : (lambda coors, domain:
get_nodes(coors, radius, eps, 'ax2'),),
'get_equator' : (lambda coors, domain:
get_nodes(coors, radius, eps, 'equator'),),
'get_volume' : (get_volume,),
}

return locals()

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large_deformation/compare_elastic_materials.py

Description
Compare various elastic materials w.r.t. uniaxial tension/compression test.
Requires Matplotlib.
source code

#!/usr/bin/env python
"""
Compare various elastic materials w.r.t. uniaxial tension/compression test.

Requires Matplotlib.
"""
from __future__ import absolute_import
from argparse import ArgumentParser, RawDescriptionHelpFormatter
import sys
import six
sys.path.append('.')

import numpy as nm

def define():
"""Define the problem to solve."""
from sfepy.discrete.fem.meshio import UserMeshIO
from sfepy.mesh.mesh_generators import gen_block_mesh
from sfepy.mechanics.matcoefs import stiffness_from_lame

def mesh_hook(mesh, mode):

"""
Generate the block mesh.
"""
if mode == 'read':
mesh = gen_block_mesh([2, 2, 3], [2, 2, 4], [0, 0, 1.5], name='el3',
verbose=False)
return mesh

elif mode == 'write':

pass

filename_mesh = UserMeshIO(mesh_hook)

options = {
'nls' : 'newton',
'ls' : 'ls',
'ts' : 'ts',
'save_times' : 'all',
}

functions = {
'linear_tension' : (linear_tension,),
'linear_compression' : (linear_compression,),
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'empty' : (lambda ts, coor, mode, region, ig: None,),
}

fields = {
'displacement' : ('real', 3, 'Omega', 1),
}

# Coefficients are chosen so that the tangent stiffness is the same for all
# material for zero strains.
# Young modulus = 10 kPa, Poisson's ratio = 0.3
materials = {
'solid' : ({
'K' : 8.333, # bulk modulus
'mu_nh' : 3.846, # shear modulus of neoHookean term
'mu_mr' : 1.923, # shear modulus of Mooney-Rivlin term
'kappa' : 1.923, # second modulus of Mooney-Rivlin term
# elasticity for LE term
'D' : stiffness_from_lame(dim=3, lam=5.769, mu=3.846),
},),
'load' : 'empty',
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
}

regions = {
'Omega' : 'all',
'Bottom' : ('vertices in (z < 0.1)', 'facet'),
'Top' : ('vertices in (z > 2.9)', 'facet'),
}

ebcs = {
'fixb' : ('Bottom', {'u.all' : 0.0}),
'fixt' : ('Top', {'u.[0,1]' : 0.0}),
}

integrals = {
'i' : 1,
'isurf' : 2,
}
equations = {
'linear' : """dw_lin_elastic.i.Omega(solid.D, v, u)
= dw_surface_ltr.isurf.Top(load.val, v)""",
'neo-Hookean' : """dw_tl_he_neohook.i.Omega(solid.mu_nh, v, u)
+ dw_tl_bulk_penalty.i.Omega(solid.K, v, u)
= dw_surface_ltr.isurf.Top(load.val, v)""",
'Mooney-Rivlin' : """dw_tl_he_neohook.i.Omega(solid.mu_mr, v, u)
+ dw_tl_he_mooney_rivlin.i.Omega(solid.kappa, v, u)
+ dw_tl_bulk_penalty.i.Omega(solid.K, v, u)
= dw_surface_ltr.isurf.Top(load.val, v)""",
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}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 5,
'eps_a' : 1e-10,
'eps_r' : 1.0,
}),
'ts' : ('ts.simple', {
't0' : 0,
't1' : 1,
'dt' : None,
'n_step' : 101, # has precedence over dt!
'verbose' : 1,
}),
}

return locals()

##
# Pressure tractions.
def linear_tension(ts, coor, mode=None, **kwargs):
if mode == 'qp':
val = nm.tile(0.1 * ts.step, (coor.shape[0], 1, 1))
return {'val' : val}

def linear_compression(ts, coor, mode=None, **kwargs):

if mode == 'qp':
val = nm.tile(-0.1 * ts.step, (coor.shape[0], 1, 1))
return {'val' : val}

def store_top_u(displacements):
"""Function _store() will be called at the end of each loading step. Top
displacements will be stored into `displacements`."""
def _store(problem, ts, state):

top = problem.domain.regions['Top']
top_u = problem.get_variables()['u'].get_state_in_region(top)
displacements.append(nm.mean(top_u[:,-1]))

return _store

def solve_branch(problem, branch_function):

displacements = {}
for key, eq in six.iteritems(problem.conf.equations):
problem.set_equations({key : eq})

load = problem.get_materials()['load']
load.set_function(branch_function)

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out = []
problem.solve(save_results=False, step_hook=store_top_u(out))
displacements[key] = nm.array(out, dtype=nm.float64)

return displacements

helps = {
'no_plot' : 'do not show plot window',
}

def main():
from sfepy.base.base import output
from sfepy.base.conf import ProblemConf, get_standard_keywords
from sfepy.discrete import Problem
from sfepy.base.plotutils import plt

parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-n', '--no-plot',
action="store_true", dest='no_plot',
default=False, help=helps['no_plot'])
options = parser.parse_args()

required, other = get_standard_keywords()

# Use this file as the input file.
conf = ProblemConf.from_file(__file__, required, other)

# Create problem instance, but do not set equations.

problem = Problem.from_conf(conf, init_equations=False)

# Solve the problem. Output is ignored, results stored by using the

# step_hook.
u_t = solve_branch(problem, linear_tension)
u_c = solve_branch(problem, linear_compression)

# Get pressure load by calling linear_*() for each time step.

ts = problem.get_timestepper()
load_t = nm.array([linear_tension(ts, nm.array([[0.0]]), 'qp')['val']
for aux in ts.iter_from(0)],
dtype=nm.float64).squeeze()
load_c = nm.array([linear_compression(ts, nm.array([[0.0]]), 'qp')['val']
for aux in ts.iter_from(0)],
dtype=nm.float64).squeeze()

# Join the branches.

displacements = {}
for key in u_t.keys():
displacements[key] = nm.r_[u_c[key][::-1], u_t[key]]
load = nm.r_[load_c[::-1], load_t]

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if plt is None:
output('matplotlib cannot be imported, printing raw data!')
output(displacements)
output(load)
else:
legend = []
for key, val in six.iteritems(displacements):
plt.plot(load, val)
legend.append(key)

plt.legend(legend, loc = 2)
plt.xlabel('tension [kPa]')
plt.ylabel('displacement [mm]')
plt.grid(True)

plt.gcf().savefig('pressure_displacement.png')

if not options.no_plot:
plt.show()

if __name__ == '__main__':
main()

large_deformation/gen_yeoh_tl_up_interactive.py

Description
This example shows the use of the dw_tl_he_genyeoh hyperelastic term, whose contribution to the deformation energy
density per unit reference volume is given by
(︀ )︀𝑝
𝑊 = 𝐾 𝐼1 − 3

where 𝐼 1 is the first main invariant of the deviatoric part of the right Cauchy-Green deformation tensor 𝐶 and K and p
are its parameters.
This term may be used to implement the generalized Yeoh hyperelastic material model [1] by adding three such terms:
(︀ )︀𝑚 (︀ )︀𝑝 (︀ )︀𝑞
𝑊 = 𝐾1 𝐼 1 − 3 + 𝐾2 𝐼 1 − 3 + 𝐾3 𝐼 1 − 3

where the coefficients 𝐾1 , 𝐾2 , 𝐾3 and exponents 𝑚, 𝑝, 𝑞 are material parameters. Only a single term is used in this
example for the sake of simplicity.
Components of the second Piola-Kirchhoff stress are in the case of an incompressible material

𝜕𝑊 −1 −𝑇
𝑆𝑖𝑗 = 2 − 𝑝 𝐹𝑖𝑘 𝐹𝑘𝑗 ,
𝜕𝐶𝑖𝑗

where 𝑝 is the hydrostatic pressure.

The large deformation is described using the total Lagrangian formulation in this example. The incompressibility is
treated by mixed displacement-pressure formulation. The weak formulation is: Find the displacement field 𝑢 and

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pressure field 𝑝 such that:

∫︁
𝑆 eff (𝑢, 𝑝) : 𝐸(𝑣) d𝑉 = 0 , ∀𝑣 ,
Ω(0)
∫︁
𝑞 (𝐽(𝑢) − 1) d𝑉 = 0 , ∀𝑞 .
Ω(0)

The following formula holds for the axial true (Cauchy) stress in the case of uniaxial stress:
(︂ )︂𝑚−1 (︂ )︂
2 2 1
𝜎(𝜆) = 𝑚 𝐾1 𝜆2 + −3 𝜆− 2 ,
3 𝜆 𝜆

where 𝜆 = 𝑙/𝑙0 is the prescribed stretch (𝑙0 and 𝑙 being the original and deformed specimen length respectively).
The boundary conditions are set so that a state of uniaxial stress is achieved, i.e. appropriate components of displace-
ment are fixed on the “Left”, “Bottom”, and “Near” faces and a monotonously increasing displacement is prescribed
on the “Right” face. This prescribed displacement is then used to calculate 𝜆 and to convert the second Piola-Kirchhoff
stress to the true (Cauchy) stress.

Note on material parameters

The three-term generalized Yeoh model is meant to be used for modelling of filled rubbers. The following choice of
parameters is suggested [1] based on experimental data and stability considerations:
𝐾1 > 0,
𝐾2 < 0,
𝐾3 > 0,
0.7 < 𝑚 < 1,
𝑚 < 𝑝 < 𝑞.

Usage Examples

Default options:

$ python examples/large_deformation/gen_yeoh_tl_up_interactive.py

To show a comparison of stress against the analytic formula:

$ python examples/large_deformation/gen_yeoh_tl_up_interactive.py -p

Using different mesh fineness:

$ python examples/large_deformation/gen_yeoh_tl_up_interactive.py \
--shape "5, 5, 5"

Different dimensions of the computational domain:

$ python examples/large_deformation/gen_yeoh_tl_up_interactive.py \
--dims "2, 1, 3"

Different length of time interval and/or number of time steps:

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$ python examples/large_deformation/gen_yeoh_tl_up_interactive.py \
-t 0,15,21

Use higher approximation order (the -t option to decrease the time step is required for convergence here):

$ python examples/large_deformation/gen_yeoh_tl_up_interactive.py \
--order 2 -t 0,2,21

Change material parameters:

$ python examples/large_deformation/gen_yeoh_tl_up_interactive.py -m 2,1

View the results using resview.py

Show pressure on deformed mesh (use PgDn/PgUp to jump forward/back):

$ python resview.py --fields=p:f1:wu:p1 domain.??.vtk

Show the axial component of stress (second Piola-Kirchhoff):

$ python resview.py --fields=stress:c0 domain.??.vtk

[1] Travis W. Hohenberger, Richard J. Windslow, Nicola M. Pugno, James J. C. Busfield. Aconstitutive Model For
Both Lowand High Strain Nonlinearities In Highly Filled Elastomers And Implementation With User-Defined Material
Subroutines In Abaqus. Rubber Chemistry And Technology, Vol. 92, No. 4, Pp. 653-686 (2019)
source code

#!/usr/bin/env python
r"""
This example shows the use of the `dw_tl_he_genyeoh` hyperelastic term, whose
contribution to the deformation energy density per unit reference volume is
given by

.. math::
W = K \, \left( \overline I_1 - 3 \right)^{p}

where :math:`\overline I_1` is the first main invariant of the deviatoric part
of the right Cauchy-Green deformation tensor :math:`\ull{C}` and `K` and `p`
are its parameters.

This term may be used to implement the generalized Yeoh hyperelastic material
model [1] by adding three such terms:

.. math::
W =
K_1 \, \left( \overline I_1 - 3 \right)^{m}
+K_2 \, \left( \overline I_1 - 3 \right)^{p}
+K_3 \, \left( \overline I_1 - 3 \right)^{q}

where the coefficients :math:`K_1, K_2, K_3` and exponents :math:`m, p, q` are
material parameters. Only a single term is used in this example for the sake of
simplicity.
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Components of the second Piola-Kirchhoff stress are in the case of an

incompressible material

.. math::
S_{ij} = 2 \, \pdiff{W}{C_{ij}} - p \, F^{-1}_{ik} \, F^{-T}_{kj} \;,

where :math:`p` is the hydrostatic pressure.

The large deformation is described using the total Lagrangian formulation in

this example. The incompressibility is treated by mixed displacement-pressure
formulation. The weak formulation is:
Find the displacement field :math:`\ul{u}` and pressure field :math:`p`
such that:

.. math::
\intl{\Omega\suz}{} \ull{S}\eff(\ul{u}, p) : \ull{E}(\ul{v})
\difd{V} = 0
\;, \quad \forall \ul{v} \;,

\intl{\Omega\suz}{} q\, (J(\ul{u})-1) \difd{V} = 0

\;, \quad \forall q \;.

The following formula holds for the axial true (Cauchy) stress in the case of
uniaxial stress:

.. math::
\sigma(\lambda) =
\frac{2}{3} \, m \, K_1 \,
\left( \lambda^2 + \frac{2}{\lambda} - 3 \right)^{m-1} \,
\left( \lambda - \frac{1}{\lambda^2} \right) \;,

where :math:`\lambda = l/l_0` is the prescribed stretch (:math:`l_0` and

:math:`l` being the original and deformed specimen length respectively).

The boundary conditions are set so that a state of uniaxial stress is achieved,
i.e. appropriate components of displacement are fixed on the "Left", "Bottom",
and "Near" faces and a monotonously increasing displacement is prescribed on
the "Right" face. This prescribed displacement is then used to calculate
:math:`\lambda` and to convert the second Piola-Kirchhoff stress to the true
(Cauchy) stress.

Note on material parameters

---------------------------

The three-term generalized Yeoh model is meant to be used for modelling of

filled rubbers. The following choice of parameters is suggested [1] based on
experimental data and stability considerations:

:math:`K_1 > 0`,

:math:`K_2 < 0`,

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:math:`K_3 > 0`,

:math:`0.7 < m < 1`,

:math:`m < p < q`.

Usage Examples
--------------

Default options::

$ python sfepy/examples/large_deformation/gen_yeoh_tl_up_interactive.py

To show a comparison of stress against the analytic formula::

$ python sfepy/examples/large_deformation/gen_yeoh_tl_up_interactive.py -p

Using different mesh fineness::

$ python sfepy/examples/large_deformation/gen_yeoh_tl_up_interactive.py \
--shape "5, 5, 5"

Different dimensions of the computational domain::

$ python sfepy/examples/large_deformation/gen_yeoh_tl_up_interactive.py \
--dims "2, 1, 3"

Different length of time interval and/or number of time steps::

$ python sfepy/examples/large_deformation/gen_yeoh_tl_up_interactive.py \
-t 0,15,21

Use higher approximation order (the ``-t`` option to decrease the time step is
required for convergence here)::

$ python sfepy/examples/large_deformation/gen_yeoh_tl_up_interactive.py \
--order 2 -t 0,2,21

Change material parameters::

$ python sfepy/examples/large_deformation/gen_yeoh_tl_up_interactive.py -m 2,1

View the results using ``resview.py``

-------------------------------------

Show pressure on deformed mesh (use PgDn/PgUp to jump forward/back)::

$ python resview.py --fields=p:f1:wu:p1 domain.??.vtk

Show the axial component of stress (second Piola-Kirchhoff)::

(continues on next page)

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(continued from previous page)

$ python resview.py --fields=stress:c0 domain.??.vtk

[1] Travis W. Hohenberger, Richard J. Windslow, Nicola M. Pugno, James J. C.

Busfield. Aconstitutive Model For Both Lowand High Strain Nonlinearities In
Highly Filled Elastomers And Implementation With User-Defined Material
Subroutines In Abaqus. Rubber Chemistry And Technology, Vol. 92, No. 4, Pp.
653-686 (2019)
"""
from __future__ import print_function, absolute_import
import argparse
import sys

SFEPY_DIR = '.'
sys.path.append(SFEPY_DIR)

import matplotlib.pyplot as plt

import numpy as np

from sfepy.base.base import IndexedStruct, Struct

from sfepy.discrete import (
FieldVariable, Material, Integral, Function, Equation, Equations, Problem)
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.discrete.fem import FEDomain, Field
from sfepy.homogenization.utils import define_box_regions
from sfepy.mesh.mesh_generators import gen_block_mesh
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.solvers.ts_solvers import SimpleTimeSteppingSolver
from sfepy.terms import Term

DIMENSION = 3

def get_displacement(ts, coors, bc=None, problem=None):

"""
Define the time-dependent displacement.
"""
out = 1. * ts.time * coors[:, 0]
return out

def _get_analytic_stress(stretches, coef, exp):

out = np.array([
2 * coef * exp * (stretch**2 + 2 / stretch - 3)**(exp - 1)
* (stretch - stretch**-2)
if (stretch**2 + 2 / stretch > 3) else 0.
for stretch in stretches])
return out

def plot_graphs(
material_parameters, global_stress, global_displacement,
undeformed_length):
"""
Plot a comparison of the nominal stress computed by the FEM and using the
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analytic formula.

Parameters
----------
material_parameters : list or tuple of float
The K_1 coefficient and exponent m.
global_displacement
The total displacement for each time step, from the FEM.
global_stress
The true (Cauchy) stress for each time step, from the FEM.
undeformed_length : float
The length of the undeformed specimen.
"""
coef, exp = material_parameters

stretch = 1 + np.array(global_displacement) / undeformed_length

# axial stress values

stress_fem_2pk = np.array([sig for sig in global_stress])
stress_fem = stress_fem_2pk * stretch
stress_analytic = _get_analytic_stress(stretch, coef, exp)

fig, (ax_stress, ax_difference) = plt.subplots(nrows=2, sharex=True)

ax_stress.plot(stretch, stress_fem, '.-', label='FEM')

ax_stress.plot(stretch, stress_analytic, '--', label='analytic')

ax_difference.plot(stretch, stress_fem - stress_analytic, '.-')

ax_stress.legend(loc='best').set_draggable(True)
ax_stress.set_ylabel(r'nominal stress $\mathrm{[Pa]}$')
ax_stress.grid()

ax_difference.set_ylabel(r'difference in nominal stress $\mathrm{[Pa]}$')

ax_difference.set_xlabel(r'stretch $\mathrm{[-]}$')
ax_difference.grid()
plt.tight_layout()
plt.show()

def stress_strain(
out, problem, _state, order=1, global_stress=None,
global_displacement=None, **_):
"""
Compute the stress and the strain and add them to the output.

Parameters
----------
out : dict
Holds the results of the finite element computation.
problem : sfepy.discrete.Problem
order : int
The approximation order of the displacement field.
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global_displacement
Total displacement for each time step, current value will be appended.
global_stress
The true (Cauchy) stress for each time step, current value will be
appended.

Returns
-------
out : dict
"""
strain = problem.evaluate(
'dw_tl_he_genyeoh.%d.Omega(m1.par, v, u)' % (2*order),
mode='el_avg', term_mode='strain', copy_materials=False)

out['green_strain'] = Struct(
name='output_data', mode='cell', data=strain, dofs=None)

stress_1 = problem.evaluate(
'dw_tl_he_genyeoh.%d.Omega(m1.par, v, u)' % (2*order),
mode='el_avg', term_mode='stress', copy_materials=False)
stress_p = problem.evaluate(
'dw_tl_bulk_pressure.%d.Omega(v, u, p)' % (2*order),
mode='el_avg', term_mode='stress', copy_materials=False)
stress = stress_1 + stress_p

out['stress'] = Struct(
name='output_data', mode='cell', data=stress, dofs=None)

global_stress.append(stress[0, 0, 0, 0])
global_displacement.append(get_displacement(
problem.ts, np.array([[1., 0, 0]]))[0])

return out

def main(cli_args):
dims = parse_argument_list(cli_args.dims, float)
shape = parse_argument_list(cli_args.shape, int)
centre = parse_argument_list(cli_args.centre, float)
material_parameters = parse_argument_list(cli_args.material_parameters,
float)
order = cli_args.order

ts_vals = cli_args.ts.split(',')
ts = {
't0' : float(ts_vals[0]), 't1' : float(ts_vals[1]),
'n_step' : int(ts_vals[2])}

do_plot = cli_args.plot

### Mesh and regions ###

mesh = gen_block_mesh(
dims, shape, centre, name='block', verbose=False)
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(continued from previous page)

domain = FEDomain('domain', mesh)

omega = domain.create_region('Omega', 'all')

lbn, rtf = domain.get_mesh_bounding_box()

box_regions = define_box_regions(3, lbn, rtf)
regions = dict([
[r, domain.create_region(r, box_regions[r][0], box_regions[r][1])]
for r in box_regions])

### Fields ###

scalar_field = Field.from_args(
'fu', np.float64, 'scalar', omega, approx_order=order-1)
vector_field = Field.from_args(
'fv', np.float64, 'vector', omega, approx_order=order)

u = FieldVariable('u', 'unknown', vector_field, history=1)

v = FieldVariable('v', 'test', vector_field, primary_var_name='u')
p = FieldVariable('p', 'unknown', scalar_field, history=1)
q = FieldVariable('q', 'test', scalar_field, primary_var_name='p')

### Material ###

coefficient, exponent = material_parameters
m_1 = Material(
'm1', par=[coefficient, exponent],
)

### Boundary conditions ###

x_sym = EssentialBC('x_sym', regions['Left'], {'u.0' : 0.0})
y_sym = EssentialBC('y_sym', regions['Near'], {'u.1' : 0.0})
z_sym = EssentialBC('z_sym', regions['Bottom'], {'u.2' : 0.0})
disp_fun = Function('disp_fun', get_displacement)
displacement = EssentialBC(
'displacement', regions['Right'], {'u.0' : disp_fun})
ebcs = Conditions([x_sym, y_sym, z_sym, displacement])

### Terms and equations ###

integral = Integral('i', order=2*order+1)

term_1 = Term.new(
'dw_tl_he_genyeoh(m1.par, v, u)',
integral, omega, m1=m_1, v=v, u=u)
term_pressure = Term.new(
'dw_tl_bulk_pressure(v, u, p)',
integral, omega, v=v, u=u, p=p)

term_volume_change = Term.new(
'dw_tl_volume(q, u)',
integral, omega, q=q, u=u, term_mode='volume')
term_volume = Term.new(
'dw_integrate(q)',
integral, omega, q=q)
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eq_balance = Equation('balance', term_1 + term_pressure)

eq_volume = Equation('volume', term_volume_change - term_volume)
equations = Equations([eq_balance, eq_volume])

### Solvers ###

ls = ScipyDirect({})
nls_status = IndexedStruct()
nls = Newton(
{'i_max' : 20},
lin_solver=ls, status=nls_status
)

### Problem ###

pb = Problem('hyper', equations=equations)
pb.set_bcs(ebcs=ebcs)
pb.set_ics(ics=Conditions([]))
tss = SimpleTimeSteppingSolver(ts, nls=nls, context=pb)
pb.set_solver(tss)

### Solution ###

axial_stress = []
axial_displacement = []
def stress_strain_fun(*args, **kwargs):
return stress_strain(
*args, order=order, global_stress=axial_stress,
global_displacement=axial_displacement, **kwargs)

pb.solve(save_results=True, post_process_hook=stress_strain_fun)

if do_plot:
plot_graphs(
material_parameters, axial_stress, axial_displacement,
undeformed_length=dims[0])

def parse_argument_list(cli_arg, type_fun=None, value_separator=','):

"""
Split the command-line argument into a list of items of given type.

Parameters
----------
cli_arg : str
type_fun : function
A function to be called on each substring of `cli_arg`; default: str.
value_separator : str
"""
if type_fun is None:
type_fun = str
out = [type_fun(value) for value in cli_arg.split(value_separator)]
return out

def parse_args():
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"""Parse command line arguments."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
'--order', type=int, default=1, help='The approximation order of the '
'displacement field [default: %(default)s]')
parser.add_argument(
'-m', '--material-parameters', default='0.5, 0.9',
help='Material parameters - coefficient and exponent - of a single '
'term of the generalized Yeoh hyperelastic model. '
'[default: %(default)s]')
parser.add_argument(
'--dims', default="1.0, 1.0, 1.0",
help='Dimensions of the block [default: %(default)s]')
parser.add_argument(
'--shape', default='2, 2, 2',
help='Shape (counts of nodes in x, y, z) of the block [default: '
'%(default)s]')
parser.add_argument(
'--centre', default='0.5, 0.5, 0.5',
help='Centre of the block [default: %(default)s]')
parser.add_argument(
'-p', '--plot', action='store_true', default=False,
help='Whether to plot a comparison with analytical formula.')
parser.add_argument(
'-t', '--ts',
type=str, default='0.0,2.0,11',
help='Start time, end time, and number of time steps [default: '
'"%(default)s"]')
return parser.parse_args()

if __name__ == '__main__':
args = parse_args()
main(args)

large_deformation/hyperelastic.py

Description
Nearly incompressible Mooney-Rivlin hyperelastic material model.
Large deformation is described using the total Lagrangian formulation. Models of this kind can be used to model e.g.
rubber or some biological materials.
Find 𝑢 such that:
∫︁ (︁ )︁
𝑆 eff (𝑢) + 𝐾(𝐽 − 1) 𝐽𝐶 −1 : 𝛿𝐸(𝑣) d𝑉 = 0 , ∀𝑣 ,
Ω(0)

where

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𝐹 deformation gradient 𝐹𝑖𝑗 = 𝜕𝑋 𝜕𝑥𝑖

𝑗
𝐽 det(𝐹 )
𝐶 right Cauchy-Green deformation tensor 𝐶 = 𝐹 𝑇 𝐹
𝜕𝑢
𝐸(𝑢) Green strain tensor 𝐸𝑖𝑗 = 21 ( 𝜕𝑋
𝜕𝑢𝑖
𝑗
+ 𝜕𝑋𝑗𝑖 + 𝜕𝑢 𝑚 𝜕𝑢𝑚
𝜕𝑋𝑖 𝜕𝑋𝑗 )
𝑆 eff (𝑢) effective second Piola-Kirchhoff stress tensor

The effective stress 𝑆 eff (𝑢) is given by:

2 1 4 2
𝑆 eff (𝑢) = 𝜇𝐽 − 3 (𝐼 − tr(𝐶)𝐶 −1 ) + 𝜅𝐽 − 3 (tr(𝐶𝐼 − 𝐶 − ((tr 𝐶)2 − tr (𝐶 2 ))𝐶 −1 ) .
3 6

source code

# -*- coding: utf-8 -*-

r"""
Nearly incompressible Mooney-Rivlin hyperelastic material model.

Large deformation is described using the total Lagrangian formulation.

Models of this kind can be used to model e.g. rubber or some biological
materials.

Find :math:`\ul{u}` such that:

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.. math::
\intl{\Omega\suz}{} \left( \ull{S}\eff(\ul{u})
+ K(J-1)\; J \ull{C}^{-1} \right) : \delta \ull{E}(\ul{v}) \difd{V}
= 0
\;, \quad \forall \ul{v} \;,

where

.. list-table::
:widths: 20 80

* - :math:`\ull{F}`
- deformation gradient :math:`F_{ij} = \pdiff{x_i}{X_j}`
* - :math:`J`
- :math:`\det(F)`
* - :math:`\ull{C}`
- right Cauchy-Green deformation tensor :math:`C = F^T F`
* - :math:`\ull{E}(\ul{u})`
- Green strain tensor :math:`E_{ij} = \frac{1}{2}(\pdiff{u_i}{X_j} +
\pdiff{u_j}{X_i} + \pdiff{u_m}{X_i}\pdiff{u_m}{X_j})`
* - :math:`\ull{S}\eff(\ul{u})`
- effective second Piola-Kirchhoff stress tensor

The effective stress :math:`\ull{S}\eff(\ul{u})` is given by:

.. math::
\ull{S}\eff(\ul{u}) = \mu J^{-\frac{2}{3}}(\ull{I}
- \frac{1}{3}\tr(\ull{C}) \ull{C}^{-1})
+ \kappa J^{-\frac{4}{3}} (\tr(\ull{C}\ull{I} - \ull{C}
- \frac{2}{6}((\tr{\ull{C}})^2 - \tr{(\ull{C}^2)})\ull{C}^{-1})
\;.
"""
from __future__ import print_function
from __future__ import absolute_import
import numpy as nm

from sfepy import data_dir

filename_mesh = data_dir + '/meshes/3d/cylinder.mesh'

options = {
'nls' : 'newton',
'ls' : 'ls',
'ts' : 'ts',
'save_times' : 'all',
'post_process_hook' : 'stress_strain',
}

field_1 = {
'name' : 'displacement',
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'dtype' : nm.float64,
'shape' : 3,
'region' : 'Omega',
'approx_order' : 1,
}

material_1 = {
'name' : 'solid',
'values' : {
'K' : 1e3, # bulk modulus
'mu' : 20e0, # shear modulus of neoHookean term
'kappa' : 10e0, # shear modulus of Mooney-Rivlin term
}
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
}

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < 0.001)', 'facet'),
'Right' : ('vertices in (x > 0.099)', 'facet'),
}

##
# Dirichlet BC + related functions.
ebcs = {
'l' : ('Left', {'u.all' : 0.0}),
'r' : ('Right', {'u.0' : 0.0, 'u.[1,2]' : 'rotate_yz'}),
}

centre = nm.array( [0, 0], dtype = nm.float64 )

def rotate_yz(ts, coor, **kwargs):

from sfepy.linalg import rotation_matrix2d

vec = coor[:,1:3] - centre

angle = 10.0 * ts.step

print('angle:', angle)

mtx = rotation_matrix2d( angle )

vec_rotated = nm.dot( vec, mtx )

displacement = vec_rotated - vec

return displacement

functions = {
'rotate_yz' : (rotate_yz,),
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}

def stress_strain( out, problem, state, extend = False ):

from sfepy.base.base import Struct, debug

ev = problem.evaluate
strain = ev('dw_tl_he_neohook.i.Omega( solid.mu, v, u )',
mode='el_avg', term_mode='strain')
out['green_strain'] = Struct(name='output_data',
mode='cell', data=strain, dofs=None)

stress = ev('dw_tl_he_neohook.i.Omega( solid.mu, v, u )',

mode='el_avg', term_mode='stress')
out['neohook_stress'] = Struct(name='output_data',
mode='cell', data=stress, dofs=None)

stress = ev('dw_tl_he_mooney_rivlin.i.Omega( solid.kappa, v, u )',

mode='el_avg', term_mode='stress')
out['mooney_rivlin_stress'] = Struct(name='output_data',
mode='cell', data=stress, dofs=None)

stress = ev('dw_tl_bulk_penalty.i.Omega( solid.K, v, u )',

mode='el_avg', term_mode= 'stress')
out['bulk_stress'] = Struct(name='output_data',
mode='cell', data=stress, dofs=None)

return out

##
# Balance of forces.
integral_1 = {
'name' : 'i',
'order' : 1,
}
equations = {
'balance' : """dw_tl_he_neohook.i.Omega( solid.mu, v, u )
+ dw_tl_he_mooney_rivlin.i.Omega( solid.kappa, v, u )
+ dw_tl_bulk_penalty.i.Omega( solid.K, v, u )
= 0""",
}

##
# Solvers etc.
solver_0 = {
'name' : 'ls',
'kind' : 'ls.scipy_direct',
}

solver_1 = {
'name' : 'newton',
'kind' : 'nls.newton',

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'i_max' : 5,
'eps_a' : 1e-10,
'eps_r' : 1.0,
'macheps' : 1e-16,
'lin_red' : 1e-2, # Linear system error < (eps_a * lin_red).
'ls_red' : 0.1,
'ls_red_warp': 0.001,
'ls_on' : 1.1,
'ls_min' : 1e-5,
'check' : 0,
'delta' : 1e-6,
}

solver_2 = {
'name' : 'ts',
'kind' : 'ts.simple',

't0' : 0,
't1' : 1,
'dt' : None,
'n_step' : 11, # has precedence over dt!
'verbose' : 1,
}

large_deformation/hyperelastic_tl_up_interactive.py

Description
Incompressible Mooney-Rivlin hyperelastic material model. In this model, the deformation energy density per unit
reference volume is given by
(︀ )︀ (︀ )︀
𝑊 = 𝐶(10) 𝐼 1 − 3 + 𝐶(01) 𝐼 2 − 3 ,

where 𝐼 1 and 𝐼 2 are the first and second main invariants of the deviatoric part of the right Cauchy-Green deformation
tensor 𝐶. The coefficients 𝐶(10) and 𝐶(01) are material parameters.
Components of the second Piola-Kirchhoff stress are in the case of an incompressible material

𝜕𝑊 −1 −𝑇
𝑆𝑖𝑗 = 2 − 𝑝 𝐹𝑖𝑘 𝐹𝑘𝑗 ,
𝜕𝐶𝑖𝑗

where 𝑝 is the hydrostatic pressure.

The large deformation is described using the total Lagrangian formulation in this example. The incompressibility is
treated by mixed displacement-pressure formulation. The weak formulation is: Find the displacement field 𝑢 and
pressure field 𝑝 such that:
∫︁
𝑆 eff (𝑢, 𝑝) : 𝐸(𝑣) d𝑉 = 0 , ∀𝑣 ,
Ω(0)
∫︁
𝑞 (𝐽(𝑢) − 1) d𝑉 = 0 , ∀𝑞 .
Ω(0)

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The following formula holds for the axial true (Cauchy) stress in the case of uniaxial stress:
(︂ )︂ (︂ )︂
𝐶(01) 2 1
𝜎(𝜆) = 2 𝐶(10) + 𝜆 − ,
𝜆 𝜆

where 𝜆 = 𝑙/𝑙0 is the prescribed stretch (𝑙0 and 𝑙 being the original and deformed specimen length respectively).
The boundary conditions are set so that a state of uniaxial stress is achieved, i.e. appropriate components of displace-
ment are fixed on the “Left”, “Bottom”, and “Near” faces and a monotonously increasing displacement is prescribed
on the “Right” face. This prescribed displacement is then used to calculate 𝜆 and to convert the second Piola-Kirchhoff
stress to the true (Cauchy) stress.

Note on material parameters

The relationship between material parameters used in the SfePy hyperelastic terms (NeoHookeanTLTerm,
MooneyRivlinTLTerm) and the ones used in this example is:

𝜇 = 2 𝐶(10) ,
𝜅 = 2 𝐶(01) .

Usage Examples

Default options:

$ python examples/large_deformation/hyperelastic_tl_up_interactive.py

To show a comparison of stress against the analytic formula:

$ python examples/large_deformation/hyperelastic_tl_up_interactive.py -p

Using different mesh fineness:

$ python examples/large_deformation/hyperelastic_tl_up_interactive.py \
--shape "5, 5, 5"

Different dimensions of the computational domain:

$ python examples/large_deformation/hyperelastic_tl_up_interactive.py \
--dims "2, 1, 3"

Different length of time interval and/or number of time steps:

$ python examples/large_deformation/hyperelastic_tl_up_interactive.py \
-t 0,15,21

Use higher approximation order (the -t option to decrease the time step is required for convergence here):

$ python examples/large_deformation/hyperelastic_tl_up_interactive.py \
--order 2 -t 0,2,21

Change material parameters:

$ python examples/large_deformation/hyperelastic_tl_up_interactive.py -m 2,1

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source code

#!/usr/bin/env python
r"""
Incompressible Mooney-Rivlin hyperelastic material model.
In this model, the deformation energy density per unit reference volume is
given by

.. math::
W = C_{(10)} \, \left( \overline I_1 - 3 \right)
+ C_{(01)} \, \left( \overline I_2 - 3 \right) \;,

where :math:`\overline I_1` and :math:`\overline I_2` are the first

and second main invariants of the deviatoric part of the right
Cauchy-Green deformation tensor :math:`\ull{C}`. The coefficients
:math:`C_{(10)}` and :math:`C_{(01)}` are material parameters.

Components of the second Piola-Kirchhoff stress are in the case of an

incompressible material

.. math::
S_{ij} = 2 \, \pdiff{W}{C_{ij}} - p \, F^{-1}_{ik} \, F^{-T}_{kj} \;,

where :math:`p` is the hydrostatic pressure.

The large deformation is described using the total Lagrangian formulation in

this example. The incompressibility is treated by mixed displacement-pressure
formulation. The weak formulation is:
Find the displacement field :math:`\ul{u}` and pressure field :math:`p`
such that:

.. math::
\intl{\Omega\suz}{} \ull{S}\eff(\ul{u}, p) : \ull{E}(\ul{v})
\difd{V} = 0
\;, \quad \forall \ul{v} \;,

\intl{\Omega\suz}{} q\, (J(\ul{u})-1) \difd{V} = 0

\;, \quad \forall q \;.

The following formula holds for the axial true (Cauchy) stress in the case of
uniaxial stress:

.. math::
\sigma(\lambda) =
2\, \left( C_{(10)} + \frac{C_{(01)}}{\lambda} \right) \,
\left( \lambda^2 - \frac{1}{\lambda} \right) \;,

where :math:`\lambda = l/l_0` is the prescribed stretch (:math:`l_0` and

:math:`l` being the original and deformed specimen length respectively).

The boundary conditions are set so that a state of uniaxial stress is achieved,
i.e. appropriate components of displacement are fixed on the "Left", "Bottom",
and "Near" faces and a monotonously increasing displacement is prescribed on
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the "Right" face. This prescribed displacement is then used to calculate
:math:`\lambda` and to convert the second Piola-Kirchhoff stress to the true
(Cauchy) stress.

Note on material parameters

---------------------------

The relationship between material parameters used in the *SfePy* hyperelastic

terms (:class:`NeoHookeanTLTerm
<sfepy.terms.terms_hyperelastic_tl.NeoHookeanTLTerm>`,
:class:`MooneyRivlinTLTerm
<sfepy.terms.terms_hyperelastic_tl.MooneyRivlinTLTerm>`)
and the ones used in this example is:

.. math::
\mu = 2\, C_{(10)} \;,

\kappa = 2\, C_{(01)} \;.

Usage Examples
--------------

Default options::

$ python sfepy/examples/large_deformation/hyperelastic_tl_up_interactive.py

To show a comparison of stress against the analytic formula::

$ python sfepy/examples/large_deformation/hyperelastic_tl_up_interactive.py -p

Using different mesh fineness::

$ python sfepy/examples/large_deformation/hyperelastic_tl_up_interactive.py \
--shape "5, 5, 5"

Different dimensions of the computational domain::

$ python sfepy/examples/large_deformation/hyperelastic_tl_up_interactive.py \
--dims "2, 1, 3"

Different length of time interval and/or number of time steps::

$ python sfepy/examples/large_deformation/hyperelastic_tl_up_interactive.py \
-t 0,15,21

Use higher approximation order (the ``-t`` option to decrease the time step is
required for convergence here)::

$ python sfepy/examples/large_deformation/hyperelastic_tl_up_interactive.py \
--order 2 -t 0,2,21

Change material parameters::

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$ python sfepy/examples/large_deformation/hyperelastic_tl_up_interactive.py -m 2,1

"""
from __future__ import print_function, absolute_import
import argparse
import sys

SFEPY_DIR = '.'
sys.path.append(SFEPY_DIR)

import matplotlib.pyplot as plt

import numpy as np

from sfepy.base.base import IndexedStruct, Struct

from sfepy.discrete import (
FieldVariable, Material, Integral, Function, Equation, Equations, Problem)
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.discrete.fem import FEDomain, Field
from sfepy.homogenization.utils import define_box_regions
from sfepy.mesh.mesh_generators import gen_block_mesh
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.solvers.ts_solvers import SimpleTimeSteppingSolver
from sfepy.terms import Term

DIMENSION = 3

def get_displacement(ts, coors, bc=None, problem=None):

"""
Define the time-dependent displacement.
"""
out = 1. * ts.time * coors[:, 0]
return out

def plot_graphs(
material_parameters, global_stress, global_displacement,
undeformed_length):
"""
Plot a comparison of the true stress computed by the FEM and using the
analytic formula.

Parameters
----------
material_parameters : list or tuple of float
The C10 and C01 coefficients.
global_displacement
The total displacement for each time step, from the FEM.
global_stress
The true (Cauchy) stress for each time step, from the FEM.
undeformed_length : float
The length of the undeformed specimen.
"""
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c10, c01 = material_parameters

stretch = 1 + np.array(global_displacement) / undeformed_length

# axial stress values

stress_fem_2pk = np.array([sig for sig in global_stress])
stress_fem = stress_fem_2pk * stretch**2
stress_analytic = 2 * (c10 + c01/stretch) * (stretch**2 - 1./stretch)

fig = plt.figure()
ax_stress = fig.add_subplot(211)
ax_difference = fig.add_subplot(212)

ax_stress.plot(stretch, stress_fem, '.-', label='FEM')

ax_stress.plot(stretch, stress_analytic, '--', label='analytic')

ax_difference.plot(stretch, stress_fem - stress_analytic, '.-')

ax_stress.legend(loc='best').draggable()
ax_stress.set_ylabel(r'true stress $\mathrm{[Pa]}$')
ax_stress.grid()

ax_difference.set_ylabel(r'difference in true stress $\mathrm{[Pa]}$')

ax_difference.set_xlabel(r'stretch $\mathrm{[-]}$')
ax_difference.grid()
plt.show()

def stress_strain(
out, problem, _state, order=1, global_stress=None,
global_displacement=None, **_):
"""
Compute the stress and the strain and add them to the output.

Parameters
----------
out : dict
Holds the results of the finite element computation.
problem : sfepy.discrete.Problem
order : int
The approximation order of the displacement field.
global_displacement
Total displacement for each time step, current value will be appended.
global_stress
The true (Cauchy) stress for each time step, current value will be
appended.

Returns
-------
out : dict
"""
strain = problem.evaluate(
'dw_tl_he_neohook.%d.Omega(m.mu, v, u)' % (2*order),
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mode='el_avg', term_mode='strain', copy_materials=False)

out['green_strain'] = Struct(
name='output_data', mode='cell', data=strain, dofs=None)

stress_10 = problem.evaluate(
'dw_tl_he_neohook.%d.Omega(m.mu, v, u)' % (2*order),
mode='el_avg', term_mode='stress', copy_materials=False)
stress_01 = problem.evaluate(
'dw_tl_he_mooney_rivlin.%d.Omega(m.kappa, v, u)' % (2*order),
mode='el_avg', term_mode='stress', copy_materials=False)
stress_p = problem.evaluate(
'dw_tl_bulk_pressure.%d.Omega(v, u, p)' % (2*order),
mode='el_avg', term_mode='stress', copy_materials=False)
stress = stress_10 + stress_01 + stress_p

out['stress'] = Struct(
name='output_data', mode='cell', data=stress, dofs=None)

global_stress.append(stress[0, 0, 0, 0])
global_displacement.append(np.max(out['u'].data[:, 0]))

return out

def main(cli_args):
dims = parse_argument_list(cli_args.dims, float)
shape = parse_argument_list(cli_args.shape, int)
centre = parse_argument_list(cli_args.centre, float)
material_parameters = parse_argument_list(cli_args.material_parameters,
float)
order = cli_args.order

ts_vals = cli_args.ts.split(',')
ts = {
't0' : float(ts_vals[0]), 't1' : float(ts_vals[1]),
'n_step' : int(ts_vals[2])}

do_plot = cli_args.plot

### Mesh and regions ###

mesh = gen_block_mesh(
dims, shape, centre, name='block', verbose=False)
domain = FEDomain('domain', mesh)

omega = domain.create_region('Omega', 'all')

lbn, rtf = domain.get_mesh_bounding_box()

box_regions = define_box_regions(3, lbn, rtf)
regions = dict([
[r, domain.create_region(r, box_regions[r][0], box_regions[r][1])]
for r in box_regions])

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### Fields ###
scalar_field = Field.from_args(
'fu', np.float64, 'scalar', omega, approx_order=order-1)
vector_field = Field.from_args(
'fv', np.float64, 'vector', omega, approx_order=order)

u = FieldVariable('u', 'unknown', vector_field, history=1)

v = FieldVariable('v', 'test', vector_field, primary_var_name='u')
p = FieldVariable('p', 'unknown', scalar_field, history=1)
q = FieldVariable('q', 'test', scalar_field, primary_var_name='p')

### Material ###

c10, c01 = material_parameters
m = Material(
'm', mu=2*c10, kappa=2*c01,
)

### Boundary conditions ###

x_sym = EssentialBC('x_sym', regions['Left'], {'u.0' : 0.0})
y_sym = EssentialBC('y_sym', regions['Near'], {'u.1' : 0.0})
z_sym = EssentialBC('z_sym', regions['Bottom'], {'u.2' : 0.0})
disp_fun = Function('disp_fun', get_displacement)
displacement = EssentialBC(
'displacement', regions['Right'], {'u.0' : disp_fun})
ebcs = Conditions([x_sym, y_sym, z_sym, displacement])

### Terms and equations ###

integral = Integral('i', order=2*order)

term_neohook = Term.new(
'dw_tl_he_neohook(m.mu, v, u)',
integral, omega, m=m, v=v, u=u)
term_mooney = Term.new(
'dw_tl_he_mooney_rivlin(m.kappa, v, u)',
integral, omega, m=m, v=v, u=u)
term_pressure = Term.new(
'dw_tl_bulk_pressure(v, u, p)',
integral, omega, v=v, u=u, p=p)

term_volume_change = Term.new(
'dw_tl_volume(q, u)',
integral, omega, q=q, u=u, term_mode='volume')
term_volume = Term.new(
'dw_integrate(q)',
integral, omega, q=q)

eq_balance = Equation('balance', term_neohook+term_mooney+term_pressure)

eq_volume = Equation('volume', term_volume_change-term_volume)
equations = Equations([eq_balance, eq_volume])

### Solvers ###

ls = ScipyDirect({})
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nls_status = IndexedStruct()
nls = Newton(
{'i_max' : 5},
lin_solver=ls, status=nls_status
)

### Problem ###

pb = Problem('hyper', equations=equations)
pb.set_bcs(ebcs=ebcs)
pb.set_ics(ics=Conditions([]))
tss = SimpleTimeSteppingSolver(ts, nls=nls, context=pb)
pb.set_solver(tss)

### Solution ###

axial_stress = []
axial_displacement = []
def stress_strain_fun(*args, **kwargs):
return stress_strain(
*args, order=order, global_stress=axial_stress,
global_displacement=axial_displacement, **kwargs)

pb.solve(save_results=True, post_process_hook=stress_strain_fun)

if do_plot:
plot_graphs(
material_parameters, axial_stress, axial_displacement,
undeformed_length=dims[0])

def parse_argument_list(cli_arg, type_fun=None, value_separator=','):

"""
Split the command-line argument into a list of items of given type.

Parameters
----------
cli_arg : str
type_fun : function
A function to be called on each substring of `cli_arg`; default: str.
value_separator : str
"""
if type_fun is None:
type_fun = str
out = [type_fun(value) for value in cli_arg.split(value_separator)]
return out

def parse_args():
"""Parse command line arguments."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
'--order', type=int, default=1, help='The approximation order of the '
'displacement field [default: %(default)s]')
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parser.add_argument(
'-m', '--material-parameters', default='1.0, 0.5',
help='Material parameters - C10, C01 - of the two-parametric '
'Mooney-Rivlin hyperelastic model. [default: %(default)s]')
parser.add_argument(
'--dims', default="1.0, 1.0, 1.0",
help='Dimensions of the block [default: %(default)s]')
parser.add_argument(
'--shape', default='4, 4, 4',
help='Shape (counts of nodes in x, y, z) of the block [default: '
'%(default)s]')
parser.add_argument(
'--centre', default='0.5, 0.5, 0.5',
help='Centre of the block [default: %(default)s]')
parser.add_argument(
'-p', '--plot', action='store_true', default=False,
help='Whether to plot a comparison with analytical formula.')
parser.add_argument(
'-t', '--ts',
type=str, default='0.0,10.0,11',
help='Start time, end time, and number of time steps [default: '
'"%(default)s"]')
return parser.parse_args()

if __name__ == '__main__':
args = parse_args()
main(args)

large_deformation/hyperelastic_ul.py

Description
Nearly incompressible Mooney-Rivlin hyperelastic material model.
Large deformation is described using the updated Lagrangian formulation. Models of this kind can be used to model
e.g. rubber or some biological materials.

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source code

# -*- coding: utf-8 -*-

r"""
Nearly incompressible Mooney-Rivlin hyperelastic material model.

Large deformation is described using the updated Lagrangian formulation.

Models of this kind can be used to model e.g. rubber or some biological
materials.
"""
from __future__ import print_function
from __future__ import absolute_import
import numpy as nm
from sfepy import data_dir

filename_mesh = data_dir + '/meshes/3d/cylinder.mesh'

options = {
'nls': 'newton',
'ls': 'ls',
'ts': 'ts',
'ulf': True,
'mesh_update_variables': ['u'],
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'output_dir': 'output',
'post_process_hook': 'stress_strain',
}

fields = {
'displacement': ('real', 3, 'Omega', 1),
}

materials = {
'solid': ({'K': 1e3, # bulk modulus
'mu': 20e0, # shear modulus of neoHookean term
'kappa': 10e0, # shear modulus of Mooney-Rivlin term
},),
}

variables = {
'u': ('unknown field', 'displacement', 0),
'v': ('test field', 'displacement', 'u'),
}

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < 0.001)', 'facet'),
'Right' : ('vertices in (x > 0.099)', 'facet'),
}

##
# Dirichlet BC + related functions.
ebcs = {
'l' : ('Left', {'u.all' : 0.0}),
'r' : ('Right', {'u.0' : 0.0, 'u.[1,2]' : 'rotate_yz'}),
}

centre = nm.array( [0, 0], dtype = nm.float64 )

def rotate_yz(ts, coor, **kwargs):

from sfepy.linalg import rotation_matrix2d

vec = coor[:,1:3] - centre

angle = 10.0 * ts.step

print('angle:', angle)

mtx = rotation_matrix2d( angle )

vec_rotated = nm.dot( vec, mtx )

displacement = vec_rotated - vec

return displacement

functions = {
'rotate_yz' : (rotate_yz,),
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}

def stress_strain( out, problem, state, extend = False ):

from sfepy.base.base import Struct

ev = problem.evaluate
strain = ev('dw_ul_he_neohook.3.Omega( solid.mu, v, u )',
mode='el_avg', term_mode='strain')
out['green_strain'] = Struct(name='output_data',
mode='cell', data=strain, dofs=None)

stress = ev('dw_ul_he_neohook.3.Omega( solid.mu, v, u )',

mode='el_avg', term_mode='stress')
out['neohook_stress'] = Struct(name='output_data',
mode='cell', data=stress, dofs=None)

stress = ev('dw_ul_he_mooney_rivlin.3.Omega( solid.kappa, v, u )',

mode='el_avg', term_mode='stress')
out['mooney_rivlin_stress'] = Struct(name='output_data',
mode='cell', data=stress, dofs=None)

stress = ev('dw_ul_bulk_penalty.3.Omega( solid.K, v, u )',

mode='el_avg', term_mode= 'stress')
out['bulk_stress'] = Struct(name='output_data',
mode='cell', data=stress, dofs=None)

return out

equations = {
'balance': """dw_ul_he_neohook.3.Omega( solid.mu, v, u )
+ dw_ul_he_mooney_rivlin.3.Omega(solid.kappa, v, u)
+ dw_ul_bulk_penalty.3.Omega( solid.K, v, u )
= 0""",
}

##
# Solvers etc.
solvers = {
'ls': ('ls.scipy_direct', {}),
'newton': ('nls.newton', {
'i_max': 25,
'eps_a': 1e-8,
'eps_r': 1.0,
'macheps': 1e-16,
'lin_red': 1e-2, # Linear system error < (eps_a * lin_red).
'ls_red': 0.1,
'ls_red_warp': 0.001,
'ls_on': 1.1,
'ls_min': 1e-5,
'check': 0,
'delta': 1e-6,
}),
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'ts': ('ts.simple', {
't0': 0,
't1': 1,
'dt': None,
'n_step': 11, # has precedence over dt!
'verbose' : 1,
}),
}

large_deformation/hyperelastic_ul_up.py

Description
Compressible Mooney-Rivlin hyperelastic material model.
Large deformation is described using the updated Lagrangian formulation. Incompressibility is treated by mixed
displacement-pressure formulation. Models of this kind can be used to model e.g. rubber or some biological ma-
terials.

source code

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# -*- coding: utf-8 -*-

r"""
Compressible Mooney-Rivlin hyperelastic material model.

Large deformation is described using the updated Lagrangian formulation.

Incompressibility is treated by mixed displacement-pressure formulation.
Models of this kind can be used to model e.g. rubber or some biological
materials.
"""
from __future__ import print_function
from __future__ import absolute_import
import numpy as nm
from sfepy import data_dir

filename_mesh = data_dir + '/meshes/3d/cylinder.mesh'

options = {
'nls': 'newton',
'ls': 'ls',
'ts': 'ts',
'ulf': True,
'mesh_update_variables': ['u'],
'output_dir': 'output',
'post_process_hook': 'stress_strain',
}

fields = {
'displacement': ('real', 'vector', 'Omega', 1),
'pressure': ('real', 'scalar', 'Omega', 0),
}

materials = {
'solid': ({'iK': 1.0 / 1e3, # bulk modulus
'mu': 20e0, # shear modulus of neoHookean term
'kappa': 10e0, # shear modulus of Mooney-Rivlin term
},),
}

variables = {
'u': ('unknown field', 'displacement', 0),
'v': ('test field', 'displacement', 'u'),
'p': ('unknown field', 'pressure', 1),
'q': ('test field', 'pressure', 'p'),
}

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < 0.001)', 'facet'),
'Right' : ('vertices in (x > 0.099)', 'facet'),
}

##
# Dirichlet BC + related functions.
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ebcs = {
'l' : ('Left', {'u.all' : 0.0}),
'r' : ('Right', {'u.0' : 0.0, 'u.[1,2]' : 'rotate_yz'}),
}

centre = nm.array( [0, 0], dtype = nm.float64 )

def rotate_yz(ts, coor, **kwargs):

from sfepy.linalg import rotation_matrix2d

vec = coor[:,1:3] - centre

angle = 10.0 * ts.step

print('angle:', angle)

mtx = rotation_matrix2d( angle )

vec_rotated = nm.dot( vec, mtx )

displacement = vec_rotated - vec

return displacement

functions = {
'rotate_yz' : (rotate_yz,),
}

def stress_strain( out, problem, state, extend = False ):

from sfepy.base.base import Struct

ev = problem.evaluate
strain = ev('dw_ul_he_neohook.3.Omega( solid.mu, v, u )',
mode='el_avg', term_mode='strain')
out['green_strain'] = Struct(name='output_data',
mode='cell', data=strain, dofs=None)

stress = ev('dw_ul_he_neohook.3.Omega( solid.mu, v, u )',

mode='el_avg', term_mode='stress')
out['neohook_stress'] = Struct(name='output_data',
mode='cell', data=stress, dofs=None)

stress = ev('dw_ul_he_mooney_rivlin.3.Omega( solid.kappa, v, u )',

mode='el_avg', term_mode='stress')
out['mooney_rivlin_stress'] = Struct(name='output_data',
mode='cell', data=stress, dofs=None)

stress = ev('dw_ul_bulk_pressure.3.Omega( v, u, p )',

mode='el_avg', term_mode= 'stress')
out['bulk_stress'] = Struct(name='output_data',
mode='cell', data=stress, dofs=None)

return out

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equations = {
'balance': """dw_ul_he_neohook.3.Omega( solid.mu, v, u )
+ dw_ul_he_mooney_rivlin.3.Omega(solid.kappa, v, u)
+ dw_ul_bulk_pressure.3.Omega( v, u, p ) = 0""",
'volume': """dw_ul_volume.3.Omega( q, u )
+ dw_ul_compressible.3.Omega( solid.iK, q, p, u ) = 0"""
}

##
# Solvers etc.
solvers = {
'ls': ('ls.scipy_direct', {}),
'newton': ('nls.newton', {
'i_max': 25,
'eps_a': 1e-8,
'eps_r': 1.0,
'macheps': 1e-16,
'lin_red': 1e-2, # Linear system error < (eps_a * lin_red).
'ls_red': 0.1,
'ls_red_warp': 0.001,
'ls_on': 1.1,
'ls_min': 1e-5,
'check': 0,
'delta': 1e-6,
}),
'ts': ('ts.simple', {
't0': 0,
't1': 1,
'dt': None,
'n_step': 11, # has precedence over dt!
'verbose' : 1,
}),
}

large_deformation/perfusion_tl.py

Description
Porous nearly incompressible hyperelastic material with fluid perfusion.
Large deformation is described using the total Lagrangian formulation. Models of this kind can be used in biomechanics
to model biological tissues, e.g. muscles.
Find 𝑢 such that:
(equilibrium equation with boundary tractions)
∫︁ (︁ )︁ ∫︁
𝑆 eff − 𝑝𝐽𝐶 −1 : 𝛿𝐸(𝑣) d𝑉 + 𝜈 · 𝐹 −1 · 𝜎 · 𝑣𝐽 d𝑆 = 0 , ∀𝑣 ,
Ω(0) Γ0
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(mass balance equation (perfusion))

∫︁ ∫︁ ∫︁
𝜕𝑞 𝜕𝑝
𝑞𝐽(𝑢) + 𝐾(𝑢(𝑛−1) ) : = 𝑞𝐽(𝑢(𝑛−1) ) , ∀𝑞 ,
𝜕𝑋 𝜕𝑋
Ω(0) Ω(0) Ω(0)

where

𝐹 deformation gradient 𝐹𝑖𝑗 = 𝜕𝑋 𝜕𝑥𝑖

𝑗
𝐽 det(𝐹 )
𝐶 right Cauchy-Green deformation tensor 𝐶 = 𝐹 𝑇 𝐹
𝜕𝑢
𝐸(𝑢) Green strain tensor 𝐸𝑖𝑗 = 21 ( 𝜕𝑋
𝜕𝑢𝑖
𝑗
+ 𝜕𝑋𝑗𝑖 + 𝜕𝑢 𝑚 𝜕𝑢𝑚
𝜕𝑋𝑖 𝜕𝑋𝑗 )
𝑆 eff (𝑢) effective second Piola-Kirchhoff stress tensor

The effective (neo-Hookean) stress 𝑆 eff (𝑢) is given by:

2 1
𝑆 eff (𝑢) = 𝜇𝐽 − 3 (𝐼 − tr(𝐶)𝐶 −1 ) .
3
The linearized deformation-dependent permeability is defined as 𝐾(𝑢) = 𝐽𝐹 −1 𝑘𝑓 (𝐽)𝐹 −𝑇 , where 𝑢 relates to the
(︁ (︁ )︁)︁2
previous time step (𝑛 − 1) and 𝑓 (𝐽) = max 0, 1 + (𝐽−1) 𝑁𝑓 expresses the dependence on volume compres-
sion/expansion.

source code

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# -*- coding: utf-8 -*-

r"""
Porous nearly incompressible hyperelastic material with fluid perfusion.

Large deformation is described using the total Lagrangian formulation.

Models of this kind can be used in biomechanics to model biological
tissues, e.g. muscles.

Find :math:`\ul{u}` such that:

(equilibrium equation with boundary tractions)

.. math::
\intl{\Omega\suz}{} \left( \ull{S}\eff - p J \ull{C}^{-1}
\right) : \delta \ull{E}(\ul{v}) \difd{V}
+ \intl{\Gamma_0\suz}{} \ul{\nu} \cdot \ull{F}^{-1} \cdot \ull{\sigma}
\cdot \ul{v} J \difd{S}
= 0
\;, \quad \forall \ul{v} \;,

(mass balance equation (perfusion))

.. math::
\intl{\Omega\suz}{} q J(\ul{u})
+ \intl{\Omega\suz}{} \ull{K}(\ul{u}\sunm) : \pdiff{q}{X} \pdiff{p}{X}
= \intl{\Omega\suz}{} q J(\ul{u}\sunm)
\;, \quad \forall q \;,

where

.. list-table::
:widths: 20 80

* - :math:`\ull{F}`
- deformation gradient :math:`F_{ij} = \pdiff{x_i}{X_j}`
* - :math:`J`
- :math:`\det(F)`
* - :math:`\ull{C}`
- right Cauchy-Green deformation tensor :math:`C = F^T F`
* - :math:`\ull{E}(\ul{u})`
- Green strain tensor :math:`E_{ij} = \frac{1}{2}(\pdiff{u_i}{X_j} +
\pdiff{u_j}{X_i} + \pdiff{u_m}{X_i}\pdiff{u_m}{X_j})`
* - :math:`\ull{S}\eff(\ul{u})`
- effective second Piola-Kirchhoff stress tensor

The effective (neo-Hookean) stress :math:`\ull{S}\eff(\ul{u})` is given

by:

.. math::
\ull{S}\eff(\ul{u}) = \mu J^{-\frac{2}{3}}(\ull{I}
- \frac{1}{3}\tr(\ull{C}) \ull{C}^{-1})
\;.
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The linearized deformation-dependent permeability is defined as

:math:`\ull{K}(\ul{u}) = J \ull{F}^{-1} \ull{k} f(J) \ull{F}^{-T}`,
where :math:`\ul{u}` relates to the previous time step :math:`(n-1)` and
:math:`f(J) = \max\left(0, \left(1 + \frac{(J -
1)}{N_f}\right)\right)^2` expresses the dependence on volume
compression/expansion.
"""
from __future__ import absolute_import
import numpy as nm

from sfepy import data_dir

filename_mesh = data_dir + '/meshes/3d/cylinder.mesh'

# Time-stepping parameters.
t0 = 0.0
t1 = 1.0
n_step = 21

from sfepy.solvers.ts import TimeStepper

ts = TimeStepper(t0, t1, None, n_step)

options = {
'nls' : 'newton',
'ls' : 'ls',
'ts' : 'ts',
'save_times' : 'all',
'post_process_hook' : 'post_process',
}

fields = {
'displacement': ('real', 3, 'Omega', 1),
'pressure' : ('real', 1, 'Omega', 1),
}

materials = {
# Perfused solid.
'ps' : ({
'mu' : 20e0, # shear modulus of neoHookean term
'k' : ts.dt * nm.eye(3, dtype=nm.float64), # reference permeability
'N_f' : 1.0, # reference porosity
},),
# Surface pressure traction.
'traction' : 'get_traction',
}

variables = {
'u' : ('unknown field', 'displacement', 0, 1),
'v' : ('test field', 'displacement', 'u'),
'p' : ('unknown field', 'pressure', 1),
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'q' : ('test field', 'pressure', 'p'),
}

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < 0.001)', 'facet'),
'Right' : ('vertices in (x > 0.099)', 'facet'),
}

##
# Dirichlet BC.
ebcs = {
'l' : ('Left', {'u.all' : 0.0, 'p.0' : 'get_pressure'}),
}

##
# Balance of forces.
integrals = {
'i1' : 1,
'i2' : 2,
}

equations = {
'force_balance'
: """dw_tl_he_neohook.i1.Omega( ps.mu, v, u )
+ dw_tl_bulk_pressure.i1.Omega( v, u, p )
+ dw_tl_surface_traction.i2.Right( traction.pressure, v, u )
= 0""",
'mass_balance'
: """dw_tl_volume.i1.Omega( q, u )
+ dw_tl_diffusion.i1.Omega( ps.k, ps.N_f, q, p, u[-1])
= dw_tl_volume.i1.Omega( q, u[-1] )"""
}

def post_process(out, problem, state, extend=False):

from sfepy.base.base import Struct, debug

val = problem.evaluate('dw_tl_he_neohook.i1.Omega( ps.mu, v, u )',

mode='el_avg', term_mode='strain')
out['green_strain'] = Struct(name='output_data',
mode='cell', data=val, dofs=None)

val = problem.evaluate('dw_tl_he_neohook.i1.Omega( ps.mu, v, u )',

mode='el_avg', term_mode='stress')
out['neohook_stress'] = Struct(name='output_data',
mode='cell', data=val, dofs=None)

val = problem.evaluate('dw_tl_bulk_pressure.i1.Omega( v, u, p )',

mode='el_avg', term_mode='stress')
out['bulk_pressure'] = Struct(name='output_data',
mode='cell', data=val, dofs=None)

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val = problem.evaluate('dw_tl_diffusion.i1.Omega( ps.k, ps.N_f, q, p, u[-1] )',
mode='el_avg', term_mode='diffusion_velocity')
out['diffusion_velocity'] = Struct(name='output_data',
mode='cell', data=val, dofs=None)

return out

##
# Solvers etc.
solver_0 = {
'name' : 'ls',
'kind' : 'ls.scipy_direct',
}

solver_1 = {
'name' : 'newton',
'kind' : 'nls.newton',

'i_max' : 7,
'eps_a' : 1e-10,
'eps_r' : 1.0,
'macheps' : 1e-16,
'lin_red' : 1e-2, # Linear system error < (eps_a * lin_red).
'ls_red' : 0.1,
'ls_red_warp': 0.001,
'ls_on' : 1.1,
'ls_min' : 1e-5,
'check' : 0,
'delta' : 1e-6,
}

solver_2 = {
'name' : 'ts',
'kind' : 'ts.simple',

't0' : t0,
't1' : t1,
'dt' : None,
'n_step' : n_step, # has precedence over dt!
'verbose' : 1,
}

##
# Functions.
def get_traction(ts, coors, mode=None):
"""
Pressure traction.

Parameters
----------
ts : TimeStepper
Time stepping info.
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coors : array_like
The physical domain coordinates where the parameters shound be defined.
mode : 'qp' or 'special'
Call mode.
"""
if mode != 'qp': return

tt = ts.nt * 2.0 * nm.pi

dim = coors.shape[1]
val = 0.05 * nm.sin(tt) * nm.eye(dim, dtype=nm.float64)
val[1,0] = val[0,1] = 0.5 * val[0,0]

shape = (coors.shape[0], 1, 1)
out = {
'pressure' : nm.tile(val, shape),
}

return out

def get_pressure(ts, coor, **kwargs):

"""Internal pressure Dirichlet boundary condition."""
tt = ts.nt * 2.0 * nm.pi

val = nm.zeros((coor.shape[0],), dtype=nm.float64)

val[:] = 1e-2 * nm.sin(tt)

return val

functions = {
'get_traction' : (lambda ts, coors, mode=None, **kwargs:
get_traction(ts, coors, mode=mode),),
'get_pressure' : (get_pressure,),
}

linear_elasticity

linear_elasticity/dispersion_analysis.py

Description
Dispersion analysis of a heterogeneous finite scale periodic cell.
The periodic cell mesh has to contain two subdomains Y1 (with the cell ids 1), Y2 (with the cell ids 2), so that different
material properties can be defined in each of the subdomains (see --pars option). The command line parameters can
be given in any consistent unit set, for example the basic SI units. The --unit-multipliers option can be used to
rescale the input units to ones more suitable to the simulation, for example to prevent having different matrix blocks
with large differences of matrix entries magnitudes. The results are then in the rescaled units.

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Usage Examples

Default material parameters, a square periodic cell with a spherical inclusion, logs also standard pressure dilatation
and shear waves, no eigenvectors:

python examples/linear_elasticity/dispersion_analysis.py meshes/2d/special/circle_in_

˓→square.mesh --log-std-waves --eigs-only

As above, with custom eigenvalue solver parameters, and different number of eigenvalues, mesh size and units used in
the calculation:

python examples/linear_elasticity/dispersion_analysis.py meshes/2d/special/circle_in_

˓→square.mesh --solver-conf="kind='eig.scipy', method='eigsh', tol=1e-10, maxiter=1000,␣

˓→which='LM', sigma=0" --log-std-waves -n 5 --range=0,640,101 --mode=omega --unit-

˓→multipliers=1e-6,1e-2,1e-3 --mesh-size=1e-2 --eigs-only

Default material parameters, a square periodic cell with a square inclusion, and a very small mesh to allow comparing
the omega and kappa modes (full matrix solver required!):

python examples/linear_elasticity/dispersion_analysis.py meshes/2d/square_2m.mesh --

˓→solver-conf="kind='eig.scipy', method='eigh'" --log-std-waves -n 10 --range=0,640,101 -

˓→-mesh-size=1e-2 --mode=omega --eigs-only --no-legends --unit-multipliers=1e-6,1e-2,1e-

˓→3 -o output/omega

python examples/linear_elasticity/dispersion_analysis.py meshes/2d/square_2m.mesh --

˓→solver-conf="kind='eig.qevp', method='companion', mode='inverted', solver={kind='eig.

˓→scipy', method='eig'}" --log-std-waves -n 500 --range=0,4000000,1001 --mesh-size=1e-2 -

˓→-mode=kappa --eigs-only --no-legends --unit-multipliers=1e-6,1e-2,1e-3 -o output/kappa

View/compare the resulting logs:

python script/plot_logs.py output/omega/frequencies.txt --no-legends -g 1 -o mode-omega.

˓→png

python script/plot_logs.py output/kappa/wave-numbers.txt --no-legends -o mode-kappa.png

python script/plot_logs.py output/kappa/wave-numbers.txt --no-legends --swap-axes -o␣
˓→mode-kappa-t.png

In contrast to the heterogeneous square periodic cell, a homogeneous square periodic cell (the region Y2 is empty):

python examples/linear_elasticity/dispersion_analysis.py meshes/2d/square_1m.mesh --

˓→solver-conf="kind='eig.scipy', method='eigh'" --log-std-waves -n 10 --range=0,640,101 -

˓→-mesh-size=1e-2 --mode=omega --eigs-only --no-legends --unit-multipliers=1e-6,1e-2,1e-

˓→3 -o output/omega-h

python script/plot_logs.py output/omega-h/frequencies.txt --no-legends -g 1 -o mode-

˓→omega-h.png

Use the Brillouin stepper:

python examples/linear_elasticity/dispersion_analysis.py meshes/2d/special/circle_in_

˓→square.mesh --log-std-waves -n=60 --eigs-only --no-legends --stepper=brillouin

python script/plot_logs.py output/frequencies.txt -g 0 --rc="'font.size':14, 'lines.

˓→linewidth' : 3, 'lines.markersize' : 4" -o brillouin-stepper-kappas.png

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python script/plot_logs.py output/frequencies.txt -g 1 --no-legends --rc="'font.size':14,

˓→ 'lines.linewidth' : 3, 'lines.markersize' : 4" -o brillouin-stepper-omegas.png

Additional arguments can be passed to the problem configuration’s define() function using the --define-kwargs
option. In this file, only the mesh vertex separation parameter mesh_eps can be used:
python examples/linear_elasticity/dispersion_analysis.py meshes/2d/special/circle_in_
˓→square.mesh --log-std-waves --eigs-only --define-kwargs="mesh_eps=1e-10" --save-regions

source code
#!/usr/bin/env python
"""
Dispersion analysis of a heterogeneous finite scale periodic cell.

The periodic cell mesh has to contain two subdomains Y1 (with the cell ids 1),
Y2 (with the cell ids 2), so that different material properties can be defined
in each of the subdomains (see ``--pars`` option). The command line parameters
can be given in any consistent unit set, for example the basic SI units. The
``--unit-multipliers`` option can be used to rescale the input units to ones
more suitable to the simulation, for example to prevent having different
matrix blocks with large differences of matrix entries magnitudes. The results
are then in the rescaled units.

Usage Examples
--------------

Default material parameters, a square periodic cell with a spherical inclusion,

logs also standard pressure dilatation and shear waves, no eigenvectors::

python sfepy/examples/linear_elasticity/dispersion_analysis.py meshes/2d/special/

˓→circle_in_square.mesh --log-std-waves --eigs-only

As above, with custom eigenvalue solver parameters, and different number of

eigenvalues, mesh size and units used in the calculation::

python sfepy/examples/linear_elasticity/dispersion_analysis.py meshes/2d/special/

˓→circle_in_square.mesh --solver-conf="kind='eig.scipy', method='eigsh', tol=1e-10,␣
˓→maxiter=1000, which='LM', sigma=0" --log-std-waves -n 5 --range=0,640,101 --mode=omega -

˓→-unit-multipliers=1e-6,1e-2,1e-3 --mesh-size=1e-2 --eigs-only

Default material parameters, a square periodic cell with a square inclusion,

and a very small mesh to allow comparing the omega and kappa modes (full matrix
solver required!)::

python sfepy/examples/linear_elasticity/dispersion_analysis.py meshes/2d/square_2m.

˓→mesh --solver-conf="kind='eig.scipy', method='eigh'" --log-std-waves -n 10 --range=0,640,
˓→101 --mesh-size=1e-2 --mode=omega --eigs-only --no-legends --unit-multipliers=1e-6,1e-

˓→2,1e-3 -o output/omega

python sfepy/examples/linear_elasticity/dispersion_analysis.py meshes/2d/square_2m.

˓→mesh --solver-conf="kind='eig.qevp', method='companion', mode='inverted', solver={kind='eig.
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˓→scipy', method='eig'}" --log-std-waves -n 500 --range=0,4000000,1001 --mesh-size=1e-2 --

˓→mode=kappa --eigs-only --no-legends --unit-multipliers=1e-6,1e-2,1e-3 -o output/kappa

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View/compare the resulting logs::

python script/plot_logs.py output/omega/frequencies.txt --no-legends -g 1 -o mode-

˓→omega.png
python script/plot_logs.py output/kappa/wave-numbers.txt --no-legends -o mode-kappa.png
python script/plot_logs.py output/kappa/wave-numbers.txt --no-legends --swap-axes -o␣
˓→mode-kappa-t.png

In contrast to the heterogeneous square periodic cell, a homogeneous

square periodic cell (the region Y2 is empty)::

python sfepy/examples/linear_elasticity/dispersion_analysis.py meshes/2d/square_1m.

˓→mesh --solver-conf="kind='eig.scipy', method='eigh'" --log-std-waves -n 10 --range=0,640,
˓→101 --mesh-size=1e-2 --mode=omega --eigs-only --no-legends --unit-multipliers=1e-6,1e-

˓→2,1e-3 -o output/omega-h

python script/plot_logs.py output/omega-h/frequencies.txt --no-legends -g 1 -o mode-

˓→omega-h.png

Use the Brillouin stepper::

python sfepy/examples/linear_elasticity/dispersion_analysis.py meshes/2d/special/

˓→circle_in_square.mesh --log-std-waves -n=60 --eigs-only --no-legends --
˓→stepper=brillouin

python script/plot_logs.py output/frequencies.txt -g 0 --rc="'font.size':14, 'lines.

˓→linewidth' : 3, 'lines.markersize' : 4" -o brillouin-stepper-kappas.png

python script/plot_logs.py output/frequencies.txt -g 1 --no-legends --rc="'font.size

˓→':14, 'lines.linewidth' : 3, 'lines.markersize' : 4" -o brillouin-stepper-omegas.png

Additional arguments can be passed to the problem configuration's

:func:`define()` function using the ``--define-kwargs`` option. In this file,
only the mesh vertex separation parameter `mesh_eps` can be used::

python sfepy/examples/linear_elasticity/dispersion_analysis.py meshes/2d/special/

˓→ circle_in_square.mesh --log-std-waves --eigs-only --define-kwargs="mesh_eps=1e-10" --
˓→save-regions

"""
from __future__ import absolute_import
import os
import sys
sys.path.append('.')
import gc
from copy import copy
from argparse import ArgumentParser, RawDescriptionHelpFormatter

import numpy as nm
import matplotlib.pyplot as plt

from sfepy.base.base import import_file, output, Struct

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from sfepy.base.conf import dict_from_string, ProblemConf
from sfepy.base.ioutils import ensure_path, remove_files_patterns, save_options
from sfepy.base.log import Log
from sfepy.discrete.fem import MeshIO
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson as stiffness
import sfepy.mechanics.matcoefs as mc
from sfepy.mechanics.units import apply_unit_multipliers, apply_units_to_pars
import sfepy.discrete.fem.periodic as per
from sfepy.discrete.fem.meshio import convert_complex_output
from sfepy.homogenization.utils import define_box_regions
from sfepy.discrete import Problem
from sfepy.mechanics.tensors import get_von_mises_stress
from sfepy.solvers import Solver
from sfepy.solvers.ts import get_print_info, TimeStepper
from sfepy.linalg.utils import output_array_stats, max_diff_csr

pars_kinds = {
'young1' : 'stress',
'poisson1' : 'one',
'density1' : 'density',
'young2' : 'stress',
'poisson2' : 'one',
'density2' : 'density',
}

def define(filename_mesh, pars, approx_order, refinement_level, solver_conf,

plane='strain', post_process=False, mesh_eps=1e-8):
io = MeshIO.any_from_filename(filename_mesh)
bbox = io.read_bounding_box()
dim = bbox.shape[1]

options = {
'absolute_mesh_path' : True,
'refinement_level' : refinement_level,
'allow_empty_regions' : True,
'post_process_hook' : 'compute_von_mises' if post_process else None,
}

fields = {
'displacement': ('complex', dim, 'Omega', approx_order),
}

materials = {
'm' : ({
'D' : {'Y1' : stiffness(dim,
young=pars.young1,
poisson=pars.poisson1,
plane=plane),
'Y2' : stiffness(dim,
young=pars.young2,
poisson=pars.poisson2,
plane=plane)},
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'density' : {'Y1' : pars.density1, 'Y2' : pars.density2},
},),
'wave' : 'get_wdir',
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
}

regions = {
'Omega' : 'all',
'Y1': 'cells of group 1',
'Y2': 'cells of group 2',
}
regions.update(define_box_regions(dim,
bbox[0], bbox[1], mesh_eps))

ebcs = {
}

if dim == 3:
epbcs = {
'periodic_x' : (['Left', 'Right'], {'u.all' : 'u.all'},
'match_x_plane'),
'periodic_y' : (['Near', 'Far'], {'u.all' : 'u.all'},
'match_y_plane'),
'periodic_z' : (['Top', 'Bottom'], {'u.all' : 'u.all'},
'match_z_plane'),
}
else:
epbcs = {
'periodic_x' : (['Left', 'Right'], {'u.all' : 'u.all'},
'match_y_line'),
'periodic_y' : (['Bottom', 'Top'], {'u.all' : 'u.all'},
'match_x_line'),
}

per.set_accuracy(mesh_eps)
functions = {
'match_x_plane' : (per.match_x_plane,),
'match_y_plane' : (per.match_y_plane,),
'match_z_plane' : (per.match_z_plane,),
'match_x_line' : (per.match_x_line,),
'match_y_line' : (per.match_y_line,),
'get_wdir' : (get_wdir,),
}

integrals = {
'i' : 2 * approx_order,
}

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equations = {
'K' : 'dw_lin_elastic.i.Omega(m.D, v, u)',
'S' : 'dw_elastic_wave.i.Omega(m.D, wave.vec, v, u)',
'R' : """1j * dw_elastic_wave_cauchy.i.Omega(m.D, wave.vec, u, v)
- 1j * dw_elastic_wave_cauchy.i.Omega(m.D, wave.vec, v, u)""",
'M' : 'dw_dot.i.Omega(m.density, v, u)',
}

solver_0 = solver_conf.copy()
solver_0['name'] = 'eig'

return locals()

def get_wdir(ts, coors, mode=None,

equations=None, term=None, problem=None, wdir=None, **kwargs):
if mode == 'special':
return {'vec' : wdir}

def set_wave_dir(pb, wdir):

materials = pb.get_materials()
wave_mat = materials['wave']
wave_mat.set_extra_args(wdir=wdir)

def save_materials(output_dir, pb, options):

stiffness = pb.evaluate('ev_integrate_mat.2.Omega(m.D, u)',
mode='el_avg', copy_materials=False, verbose=False)
young, poisson = mc.youngpoisson_from_stiffness(stiffness,
plane=options.plane)
density = pb.evaluate('ev_integrate_mat.2.Omega(m.density, u)',
mode='el_avg', copy_materials=False, verbose=False)

out = {}
out['young'] = Struct(name='young', mode='cell',
data=young[..., None, None])
out['poisson'] = Struct(name='poisson', mode='cell',
data=poisson[..., None, None])
out['density'] = Struct(name='density', mode='cell', data=density)
materials_filename = os.path.join(output_dir, 'materials.vtk')
pb.save_state(materials_filename, out=out)

def get_std_wave_fun(pb, options):

stiffness = pb.evaluate('ev_integrate_mat.2.Omega(m.D, u)',
mode='el_avg', copy_materials=False, verbose=False)
young, poisson = mc.youngpoisson_from_stiffness(stiffness,
plane=options.plane)
density = pb.evaluate('ev_integrate_mat.2.Omega(m.density, u)',
mode='el_avg', copy_materials=False, verbose=False)

lam, mu = mc.lame_from_youngpoisson(young, poisson,

plane=options.plane)
alam = nm.average(lam)
amu = nm.average(mu)
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adensity = nm.average(density)

cp = nm.sqrt((alam + 2.0 * amu) / adensity)

cs = nm.sqrt(amu / adensity)
output('average p-wave speed:', cp)
output('average shear wave speed:', cs)

log_names = [r'$\omega_p$', r'$\omega_s$']

log_plot_kwargs = [{'ls' : '--', 'color' : 'k'},
{'ls' : '--', 'color' : 'gray'}]

if options.mode == 'omega':
fun = lambda wmag, wdir: (cp * wmag, cs * wmag)

else:
fun = lambda wmag, wdir: (wmag / cp, wmag / cs)

return fun, log_names, log_plot_kwargs

def get_stepper(rng, pb, options):

if options.stepper == 'linear':
stepper = TimeStepper(rng[0], rng[1], dt=None, n_step=rng[2])
return stepper

bbox = pb.domain.mesh.get_bounding_box()

bzone = 2.0 * nm.pi / (bbox[1] - bbox[0])

num = rng[2] // 3

class BrillouinStepper(Struct):
"""
Step over 1. Brillouin zone in xy plane.
"""
def __init__(self, t0, t1, dt=None, n_step=None, step=None, **kwargs):
Struct.__init__(self, t0=t0, t1=t1, dt=dt, n_step=n_step, step=step)

self.n_digit, self.format, self.suffix = get_print_info(self.n_step)

def __iter__(self):
ts = TimeStepper(0, bzone[0], dt=None, n_step=num)
for ii, val in ts:
yield ii, val, nm.array([1.0, 0.0])
if ii == (num-2): break

ts = TimeStepper(0, bzone[1], dt=None, n_step=num)

for ii, k1 in ts:
wdir = nm.array([bzone[0], k1])
val = nm.linalg.norm(wdir)
wdir = wdir / val
yield num + ii, val, wdir
if ii == (num-2): break
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wdir = nm.array([bzone[0], bzone[1]])

val = nm.linalg.norm(wdir)
wdir = wdir / val
ts = TimeStepper(0, 1, dt=None, n_step=num)
for ii, _ in ts:
yield 2 * num + ii, val * (1.0 - float(ii)/(num-1)), wdir

stepper = BrillouinStepper(0, 1, n_step=rng[2])

return stepper

def compute_von_mises(out, pb, state, extend=False, wmag=None, wdir=None):

"""
Calculate the von Mises stress.
"""
stress = pb.evaluate('ev_cauchy_stress.i.Omega(m.D, u)', mode='el_avg')

vms = get_von_mises_stress(stress.squeeze())
vms.shape = (vms.shape[0], 1, 1, 1)
out['von_mises_stress'] = Struct(name='output_data', mode='cell',
data=vms)

return out

def save_eigenvectors(filename, svecs, wmag, wdir, pb):

if svecs is None: return

variables = pb.set_default_state()
# Make full eigenvectors (add DOFs fixed by boundary conditions).
vecs = nm.empty((variables.di.ptr[-1], svecs.shape[1]),
dtype=svecs.dtype)
for ii in range(svecs.shape[1]):
vecs[:, ii] = variables.make_full_vec(svecs[:, ii])

# Save the eigenvectors.

out = {}

pp_name = pb.conf.options.get('post_process_hook')
pp = getattr(pb.conf.funmod, pp_name if pp_name is not None else '',
lambda out, *args, **kwargs: out)

for ii in range(svecs.shape[1]):
variables.set_state(vecs[:, ii])
aux = variables.create_output()
aux2 = {}
pp(aux2, pb, variables, wmag=wmag, wdir=wdir)
aux.update(convert_complex_output(aux2))
out.update({key + '%03d' % ii : aux[key] for key in aux})

pb.save_state(filename, out=out)

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def assemble_matrices(define, mod, pars, set_wave_dir, options, wdir=None):
"""
Assemble the blocks of dispersion eigenvalue problem matrices.
"""
define_dict = define(filename_mesh=options.mesh_filename,
pars=pars,
approx_order=options.order,
refinement_level=options.refine,
solver_conf=options.solver_conf,
plane=options.plane,
post_process=options.post_process,
**options.define_kwargs)

conf = ProblemConf.from_dict(define_dict, mod)

pb = Problem.from_conf(conf)
pb.dispersion_options = options
pb.set_output_dir(options.output_dir)
dim = pb.domain.shape.dim

# Set the normalized wave vector direction to the material(s).

if wdir is None:
wdir = nm.asarray(options.wave_dir[:dim], dtype=nm.float64)
wdir = wdir / nm.linalg.norm(wdir)
set_wave_dir(pb, wdir)

bbox = pb.domain.mesh.get_bounding_box()
size = (bbox[1] - bbox[0]).max()
scaling0 = apply_unit_multipliers([1.0], ['length'],
options.unit_multipliers)[0]
scaling = scaling0
if options.mesh_size is not None:
scaling *= options.mesh_size / size
output('scaling factor of periodic cell mesh coordinates:', scaling)
output('new mesh size with applied unit multipliers:', scaling * size)
pb.domain.mesh.coors[:] *= scaling
pb.set_mesh_coors(pb.domain.mesh.coors, update_fields=True)

bzone = 2.0 * nm.pi / (scaling * size)

output('1. Brillouin zone size:', bzone * scaling0)
output('1. Brillouin zone size with applied unit multipliers:', bzone)

pb.time_update()
pb.update_materials()

# Assemble the matrices.

mtxs = {}
for key, eq in pb.equations.iteritems():
mtxs[key] = mtx = pb.mtx_a.copy()
mtx = eq.evaluate(mode='weak', dw_mode='matrix', asm_obj=mtx)
mtx.eliminate_zeros()
output_array_stats(mtx.data, 'nonzeros in %s' % key)
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output('symmetry checks:')
output('%s - %s^T:' % (key, key), max_diff_csr(mtx, mtx.T))
output('%s - %s^H:' % (key, key), max_diff_csr(mtx, mtx.H))

return pb, wdir, bzone, mtxs

def setup_n_eigs(options, pb, mtxs):

"""
Setup the numbers of eigenvalues based on options and numbers of DOFs.
"""
solver_n_eigs = n_eigs = options.n_eigs
n_dof = mtxs['K'].shape[0]
if options.mode == 'omega':
if options.n_eigs > n_dof:
n_eigs = n_dof
solver_n_eigs = None

else:
if options.n_eigs > 2 * n_dof:
n_eigs = 2 * n_dof
solver_n_eigs = None

return solver_n_eigs, n_eigs

def build_evp_matrices(mtxs, val, mode, pb):

"""
Build the matrices of the dispersion eigenvalue problem.
"""
if mode == 'omega':
mtx_a = mtxs['K'] + val**2 * mtxs['S'] + val * mtxs['R']
output('A - A^H:', max_diff_csr(mtx_a, mtx_a.H))

evp_mtxs = (mtx_a, mtxs['M'])

else:
evp_mtxs = (mtxs['S'], mtxs['R'], mtxs['K'] - val**2 * mtxs['M'])

return evp_mtxs

def process_evp_results(eigs, svecs, val, wdir, bzone, pb, mtxs, options,

std_wave_fun=None):
"""
Transform eigenvalues to either omegas or kappas, depending on `mode`.
Transform eigenvectors, if available, depending on `mode`.
Return also the values to log.
"""
if options.mode == 'omega':
omegas = nm.sqrt(eigs)

output('eigs, omegas:')
for ii, om in enumerate(omegas):
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output('{:>3}. {: .10e}, {:.10e}'.format(ii, eigs[ii], om))

if options.stepper == 'linear':
out = tuple(eigs) + tuple(omegas)

else:
out = tuple(val * wdir) + tuple(omegas)

if std_wave_fun is not None:

out = out + std_wave_fun(val, wdir)

return omegas, svecs, out

else:
kappas = eigs.copy()
rks = kappas.copy()

# Mask modes far from 1. Brillouin zone.

max_kappa = 1.2 * bzone
kappas[kappas.real > max_kappa] = nm.nan

# Mask non-physical modes.

kappas[kappas.real < 0] = nm.nan
kappas[nm.abs(kappas.imag) > 1e-10] = nm.nan
out = tuple(kappas.real)

output('raw kappas, masked real part:',)

for ii, kr in enumerate(kappas.real):
output('{:>3}. {: 23.5e}, {:.10e}'.format(ii, rks[ii], kr))

if svecs is not None:

n_dof = mtxs['K'].shape[0]
# Select only vectors corresponding to physical modes.
ii = nm.isfinite(kappas.real)
svecs = svecs[:n_dof, ii]

if std_wave_fun is not None:

out = out + tuple(ii if ii <= max_kappa else nm.nan
for ii in std_wave_fun(val, wdir))

return kappas, svecs, out

helps = {
'pars' :
'material parameters in Y1, Y2 subdomains in basic units.'
' The default parameters are:'
' young1, poisson1, density1, young2, poisson2, density2'
' [default: %(default)s]',
'conf' :
'if given, an alternative problem description file with apply_units() and'
' define() functions [default: %(default)s]',
'define_kwargs' : 'additional keyword arguments passed to define()',
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'mesh_size' :
'desired mesh size (max. of bounding box dimensions) in basic units'
' - the input periodic cell mesh is rescaled to this size'
' [default: %(default)s]',
'unit_multipliers' :
'basic unit multipliers (time, length, mass) [default: %(default)s]',
'plane' :
'for 2D problems, plane strain or stress hypothesis selection'
' [default: %(default)s]',
'wave_dir' : 'the wave vector direction (will be normalized)'
' [default: %(default)s]',
'mode' : 'solution mode: omega = solve a generalized EVP for omega,'
' kappa = solve a quadratic generalized EVP for kappa'
' [default: %(default)s]',
'stepper' : 'the range stepper. For "brillouin", only the number'
' of items from --range is used'
' [default: %(default)s]',
'range' : 'the wave vector magnitude / frequency range'
' (like numpy.linspace) depending on the mode option'
' [default: %(default)s]',
'order' : 'displacement field approximation order [default: %(default)s]',
'refine' : 'number of uniform mesh refinements [default: %(default)s]',
'n_eigs' : 'the number of eigenvalues to compute [default: %(default)s]',
'eigs_only' : 'compute only eigenvalues, not eigenvectors',
'post_process' : 'post-process eigenvectors',
'solver_conf' : 'eigenvalue problem solver configuration options'
' [default: %(default)s]',
'save_regions' : 'save defined regions into'
' <output_directory>/regions.vtk',
'save_materials' : 'save material parameters into'
' <output_directory>/materials.vtk',
'log_std_waves' : 'log also standard pressure dilatation and shear waves',
'no_legends' :
'do not show legends in the log plots',
'no_show' :
'do not show the log figure',
'silent' : 'do not print messages to screen',
'clear' :
'clear old solution files from output directory',
'output_dir' :
'output directory [default: %(default)s]',
'mesh_filename' :
'input periodic cell mesh file name [default: %(default)s]',
}

def main():
# Aluminium and epoxy.
default_pars = '70e9,0.35,2.799e3,3.8e9,0.27,1.142e3'
default_solver_conf = ("kind='eig.scipy',method='eigsh',tol=1.0e-5,"
"maxiter=1000,which='LM',sigma=0.0")

parser = ArgumentParser(description=__doc__,
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formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--pars', metavar='name1=value1,name2=value2,...'
' or value1,value2,...',
action='store', dest='pars',
default=default_pars, help=helps['pars'])
parser.add_argument('--conf', metavar='filename',
action='store', dest='conf',
default=None, help=helps['conf'])
parser.add_argument('--define-kwargs', metavar='dict-like',
action='store', dest='define_kwargs',
default=None, help=helps['define_kwargs'])
parser.add_argument('--mesh-size', type=float, metavar='float',
action='store', dest='mesh_size',
default=None, help=helps['mesh_size'])
parser.add_argument('--unit-multipliers',
metavar='c_time,c_length,c_mass',
action='store', dest='unit_multipliers',
default='1.0,1.0,1.0', help=helps['unit_multipliers'])
parser.add_argument('--plane', action='store', dest='plane',
choices=['strain', 'stress'],
default='strain', help=helps['plane'])
parser.add_argument('--wave-dir', metavar='float,float[,float]',
action='store', dest='wave_dir',
default='1.0,0.0,0.0', help=helps['wave_dir'])
parser.add_argument('--mode', action='store', dest='mode',
choices=['omega', 'kappa'],
default='omega', help=helps['mode'])
parser.add_argument('--stepper', action='store', dest='stepper',
choices=['linear', 'brillouin'],
default='linear', help=helps['stepper'])
parser.add_argument('--range', metavar='start,stop,count',
action='store', dest='range',
default='0,6.4,33', help=helps['range'])
parser.add_argument('--order', metavar='int', type=int,
action='store', dest='order',
default=1, help=helps['order'])
parser.add_argument('--refine', metavar='int', type=int,
action='store', dest='refine',
default=0, help=helps['refine'])
parser.add_argument('-n', '--n-eigs', metavar='int', type=int,
action='store', dest='n_eigs',
default=6, help=helps['n_eigs'])
group = parser.add_mutually_exclusive_group()
group.add_argument('--eigs-only',
action='store_true', dest='eigs_only',
default=False, help=helps['eigs_only'])
group.add_argument('--post-process',
action='store_true', dest='post_process',
default=False, help=helps['post_process'])
parser.add_argument('--solver-conf', metavar='dict-like',
action='store', dest='solver_conf',
default=default_solver_conf, help=helps['solver_conf'])
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parser.add_argument('--save-regions',
action='store_true', dest='save_regions',
default=False, help=helps['save_regions'])
parser.add_argument('--save-materials',
action='store_true', dest='save_materials',
default=False, help=helps['save_materials'])
parser.add_argument('--log-std-waves',
action='store_true', dest='log_std_waves',
default=False, help=helps['log_std_waves'])
parser.add_argument('--no-legends',
action='store_false', dest='show_legends',
default=True, help=helps['no_legends'])
parser.add_argument('--no-show',
action='store_false', dest='show',
default=True, help=helps['no_show'])
parser.add_argument('--silent',
action='store_true', dest='silent',
default=False, help=helps['silent'])
parser.add_argument('-c', '--clear',
action='store_true', dest='clear',
default=False, help=helps['clear'])
parser.add_argument('-o', '--output-dir', metavar='path',
action='store', dest='output_dir',
default='output', help=helps['output_dir'])
parser.add_argument('mesh_filename', default='',
help=helps['mesh_filename'])
options = parser.parse_args()

output_dir = options.output_dir

output.set_output(filename=os.path.join(output_dir,'output_log.txt'),
combined=options.silent == False)

if options.conf is not None:

mod = import_file(options.conf)

else:
mod = sys.modules[__name__]

pars_kinds = mod.pars_kinds
define = mod.define
set_wave_dir = mod.set_wave_dir
setup_n_eigs = mod.setup_n_eigs
build_evp_matrices = mod.build_evp_matrices
save_materials = mod.save_materials
get_std_wave_fun = mod.get_std_wave_fun
get_stepper = mod.get_stepper
process_evp_results = mod.process_evp_results
save_eigenvectors = mod.save_eigenvectors

try:
options.pars = dict_from_string(options.pars)
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except:
aux = [float(ii) for ii in options.pars.split(',')]
options.pars = {key : aux[ii]
for ii, key in enumerate(pars_kinds.keys())}

options.unit_multipliers = [float(ii)
for ii in options.unit_multipliers.split(',')]
options.wave_dir = [float(ii)
for ii in options.wave_dir.split(',')]
aux = options.range.split(',')
options.range = [float(aux[0]), float(aux[1]), int(aux[2])]
options.solver_conf = dict_from_string(options.solver_conf)
options.define_kwargs = dict_from_string(options.define_kwargs)

if options.clear:
remove_files_patterns(output_dir,
['*.h5', '*.vtk', '*.txt'],
ignores=['output_log.txt'],
verbose=True)

filename = os.path.join(output_dir, 'options.txt')

ensure_path(filename)
save_options(filename, [('options', vars(options))],
quote_command_line=True)

pars = apply_units_to_pars(options.pars, pars_kinds,

options.unit_multipliers)
output('material parameter names and kinds:')
output(pars_kinds)
output('material parameters with applied unit multipliers:')
output(pars)

pars = Struct(**pars)

if options.mode == 'omega':
rng = copy(options.range)
rng[:2] = apply_unit_multipliers(options.range[:2],
['wave_number', 'wave_number'],
options.unit_multipliers)
output('wave number range with applied unit multipliers:', rng)

else:
if options.stepper == 'brillouin':
raise ValueError('Cannot use "brillouin" stepper in kappa mode!')

rng = copy(options.range)
rng[:2] = apply_unit_multipliers(options.range[:2],
['frequency', 'frequency'],
options.unit_multipliers)
output('frequency range with applied unit multipliers:', rng)

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pb, wdir, bzone, mtxs = assemble_matrices(define, mod, pars, set_wave_dir,
options)
dim = pb.domain.shape.dim

if dim != 2:
options.plane = 'strain'

if options.save_regions:
pb.save_regions_as_groups(os.path.join(output_dir, 'regions'))

if options.save_materials:
save_materials(output_dir, pb, options)

conf = pb.solver_confs['eig']
eig_solver = Solver.any_from_conf(conf)

n_eigs, options.n_eigs = setup_n_eigs(options, pb, mtxs)

get_color = lambda ii: plt.cm.viridis((float(ii)

/ (max(options.n_eigs, 2) - 1)))
plot_kwargs = [{'color' : get_color(ii), 'ls' : '', 'marker' : 'o'}
for ii in range(options.n_eigs)]
get_color_dim = lambda ii: plt.cm.viridis((float(ii) / (max(dim, 2) -1)))
plot_kwargs_dim = [{'color' : get_color_dim(ii), 'ls' : '', 'marker' : 'o'}
for ii in range(dim)]

log_names = []
log_plot_kwargs = []
if options.log_std_waves:
std_wave_fun, log_names, log_plot_kwargs = get_std_wave_fun(
pb, options)

else:
std_wave_fun = None

stepper = get_stepper(rng, pb, options)

if options.mode == 'omega':
eigenshapes_filename = os.path.join(output_dir,
'frequency-eigenshapes-%s.vtk'
% stepper.suffix)

if options.stepper == 'linear':
log = Log([[r'$\lambda_{%d}$' % ii for ii in range(options.n_eigs)],
[r'$\omega_{%d}$'
% ii for ii in range(options.n_eigs)] + log_names],
plot_kwargs=[plot_kwargs, plot_kwargs + log_plot_kwargs],
formats=[['{:.12e}'] * options.n_eigs,
['{:.12e}'] * (options.n_eigs + len(log_names))],
yscales=['linear', 'linear'],
xlabels=[r'$\kappa$', r'$\kappa$'],
ylabels=[r'eigenvalues $\lambda_i$',
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r'frequencies $\omega_i$'],
show_legends=options.show_legends,
is_plot=options.show,
log_filename=os.path.join(output_dir, 'frequencies.txt'),
aggregate=1000, sleep=0.1)

else:
log = Log([[r'$\kappa_{%d}$'% ii for ii in range(dim)],
[r'$\omega_{%d}$'
% ii for ii in range(options.n_eigs)] + log_names],
plot_kwargs=[plot_kwargs_dim,
plot_kwargs + log_plot_kwargs],
formats=[['{:.12e}'] * dim,
['{:.12e}'] * (options.n_eigs + len(log_names))],
yscales=['linear', 'linear'],
xlabels=[r'', r''],
ylabels=[r'wave vector $\kappa$',
r'frequencies $\omega_i$'],
show_legends=options.show_legends,
is_plot=options.show,
log_filename=os.path.join(output_dir, 'frequencies.txt'),
aggregate=1000, sleep=0.1)

for aux in stepper:

if options.stepper == 'linear':
iv, wmag = aux

else:
iv, wmag, wdir = aux

output('step %d: wave vector %s' % (iv, wmag * wdir))

if options.stepper == 'brillouin':
pb, _, bzone, mtxs = assemble_matrices(
define, mod, pars, set_wave_dir, options, wdir=wdir)

evp_mtxs = build_evp_matrices(mtxs, wmag, options.mode, pb)

if options.eigs_only:
eigs = eig_solver(*evp_mtxs, n_eigs=n_eigs,
eigenvectors=False)
svecs = None

else:
eigs, svecs = eig_solver(*evp_mtxs, n_eigs=n_eigs,
eigenvectors=True)

omegas, svecs, out = process_evp_results(

eigs, svecs, wmag, wdir, bzone, pb, mtxs, options,
std_wave_fun=std_wave_fun
)
if options.stepper == 'linear':
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log(*out, x=[wmag, wmag])

else:
log(*out, x=[iv, iv])

save_eigenvectors(eigenshapes_filename % iv, svecs, wmag, wdir, pb)

gc.collect()

log(save_figure=os.path.join(output_dir, 'frequencies.png'))
log(finished=True)

else:
eigenshapes_filename = os.path.join(output_dir,
'wave-number-eigenshapes-%s.vtk'
% stepper.suffix)

log = Log([[r'$\kappa_{%d}$' % ii for ii in range(options.n_eigs)]

+ log_names],
plot_kwargs=[plot_kwargs + log_plot_kwargs],
formats=[['{:.12e}'] * (options.n_eigs + len(log_names))],
yscales=['linear'],
xlabels=[r'$\omega$'],
ylabels=[r'wave numbers $\kappa_i$'],
show_legends=options.show_legends,
is_plot=options.show,
log_filename=os.path.join(output_dir, 'wave-numbers.txt'),
aggregate=1000, sleep=0.1)
for io, omega in stepper:
output('step %d: frequency %s' % (io, omega))

evp_mtxs = build_evp_matrices(mtxs, omega, options.mode, pb)

if options.eigs_only:
eigs = eig_solver(*evp_mtxs, n_eigs=n_eigs,
eigenvectors=False)
svecs = None

else:
eigs, svecs = eig_solver(*evp_mtxs, n_eigs=n_eigs,
eigenvectors=True)

kappas, svecs, out = process_evp_results(

eigs, svecs, omega, wdir, bzone, pb, mtxs, options,
std_wave_fun=std_wave_fun
)
log(*out, x=[omega])

save_eigenvectors(eigenshapes_filename % io, svecs, kappas, wdir,

pb)

gc.collect()
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log(save_figure=os.path.join(output_dir, 'wave-numbers.png'))
log(finished=True)

if __name__ == '__main__':
main()

linear_elasticity/elastic_contact_planes.py

Description
Elastic contact planes simulating an indentation test.
Four contact planes bounded by polygons (triangles in this case) form a very rigid pyramid shape simulating an indentor.
Find 𝑢 such that:
∫︁ 4 ∫︁
∑︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) + 𝑣 · 𝑓 𝑖 (𝑑(𝑢))𝑛𝑖 = 0 ,
Ω 𝑖=1 Γ𝑖

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

Notes

Even though the material is linear elastic and small deformations are used, the problem is highly nonlinear due to
contacts with the planes.
Checking the tangent matrix by finite differences by setting ‘check’ in ‘nls’ solver configuration to nonzero is rather
tricky - the active contact points must not change during the test. This can be ensured by a sufficient initial penetration
and large enough contact boundary polygons (hard!), or by tweaking the dw_contact_plane term to mask points only
by undeformed coordinates.

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source code

r"""
Elastic contact planes simulating an indentation test.

Four contact planes bounded by polygons (triangles in this case) form a very
rigid pyramid shape simulating an indentor.

Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
+ \sum_{i=1}^4 \int_{\Gamma_i} \ul{v} \cdot f^i(d(\ul{u})) \ul{n^i}
= 0 \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl} + \delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.

Notes
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-----

Even though the material is linear elastic and small deformations are used, the
problem is highly nonlinear due to contacts with the planes.

Checking the tangent matrix by finite differences by setting 'check' in 'nls'

solver configuration to nonzero is rather tricky - the active contact points
must not change during the test. This can be ensured by a sufficient initial
penetration and large enough contact boundary polygons (hard!), or by tweaking
the dw_contact_plane term to mask points only by undeformed coordinates.
"""
from __future__ import absolute_import
from sfepy import data_dir
from sfepy.mechanics.matcoefs import stiffness_from_lame
from six.moves import range

filename_mesh = data_dir + '/meshes/3d/cube_medium_hexa.mesh'

k = 1e5 # Elastic plane stiffness for positive penetration.

f0 = 1e2 # Force at zero penetration.
dn = 0.2 # x or y component magnitude of normals.
ds = 0.25 # Boundary polygon size in horizontal directions.
az = 0.4 # Anchor z coordinate.

options = {
'ts' : 'ts',
'nls' : 'newton',
'ls' : 'lsd',

'output_format': 'vtk',
}

fields = {
'displacement': ('real', 3, 'Omega', 1),
}

materials = {
'solid' : ({
'D': stiffness_from_lame(dim=3, lam=5.769, mu=3.846),
},),
'cp0' : ({
'f' : [k, f0],
'.n' : [dn, 0.0, 1.0],
'.a' : [0.0, 0.0, az],
'.bs' : [[0.0, 0.0, az],
[-ds, -ds, az],
[-ds, ds, az]],
},),
'cp1' : ({
'f' : [k, f0],
'.n' : [-dn, 0.0, 1.0],
'.a' : [0.0, 0.0, az],
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'.bs' : [[0.0, 0.0, az],
[ds, -ds, az],
[ds, ds, az]],
},),
'cp2' : ({
'f' : [k, f0],
'.n' : [0.0, dn, 1.0],
'.a' : [0.0, 0.0, az],
'.bs' : [[0.0, 0.0, az],
[-ds, -ds, az],
[ds, -ds, az]],
},),
'cp3' : ({
'f' : [k, f0],
'.n' : [0.0, -dn, 1.0],
'.a' : [0.0, 0.0, az],
'.bs' : [[0.0, 0.0, az],
[-ds, ds, az],
[ds, ds, az]],
},),
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
}

regions = {
'Omega' : 'all',
'Bottom' : ('vertices in (z < -0.499)', 'facet'),
'Top' : ('vertices in (z > 0.499)', 'facet'),
}

ebcs = {
'fixed' : ('Bottom', {'u.all' : 0.0}),
}

equations = {
'elasticity' :
"""dw_lin_elastic.2.Omega(solid.D, v, u)
+ dw_contact_plane.2.Top(cp0.f, cp0.n, cp0.a, cp0.bs, v, u)
+ dw_contact_plane.2.Top(cp1.f, cp1.n, cp1.a, cp1.bs, v, u)
+ dw_contact_plane.2.Top(cp2.f, cp2.n, cp2.a, cp2.bs, v, u)
+ dw_contact_plane.2.Top(cp3.f, cp3.n, cp3.a, cp3.bs, v, u)
= 0""",
}

solvers = {
'lsd' : ('ls.scipy_direct', {}),
'lsi' : ('ls.petsc', {
'method' : 'cg',
'eps_r' : 1e-8,
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'i_max' : 3000,
}),
'newton' : ('nls.newton', {
'i_max' : 10,
'eps_a' : 1e-10,
'check' : 0,
'delta' : 1e-6,
}),
}

def main():
import os

import numpy as nm
import matplotlib.pyplot as plt

from sfepy.discrete.fem import MeshIO

import sfepy.linalg as la
from sfepy.mechanics.contact_bodies import (ContactPlane, plot_polygon,
plot_points)

conf_dir = os.path.dirname(__file__)
io = MeshIO.any_from_filename(filename_mesh, prefix_dir=conf_dir)
bb = io.read_bounding_box()
outline = [vv for vv in la.combine(zip(*bb))]

ax = plot_points(None, nm.array(outline), 'r*')

for name in ['cp%d' % ii for ii in range(4)]:
cpc = materials[name][0]
cp = ContactPlane(cpc['.a'], cpc['.n'], cpc['.bs'])

v1, v2 = la.get_perpendiculars(cp.normal)

ax = plot_polygon(ax, cp.bounds)
ax = plot_polygon(ax, nm.r_[cp.anchor[None, :],
cp.anchor[None, :] + cp.normal[None, :]])
ax = plot_polygon(ax, nm.r_[cp.anchor[None, :],
cp.anchor[None, :] + v1])
ax = plot_polygon(ax, nm.r_[cp.anchor[None, :],
cp.anchor[None, :] + v2])

plt.show()

if __name__ == '__main__':
main()

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linear_elasticity/elastic_contact_sphere.py

Description
Elastic contact sphere simulating an indentation test.
Find 𝑢 such that:
∫︁ ∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) + 𝑣 · 𝑓 (𝑑(𝑢))𝑛(𝑢) = 0 ,
Ω Γ

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

Notes

Even though the material is linear elastic and small deformations are used, the problem is highly nonlinear due to
contacts with the sphere. See also elastic_contact_planes.py example.

source code

r"""
Elastic contact sphere simulating an indentation test.
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Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
+ \int_{\Gamma} \ul{v} \cdot f(d(\ul{u})) \ul{n}(\ul{u})
= 0 \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl} + \delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.

Notes
-----

Even though the material is linear elastic and small deformations are used, the
problem is highly nonlinear due to contacts with the sphere. See also
elastic_contact_planes.py example.
"""
from __future__ import absolute_import
from sfepy import data_dir
from sfepy.mechanics.matcoefs import stiffness_from_lame

filename_mesh = data_dir + '/meshes/3d/cube_medium_hexa.mesh'

k = 1e5 # Elastic sphere stiffness for positive penetration.

f0 = 1e-2 # Force at zero penetration.

options = {
'nls' : 'newton',
'ls' : 'ls',

'output_format': 'vtk',
}

fields = {
'displacement': ('real', 3, 'Omega', 1),
}

materials = {
'solid' : ({
'D': stiffness_from_lame(dim=3, lam=5.769, mu=3.846),
},),
'cs' : ({
'f' : [k, f0],
'.c' : [0.0, 0.0, 1.2],
'.r' : 0.8,
},),
}
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variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
}

regions = {
'Omega' : 'all',
'Bottom' : ('vertices in (z < -0.499)', 'facet'),
'Top' : ('vertices in (z > 0.499)', 'facet'),
}

ebcs = {
'fixed' : ('Bottom', {'u.all' : 0.0}),
}

equations = {
'elasticity' :
"""dw_lin_elastic.2.Omega(solid.D, v, u)
+ dw_contact_sphere.2.Top(cs.f, cs.c, cs.r, v, u)
= 0""",
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 20,
'eps_a' : 1e-1,
'ls_on' : 2.0,
'check' : 0,
'delta' : 1e-6,
}),
}

def main():
import os

import numpy as nm
import matplotlib.pyplot as plt

from sfepy.discrete.fem import MeshIO

import sfepy.linalg as la
from sfepy.mechanics.contact_bodies import ContactSphere, plot_points

conf_dir = os.path.dirname(__file__)
io = MeshIO.any_from_filename(filename_mesh, prefix_dir=conf_dir)
bb = io.read_bounding_box()
outline = [vv for vv in la.combine(zip(*bb))]

ax = plot_points(None, nm.array(outline), 'r*')

csc = materials['cs'][0]
cs = ContactSphere(csc['.c'], csc['.r'])
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pps = (bb[1] - bb[0]) * nm.random.rand(5000, 3) + bb[0]

mask = cs.mask_points(pps, 0.0)

ax = plot_points(ax, cs.centre[None, :], 'b*', ms=30)

ax = plot_points(ax, pps[mask], 'kv')
ax = plot_points(ax, pps[~mask], 'r.')

plt.show()

if __name__ == '__main__':
main()

linear_elasticity/elastic_shifted_periodic.py

Description
Linear elasticity with linear combination constraints and periodic boundary conditions.
The linear combination constraints are used to apply periodic boundary conditions with a shift in the second axis
direction.
Find 𝑢 such that:
∫︁ ∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) = − 𝑣·𝜎·𝑛, ∀𝑣 ,
Ω Γ𝑏𝑜𝑡𝑡𝑜𝑚
𝑢 = 0 on Γ𝑙𝑒𝑓 𝑡 ,
𝑢1 = 𝑢2 = 0 on Γ𝑟𝑖𝑔ℎ𝑡 ,
𝑢(𝑥) = 𝑢(𝑦) for 𝑥 ∈ Γ𝑏𝑜𝑡𝑡𝑜𝑚 , 𝑦 ∈ Γ𝑡𝑜𝑝 , 𝑦 = 𝑃1 (𝑥) ,
𝑢(𝑥) = 𝑢(𝑦) + 𝑎(𝑦) for 𝑥 ∈ Γ𝑛𝑒𝑎𝑟 , 𝑦 ∈ Γ𝑓 𝑎𝑟 , 𝑦 = 𝑃2 (𝑥) ,

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 ,

and the traction 𝜎 · 𝑛 = 𝑝¯𝐼 · 𝑛 is given in terms of traction pressure 𝑝¯. The function 𝑎(𝑦) is given (the shift), 𝑃1 and
𝑃2 are the periodic coordinate mappings.
View the results using:

$ ./postproc.py block.vtk --wireframe -b --only-names=u -d'u,plot_displacements,rel_

˓→scaling=1,color_kind="scalars",color_name="von_mises_stress"'

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source code

r"""
Linear elasticity with linear combination constraints and periodic boundary
conditions.

The linear combination constraints are used to apply periodic boundary

conditions with a shift in the second axis direction.

Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
= - \int_{\Gamma_{bottom}} \ul{v} \cdot \ull{\sigma} \cdot \ul{n}
\;, \quad \forall \ul{v} \;,

\ul{u} = 0 \mbox{ on } \Gamma_{left} \;,

u_1 = u_2 = 0 \mbox{ on } \Gamma_{right} \;,

\ul{u}(\ul{x}) = \ul{u}(\ul{y}) \mbox{ for }

\ul{x} \in \Gamma_{bottom}, \ul{y} \in \Gamma_{top},
\ul{y} = P_1(\ul{x}) \;,
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\ul{u}(\ul{x}) = \ul{u}(\ul{y}) + a(\ul{y}) \mbox{ for }

\ul{x} \in \Gamma_{near}, \ul{y} \in \Gamma_{far},
\ul{y} = P_2(\ul{x}) \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;,

and the traction :math:`\ull{\sigma} \cdot \ul{n} = \bar{p} \ull{I} \cdot

\ul{n}` is given in terms of traction pressure :math:`\bar{p}`. The function
:math:`a(\ul{y})` is given (the shift), :math:`P_1` and :math:`P_2` are the
periodic coordinate mappings.

View the results using::

$ ./postproc.py block.vtk --wireframe -b --only-names=u -d'u,plot_displacements,rel_

˓→scaling=1,color_kind="scalars",color_name="von_mises_stress"'
"""
from __future__ import absolute_import
import numpy as nm

from sfepy.mechanics.matcoefs import stiffness_from_lame

from sfepy.mechanics.tensors import get_von_mises_stress
import sfepy.discrete.fem.periodic as per
from sfepy import data_dir

filename_mesh = data_dir + '/meshes/3d/block.mesh'

options = {
'nls' : 'newton',
'ls' : 'ls',
'post_process_hook' : 'post_process'
}

def post_process(out, pb, state, extend=False):

"""
Calculate and output strain and stress for given displacements.
"""
from sfepy.base.base import Struct

ev = pb.evaluate
stress = ev('ev_cauchy_stress.2.Omega(solid.D, u)', mode='el_avg')

vms = get_von_mises_stress(stress.squeeze())
vms.shape = (vms.shape[0], 1, 1, 1)
out['von_mises_stress'] = Struct(name='output_data', mode='cell',
data=vms, dofs=None)

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return out

def linear_tension(ts, coor, mode=None, **kwargs):

if mode == 'qp':
val = 0.1 * nm.sin(coor[:, 0] / 10.)

return {'val' : val.reshape((coor.shape[0], 1, 1))}

def get_shift(ts, coors, region=None):

val = nm.zeros_like(coors, dtype=nm.float64)

val[:, 1] = 0.1 * coors[:, 0]

return val

functions = {
'get_shift' : (get_shift,),
'linear_tension' : (linear_tension,),
'match_y_plane' : (per.match_y_plane,),
'match_z_plane' : (per.match_z_plane,),
}

fields = {
'displacement': ('real', 3, 'Omega', 1),
}

materials = {
'solid' : ({
'D' : stiffness_from_lame(3, lam=5.769, mu=3.846),
},),
'load' : (None, 'linear_tension')
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
}

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < -4.99)', 'facet'),
'Right' : ('vertices in (x > 4.99)', 'facet'),
'Bottom' : ('vertices in (z < -0.99)', 'facet'),
'Top' : ('vertices in (z > 0.99)', 'facet'),
'Near' : ('vertices in (y < -0.99)', 'facet'),
'Far' : ('vertices in (y > 0.99)', 'facet'),
}

ebcs = {
'fix1' : ('Left', {'u.all' : 0.0}),
'fix2' : ('Right', {'u.[1,2]' : 0.0}),
}

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epbcs = {
'periodic' : (['Bottom', 'Top'], {'u.all' : 'u.all'}, 'match_z_plane'),
}

lcbcs = {
'shifted' : (('Near', 'Far'),
{'u.all' : 'u.all'},
'match_y_plane', 'shifted_periodic',
'get_shift'),
}

equations = {
'elasticity' : """
dw_lin_elastic.2.Omega(solid.D, v, u)
= -dw_surface_ltr.2.Bottom(load.val, v)
""",
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
}),
}

linear_elasticity/elastodynamic.py

Description
The linear elastodynamics solution of an iron plate impact problem.
Find 𝑢 such that:

𝜕2𝑢
∫︁ ∫︁
𝜌𝑣 2 + 𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) = 0 , ∀𝑣 ,
Ω 𝜕𝑡 Ω

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

Notes

The used elastodynamics solvers expect that the total vector of DOFs contains three blocks in this order: the dis-
placements, the velocities, and the accelerations. This is achieved by defining three unknown variables 'u', 'du',
'ddu' and the corresponding test variables, see the variables definition. Then the solver can automatically extract
the mass, damping (zero here), and stiffness matrices as diagonal blocks of the global matrix. Note also the use of
the 'dw_zero' (do-nothing) term that prevents the velocity-related variables to be removed from the equations in the
absence of a damping term.

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Usage Examples

Run with the default settings (the Newmark method, 3D problem, results stored in output/ed/):

python simple.py examples/linear_elasticity/elastodynamic.py

Solve using the Bathe method:

python simple.py examples/linear_elasticity/elastodynamic.py -O "ts='tsb'"

View the resulting deformation using:

• color by 𝑢:

python postproc.py output/ed/user_block.h5 -b --wireframe --only-names=u -d 'u,plot_

˓→displacements,rel_scaling=1e3'

• color by 𝑒(𝑢):

python postproc.py output/ed/user_block.h5 -b --wireframe --only-names=u -d 'u,plot_

˓→displacements,rel_scaling=1e3,color_kind="tensors",color_name="cauchy_strain"'

• color by 𝜎(𝑢):

python postproc.py output/ed/user_block.h5 -b --wireframe --only-names=u -d 'u,plot_

˓→displacements,rel_scaling=1e3,color_kind="tensors",color_name="cauchy_stress"'

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r"""
The linear elastodynamics solution of an iron plate impact problem.

Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} \rho \ul{v} \pddiff{\ul{u}}{t}
+ \int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
= 0
\;, \quad \forall \ul{v} \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.

Notes
-----

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The used elastodynamics solvers expect that the total vector of DOFs contains
three blocks in this order: the displacements, the velocities, and the
accelerations. This is achieved by defining three unknown variables ``'u'``,
``'du'``, ``'ddu'`` and the corresponding test variables, see the `variables`
definition. Then the solver can automatically extract the mass, damping (zero
here), and stiffness matrices as diagonal blocks of the global matrix. Note
also the use of the ``'dw_zero'`` (do-nothing) term that prevents the
velocity-related variables to be removed from the equations in the absence of a
damping term.

Usage Examples
--------------

Run with the default settings (the Newmark method, 3D problem, results stored
in ``output/ed/``)::

python simple.py sfepy/examples/linear_elasticity/elastodynamic.py

Solve using the Bathe method::

python simple.py sfepy/examples/linear_elasticity/elastodynamic.py -O "ts='tsb'"

View the resulting deformation using:

- color by :math:`\ul{u}`::

python postproc.py output/ed/user_block.h5 -b --wireframe --only-names=u -d 'u,plot_

˓→displacements,rel_scaling=1e3'

- color by :math:`\ull{e}(\ul{u})`::

python postproc.py output/ed/user_block.h5 -b --wireframe --only-names=u -d 'u,plot_

˓→displacements,rel_scaling=1e3,color_kind="tensors",color_name="cauchy_strain"'

- color by :math:`\ull{\sigma}(\ul{u})`::

python postproc.py output/ed/user_block.h5 -b --wireframe --only-names=u -d 'u,plot_

˓→displacements,rel_scaling=1e3,color_kind="tensors",color_name="cauchy_stress"'
"""
from __future__ import absolute_import

import numpy as nm

import sfepy.mechanics.matcoefs as mc
from sfepy.discrete.fem.meshio import UserMeshIO
from sfepy.mesh.mesh_generators import gen_block_mesh

plane = 'strain'
dim = 3

# Material parameters.
E = 200e9
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nu = 0.3
rho = 7800.0

lam, mu = mc.lame_from_youngpoisson(E, nu, plane=plane)

# Longitudinal and shear wave propagation speeds.
cl = nm.sqrt((lam + 2.0 * mu) / rho)
cs = nm.sqrt(mu / rho)

# Initial velocity.
v0 = 1.0

# Mesh dimensions and discretization.

d = 2.5e-3
if dim == 3:
L = 4 * d
dims = [L, d, d]

shape = [21, 6, 6]
#shape = [101, 26, 26]

else:
L = 2 * d
dims = [L, 2 * d]

shape = [61, 61]

# shape = [361, 361]

# Element size.
H = L / (shape[0] - 1)

# Time-stepping parameters.
# Note: the Courant number C0 = dt * cl / H
dt = H / cl # C0 = 1

if dim == 3:
t1 = 0.9 * L / cl

else:
t1 = 1.5 * d / cl

def mesh_hook(mesh, mode):

"""
Generate the block mesh.
"""
if mode == 'read':
mesh = gen_block_mesh(dims, shape, 0.5 * nm.array(dims),
name='user_block', verbose=False)
return mesh

elif mode == 'write':

pass

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def post_process(out, problem, state, extend=False):
"""
Calculate and output strain and stress for given displacements.
"""
from sfepy.base.base import Struct

ev = problem.evaluate
strain = ev('ev_cauchy_strain.i.Omega(u)', mode='el_avg', verbose=False)
stress = ev('ev_cauchy_stress.i.Omega(solid.D, u)', mode='el_avg',
copy_materials=False, verbose=False)

out['cauchy_strain'] = Struct(name='output_data', mode='cell',

data=strain, dofs=None)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)

return out

filename_mesh = UserMeshIO(mesh_hook)

regions = {
'Omega' : 'all',
'Impact' : ('vertices in (x < 1e-12)', 'facet'),
}
if dim == 3:
regions.update({
'Symmetry-y' : ('vertices in (y < 1e-12)', 'facet'),
'Symmetry-z' : ('vertices in (z < 1e-12)', 'facet'),
})

# Iron.
materials = {
'solid' : ({
'D': mc.stiffness_from_youngpoisson(dim=dim, young=E, poisson=nu,
plane=plane),
'rho': rho,
},),
}

fields = {
'displacement': ('real', 'vector', 'Omega', 1),
}

integrals = {
'i' : 2,
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'du' : ('unknown field', 'displacement', 1),
'ddu' : ('unknown field', 'displacement', 2),
'v' : ('test field', 'displacement', 'u'),
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'dv' : ('test field', 'displacement', 'du'),
'ddv' : ('test field', 'displacement', 'ddu'),
}

ebcs = {
'Impact' : ('Impact', {'u.0' : 0.0, 'du.0' : 0.0, 'ddu.0' : 0.0}),
}
if dim == 3:
ebcs.update({
'Symmtery-y' : ('Symmetry-y',
{'u.1' : 0.0, 'du.1' : 0.0, 'ddu.1' : 0.0}),
'Symmetry-z' : ('Symmetry-z',
{'u.2' : 0.0, 'du.2' : 0.0, 'ddu.2' : 0.0}),
})

def get_ic(coor, ic, mode='u'):

val = nm.zeros_like(coor)
if mode == 'u':
val[:, 0] = 0.0

elif mode == 'du':

val[:, 0] = -1.0

return val

functions = {
'get_ic_u' : (get_ic,),
'get_ic_du' : (lambda coor, ic: get_ic(coor, None, mode='du'),),
}

ics = {
'ic' : ('Omega', {'u.all' : 'get_ic_u', 'du.all' : 'get_ic_du'}),
}

equations = {
'balance_of_forces' :
"""dw_dot.i.Omega(solid.rho, ddv, ddu)
+ dw_zero.i.Omega(dv, du)
+ dw_lin_elastic.i.Omega(solid.D, v, u) = 0""",
}

solvers = {
'ls' : ('ls.scipy_direct', {
'use_presolve' : True,
}),
'ls-i' : ('ls.petsc', {
'method' : 'cg',
'precond' : 'icc',
'i_max' : 150,
'eps_a' : 1e-32,
'eps_r' : 1e-8,
'verbose' : 2,
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}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-6,
'eps_r' : 1e-6,
}),
'tsvv' : ('ts.velocity_verlet', {
# Excplicit method -> requires at least 10x smaller dt than the other
# time-stepping solvers.
't0' : 0.0,
't1' : t1,
'dt' : dt,
'n_step' : None,

'is_linear' : True,

'verbose' : 1,
}),
'tsn' : ('ts.newmark', {
't0' : 0.0,
't1' : t1,
'dt' : dt,
'n_step' : None,

'is_linear' : True,

'beta' : 0.25,
'gamma' : 0.5,

'verbose' : 1,
}),
'tsga' : ('ts.generalized_alpha', {
't0' : 0.0,
't1' : t1,
'dt' : dt,
'n_step' : None,

'is_linear' : True,

'rho_inf' : 0.5,
'alpha_m' : None,
'alpha_f' : None,
'beta' : None,
'gamma' : None,

'verbose' : 1,
}),
'tsb' : ('ts.bathe', {
't0' : 0.0,
't1' : t1,
'dt' : dt,
'n_step' : None,
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'is_linear' : True,

'verbose' : 1,
}),
}

options = {
'ts' : 'tsn',
# 'ts' : 'tsb',
'nls' : 'newton',
# 'ls' : 'ls-i',
'ls' : 'ls',

'save_times' : 20,

'active_only' : False,

'output_format' : 'h5',
'output_dir' : 'output/ed',
'post_process_hook' : 'post_process',
}

linear_elasticity/its2D_1.py

Description
Diametrically point loaded 2-D disk. See Primer.
Find 𝑢 such that:
∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) = 0 , ∀𝑣 ,
Ω

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

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source code

r"""
Diametrically point loaded 2-D disk. See :ref:`sec-primer`.

Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
= 0
\;, \quad \forall \ul{v} \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.
"""
from __future__ import absolute_import
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
from sfepy.discrete.fem.utils import refine_mesh
from sfepy import data_dir
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# Fix the mesh file name if you run this file outside the SfePy directory.
filename_mesh = data_dir + '/meshes/2d/its2D.mesh'

refinement_level = 0
filename_mesh = refine_mesh(filename_mesh, refinement_level)

output_dir = '.' # set this to a valid directory you have write access to

young = 2000.0 # Young's modulus [MPa]

poisson = 0.4 # Poisson's ratio

options = {
'output_dir' : output_dir,
}

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < 0.001)', 'facet'),
'Bottom' : ('vertices in (y < 0.001)', 'facet'),
'Top' : ('vertex 2', 'vertex'),
}

materials = {
'Asphalt' : ({'D': stiffness_from_youngpoisson(2, young, poisson)},),
'Load' : ({'.val' : [0.0, -1000.0]},),
}

fields = {
'displacement': ('real', 'vector', 'Omega', 1),
}

equations = {
'balance_of_forces' :
"""dw_lin_elastic.2.Omega(Asphalt.D, v, u)
= dw_point_load.0.Top(Load.val, v)""",
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
}

ebcs = {
'XSym' : ('Bottom', {'u.1' : 0.0}),
'YSym' : ('Left', {'u.0' : 0.0}),
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
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'eps_a' : 1e-6,
}),
}

linear_elasticity/its2D_2.py

Description
Diametrically point loaded 2-D disk with postprocessing. See Primer.
Find 𝑢 such that:
∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) = 0 , ∀𝑣 ,
Ω

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

source code

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r"""
Diametrically point loaded 2-D disk with postprocessing. See
:ref:`sec-primer`.

Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
= 0
\;, \quad \forall \ul{v} \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.
"""

from __future__ import absolute_import

from sfepy.examples.linear_elasticity.its2D_1 import *

from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson

def stress_strain(out, pb, state, extend=False):

"""
Calculate and output strain and stress for given displacements.
"""
from sfepy.base.base import Struct

ev = pb.evaluate
strain = ev('ev_cauchy_strain.2.Omega(u)', mode='el_avg')
stress = ev('ev_cauchy_stress.2.Omega(Asphalt.D, u)', mode='el_avg',
copy_materials=False)

out['cauchy_strain'] = Struct(name='output_data', mode='cell',

data=strain, dofs=None)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)

return out

asphalt = materials['Asphalt'][0]
asphalt.update({'D' : stiffness_from_youngpoisson(2, young, poisson)})
options.update({'post_process_hook' : 'stress_strain',})

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linear_elasticity/its2D_3.py

Description
Diametrically point loaded 2-D disk with nodal stress calculation. See Primer.
Find 𝑢 such that:
∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) = 0 , ∀𝑣 ,
Ω

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

source code

r"""
Diametrically point loaded 2-D disk with nodal stress calculation. See
:ref:`sec-primer`.

Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
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= 0
\;, \quad \forall \ul{v} \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.
"""
from __future__ import print_function
from __future__ import absolute_import
from sfepy.examples.linear_elasticity.its2D_1 import *

from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson

from sfepy.discrete.fem.geometry_element import geometry_data
from sfepy.discrete import FieldVariable
from sfepy.discrete.fem import Field
import numpy as nm

gdata = geometry_data['2_3']
nc = len(gdata.coors)

def nodal_stress(out, pb, state, extend=False, integrals=None):

'''
Calculate stresses at nodal points.
'''

# Point load.
mat = pb.get_materials()['Load']
P = 2.0 * mat.get_data('special', 'val')[1]

# Calculate nodal stress.

pb.time_update()

if integrals is None: integrals = pb.get_integrals()

stress = pb.evaluate('ev_cauchy_stress.ivn.Omega(Asphalt.D, u)', mode='qp',

integrals=integrals, copy_materials=False)
sfield = Field.from_args('stress', nm.float64, (3,),
pb.domain.regions['Omega'])
svar = FieldVariable('sigma', 'parameter', sfield,
primary_var_name='(set-to-None)')
svar.set_from_qp(stress, integrals['ivn'])

print('\n==================================================================')
print('Given load = %.2f N' % -P)
print('\nAnalytical solution')
print('===================')
print('Horizontal tensile stress = %.5e MPa/mm' % (-2.*P/(nm.pi*150.)))
print('Vertical compressive stress = %.5e MPa/mm' % (-6.*P/(nm.pi*150.)))
print('\nFEM solution')
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print('============')
print('Horizontal tensile stress = %.5e MPa/mm' % (svar()[0]))
print('Vertical compressive stress = %.5e MPa/mm' % (-svar()[1]))
print('==================================================================')
return out

asphalt = materials['Asphalt'][0]
asphalt.update({'D' : stiffness_from_youngpoisson(2, young, poisson)})
options.update({'post_process_hook' : 'nodal_stress',})

integrals = {
'ivn' : ('custom', gdata.coors, [gdata.volume / nc] * nc),
}

linear_elasticity/its2D_4.py

Description
Diametrically point loaded 2-D disk with postprocessing and probes. See Primer.
Use it as follows (assumes running from the sfepy directory; on Windows, you may need to prefix all the commands
with “python ” and remove “./”):
1. solve the problem:

./simple.py examples/linear_elasticity/its2D_4.py

2. optionally, view the results:

./postproc.py its2D.h5 -b

3. optionally, convert results to VTK, and view again:

./extractor.py -d its2D.h5
./postproc.py its2D.vtk -b

4. probe the data:

./probe.py examples/linear_elasticity/its2D_4.py its2D.h5

Find 𝑢 such that:

∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) = 0 , ∀𝑣 ,
Ω

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

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source code

r"""
Diametrically point loaded 2-D disk with postprocessing and probes. See
:ref:`sec-primer`.

Use it as follows (assumes running from the sfepy directory; on Windows, you
may need to prefix all the commands with "python " and remove "./"):

1. solve the problem::

./simple.py sfepy/examples/linear_elasticity/its2D_4.py

2. optionally, view the results::

./postproc.py its2D.h5 -b

3. optionally, convert results to VTK, and view again::

./extractor.py -d its2D.h5
./postproc.py its2D.vtk -b

4. probe the data::

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(continued from previous page)

./probe.py sfepy/examples/linear_elasticity/its2D_4.py its2D.h5

Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
= 0
\;, \quad \forall \ul{v} \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.
"""
from __future__ import absolute_import
from sfepy.examples.linear_elasticity.its2D_1 import *

from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson

from six.moves import range

def stress_strain(out, pb, state, extend=False):

"""
Calculate and output strain and stress for given displacements.
"""
from sfepy.base.base import Struct

ev = pb.evaluate
strain = ev('ev_cauchy_strain.2.Omega(u)', mode='el_avg')
stress = ev('ev_cauchy_stress.2.Omega(Asphalt.D, u)', mode='el_avg')

out['cauchy_strain'] = Struct(name='output_data', mode='cell',

data=strain, dofs=None)
out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)

return out

def gen_lines(problem):
from sfepy.discrete.probes import LineProbe
ps0 = [[0.0, 0.0], [ 0.0, 0.0]]
ps1 = [[75.0, 0.0], [ 0.0, 75.0]]

# Use adaptive probe with 10 inital points.

n_point = -10

labels = ['%s -> %s' % (p0, p1) for p0, p1 in zip(ps0, ps1)]
probes = []
for ip in range(len(ps0)):
p0, p1 = ps0[ip], ps1[ip]
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probes.append(LineProbe(p0, p1, n_point))

return probes, labels

def probe_hook(data, probe, label, problem):

import matplotlib.pyplot as plt
import matplotlib.font_manager as fm

def get_it(name, var_name):

var = problem.create_variables([var_name])[var_name]
var.set_data(data[name].data)

pars, vals = probe(var)

vals = vals.squeeze()
return pars, vals

results = {}
results['u'] = get_it('u', 'u')
results['cauchy_strain'] = get_it('cauchy_strain', 's')
results['cauchy_stress'] = get_it('cauchy_stress', 's')

fig = plt.figure()
plt.clf()
fig.subplots_adjust(hspace=0.4)
plt.subplot(311)
pars, vals = results['u']
for ic in range(vals.shape[1]):
plt.plot(pars, vals[:,ic], label=r'$u_{%d}$' % (ic + 1),
lw=1, ls='-', marker='+', ms=3)
plt.ylabel('displacements')
plt.xlabel('probe %s' % label, fontsize=8)
plt.legend(loc='best', prop=fm.FontProperties(size=10))

sym_indices = ['11', '22', '12']

plt.subplot(312)
pars, vals = results['cauchy_strain']
for ic in range(vals.shape[1]):
plt.plot(pars, vals[:,ic], label=r'$e_{%s}$' % sym_indices[ic],
lw=1, ls='-', marker='+', ms=3)
plt.ylabel('Cauchy strain')
plt.xlabel('probe %s' % label, fontsize=8)
plt.legend(loc='best', prop=fm.FontProperties(size=8))

plt.subplot(313)
pars, vals = results['cauchy_stress']
for ic in range(vals.shape[1]):
plt.plot(pars, vals[:,ic], label=r'$\sigma_{%s}$' % sym_indices[ic],
lw=1, ls='-', marker='+', ms=3)
plt.ylabel('Cauchy stress')
plt.xlabel('probe %s' % label, fontsize=8)
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plt.legend(loc='best', prop=fm.FontProperties(size=8))

return plt.gcf(), results

materials['Asphalt'][0].update({'D' : stiffness_from_youngpoisson(2, young, poisson)})

# Update fields and variables to be able to use probes for tensors.

fields.update({
'sym_tensor': ('real', 3, 'Omega', 0),
})

variables.update({
's' : ('parameter field', 'sym_tensor', None),
})

options.update({
'output_format' : 'h5', # VTK reader cannot read cell data yet for probing
'post_process_hook' : 'stress_strain',
'gen_probes' : 'gen_lines',
'probe_hook' : 'probe_hook',
})

linear_elasticity/its2D_interactive.py

Description
Diametrically point loaded 2-D disk, using commands for interactive use. See Primer.
The script combines the functionality of all the its2D_?.py examples and allows setting various simulation parameters,
namely:
• material parameters
• displacement field approximation order
• uniform mesh refinement level
The example shows also how to probe the results as in linear_elasticity/its2D_4.py, and how to display the results using
Mayavi. Using sfepy.discrete.probes allows correct probing of fields with the approximation order greater than
one.
In the SfePy top-level directory the following command can be used to get usage information:

python examples/linear_elasticity/its2D_interactive.py -h

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Notes

The --probe and --show options work simultaneously only if Mayavi and Matplotlib use the same backend type (for
example wx).
source code

#!/usr/bin/env python
"""
Diametrically point loaded 2-D disk, using commands for interactive use. See
:ref:`sec-primer`.

The script combines the functionality of all the ``its2D_?.py`` examples and
allows setting various simulation parameters, namely:

- material parameters
- displacement field approximation order
- uniform mesh refinement level

The example shows also how to probe the results as in

:ref:`linear_elasticity-its2D_4`, and how to display the results using Mayavi.
Using :mod:`sfepy.discrete.probes` allows correct probing of fields with the
approximation order greater than one.

In the SfePy top-level directory the following command can be used to get usage
information::

python sfepy/examples/linear_elasticity/its2D_interactive.py -h

Notes
-----

The ``--probe`` and ``--show`` options work simultaneously only if Mayavi and
Matplotlib use the same backend type (for example wx).
"""
from __future__ import absolute_import
import sys
from six.moves import range
sys.path.append('.')
from argparse import ArgumentParser, RawDescriptionHelpFormatter

import numpy as nm
import matplotlib.pyplot as plt

from sfepy.base.base import assert_, output, ordered_iteritems, IndexedStruct

from sfepy.discrete import (FieldVariable, Material, Integral, Integrals,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
from sfepy.solvers.auto_fallback import AutoDirect
from sfepy.solvers.nls import Newton
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from sfepy.discrete.fem.geometry_element import geometry_data
from sfepy.discrete.probes import LineProbe
from sfepy.discrete.projections import project_by_component

from sfepy.examples.linear_elasticity.its2D_2 import stress_strain

from sfepy.examples.linear_elasticity.its2D_3 import nodal_stress

def gen_lines(problem):
"""
Define two line probes.

Additional probes can be added by appending to `ps0` (start points) and

`ps1` (end points) lists.
"""
ps0 = [[0.0, 0.0], [0.0, 0.0]]
ps1 = [[75.0, 0.0], [0.0, 75.0]]

# Use enough points for higher order approximations.

n_point = 1000

labels = ['%s -> %s' % (p0, p1) for p0, p1 in zip(ps0, ps1)]
probes = []
for ip in range(len(ps0)):
p0, p1 = ps0[ip], ps1[ip]
probes.append(LineProbe(p0, p1, n_point))

return probes, labels

def probe_results(u, strain, stress, probe, label):

"""
Probe the results using the given probe and plot the probed values.
"""
results = {}

pars, vals = probe(u)

results['u'] = (pars, vals)
pars, vals = probe(strain)
results['cauchy_strain'] = (pars, vals)
pars, vals = probe(stress)
results['cauchy_stress'] = (pars, vals)

fig = plt.figure()
plt.clf()
fig.subplots_adjust(hspace=0.4)
plt.subplot(311)
pars, vals = results['u']
for ic in range(vals.shape[1]):
plt.plot(pars, vals[:,ic], label=r'$u_{%d}$' % (ic + 1),
lw=1, ls='-', marker='+', ms=3)
plt.ylabel('displacements')
plt.xlabel('probe %s' % label, fontsize=8)
plt.legend(loc='best', fontsize=10)
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sym_indices = ['11', '22', '12']

plt.subplot(312)
pars, vals = results['cauchy_strain']
for ic in range(vals.shape[1]):
plt.plot(pars, vals[:,ic], label=r'$e_{%s}$' % sym_indices[ic],
lw=1, ls='-', marker='+', ms=3)
plt.ylabel('Cauchy strain')
plt.xlabel('probe %s' % label, fontsize=8)
plt.legend(loc='best', fontsize=10)

plt.subplot(313)
pars, vals = results['cauchy_stress']
for ic in range(vals.shape[1]):
plt.plot(pars, vals[:,ic], label=r'$\sigma_{%s}$' % sym_indices[ic],
lw=1, ls='-', marker='+', ms=3)
plt.ylabel('Cauchy stress')
plt.xlabel('probe %s' % label, fontsize=8)
plt.legend(loc='best', fontsize=10)

return fig, results

helps = {
'young' : "the Young's modulus [default: %(default)s]",
'poisson' : "the Poisson's ratio [default: %(default)s]",
'load' : "the vertical load value (negative means compression)"
" [default: %(default)s]",
'order' : 'displacement field approximation order [default: %(default)s]',
'refine' : 'uniform mesh refinement level [default: %(default)s]',
'probe' : 'probe the results',
'show' : 'show the results figure',
}

def main():
from sfepy import data_dir

parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('--young', metavar='float', type=float,
action='store', dest='young',
default=2000.0, help=helps['young'])
parser.add_argument('--poisson', metavar='float', type=float,
action='store', dest='poisson',
default=0.4, help=helps['poisson'])
parser.add_argument('--load', metavar='float', type=float,
action='store', dest='load',
default=-1000.0, help=helps['load'])
parser.add_argument('--order', metavar='int', type=int,
action='store', dest='order',
default=1, help=helps['order'])
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parser.add_argument('-r', '--refine', metavar='int', type=int,
action='store', dest='refine',
default=0, help=helps['refine'])
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
parser.add_argument('-p', '--probe',
action="store_true", dest='probe',
default=False, help=helps['probe'])
options = parser.parse_args()

assert_((0.0 < options.poisson < 0.5),

"Poisson's ratio must be in ]0, 0.5[!")
assert_((0 < options.order),
'displacement approximation order must be at least 1!')

output('using values:')
output(" Young's modulus:", options.young)
output(" Poisson's ratio:", options.poisson)
output(' vertical load:', options.load)
output('uniform mesh refinement level:', options.refine)

# Build the problem definition.

mesh = Mesh.from_file(data_dir + '/meshes/2d/its2D.mesh')
domain = FEDomain('domain', mesh)

if options.refine > 0:
for ii in range(options.refine):
output('refine %d...' % ii)
domain = domain.refine()
output('... %d nodes %d elements'
% (domain.shape.n_nod, domain.shape.n_el))

omega = domain.create_region('Omega', 'all')

left = domain.create_region('Left',
'vertices in x < 0.001', 'facet')
bottom = domain.create_region('Bottom',
'vertices in y < 0.001', 'facet')
top = domain.create_region('Top', 'vertex 2', 'vertex')

field = Field.from_args('fu', nm.float64, 'vector', omega,

approx_order=options.order)

u = FieldVariable('u', 'unknown', field)

v = FieldVariable('v', 'test', field, primary_var_name='u')

D = stiffness_from_youngpoisson(2, options.young, options.poisson)

asphalt = Material('Asphalt', D=D)

load = Material('Load', values={'.val' : [0.0, options.load]})

integral = Integral('i', order=2*options.order)

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integral0 = Integral('i', order=0)

t1 = Term.new('dw_lin_elastic(Asphalt.D, v, u)',
integral, omega, Asphalt=asphalt, v=v, u=u)
t2 = Term.new('dw_point_load(Load.val, v)',
integral0, top, Load=load, v=v)
eq = Equation('balance', t1 - t2)
eqs = Equations([eq])

xsym = EssentialBC('XSym', bottom, {'u.1' : 0.0})

ysym = EssentialBC('YSym', left, {'u.0' : 0.0})

ls = AutoDirect({})

nls_status = IndexedStruct()
nls = Newton({}, lin_solver=ls, status=nls_status)

pb = Problem('elasticity', equations=eqs)

pb.set_bcs(ebcs=Conditions([xsym, ysym]))

pb.set_solver(nls)

# Solve the problem.

variables = pb.solve()
output(nls_status)

# Postprocess the solution.

out = variables.create_output()
out = stress_strain(out, pb, variables, extend=True)
pb.save_state('its2D_interactive.vtk', out=out)

gdata = geometry_data['2_3']
nc = len(gdata.coors)

integral_vn = Integral('ivn', coors=gdata.coors,

weights=[gdata.volume / nc] * nc)

nodal_stress(out, pb, variables, integrals=Integrals([integral_vn]))

if options.probe:
# Probe the solution.
probes, labels = gen_lines(pb)

sfield = Field.from_args('sym_tensor', nm.float64, 3, omega,

approx_order=options.order - 1)
stress = FieldVariable('stress', 'parameter', sfield,
primary_var_name='(set-to-None)')
strain = FieldVariable('strain', 'parameter', sfield,
primary_var_name='(set-to-None)')

cfield = Field.from_args('component', nm.float64, 1, omega,

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approx_order=options.order - 1)
component = FieldVariable('component', 'parameter', cfield,
primary_var_name='(set-to-None)')

ev = pb.evaluate
order = 2 * (options.order - 1)
strain_qp = ev('ev_cauchy_strain.%d.Omega(u)' % order, mode='qp')
stress_qp = ev('ev_cauchy_stress.%d.Omega(Asphalt.D, u)' % order,
mode='qp', copy_materials=False)

project_by_component(strain, strain_qp, component, order)

project_by_component(stress, stress_qp, component, order)

all_results = []
for ii, probe in enumerate(probes):
fig, results = probe_results(u, strain, stress, probe, labels[ii])

fig.savefig('its2D_interactive_probe_%d.png' % ii)
all_results.append(results)

for ii, results in enumerate(all_results):

output('probe %d:' % ii)
output.level += 2
for key, res in ordered_iteritems(results):
output(key + ':')
val = res[1]
output(' min: %+.2e, mean: %+.2e, max: %+.2e'
% (val.min(), val.mean(), val.max()))
output.level -= 2

if options.show:
# Show the solution. If the approximation order is greater than 1, the
# extra DOFs are simply thrown away.
from sfepy.postprocess.viewer import Viewer

view = Viewer('its2D_interactive.vtk')
view(vector_mode='warp_norm', rel_scaling=1,
is_scalar_bar=True, is_wireframe=True)

if __name__ == '__main__':
main()

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linear_elasticity/linear_elastic.py

Description
Linear elasticity with given displacements.
Find 𝑢 such that:
∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) = 0 , ∀𝑣 ,
Ω

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

This example models a cylinder that is fixed at one end while the second end has a specified displacement of 0.01 in the
x direction (this boundary condition is named 'Displaced'). There is also a specified displacement of 0.005 in the z
direction for points in the region labeled 'SomewhereTop'. This boundary condition is named 'PerturbedSurface'.
The region 'SomewhereTop' is specified as those vertices for which:

(z > 0.017) & (x > 0.03) & (x < 0.07)

The displacement field (three DOFs/node) in the 'Omega region' is approximated using P1 (four-node tetrahedral)
finite elements. The material is linear elastic and its properties are specified as Lamé parameters 𝜆 and 𝜇 (see http:
//en.wikipedia.org/wiki/Lam%C3%A9_parameters)
The output is the displacement for each vertex, saved by default to cylinder.vtk. View the results using:

$ ./postproc.py cylinder.vtk --wireframe -b --only-names=u -d'u,plot_displacements,rel_

˓→scaling=1'

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source code

# -*- coding: utf-8 -*-

r"""
Linear elasticity with given displacements.

Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
= 0
\;, \quad \forall \ul{v} \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.

This example models a cylinder that is fixed at one end while the second end
has a specified displacement of 0.01 in the x direction (this boundary
condition is named ``'Displaced'``). There is also a specified displacement of
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0.005 in the z direction for points in the region labeled
``'SomewhereTop'``. This boundary condition is named
``'PerturbedSurface'``. The region ``'SomewhereTop'`` is specified as those
vertices for which::

(z > 0.017) & (x > 0.03) & (x < 0.07)

The displacement field (three DOFs/node) in the ``'Omega region'`` is

approximated using P1 (four-node tetrahedral) finite elements. The material is
linear elastic and its properties are specified as Lamé parameters
:math:`\lambda` and :math:`\mu` (see
http://en.wikipedia.org/wiki/Lam%C3%A9_parameters)

The output is the displacement for each vertex, saved by default to

cylinder.vtk. View the results using::

$ ./postproc.py cylinder.vtk --wireframe -b --only-names=u -d'u,plot_displacements,rel_

˓→scaling=1'
"""
from __future__ import absolute_import
from sfepy import data_dir
from sfepy.mechanics.matcoefs import stiffness_from_lame

filename_mesh = data_dir + '/meshes/3d/cylinder.mesh'

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < 0.001)', 'facet'),
'Right' : ('vertices in (x > 0.099)', 'facet'),
'SomewhereTop' : ('vertices in (z > 0.017) & (x > 0.03) & (x < 0.07)',
'vertex'),
}

materials = {
'solid' : ({'D': stiffness_from_lame(dim=3, lam=1e1, mu=1e0)},),
}

fields = {
'displacement': ('real', 'vector', 'Omega', 1),
}

integrals = {
'i' : 1,
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
}

ebcs = {
'Fixed' : ('Left', {'u.all' : 0.0}),
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'Displaced' : ('Right', {'u.0' : 0.01, 'u.[1,2]' : 0.0}),
'PerturbedSurface' : ('SomewhereTop', {'u.2' : 0.005}),
}

equations = {
'balance_of_forces' :
"""dw_lin_elastic.i.Omega(solid.D, v, u) = 0""",
}

solvers = {
'ls': ('ls.auto_direct', {}),
'newton': ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
}),
}

linear_elasticity/linear_elastic_damping.py

Description
Time-dependent linear elasticity with a simple damping.
Find 𝑢 such that:
∫︁ ∫︁
𝜕𝑢
𝑐𝑣· + 𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) = 0 , ∀𝑣 ,
Ω 𝜕𝑡 Ω

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

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source code

r"""
Time-dependent linear elasticity with a simple damping.

Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} c\ \ul{v} \cdot \pdiff{\ul{u}}{t}
+ \int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
= 0
\;, \quad \forall \ul{v} \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.
"""
from __future__ import print_function
from __future__ import absolute_import
from copy import deepcopy
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import numpy as nm
from sfepy.examples.linear_elasticity.linear_elastic import \
filename_mesh, materials, regions, fields, ebcs, \
integrals, solvers

def print_times(problem, state):

print(nm.array(problem.ts.times))

options = {
'ts' : 'ts',
'save_times' : 'all',
'post_process_hook_final' : print_times,
'output_format' : 'h5',
}

variables = {
'u' : ('unknown field', 'displacement', 0, 1),
'v' : ('test field', 'displacement', 'u'),
}

# Put density to 'solid'.

materials = deepcopy(materials)
materials['solid'][0].update({'c' : 1000.0})

# Moving the PerturbedSurface region.

ebcs = deepcopy(ebcs)
ebcs['PerturbedSurface'][1].update({'u.0' : 'ebc_sin'})

def ebc_sin(ts, coors, **kwargs):

val = 0.01 * nm.sin(2.0*nm.pi*ts.nt)
return nm.tile(val, (coors.shape[0],))

equations = {
'balance_of_forces in time' :
"""dw_dot.i.Omega( solid.c, v, du/dt )
+ dw_lin_elastic.i.Omega( solid.D, v, u ) = 0""",
}

def adapt_time_step(ts, status, adt, problem, verbose=False):

if ts.time > 0.5:
ts.set_time_step(0.1)

return True

solvers = deepcopy(solvers) # Do not spoil linear_elastic.py namespace in tests.

solvers.update({
'ts' : ('ts.adaptive', {
't0' : 0.0,
't1' : 1.0,
'dt' : None,
'n_step' : 101,
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'adapt_fun' : adapt_time_step,
'verbose' : 1,
}),
})

ls = solvers['ls']
ls[1].update({'use_presolve' : True})

functions = {
'ebc_sin' : (ebc_sin,),
}

linear_elasticity/linear_elastic_iga.py

Description
Linear elasticity solved in a single patch NURBS domain using the isogeometric analysis (IGA) approach.
Find 𝑢 such that:
∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) = 0 , ∀𝑣 ,
Ω

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

The domain geometry was created by:

$ ./script/gen_iga_patch.py -d [1,0.5,0.1] -s [11,5,3] --degrees [2,2,2] -o meshes/iga/

˓→block3d.iga

View the results using:

$ ./postproc.py block3d.vtk --wireframe -b

$ ./postproc.py block3d.vtk --wireframe -b -d 'u,plot_displacements,rel_scaling=1e0'

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source code
r"""
Linear elasticity solved in a single patch NURBS domain using the isogeometric
analysis (IGA) approach.

Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
= 0
\;, \quad \forall \ul{v} \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.

The domain geometry was created by::

$ ./script/gen_iga_patch.py -d [1,0.5,0.1] -s [11,5,3] --degrees [2,2,2] -o meshes/iga/

˓→block3d.iga
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View the results using::

$ ./postproc.py block3d.vtk --wireframe -b

$ ./postproc.py block3d.vtk --wireframe -b -d 'u,plot_displacements,rel_scaling=1e0'
"""
from __future__ import absolute_import
from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy import data_dir

filename_domain = data_dir + '/meshes/iga/block3d.iga'

regions = {
'Omega' : 'all',
'Gamma1' : ('vertices of set xi00', 'facet'),
'Gamma2' : ('vertices of set xi01', 'facet'),
}

materials = {
'solid' : ({
'D' : stiffness_from_lame(3, lam=5.769, mu=3.846),
},),
}

fields = {
'displacement': ('real', 'vector', 'Omega', None, 'H1', 'iga'),
}

integrals = {
'i' : 3,
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
}

ebcs = {
'u1' : ('Gamma1', {'u.all' : 0.0}),
'u2' : ('Gamma2', {'u.0' : 0.1, 'u.[1,2]' : 'get_ebcs'}),
}

def get_ebcs(ts, coors, **kwargs):

import numpy as nm

aux = nm.empty_like(coors[:, 1:])

aux[:, 0] = 0.1 * coors[:, 1]
aux[:, 1] = -0.05 + 0.03 * nm.sin(coors[:, 1] * 5 * nm.pi)

return aux

functions = {
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'get_ebcs' : (get_ebcs,),
}

equations = {
'balance_of_forces' : """dw_lin_elastic.i.Omega(solid.D, v, u) = 0""",
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
}),
}

linear_elasticity/linear_elastic_interactive.py

Description
missing description!
source code
#!/usr/bin/env python
from argparse import ArgumentParser
import numpy as nm

import sys
sys.path.append('.')

from sfepy.base.base import IndexedStruct

from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.solvers.ls import ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.postprocess.viewer import Viewer
from sfepy.mechanics.matcoefs import stiffness_from_lame

def shift_u_fun(ts, coors, bc=None, problem=None, shift=0.0):

"""
Define a displacement depending on the y coordinate.
"""
val = shift * coors[:,1]**2

return val

helps = {
'show' : 'show the results figure',
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}

def main():
from sfepy import data_dir

parser = ArgumentParser()
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
options = parser.parse_args()

mesh = Mesh.from_file(data_dir + '/meshes/2d/rectangle_tri.mesh')

domain = FEDomain('domain', mesh)

min_x, max_x = domain.get_mesh_bounding_box()[:,0]

eps = 1e-8 * (max_x - min_x)
omega = domain.create_region('Omega', 'all')
gamma1 = domain.create_region('Gamma1',
'vertices in x < %.10f ' % (min_x + eps),
'facet')
gamma2 = domain.create_region('Gamma2',
'vertices in x > %.10f ' % (max_x - eps),
'facet')

field = Field.from_args('fu', nm.float64, 'vector', omega,

approx_order=2)

u = FieldVariable('u', 'unknown', field)

v = FieldVariable('v', 'test', field, primary_var_name='u')

m = Material('m', D=stiffness_from_lame(dim=2, lam=1.0, mu=1.0))

f = Material('f', val=[[0.02], [0.01]])

integral = Integral('i', order=3)

t1 = Term.new('dw_lin_elastic(m.D, v, u)',
integral, omega, m=m, v=v, u=u)
t2 = Term.new('dw_volume_lvf(f.val, v)', integral, omega, f=f, v=v)
eq = Equation('balance', t1 + t2)
eqs = Equations([eq])

fix_u = EssentialBC('fix_u', gamma1, {'u.all' : 0.0})

bc_fun = Function('shift_u_fun', shift_u_fun,

extra_args={'shift' : 0.01})
shift_u = EssentialBC('shift_u', gamma2, {'u.0' : bc_fun})

ls = ScipyDirect({})

nls_status = IndexedStruct()
nls = Newton({}, lin_solver=ls, status=nls_status)
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pb = Problem('elasticity', equations=eqs)
pb.save_regions_as_groups('regions')

pb.set_bcs(ebcs=Conditions([fix_u, shift_u]))

pb.set_solver(nls)

status = IndexedStruct()
variables = pb.solve(status=status)

print('Nonlinear solver status:\n', nls_status)

print('Stationary solver status:\n', status)

pb.save_state('linear_elasticity.vtk', variables)

if options.show:
view = Viewer('linear_elasticity.vtk')
view(vector_mode='warp_norm', rel_scaling=2,
is_scalar_bar=True, is_wireframe=True)

if __name__ == '__main__':
main()

linear_elasticity/linear_elastic_tractions.py

Description
Linear elasticity with pressure traction load on a surface and constrained to one-dimensional motion.
Find 𝑢 such that:
∫︁ ∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) = − 𝑣·𝜎·𝑛, ∀𝑣 ,
Ω Γ𝑟𝑖𝑔ℎ𝑡

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

and 𝜎 · 𝑛 = 𝑝¯𝐼 · 𝑛 with given traction pressure 𝑝¯.

The function verify_tractions() is called after the solution to verify that the inner surface tractions correspond to
the load applied to the external surface. Try running the example with different approximation orders and/or uniform
refinement levels:
• the default options:

python simple.py examples/linear_elasticity/linear_elastic_tractions.py -O␣

˓→refinement_level=0 -d approx_order=1

• refine once:

python simple.py examples/linear_elasticity/linear_elastic_tractions.py -O␣

˓→refinement_level=1 -d approx_order=1

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• use the tri-quadratic approximation (Q2):

python simple.py examples/linear_elasticity/linear_elastic_tractions.py -O␣
˓→refinement_level=0 -d approx_order=2

source code
r"""
Linear elasticity with pressure traction load on a surface and constrained to
one-dimensional motion.

Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
= - \int_{\Gamma_{right}} \ul{v} \cdot \ull{\sigma} \cdot \ul{n}
\;, \quad \forall \ul{v} \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.
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and :math:`\ull{\sigma} \cdot \ul{n} = \bar{p} \ull{I} \cdot \ul{n}`

with given traction pressure :math:`\bar{p}`.

The function :func:`verify_tractions()` is called after the solution to verify

that the inner surface tractions correspond to the load applied to the external
surface. Try running the example with different approximation orders and/or uniform␣
˓→refinement levels:

- the default options::

python simple.py sfepy/examples/linear_elasticity/linear_elastic_tractions.py -O␣

˓→refinement_level=0 -d approx_order=1

- refine once::

python simple.py sfepy/examples/linear_elasticity/linear_elastic_tractions.py -O␣

˓→refinement_level=1 -d approx_order=1

- use the tri-quadratic approximation (Q2)::

python simple.py sfepy/examples/linear_elasticity/linear_elastic_tractions.py -O␣

˓→refinement_level=0 -d approx_order=2
"""
from __future__ import absolute_import
import numpy as nm
from sfepy.base.base import output
from sfepy.mechanics.matcoefs import stiffness_from_lame

def linear_tension(ts, coor, mode=None, **kwargs):

if mode == 'qp':
val = nm.tile(1.0, (coor.shape[0], 1, 1))

return {'val' : val}

def verify_tractions(out, problem, state, extend=False):

"""
Verify that the inner surface tractions correspond to the load applied
to the external surface.
"""
from sfepy.mechanics.tensors import get_full_indices
from sfepy.discrete import Material, Function

load_force = problem.evaluate(
'ev_integrate_mat.2.Right(load.val, u)'
)
output('surface load force:', load_force)

def eval_force(region_name):
strain = problem.evaluate(
'ev_cauchy_strain.i.%s(u)' % region_name, mode='qp',
verbose=False,
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)
D = problem.evaluate(
'ev_integrate_mat.i.%s(solid.D, u)' % region_name,
mode='qp',
verbose=False,
)

normal = nm.array([1, 0, 0], dtype=nm.float64)

s2f = get_full_indices(len(normal))
stress = nm.einsum('cqij,cqjk->cqik', D, strain)
# Full (matrix) form of stress.
mstress = stress[..., s2f, 0]

# Force in normal direction.

force = nm.einsum('cqij,i,j->cq', mstress, normal, normal)

def get_force(ts, coors, mode=None, **kwargs):

if mode == 'qp':
return {'force' : force.reshape(coors.shape[0], 1, 1)}
aux = Material('aux', function=Function('get_force', get_force))

middle_force = - problem.evaluate(
'ev_integrate_mat.i.%s(aux.force, u)' % region_name,
aux=aux,
verbose=False,
)
output('%s section axial force:' % region_name, middle_force)

eval_force('Left')
eval_force('Middle')
eval_force('Right')

return out

def define(approx_order=1):
"""Define the problem to solve."""
from sfepy import data_dir

filename_mesh = data_dir + '/meshes/3d/block.mesh'

options = {
'nls' : 'newton',
'ls' : 'ls',
'post_process_hook' : 'verify_tractions',
}

functions = {
'linear_tension' : (linear_tension,),
}

fields = {
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'displacement': ('real', 3, 'Omega', approx_order),
}

materials = {
'solid' : ({'D': stiffness_from_lame(3, lam=5.769, mu=3.846)},),
'load' : (None, 'linear_tension')
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
}

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < -4.99)', 'facet'),
# Use a parent region to select only facets belonging to cells in the
# parent region. Otherwise, each facet is in the region two times, with
# opposite normals.
'Middle' : ('vertices in (x > -1e-10) & (x < 1e-10)', 'facet', 'Rhalf'),
'Rhalf' : 'vertices in x > -1e-10',
'Right' : ('vertices in (x > 4.99)', 'facet'),
}

ebcs = {
'fixb' : ('Left', {'u.all' : 0.0}),
'fixt' : ('Right', {'u.[1,2]' : 0.0}),
}

integrals = {
'i' : 2 * approx_order,
}

##
# Balance of forces.
equations = {
'elasticity' :
"""dw_lin_elastic.i.Omega( solid.D, v, u )
= - dw_surface_ltr.i.Right( load.val, v )""",
}

##
# Solvers etc.
solvers = {
'ls' : ('ls.auto_direct', {}),
'newton' : ('nls.newton',
{ 'i_max' : 1,
'eps_a' : 1e-10,
'eps_r' : 1.0,
'macheps' : 1e-16,
# Linear system error < (eps_a * lin_red).
'lin_red' : 1e-2,
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'ls_red' : 0.1,
'ls_red_warp' : 0.001,
'ls_on' : 1.1,
'ls_min' : 1e-5,
'check' : 0,
'delta' : 1e-6,
})
}

return locals()

linear_elasticity/linear_elastic_up.py

Description
Nearly incompressible linear elasticity in mixed displacement-pressure formulation with comments.
Find 𝑢, 𝑝 such that:
∫︁ ∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) − 𝑝∇·𝑣 =0, ∀𝑣 ,
Ω Ω
∫︁ ∫︁
− 𝑞∇·𝑢− 𝛾𝑞𝑝 = 0 , ∀𝑞 .
Ω Ω

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source code

r"""
Nearly incompressible linear elasticity in mixed displacement-pressure
formulation with comments.

Find :math:`\ul{u}`, :math:`p` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
- \int_{\Omega} p\ \nabla \cdot \ul{v}
= 0
\;, \quad \forall \ul{v} \;,

- \int_{\Omega} q\ \nabla \cdot \ul{u}

- \int_{\Omega} \gamma q p
= 0
\;, \quad \forall q \;.
"""
#!
#! Linear Elasticity
#! =================
#$ \centerline{Example input file, \today}

#! This file models a cylinder that is fixed at one end while the
#! second end has a specified displacement of 0.02 in the x direction
#! (this boundary condition is named PerturbedSurface).
#! The output is the displacement for each node, saved by default to
#! simple_out.vtk. The material is linear elastic.
from __future__ import absolute_import
from sfepy import data_dir

from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson_mixed, bulk_from_

˓→youngpoisson

#! Mesh
#! ----

dim = 3
approx_u = '3_4_P1'
approx_p = '3_4_P0'
order = 2
filename_mesh = data_dir + '/meshes/3d/cylinder.mesh'
#! Regions
#! -------
#! Whole domain 'Omega', left and right ends.
regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < 0.001)', 'facet'),
'Right' : ('vertices in (x > 0.099)', 'facet'),
}
#! Materials
#! ---------
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#! The linear elastic material model is used.
materials = {
'solid' : ({'D' : stiffness_from_youngpoisson_mixed(dim, 0.7e9, 0.4),
'gamma' : 1.0/bulk_from_youngpoisson(0.7e9, 0.4)},),
}
#! Fields
#! ------
#! A field is used to define the approximation on a (sub)domain
fields = {
'displacement': ('real', 'vector', 'Omega', 1),
'pressure' : ('real', 'scalar', 'Omega', 0),
}
#! Integrals
#! ---------
#! Define the integral type Volume/Surface and quadrature rule.
integrals = {
'i' : order,
}
#! Variables
#! ---------
#! Define displacement and pressure fields and corresponding fields
#! for test variables.
variables = {
'u' : ('unknown field', 'displacement'),
'v' : ('test field', 'displacement', 'u'),
'p' : ('unknown field', 'pressure'),
'q' : ('test field', 'pressure', 'p'),
}
#! Boundary Conditions
#! -------------------
#! The left end of the cylinder is fixed (all DOFs are zero) and
#! the 'right' end has non-zero displacements only in the x direction.
ebcs = {
'Fixed' : ('Left', {'u.all' : 0.0}),
'PerturbedSurface' : ('Right', {'u.0' : 0.02, 'u.1' : 0.0}),
}
#! Equations
#! ---------
#! The weak formulation of the linear elastic problem.
equations = {
'balance_of_forces' :
""" dw_lin_elastic.i.Omega( solid.D, v, u )
- dw_stokes.i.Omega( v, p )
= 0 """,
'pressure constraint' :
"""- dw_stokes.i.Omega( u, q )
- dw_dot.i.Omega( solid.gamma, q, p )
= 0""",
}
#! Solvers
#! -------
#! Define linear and nonlinear solver.
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#! Even linear problems are solved by a nonlinear solver - only one
#! iteration is needed and the final residual is obtained for free.
solvers = {
'ls': ('ls.schur_mumps', {
'schur_variables': ['p'],
'fallback': 'ls2'
}),
'ls2': ('ls.scipy_umfpack', {'fallback': 'ls3'}),
'ls3': ('ls.scipy_superlu', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-2,
'eps_r' : 1e-10,
}),
}
#! Options
#! -------
#! Various problem-specific options.
options = {
'output_dir' : './output',
'absolute_mesh_path' : True,
}

linear_elasticity/linear_viscoelastic.py

Description
Linear viscoelasticity with pressure traction load on a surface and constrained to one-dimensional motion.
The fading memory terms require an unloaded initial configuration, so the load starts in the second time step. The load
is then held for the first half of the total time interval, and released afterwards.
This example uses exponential fading memory kernel ℋ𝑖𝑗𝑘𝑙 (𝑡) = ℋ𝑖𝑗𝑘𝑙 (0)𝑒−𝑑𝑡 with decay 𝑑. Two equation kinds
are supported - ‘th’ and ‘eth’. In ‘th’ mode the tabulated kernel is linearly interpolated to required times using
interp_conv_mat(). In ‘eth’ mode, the computation is exact for exponential kernels.
Find 𝑢 such that:
∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢)
Ω
∫︁ [︂∫︁ 𝑡 ]︂
𝜕𝑢
+ ℋ𝑖𝑗𝑘𝑙 (𝑡 − 𝜏 ) 𝑒𝑘𝑙 ( (𝜏 )) d𝜏 𝑒𝑖𝑗 (𝑣)
Ω 0 𝜕𝜏
∫︁
=− 𝑣 · 𝜎 · 𝑛 , ∀𝑣 ,
Γ𝑟𝑖𝑔ℎ𝑡

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 ,

ℋ𝑖𝑗𝑘𝑙 (0) has the same structure as 𝐷𝑖𝑗𝑘𝑙 and 𝜎 · 𝑛 = 𝑝¯𝐼 · 𝑛 with given traction pressure 𝑝¯.

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Notes

Because this example is run also as a test, it uses by default very few time steps. Try changing that.

Visualization

The output file is assumed to be ‘block.h5’ in the working directory. Change it appropriately for your situation.

Deforming mesh

Try to play with the following:

$ ./postproc.py block.h5 -b --only-names=u -d 'u,plot_displacements,rel_scaling=1e0,

˓→opacity=1.0,color_name="viscous_stress",color_kind="tensors"' --wireframe

Use:

$ ./postproc.py -l block.h5

to see names and kinds of variables.

Time history plots

Run the following:

$ python examples/linear_elasticity/linear_viscoelastic.py -h
$ python examples/linear_elasticity/linear_viscoelastic.py block.h5

Try comparing ‘th’ and ‘eth’ versions, e.g., for n_step = 201, and f_n_step = 51. There is a visible notch on viscous
stress curves in the ‘th’ mode, as the fading memory kernel is cut off before it goes close enough to zero.

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source code

#!/usr/bin/env python
r"""
Linear viscoelasticity with pressure traction load on a surface and constrained
to one-dimensional motion.

The fading memory terms require an unloaded initial configuration, so the load
starts in the second time step. The load is then held for the first half of the
total time interval, and released afterwards.

This example uses exponential fading memory kernel

:math:`\Hcal_{ijkl}(t) = \Hcal_{ijkl}(0) e^{-d t}` with decay
:math:`d`. Two equation kinds are supported - 'th' and 'eth'. In 'th'
mode the tabulated kernel is linearly interpolated to required times
using :func:`interp_conv_mat()`. In 'eth' mode, the computation is exact
for exponential kernels.

Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u}) \\
+ \int_{\Omega} \left [\int_0^t
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\Hcal_{ijkl}(t-\tau)\,e_{kl}(\pdiff{\ul{u}}{\tau}(\tau)) \difd{\tau}
\right]\,e_{ij}(\ul{v}) \\
= - \int_{\Gamma_{right}} \ul{v} \cdot \ull{\sigma} \cdot \ul{n}
\;, \quad \forall \ul{v} \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;,

:math:`\Hcal_{ijkl}(0)` has the same structure as :math:`D_{ijkl}` and

:math:`\ull{\sigma} \cdot \ul{n} = \bar{p} \ull{I} \cdot \ul{n}` with
given traction pressure :math:`\bar{p}`.

Notes
-----

Because this example is run also as a test, it uses by default very few time
steps. Try changing that.

Visualization
-------------

The output file is assumed to be 'block.h5' in the working directory. Change it

appropriately for your situation.

Deforming mesh
^^^^^^^^^^^^^^

Try to play with the following::

$ ./postproc.py block.h5 -b --only-names=u -d 'u,plot_displacements,rel_scaling=1e0,

˓→opacity=1.0,color_name="viscous_stress",color_kind="tensors"' --wireframe

Use::

$ ./postproc.py -l block.h5

to see names and kinds of variables.

Time history plots

^^^^^^^^^^^^^^^^^^

Run the following::

$ python sfepy/examples/linear_elasticity/linear_viscoelastic.py -h
$ python sfepy/examples/linear_elasticity/linear_viscoelastic.py block.h5

Try comparing 'th' and 'eth' versions, e.g., for n_step = 201, and f_n_step =
51. There is a visible notch on viscous stress curves in the 'th' mode, as the
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(continued from previous page)

fading memory kernel is cut off before it goes close enough to zero.
"""
from __future__ import absolute_import
import numpy as nm

import sys
sys.path.append('.')

from sfepy.base.base import output

from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.homogenization.utils import interp_conv_mat
from sfepy import data_dir
import six

def linear_tension(ts, coors, mode=None, verbose=True, **kwargs):

if mode == 'qp':
val = 1.0 * ((ts.step > 0) and (ts.nt <= 0.5))

if verbose:
output('load:', val)

val = nm.tile(val, (coors.shape[0], 1, 1))

return {'val' : val}

def get_exp_fading_kernel(coef0, decay, times):

val = coef0[None, ...] * nm.exp(-decay * times[:, None, None])
return val

def get_th_pars(ts, coors, mode=None, times=None, kernel=None, **kwargs):

out = {}

if mode == 'special':
out['H'] = interp_conv_mat(kernel, ts, times)

elif mode == 'qp':

out['H0'] = kernel[0][None, ...]
out['Hd'] = nm.array([[[kernel[1, 0, 0] / kernel[0, 0, 0]]]])

return out

filename_mesh = data_dir + '/meshes/3d/block.mesh'

## Configure below. ##

# Time stepping times.

t0 = 0.0
t1 = 20.0
n_step = 21

# Fading memory times.

f_t0 = 0.0
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f_t1 = 5.0
f_n_step = 6

decay = 0.8
mode = 'eth'

## Configure above. ##

times = nm.linspace(f_t0, f_t1, f_n_step)

kernel = get_exp_fading_kernel(stiffness_from_lame(3, lam=1.0, mu=1.0),
decay, times)

dt = (t1 - t0) / (n_step - 1)

fading_memory_length = min(int((f_t1 - f_t0) / dt) + 1, n_step)
output('fading memory length:', fading_memory_length)

def post_process(out, pb, state, extend=False):

"""
Calculate and output strain and stress for given displacements.
"""
from sfepy.base.base import Struct

ev = pb.evaluate
strain = ev('ev_cauchy_strain.2.Omega(u)', mode='el_avg')
out['cauchy_strain'] = Struct(name='output_data', mode='cell',
data=strain, dofs=None)

estress = ev('ev_cauchy_stress.2.Omega(solid.D, u)', mode='el_avg')

out['cauchy_stress'] = Struct(name='output_data', mode='cell',
data=estress, dofs=None)

ts = pb.get_timestepper()
if mode == 'th':
vstress = ev('ev_cauchy_stress_th.2.Omega(ts, th.H, du/dt)',
ts=ts, mode='el_avg')
out['viscous_stress'] = Struct(name='output_data', mode='cell',
data=vstress, dofs=None)

else:
# The eth terms require 'preserve_caches=True' in order to have correct
# fading memory history.
vstress = ev('ev_cauchy_stress_eth.2.Omega(ts, th.H0, th.Hd, du/dt)',
ts=ts, mode='el_avg', preserve_caches=True)
out['viscous_stress'] = Struct(name='output_data', mode='cell',
data=vstress, dofs=None)

out['total_stress'] = Struct(name='output_data', mode='cell',

data=estress + vstress, dofs=None)

return out

options = {
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'ts' : 'ts',
'nls' : 'newton',
'ls' : 'ls',

'output_format' : 'h5',
'post_process_hook' : 'post_process',
}

functions = {
'linear_tension' : (linear_tension,),
'get_pars' : (lambda ts, coors, mode=None, **kwargs:
get_th_pars(ts, coors, mode, times=times, kernel=kernel,
**kwargs),),
}

fields = {
'displacement': ('real', 3, 'Omega', 1),
}

materials = {
'solid' : ({
'D' : stiffness_from_lame(3, lam=5.769, mu=3.846),
},),
'th' : 'get_pars',
'load' : 'linear_tension',
}

variables = {
'u' : ('unknown field', 'displacement', 0, fading_memory_length),
'v' : ('test field', 'displacement', 'u'),
}

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < -4.99)', 'facet'),
'Right' : ('vertices in (x > 4.99)', 'facet'),
}

ebcs = {
'fixb' : ('Left', {'u.all' : 0.0}),
'fixt' : ('Right', {'u.[1,2]' : 0.0}),
}

if mode == 'th':
# General form with tabulated kernel.
equations = {
'elasticity' :
"""dw_lin_elastic.2.Omega( solid.D, v, u )
+ dw_lin_elastic_th.2.Omega( ts, th.H, v, du/dt )
= - dw_surface_ltr.2.Right( load.val, v )""",
}

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else:
# Fast form that is exact for exponential kernels.
equations = {
'elasticity' :
"""dw_lin_elastic.2.Omega( solid.D, v, u )
+ dw_lin_elastic_eth.2.Omega( ts, th.H0, th.Hd, v, du/dt )
= - dw_surface_ltr.2.Right( load.val, v )""",
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
}),
'ts' : ('ts.simple', {
't0' : t0,
't1' : t1,
'dt' : None,
'n_step' : n_step,
'quasistatic' : True,
'verbose' : 1,
}),
}

def main():
"""
Plot the load, displacement, strain and stresses w.r.t. time.
"""
from argparse import ArgumentParser, RawDescriptionHelpFormatter
import matplotlib.pyplot as plt

import sfepy.postprocess.time_history as th

msgs = {
'node': 'plot displacements in given node [default: %(default)s]',
'element': 'plot tensors in given element [default: %(default)s]',
}

parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument(metavar='OUTPUT_FILE', dest='output_file',
help='output file in HDF5 format')
parser.add_argument('-n', '--node', type=int, metavar='ii',
action='store', dest='node',
default=512, help=msgs['node'])
parser.add_argument('-e', '--element', type=int, metavar='ii',
action='store', dest='element',
default=299, help=msgs['element'])
options = parser.parse_args()

filename = options.output_file
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tensor_names = ['cauchy_strain',
'cauchy_stress', 'viscous_stress', 'total_stress']
extract = ('u n %d, ' % options.node) \
+ ', '.join('%s e %d' % (name, options.element)
for name in tensor_names)
ths, ts = th.extract_time_history(filename, extract)

load = [linear_tension(ts, nm.array([0]),

mode='qp', verbose=False)['val'].squeeze()
for ii in ts]
load = nm.array(load)

normalized_kernel = kernel[:, 0, 0] / kernel[0, 0, 0]

plt.figure(1, figsize=(8, 10))

plt.subplots_adjust(hspace=0.3,
top=0.95, bottom=0.05, left=0.07, right=0.95)

plt.subplot(311)
plt.plot(times, normalized_kernel, lw=3)
plt.title('fading memory decay')
plt.xlabel('time')

plt.subplot(312)
plt.plot(ts.times, load, lw=3)
plt.title('load')
plt.xlabel('time')

displacements = ths['u'][options.node]

plt.subplot(313)
plt.plot(ts.times, displacements, lw=3)
plt.title('displacement components, node %d' % options.node)
plt.xlabel('time')

plt.figure(2, figsize=(8, 10))

plt.subplots_adjust(hspace=0.35,
top=0.95, bottom=0.05, left=0.07, right=0.95)

for ii, tensor_name in enumerate(tensor_names):

tensor = ths[tensor_name][options.element]

plt.subplot(411 + ii)
plt.plot(ts.times, tensor, lw=3)
plt.title('%s components, element %d' % (tensor_name, options.element))
plt.xlabel('time')

plt.show()

if __name__ == '__main__':
main()

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linear_elasticity/material_nonlinearity.py

Description
Example demonstrating how a linear elastic term can be used to solve an elasticity problem with a material nonlinearity.
∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) = 0 , ∀𝑣 ,
Ω

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

source code

# -*- coding: utf-8 -*-

r"""
Example demonstrating how a linear elastic term can be used to solve an
elasticity problem with a material nonlinearity.

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
= 0
\;, \quad \forall \ul{v} \;,
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(continued from previous page)

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.
"""
from __future__ import absolute_import
import numpy as nm

from sfepy.linalg import norm_l2_along_axis

from sfepy import data_dir
from sfepy.mechanics.matcoefs import stiffness_from_lame

filename_mesh = data_dir + '/meshes/3d/cylinder.mesh'

def post_process(out, pb, state, extend=False):

from sfepy.base.base import Struct

mu = pb.evaluate('ev_integrate_mat.2.Omega(nonlinear.mu, u)',
mode='el_avg', copy_materials=False, verbose=False)
out['mu'] = Struct(name='mu', mode='cell', data=mu, dofs=None)

strain = pb.evaluate('ev_cauchy_strain.2.Omega(u)', mode='el_avg')

out['strain'] = Struct(name='strain', mode='cell', data=strain, dofs=None)

return out

strains = [None]

def get_pars(ts, coors, mode='qp',

equations=None, term=None, problem=None, **kwargs):
"""
The material nonlinearity function - the Lamé coefficient `mu`
depends on the strain.
"""
if mode != 'qp': return

val = nm.empty(coors.shape[0], dtype=nm.float64)

val.fill(1e0)

order = term.integral.order
uvar = equations.variables['u']

strain = problem.evaluate('ev_cauchy_strain.%d.Omega(u)' % order,

u=uvar, mode='qp')
if ts.step > 0:
strain0 = strains[-1]

else:
strain0 = strain
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dstrain = (strain - strain0) / ts.dt

dstrain.shape = (strain.shape[0] * strain.shape[1], strain.shape[2])

norm = norm_l2_along_axis(dstrain)

val += norm

# Store history.
strains[0] = strain
return {'D': stiffness_from_lame(dim=3, lam=1e1, mu=val),
'mu': val.reshape(-1, 1, 1)}

def pull(ts, coors, **kwargs):

val = nm.empty_like(coors[:,0])
val.fill(0.01 * ts.step)

return val

functions = {
'get_pars' : (get_pars,),
'pull' : (pull,),
}

options = {
'ts' : 'ts',
'output_format' : 'h5',
'save_times' : 'all',

'post_process_hook' : 'post_process',
}

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < 0.001)', 'facet'),
'Right' : ('vertices in (x > 0.099)', 'facet'),
}

materials = {
'nonlinear' : 'get_pars',
}

fields = {
'displacement': ('real', 'vector', 'Omega', 1),
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
}

ebcs = {
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'Fixed' : ('Left', {'u.all' : 0.0}),
'Displaced' : ('Right', {'u.0' : 'pull', 'u.[1,2]' : 0.0}),
}

equations = {
'balance_of_forces in time' :
"""dw_lin_elastic.2.Omega(nonlinear.D, v, u) = 0""",
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton',
{'i_max' : 1,
'eps_a' : 1e-10,
'eps_r' : 1.0,
}),
'ts' : ('ts.simple',
{'t0' : 0.0,
't1' : 1.0,
'dt' : None,
'n_step' : 5,
'quasistatic' : True,
'verbose' : 1,
}),
}

linear_elasticity/modal_analysis.py

Description
Modal analysis of a linear elastic block in 2D or 3D.
The dimension of the problem is determined by the length of the vector in --dims option.
Optionally, a mesh file name can be given as a positional argument. In that case, the mesh generation options are
ignored.
The default material properties correspond to aluminium in the following units:
• length: m
• mass: kg
• stiffness / stress: Pa
• density: kg / m^3

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Examples

• Run with the default arguments, show results (color = strain):

python examples/linear_elasticity/modal_analysis.py --show

• Fix bottom surface of the domain, show 9 eigen-shapes:

python examples/linear_elasticity/modal_analysis.py -b cantilever -n 9 --show

• Increase mesh resolution:

python examples/linear_elasticity/modal_analysis.py -s 31,31 -n 9 --show

• Use 3D domain:
python examples/linear_elasticity/modal_analysis.py -d 1,1,1 -c 0,0,0 -s 8,8,8 --
˓→show

• Change the eigenvalue problem solver to LOBPCG:

python examples/linear_elasticity/modal_analysis.py --solver="eig.scipy_lobpcg,i_
˓→max:100,largest:False" --show

See sfepy.solvers.eigen for available solvers.

source code
#!/usr/bin/env python
"""
Modal analysis of a linear elastic block in 2D or 3D.

The dimension of the problem is determined by the length of the vector

in ``--dims`` option.

Optionally, a mesh file name can be given as a positional argument. In that

case, the mesh generation options are ignored.

The default material properties correspond to aluminium in the following units:

- length: m
- mass: kg
- stiffness / stress: Pa
- density: kg / m^3

Examples
--------

- Run with the default arguments, show results (color = strain)::

python sfepy/examples/linear_elasticity/modal_analysis.py --show

- Fix bottom surface of the domain, show 9 eigen-shapes::

python sfepy/examples/linear_elasticity/modal_analysis.py -b cantilever -n 9 --show

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(continued from previous page)

- Increase mesh resolution::

python sfepy/examples/linear_elasticity/modal_analysis.py -s 31,31 -n 9 --show

- Use 3D domain::

python sfepy/examples/linear_elasticity/modal_analysis.py -d 1,1,1 -c 0,0,0 -s 8,8,8␣

˓→--show

- Change the eigenvalue problem solver to LOBPCG::

python sfepy/examples/linear_elasticity/modal_analysis.py --solver="eig.scipy_lobpcg,

˓→i_max:100,largest:False" --show

See :mod:`sfepy.solvers.eigen` for available solvers.

"""
from __future__ import absolute_import
import sys
import six
from six.moves import range
sys.path.append('.')
from argparse import ArgumentParser, RawDescriptionHelpFormatter

import numpy as nm
import scipy.sparse.linalg as sla

from sfepy.base.base import assert_, output, Struct

from sfepy.discrete import (FieldVariable, Material, Integral, Integrals,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
from sfepy.mesh.mesh_generators import gen_block_mesh
from sfepy.solvers import Solver

helps = {
'dims' :
'dimensions of the block [default: %(default)s]',
'centre' :
'centre of the block [default: %(default)s]',
'shape' :
'numbers of vertices along each axis [default: %(default)s]',
'bc_kind' :
'kind of Dirichlet boundary conditions on the bottom and top surfaces,'
' one of: free, cantilever, fixed [default: %(default)s]',
'axis' :
'the axis index of the block that the bottom and top surfaces are related'
' to [default: %(default)s]',
'young' : "the Young's modulus [default: %(default)s]",
'poisson' : "the Poisson's ratio [default: %(default)s]",
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'density' : "the material density [default: %(default)s]",
'order' : 'displacement field approximation order [default: %(default)s]',
'n_eigs' : 'the number of eigenvalues to compute [default: %(default)s]',
'ignore' : 'if given, the number of eigenvalues to ignore (e.g. rigid'
' body modes); has precedence over the default setting determined by'
' --bc-kind [default: %(default)s]',
'solver' : 'the eigenvalue problem solver to use. It should be given'
' as a comma-separated list: solver_kind,option0:value0,option1:value1,...'
' [default: %(default)s]',
'show' : 'show the results figure',
}

def main():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('-d', '--dims', metavar='dims',
action='store', dest='dims',
default='[1.0, 1.0]', help=helps['dims'])
parser.add_argument('-c', '--centre', metavar='centre',
action='store', dest='centre',
default='[0.0, 0.0]', help=helps['centre'])
parser.add_argument('-s', '--shape', metavar='shape',
action='store', dest='shape',
default='[11, 11]', help=helps['shape'])
parser.add_argument('-b', '--bc-kind', metavar='kind',
action='store', dest='bc_kind',
choices=['free', 'cantilever', 'fixed'],
default='free', help=helps['bc_kind'])
parser.add_argument('-a', '--axis', metavar='0, ..., dim, or -1',
type=int, action='store', dest='axis',
default=-1, help=helps['axis'])
parser.add_argument('--young', metavar='float', type=float,
action='store', dest='young',
default=6.80e+10, help=helps['young'])
parser.add_argument('--poisson', metavar='float', type=float,
action='store', dest='poisson',
default=0.36, help=helps['poisson'])
parser.add_argument('--density', metavar='float', type=float,
action='store', dest='density',
default=2700.0, help=helps['density'])
parser.add_argument('--order', metavar='int', type=int,
action='store', dest='order',
default=1, help=helps['order'])
parser.add_argument('-n', '--n-eigs', metavar='int', type=int,
action='store', dest='n_eigs',
default=6, help=helps['n_eigs'])
parser.add_argument('-i', '--ignore', metavar='int', type=int,
action='store', dest='ignore',
default=None, help=helps['ignore'])
parser.add_argument('--solver', metavar='solver', action='store',
dest='solver',
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default= \
"eig.scipy,method:'eigsh',tol:1e-5,maxiter:1000",
help=helps['solver'])
parser.add_argument('--show',
action="store_true", dest='show',
default=False, help=helps['show'])
parser.add_argument('filename', nargs='?', default=None)
options = parser.parse_args()

aux = options.solver.split(',')
kwargs = {}
for option in aux[1:]:
key, val = option.split(':')
kwargs[key.strip()] = eval(val)
eig_conf = Struct(name='evp', kind=aux[0], **kwargs)

output('using values:')
output(" Young's modulus:", options.young)
output(" Poisson's ratio:", options.poisson)
output(' density:', options.density)
output('displacement field approximation order:', options.order)
output('requested %d eigenvalues' % options.n_eigs)
output('using eigenvalue problem solver:', eig_conf.kind)
output.level += 1
for key, val in six.iteritems(kwargs):
output('%s: %r' % (key, val))
output.level -= 1

assert_((0.0 < options.poisson < 0.5),

"Poisson's ratio must be in ]0, 0.5[!")
assert_((0 < options.order),
'displacement approximation order must be at least 1!')

filename = options.filename
if filename is not None:
mesh = Mesh.from_file(filename)
dim = mesh.dim
dims = nm.diff(mesh.get_bounding_box(), axis=0)

else:
dims = nm.array(eval(options.dims), dtype=nm.float64)
dim = len(dims)

centre = nm.array(eval(options.centre), dtype=nm.float64)[:dim]

shape = nm.array(eval(options.shape), dtype=nm.int32)[:dim]

output('dimensions:', dims)
output('centre: ', centre)
output('shape: ', shape)

mesh = gen_block_mesh(dims, shape, centre, name='mesh')

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output('axis: ', options.axis)
assert_((-dim <= options.axis < dim), 'invalid axis value!')

eig_solver = Solver.any_from_conf(eig_conf)

# Build the problem definition.

domain = FEDomain('domain', mesh)

bbox = domain.get_mesh_bounding_box()
min_coor, max_coor = bbox[:, options.axis]
eps = 1e-8 * (max_coor - min_coor)
ax = 'xyz'[:dim][options.axis]

omega = domain.create_region('Omega', 'all')

bottom = domain.create_region('Bottom',
'vertices in (%s < %.10f )'
% (ax, min_coor + eps),
'facet')
bottom_top = domain.create_region('BottomTop',
'r.Bottom +v vertices in (%s > %.10f )'
% (ax, max_coor - eps),
'facet')

field = Field.from_args('fu', nm.float64, 'vector', omega,

approx_order=options.order)

u = FieldVariable('u', 'unknown', field)

v = FieldVariable('v', 'test', field, primary_var_name='u')

mtx_d = stiffness_from_youngpoisson(dim, options.young, options.poisson)

m = Material('m', D=mtx_d, rho=options.density)

integral = Integral('i', order=2*options.order)

t1 = Term.new('dw_lin_elastic(m.D, v, u)', integral, omega, m=m, v=v, u=u)

t2 = Term.new('dw_dot(m.rho, v, u)', integral, omega, m=m, v=v, u=u)
eq1 = Equation('stiffness', t1)
eq2 = Equation('mass', t2)
lhs_eqs = Equations([eq1, eq2])

pb = Problem('modal', equations=lhs_eqs)

if options.bc_kind == 'free':
pb.time_update()
n_rbm = dim * (dim + 1) // 2

elif options.bc_kind == 'cantilever':

fixed = EssentialBC('Fixed', bottom, {'u.all' : 0.0})
pb.time_update(ebcs=Conditions([fixed]))
n_rbm = 0

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elif options.bc_kind == 'fixed':
fixed = EssentialBC('Fixed', bottom_top, {'u.all' : 0.0})
pb.time_update(ebcs=Conditions([fixed]))
n_rbm = 0

else:
raise ValueError('unsupported BC kind! (%s)' % options.bc_kind)

if options.ignore is not None:

n_rbm = options.ignore

pb.update_materials()

# Assemble stiffness and mass matrices.

mtx_k = eq1.evaluate(mode='weak', dw_mode='matrix', asm_obj=pb.mtx_a)
mtx_m = mtx_k.copy()
mtx_m.data[:] = 0.0
mtx_m = eq2.evaluate(mode='weak', dw_mode='matrix', asm_obj=mtx_m)

try:
eigs, svecs = eig_solver(mtx_k, mtx_m, options.n_eigs + n_rbm,
eigenvectors=True)

except sla.ArpackNoConvergence as ee:

eigs = ee.eigenvalues
svecs = ee.eigenvectors
output('only %d eigenvalues converged!' % len(eigs))

output('%d eigenvalues converged (%d ignored as rigid body modes)' %

(len(eigs), n_rbm))

eigs = eigs[n_rbm:]
svecs = svecs[:, n_rbm:]

omegas = nm.sqrt(eigs)
freqs = omegas / (2 * nm.pi)

output('number | eigenvalue | angular frequency '

'| frequency')
for ii, eig in enumerate(eigs):
output('%6d | %17.12e | %17.12e | %17.12e'
% (ii + 1, eig, omegas[ii], freqs[ii]))

# Make full eigenvectors (add DOFs fixed by boundary conditions).

variables = pb.set_default_state()

vecs = nm.empty((variables.di.ptr[-1], svecs.shape[1]),

dtype=nm.float64)
for ii in range(svecs.shape[1]):
vecs[:, ii] = variables.make_full_vec(svecs[:, ii])

# Save the eigenvectors.

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out = {}
for ii in range(eigs.shape[0]):
variables.set_state(vecs[:, ii])
aux = variables.create_output()
strain = pb.evaluate('ev_cauchy_strain.i.Omega(u)',
integrals=Integrals([integral]),
mode='el_avg', verbose=False)
out['u%03d' % ii] = aux.popitem()[1]
out['strain%03d' % ii] = Struct(mode='cell', data=strain)

pb.save_state('eigenshapes.vtk', out=out)
pb.save_regions_as_groups('regions')

if len(eigs) and options.show:

# Show the solution. If the approximation order is greater than 1, the
# extra DOFs are simply thrown away.
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.domain_specific import DomainSpecificPlot

scaling = 0.05 * dims.max() / nm.abs(vecs).max()

ds = {}
for ii in range(eigs.shape[0]):
pd = DomainSpecificPlot('plot_displacements',
['rel_scaling=%s' % scaling,
'color_kind="tensors"',
'color_name="strain%03d"' % ii])
ds['u%03d' % ii] = pd

view = Viewer('eigenshapes.vtk')
view(domain_specific=ds, only_names=sorted(ds.keys()),
is_scalar_bar=False, is_wireframe=True)

if __name__ == '__main__':
main()

linear_elasticity/nodal_lcbcs.py

Description
Linear elasticity with nodal linear combination constraints.
Find 𝑢 such that:
∫︁ ∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) = − 𝑣·𝜎·𝑛, ∀𝑣 ,
Ω Γ𝑟𝑖𝑔ℎ𝑡

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

and 𝜎 · 𝑛 = 𝑝¯𝐼 · 𝑛 with given traction pressure 𝑝¯. The constraints are given in terms of coefficient matrices and

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right-hand sides, see the lcbcs keyword below. For instance, 'nlcbc1' in the 3D mesh case corresponds to

𝑢0 − 𝑢1 + 𝑢2 = 0
𝑢0 + 0.5𝑢1 + 0.1𝑢2 = 0.05

that should hold in the 'Top' region.

This example demonstrates how to pass command line options to a problem description file using --define option of
simple.py. Try:

python simple.py examples/linear_elasticity/nodal_lcbcs.py --define='dim: 3'

to use a 3D mesh, instead of the default 2D mesh. The example also shows that the nodal constraints can be used in
place of the Dirichlet boundary conditions. Try:

python simple.py examples/linear_elasticity/nodal_lcbcs.py --define='use_ebcs: False'

to replace ebcs with the 'nlcbc4' constraints. The results should be the same for the two cases. Both options can be
combined:

python simple.py examples/linear_elasticity/nodal_lcbcs.py --define='dim: 3, use_ebcs:␣

˓→False'

The post_process() function is used both to compute the von Mises stress and to verify the linear combination
constraints.
View the 2D results using:

python postproc.py square_quad.vtk --wireframe -b

python postproc.py square_quad.vtk --wireframe -b --only-names=u -d'u,plot_displacements,

˓→rel_scaling=1,color_kind="scalars",color_name="von_mises_stress"'

View the 3D results using:

python postproc.py cube_medium_tetra.vtk --wireframe -b

python postproc.py cube_medium_tetra.vtk --wireframe -b --only-names=u -d'u,plot_

˓→displacements,rel_scaling=1,color_kind="scalars",color_name="von_mises_stress"'

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source code

r"""
Linear elasticity with nodal linear combination constraints.

Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
= - \int_{\Gamma_{right}} \ul{v} \cdot \ull{\sigma} \cdot \ul{n}
\;, \quad \forall \ul{v} \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.

and :math:`\ull{\sigma} \cdot \ul{n} = \bar{p} \ull{I} \cdot \ul{n}` with given
traction pressure :math:`\bar{p}`. The constraints are given in terms of
coefficient matrices and right-hand sides, see the ``lcbcs`` keyword below. For
instance, ``'nlcbc1'`` in the 3D mesh case corresponds to
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.. math::
u_0 - u_1 + u_2 = 0 \\
u_0 + 0.5 u_1 + 0.1 u_2 = 0.05

that should hold in the ``'Top'`` region.

This example demonstrates how to pass command line options to a problem

description file using ``--define`` option of ``simple.py``. Try::

python simple.py sfepy/examples/linear_elasticity/nodal_lcbcs.py --define='dim: 3'

to use a 3D mesh, instead of the default 2D mesh. The example also shows that
the nodal constraints can be used in place of the Dirichlet boundary
conditions. Try::

python simple.py sfepy/examples/linear_elasticity/nodal_lcbcs.py --define='use_ebcs:␣

˓→False'

to replace ``ebcs`` with the ``'nlcbc4'`` constraints. The results should be

the same for the two cases. Both options can be combined::

python simple.py sfepy/examples/linear_elasticity/nodal_lcbcs.py --define='dim: 3, use_

˓→ebcs: False'

The :func:`post_process()` function is used both to compute the von Mises

stress and to verify the linear combination constraints.

View the 2D results using::

python postproc.py square_quad.vtk --wireframe -b

python postproc.py square_quad.vtk --wireframe -b --only-names=u -d'u,plot_

˓→displacements,rel_scaling=1,color_kind="scalars",color_name="von_mises_stress"'

View the 3D results using::

python postproc.py cube_medium_tetra.vtk --wireframe -b

python postproc.py cube_medium_tetra.vtk --wireframe -b --only-names=u -d'u,plot_

˓→displacements,rel_scaling=1,color_kind="scalars",color_name="von_mises_stress"'
"""
from __future__ import absolute_import
import numpy as nm

from sfepy.base.base import output, assert_

from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.mechanics.tensors import get_von_mises_stress
from sfepy import data_dir

def post_process(out, pb, state, extend=False):

"""
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Calculate and output strain and stress for given displacements.
"""
from sfepy.base.base import Struct

ev = pb.evaluate
stress = ev('ev_cauchy_stress.2.Omega(m.D, u)', mode='el_avg')

vms = get_von_mises_stress(stress.squeeze())
vms.shape = (vms.shape[0], 1, 1, 1)
out['von_mises_stress'] = Struct(name='output_data', mode='cell',
data=vms, dofs=None)

dim = pb.domain.shape.dim

us = state().reshape((-1, dim))

field = pb.fields['displacement']

if dim == 2:
ii = field.get_dofs_in_region(pb.domain.regions['Top'])
output('top LCBC (u.0 - u.1 = 0):')
output('\n', nm.c_[us[ii], nm.diff(us[ii], 1)])

ii = field.get_dofs_in_region(pb.domain.regions['Bottom'])
output('bottom LCBC (u.0 + u.1 = -0.1):')
output('\n', nm.c_[us[ii], nm.sum(us[ii], 1)])

ii = field.get_dofs_in_region(pb.domain.regions['Right'])
output('right LCBC (u.0 + u.1 = linspace(0, 0.1)):')
output('\n', nm.c_[us[ii], nm.sum(us[ii], 1)])

else:
ii = field.get_dofs_in_region(pb.domain.regions['Top'])
output('top LCBC (u.0 - u.1 + u.2 = 0):')
output('\n', nm.c_[us[ii], us[ii, 0] - us[ii, 1] + us[ii, 2]])
output('top LCBC (u.0 + 0.5 u.1 + 0.1 u.2 = 0.05):')
output('\n', nm.c_[us[ii],
us[ii, 0] + 0.5 * us[ii, 1] + 0.1 * us[ii, 2]])

ii = field.get_dofs_in_region(pb.domain.regions['Bottom'])
output('bottom LCBC (u.2 - 0.1 u.1 = 0.2):')
output('\n', nm.c_[us[ii], us[ii, 2] - 0.1 * us[ii, 1]])

ii = field.get_dofs_in_region(pb.domain.regions['Right'])
output('right LCBC (u.0 + u.1 + u.2 = linspace(0, 0.1)):')
output('\n', nm.c_[us[ii], nm.sum(us[ii], 1)])

return out

def define(dim=2, use_ebcs=True):

assert_(dim in (2, 3))

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if dim == 2:
filename_mesh = data_dir + '/meshes/2d/square_quad.mesh'

else:
filename_mesh = data_dir + '/meshes/3d/cube_medium_tetra.mesh'

options = {
'nls' : 'newton',
'ls' : 'ls',
'post_process_hook' : 'post_process'
}

def get_constraints(ts, coors, region=None):

mtx = nm.ones((coors.shape[0], 1, dim), dtype=nm.float64)

rhs = nm.arange(coors.shape[0], dtype=nm.float64)[:, None]

rhs *= 0.1 / (coors.shape[0] - 1)

return mtx, rhs

functions = {
'get_constraints' : (get_constraints,),
}

fields = {
'displacement': ('real', dim, 'Omega', 1),
}

materials = {
'm' : ({
'D' : stiffness_from_lame(dim, lam=5.769, mu=3.846),
},),
'load' : ({'val' : -1.0},),
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
}

regions = {
'Omega' : 'all',
'Bottom' : ('vertices in (y < -0.499) -v r.Left', 'facet'),
'Top' : ('vertices in (y > 0.499) -v r.Left', 'facet'),
'Left' : ('vertices in (x < -0.499)', 'facet'),
'Right' : ('vertices in (x > 0.499) -v (r.Bottom +v r.Top)', 'facet'),
}

if dim == 2:
lcbcs = {
'nlcbc1' : ('Top', {'u.all' : None}, None, 'nodal_combination',
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([[1.0, -1.0]], [0.0])),
'nlcbc2' : ('Bottom', {'u.all' : None}, None, 'nodal_combination',
([[1.0, 1.0]], [-0.1])),
'nlcbc3' : ('Right', {'u.all' : None}, None, 'nodal_combination',
'get_constraints'),
}

else:
lcbcs = {
'nlcbc1' : ('Top', {'u.all' : None}, None, 'nodal_combination',
([[1.0, -1.0, 1.0], [1.0, 0.5, 0.1]], [0.0, 0.05])),
'nlcbc2' : ('Bottom', {'u.[2,1]' : None}, None, 'nodal_combination',
([[1.0, -0.1]], [0.2])),
'nlcbc3' : ('Right', {'u.all' : None}, None, 'nodal_combination',
'get_constraints'),
}

if use_ebcs:
ebcs = {
'fix' : ('Left', {'u.all' : 0.0}),
}

else:
ebcs = {}

lcbcs.update({
'nlcbc4' : ('Left', {'u.all' : None}, None, 'nodal_combination',
(nm.eye(dim), nm.zeros(dim))),
})

equations = {
'elasticity' : """
dw_lin_elastic.2.Omega(m.D, v, u)
= -dw_surface_ltr.2.Right(load.val, v)
""",
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
}),
}

return locals()

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linear_elasticity/prestress_fibres.py

Description
Linear elasticity with a given prestress in one subdomain and a (pre)strain fibre reinforcement in the other.
Find 𝑢 such that:
∫︁ ∫︁ ∫︁
𝑓
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) + 𝜎𝑖𝑗 𝑒𝑖𝑗 (𝑣) + 𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣) (𝑑𝑘 𝑑𝑙 ) = 0 , ∀𝑣 ,
Ω Ω1 Ω2

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

𝑓
The stiffness of fibres 𝐷𝑖𝑗𝑘𝑙 is defined analogously, 𝑑 is the unit fibre direction vector and 𝜎𝑖𝑗 is the prestress.

Visualization

Use the following to see the deformed structure with 10x magnified displacements:

$ ./postproc.py block.vtk -b --vector-mode=warp_norm -s 1 --wireframe

source code

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r"""
Linear elasticity with a given prestress in one subdomain and a (pre)strain
fibre reinforcement in the other.

Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
+ \int_{\Omega_1} \sigma_{ij} e_{ij}(\ul{v})
+ \int_{\Omega_2} D^f_{ijkl} e_{ij}(\ul{v}) \left(d_k d_l\right)
= 0
\;, \quad \forall \ul{v} \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.

The stiffness of fibres :math:`D^f_{ijkl}` is defined analogously,

:math:`\ul{d}` is the unit fibre direction vector and :math:`\sigma_{ij}` is
the prestress.

Visualization
-------------

Use the following to see the deformed structure with 10x magnified
displacements::

$ ./postproc.py block.vtk -b --vector-mode=warp_norm -s 1 --wireframe

"""
from __future__ import absolute_import
import numpy as nm
from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy import data_dir

filename_mesh = data_dir + '/meshes/3d/block.mesh'

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < -4.99)', 'facet'),
'Omega1' : 'vertices in (x < 0.001)',
'Omega2' : 'vertices in (x > -0.001)',
}

materials = {
'solid' : ({
'D' : stiffness_from_lame(3, lam=1e2, mu=1e1),
'prestress' : 0.1 * nm.array([[1.0], [1.0], [1.0],
[0.5], [0.5], [0.5]],
dtype=nm.float64),
'DF' : stiffness_from_lame(3, lam=8e0, mu=8e-1),
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'nu' : nm.array([[-0.5], [0.0], [0.5]], dtype=nm.float64),
},),
}

fields = {
'displacement': ('real', 'vector', 'Omega', 1),
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
}

ebcs = {
'Fixed' : ('Left', {'u.all' : 0.0}),
}

equations = {
'balance_of_forces' :
"""dw_lin_elastic.2.Omega( solid.D, v, u )
+ dw_lin_prestress.2.Omega1( solid.prestress, v )
+ dw_lin_strain_fib.2.Omega2( solid.DF, solid.nu, v )
= 0""",
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
}),
}

linear_elasticity/shell10x_cantilever.py

Description
Bending of a long thin cantilever beam computed using the dw_shell10x term.
Find displacements of the central plane 𝑢, and rotations 𝛼 such that:
∫︁ ∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣, 𝛽)𝑒𝑘𝑙 (𝑢, 𝛼) = − 𝑣·𝑓 , ∀𝑣 ,
Ω Γ𝑟𝑖𝑔ℎ𝑡

where 𝐷𝑖𝑗𝑘𝑙 is the isotropic elastic tensor, given using the Young’s modulus 𝐸 and the Poisson’s ratio 𝜈.
The variable u below holds both 𝑢 and 𝛼 DOFs. For visualization, it is saved as two fields u_disp and u_rot, corre-
sponding to 𝑢 and 𝛼, respectively.
See also linear_elasticity/shell10x_cantilever_interactive.py example.
View the results using:

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python postproc.py shell10x.vtk -d 'u_disp,plot_displacements,rel_scaling=1.0' --opacity=

˓→'wireframe=0.5' -b --wireframe

source code

r"""
Bending of a long thin cantilever beam computed using the
:class:`dw_shell10x <sfepy.terms.terms_shells.Shell10XTerm>` term.

Find displacements of the central plane :math:`\ul{u}`, and rotations

:math:`\ul{\alpha}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}, \ul{\beta})
e_{kl}(\ul{u}, \ul{\alpha})
= - \int_{\Gamma_{right}} \ul{v} \cdot \ul{f}
\;, \quad \forall \ul{v} \;,

where :math:`D_{ijkl}` is the isotropic elastic tensor, given using the Young's
modulus :math:`E` and the Poisson's ratio :math:`\nu`.

The variable ``u`` below holds both :math:`\ul{u}` and :math:`\ul{\alpha}`

DOFs. For visualization, it is saved as two fields ``u_disp`` and ``u_rot``,
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(continued from previous page)

corresponding to :math:`\ul{u}` and :math:`\ul{\alpha}`, respectively.

See also :ref:`linear_elasticity-shell10x_cantilever_interactive` example.

View the results using::

python postproc.py shell10x.vtk -d 'u_disp,plot_displacements,rel_scaling=1.0' --

˓→opacity='wireframe=0.5' -b --wireframe
"""
from __future__ import absolute_import
from sfepy.base.base import output
from sfepy.discrete.fem.meshio import UserMeshIO
from sfepy.discrete import Integral
import sfepy.mechanics.shell10x as sh

import sfepy.examples.linear_elasticity.shell10x_cantilever_interactive as sci

# Beam dimensions.
dims = [0.2, 0.01, 0.001]
thickness = dims[2]

transform = 'bend' # None, 'bend' or 'twist'

# Mesh resolution: increase to improve accuracy.

shape = [11, 2]

# Material parameters.
young = 210e9
poisson = 0.3

# Loading force.
force = -1.0

def mesh_hook(mesh, mode):

"""
Generate the beam mesh.
"""
if mode == 'read':
mesh = sci.make_mesh(dims[:2], shape, transform=transform)
return mesh

def post_process(out, problem, state, extend=False):

u = problem.get_variables()['u']
gamma2 = problem.domain.regions['Gamma2']

dofs = u.get_state_in_region(gamma2)
output('DOFs along the loaded edge:')
output('\n%s' % dofs)

if transform != 'twist':
label, ii = {None : ('u_3', 2), 'bend' : ('u_1', 0)}[transform]

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u_exact = sci.get_analytical_displacement(dims, young, force,
transform=transform)
output('max. %s displacement:' % label, dofs[0, ii])
output('analytical value:', u_exact)

return out

filename_mesh = UserMeshIO(mesh_hook)

options = {
'nls' : 'newton',
'ls' : 'ls',
'post_process_hook' : 'post_process',
}

if transform is None:
pload = [[0.0, 0.0, force / shape[1], 0.0, 0.0, 0.0]] * shape[1]

elif transform == 'bend':

pload = [[force / shape[1], 0.0, 0.0, 0.0, 0.0, 0.0]] * shape[1]

elif transform == 'twist':

pload = [[0.0, force / shape[1], 0.0, 0.0, 0.0, 0.0]] * shape[1]

materials = {
'm' : ({
'D' : sh.create_elastic_tensor(young=young, poisson=poisson),
'.drill' : 1e-7,
},),
'load' : ({
'.val' : pload,
},)
}

xmin = (-0.5 + 1e-12) * dims[0]

xmax = (0.5 - 1e-12) * dims[0]

regions = {
'Omega' : 'all',
'Gamma1' : ('vertices in (x < %.14f )' % xmin, 'facet'),
'Gamma2' : ('vertices in (x > %.14f )' % xmax, 'facet'),
}

fields = {
'fu': ('real', 6, 'Omega', 1, 'H1', 'shell10x'),
}

variables = {
'u' : ('unknown field', 'fu', 0),
'v' : ('test field', 'fu', 'u'),
}

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ebcs = {
'fix' : ('Gamma1', {'u.all' : 0.0}),
}

# Custom integral.
aux = Integral('i', order=3)
qp_coors, qp_weights = aux.get_qp('3_8')
qp_coors[:, 2] = thickness * (qp_coors[:, 2] - 0.5)
qp_weights *= thickness

integrals = {
'i' : ('custom', qp_coors, qp_weights),
}

equations = {
'elasticity' :
"""dw_shell10x.i.Omega(m.D, m.drill, v, u)
= dw_point_load.i.Gamma2(load.val, v)""",
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-7,
}),
}

linear_elasticity/shell10x_cantilever_interactive.py

Description
Bending of a long thin cantilever beam computed using the dw_shell10x term.
Find displacements of the central plane 𝑢, and rotations 𝛼 such that:
∫︁ ∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣, 𝛽)𝑒𝑘𝑙 (𝑢, 𝛼) = − 𝑣·𝑓 , ∀𝑣 ,
Ω Γ𝑟𝑖𝑔ℎ𝑡

where 𝐷𝑖𝑗𝑘𝑙 is the isotropic elastic tensor, given using the Young’s modulus 𝐸 and the Poisson’s ratio 𝜈.
The variable u below holds both 𝑢 and 𝛼 DOFs. For visualization, it is saved as two fields u_disp and u_rot, corre-
sponding to 𝑢 and 𝛼, respectively.
The material, loading and discretization parameters can be given using command line options.
Besides the default straight beam, two coordinate transformations can be applied (see the --transform option):
• bend: the beam is bent
• twist: the beam is twisted
For the straight and bent beam a comparison with the analytical solution coming from the Euler-Bernoulli theory is
shown.
See also linear_elasticity/shell10x_cantilever.py example.

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Usage Examples

See all options:

python examples/linear_elasticity/shell10x_cantilever_interactive.py -h

Apply the bending transformation to the beam domain coordinates, plot convergence curves w.r.t. number of elements:

python examples/linear_elasticity/shell10x_cantilever_interactive.py output -t bend -p

Apply the twisting transformation to the beam domain coordinates, change number of cells, show the solution:

python examples/linear_elasticity/shell10x_cantilever_interactive.py output -t twist -n␣

˓→2,51,3 -s

source code

#!/usr/bin/env python
r"""
Bending of a long thin cantilever beam computed using the
:class:`dw_shell10x <sfepy.terms.terms_shells.Shell10XTerm>` term.

Find displacements of the central plane :math:`\ul{u}`, and rotations

:math:`\ul{\alpha}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}, \ul{\beta})
e_{kl}(\ul{u}, \ul{\alpha})
= - \int_{\Gamma_{right}} \ul{v} \cdot \ul{f}
\;, \quad \forall \ul{v} \;,

where :math:`D_{ijkl}` is the isotropic elastic tensor, given using the Young's
modulus :math:`E` and the Poisson's ratio :math:`\nu`.

The variable ``u`` below holds both :math:`\ul{u}` and :math:`\ul{\alpha}`

DOFs. For visualization, it is saved as two fields ``u_disp`` and ``u_rot``,
corresponding to :math:`\ul{u}` and :math:`\ul{\alpha}`, respectively.

The material, loading and discretization parameters can be given using command
line options.

Besides the default straight beam, two coordinate transformations can be applied
(see the ``--transform`` option):

- bend: the beam is bent

- twist: the beam is twisted

For the straight and bent beam a comparison with the analytical solution
coming from the Euler-Bernoulli theory is shown.

See also :ref:`linear_elasticity-shell10x_cantilever` example.

Usage Examples
--------------
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See all options::

python sfepy/examples/linear_elasticity/shell10x_cantilever_interactive.py -h

Apply the bending transformation to the beam domain coordinates, plot

convergence curves w.r.t. number of elements::

python sfepy/examples/linear_elasticity/shell10x_cantilever_interactive.py output -t␣

˓→bend -p

Apply the twisting transformation to the beam domain coordinates, change number of cells,
˓→ show the solution::

python sfepy/examples/linear_elasticity/shell10x_cantilever_interactive.py output -t␣

˓→twist -n 2,51,3 -s
"""
from __future__ import absolute_import
from argparse import RawDescriptionHelpFormatter, ArgumentParser
import os
import sys
from six.moves import range
sys.path.append('.')

import numpy as nm

from sfepy.base.base import output, IndexedStruct

from sfepy.base.ioutils import ensure_path
from sfepy.discrete import (FieldVariable, Material, Integral,
Equation, Equations, Problem)
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.solvers.solvers import use_first_available
from sfepy.solvers.ls import MUMPSSolver, ScipyDirect
from sfepy.solvers.nls import Newton
from sfepy.linalg import make_axis_rotation_matrix
from sfepy.mechanics.tensors import transform_data
from sfepy.mesh.mesh_generators import gen_block_mesh
import sfepy.mechanics.shell10x as sh

def make_mesh(dims, shape, transform=None):

"""
Generate a 2D rectangle mesh in 3D space, and optionally apply a coordinate
transform.
"""
_mesh = gen_block_mesh(dims, shape, [0, 0], name='shell10x', verbose=False)

coors = nm.c_[_mesh.coors, nm.zeros(_mesh.n_nod, dtype=nm.float64)]

coors = nm.ascontiguousarray(coors)

conns = [_mesh.get_conn(_mesh.descs[0])]
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mesh = Mesh.from_data(_mesh.name, coors, _mesh.cmesh.vertex_groups, conns,

[_mesh.cmesh.cell_groups], _mesh.descs)

if transform == 'bend':
bbox = mesh.get_bounding_box()
x0, x1 = bbox[:, 0]

angles = 0.5 * nm.pi * (coors[:, 0] - x0) / (x1 - x0)

mtx = make_axis_rotation_matrix([0, -1, 0], angles[:, None, None])

coors = mesh.coors.copy()
coors[:, 0] = 0
coors[:, 2] = (x1 - x0)

mesh.coors[:] = transform_data(coors, mtx=mtx)

mesh.coors[:, 0] -= 0.5 * (x1 - x0)

elif transform == 'twist':

bbox = mesh.get_bounding_box()
x0, x1 = bbox[:, 0]

angles = 0.5 * nm.pi * (coors[:, 0] - x0) / (x1 - x0)

mtx = make_axis_rotation_matrix([-1, 0, 0], angles[:, None, None])

mesh.coors[:] = transform_data(mesh.coors, mtx=mtx)

return mesh

def make_domain(dims, shape, transform=None):

"""
Generate a 2D rectangle domain in 3D space, define regions.
"""
xmin = (-0.5 + 1e-12) * dims[0]
xmax = (0.5 - 1e-12) * dims[0]

mesh = make_mesh(dims, shape, transform=transform)

domain = FEDomain('domain', mesh)
domain.create_region('Omega', 'all')
domain.create_region('Gamma1', 'vertices in (x < %.14f )' % xmin, 'facet')
domain.create_region('Gamma2', 'vertices in (x > %.14f )' % xmax, 'facet')

return domain

def solve_problem(shape, dims, young, poisson, force, transform=None):

domain = make_domain(dims[:2], shape, transform=transform)

omega = domain.regions['Omega']
gamma1 = domain.regions['Gamma1']
gamma2 = domain.regions['Gamma2']

field = Field.from_args('fu', nm.float64, 6, omega, approx_order=1,

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poly_space_base='shell10x')
u = FieldVariable('u', 'unknown', field)
v = FieldVariable('v', 'test', field, primary_var_name='u')

thickness = dims[2]
if transform is None:
pload = [[0.0, 0.0, force / shape[1], 0.0, 0.0, 0.0]] * shape[1]

elif transform == 'bend':

pload = [[force / shape[1], 0.0, 0.0, 0.0, 0.0, 0.0]] * shape[1]

elif transform == 'twist':

pload = [[0.0, force / shape[1], 0.0, 0.0, 0.0, 0.0]] * shape[1]

m = Material('m', D=sh.create_elastic_tensor(young=young, poisson=poisson),

values={'.drill' : 1e-7})
load = Material('load', values={'.val' : pload})

aux = Integral('i', order=3)

qp_coors, qp_weights = aux.get_qp('3_8')
qp_coors[:, 2] = thickness * (qp_coors[:, 2] - 0.5)
qp_weights *= thickness

integral = Integral('i', coors=qp_coors, weights=qp_weights, order='custom')

t1 = Term.new('dw_shell10x(m.D, m.drill, v, u)',

integral, omega, m=m, v=v, u=u)
t2 = Term.new('dw_point_load(load.val, v)',
integral, gamma2, load=load, v=v)
eq = Equation('balance', t1 - t2)
eqs = Equations([eq])

fix_u = EssentialBC('fix_u', gamma1, {'u.all' : 0.0})

ls = use_first_available([(MUMPSSolver, {}), (ScipyDirect, {})])

nls_status = IndexedStruct()
nls = Newton({}, lin_solver=ls, status=nls_status)

pb = Problem('elasticity with shell10x', equations=eqs)

pb.set_bcs(ebcs=Conditions([fix_u]))
pb.set_solver(nls)

state = pb.solve()

return pb, state, u, gamma2

def get_analytical_displacement(dims, young, force, transform=None):

"""
Returns the analytical value of the max. displacement according to
Euler-Bernoulli theory.
"""
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l, b, h = dims

if transform is None:
moment = b * h**3 / 12.0
u = force * l**3 / (3 * young * moment)

elif transform == 'bend':

u = force * 3.0 * nm.pi * l**3 / (young * b * h**3)

elif transform == 'twist':

u = None

return u

helps = {
'output_dir' : 'output directory',
'dims' :
'dimensions of the cantilever [default: %(default)s]',
'nx' :
'the range for the numbers of cells in the x direction'
' [default: %(default)s]',
'transform' :
'the transformation of the domain coordinates [default: %(default)s]',
'young' : "the Young's modulus [default: %(default)s]",
'poisson' : "the Poisson's ratio [default: %(default)s]",
'force' : "the force load [default: %(default)s]",
'plot' : 'plot the max. displacement w.r.t. number of cells',
'scaling' : 'the displacement scaling, with --show [default: %(default)s]',
'show' : 'show the results figure',
'silent' : 'do not print messages to screen',
}

def main():
parser = ArgumentParser(description=__doc__.rstrip(),
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('output_dir', help=helps['output_dir'])
parser.add_argument('-d', '--dims', metavar='l,w,t',
action='store', dest='dims',
default='0.2,0.01,0.001', help=helps['dims'])
parser.add_argument('-n', '--nx', metavar='start,stop,step',
action='store', dest='nx',
default='2,103,10', help=helps['nx'])
parser.add_argument('-t', '--transform', choices=['none', 'bend', 'twist'],
action='store', dest='transform',
default='none', help=helps['transform'])
parser.add_argument('--young', metavar='float', type=float,
action='store', dest='young',
default=210e9, help=helps['young'])
parser.add_argument('--poisson', metavar='float', type=float,
action='store', dest='poisson',
default=0.3, help=helps['poisson'])
parser.add_argument('--force', metavar='float', type=float,
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action='store', dest='force',
default=-1.0, help=helps['force'])
parser.add_argument('-p', '--plot',
action="store_true", dest='plot',
default=False, help=helps['plot'])
parser.add_argument('--u-scaling', metavar='float', type=float,
action='store', dest='scaling',
default=1.0, help=helps['scaling'])
parser.add_argument('-s', '--show',
action="store_true", dest='show',
default=False, help=helps['show'])
parser.add_argument('--silent',
action='store_true', dest='silent',
default=False, help=helps['silent'])
options = parser.parse_args()

dims = nm.array([float(ii) for ii in options.dims.split(',')],

dtype=nm.float64)
nxs = tuple([int(ii) for ii in options.nx.split(',')])
young = options.young
poisson = options.poisson
force = options.force

output_dir = options.output_dir

odir = lambda filename: os.path.join(output_dir, filename)

filename = odir('output_log.txt')
ensure_path(filename)
output.set_output(filename=filename, combined=options.silent == False)

output('output directory:', output_dir)

output('using values:')
output(" dimensions:", dims)
output(" nx range:", nxs)
output(" Young's modulus:", options.young)
output(" Poisson's ratio:", options.poisson)
output(' force:', options.force)
output(' transform:', options.transform)

if options.transform == 'none':
options.transform = None

u_exact = get_analytical_displacement(dims, young, force,

transform=options.transform)

if options.transform is None:
ilog = 2
labels = ['u_3']

elif options.transform == 'bend':

ilog = 0
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labels = ['u_1']

elif options.transform == 'twist':

ilog = [0, 1, 2]
labels = ['u_1', 'u_2', 'u_3']

label = ', '.join(labels)

log = []
for nx in range(*nxs):
shape = (nx, 2)

pb, state, u, gamma2 = solve_problem(shape, dims, young, poisson, force,

transform=options.transform)

dofs = u.get_state_in_region(gamma2)
output('DOFs along the loaded edge:')
output('\n%s' % dofs)

log.append([nx - 1] + nm.array(dofs[0, ilog], ndmin=1).tolist())

pb.save_state(odir('shell10x_cantilever.vtk'), state)

log = nm.array(log)

output('max. %s displacement w.r.t. number of cells:' % label)

output('\n%s' % log)
output('analytical value:', u_exact)

if options.plot:
import matplotlib.pyplot as plt

plt.rcParams.update({
'lines.linewidth' : 3,
'font.size' : 16,
})

fig, ax1 = plt.subplots()

fig.suptitle('max. $%s$ displacement' % label)

for ic in range(log.shape[1] - 1):

ax1.plot(log[:, 0], log[:, ic + 1], label=r'$%s$' % labels[ic])
ax1.set_xlabel('# of cells')
ax1.set_ylabel(r'$%s$' % label)
ax1.grid(which='both')

lines1, labels1 = ax1.get_legend_handles_labels()

if u_exact is not None:

ax1.hlines(u_exact, log[0, 0], log[-1, 0],
'r', 'dotted', label=r'$%s^{analytical}$' % label)

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ax2 = ax1.twinx()
# Assume single log column.
ax2.semilogy(log[:, 0], nm.abs(log[:, 1] - u_exact), 'g',
label=r'$|%s - %s^{analytical}|$' % (label, label))
ax2.set_ylabel(r'$|%s - %s^{analytical}|$' % (label, label))

lines2, labels2 = ax2.get_legend_handles_labels()

else:
lines2, labels2 = [], []

ax1.legend(lines1 + lines2, labels1 + labels2, loc='best')

plt.tight_layout()
ax1.set_xlim([log[0, 0] - 2, log[-1, 0] + 2])

suffix = {None: 'straight',

'bend' : 'bent', 'twist' : 'twisted'}[options.transform]
fig.savefig(odir('shell10x_cantilever_convergence_%s.png' % suffix))

plt.show()

if options.show:
from sfepy.postprocess.viewer import Viewer
from sfepy.postprocess.domain_specific import DomainSpecificPlot

ds = {'u_disp' :
DomainSpecificPlot('plot_displacements',
['rel_scaling=%f ' % options.scaling])}
view = Viewer(odir('shell10x_cantilever.vtk'))
view(domain_specific=ds, is_scalar_bar=True, is_wireframe=True,
opacity={'wireframe' : 0.5})

if __name__ == '__main__':
main()

linear_elasticity/two_bodies_contact.py

Description
Contact of two elastic bodies with a penalty function for enforcing the contact constraints.
Find 𝑢 such that:
∫︁ ∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) + 𝜀𝑁 ⟨𝑔𝑁 (𝑢)⟩𝑛𝑣 = 0 , ∀𝑣 ,
Ω Γ𝑐

where 𝜀𝑁 ⟨𝑔𝑁 (𝑢)⟩ is the penalty function, 𝜀𝑁 is the normal penalty parameter, ⟨𝑔𝑁 (𝑢)⟩ are the Macaulay’s brackets of
the gap function 𝑔𝑁 (𝑢) and

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

Usage examples:

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./simple.py examples/linear_elasticity/two_bodies_contact.py --save-regions-as-groups --

˓→save-ebc-nodes

./postproc.py two_bodies.mesh.vtk -b --wire

./postproc.py two_bodies.mesh.vtk -b --wire -d 'u,plot_displacements,rel_scaling=1.0'

./script/plot_logs.py log.txt

./postproc.py --wire two_bodies.mesh_ebc_nodes.vtk

./postproc.py --wire two_bodies.mesh_regions.vtk

source code

r"""
Contact of two elastic bodies with a penalty function for enforcing the contact
constraints.

Find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
+ \int_{\Gamma_{c}} \varepsilon_N \langle g_N(\ul{u}) \rangle \ul{n} \ul{v}
= 0
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\;, \quad \forall \ul{v} \;,

where :math:`\varepsilon_N \langle g_N(\ul{u}) \rangle` is the penalty

function, :math:`\varepsilon_N` is the normal penalty parameter, :math:`\langle
g_N(\ul{u}) \rangle` are the Macaulay's brackets of the gap function
:math:`g_N(\ul{u})` and

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.

Usage examples::

./simple.py sfepy/examples/linear_elasticity/two_bodies_contact.py --save-regions-as-

˓→groups --save-ebc-nodes

./postproc.py two_bodies.mesh.vtk -b --wire

./postproc.py two_bodies.mesh.vtk -b --wire -d 'u,plot_displacements,rel_scaling=1.0'

./script/plot_logs.py log.txt

./postproc.py --wire two_bodies.mesh_ebc_nodes.vtk

./postproc.py --wire two_bodies.mesh_regions.vtk
"""
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
from sfepy.discrete.fem.meshio import UserMeshIO

import numpy as nm

dim = 2

if dim == 2:
dims0 = [1.0, 0.5]
shape0 = [4, 4]
centre0 = [0, -0.25]

dims1 = [1.0, 0.5]

shape1 = [3, 3]
centre1 = [0, 0.25]

shift1 = [0.0, -0.1]

else:
dims0 = [1.0, 1.0, 0.5]
shape0 = [2, 2, 2]
centre0 = [0, 0, -0.25]

dims1 = [1.0, 1.0, 0.5]

shape1 = [2, 2, 2]
centre1 = [0, 0, 0.25]

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shift1 = [0.0, 0.0, -0.1]

def get_bbox(dims, centre, eps=0.0):

dims = nm.asarray(dims)
centre = nm.asarray(centre)

bbox = nm.r_[[centre - (0.5 - eps) * dims], [centre + (0.5 - eps) * dims]]

return bbox

def gen_two_bodies(dims0, shape0, centre0, dims1, shape1, centre1, shift1):

from sfepy.discrete.fem import Mesh
from sfepy.mesh.mesh_generators import gen_block_mesh

m0 = gen_block_mesh(dims0, shape0, centre0)

m1 = gen_block_mesh(dims1, shape1, centre1)

coors = nm.concatenate((m0.coors, m1.coors + shift1), axis=0)

desc = m0.descs[0]
c0 = m0.get_conn(desc)
c1 = m1.get_conn(desc)
conn = nm.concatenate((c0, c1 + m0.n_nod), axis=0)

ngroups = nm.zeros(coors.shape[0], dtype=nm.int32)

ngroups[m0.n_nod:] = 1

mat_id = nm.zeros(conn.shape[0], dtype=nm.int32)

mat_id[m0.n_el:] = 1

name = 'two_bodies.mesh'

mesh = Mesh.from_data(name, coors, ngroups, [conn], [mat_id], m0.descs)

return mesh

def mesh_hook(mesh, mode):

if mode == 'read':
return gen_two_bodies(dims0, shape0, centre0,
dims1, shape1, centre1, shift1)

elif mode == 'write':

pass

def post_process(out, pb, state, extend=False):

from sfepy.base.base import Struct
from sfepy.discrete.fem import extend_cell_data

ev = pb.evaluate
gap = ev('dw_contact.i.Contact(contact.epss, v, u)',
mode='el_avg', term_mode='gap')
gap = extend_cell_data(gap, pb.domain, 'Contact', val=0.0, is_surface=True)
out['gap'] = Struct(name='output_data',
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mode='cell', data=gap, dofs=None)

return out

filename_mesh = UserMeshIO(mesh_hook)

options = {
'nls' : 'newton',
'ls' : 'ls',
'post_process_hook' : 'post_process',
}

fields = {
'displacement': ('real', dim, 'Omega', 1),
}

materials = {
'solid' : ({'D': stiffness_from_youngpoisson(dim,
young=1.0, poisson=0.3)},),
'contact' : ({'.epss' : 1e1},),
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
}

bbox0 = get_bbox(dims0, centre0, eps=1e-5)

bbox1 = get_bbox(dims1, nm.asarray(centre1) + nm.asarray(shift1), eps=1e-5)

if dim == 2:
regions = {
'Omega' : 'all',
'Omega0' : 'cells of group 0',
'Omega1' : 'cells of group 1',
'Bottom' : ('vertices in (y < %f )' % bbox0[0, 1], 'facet'),
'Top' : ('vertices in (y > %f )' % bbox1[1, 1], 'facet'),
'Contact0' : ('(vertices in (y > %f ) *v r.Omega0)' % bbox0[1, 1],
'facet'),
'Contact1' : ('(vertices in (y < %f ) *v r.Omega1)' % bbox1[0, 1],
'facet'),
'Contact' : ('r.Contact0 +s r.Contact1', 'facet')
}

else:
regions = {
'Omega' : 'all',
'Omega0' : 'cells of group 0',
'Omega1' : 'cells of group 1',
'Bottom' : ('vertices in (z < %f )' % bbox0[0, 2], 'facet'),
'Top' : ('vertices in (z > %f )' % bbox1[1, 2], 'facet'),
'Contact0' : ('(vertices in (z > %f ) *v r.Omega0)' % bbox0[1, 2],
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'facet'),
'Contact1' : ('(vertices in (z < %f ) *v r.Omega1)' % bbox1[0, 2],
'facet'),
'Contact' : ('r.Contact0 +s r.Contact1', 'facet')
}

ebcs = {
'fixb' : ('Bottom', {'u.all' : 0.0}),
'fixt' : ('Top', {'u.all' : 0.0}),
}

integrals = {
'i' : 10,
}

equations = {
'elasticity' :
"""dw_lin_elastic.2.Omega(solid.D, v, u)
+ dw_contact.i.Contact(contact.epss, v, u)
= 0""",
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 5,
'eps_a' : 1e-6,
'eps_r' : 1.0,
'macheps' : 1e-16,
# Linear system error < (eps_a * lin_red).
'lin_red' : 1e-2,
'ls_red' : 0.1,
'ls_red_warp' : 0.001,
'ls_on' : 100.1,
'ls_min' : 1e-5,
'check' : 0,
'delta' : 1e-8,
# 'log' : {'text' : 'log.txt', 'plot' : None},
})
}

miscellaneous

miscellaneous/live_plot.py

Description
missing description!
source code

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from __future__ import print_function

from __future__ import absolute_import
import os
import sys
sys.path.append( '.' )

import numpy as nm

from sfepy.base.base import output, pause

from sfepy.base.log import Log

def main():
cwd = os.path.split(os.path.join(os.getcwd(), __file__))[0]

log = Log((['sin(x) + i sin(x**2)', 'cos(x)'], ['exp(x)']),

yscales=['linear', 'log'],
xlabels=['angle', None], ylabels=[None, 'a function'],
aggregate=1000, sleep=0.05,
log_filename=os.path.join(cwd, 'live_plot.log'))
log2 = Log([['x^3']],
yscales=['linear'],
xlabels=['x'], ylabels=['a cubic function'],
aggregate=1000, sleep=0.05,
log_filename=os.path.join(cwd, 'live_plot2.log'),
formats=[['{:.5e}']])

added = 0
for x in nm.linspace(0, 4.0 * nm.pi, 200):
output('x: ', x)

if x < (2.0 * nm.pi):

log(nm.sin(x)+1j*nm.sin(x**2), nm.cos(x), nm.exp(x), x=[x, None])

else:
if added:
log(nm.sin(x)+1j*nm.sin(x**2), nm.cos(x), nm.exp(x), x**2,
x=[x, None, x])
else:
log.plot_vlines(color='r', linewidth=2)
log.add_group(['x^2'], yscale='linear', xlabel='new x',
ylabel='square', formats=['%+g'])
added += 1

if (added == 20) or (added == 50):

log.plot_vlines([2], color='g', linewidth=2)

log2(x*x*x, x=[x])

print(log)
print(log2)
pause()

log(finished=True)
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log2(finished=True)

if __name__ == '__main__':
main()

multi_physics

multi_physics/biot.py

Description
Biot problem - deformable porous medium.
Find 𝑢, 𝑝 such that:
∫︁ ∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) − 𝑝 𝛼𝑖𝑗 𝑒𝑖𝑗 (𝑣) = 0 , ∀𝑣 ,
Ω Ω
∫︁ ∫︁
𝑞 𝛼𝑖𝑗 𝑒𝑖𝑗 (𝑢) + 𝐾𝑖𝑗 ∇𝑖 𝑞∇𝑗 𝑝 = 0 , ∀𝑞 ,
Ω Ω

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

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source code

r"""
Biot problem - deformable porous medium.

Find :math:`\ul{u}`, :math:`p` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
- \int_{\Omega} p\ \alpha_{ij} e_{ij}(\ul{v})
= 0
\;, \quad \forall \ul{v} \;,

\int_{\Omega} q\ \alpha_{ij} e_{ij}(\ul{u})

+ \int_{\Omega} K_{ij} \nabla_i q \nabla_j p
= 0
\;, \quad \forall q \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.
"""
from __future__ import absolute_import
import numpy as nm

from sfepy import data_dir

from sfepy.mechanics.matcoefs import stiffness_from_lame

filename_mesh = data_dir + '/meshes/3d/cube_medium_hexa.mesh'

regions = {
'Omega' : 'all',
'Bottom' : ('vertices in (z < -0.4999999)', 'facet'),
'Top' : ('vertices in (z > 0.4999999)', 'facet'),
'Left' : ('vertices in (x < -0.4999999)', 'facet'),
}

field_1 = {
'name' : 'displacement',
'dtype' : nm.float64,
'shape' : (3,),
'region' : 'Omega',
'approx_order' : 1,
}

field_2 = {
'name' : 'pressure',
'dtype' : nm.float64,
'shape' : (1,),
'region' : 'Omega',
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'approx_order' : 1,
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
'p' : ('unknown field', 'pressure', 1),
'q' : ('test field', 'pressure', 'p'),
}

ebcs = {
'fix_u' : ('Bottom', {'u.all' : 0.0}),
'load_u' : ('Top', {'u.2' : 0.2}),
'load_p' : ('Left', {'p.all' : 1.0}),
}

material_1 = {
'name' : 'm',
'values' : {
'D': stiffness_from_lame(dim=3, lam=1.7, mu=0.3),
'alpha' : nm.array( [[0.132], [0.132], [0.132],
[0.092], [0.092], [0.092]],
dtype = nm.float64 ),
'K' : nm.array( [[2.0, 0.2, 0.0], [0.2, 1.0, 0.0], [0.0, 0.0, 0.5]],
dtype = nm.float64 ),
}
}

integral_1 = {
'name' : 'i1',
'order' : 1,
}

integral_2 = {
'name' : 'i2',
'order' : 2,
}

equations = {
'eq_1' :
"""dw_lin_elastic.i2.Omega( m.D, v, u )
- dw_biot.i1.Omega( m.alpha, v, p )
= 0""",
'eq_2' :
"""dw_biot.i1.Omega( m.alpha, u, q ) + dw_diffusion.i1.Omega( m.K, q, p )
= 0""",
}

solver_0 = {
'name' : 'ls_d',
'kind' : 'ls.scipy_direct',
}
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solver_1 = {
'name' : 'newton',
'kind' : 'nls.newton',

'i_max' : 1,
'eps_a' : 1e-10,
'eps_r' : 1.0,
'macheps' : 1e-16,
'lin_red' : 1e-2, # Linear system error < (eps_a * lin_red).
'ls_red' : 0.1,
'ls_red_warp' : 0.001,
'ls_on' : 1.1,
'ls_min' : 1e-5,
'check' : 0,
'delta' : 1e-6,
}

multi_physics/biot_npbc.py

Description
Biot problem - deformable porous medium with the no-penetration boundary condition on a boundary region.
Find 𝑢, 𝑝 such that:
∫︁ ∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) − 𝑝 𝛼𝑖𝑗 𝑒𝑖𝑗 (𝑣) = 0 , ∀𝑣 ,
Ω
∫︁ ∫︁ Ω
𝑞 𝛼𝑖𝑗 𝑒𝑖𝑗 (𝑢) + 𝐾𝑖𝑗 ∇𝑖 𝑞∇𝑗 𝑝 = 0 , ∀𝑞 ,
Ω Ω
𝑢 · 𝑛 = 0 on Γ𝑤𝑎𝑙𝑙𝑠 ,

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

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source code

r"""
Biot problem - deformable porous medium with the no-penetration boundary
condition on a boundary region.

Find :math:`\ul{u}`, :math:`p` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
- \int_{\Omega} p\ \alpha_{ij} e_{ij}(\ul{v})
= 0
\;, \quad \forall \ul{v} \;,

\int_{\Omega} q\ \alpha_{ij} e_{ij}(\ul{u})

+ \int_{\Omega} K_{ij} \nabla_i q \nabla_j p
= 0
\;, \quad \forall q \;,

\ul{u} \cdot \ul{n} = 0 \mbox{ on } \Gamma_{walls} \;,

where

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.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.
"""
from __future__ import absolute_import
import os
import numpy as nm

from sfepy.linalg import get_coors_in_tube

from sfepy.mechanics.matcoefs import stiffness_from_lame

def define():
from sfepy import data_dir

filename = data_dir + '/meshes/3d/cylinder.mesh'

output_dir = 'output'
return define_input(filename, output_dir)

def cinc_simple(coors, mode):

axis = nm.array([1, 0, 0], nm.float64)
if mode == 0: # In
centre = nm.array([0.0, 0.0, 0.0], nm.float64)
radius = 0.019
length = 0.00002
elif mode == 1: # Out
centre = nm.array([0.1, 0.0, 0.0], nm.float64)
radius = 0.019
length = 0.00002
elif mode == 2: # Rigid
centre = nm.array([0.05, 0.0, 0.0], nm.float64)
radius = 0.015
length = 0.03
else:
raise ValueError('unknown mode %s!' % mode)

return get_coors_in_tube(coors,
centre, axis, -1, radius, length)

def define_regions(filename):
if filename.find('simple.mesh'):
dim = 3
regions = {
'Omega' : 'all',
'Walls' : ('vertices of surface -v (r.Outlet +f r.Inlet)', 'facet'),
'Inlet' : ('vertices by cinc_simple0', 'facet'),
'Outlet' : ('vertices by cinc_simple1', 'facet'),
'Rigid' : 'vertices by cinc_simple2',
}

else:
raise ValueError('unknown mesh %s!' % filename)
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return regions, dim

def get_pars(ts, coor, mode, output_dir='.', **kwargs):

if mode == 'qp':
n_nod, dim = coor.shape
sym = (dim + 1) * dim // 2

out = {}
out['D'] = nm.tile(stiffness_from_lame(dim, lam=1.7, mu=0.3),
(coor.shape[0], 1, 1))

aa = nm.zeros((sym, 1), dtype=nm.float64)

aa[:dim] = 0.132
aa[dim:sym] = 0.092
out['alpha'] = nm.tile(aa, (coor.shape[0], 1, 1))

perm = nm.eye(dim, dtype=nm.float64)

out['K'] = nm.tile(perm, (coor.shape[0], 1, 1))

return out

def post_process(out, pb, state, extend=False):

from sfepy.base.base import Struct

dvel = pb.evaluate('ev_diffusion_velocity.i.Omega( m.K, p )',

mode='el_avg')
out['dvel'] = Struct(name='output_data',
mode='cell', data=dvel, dofs=None)

stress = pb.evaluate('ev_cauchy_stress.i.Omega( m.D, u )',

mode='el_avg')
out['cauchy_stress'] = Struct(name='output_data',
mode='cell', data=stress, dofs=None)
return out

def define_input(filename, output_dir):

filename_mesh = filename
options = {
'output_dir' : output_dir,
'output_format' : 'vtk',
'post_process_hook' : 'post_process',

'ls' : 'ls',
'nls' : 'newton',
}

functions = {
'cinc_simple0' : (lambda coors, domain:
cinc_simple(coors, 0),),
'cinc_simple1' : (lambda coors, domain:
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cinc_simple(coors, 1),),
'cinc_simple2' : (lambda coors, domain:
cinc_simple(coors, 2),),
'get_pars' : (lambda ts, coors, mode=None, **kwargs:
get_pars(ts, coors, mode,
output_dir=output_dir, **kwargs),),
}
regions, dim = define_regions(filename_mesh)

field_1 = {
'name' : 'displacement',
'dtype' : nm.float64,
'shape' : dim,
'region' : 'Omega',
'approx_order' : 1,
}
field_2 = {
'name' : 'pressure',
'dtype' : nm.float64,
'shape' : 1,
'region' : 'Omega',
'approx_order' : 1,
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
'p' : ('unknown field', 'pressure', 1),
'q' : ('test field', 'pressure', 'p'),
}

ebcs = {
'inlet' : ('Inlet', {'p.0' : 1.0, 'u.all' : 0.0}),
'outlet' : ('Outlet', {'p.0' : -1.0}),
}

lcbcs = {
'rigid' : ('Outlet', {'u.all' : None}, None, 'rigid'),
'no_penetration' : ('Walls', {'u.all' : None}, None,
'no_penetration', None),
}

material_1 = {
'name' : 'm',
'function' : 'get_pars',
}

integral_1 = {
'name' : 'i',
'order' : 2,
}

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equations = {
'eq_1' :
"""dw_lin_elastic.i.Omega( m.D, v, u )
- dw_biot.i.Omega( m.alpha, v, p )
= 0""",
'eq_2' :
"""dw_biot.i.Omega( m.alpha, u, q )
+ dw_diffusion.i.Omega( m.K, q, p )
= 0""",
}

solver_0 = {
'name' : 'ls',
'kind' : 'ls.scipy_direct', # Direct solver.
}

solver_1 = {
'name' : 'newton',
'kind' : 'nls.newton',
}

return locals()

multi_physics/biot_npbc_lagrange.py

Description
Biot problem - deformable porous medium with the no-penetration boundary condition on a boundary region enforced
using Lagrange multipliers.
The non-penetration condition is enforced weakly using the Lagrange multiplier 𝜆. There is also a rigid body movement
constraint imposed on the Γ𝑜𝑢𝑡𝑙𝑒𝑡 region using the linear combination boundary conditions.
Find 𝑢, 𝑝 and 𝜆 such that:
∫︁ ∫︁ ∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) − 𝑝 𝛼𝑖𝑗 𝑒𝑖𝑗 (𝑣) + 𝜆𝑛 · 𝑣 = 0 , ∀𝑣 ,
Ω Ω Γ
∫︁ ∫︁ 𝑤𝑎𝑙𝑙𝑠
𝑞 𝛼𝑖𝑗 𝑒𝑖𝑗 (𝑢) + 𝐾𝑖𝑗 ∇𝑖 𝑞∇𝑗 𝑝 = 0 , ∀𝑞 ,
Ω Ω
∫︁
ˆ ·𝑢=0,
𝜆𝑛 ˆ,
∀𝜆
Γ𝑤𝑎𝑙𝑙𝑠
𝑢 · 𝑛 = 0 on Γ𝑤𝑎𝑙𝑙𝑠 ,

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

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source code

r"""
Biot problem - deformable porous medium with the no-penetration boundary
condition on a boundary region enforced using Lagrange multipliers.

The non-penetration condition is enforced weakly using the Lagrange

multiplier :math:`\lambda`. There is also a rigid body movement
constraint imposed on the :math:`\Gamma_{outlet}` region using the
linear combination boundary conditions.

Find :math:`\ul{u}`, :math:`p` and :math:`\lambda` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
- \int_{\Omega} p\ \alpha_{ij} e_{ij}(\ul{v})
+ \int_{\Gamma_{walls}} \lambda \ul{n} \cdot \ul{v}
= 0
\;, \quad \forall \ul{v} \;,

\int_{\Omega} q\ \alpha_{ij} e_{ij}(\ul{u})

+ \int_{\Omega} K_{ij} \nabla_i q \nabla_j p
= 0
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\;, \quad \forall q \;,

\int_{\Gamma_{walls}} \hat\lambda \ul{n} \cdot \ul{u}

= 0
\;, \quad \forall \hat\lambda \;,

\ul{u} \cdot \ul{n} = 0 \mbox{ on } \Gamma_{walls} \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.
"""
from __future__ import absolute_import
from sfepy.examples.multi_physics.biot_npbc import (cinc_simple,
define_regions, get_pars)

def define():
from sfepy import data_dir

filename = data_dir + '/meshes/3d/cylinder.mesh'

output_dir = 'output'
return define_input(filename, output_dir)

def post_process(out, pb, state, extend=False):

from sfepy.base.base import Struct

dvel = pb.evaluate('ev_diffusion_velocity.2.Omega( m.K, p )',

mode='el_avg')
out['dvel'] = Struct(name='output_data', var_name='p',
mode='cell', data=dvel, dofs=None)

stress = pb.evaluate('ev_cauchy_stress.2.Omega( m.D, u )',

mode='el_avg')
out['cauchy_stress'] = Struct(name='output_data', var_name='u',
mode='cell', data=stress, dofs=None)
return out

def define_input(filename, output_dir):

filename_mesh = filename
options = {
'output_dir' : output_dir,
'output_format' : 'vtk',
'post_process_hook' : 'post_process',
## 'file_per_var' : True,

'ls' : 'ls',
'nls' : 'newton',
}
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functions = {
'cinc_simple0' : (lambda coors, domain:
cinc_simple(coors, 0),),
'cinc_simple1' : (lambda coors, domain:
cinc_simple(coors, 1),),
'cinc_simple2' : (lambda coors, domain:
cinc_simple(coors, 2),),
'get_pars' : (lambda ts, coors, mode=None, **kwargs:
get_pars(ts, coors, mode,
output_dir=output_dir, **kwargs),),
}
regions, dim = define_regions(filename_mesh)

fields = {
'displacement': ('real', 'vector', 'Omega', 1),
'pressure': ('real', 'scalar', 'Omega', 1),
'multiplier': ('real', 'scalar', 'Walls', 1),
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
'p' : ('unknown field', 'pressure', 1),
'q' : ('test field', 'pressure', 'p'),
'ul' : ('unknown field', 'multiplier', 2),
'vl' : ('test field', 'multiplier', 'ul'),
}

ebcs = {
'inlet' : ('Inlet', {'p.0' : 1.0, 'u.all' : 0.0}),
'outlet' : ('Outlet', {'p.0' : -1.0}),
}

lcbcs = {
'rigid' : ('Outlet', {'u.all' : None}, None, 'rigid'),
}

materials = {
'm' : 'get_pars',
}

equations = {
'eq_1' :
"""dw_lin_elastic.2.Omega( m.D, v, u )
- dw_biot.2.Omega( m.alpha, v, p )
+ dw_non_penetration.2.Walls( v, ul )
= 0""",
'eq_2' :
"""dw_biot.2.Omega( m.alpha, u, q )
+ dw_diffusion.2.Omega( m.K, q, p )
= 0""",
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'eq_3' :
"""dw_non_penetration.2.Walls( u, vl )
= 0""",
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {}),
}

return locals()

multi_physics/biot_parallel_interactive.py

Description
Parallel assembling and solving of a Biot problem (deformable porous medium), using commands for interactive use.
Find 𝑢, 𝑝 such that:
∫︁ ∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) − 𝑝 𝛼𝑖𝑗 𝑒𝑖𝑗 (𝑣) = 0 , ∀𝑣 ,
Ω
∫︁ ∫︁ Ω
𝑞 𝛼𝑖𝑗 𝑒𝑖𝑗 (𝑢) + 𝐾𝑖𝑗 ∇𝑖 𝑞∇𝑗 𝑝 = 0 , ∀𝑞 ,
Ω Ω

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

Important Notes

• This example requires petsc4py, mpi4py and (optionally) pymetis with their dependencies installed!
• This example generates a number of files - do not use an existing non-empty directory for the output_dir
argument.
• Use the --clear option with care!

Notes

• Each task is responsible for a subdomain consisting of a set of cells (a cell region).
• Each subdomain owns PETSc DOFs within a consecutive range.
• When both global and task-local variables exist, the task-local variables have _i suffix.
• This example shows how to use a nonlinear solver from PETSc.
• This example can serve as a template for solving a (non)linear multi-field problem - just replace the equations in
create_local_problem().
• The material parameter 𝛼𝑖𝑗 is artificially high to be able to see the pressure influence on displacements.
• The command line options are saved into <output_dir>/options.txt file.

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Usage Examples

See all options:

$ python examples/multi_physics/biot_parallel_interactive.py -h

See PETSc options:

$ python examples/multi_physics/biot_parallel_interactive.py -help

Single process run useful for debugging with debug():

$ python examples/multi_physics/biot_parallel_interactive.py output-parallel

Parallel runs:

$ mpiexec -n 3 python examples/multi_physics/biot_parallel_interactive.py output-

˓→parallel -2 --shape=101,101

$ mpiexec -n 3 python examples/multi_physics/biot_parallel_interactive.py output-

˓→parallel -2 --shape=101,101 --metis

$ mpiexec -n 8 python examples/multi_physics/biot_parallel_interactive.py output-

˓→parallel -2 --shape 101,101 --metis -snes_monitor -snes_view -snes_converged_reason -

˓→ksp_monitor

Using FieldSplit preconditioner:

$ mpiexec -n 2 python examples/multi_physics/biot_parallel_interactive.py output-

˓→parallel --shape=101,101 -snes_monitor -snes_converged_reason -ksp_monitor -pc_type␣

˓→fieldsplit

$ mpiexec -n 8 python examples/multi_physics/biot_parallel_interactive.py output-

˓→parallel --shape=1001,1001 --metis -snes_monitor -snes_converged_reason -ksp_monitor -

˓→pc_type fieldsplit -pc_fieldsplit_type additive

View the results using (strip linearization or approximation orders one):

$ python postproc.py output-parallel/sol.h5 --wireframe -b -d'p,plot_warp_scalar:u,plot_

˓→displacements'

View the results using (adaptive linearization):

$ python postproc.py output-parallel/sol_u.h5 --wireframe -b -d'u,plot_displacements'

$ python postproc.py output-parallel/sol_p.h5 --wireframe -b -d'p,plot_warp_scalar'

source code

#!/usr/bin/env python
r"""
Parallel assembling and solving of a Biot problem (deformable porous medium),
using commands for interactive use.

Find :math:`\ul{u}`, :math:`p` such that:

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.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
- \int_{\Omega} p\ \alpha_{ij} e_{ij}(\ul{v})
= 0
\;, \quad \forall \ul{v} \;,

\int_{\Omega} q\ \alpha_{ij} e_{ij}(\ul{u})

+ \int_{\Omega} K_{ij} \nabla_i q \nabla_j p
= 0
\;, \quad \forall q \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.

Important Notes
---------------

- This example requires petsc4py, mpi4py and (optionally) pymetis with their
dependencies installed!
- This example generates a number of files - do not use an existing non-empty
directory for the ``output_dir`` argument.
- Use the ``--clear`` option with care!

Notes
-----

- Each task is responsible for a subdomain consisting of a set of cells (a cell

region).
- Each subdomain owns PETSc DOFs within a consecutive range.
- When both global and task-local variables exist, the task-local
variables have ``_i`` suffix.
- This example shows how to use a nonlinear solver from PETSc.
- This example can serve as a template for solving a (non)linear multi-field
problem - just replace the equations in :func:`create_local_problem()`.
- The material parameter :math:`\alpha_{ij}` is artificially high to be able to
see the pressure influence on displacements.
- The command line options are saved into <output_dir>/options.txt file.

Usage Examples
--------------

See all options::

$ python sfepy/examples/multi_physics/biot_parallel_interactive.py -h

See PETSc options::

(continues on next page)

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(continued from previous page)

$ python sfepy/examples/multi_physics/biot_parallel_interactive.py -help

Single process run useful for debugging with :func:`debug()

<sfepy.base.base.debug>`::

$ python sfepy/examples/multi_physics/biot_parallel_interactive.py output-parallel

Parallel runs::

$ mpiexec -n 3 python sfepy/examples/multi_physics/biot_parallel_interactive.py output-

˓→parallel -2 --shape=101,101

$ mpiexec -n 3 python sfepy/examples/multi_physics/biot_parallel_interactive.py output-

˓→parallel -2 --shape=101,101 --metis

$ mpiexec -n 8 python sfepy/examples/multi_physics/biot_parallel_interactive.py output-

˓→parallel -2 --shape 101,101 --metis -snes_monitor -snes_view -snes_converged_reason -
˓→ksp_monitor

Using FieldSplit preconditioner::

$ mpiexec -n 2 python sfepy/examples/multi_physics/biot_parallel_interactive.py output-

˓→parallel --shape=101,101 -snes_monitor -snes_converged_reason -ksp_monitor -pc_type␣
˓→fieldsplit

$ mpiexec -n 8 python sfepy/examples/multi_physics/biot_parallel_interactive.py output-

˓→parallel --shape=1001,1001 --metis -snes_monitor -snes_converged_reason -ksp_monitor -
˓→pc_type fieldsplit -pc_fieldsplit_type additive

View the results using (strip linearization or approximation orders one)::

$ python postproc.py output-parallel/sol.h5 --wireframe -b -d'p,plot_warp_scalar:u,plot_

˓→displacements'

View the results using (adaptive linearization)::

$ python postproc.py output-parallel/sol_u.h5 --wireframe -b -d'u,plot_displacements'

$ python postproc.py output-parallel/sol_p.h5 --wireframe -b -d'p,plot_warp_scalar'
"""
from __future__ import absolute_import
from argparse import RawDescriptionHelpFormatter, ArgumentParser
import os
import sys
sys.path.append('.')

import numpy as nm

from sfepy.base.base import output, Struct

from sfepy.base.ioutils import ensure_path, remove_files_patterns, save_options
from sfepy.base.timing import Timer
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.discrete.common.region import Region
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from sfepy.discrete import (FieldVariable, Material, Integral, Function,
Equation, Equations, Problem)
from sfepy.discrete.conditions import Conditions, EssentialBC
from sfepy.terms import Term
from sfepy.solvers.ls import PETScKrylovSolver
from sfepy.solvers.nls import PETScNonlinearSolver
from sfepy.mechanics.matcoefs import stiffness_from_lame

import sfepy.parallel.parallel as pl
from sfepy.parallel.evaluate import PETScParallelEvaluator

def create_local_problem(omega_gi, orders):

"""
Local problem definition using a domain corresponding to the global region
`omega_gi`.
"""
order_u, order_p = orders

mesh = omega_gi.domain.mesh

# All tasks have the whole mesh.

bbox = mesh.get_bounding_box()
min_x, max_x = bbox[:, 0]
eps_x = 1e-8 * (max_x - min_x)

min_y, max_y = bbox[:, 1]

eps_y = 1e-8 * (max_y - min_y)

mesh_i = Mesh.from_region(omega_gi, mesh, localize=True)

domain_i = FEDomain('domain_i', mesh_i)
omega_i = domain_i.create_region('Omega', 'all')

gamma1_i = domain_i.create_region('Gamma1',
'vertices in (x < %.10f )'
% (min_x + eps_x),
'facet', allow_empty=True)
gamma2_i = domain_i.create_region('Gamma2',
'vertices in (x > %.10f )'
% (max_x - eps_x),
'facet', allow_empty=True)
gamma3_i = domain_i.create_region('Gamma3',
'vertices in (y < %.10f )'
% (min_y + eps_y),
'facet', allow_empty=True)

field1_i = Field.from_args('fu', nm.float64, mesh.dim, omega_i,

approx_order=order_u)

field2_i = Field.from_args('fp', nm.float64, 1, omega_i,

approx_order=order_p)

output('field 1: number of local DOFs:', field1_i.n_nod)

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output('field 2: number of local DOFs:', field2_i.n_nod)

u_i = FieldVariable('u_i', 'unknown', field1_i, order=0)

v_i = FieldVariable('v_i', 'test', field1_i, primary_var_name='u_i')
p_i = FieldVariable('p_i', 'unknown', field2_i, order=1)
q_i = FieldVariable('q_i', 'test', field2_i, primary_var_name='p_i')

if mesh.dim == 2:
alpha = 1e2 * nm.array([[0.132], [0.132], [0.092]])

else:
alpha = 1e2 * nm.array([[0.132], [0.132], [0.132],
[0.092], [0.092], [0.092]])

mat = Material('m', D=stiffness_from_lame(mesh.dim, lam=10, mu=5),

k=1, alpha=alpha)
integral = Integral('i', order=2*(max(order_u, order_p)))

t11 = Term.new('dw_lin_elastic(m.D, v_i, u_i)',

integral, omega_i, m=mat, v_i=v_i, u_i=u_i)
t12 = Term.new('dw_biot(m.alpha, v_i, p_i)',
integral, omega_i, m=mat, v_i=v_i, p_i=p_i)
t21 = Term.new('dw_biot(m.alpha, u_i, q_i)',
integral, omega_i, m=mat, u_i=u_i, q_i=q_i)
t22 = Term.new('dw_laplace(m.k, q_i, p_i)',
integral, omega_i, m=mat, q_i=q_i, p_i=p_i)

eq1 = Equation('eq1', t11 - t12)

eq2 = Equation('eq1', t21 + t22)
eqs = Equations([eq1, eq2])

ebc1 = EssentialBC('ebc1', gamma1_i, {'u_i.all' : 0.0})

ebc2 = EssentialBC('ebc2', gamma2_i, {'u_i.0' : 0.05})
def bc_fun(ts, coors, **kwargs):
val = 0.3 * nm.sin(4 * nm.pi * (coors[:, 0] - min_x) / (max_x - min_x))
return val

fun = Function('bc_fun', bc_fun)

ebc3 = EssentialBC('ebc3', gamma3_i, {'p_i.all' : fun})

pb = Problem('problem_i', equations=eqs, active_only=False)

pb.time_update(ebcs=Conditions([ebc1, ebc2, ebc3]))
pb.update_materials()

return pb

def solve_problem(mesh_filename, options, comm):

order_u = options.order_u
order_p = options.order_p

rank, size = comm.Get_rank(), comm.Get_size()

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output('rank', rank, 'of', size)

stats = Struct()
timer = Timer('solve_timer')

timer.start()
mesh = Mesh.from_file(mesh_filename)
stats.t_read_mesh = timer.stop()

timer.start()
if rank == 0:
cell_tasks = pl.partition_mesh(mesh, size, use_metis=options.metis,
verbose=True)

else:
cell_tasks = None

stats.t_partition_mesh = timer.stop()

output('creating global domain and fields...')

timer.start()

domain = FEDomain('domain', mesh)

omega = domain.create_region('Omega', 'all')
field1 = Field.from_args('fu', nm.float64, mesh.dim, omega,
approx_order=order_u)
field2 = Field.from_args('fp', nm.float64, 1, omega,
approx_order=order_p)
fields = [field1, field2]

stats.t_create_global_fields = timer.stop()
output('...done in', timer.dt)

output('distributing fields...')
timer.start()

distribute = pl.distribute_fields_dofs
lfds, gfds = distribute(fields, cell_tasks,
is_overlap=True,
use_expand_dofs=True,
save_inter_regions=options.save_inter_regions,
output_dir=options.output_dir,
comm=comm, verbose=True)

stats.t_distribute_fields_dofs = timer.stop()
output('...done in', timer.dt)

output('creating local problem...')

timer.start()

cells = lfds[0].cells

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omega_gi = Region.from_cells(cells, domain)
omega_gi.finalize()
omega_gi.update_shape()

pb = create_local_problem(omega_gi, [order_u, order_p])

variables = pb.get_initial_state()

variables.fill_state(0.0)
variables.apply_ebc()

stats.t_create_local_problem = timer.stop()
output('...done in', timer.dt)

output('allocating global system...')

timer.start()

sizes, drange, pdofs = pl.setup_composite_dofs(lfds, fields, variables,

verbose=True)
pmtx, psol, prhs = pl.create_petsc_system(pb.mtx_a, sizes, pdofs, drange,
is_overlap=True, comm=comm,
verbose=True)

stats.t_allocate_global_system = timer.stop()
output('...done in', timer.dt)

output('creating solver...')
timer.start()

conf = Struct(method='bcgsl', precond='jacobi', sub_precond='none',

i_max=10000, eps_a=1e-50, eps_r=1e-6, eps_d=1e4,
verbose=True)
status = {}
ls = PETScKrylovSolver(conf, comm=comm, mtx=pmtx, status=status)

field_ranges = {}
for ii, variable in enumerate(variables.iter_state(ordered=True)):
field_ranges[variable.name] = lfds[ii].petsc_dofs_range

ls.set_field_split(field_ranges, comm=comm)

ev = PETScParallelEvaluator(pb, pdofs, drange, True,

psol, comm, verbose=True)

nls_status = {}
conf = Struct(method='newtonls',
i_max=5, eps_a=0, eps_r=1e-5, eps_s=0.0,
verbose=True)
nls = PETScNonlinearSolver(conf, pmtx=pmtx, prhs=prhs, comm=comm,
fun=ev.eval_residual,
fun_grad=ev.eval_tangent_matrix,
lin_solver=ls, status=nls_status)
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stats.t_create_solver = timer.stop()
output('...done in', timer.dt)

output('solving...')
timer.start()

variables.apply_ebc()

ev.psol_i[...] = variables()
ev.gather(psol, ev.psol_i)

psol = nls(psol)

ev.scatter(ev.psol_i, psol)
sol0_i = ev.psol_i[...]

stats.t_solve = timer.stop()
output('...done in', timer.dt)

output('saving solution...')
timer.start()

variables.set_state(sol0_i)
out = variables.create_output()

filename = os.path.join(options.output_dir, 'sol_%02d.h5' % comm.rank)

pb.domain.mesh.write(filename, io='auto', out=out)

gather_to_zero = pl.create_gather_to_zero(psol)

psol_full = gather_to_zero(psol)

if comm.rank == 0:
sol = psol_full[...].copy()

u = FieldVariable('u', 'parameter', field1,

primary_var_name='(set-to-None)')
remap = gfds[0].id_map
ug = sol[remap]

p = FieldVariable('p', 'parameter', field2,

primary_var_name='(set-to-None)')
remap = gfds[1].id_map
pg = sol[remap]

if (((order_u == 1) and (order_p == 1))

or (options.linearization == 'strip')):
out = u.create_output(ug)
out.update(p.create_output(pg))
filename = os.path.join(options.output_dir, 'sol.h5')
mesh.write(filename, io='auto', out=out)
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else:
out = u.create_output(ug, linearization=Struct(kind='adaptive',
min_level=0,
max_level=order_u,
eps=1e-3))

filename = os.path.join(options.output_dir, 'sol_u.h5')

out['u'].mesh.write(filename, io='auto', out=out)

out = p.create_output(pg, linearization=Struct(kind='adaptive',

min_level=0,
max_level=order_p,
eps=1e-3))

filename = os.path.join(options.output_dir, 'sol_p.h5')

out['p'].mesh.write(filename, io='auto', out=out)

stats.t_save_solution = timer.stop()
output('...done in', timer.dt)

stats.t_total = timer.total

stats.n_dof = sizes[1]
stats.n_dof_local = sizes[0]
stats.n_cell = omega.shape.n_cell
stats.n_cell_local = omega_gi.shape.n_cell

return stats

helps = {
'output_dir' :
'output directory',
'dims' :
'dimensions of the block [default: %(default)s]',
'shape' :
'shape (counts of nodes in x, y, z) of the block [default: %(default)s]',
'centre' :
'centre of the block [default: %(default)s]',
'2d' :
'generate a 2D rectangle, the third components of the above'
' options are ignored',
'u-order' :
'displacement field approximation order',
'p-order' :
'pressure field approximation order',
'linearization' :
'linearization used for storing the results with approximation order > 1'
' [default: %(default)s]',
'metis' :
'use metis for domain partitioning',
'save_inter_regions' :
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'save inter-task regions for debugging partitioning problems',
'stats_filename' :
'name of the stats file for storing elapsed time statistics',
'new_stats' :
'create a new stats file with a header line (overwrites existing!)',
'silent' : 'do not print messages to screen',
'clear' :
'clear old solution files from output directory'
' (DANGEROUS - use with care!)',
}

def main():
parser = ArgumentParser(description=__doc__.rstrip(),
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('output_dir', help=helps['output_dir'])
parser.add_argument('--dims', metavar='dims',
action='store', dest='dims',
default='1.0,1.0,1.0', help=helps['dims'])
parser.add_argument('--shape', metavar='shape',
action='store', dest='shape',
default='11,11,11', help=helps['shape'])
parser.add_argument('--centre', metavar='centre',
action='store', dest='centre',
default='0.0,0.0,0.0', help=helps['centre'])
parser.add_argument('-2', '--2d',
action='store_true', dest='is_2d',
default=False, help=helps['2d'])
parser.add_argument('--u-order', metavar='int', type=int,
action='store', dest='order_u',
default=1, help=helps['u-order'])
parser.add_argument('--p-order', metavar='int', type=int,
action='store', dest='order_p',
default=1, help=helps['p-order'])
parser.add_argument('--linearization', choices=['strip', 'adaptive'],
action='store', dest='linearization',
default='strip', help=helps['linearization'])
parser.add_argument('--metis',
action='store_true', dest='metis',
default=False, help=helps['metis'])
parser.add_argument('--save-inter-regions',
action='store_true', dest='save_inter_regions',
default=False, help=helps['save_inter_regions'])
parser.add_argument('--stats', metavar='filename',
action='store', dest='stats_filename',
default=None, help=helps['stats_filename'])
parser.add_argument('--new-stats',
action='store_true', dest='new_stats',
default=False, help=helps['new_stats'])
parser.add_argument('--silent',
action='store_true', dest='silent',
default=False, help=helps['silent'])
parser.add_argument('--clear',
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action='store_true', dest='clear',
default=False, help=helps['clear'])
options, petsc_opts = parser.parse_known_args()

comm = pl.PETSc.COMM_WORLD

output_dir = options.output_dir

filename = os.path.join(output_dir, 'output_log_%02d.txt' % comm.rank)

if comm.rank == 0:
ensure_path(filename)
comm.barrier()

output.prefix = 'sfepy_%02d:' % comm.rank

output.set_output(filename=filename, combined=options.silent == False)

output('petsc options:', petsc_opts)

mesh_filename = os.path.join(options.output_dir, 'para.h5')

dim = 2 if options.is_2d else 3

dims = nm.array(eval(options.dims), dtype=nm.float64)[:dim]
shape = nm.array(eval(options.shape), dtype=nm.int32)[:dim]
centre = nm.array(eval(options.centre), dtype=nm.float64)[:dim]

output('dimensions:', dims)
output('shape: ', shape)
output('centre: ', centre)

if comm.rank == 0:
from sfepy.mesh.mesh_generators import gen_block_mesh

if options.clear:
remove_files_patterns(output_dir,
['*.h5', '*.mesh', '*.txt'],
ignores=['output_log_%02d.txt' % ii
for ii in range(comm.size)],
verbose=True)

save_options(os.path.join(output_dir, 'options.txt'),
[('options', vars(options))])

mesh = gen_block_mesh(dims, shape, centre, name='block-fem',

verbose=True)
mesh.write(mesh_filename, io='auto')

comm.barrier()

output('field u order:', options.order_u)

output('field p order:', options.order_p)

stats = solve_problem(mesh_filename, options, comm)

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output(stats)

if options.stats_filename:
from sfepy.examples.diffusion.poisson_parallel_interactive import save_stats
if comm.rank == 0:
ensure_path(options.stats_filename)
comm.barrier()

pars = Struct(dim=dim, shape=shape, order=options.order_u)

pl.call_in_rank_order(
lambda rank, comm:
save_stats(options.stats_filename, pars, stats, options.new_stats,
rank, comm),
comm
)

if __name__ == '__main__':
main()

multi_physics/biot_short_syntax.py

Description
Biot problem - deformable porous medium with a no-penetration boundary condition imposed in the weak sense on a
boundary region, using the short syntax of keywords.
The Biot coefficient tensor 𝛼𝑖𝑗 is non-symmetric. The mesh resolution can be changed by editing the shape variable.
This example demonstrates how to set up various linear solvers and preconditioners (see solvers dict):
• ‘direct’ (a direct solver from SciPy), ‘iterative-s’ (an iterative solver from SciPy), ‘iterative-p’ (an iterative solver
from PETSc) solvers can be used as the main linear solver.
• ‘direct’, ‘cg-s’ (several iterations of CG from SciPy), ‘cg-p’ (several iterations of CG from PETSc), ‘pyamg’ (an
algebraic multigrid solver) solvers can be used as preconditioners for the matrix blocks on the diagonal.
See setup_precond() and try to modify it.
The PETSc solvers can be configured also using command line options. For example, set 'ls' : 'iterative-p'
in options, and run:

python simple.py examples/multi_physics/biot_short_syntax.py -ksp_monitor

or simply run:

python simple.py examples/multi_physics/biot_short_syntax.py -O "ls='iterative-p'"

to monitor the PETSc iterative solver convergence. It will diverge without preconditioning, see matvec_bj(),
matvec_j() for further details.
The PETSc options can also be set in the solver configuration - try uncommenting the 'ksp_*' or 'pc_*' parameters
in 'iterative-p'. Uncommenting all the lines leads to, among other things, using the GMRES method with no
preconditioning and the condition number estimate computation. Compare the condition number estimates with and
without a preconditioning (try, for example, using 'precond' : 'mg' or 'pc_type' : 'mg').

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Find 𝑢, 𝑝 such that:

∫︁ ∫︁ ∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) − 𝑝 𝛼𝑖𝑗 𝑒𝑖𝑗 (𝑣) + 𝜀(𝑛 · 𝑣)(𝑛 · 𝑢) = 0 , ∀𝑣 ,
Ω Ω Γ𝑇 𝐵
∫︁ ∫︁
− 𝑞 𝛼𝑖𝑗 𝑒𝑖𝑗 (𝑢) − 𝐾𝑖𝑗 ∇𝑖 𝑞∇𝑗 𝑝 = 0 , ∀𝑞 ,
Ω Ω

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

source code

r"""
Biot problem - deformable porous medium with a no-penetration boundary
condition imposed in the weak sense on a boundary region, using the short
syntax of keywords.

The Biot coefficient tensor :math:`\alpha_{ij}` is non-symmetric. The mesh

resolution can be changed by editing the `shape` variable.

This example demonstrates how to set up various linear solvers and

preconditioners (see `solvers` dict):

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- `'direct'` (a direct solver from SciPy), `'iterative-s'` (an iterative solver
from SciPy), `'iterative-p'` (an iterative solver from PETSc) solvers can be
used as the main linear solver.
- `'direct'`, `'cg-s'` (several iterations of CG from SciPy), `'cg-p'` (several
iterations of CG from PETSc), `'pyamg'` (an algebraic multigrid solver)
solvers can be used as preconditioners for the matrix blocks on the diagonal.

See :func:`setup_precond()` and try to modify it.

The PETSc solvers can be configured also using command line options. For
example, set ``'ls' : 'iterative-p'`` in `options`, and run::

python simple.py sfepy/examples/multi_physics/biot_short_syntax.py -ksp_monitor

or simply run::

python simple.py sfepy/examples/multi_physics/biot_short_syntax.py -O "ls='iterative-p'"

to monitor the PETSc iterative solver convergence. It will diverge without

preconditioning, see :func:`matvec_bj()`, :func:`matvec_j()` for further
details.

The PETSc options can also be set in the solver configuration - try
uncommenting the ``'ksp_*'`` or ``'pc_*'`` parameters in ``'iterative-p'``.
Uncommenting all the lines leads to, among other things, using the GMRES method
with no preconditioning and the condition number estimate computation. Compare
the condition number estimates with and without a preconditioning (try, for
example, using ``'precond' : 'mg'`` or ``'pc_type' : 'mg'``).

Find :math:`\ul{u}`, :math:`p` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
- \int_{\Omega} p\ \alpha_{ij} e_{ij}(\ul{v})
+ \int_{\Gamma_{TB}} \varepsilon (\ul{n} \cdot \ul{v}) (\ul{n} \cdot \ul{u})
= 0
\;, \quad \forall \ul{v} \;,

- \int_{\Omega} q\ \alpha_{ij} e_{ij}(\ul{u})

- \int_{\Omega} K_{ij} \nabla_i q \nabla_j p
= 0
\;, \quad \forall q \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.
"""
from __future__ import absolute_import
import numpy as nm
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from sfepy.base.base import Struct

from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.discrete.fem.meshio import UserMeshIO
from sfepy.mesh.mesh_generators import gen_block_mesh

def get_pars(ts, coor, mode, **kwargs):

"""
Define the material parameters.
"""
if mode == 'qp':
n_nod, dim = coor.shape

out = {}
out['D'] = stiffness_from_lame(dim, lam=1.7, mu=0.3)[None, ...]

out['alpha'] = nm.array([[[0.132, 0.092],

[0.052, 0.132]]])

out['K'] = nm.eye(dim, dtype=nm.float64)[None, ...]

out['np_eps'] = nm.array([[[1e5]]])

return out

def post_process(out, pb, state, extend=False):

"""
Compute derived quantities of interest..
"""
from sfepy.base.base import Struct

dvel = pb.evaluate('ev_diffusion_velocity.i.Omega(m.K, p)',

mode='el_avg')
out['dvel'] = Struct(name='output_data',
mode='cell', data=dvel, dofs=None)

stress = pb.evaluate('ev_cauchy_stress.i.Omega(m.D, u)',

mode='el_avg')
out['cauchy_stress'] = Struct(name='output_data',
mode='cell', data=stress, dofs=None)

return out

# Mesh dimensions.
dims = [0.1, 0.1]

# Mesh resolution: increase to improve accuracy.

shape = [21, 21]

def mesh_hook(mesh, mode):

"""
Generate the block mesh.
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"""
if mode == 'read':
mesh = gen_block_mesh(dims, shape, [0, 0], name='user_block',
verbose=False)
return mesh

elif mode == 'write':

pass

filename_mesh = UserMeshIO(mesh_hook)

materials = {
'coef' : ({'val' : 1.0},),
}

regions = {
'Omega' : 'all', # or 'cells of group 6'
'GammaL' : ('vertices in (x < -0.0499)', 'facet'),
'GammaR' : ('vertices in (x > 0.0499)', 'facet'),
'GammaTB' : ('vertices of surface -s (r.GammaL +s r.GammaR)', 'facet')
}

fields = {
'displacement': ('real', 'vector', 'Omega', 1),
'pressure': ('real', 'scalar', 'Omega', 1),
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
'p' : ('unknown field', 'pressure', 1),
'q' : ('test field', 'pressure', 'p'),
}

ebcs = {
'inlet' : ('GammaL', {'p.0' : 1.0, 'u.all' : 0.0}),
'outlet' : ('GammaR', {'p.0' : 0.0}),
}

integrals = {
'i' : 2,
}

materials = {
'm' : 'get_pars',
}

functions = {
'get_pars' : (get_pars,),
}

equations = {
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'eq_1' :
"""+ dw_lin_elastic.i.Omega(m.D, v, u)
- dw_biot.i.Omega(m.alpha, v, p)
+ dw_non_penetration_p.i.GammaTB(m.np_eps, v, u)
= 0""",
'eq_2' :
"""- dw_biot.i.Omega(m.alpha, u, q)
- dw_diffusion.i.Omega(m.K, q, p)
= 0""",
}

def setup_precond(mtx, problem):

"""
Setup a preconditioner for `mtx`.
"""
import scipy.sparse.linalg as spla
from sfepy.solvers import Solver

# Get active DOF indices for u, p.

adi = problem.get_variables().adi
iu = adi.indx['u']
ip = adi.indx['p']

# Get the diagonal blocks of the linear system matrix.

K = mtx[iu, iu]
M = mtx[ip, ip]

# Create solvers for K, M blocks to be used in matvec_bj(). A different

# solver for each block could be used.
conf = problem.solver_confs['direct']
# conf = problem.solver_confs['cg-s']
# conf = problem.solver_confs['cg-p']
# conf = problem.solver_confs['pyamg']
ls1 = Solver.any_from_conf(conf, mtx=K, context=problem)
ls2 = Solver.any_from_conf(conf, mtx=M, context=problem)

def matvec_bj(vec):
"""
The application of the Block Jacobi preconditioner.

The exact version (as with the `'direct'` solver) can be obtained also
by using the following PETSs command-line options, together with the
`'iterative-p'` solver::

-ksp_monitor -pc_type fieldsplit -pc_fieldsplit_type additive -fieldsplit_u_

˓→ksp_type preonly -fieldsplit_u_pc_type lu -fieldsplit_p_ksp_type preonly -fieldsplit_p_
˓→pc_type lu

The inexact version (20 iterations of a CG solver for each block, as

with the `'cg-s'` or `'cg-p'` solvers) can be obtained also by using
the following PETSs command-line options, together with the
`'iterative-p'` solver::
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-ksp_monitor -pc_type fieldsplit -pc_fieldsplit_type additive -fieldsplit_u_

˓→ksp_type cg -fieldsplit_u_pc_type none -fieldsplit_p_ksp_type cg -fieldsplit_p_pc_type␣
˓→none -fieldsplit_u_ksp_max_it 20 -fieldsplit_p_ksp_max_it 20

"""
vu = ls1(vec[iu])
vp = ls2(vec[ip])

return nm.r_[vu, vp]

def matvec_j(vec):
"""
The application of the Jacobi (diagonal) preconditioner.

The same effect can be obtained also by using the following PETSs
command-line options, together with the `'iterative-p'` solver::

-ksp_monitor -pc_type jacobi

"""
D = mtx.diagonal()

return vec / D

# Create the preconditioner, using one of matvec_bj() or matvec_j().

precond = Struct(name='precond', shape=mtx.shape, matvec=matvec_bj)
precond = spla.aslinearoperator(precond)

return precond

method = 'gmres'
i_max = 20
eps_r = 1e-8

solvers = {
'direct' : ('ls.scipy_direct', {}),

'iterative-s' : ('ls.scipy_iterative', {
'method' : method,
'i_max' : i_max,
'eps_r' : eps_r,
'setup_precond': setup_precond,
'verbose' : 2,
}),
'cg-s' : ('ls.scipy_iterative', {
'method' : 'cg',
'i_max' : 20,
'eps_r' : 1e-6,
'verbose' : 0,
}),

'iterative-p' : ('ls.petsc', {
'method' : method,
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'precond' : 'none',
'i_max' : i_max,
'eps_r' : eps_r,
'verbose' : 2,
# 'ksp_converged_reason' : None,
# 'ksp_monitor_true_residual' : None,
# 'ksp_monitor_singular_value' : None,
# 'ksp_final_residual' : None,
# 'ksp_type' : 'gmres', # Overrides `method`.
# 'ksp_max_it' : 500,
# 'ksp_gmres_restart' : 1000,
# 'pc_type' : 'none', # Overrides `precond`.
}),
'cg-p' : ('ls.petsc', {
'method' : 'cg',
'precond' : 'none',
'i_max' : 20,
'eps_r' : 1e-6,
'verbose' : 0,
}),

'pyamg' : ('ls.pyamg', {
'method' : 'smoothed_aggregation_solver',
'i_max' : 20,
'eps_r' : 1e-6,
'verbose' : 0,
}),

'newton' : ('nls.newton',
{'i_max' : 1,
'eps_r' : 1e-6,
'eps_a' : 1.0,
}),
}

options = {
'nls' : 'newton',
'ls' : 'iterative-s',

'post_process_hook' : 'post_process',
}

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multi_physics/piezo_elasticity.py

Description
Piezo-elasticity problem - linear elastic material with piezoelectric effects.
Find 𝑢, 𝜑 such that:
∫︁ ∫︁ ∫︁
−𝜔 2 𝜌𝑣·𝑢+ 𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) − 𝑔𝑘𝑖𝑗 𝑒𝑖𝑗 (𝑣)∇𝑘 𝜑 = 0 , ∀𝑣 ,
𝑌 𝑌 𝑌2
∫︁ ∫︁
𝑔𝑘𝑖𝑗 𝑒𝑖𝑗 (𝑢)∇𝑘 𝜓 + 𝐾𝑖𝑗 ∇𝑖 𝜓∇𝑗 𝜑 = 0 , ∀𝜓 ,
𝑌2 𝑌

where

𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 .

source code

r"""
Piezo-elasticity problem - linear elastic material with piezoelectric
effects.

Find :math:`\ul{u}`, :math:`\phi` such that:

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.. math::
- \omega^2 \int_{Y} \rho\ \ul{v} \cdot \ul{u}
+ \int_{Y} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
- \int_{Y_2} g_{kij}\ e_{ij}(\ul{v}) \nabla_k \phi
= 0
\;, \quad \forall \ul{v} \;,

\int_{Y_2} g_{kij}\ e_{ij}(\ul{u}) \nabla_k \psi

+ \int_{Y} K_{ij} \nabla_i \psi \nabla_j \phi
= 0
\;, \quad \forall \psi \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;.
"""
from __future__ import absolute_import
import os
import numpy as nm

from sfepy import data_dir

from sfepy.discrete.fem import MeshIO
from sfepy.mechanics.matcoefs import stiffness_from_lame
import six

def post_process(out, pb, state, extend=False):

"""
Calculate and output the strain and stresses for the given state.
"""
from sfepy.base.base import Struct
from sfepy.discrete.fem import extend_cell_data

ev = pb.evaluate
strain = ev('ev_cauchy_strain.i.Y(u)', mode='el_avg')
stress = ev('ev_cauchy_stress.i.Y(inclusion.D, u)', mode='el_avg')

piezo = -ev('ev_piezo_stress.i.Y2(inclusion.coupling, phi)',

mode='el_avg')
piezo = extend_cell_data(piezo, pb.domain, 'Y2', val=0.0)

piezo_strain = ev('ev_piezo_strain.i.Y(inclusion.coupling, u)',

mode='el_avg')

out['cauchy_strain'] = Struct(name='output_data', mode='cell',

data=strain, dofs=None)
out['elastic_stress'] = Struct(name='output_data', mode='cell',
data=stress, dofs=None)
out['piezo_stress'] = Struct(name='output_data', mode='cell',
data=piezo, dofs=None)
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out['piezo_strain'] = Struct(name='output_data', mode='cell',
data=piezo_strain, dofs=None)
out['total_stress'] = Struct(name='output_data', mode='cell',
data=stress + piezo, dofs=None)

return out

filename_mesh = data_dir + '/meshes/2d/special/circle_in_square.mesh'

## filename_mesh = data_dir + '/meshes/2d/special/circle_in_square_small.mesh'
## filename_mesh = data_dir + '/meshes/3d/special/cube_sphere.mesh'
## filename_mesh = data_dir + '/meshes/2d/special/cube_cylinder.mesh'

omega = 1
omega_squared = omega**2

conf_dir = os.path.dirname(__file__)
io = MeshIO.any_from_filename(filename_mesh, prefix_dir=conf_dir)
bbox, dim = io.read_bounding_box(ret_dim=True)

geom = {3 : '3_4', 2 : '2_3'}[dim]

x_left, x_right = bbox[:,0]

options = {
'post_process_hook' : 'post_process',
}

regions = {
'Y' : 'all',
'Y1' : 'cells of group 1',
'Y2' : 'cells of group 2',
'Y2_Surface': ('r.Y1 *v r.Y2', 'facet'),
'Left' : ('vertices in (x < %f )' % (x_left + 1e-3), 'facet'),
'Right' : ('vertices in (x > %f )' % (x_right - 1e-3), 'facet'),
}

fields = {
'displacement' : ('real', dim, 'Y', 1),
'potential' : ('real', 1, 'Y', 1),
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
'phi' : ('unknown field', 'potential', 1),
'psi' : ('test field', 'potential', 'phi'),
}

ebcs = {
'u1' : ('Left', {'u.all' : 0.0}),
'u2' : ('Right', {'u.0' : 0.1}),
'phi' : ('Y2_Surface', {'phi.all' : 0.0}),
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}

def get_inclusion_pars(ts, coor, mode=None, **kwargs):

"""TODO: implement proper 3D -> 2D transformation of constitutive
matrices."""
if mode == 'qp':
_, dim = coor.shape
sym = (dim + 1) * dim // 2

dielectric = nm.eye(dim, dtype=nm.float64)

# !!!
coupling = nm.ones((dim, sym), dtype=nm.float64)
# coupling[0,1] = 0.2

out = {
# Lame coefficients in 1e+10 Pa.
'D' : stiffness_from_lame(dim=2, lam=0.1798, mu=0.148),
# dielectric tensor
'dielectric' : dielectric,
# piezoelectric coupling
'coupling' : coupling,
'density' : nm.array([[0.1142]]), # in 1e4 kg/m3
}

for key, val in six.iteritems(out):

out[key] = val[None, ...]

return out

materials = {
'inclusion' : (None, 'get_inclusion_pars')
}

functions = {
'get_inclusion_pars' : (get_inclusion_pars,),
}

integrals = {
'i' : 2,
}

equations = {
'1' : """- %f * dw_dot.i.Y(inclusion.density, v, u)
+ dw_lin_elastic.i.Y(inclusion.D, v, u)
- dw_piezo_coupling.i.Y2(inclusion.coupling, v, phi)
= 0""" % omega_squared,
'2' : """dw_piezo_coupling.i.Y2(inclusion.coupling, u, psi)
+ dw_diffusion.i.Y(inclusion.dielectric, psi, phi)
= 0""",
}

solvers = {
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'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton',
{'i_max' : 1,
'eps_a' : 1e-10,
}),
}

multi_physics/piezo_elasticity_macro.py

Description
Piezo-elasticity problem - homogenization of a piezoelectric linear elastic matrix with embedded metalic electrodes,
see [1] for details.
[1] E.Rohan, V.Lukes: Homogenization of the fluid-saturated piezoelectric porous media. International Journal of
Solids and Structures 147, 2018, pages 110-125. https://doi.org/10.1016/j.ijsolstr.2018.05.017

source code

r"""
Piezo-elasticity problem - homogenization of a piezoelectric linear elastic
matrix with embedded metalic electrodes, see [1] for details.
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[1] E.Rohan, V.Lukes: Homogenization of the fluid-saturated piezoelectric

porous media. International Journal of Solids and Structures 147, 2018,
pages 110-125. https://doi.org/10.1016/j.ijsolstr.2018.05.017
"""

import numpy as nm
from sfepy import data_dir, base_dir
from sfepy.base.base import Struct
from sfepy.homogenization.micmac import get_homog_coefs_linear
import os.path as osp
from sfepy.homogenization.recovery import recover_micro_hook_eps
from sfepy.discrete.projections import make_l2_projection_data

def linear_projection(pb, data_qp):

svar = pb.create_variables(['svar'])['svar']
aux = []
for ii in range(data_qp.shape[2]):
make_l2_projection_data(svar, data_qp[..., ii, :].copy())
aux.append(svar())

return nm.ascontiguousarray(nm.array(aux).T)

def post_process(out, pb, state, extend=False):

# evaluate macroscopic strain
strain = pb.evaluate('ev_cauchy_strain.i2.Omega(u)', mode='el_avg')
out['e'] = Struct(name='output_data', mode='cell', dofs=None,
var_name='u', data=strain)

# micro recovery
rreg = pb.domain.regions['Recovery']
dim = rreg.dim

state_dict = state.get_state_parts()
displ = state_dict['u']
strain_qp = pb.evaluate('ev_cauchy_strain.i2.Omega(u)', mode='qp')

nodal_data = {
'u': displ.reshape((displ.shape[0] // dim, dim)), # displacement
'strain': linear_projection(pb, strain_qp), # strain
}
const_data = {
'phi': pb.conf.phi, # el. potentials
}
def_args = {
'eps0': pb.conf.eps0,
'filename_mesh': pb.conf.filename_mesh_micro,
}
pvar = pb.create_variables(['svar'])

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recover_micro_hook_eps(pb.conf.filename_micro, rreg,
pvar['svar'], nodal_data, const_data, pb.conf.eps0,
define_args=def_args)

return out

def get_homog_fun(fname):
return lambda ts, coors, mode=None, problem=None, **kwargs:\
get_homog(coors, mode, problem, fname, **kwargs)

def get_homog(coors, mode, pb, micro_filename, **kwargs):

if not (mode == 'qp'):
return

nqp = coors.shape[0]
coefs_filename = osp.join(pb.conf.options.get('output_dir', '.'),
'coefs_piezo.h5')

def_args = {
'eps0': pb.conf.eps0,
'filename_mesh': pb.conf.filename_mesh_micro,
}

coefs = get_homog_coefs_linear(0, 0, None,

micro_filename=micro_filename,
coefs_filename=coefs_filename,
define_args=def_args)

Vf = coefs['V0'] * pb.conf.phi[0] + coefs['V1'] * pb.conf.phi[1]

out = {
'A': nm.tile(coefs['A'], (nqp, 1, 1)),
'Vf': nm.tile(Vf[:, nm.newaxis], (nqp, 1, 1)),
}

return out

def define():
eps0 = 1. / 30 # real size of the reference cell

phi = nm.array([1, -1]) * 1e4 # prescribed el. potential

filename_mesh = data_dir + '/meshes/3d/cube_medium_hexa.mesh'

# define the micro problem - homogenization procedure

filename_micro = base_dir +\
'/examples/multi_physics/piezo_elasticity_micro.py'
filename_mesh_micro = data_dir + '/meshes/3d/piezo_mesh_micro.vtk'

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fields = {
'displacement': ('real', 'vector', 'Omega', 1),
'sfield': ('real', 'scalar', 'Omega', 1),
}

variables = {
'u': ('unknown field', 'displacement'),
'v': ('test field', 'displacement', 'u'),
'svar': ('parameter field', 'sfield', 'set-to-none'),
}

# define material - homogenization

functions = {
'get_homog': (get_homog_fun(filename_micro),),
}

materials = {
'hom': 'get_homog',
}

integrals = {
'i2': 2,
}

regions = {
'Omega': 'all',
'Left': ('vertices in (x < -0.4999)', 'facet'),
'Recovery': ('cell 266'),
}

ebcs = {
'fixed_u': ('Left', {'u.all': 0.0}),
}

equations = {
'balance_of_forces': """
dw_lin_elastic.i2.Omega(hom.A, v, u)
=
- dw_lin_prestress.i2.Omega(hom.Vf, v)""",
}

solvers = {
'ls': ('ls.scipy_direct', {}),
'newton': ('nls.newton',
{'i_max': 10,
'eps_a': 1e-3,
'eps_r': 1e-3,
'problem': 'nonlinear',
})
}

options = {
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'output_dir': 'output',
'nls': 'newton',
'post_process_hook': 'post_process',
}

return locals()

multi_physics/piezo_elasticity_micro.py

Description
Piezo-elasticity problem - homogenization of a piezoelectric linear elastic matrix with embedded metalic electrodes,
see [1] for details.
[1] E.Rohan, V.Lukes: Homogenization of the fluid-saturated piezoelectric porous media. International Journal of
Solids and Structures 147, 2018, pages 110-125. https://doi.org/10.1016/j.ijsolstr.2018.05.017
source code

r"""
Piezo-elasticity problem - homogenization of a piezoelectric linear elastic
matrix with embedded metalic electrodes, see [1] for details.

[1] E.Rohan, V.Lukes: Homogenization of the fluid-saturated piezoelectric

porous media. International Journal of Solids and Structures 147, 2018,
pages 110-125. https://doi.org/10.1016/j.ijsolstr.2018.05.017
"""

import numpy as nm
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
from sfepy.homogenization.utils import coor_to_sym, define_box_regions
from sfepy.discrete.fem.mesh import Mesh
from sfepy.base.base import Struct
import sfepy.discrete.fem.periodic as per
import sfepy.homogenization.coefs_base as cb

# Recover fields at the microscpopic level

def recovery_micro(pb, corrs, macro):
eps0 = macro['eps0']
mesh = pb.domain.mesh
regions = pb.domain.regions
dim = mesh.dim
Ymc_map = regions['Ymc'].get_entities(0)
Ym_map = regions['Ym'].get_entities(0)
# deformation
u1, phi = 0, 0

for ii in range(2):
u1 += corrs['corrs_k%d' % ii]['u'] * macro['phi'][ii]
phi += corrs['corrs_k%d' % ii]['r'] * macro['phi'][ii]

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for ii in range(dim):
for jj in range(dim):
kk = coor_to_sym(ii, jj, dim)
phi += corrs['corrs_rs']['r_%d%d' % (ii, jj)]\
* nm.expand_dims(macro['strain'][Ym_map, kk], axis=1)
u1 += corrs['corrs_rs']['u_%d%d' % (ii, jj)]\
* nm.expand_dims(macro['strain'][Ymc_map, kk], axis=1)

u = macro['u'][Ymc_map, :] + eps0 * u1
mvar = pb.create_variables(['u', 'r', 'svar'])
e_mac_Ymc = [None] * macro['strain'].shape[1]

for ii in range(dim):
for jj in range(dim):
kk = coor_to_sym(ii, jj, dim)
mvar['svar'].set_data(macro['strain'][:, kk])
mac_e_Ymc = pb.evaluate('ev_integrate.i2.Ymc(svar)',
mode='el_avg',
var_dict={'svar': mvar['svar']})

e_mac_Ymc[kk] = mac_e_Ymc.squeeze()

e_mac_Ymc = nm.vstack(e_mac_Ymc).T[:, nm.newaxis, :, nm.newaxis]

mvar['r'].set_data(phi)
E_mic = pb.evaluate('ev_grad.i2.Ym(r)',
mode='el_avg',
var_dict={'r': mvar['r']}) / eps0

mvar['u'].set_data(u1)
e_mic = pb.evaluate('ev_cauchy_strain.i2.Ymc(u)',
mode='el_avg',
var_dict={'u': mvar['u']})
e_mic += e_mac_Ymc

out = {
'u0': (macro['u'][Ymc_map, :], 'u', 'p'),
'u': (u, 'u', 'p'),
'u1': (u1, 'u', 'p'),
'e_mic': (e_mic, 'u', 'c'),
'phi': (phi, 'r', 'p'),
'E_mic': (E_mic, 'r', 'c'),
}

out_struct = {}
for k, v in out.items():
out_struct[k] = Struct(name='output_data',
mode='cell' if v[2] == 'c' else 'vertex',
data=v[0],
var_name=v[1],
dofs=None)

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return out_struct

# Define the local problems and the homogenized coefficients,

# eps0 is the real size of the reference cell.
def define(eps0=1e-3, filename_mesh='meshes/3d/piezo_mesh_micro.vtk'):

mesh = Mesh.from_file(filename_mesh)
bbox = mesh.get_bounding_box()
regions = define_box_regions(mesh.dim, bbox[0], bbox[1], eps=1e-3)

regions.update({
'Ymc': 'all',
# matrix
'Ym': 'cells of group 1',
'Ym_left': ('r.Ym *v r.Left', 'vertex'),
'Ym_right': ('r.Ym *v r.Right', 'vertex'),
'Ym_bottom': ('r.Ym *v r.Bottom', 'vertex'),
'Ym_top': ('r.Ym *v r.Top', 'vertex'),
'Ym_far': ('r.Ym *v r.Far', 'vertex'),
'Ym_near': ('r.Ym *v r.Near', 'vertex'),
'Gamma_ms': ('r.Ym *v r.Yc', 'facet', 'Ym'),
# conductors
'Yc': ('r.Yc1 +c r.Yc2', 'cell'),
'Yc1': 'cells of group 2',
'Yc2': 'cells of group 3',
'Gamma_s1': ('r.Ym *v r.Yc1', 'facet', 'Ym'),
'Gamma_s2': ('r.Ym *v r.Yc2', 'facet', 'Ym'),
})

options = {
'coefs_filename': 'coefs_piezo',
'volume': {'value': nm.prod(bbox[1] - bbox[0])},
'coefs': 'coefs',
'requirements': 'requirements',
'output_dir': 'output',
'file_per_var': True,
'absolute_mesh_path': True,
'multiprocessing': False,
'recovery_hook': recovery_micro,
}

fields = {
'displacement': ('real', 'vector', 'Ymc', 1),
'potential': ('real', 'scalar', 'Ym', 1),
'sfield': ('real', 'scalar', 'Ymc', 1),
}

variables = {
# displacement
'u': ('unknown field', 'displacement'),
'v': ('test field', 'displacement', 'u'),
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'Pi_u': ('parameter field', 'displacement', 'u'),
'U1': ('parameter field', 'displacement', '(set-to-None)'),
'U2': ('parameter field', 'displacement', '(set-to-None)'),
# potential
'r': ('unknown field', 'potential'),
's': ('test field', 'potential', 'r'),
'Pi_r': ('parameter field', 'potential', 'r'),
'R1': ('parameter field', 'potential', '(set-to-None)'),
'R2': ('parameter field', 'potential', '(set-to-None)'),
# auxiliary
'svar': ('parameter field', 'sfield', '(set-to-None)'),
}

epbcs = {
'p_ux': (['Left', 'Right'], {'u.all': 'u.all'}, 'match_x_plane'),
'p_uy': (['Near', 'Far'], {'u.all': 'u.all'}, 'match_y_plane'),
'p_uz': (['Bottom', 'Top'], {'u.all': 'u.all'}, 'match_z_plane'),
'p_rx': (['Ym_left', 'Ym_right'], {'r.0': 'r.0'}, 'match_x_plane'),
'p_ry': (['Ym_near', 'Ym_far'], {'r.0': 'r.0'}, 'match_y_plane'),
'p_rz': (['Ym_bottom', 'Ym_top'], {'r.0': 'r.0'}, 'match_z_plane'),
}

periodic = {
'per_u': ['per_u_x', 'per_u_y', 'per_u_z'],
'per_r': ['per_r_x', 'per_r_y', 'per_r_z'],
}

# rescale piezoelectric material parameters

mat_g_sc, mat_d_sc = (eps0, eps0**2)

materials = {
'elastic': ({
'D': {
'Ym': nm.array([[1.504, 0.656, 0.659, 0, 0, 0],
[0.656, 1.504, 0.659, 0, 0, 0],
[0.659, 0.659, 1.455, 0, 0, 0],
[0, 0, 0, 0.424, 0, 0],
[0, 0, 0, 0, 0.439, 0],
[0, 0, 0, 0, 0, 0.439]]) * 1e11,
'Yc': stiffness_from_youngpoisson(3, 200e9, 0.25)}},),
'piezo': ({
'g': nm.array([[0, 0, 0, 0, 11.404, 0],
[0, 0, 0, 0, 0, 11.404],
[-4.322, -4.322, 17.360, 0, 0, 0]]) / mat_g_sc,
'd': nm.array([[1.284, 0, 0],
[0, 1.284, 0],
[0, 0, 1.505]]) * 1e-8 / mat_d_sc},),
}

functions = {
'match_x_plane': (per.match_x_plane,),
'match_y_plane': (per.match_y_plane,),
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'match_z_plane': (per.match_z_plane,),
}

ebcs = {
'fixed_u': ('Corners', {'u.all': 0.0}),
'fixed_r': ('Gamma_ms', {'r.all': 0.0}),
'fixed_r1_s1': ('Gamma_s1', {'r.0': 1.0}),
'fixed_r0_s1': ('Gamma_s1', {'r.0': 0.0}),
'fixed_r1_s2': ('Gamma_s2', {'r.0': 1.0}),
'fixed_r0_s2': ('Gamma_s2', {'r.0': 0.0}),
}

integrals = {
'i2': 2,
}

solvers = {
'ls_d': ('ls.scipy_direct', {}),
'ls_i': ('ls.scipy_iterative', {}),
'ns_ea6': ('nls.newton', {'eps_a': 1e6, 'eps_r': 1e-3,}),
'ns_ea0': ('nls.newton', {'eps_a': 1e0, 'eps_r': 1e-3,}),
}

coefs = {
'A1': {
'status': 'auxiliary',
'requires': ['pis_u', 'corrs_rs'],
'expression': 'dw_lin_elastic.i2.Ymc(elastic.D, U1, U2)',
'set_variables': [('U1', ('corrs_rs', 'pis_u'), 'u'),
('U2', ('corrs_rs', 'pis_u'), 'u')],
'class': cb.CoefSymSym,
},
'A2': {
'status': 'auxiliary',
'requires': ['corrs_rs'],
'expression': 'dw_diffusion.i2.Ym(piezo.d, R1, R2)',
'set_variables': [('R1', 'corrs_rs', 'r'),
('R2', 'corrs_rs', 'r')],
'class': cb.CoefSymSym,
},
'A': {
'requires': ['c.A1', 'c.A2'],
'expression': 'c.A1 + c.A2',
'class': cb.CoefEval,
},
'vol': {
'regions': ['Ym', 'Yc1', 'Yc2'],
'expression': 'ev_volume.i2.%s(svar)',
'class': cb.VolumeFractions,
},
'eps0': {
'requires': [],
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'expression': '%e' % eps0,
'class': cb.CoefEval,
},
'filenames': {},
}

requirements = {
'pis_u': {
'variables': ['u'],
'class': cb.ShapeDimDim,
},
'pis_r': {
'variables': ['r'],
'class': cb.ShapeDim,
},
'corrs_rs': {
'requires': ['pis_u'],
'ebcs': ['fixed_u', 'fixed_r'],
'epbcs': ['p_ux', 'p_uy', 'p_uz', 'p_rx', 'p_ry', 'p_rz'],
'equations': {
'eq1':
"""dw_lin_elastic.i2.Ymc(elastic.D, v, u)
- dw_piezo_coupling.i2.Ym(piezo.g, v, r)
= - dw_lin_elastic.i2.Ymc(elastic.D, v, Pi_u)""",
'eq2':
"""
- dw_piezo_coupling.i2.Ym(piezo.g, u, s)
- dw_diffusion.i2.Ym(piezo.d, s, r)
= dw_piezo_coupling.i2.Ym(piezo.g, Pi_u, s)""",
},
'set_variables': [('Pi_u', 'pis_u', 'u')],
'class': cb.CorrDimDim,
'save_name': 'corrs_rs',
'solvers': {'ls': 'ls_i', 'nls': 'ns_ea6'},
},
}

# define requirements and coefficients related to conductors

bc_conductors = [
['fixed_r1_s1', 'fixed_r0_s2'], # phi = 1 on S1, phi = 0 on S2
['fixed_r1_s2', 'fixed_r0_s1'], # phi = 0 on S1, phi = 1 on S2
]

for k in range(2):
sk = '%d' % k

requirements.update({
'corrs_k' + sk: {
'requires': ['pis_r'],
'ebcs': ['fixed_u'] + bc_conductors[k],
'epbcs': ['p_ux', 'p_uy', 'p_uz', 'p_rx', 'p_ry', 'p_rz'],
'equations': {
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'eq1':
"""dw_lin_elastic.i2.Ymc(elastic.D, v, u)
- dw_piezo_coupling.i2.Ym(piezo.g, v, r)
= 0""",
'eq2':
"""
- dw_piezo_coupling.i2.Ym(piezo.g, u, s)
- dw_diffusion.i2.Ym(piezo.d, s, r)
= 0"""
},
'class': cb.CorrOne,
'save_name': 'corrs_k' + sk,
'solvers': {'ls': 'ls_d', 'nls': 'ns_ea0'},
},
})

coefs.update({
'V1_' + sk: {
'status': 'auxiliary',
'requires': ['pis_u', 'corrs_k' + sk],
'expression': 'dw_lin_elastic.i2.Ymc(elastic.D, U1, U2)',
'set_variables': [('U1', 'corrs_k' + sk, 'u'),
('U2', 'pis_u', 'u')],
'class': cb.CoefSym,
},
'V2_' + sk: {
'status': 'auxiliary',
'requires': ['pis_u', 'corrs_k' + sk],
'expression': 'dw_piezo_coupling.i2.Ym(piezo.g, U1, R1)',
'set_variables': [('R1', 'corrs_k' + sk, 'r'),
('U1', 'pis_u', 'u')],
'class': cb.CoefSym,
},
'V' + sk: {
'requires': ['c.V1_' + sk, 'c.V2_' + sk],
'expression': 'c.V1_%s - c.V2_%s' % (sk, sk),
'class': cb.CoefEval,
},
})

return locals()

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multi_physics/thermal_electric.py

Description
First solve the stationary electric conduction problem. Then use its results to solve the evolutionary heat conduction
problem.
Run this example as on a command line:

$ python <path_to_this_file>/thermal_electric.py

source code

#!/usr/bin/env python
"""
First solve the stationary electric conduction problem. Then use its
results to solve the evolutionary heat conduction problem.

Run this example as on a command line::

$ python <path_to_this_file>/thermal_electric.py
"""
from __future__ import absolute_import
import sys
sys.path.append( '.' )
import os

from sfepy import data_dir

filename_mesh = data_dir + '/meshes/2d/special/circle_in_square.mesh'

# Time stepping for the heat conduction problem.

t0 = 0.0
t1 = 0.5
n_step = 11

# Material parameters.
specific_heat = 1.2

##########

cwd = os.path.split(os.path.join(os.getcwd(), __file__))[0]

options = {
'absolute_mesh_path' : True,
'output_dir' : os.path.join(cwd, 'output')
}

regions = {
'Omega' : 'all',
'Omega1' : 'cells of group 1',
'Omega2' : 'cells of group 2',
'Omega2_Surface': ('r.Omega1 *v r.Omega2', 'facet'),
'Left' : ('vertices in (x < %f )' % -0.4999, 'facet'),
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'Right' : ('vertices in (x > %f )' % 0.4999, 'facet'),
}

materials = {
'm' : ({
'thermal_conductivity' : 2.0,
'electric_conductivity' : 1.5,
},),
}

# The fields use the same approximation, so a single field could be used
# instead.
fields = {
'temperature': ('real', 1, 'Omega', 1),
'potential' : ('real', 1, 'Omega', 1),
}

variables = {
'T' : ('unknown field', 'temperature', 0, 1),
's' : ('test field', 'temperature', 'T'),
'phi' : ('unknown field', 'potential', 1),
'psi' : ('test field', 'potential', 'phi'),
'phi_known' : ('parameter field', 'potential', '(set-to-None)'),
}

ics = {
'ic' : ('Omega', {'T.0' : 0.0}),
}

ebcs = {
'left' : ('Left', {'T.0' : 0.0, 'phi.0' : 0.0}),
'right' : ('Right', {'T.0' : 2.0, 'phi.0' : 0.0}),
'inside' : ('Omega2_Surface', {'phi.0' : 'set_electric_bc'}),
}

def set_electric_bc(coor):
y = coor[:,1]
ymin, ymax = y.min(), y.max()
val = 2.0 * (((y - ymin) / (ymax - ymin)) - 0.5)
return val

functions = {
'set_electric_bc' : (lambda ts, coor, bc, problem, **kwargs:
set_electric_bc(coor),),
}

equations = {
'2' : """%.12e * dw_dot.2.Omega( s, dT/dt )
+ dw_laplace.2.Omega( m.thermal_conductivity, s, T )
= dw_electric_source.2.Omega( m.electric_conductivity,
s, phi_known ) """ % specific_heat,
'1' : """dw_laplace.2.Omega( m.electric_conductivity, psi, phi ) = 0""",
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}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
'problem' : 'nonlinear',
}),
'ts' : ('ts.simple', {
't0' : t0,
't1' : t1,
'dt' : None,
'n_step' : n_step, # has precedence over dt!
'verbose' : 1,
}),
}

def main():
from sfepy.base.base import output
from sfepy.base.conf import ProblemConf, get_standard_keywords
from sfepy.discrete import Problem

output.prefix = 'therel:'

required, other = get_standard_keywords()

conf = ProblemConf.from_file(__file__, required, other)

problem = Problem.from_conf(conf, init_equations=False)

# Setup output directory according to options above.

problem.setup_default_output()

# First solve the stationary electric conduction problem.

problem.set_equations({'eq' : conf.equations['1']})
state_el = problem.solve()
problem.save_state(problem.get_output_name(suffix = 'el'), state_el)

# Then solve the evolutionary heat conduction problem, using state_el.

problem.set_equations({'eq' : conf.equations['2']})
phi_var = problem.get_variables()['phi_known']
phi_var.set_data(state_el())
problem.solve()

output('results saved in %s' % problem.get_output_name(suffix = '*'))

if __name__ == '__main__':
main()

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multi_physics/thermo_elasticity.py

Description
Thermo-elasticity with a given temperature distribution.
Uses dw_biot term with an isotropic coefficient for thermo-elastic coupling.
For given body temperature 𝑇 and background temperature 𝑇0 find 𝑢 such that:
∫︁ ∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) − (𝑇 − 𝑇0 ) 𝛼𝑖𝑗 𝑒𝑖𝑗 (𝑣) = 0 , ∀𝑣 ,
Ω Ω

where
𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 ,

𝛼𝑖𝑗 = (3𝜆 + 2𝜇)𝛼𝛿𝑖𝑗

and 𝛼 is the thermal expansion coefficient.

source code

r"""
Thermo-elasticity with a given temperature distribution.

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(continued from previous page)

Uses `dw_biot` term with an isotropic coefficient for thermo-elastic coupling.

For given body temperature :math:`T` and background temperature

:math:`T_0` find :math:`\ul{u}` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
- \int_{\Omega} (T - T_0)\ \alpha_{ij} e_{ij}(\ul{v})
= 0
\;, \quad \forall \ul{v} \;,

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;, \\

\alpha_{ij} = (3 \lambda + 2 \mu) \alpha \delta_{ij}

and :math:`\alpha` is the thermal expansion coefficient.

"""
from __future__ import absolute_import
import numpy as np

from sfepy.base.base import Struct

from sfepy.mechanics.matcoefs import stiffness_from_lame
from sfepy.mechanics.tensors import get_von_mises_stress
from sfepy import data_dir

# Material parameters.
lam = 10.0
mu = 5.0
thermal_expandability = 1.25e-5
T0 = 20.0 # Background temperature.

filename_mesh = data_dir + '/meshes/3d/block.mesh'

def get_temperature_load(ts, coors, region=None):

"""
Temperature load depends on the `x` coordinate.
"""
x = coors[:, 0]
return (x - x.min())**2 - T0

def post_process(out, pb, state, extend=False):

"""
Compute derived quantities: strain, stresses. Store also the loading
temperature.
"""
ev = pb.evaluate

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strain = ev('ev_cauchy_strain.2.Omega( u )', mode='el_avg')
out['cauchy_strain'] = Struct(name='output_data',
mode='cell', data=strain,
dofs=None)

e_stress = ev('ev_cauchy_stress.2.Omega( solid.D, u )', mode='el_avg')

out['elastic_stress'] = Struct(name='output_data',
mode='cell', data=e_stress,
dofs=None)

t_stress = ev('ev_biot_stress.2.Omega( solid.alpha, T )', mode='el_avg')

out['thermal_stress'] = Struct(name='output_data',
mode='cell', data=t_stress,
dofs=None)

out['total_stress'] = Struct(name='output_data',
mode='cell', data=e_stress + t_stress,
dofs=None)

out['von_mises_stress'] = aux = out['total_stress'].copy()

vms = get_von_mises_stress(aux.data.squeeze())
vms.shape = (vms.shape[0], 1, 1, 1)
out['von_mises_stress'].data = vms

val = pb.get_variables()['T']()
val.shape = (val.shape[0], 1)
out['T'] = Struct(name='output_data',
mode='vertex', data=val + T0,
dofs=None)
return out

options = {
'post_process_hook' : 'post_process',

'nls' : 'newton',
'ls' : 'ls',
}

functions = {
'get_temperature_load' : (get_temperature_load,),
}

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < -4.99)', 'facet'),
}

fields = {
'displacement': ('real', 3, 'Omega', 1),
'temperature': ('real', 1, 'Omega', 1),
}

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variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
'T' : ('parameter field', 'temperature',
{'setter' : 'get_temperature_load'}),
}

ebcs = {
'fix_u' : ('Left', {'u.all' : 0.0}),
}

eye_sym = np.array([[1], [1], [1], [0], [0], [0]], dtype=np.float64)

materials = {
'solid' : ({
'D' : stiffness_from_lame(3, lam=lam, mu=mu),
'alpha' : (3.0 * lam + 2.0 * mu) * thermal_expandability * eye_sym
},),
}

equations = {
'balance_of_forces' :
"""dw_lin_elastic.2.Omega( solid.D, v, u )
- dw_biot.2.Omega( solid.alpha, v, T )
= 0""",
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
}),
}

multi_physics/thermo_elasticity_ess.py

Description
Thermo-elasticity with a computed temperature demonstrating equation sequence solver.
Uses dw_biot term with an isotropic coefficient for thermo-elastic coupling.
The equation sequence solver ('ess' in solvers) automatically solves first the temperature distribution and then the
elasticity problem with the already computed temperature.
Find 𝑢, 𝑇 such that:
∫︁ ∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) − (𝑇 − 𝑇0 ) 𝛼𝑖𝑗 𝑒𝑖𝑗 (𝑣) = 0 , ∀𝑣 ,
Ω Ω
∫︁
∇𝑠 · ∇𝑇 = 0 , ∀𝑠 .
Ω

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where
𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙 ,

𝛼𝑖𝑗 = (3𝜆 + 2𝜇)𝛼𝛿𝑖𝑗 ,

𝑇0 is the background temperature and 𝛼 is the thermal expansion coefficient.

Notes

The gallery image was produced by (plus proper view settings):

./postproc.py block.vtk -d'u,plot_displacements,rel_scaling=1000,color_kind="scalars",

˓→color_name="T"' --wireframe --only-names=u -b

source code

r"""
Thermo-elasticity with a computed temperature demonstrating equation sequence
solver.

Uses `dw_biot` term with an isotropic coefficient for thermo-elastic coupling.

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The equation sequence solver (``'ess'`` in ``solvers``) automatically solves
first the temperature distribution and then the elasticity problem with the
already computed temperature.

Find :math:`\ul{u}`, :math:`T` such that:

.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
- \int_{\Omega} (T - T_0)\ \alpha_{ij} e_{ij}(\ul{v})
= 0
\;, \quad \forall \ul{v} \;,

\int_{\Omega} \nabla s \cdot \nabla T

= 0
\;, \quad \forall s \;.

where

.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \delta_{ij} \delta_{kl}
\;, \\

\alpha_{ij} = (3 \lambda + 2 \mu) \alpha \delta_{ij} \;,

:math:`T_0` is the background temperature and :math:`\alpha` is the thermal

expansion coefficient.

Notes
-----
The gallery image was produced by (plus proper view settings)::

./postproc.py block.vtk -d'u,plot_displacements,rel_scaling=1000,color_kind="scalars",

˓→color_name="T"' --wireframe --only-names=u -b
"""
from __future__ import absolute_import
import numpy as np

from sfepy.mechanics.matcoefs import stiffness_from_lame

from sfepy import data_dir

# Material parameters.
lam = 10.0
mu = 5.0
thermal_expandability = 1.25e-5
T0 = 20.0 # Background temperature.

filename_mesh = data_dir + '/meshes/3d/block.mesh'

options = {
'nls' : 'newton',
'ls' : 'ls',
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'block_solve' : True,
}

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < -4.99)', 'facet'),
'Right' : ('vertices in (x > 4.99)', 'facet'),
'Bottom' : ('vertices in (z < -0.99)', 'facet'),
}

fields = {
'displacement': ('real', 3, 'Omega', 1),
'temperature': ('real', 1, 'Omega', 1),
}

variables = {
'u' : ('unknown field', 'displacement', 0),
'v' : ('test field', 'displacement', 'u'),
'T' : ('unknown field', 'temperature', 1),
's' : ('test field', 'temperature', 'T'),
}

ebcs = {
'u0' : ('Left', {'u.all' : 0.0}),
't0' : ('Left', {'T.0' : 20.0}),
't2' : ('Bottom', {'T.0' : 0.0}),
't1' : ('Right', {'T.0' : 30.0}),
}

eye_sym = np.array([[1], [1], [1], [0], [0], [0]], dtype=np.float64)

materials = {
'solid' : ({
'D' : stiffness_from_lame(3, lam=lam, mu=mu),
'alpha' : (3.0 * lam + 2.0 * mu) * thermal_expandability * eye_sym
},),
}

equations = {
'balance_of_forces' : """
+ dw_lin_elastic.2.Omega(solid.D, v, u)
- dw_biot.2.Omega(solid.alpha, v, T)
= 0
""",
'temperature' : """
+ dw_laplace.1.Omega(s, T)
= 0
"""
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
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'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
}),
}

navier_stokes

navier_stokes/navier_stokes.py

Description
Navier-Stokes equations for incompressible fluid flow.
Find 𝑢, 𝑝 such that:
∫︁ ∫︁ ∫︁
𝜈 ∇𝑣 : ∇𝑢 + ((𝑢 · ∇)𝑢) · 𝑣 − 𝑝∇·𝑣 =0, ∀𝑣 ,
Ω Ω
∫︁Ω
𝑞∇·𝑢=0, ∀𝑞 .
Ω

source code

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r"""
Navier-Stokes equations for incompressible fluid flow.

Find :math:`\ul{u}`, :math:`p` such that:

.. math::
\int_{\Omega} \nu\ \nabla \ul{v} : \nabla \ul{u}
+ \int_{\Omega} ((\ul{u} \cdot \nabla) \ul{u}) \cdot \ul{v}
- \int_{\Omega} p\ \nabla \cdot \ul{v}
= 0
\;, \quad \forall \ul{v} \;,

\int_{\Omega} q\ \nabla \cdot \ul{u}

= 0
\;, \quad \forall q \;.
"""
from __future__ import absolute_import
from sfepy import data_dir

filename_mesh = data_dir + '/meshes/3d/elbow2.mesh'

options = {
'nls' : 'newton',
'ls' : 'ls',
'post_process_hook' : 'verify_incompressibility',

# Options for saving higher-order variables.

# Possible kinds:
# 'strip' ... just remove extra DOFs (ignores other linearization
# options)
# 'adaptive' ... adaptively refine linear element mesh.
'linearization' : {
'kind' : 'strip',
'min_level' : 1, # Min. refinement level to achieve everywhere.
'max_level' : 2, # Max. refinement level.
'eps' : 1e-1, # Relative error tolerance.
},
}

field_1 = {
'name' : '3_velocity',
'dtype' : 'real',
'shape' : (3,),
'region' : 'Omega',
'approx_order' : '1B',
}

field_2 = {
'name' : 'pressure',
'dtype' : 'real',
'shape' : (1,),
'region' : 'Omega',
'approx_order' : 1,
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}

# Can use logical operations '&' (and), '|' (or).

region_1000 = {
'name' : 'Omega',
'select' : 'cells of group 6',
}

region_0 = {
'name' : 'Walls',
'select' : 'vertices of surface -v (r.Outlet +v r.Inlet)',
'kind' : 'facet',
}
region_1 = {
'name' : 'Inlet',
'select' : 'vertices by cinc0', # In
'kind' : 'facet',
}
region_2 = {
'name' : 'Outlet',
'select' : 'vertices by cinc1', # Out
'kind' : 'facet',
}

ebc_1 = {
'name' : 'Walls',
'region' : 'Walls',
'dofs' : {'u.all' : 0.0},
}
ebc_2 = {
'name' : 'Inlet',
'region' : 'Inlet',
'dofs' : {'u.1' : 1.0, 'u.[0,2]' : 0.0},
}

material_1 = {
'name' : 'fluid',
'values' : {
'viscosity' : 1.25e-3,
'density' : 1e0,
},
}

variable_1 = {
'name' : 'u',
'kind' : 'unknown field',
'field' : '3_velocity',
'order' : 0,
}
variable_2 = {
'name' : 'v',
'kind' : 'test field',
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'field' : '3_velocity',
'dual' : 'u',
}
variable_3 = {
'name' : 'p',
'kind' : 'unknown field',
'field' : 'pressure',
'order' : 1,
}
variable_4 = {
'name' : 'q',
'kind' : 'test field',
'field' : 'pressure',
'dual' : 'p',
}
variable_5 = {
'name' : 'pp',
'kind' : 'parameter field',
'field' : 'pressure',
'like' : 'p',
}

integral_1 = {
'name' : 'i1',
'order' : 2,
}
integral_2 = {
'name' : 'i2',
'order' : 3,
}

##
# Stationary Navier-Stokes equations.
equations = {
'balance' :
"""+ dw_div_grad.i2.Omega( fluid.viscosity, v, u )
+ dw_convect.i2.Omega( v, u )
- dw_stokes.i1.Omega( v, p ) = 0""",
'incompressibility' :
"""dw_stokes.i1.Omega( u, q ) = 0""",
}

solver_0 = {
'name' : 'ls',
'kind' : 'ls.scipy_direct',
}

solver_1 = {
'name' : 'newton',
'kind' : 'nls.newton',

'i_max' : 5,
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'eps_a' : 1e-8,
'eps_r' : 1.0,
'macheps' : 1e-16,
'lin_red' : 1e-2, # Linear system error < (eps_a * lin_red).
'ls_red' : 0.1,
'ls_red_warp' : 0.001,
'ls_on' : 0.99999,
'ls_min' : 1e-5,
'check' : 0,
'delta' : 1e-6,
}

def verify_incompressibility(out, problem, variables, extend=False):

"""This hook is normally used for post-processing (additional results can
be inserted into `out` dictionary), but here we just verify the weak
incompressibility condition."""
from sfepy.base.base import nm, output, assert_

one = nm.ones((variables['p'].field.n_nod,), dtype=nm.float64)

variables.set_state_parts({'p' : one})
zero = problem.evaluate('dw_stokes.i1.Omega(u, p)')
output('div(u) = %.3e' % zero)

assert_(abs(zero) < 1e-14)

return out

##
# Functions.
import os.path as op
import sys

sys.path.append(data_dir) # Make installed example work.

import sfepy.examples.navier_stokes.utils as utils

cinc_name = 'cinc_' + op.splitext(op.basename(filename_mesh))[0]

cinc = getattr(utils, cinc_name)

functions = {
'cinc0' : (lambda coors, domain=None: cinc(coors, 0),),
'cinc1' : (lambda coors, domain=None: cinc(coors, 1),),
}

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navier_stokes/navier_stokes2d.py

Description
Navier-Stokes equations for incompressible fluid flow in 2D.
Find 𝑢, 𝑝 such that:
∫︁ ∫︁ ∫︁
𝜈 ∇𝑣 : ∇𝑢 + ((𝑢 · ∇)𝑢) · 𝑣 − 𝑝∇·𝑣 =0, ∀𝑣 ,
Ω Ω
∫︁Ω
𝑞∇·𝑢=0, ∀𝑞 .
Ω

The mesh is created by gen_block_mesh() function.

View the results using:

$ ./postproc.py user_block.vtk -b

source code

# -*- coding: utf-8 -*-

r"""
Navier-Stokes equations for incompressible fluid flow in 2D.

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Find :math:`\ul{u}`, :math:`p` such that:

.. math::
\int_{\Omega} \nu\ \nabla \ul{v} : \nabla \ul{u}
+ \int_{\Omega} ((\ul{u} \cdot \nabla) \ul{u}) \cdot \ul{v}
- \int_{\Omega} p\ \nabla \cdot \ul{v}
= 0
\;, \quad \forall \ul{v} \;,

\int_{\Omega} q\ \nabla \cdot \ul{u}

= 0
\;, \quad \forall q \;.

The mesh is created by ``gen_block_mesh()`` function.

View the results using::

$ ./postproc.py user_block.vtk -b
"""
from __future__ import absolute_import
from sfepy.discrete.fem.meshio import UserMeshIO
from sfepy.mesh.mesh_generators import gen_block_mesh

# Mesh dimensions.
dims = [0.1, 0.1]

# Mesh resolution: increase to improve accuracy.

shape = [51, 51]

def mesh_hook(mesh, mode):

"""
Generate the block mesh.
"""
if mode == 'read':
mesh = gen_block_mesh(dims, shape, [0, 0], name='user_block',
verbose=False)
return mesh

elif mode == 'write':

pass

filename_mesh = UserMeshIO(mesh_hook)

regions = {
'Omega' : 'all',
'Left' : ('vertices in (x < -0.0499)', 'facet'),
'Right' : ('vertices in (x > 0.0499)', 'facet'),
'Bottom' : ('vertices in (y < -0.0499)', 'facet'),
'Top' : ('vertices in (y > 0.0499)', 'facet'),
'Walls' : ('r.Left +v r.Right +v r.Bottom', 'facet'),
}

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materials = {
'fluid' : ({'viscosity' : 1.00e-2},),
}

fields = {
'velocity': ('real', 'vector', 'Omega', 2),
'pressure': ('real', 'scalar', 'Omega', 1),
}

variables = {
'u' : ('unknown field', 'velocity', 0),
'v' : ('test field', 'velocity', 'u'),
'p' : ('unknown field', 'pressure', 1),
'q' : ('test field', 'pressure', 'p'),
}

ebcs = {
'1_Walls' : ('Walls', {'u.all' : 0.0}),
'0_Driven' : ('Top', {'u.0' : 1.0, 'u.1' : 0.0}),
'Pressure' : ('Bottom', {'p.0' : 0.0}),
}

integrals = {
'i' : 4,
}

equations = {
'balance' :
"""+ dw_div_grad.i.Omega(fluid.viscosity, v, u)
+ dw_convect.i.Omega(v, u)
- dw_stokes.i.Omega(v, p) = 0""",

'incompressibility' :
"""dw_stokes.i.Omega(u, q) = 0""",
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 15,
'eps_a' : 1e-10,
'eps_r' : 1.0,
}),
}

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navier_stokes/navier_stokes2d_iga.py

Description
Navier-Stokes equations for incompressible fluid flow in 2D solved in a single patch NURBS domain using the isoge-
ometric analysis (IGA) approach.
Find 𝑢, 𝑝 such that:
∫︁ ∫︁ ∫︁
𝜈 ∇𝑣 : ∇𝑢 + ((𝑢 · ∇)𝑢) · 𝑣 − 𝑝∇·𝑣 =0, ∀𝑣 ,
Ω Ω
∫︁Ω
𝑞∇·𝑢=0, ∀𝑞 .
Ω

The domain geometry was created by:

$ ./script/gen_iga_patch.py -2 -d 0.1,0.1 -s 10,10 -o meshes/iga/block2d.iga

View the results using:

$ ./postproc.py block2d.vtk -b

source code

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# -*- coding: utf-8 -*-

r"""
Navier-Stokes equations for incompressible fluid flow in 2D solved in a single
patch NURBS domain using the isogeometric analysis (IGA) approach.

Find :math:`\ul{u}`, :math:`p` such that:

.. math::
\int_{\Omega} \nu\ \nabla \ul{v} : \nabla \ul{u}
+ \int_{\Omega} ((\ul{u} \cdot \nabla) \ul{u}) \cdot \ul{v}
- \int_{\Omega} p\ \nabla \cdot \ul{v}
= 0
\;, \quad \forall \ul{v} \;,

\int_{\Omega} q\ \nabla \cdot \ul{u}

= 0
\;, \quad \forall q \;.

The domain geometry was created by::

$ ./script/gen_iga_patch.py -2 -d 0.1,0.1 -s 10,10 -o meshes/iga/block2d.iga

View the results using::

$ ./postproc.py block2d.vtk -b
"""
from __future__ import absolute_import
from sfepy import data_dir

filename_domain = data_dir + '/meshes/iga/block2d.iga'

regions = {
'Omega' : 'all',
'Left' : ('vertices of set xi00', 'facet'),
'Right' : ('vertices of set xi01', 'facet'),
'Bottom' : ('vertices of set xi10', 'facet'),
'Top' : ('vertices of set xi11', 'facet'),
'Walls' : ('r.Left +v r.Right +v r.Bottom', 'facet'),
}

materials = {
'fluid' : ({'viscosity' : 1.00e-2},),
}

fields = {
'velocity': ('real', 'vector', 'Omega', 'iga+1', 'H1', 'iga'),
'pressure': ('real', 'scalar', 'Omega', 'iga', 'H1', 'iga'),
}

variables = {
'u' : ('unknown field', 'velocity', 0),
'v' : ('test field', 'velocity', 'u'),
'p' : ('unknown field', 'pressure', 1),
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'q' : ('test field', 'pressure', 'p'),
}

ebcs = {
'1_Walls' : ('Walls', {'u.all' : 0.0}),
'0_Driven' : ('Top', {'u.0' : 1.0, 'u.1' : 0.0}),
'Pressure' : ('Bottom', {'p.0' : 0.0}),
}

integrals = {
'i' : 6,
}

equations = {
'balance' :
"""+ dw_div_grad.i.Omega(fluid.viscosity, v, u)
+ dw_convect.i.Omega(v, u)
- dw_stokes.i.Omega(v, p) = 0""",

'incompressibility' :
"""dw_stokes.i.Omega(u, q) = 0""",
}

solvers = {
'ls' : ('ls.scipy_direct', {}),
'newton' : ('nls.newton', {
'i_max' : 15,
'eps_a' : 1e-10,
'eps_r' : 1.0,
}),
}

navier_stokes/stabilized_navier_stokes.py

Description
Stabilized Navier-Stokes problem with grad-div, SUPG and PSPG stabilization solved by a custom Oseen solver.
The stabilization terms are described in [1].
[1] G. Matthies and G. Lube. On streamline-diffusion methods of inf-sup stable discretisations of the generalised Oseen
problem. Number 2007-02 in Preprint Series of Institut fuer Numerische und Angewandte Mathematik, Georg-August-
Universitaet Goettingen, 2007.
Find 𝑢, 𝑝 such that:
∫︀ ∫︀ ∫︀
Ω
𝜈∫︀ ∇𝑣 : ∇𝑢 Ω ((𝑏 · ∇)𝑢) · 𝑣 − Ω 𝑝 ∇ · 𝑣
+𝛾∑︀Ω (∇ · ∫︀𝑢) · (∇ · 𝑣)
+ 𝐾∈ℐℎ ∫︀𝑇𝐾 𝛿𝐾 ((𝑏 · ∇)𝑢) · ((𝑏 · ∇)𝑣)
∑︀
+ 𝐾∈ℐℎ 𝑇𝐾 𝛿𝐾 ∇𝑝 · ((𝑏 · ∇)𝑣) = 0 , ∀𝑣 ,
∫︀
𝑞 ∇ · 𝑢 ∫︀
Ω∑︀
+ 𝐾∈ℐℎ ∫︀𝑇𝐾 𝜏𝐾 ((𝑏 · ∇)𝑢) · ∇𝑞
∑︀
+ 𝐾∈ℐℎ 𝑇𝐾 𝜏𝐾 ∇𝑝 · ∇𝑞 = 0 , ∀𝑞 .

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source code

r"""
Stabilized Navier-Stokes problem with grad-div, SUPG and PSPG stabilization
solved by a custom Oseen solver.

The stabilization terms are described in [1].

[1] G. Matthies and G. Lube. On streamline-diffusion methods of inf-sup stable

discretisations of the generalised Oseen problem. Number 2007-02 in Preprint
Series of Institut fuer Numerische und Angewandte Mathematik,
Georg-August-Universitaet Goettingen, 2007.

Find :math:`\ul{u}`, :math:`p` such that:

.. math::
\begin{array}{l}
\int_{\Omega} \nu\ \nabla \ul{v} : \nabla \ul{u}
\int_{\Omega} ((\ul{b} \cdot \nabla) \ul{u}) \cdot \ul{v}
- \int_{\Omega} p\ \nabla \cdot \ul{v} \\
+ \gamma \int_{\Omega} (\nabla\cdot\ul{u}) \cdot (\nabla\cdot\ul{v}) \\
+ \sum_{K \in \Ical_h}\int_{T_K} \delta_K\ ((\ul{b} \cdot \nabla)
\ul{u})\cdot ((\ul{b} \cdot \nabla) \ul{v}) \\
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+ \sum_{K \in \Ical_h}\int_{T_K} \delta_K\ \nabla p\cdot ((\ul{b} \cdot
\nabla) \ul{v})
= 0
\;, \quad \forall \ul{v} \;,
\end{array}

\begin{array}{l}
\int_{\Omega} q\ \nabla \cdot \ul{u} \\
+ \sum_{K \in \Ical_h}\int_{T_K} \tau_K\ ((\ul{b} \cdot \nabla) \ul{u})
\cdot \nabla q \\
+ \sum_{K \in \Ical_h}\int_{T_K} \tau_K\ \nabla p \cdot \nabla q
= 0
\;, \quad \forall q \;.
\end{array}
"""
from __future__ import absolute_import
from sfepy.solvers.oseen import StabilizationFunction
from sfepy import data_dir

filename_mesh = data_dir + '/meshes/3d/elbow2.mesh'

options = {
'solution' : 'steady',
'nls' : 'oseen',
'ls' : 'ls',
}

regions = {
'Omega' : 'all',
'Walls' : ('vertices of surface -v (r.Outlet +v r.Inlet)', 'facet'),
'Inlet' : ('vertices by cinc0', 'facet'),
'Outlet' : ('vertices by cinc1', 'facet'),
}

fields = {
'velocity' : ('real', 3, 'Omega', 1),
'pressure' : ('real', 1, 'Omega', 1),
}

variables = {
'u' : ('unknown field', 'velocity', 0),
'v' : ('test field', 'velocity', 'u'),
'b' : ('parameter field', 'velocity', 'u'),
'p' : ('unknown field', 'pressure', 1),
'q' : ('test field', 'pressure', 'p'),
}

ebcs = {
'Walls_velocity' : ('Walls', {'u.all' : 0.0}),
'Inlet_velocity' : ('Inlet', {'u.1' : 1.0, 'u.[0,2]' : 0.0}),
}

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materials = {
'fluid' : ({'viscosity' : 1.25e-5,
'density' : 1e0},),
'stabil' : 'stabil',
}

integrals = {
'i1' : 2,
'i2' : 3,
}

##
# Stationary Navier-Stokes equations with grad-div, SUPG and PSPG stabilization.
equations = {
'balance' :
""" dw_div_grad.i2.Omega( fluid.viscosity, v, u )
+ dw_lin_convect.i2.Omega( v, b, u )
- dw_stokes.i1.Omega( v, p )
+ dw_st_grad_div.i1.Omega( stabil.gamma, v, u )
+ dw_st_supg_c.i1.Omega( stabil.delta, v, b, u )
+ dw_st_supg_p.i1.Omega( stabil.delta, v, b, p )
= 0""",
'incompressibility' :
""" dw_stokes.i1.Omega( u, q )
+ dw_st_pspg_c.i1.Omega( stabil.tau, q, b, u )
+ dw_st_pspg_p.i1.Omega( stabil.tau, q, p )
= 0""",
}

solver_1 = {
'name' : 'oseen',
'kind' : 'nls.oseen',

'stabil_mat' : 'stabil',

'adimensionalize' : False,
'check_navier_stokes_residual' : False,

'i_max' : 10,
'eps_a' : 1e-8,
'eps_r' : 1.0,
'macheps' : 1e-16,
'lin_red' : 1e-2, # Linear system error < (eps_a * lin_red).

# Uncomment the following to get a convergence log.

## 'log' : {'text' : 'oseen_log.txt',
## 'plot' : 'oseen_log.png'},
}

solver_2 = {
'name' : 'ls',
'kind' : 'ls.scipy_direct',
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}

##
# Functions.
import os.path as op
import sys

sys.path.append(data_dir) # Make installed example work.

import sfepy.examples.navier_stokes.utils as utils

cinc_name = 'cinc_' + op.splitext(op.basename(filename_mesh))[0]

cinc = getattr(utils, cinc_name)

name_map = {'p' : 'p', 'q' : 'q', 'u' : 'u', 'b' : 'b', 'v' : 'v',
'fluid' : 'fluid', 'omega' : 'omega', 'i1' : 'i1', 'i2' : 'i2',
'viscosity' : 'viscosity', 'velocity' : 'velocity',
'gamma' : 'gamma', 'delta' : 'delta', 'tau' : 'tau'}

functions = {
'cinc0' : (lambda coors, domain=None: cinc(coors, 0),),
'cinc1' : (lambda coors, domain=None: cinc(coors, 1),),
'stabil' : (StabilizationFunction(name_map),),
}

navier_stokes/stokes.py

Description
Stokes equations for incompressible fluid flow.
This example demonstrates fields defined on subdomains as well as use of periodic boundary conditions.
Find 𝑢, 𝑝 such that:
∫︁ ∫︁
𝜈 ∇𝑣 : ∇𝑢 − 𝑝∇·𝑣 =0, ∀𝑣 ,
𝑌1 ∪𝑌2 𝑌1 ∪𝑌2
∫︁
𝑞∇·𝑢=0, ∀𝑞 .
𝑌1 ∪𝑌2

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r"""
Stokes equations for incompressible fluid flow.

This example demonstrates fields defined on subdomains as well as use of

periodic boundary conditions.

Find :math:`\ul{u}`, :math:`p` such that:

.. math::
\int_{Y_1 \cup Y_2} \nu\ \nabla \ul{v} : \nabla \ul{u}
- \int_{Y_1 \cup Y_2} p\ \nabla \cdot \ul{v}
= 0
\;, \quad \forall \ul{v} \;,

\int_{Y_1 \cup Y_2} q\ \nabla \cdot \ul{u}

= 0
\;, \quad \forall q \;.
"""
from __future__ import absolute_import
from sfepy import data_dir
from sfepy.discrete.fem.periodic import match_y_line
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filename_mesh = data_dir + '/meshes/2d/special/channels_symm944t.mesh'

if filename_mesh.find( 'symm' ):
region_1 = {
'name' : 'Y1',
'select' : """cells of group 3""",
}
region_2 = {
'name' : 'Y2',
'select' : """cells of group 4 +c cells of group 6
+c cells of group 8""",
}
region_4 = {
'name' : 'Y1Y2',
'select' : """r.Y1 +c r.Y2""",
}
region_5 = {
'name' : 'Walls',
'select' : """r.EBCGamma1 +v r.EBCGamma2""",
'kind' : 'facet',
}
region_310 = {
'name' : 'EBCGamma1',
'select' : """(cells of group 1 *v cells of group 3)
+v
(cells of group 2 *v cells of group 3)
""",
'kind' : 'facet',
}
region_320 = {
'name' : 'EBCGamma2',
'select' : """(cells of group 5 *v cells of group 4)
+v
(cells of group 1 *v cells of group 4)
+v
(cells of group 7 *v cells of group 6)
+v
(cells of group 2 *v cells of group 6)
+v
(cells of group 9 *v cells of group 8)
+v
(cells of group 2 *v cells of group 8)
""",
'kind' : 'facet',
}

w2 = 0.499
# Sides.
region_20 = {
'name' : 'Left',
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'select' : 'vertices in (x < %.3f )' % -w2,
'kind' : 'facet',
}
region_21 = {
'name' : 'Right',
'select' : 'vertices in (x > %.3f )' % w2,
'kind' : 'facet',
}
region_22 = {
'name' : 'Bottom',
'select' : 'vertices in (y < %.3f )' % -w2,
'kind' : 'facet',
}
region_23 = {
'name' : 'Top',
'select' : 'vertices in (y > %.3f )' % w2,
'kind' : 'facet',
}

field_1 = {
'name' : '2_velocity',
'dtype' : 'real',
'shape' : (2,),
'region' : 'Y1Y2',
'approx_order' : 2,
}

field_2 = {
'name' : 'pressure',
'dtype' : 'real',
'shape' : (1,),
'region' : 'Y1Y2',
'approx_order' : 1,
}

variable_1 = {
'name' : 'u',
'kind' : 'unknown field',
'field' : '2_velocity',
'order' : 0,
}
variable_2 = {
'name' : 'v',
'kind' : 'test field',
'field' : '2_velocity',
'dual' : 'u',
}
variable_3 = {
'name' : 'p',
'kind' : 'unknown field',
'field' : 'pressure',
'order' : 1,
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}
variable_4 = {
'name' : 'q',
'kind' : 'test field',
'field' : 'pressure',
'dual' : 'p',
}

integral_1 = {
'name' : 'i',
'order' : 2,
}

equations = {
'balance' :
"""dw_div_grad.i.Y1Y2( fluid.viscosity, v, u )
- dw_stokes.i.Y1Y2( v, p ) = 0""",
'incompressibility' :
"""dw_stokes.i.Y1Y2( u, q ) = 0""",
}

material_1 = {
'name' : 'fluid',
'values' : {
'viscosity' : 1.0,
'density' : 1e0,
},
}

ebc_1 = {
'name' : 'walls',
'region' : 'Walls',
'dofs' : {'u.all' : 0.0},
}
ebc_2 = {
'name' : 'top_velocity',
'region' : 'Top',
'dofs' : {'u.1' : -1.0, 'u.0' : 0.0},
}
ebc_10 = {
'name' : 'bottom_pressure',
'region' : 'Bottom',
'dofs' : {'p.0' : 0.0},
}

epbc_1 = {
'name' : 'u_rl',
'region' : ['Left', 'Right'],
'dofs' : {'u.all' : 'u.all', 'p.0' : 'p.0'},
'match' : 'match_y_line',
}

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functions = {
'match_y_line' : (match_y_line,),
}

solver_0 = {
'name' : 'ls',
'kind' : 'ls.scipy_direct',
}

solver_1 = {
'name' : 'newton',
'kind' : 'nls.newton',

'i_max' : 2,
'eps_a' : 1e-8,
'eps_r' : 1e-2,
'macheps' : 1e-16,
'lin_red' : 1e-2, # Linear system error < (eps_a * lin_red).
'ls_red' : 0.1,
'ls_red_warp' : 0.001,
'ls_on' : 1.1,
'ls_min' : 1e-5,
'check' : 0,
'delta' : 1e-6,
}

save_format = 'hdf5' # 'hdf5' or 'vtk'

navier_stokes/stokes_slip_bc.py

Description
Incompressible Stokes flow with Navier (slip) boundary conditions, flow driven by a moving wall and a small diffusion
for stabilization.
This example demonstrates the use of no-penetration and edge direction boundary conditions together with Navier or
slip boundary conditions. Alternatively the no-penetration boundary conditions can be applied in a weak sense using
the penalty term dw_non_penetration_p.
Find 𝑢, 𝑝 such that:
∫︁ ∫︁ ∫︁ ∫︁
𝜈 ∇𝑣 : ∇𝑢 − 𝑝∇·𝑣+ 𝛽𝑣 · (𝑢 − 𝑢𝑑 ) + 𝛽𝑣 · 𝑢 = 0 , ∀𝑣 ,
Ω Ω Γ1 Γ
∫︁ ∫︁ 2
𝜇∇𝑞 · ∇𝑝 + 𝑞∇·𝑢=0, ∀𝑞 ,
Ω Ω

where 𝜈 is the fluid viscosity, 𝛽 is the slip coefficient, 𝜇 is the (small) numerical diffusion coefficient, Γ1 is the top wall
that moves with the given driving velocity 𝑢𝑑 and Γ2 are the remaining walls. The Navier conditions are in effect on
both Γ1 , Γ2 and are expressed by the corresponding integrals in the equations above.
The no-penetration boundary conditions are applied on Γ1 , Γ2 , except the vertices of the block edges, where the edge
direction boundary conditions are applied.
The penalty term formulation is given by the following equations.

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Find 𝑢, 𝑝 such that:

∫︁ ∫︁ ∫︁ ∫︁ ∫︁
𝜈 ∇𝑣 : ∇𝑢 − 𝑝∇·𝑣+ 𝛽𝑣 · (𝑢 − 𝑢𝑑 ) + 𝛽𝑣 · 𝑢 + 𝜖(𝑛 · 𝑣)(𝑛 · 𝑢) = 0 , ∀𝑣 ,
Ω Ω Γ1 Γ2 Γ1 ∪Γ2
∫︁ ∫︁
𝜇∇𝑞 · ∇𝑝 + 𝑞∇·𝑢=0, ∀𝑞 ,
Ω Ω

where 𝜖 is the penalty coefficient (sufficiently large). The no-penetration boundary conditions are applied on Γ1 , Γ2 .
Optionally, Dirichlet boundary conditions can be applied on the inlet in the both cases, see below.
For large meshes use the 'ls_i' linear solver - PETSc + petsc4py are needed in that case.
Several parameters can be set using the --define option of simple.py, see define() and the examples below.

Examples

Specify the inlet velocity and a finer mesh:

python3 simple.py examples/navier_stokes/stokes_slip_bc -d shape="(11,31,31),u_inlet=0.5"

python3 resview.py -f p:p0 u:o.4:p1 u:g:f0.2:p1 -- user_block.vtk

Use the penalty term formulation and einsum-based terms with the default (numpy) backend:

python3 simple.py examples/navier_stokes/stokes_slip_bc -d "mode=penalty,term_mode=einsum

˓→"

python3 resview.py -f p:p0 u:o.4:p1 u:g:f0.2:p1 -- user_block.vtk

Change backend to opt_einsum (needs to be installed) and use the quadratic velocity approximation order:

python3 simple.py examples/navier_stokes/stokes_slip_bc -d "u_order=2,mode=penalty,term_

˓→mode=einsum,backend=opt_einsum,optimize=auto"

python3 resview.py -f p:p0 u:o.4:p1 u:g:f0.2:p1 -- user_block.vtk

Note the pressure field distribution improvement w.r.t. the previous examples. IfPETSc + petsc4py are installed, try
using the iterative solver to speed up the solution:

python3 simple.py examples/navier_stokes/stokes_slip_bc -d "u_order=2,ls=ls_i,

˓→mode=penalty,term_mode=einsum,backend=opt_einsum,optimize=auto"

python3 resview.py -f p:p0 u:o.4:p1 u:g:f0.2:p1 -- user_block.vtk

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source code

r"""
Incompressible Stokes flow with Navier (slip) boundary conditions, flow driven
by a moving wall and a small diffusion for stabilization.

This example demonstrates the use of `no-penetration` and `edge direction`

boundary conditions together with Navier or slip boundary conditions.
Alternatively the `no-penetration` boundary conditions can be applied in a weak
sense using the penalty term ``dw_non_penetration_p``.

Find :math:`\ul{u}`, :math:`p` such that:

.. math::
\int_{\Omega} \nu\ \nabla \ul{v} : \nabla \ul{u}
- \int_{\Omega} p\ \nabla \cdot \ul{v}
+ \int_{\Gamma_1} \beta \ul{v} \cdot (\ul{u} - \ul{u}_d)
+ \int_{\Gamma_2} \beta \ul{v} \cdot \ul{u}
= 0
\;, \quad \forall \ul{v} \;,

\int_{\Omega} \mu \nabla q \cdot \nabla p

+ \int_{\Omega} q\ \nabla \cdot \ul{u}
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(continued from previous page)

= 0
\;, \quad \forall q \;,

where :math:`\nu` is the fluid viscosity, :math:`\beta` is the slip

coefficient, :math:`\mu` is the (small) numerical diffusion coefficient,
:math:`\Gamma_1` is the top wall that moves with the given driving velocity
:math:`\ul{u}_d` and :math:`\Gamma_2` are the remaining walls. The Navier
conditions are in effect on both :math:`\Gamma_1`, :math:`\Gamma_2` and are
expressed by the corresponding integrals in the equations above.

The `no-penetration` boundary conditions are applied on :math:`\Gamma_1`,

:math:`\Gamma_2`, except the vertices of the block edges, where the `edge
direction` boundary conditions are applied.

The penalty term formulation is given by the following equations.

Find :math:`\ul{u}`, :math:`p` such that:

.. math::
\int_{\Omega} \nu\ \nabla \ul{v} : \nabla \ul{u}
- \int_{\Omega} p\ \nabla \cdot \ul{v}
+ \int_{\Gamma_1} \beta \ul{v} \cdot (\ul{u} - \ul{u}_d)
+ \int_{\Gamma_2} \beta \ul{v} \cdot \ul{u}
+ \int_{\Gamma_1 \cup \Gamma_2} \epsilon (\ul{n} \cdot \ul{v})
(\ul{n} \cdot \ul{u})
= 0
\;, \quad \forall \ul{v} \;,

\int_{\Omega} \mu \nabla q \cdot \nabla p

+ \int_{\Omega} q\ \nabla \cdot \ul{u}
= 0
\;, \quad \forall q \;,

where :math:`\epsilon` is the penalty coefficient (sufficiently large). The

`no-penetration` boundary conditions are applied on :math:`\Gamma_1`,
:math:`\Gamma_2`.

Optionally, Dirichlet boundary conditions can be applied on

the inlet in the both cases, see below.

For large meshes use the ``'ls_i'`` linear solver - PETSc + petsc4py are needed
in that case.

Several parameters can be set using the ``--define`` option of ``simple.py``,

see :func:`define()` and the examples below.

Examples
--------

Specify the inlet velocity and a finer mesh::

python3 simple.py sfepy/examples/navier_stokes/stokes_slip_bc -d shape="(11,31,31),u_

˓→inlet=0.5" (continues on next page)

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python3 resview.py -f p:p0 u:o.4:p1 u:g:f0.2:p1 -- user_block.vtk

Use the penalty term formulation and einsum-based terms with the default
(numpy) backend::

python3 simple.py sfepy/examples/navier_stokes/stokes_slip_bc -d "mode=penalty,term_

˓→mode=einsum"
python3 resview.py -f p:p0 u:o.4:p1 u:g:f0.2:p1 -- user_block.vtk

Change backend to opt_einsum (needs to be installed) and use the quadratic velocity␣
˓→approximation order::

python3 simple.py sfepy/examples/navier_stokes/stokes_slip_bc -d "u_order=2,

˓→mode=penalty,term_mode=einsum,backend=opt_einsum,optimize=auto"
python3 resview.py -f p:p0 u:o.4:p1 u:g:f0.2:p1 -- user_block.vtk

Note the pressure field distribution improvement w.r.t. the previous examples. IfPETSc +␣
˓→petsc4py are installed, try using the iterative solver to speed up the solution::

python3 simple.py sfepy/examples/navier_stokes/stokes_slip_bc -d "u_order=2,ls=ls_i,

˓→mode=penalty,term_mode=einsum,backend=opt_einsum,optimize=auto"
python3 resview.py -f p:p0 u:o.4:p1 u:g:f0.2:p1 -- user_block.vtk
"""
import os
from functools import partial
import numpy as nm

from sfepy.base.base import assert_, output

from sfepy.discrete.fem.meshio import UserMeshIO
from sfepy.mesh.mesh_generators import gen_block_mesh
from sfepy.homogenization.utils import define_box_regions

def define(dims=(3, 1, 0.5), shape=(11, 15, 15), u_order=1, refine=0,

ls='ls_d', u_inlet=None, mode='lcbc', term_mode='original',
backend='numpy', optimize='optimal', verbosity=0, output_dir='',
save_lcbc_vecs=False):
"""
Parameters
----------
dims : tuple
The block domain dimensions.
shape : tuple
The mesh resolution: increase to improve accuracy.
u_order : int
The velocity field approximation order.
refine : int
The refinement level.
ls : 'ls_d' or 'ls_i'
The pre-configured linear solver name.
u_inlet : float, optional
The x-component of the inlet velocity.
mode : 'lcbc' or 'penalty'
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The alternative formulations.
term_mode : 'original' or 'einsum'
The switch to use either the original or new experimental einsum-based
terms.
backend : str
The einsum mode backend.
optimize : str
The einsum mode optimization (backend dependent).
verbosity : 0, 1, 2, 3
The verbosity level of einsum-based terms.
output_dir : str
The output directory.
save_lcbc_vecs : bool
If True, save the no_penetration and edge_direction LCBC vectors.
"""
output('dims: {}, shape: {}, u_order: {}, refine: {}, u_inlet: {}'
.format(dims, shape, u_order, refine, u_inlet))
output('linear solver: {}'.format(ls))
output('mode: {}, term_mode: {}'.format(mode, term_mode))
if term_mode == 'einsum':
output('backend: {}, optimize: {}, verbosity: {}'
.format(backend, optimize, verbosity))

assert_(mode in {'lcbc', 'penalty'})

assert_(term_mode in {'original', 'einsum'})
if u_order > 1:
assert_(mode == 'penalty', msg='set mode=penalty to use u_order > 1!')
dims = nm.array(dims, dtype=nm.float64)
shape = nm.array(shape, dtype=nm.int32)

def mesh_hook(mesh, mode):

"""
Generate the block mesh.
"""
if mode == 'read':
mesh = gen_block_mesh(dims, shape, [0, 0, 0], name='user_block',
verbose=False)
return mesh

elif mode == 'write':

pass

filename_mesh = UserMeshIO(mesh_hook)

regions = define_box_regions(3, 0.5 * dims)

regions.update({
'Omega' : 'all',
'Edges_v' : ("""(r.Near *v r.Bottom) +v
(r.Bottom *v r.Far) +v
(r.Far *v r.Top) +v
(r.Top *v r.Near)""", 'edge'),
'Gamma1_f' : ('copy r.Top', 'face'),
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'Gamma2_f' : ('r.Near +v r.Bottom +v r.Far', 'face'),
'Gamma_f' : ('r.Gamma1_f +v r.Gamma2_f', 'face'),
'Gamma_v' : ('r.Gamma_f -v r.Edges_v', 'face'),
'Inlet_f' : ('r.Left -v r.Gamma_f', 'face'),
})

fields = {
'velocity' : ('real', 3, 'Omega', u_order),
'pressure' : ('real', 1, 'Omega', 1),
}

def get_u_d(ts, coors, region=None):

"""
Given stator velocity.
"""
out = nm.zeros_like(coors)
out[:] = [1.0, 1.0, 0.0]

return out

functions = {
'get_u_d' : (get_u_d,),
}

variables = {
'u' : ('unknown field', 'velocity', 0),
'v' : ('test field', 'velocity', 'u'),
'u_d' : ('parameter field', 'velocity',
{'setter' : 'get_u_d'}),
'p' : ('unknown field', 'pressure', 1),
'q' : ('test field', 'pressure', 'p'),
}

materials = {
'm' : ({
'nu' : 1e-3,
'beta' : 1e-2,
'mu' : 1e-10,
},),
}

ebcs = {
}
if u_inlet is not None:
ebcs['inlet'] = ('Inlet_f', {'u.0' : u_inlet, 'u.[1, 2]' : 0.0})

indir = partial(os.path.join, output_dir)

if mode == 'lcbc':
lcbcs = {
'walls' : ('Gamma_v', {'u.all' : None}, None, 'no_penetration',
indir('normals_Gamma.vtk') if save_lcbc_vecs else None),
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'edges' : ('Edges_v', [(-0.5, 1.5)], {'u.all' : None}, None,
'edge_direction',
indir('edges_Edges.vtk') if save_lcbc_vecs else None),
}

if term_mode == 'original':
equations = {
'balance' :
"""dw_div_grad.5.Omega(m.nu, v, u)
- dw_stokes.5.Omega(v, p)
+ dw_dot.5.Gamma1_f(m.beta, v, u)
+ dw_dot.5.Gamma2_f(m.beta, v, u)
=
+ dw_dot.5.Gamma1_f(m.beta, v, u_d)""",
'incompressibility' :
"""dw_laplace.5.Omega(m.mu, q, p)
+ dw_stokes.5.Omega(u, q) = 0""",
}

else:
equations = {
'balance' :
"""de_div_grad.5.Omega(m.nu, v, u)
- de_stokes.5.Omega(v, p)
+ de_dot.5.Gamma1_f(m.beta, v, u)
+ de_dot.5.Gamma2_f(m.beta, v, u)
=
+ de_dot.5.Gamma1_f(m.beta, v, u_d)""",
'incompressibility' :
"""de_laplace.5.Omega(m.mu, q, p)
+ de_stokes.5.Omega(u, q) = 0""",
}

else:
materials['m'][0]['np_eps'] = 1e3

if term_mode == 'original':
equations = {
'balance' :
"""dw_div_grad.5.Omega(m.nu, v, u)
- dw_stokes.5.Omega(v, p)
+ dw_dot.5.Gamma1_f(m.beta, v, u)
+ dw_dot.5.Gamma2_f(m.beta, v, u)
+ dw_non_penetration_p.5.Gamma1_f(m.np_eps, v, u)
+ dw_non_penetration_p.5.Gamma2_f(m.np_eps, v, u)
=
+ dw_dot.5.Gamma1_f(m.beta, v, u_d)""",
'incompressibility' :
"""dw_laplace.5.Omega(m.mu, q, p)
+ dw_stokes.5.Omega(u, q) = 0""",
}

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else:
equations = {
'balance' :
"""de_div_grad.5.Omega(m.nu, v, u)
- de_stokes.5.Omega(v, p)
+ de_dot.5.Gamma1_f(m.beta, v, u)
+ de_dot.5.Gamma2_f(m.beta, v, u)
+ de_non_penetration_p.5.Gamma1_f(m.np_eps, v, u)
+ de_non_penetration_p.5.Gamma2_f(m.np_eps, v, u)
=
+ de_dot.5.Gamma1_f(m.beta, v, u_d)""",
'incompressibility' :
"""de_laplace.5.Omega(m.mu, q, p)
+ de_stokes.5.Omega(u, q) = 0""",
}

solvers = {
'ls_d' : ('ls.auto_direct', {}),
'ls_i' : ('ls.petsc', {
'method' : 'bcgsl', # ksp_type
'precond' : 'bjacobi', # pc_type
'sub_precond' : 'ilu', # sub_pc_type
'eps_a' : 0.0, # abstol
'eps_r' : 1e-12, # rtol
'eps_d' : 1e10, # Divergence tolerance.
'i_max' : 200, # maxits
}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-10,
}),
}

options = {
'nls' : 'newton',
'ls' : ls,
'eterm': {
'verbosity' : verbosity,
'backend_args' : {
'backend' : backend,
'optimize' : optimize,
'layout' : None,
},
},
'refinement_level' : refine,
'output_dir' : output_dir,
}

return locals()

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navier_stokes/utils.py

Description
missing description!
source code

##
# Functions.
from __future__ import absolute_import
import numpy as nm

from sfepy.linalg import get_coors_in_tube

# last revision: 01.08.2007

def cinc_cylinder(coors, mode):
axis = nm.array([1, 0, 0], nm.float64)
if mode == 0: # In
centre = nm.array([-0.00001, 0.0, 0.0], nm.float64)
radius = 0.019
length = 0.00002
elif mode == 1: # Out
centre = nm.array([0.09999, 0.0, 0.0], nm.float64)
radius = 0.019
length = 0.00002
else:
centre = nm.array([0.05, 0.0, 0.0], nm.float64)
radius = 0.012
length = 0.04

return get_coors_in_tube(coors, centre, axis, -1.0, radius, length)

def cinc_elbow2(coors, mode):

if mode == 0: # In
centre = nm.array([0.0, -0.00001, 0.0], nm.float64)
else: # Out
centre = nm.array([0.2, -0.00001, 0.0], nm.float64)

axis = nm.array([0, 1, 0], nm.float64)

radius = 0.029
length = 0.00002

return get_coors_in_tube(coors, centre, axis, -1.0, radius, length)

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phononic

phononic/band_gaps.py

Description
Acoustic band gaps in a strongly heterogeneous elastic body, detected using homogenization techniques.
A reference periodic cell contains two domains: the stiff matrix 𝑌𝑚 and the soft (but heavy) inclusion 𝑌𝑐 .
source code

"""
Acoustic band gaps in a strongly heterogeneous elastic body, detected using
homogenization techniques.

A reference periodic cell contains two domains: the stiff matrix :math:`Y_m`
and the soft (but heavy) inclusion :math:`Y_c`.
"""
from __future__ import absolute_import
from sfepy import data_dir
from sfepy.base.base import Struct
from sfepy.base.ioutils import InDir
from sfepy.homogenization.coefficients import Coefficients

from sfepy.examples.phononic.band_gaps_conf import (BandGapsConf, get_pars,

clip, clip_sqrt)

clip, clip_sqrt # Make pyflakes happy...

incwd = InDir(__file__)

filename = data_dir + '/meshes/2d/special/circle_in_square.mesh'

output_dir = incwd('output/band_gaps')

# aluminium, SI units
D_m = get_pars(2, 5.898e10, 2.681e10)
density_m = 2799.0

# epoxy, SI units
D_c = get_pars(2, 1.798e9, 1.48e9)
density_c = 1142.0

mat_pars = Coefficients(D_m=D_m, density_m=density_m,

D_c=D_c, density_c=density_c)

region_selects = Struct(matrix='cells of group 1',

inclusion='cells of group 2')

corrs_save_names = {'evp' : 'evp', 'corrs_rs' : 'corrs_rs'}

options = {
'plot_transform_angle' : None,
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'plot_transform_wave' : ('clip_sqrt', (0, 7000)),
'plot_transform' : ('clip', (-7000, 7000)),

'fig_name' : 'band_gaps',
'fig_name_angle' : 'band_gaps_angle',
'fig_name_wave' : 'band_gaps_wave',
'fig_suffix' : '.pdf',

'coefs_filename' : 'coefs.txt',

'incident_wave_dir' : [1.0, 1.0],

'plot_options' : {
'show' : True,
'legend' : True,
},
'plot_labels' : {
'band_gaps' : {
'resonance' : r'$\lambda^r$',
'masked' : r'masked $\lambda^r$',
'eig_min' : r'min eig($M$)',
'eig_max' : r'max eig($M$)',
'x_axis' : r'$\sqrt{\lambda}$, $\omega$',
'y_axis' : r'eigenvalues of mass matrix $M$',
},
},
'plot_rsc' : {
'params' : {'axes.labelsize': 'x-large',
'font.size': 14,
'legend.fontsize': 'large',
'legend.loc': 'upper right',
'xtick.labelsize': 'large',
'ytick.labelsize': 'large',
'text.usetex': True},
},
'multiprocessing' : False,
'float_format' : '%.16e',
}

evp_options = {
'eigensolver' : 'eig.sgscipy',
'save_eig_vectors' : (12, 0),
'scale_epsilon' : 1.0,
'elasticity_contrast' : 1.0,
}

eigenmomenta_options = {
# eigenmomentum threshold,
'threshold' : 1e-2,
# eigenmomentum threshold is relative w.r.t. largest one,
'threshold_is_relative' : True,
}
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band_gaps_options = {
'eig_range' : (0, 30), # -> freq_range
# = sqrt(eigs[slice(*eig_range)][[0, -1]])
# 'fixed_freq_range' : (0.1, 3e7),
'freq_margins' : (10, 10), # % of freq_range
'freq_eps' : 1e-7, # frequency
'zero_eps' : 1e-12, # zero finding
'freq_step' : 0.0001, # % of freq_range

'log_save_name' : 'band_gaps.log',
'raw_log_save_name' : 'raw_eigensolution.npz',
}

conf = BandGapsConf(filename, 1, region_selects, mat_pars, options,

evp_options, eigenmomenta_options, band_gaps_options,
corrs_save_names=corrs_save_names, incwd=incwd,
output_dir=output_dir)

define = lambda: conf.conf.to_dict()

phononic/band_gaps_conf.py

Description
Configuration classes for acoustic band gaps in a strongly heterogeneous elastic body.
source code
"""
Configuration classes for acoustic band gaps in a strongly heterogeneous
elastic body.
"""
from __future__ import absolute_import
import numpy as nm

from sfepy.base.base import get_default, import_file, Struct

from sfepy.base.conf import ProblemConf
from sfepy.discrete.fem import MeshIO
import sfepy.discrete.fem.periodic as per
from sfepy.mechanics.matcoefs import stiffness_from_lame, TransformToPlane
from sfepy.homogenization.utils import define_box_regions, get_lattice_volume
import sfepy.homogenization.coefs_base as cb
import sfepy.homogenization.coefs_phononic as cp

per.set_accuracy(1e-8)

def get_pars(dim, lam, mu):

c = stiffness_from_lame(3, lam, mu)
if dim == 2:
tr = TransformToPlane()
try:
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c = tr.tensor_plane_stress(c3=c)
except:
sym = (dim + 1) * dim // 2
c = nm.zeros((sym, sym), dtype=nm.float64)

return c

def set_coef_d(variables, ir, ic, mode, pis, corrs_rs):

mode2var = {'row' : 'u1_m', 'col' : 'u2_m'}

val = pis.states[ir, ic]['u_m'] + corrs_rs.states[ir, ic]['u_m']

variables[mode2var[mode]].set_data(val)

class BandGapsConf(Struct):
"""
Configuration class for acoustic band gaps in a strongly heterogeneous
elastic body.
"""

def __init__(self, filename, approx, region_selects, mat_pars, options,

evp_options, eigenmomenta_options, band_gaps_options,
coefs_save_name='coefs',
corrs_save_names=None,
incwd=None,
output_dir=None, **kwargs):
Struct.__init__(self, approx=approx, region_selects=region_selects,
mat_pars=mat_pars, options=options,
evp_options=evp_options,
eigenmomenta_options=eigenmomenta_options,
band_gaps_options=band_gaps_options,
**kwargs)
self.incwd = get_default(incwd, lambda x: x)

self.conf = Struct()
self.conf.filename_mesh = self.incwd(filename)

output_dir = get_default(output_dir, self.incwd('output'))

default = {'evp' : 'evp', 'corrs_rs' : 'corrs_rs'}

self.corrs_save_names = get_default(corrs_save_names,
default)

io = MeshIO.any_from_filename(self.conf.filename_mesh)
self.bbox, self.dim = io.read_bounding_box(ret_dim=True)
rpc_axes = nm.eye(self.dim, dtype=nm.float64) \
* (self.bbox[1] - self.bbox[0])

self.conf.options = options
self.conf.options.update({
'output_dir' : output_dir,

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'volume' : {
'value' : get_lattice_volume(rpc_axes),
},

'coefs' : 'coefs',
'requirements' : 'requirements',

'coefs_filename' : coefs_save_name,
})

self.conf.mat_pars = mat_pars

self.conf.solvers = self.define_solvers()
self.conf.regions = self.define_regions()
self.conf.materials = self.define_materials()
self.conf.fields = self.define_fields()
self.conf.variables = self.define_variables()
(self.conf.ebcs, self.conf.epbcs,
self.conf.lcbcs, self.all_periodic) = self.define_bcs()
self.conf.functions = self.define_functions()
self.conf.integrals = self.define_integrals()

self.equations, self.expr_coefs = self.define_equations()

self.conf.coefs = self.define_coefs()
self.conf.requirements = self.define_requirements()

def __call__(self):
return ProblemConf.from_dict(self.conf.__dict__,
import_file(__file__))

def define_solvers(self):
solvers = {
'ls_d' : ('ls.scipy_direct', {}),
'ls_i' : ('ls.scipy_iterative', {
'method' : 'cg',
'i_max' : 1000,
'eps_a' : 1e-12,
}),
'newton' : ('nls.newton', {
'i_max' : 1,
'eps_a' : 1e-4,
}),
}

return solvers

def define_regions(self):
regions = {
'Y' : 'all',
'Y_m' : self.region_selects.matrix,
'Y_c' : self.region_selects.inclusion,
'Gamma_mc': ('r.Y_m *v r.Y_c', 'facet'),
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}

regions.update(define_box_regions(self.dim,
self.bbox[0], self.bbox[1], 1e-5))

return regions

def define_materials(self):
materials = {
'm' : ({
'D_m' : self.mat_pars.D_m,
'density_m' : self.mat_pars.density_m,
'D_c' : self.mat_pars.D_c,
'density_c' : self.mat_pars.density_c,
}, None, None, {'special_constant' : True}),
}
return materials

def define_fields(self):
fields = {
'vector_Y_m' : ('real', self.dim, 'Y_m', self.approx),
'vector_Y_c' : ('real', self.dim, 'Y_c', self.approx),

'scalar_Y' : ('real', 1, 'Y', 1),

}
return fields

def define_variables(self):
variables = {
'u_m' : ('unknown field', 'vector_Y_m'),
'v_m' : ('test field', 'vector_Y_m', 'u_m'),
'Pi' : ('parameter field', 'vector_Y_m', '(set-to-None)'),
'u1_m' : ('parameter field', 'vector_Y_m', '(set-to-None)'),
'u2_m' : ('parameter field', 'vector_Y_m', '(set-to-None)'),

'u_c' : ('unknown field', 'vector_Y_c'),

'v_c' : ('test field', 'vector_Y_c', 'u_c'),

'aux' : ('parameter field', 'scalar_Y', '(set-to-None)'),

}
return variables

def define_bcs(self):
ebcs = {
'fixed_corners' : ('Corners', {'u_m.all' : 0.0}),
'fixed_gamma_mc' : ('Gamma_mc', {'u_c.all' : 0.0}),
}

epbcs = {}
all_periodic = []
for vn in ['u_m']:
val = {'%s.all' % vn : '%s.all' % vn}
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epbcs.update({
'periodic_%s_x' % vn : (['Left', 'Right'], val,
'match_y_line'),
'periodic_%s_y' % vn : (['Top', 'Bottom'], val,
'match_x_line'),
})
all_periodic.extend(['periodic_%s_x' % vn, 'periodic_%s_y' % vn])

lcbcs = {}

return ebcs, epbcs, lcbcs, all_periodic

def define_functions(self):
functions = {
'match_x_line' : (per.match_x_line,),
'match_y_line' : (per.match_y_line,),
}

return functions

def define_integrals(self):
integrals = {
'i' : 2,
}

return integrals

def define_equations(self):
equations = {}
equations['corrs_rs'] = {
'balance_of_forces' :
"""dw_lin_elastic.i.Y_m( m.D_m, v_m, u_m )
= - dw_lin_elastic.i.Y_m( m.D_m, v_m, Pi )""",
}
equations['evp'] = {
'lhs' : """dw_lin_elastic.i.Y_c( m.D_c, v_c, u_c )""",
'rhs' : """dw_dot.i.Y_c( m.density_c, v_c, u_c )""",
}

expr_coefs = {
'D' : """dw_lin_elastic.i.Y_m( m.D_m, u1_m, u2_m )""",
'VF' : """ev_volume.i.%s(aux)""",
'ema' : """ev_integrate.i.Y_c( m.density_c, u_c )""",
}

return equations, expr_coefs

def define_coefs(self):
from copy import copy

ema_options = copy(self.eigenmomenta_options)
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ema_options.update({'var_name' : 'u_c'})

coefs = {
# Basic.
'VF' : {
'regions' : ['Y_m', 'Y_c'],
'expression' : self.expr_coefs['VF'],
'class' : cb.VolumeFractions,
},
'dv_info' : {
'requires' : ['c.VF'],
'region_to_material' : {'Y_m' : ('m', 'density_m'),
'Y_c' : ('m', 'density_c'),},
'class' : cp.DensityVolumeInfo,
},

'eigenmomenta' : {
'requires' : ['evp', 'c.dv_info'],
'expression' : self.expr_coefs['ema'],
'options' : ema_options,
'class' : cp.Eigenmomenta,
},
'M' : {
'requires' : ['evp', 'c.dv_info', 'c.eigenmomenta'],
'class' : cp.AcousticMassTensor,
},
'band_gaps' : {
'requires' : ['evp', 'c.eigenmomenta', 'c.M'],
'options' : self.band_gaps_options,
'class' : cp.BandGaps,
},

# Dispersion.
'D' : {
'requires' : ['pis', 'corrs_rs'],
'expression' : self.expr_coefs['D'],
'set_variables' : set_coef_d,
'class' : cb.CoefSymSym,
},
'Gamma' : {
'requires' : ['c.D'],
'options' : {
'mode' : 'simple',
'incident_wave_dir' : None,
},
'class' : cp.ChristoffelAcousticTensor,
},
'dispersion' : {
'requires' : ['evp', 'c.eigenmomenta', 'c.M', 'c.Gamma'],
'options' : self.band_gaps_options,
'class' : cp.BandGaps,
},
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'polarization_angles' : {
'requires' : ['c.dispersion'],
'options' : {
'incident_wave_dir' : None,
},
'class' : cp.PolarizationAngles,
},

# Phase velocity.
'phase_velocity' : {
'requires' : ['c.dv_info', 'c.Gamma'],
'options' : {
'eigensolver' : 'eig.sgscipy',
},
'class' : cp.PhaseVelocity,
},
'filenames' : {},
}

return coefs

def define_requirements(self):
requirements = {
# Basic.
'evp' : {
'ebcs' : ['fixed_gamma_mc'],
'epbcs' : None,
'equations' : self.equations['evp'],
'save_name' : self.corrs_save_names['evp'],
'options' : self.evp_options,
'class' : cp.SimpleEVP,
},

# Dispersion.
'pis' : {
'variables' : ['u_m'],
'class' : cb.ShapeDimDim,
},
'corrs_rs' : {
'requires' : ['pis'],
'ebcs' : ['fixed_corners'],
'epbcs' : self.all_periodic,
'equations' : self.equations['corrs_rs'],
'set_variables' : [('Pi', 'pis', 'u_m')],
'save_name' : self.corrs_save_names['corrs_rs'],
'is_linear' : True,
'class' : cb.CorrDimDim,
},
}
return requirements

class BandGapsRigidConf(BandGapsConf):
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"""
Configuration class for acoustic band gaps in a strongly heterogeneous
elastic body with rigid inclusions.
"""

def define_regions(self):
regions = BandGapsConf.define_regions(self)
regions['Y_cr'] = regions['Y_c']
regions.update({
'Y_r' : 'vertices by select_yr',
'Y_c' : 'r.Y_cr -c r.Y_r',
})
return regions

def define_materials(self):
materials = BandGapsConf.define_materials(self)
materials['m'][0].update({
'D_r' : self.mat_pars.D_r,
'density_r' : self.mat_pars.density_r,
})
return materials

def define_fields(self):
fields = {
'vector_Y_cr' : ('real', self.dim, 'Y_cr', self.approx),

'scalar_Y' : ('real', 1, 'Y', 1),

}
return fields

def define_variables(self):
variables = {
'u' : ('unknown field', 'vector_Y_cr'),
'v' : ('test field', 'vector_Y_cr', 'u'),

'aux' : ('parameter field', 'scalar_Y', '(set-to-None)'),

}
return variables

def define_bcs(self):
ebcs = {
'fixed_gamma_mc' : ('Gamma_mc', {'u.all' : 0.0}),
}
lcbcs ={
'rigid' : ('Y_r',{'u.all' : None}, None, 'rigid'),
}

return ebcs, {}, lcbcs, []

def define_functions(self):
functions = BandGapsConf.define_functions(self)
functions.update({
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'select_yr' : (self.select_yr,),
})

return functions

def define_equations(self):
equations = {}

# dw_lin_elastic.i.Y_r( m.D_r, v, u ) should have no effect!

equations['evp'] = {
'lhs' : """dw_lin_elastic.i.Y_c( m.D_c, v, u )
+ dw_lin_elastic.i.Y_r( m.D_r, v, u )""",
'rhs' : """dw_dot.i.Y_c( m.density_c, v, u )
+ dw_dot.i.Y_r( m.density_r, v, u )""",
}

expr_coefs = {
'VF' : """ev_volume.i.%s(aux)""",
'ema' : """ev_integrate.i.Y_c( m.density_c, u )
+ ev_integrate.i.Y_r( m.density_r, u )""",
}

return equations, expr_coefs

def define_coefs(self):
from copy import copy

ema_options = copy(self.eigenmomenta_options)
ema_options.update({'var_name' : 'u'})

coefs = {
# Basic.
'VF' : {
'regions' : ['Y_m', 'Y_cr', 'Y_c', 'Y_r'],
'expression' : self.expr_coefs['VF'],
'class' : cb.VolumeFractions,
},
'dv_info' : {
'requires' : ['c.VF'],
'region_to_material' : {'Y_m' : ('m', 'density_m'),
'Y_c' : ('m', 'density_c'),
'Y_r' : ('m', 'density_r'),},
'class' : cp.DensityVolumeInfo,
},

'eigenmomenta' : {
'requires' : ['evp', 'c.dv_info'],
'expression' : self.expr_coefs['ema'],
'options' : ema_options,
'class' : cp.Eigenmomenta,
},
'M' : {
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'requires' : ['evp', 'c.dv_info', 'c.eigenmomenta'],
'class' : cp.AcousticMassTensor,
},
'band_gaps' : {
'requires' : ['evp', 'c.eigenmomenta', 'c.M'],
'options' : self.band_gaps_options,
'class' : cp.BandGaps,
},

'filenames' : {},
}

return coefs

def define_requirements(self):
requirements = {
# Basic.
'evp' : {
'ebcs' : ['fixed_gamma_mc'],
'epbcs' : None,
'lcbcs' : ['rigid'],
'equations' : self.equations['evp'],
'save_name' : self.corrs_save_names['evp'],
'options' : self.evp_options,
'class' : cp.SimpleEVP,
},
}
return requirements

def clip(data, plot_range):

return nm.clip(data, *plot_range)

def clip_sqrt(data, plot_range):

return nm.clip(nm.sqrt(data), *plot_range)

def normalize(data, plot_range):

aux = nm.arctan(data)
return clip(aux, plot_range)

phononic/band_gaps_rigid.py

Description
Acoustic band gaps in a strongly heterogeneous elastic body with a rigid inclusion, detected using homogenization
techniques.
A reference periodic cell contains three domains: the stiff matrix 𝑌𝑚 and the soft inclusion 𝑌𝑐 enclosing the rigid heavy
sub-inclusion 𝑌𝑟 .
source code

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"""
Acoustic band gaps in a strongly heterogeneous elastic body with a rigid
inclusion, detected using homogenization techniques.

A reference periodic cell contains three domains: the stiff matrix :math:`Y_m`
and the soft inclusion :math:`Y_c` enclosing the rigid heavy sub-inclusion
:math:`Y_r`.
"""
from __future__ import absolute_import
import numpy as nm

from sfepy import data_dir

from sfepy.base.base import Struct
from sfepy.base.ioutils import InDir
from sfepy.discrete.fem import extend_cell_data
from sfepy.linalg import norm_l2_along_axis
from sfepy.homogenization.coefficients import Coefficients

from sfepy.examples.phononic.band_gaps_conf import (BandGapsRigidConf,

get_pars, normalize)

normalize # Make pyflakes happy...

incwd = InDir(__file__)

dim = 2

if dim == 3:
filename = data_dir + '/meshes/3d/special/cube_sphere.mesh'

else:
filename = data_dir + '/meshes/2d/special/circle_in_square.mesh'

output_dir = incwd('output/band_gaps_rigid')

# Rigid inclusion diameter.

yr_diameter = 0.125

# aluminium, SI units
D_m = get_pars(2, 5.898e10, 2.681e10)
density_m = 2799.0

# epoxy, SI units
D_c = get_pars(2, 1.798e9, 1.48e9)
density_c = 1142.0

# lead, SI units, does not matter

D_r = get_pars(dim, 4.074e10, 5.556e9)
density_r = 11340.0

mat_pars = Coefficients(D_m=D_m, density_m=density_m,

D_c=D_c, density_c=density_c,
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D_r=D_r, density_r=density_r)

region_selects = Struct(matrix='cells of group 1',

inclusion='cells of group 2')

corrs_save_names = {'evp' : 'evp'}

evp_options = {
'eigensolver' : 'eig.sgscipy',
'save_eig_vectors' : (12, 0),
'scale_epsilon' : 1.0,
'elasticity_contrast' : 1.0,
}

eigenmomenta_options = {
# eigenmomentum threshold,
'threshold' : 1e-1,
# eigenmomentum threshold is relative w.r.t. largest one,
'threshold_is_relative' : True,
}

band_gaps_options = {
'fixed_freq_range' : (0., 35000.), # overrides eig_range!

'freq_eps' : 1e-7, # frequency

'zero_eps' : 1e-12, # zero finding
'freq_step' : 0.01, # % of freq_range

'log_save_name' : 'band_gaps.log',
'raw_log_save_name' : 'raw_eigensolution.npz',
}

options = {
'post_process_hook' : 'post_process',

'plot_transform' : ('normalize', (-2, 2)),

'fig_name' : 'band_gaps',
'fig_suffix' : '.pdf',

'coefs_filename' : 'coefs.txt',

'plot_options' : {
'show' : True, # Show figure.
'legend' : True, # Show legend.
},
'float_format' : '%.16e',
}

def select_yr_circ(coors, diameter=None):

r = norm_l2_along_axis(coors)
out = nm.where(r < diameter)[0]
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if out.shape[0] <= 3:
raise ValueError('too few nodes selected! (%d)' % out.shape[0])

return out

def _select_yr_circ(coors, domain=None, diameter=None):

return select_yr_circ(coors, diameter=yr_diameter)

def post_process(out, problem, mtx_phi):

for key in list(out.keys()):
ii = int(key[1:])
vec = mtx_phi[:,ii].copy()
problem.set_default_state(vec)

strain = problem.evaluate('ev_cauchy_strain.i.Y_c(u)',
verbose=False, mode='el_avg')
strain = extend_cell_data(strain, problem.domain, 'Y_c')
out['strain%03d' % ii] = Struct(name='output_data',
mode='cell', data=strain,
dofs=None)
return out

conf = BandGapsRigidConf(filename, 1, region_selects, mat_pars, options,

evp_options, eigenmomenta_options, band_gaps_options,
corrs_save_names=corrs_save_names, incwd=incwd,
output_dir=output_dir, select_yr=_select_yr_circ)

define = lambda: conf.conf.to_dict()

quantum

quantum/boron.py

Description
Boron atom with 1 electron.
See quantum/quantum_common.py.

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source code

"""
Boron atom with 1 electron.

See :ref:`quantum-quantum_common`.
"""
from __future__ import absolute_import
from sfepy.linalg import norm_l2_along_axis

from sfepy.examples.quantum.quantum_common import common

def get_exact(n_eigs, box_size, dim):

Z = 5
if dim == 2:
eigs = [-float(Z)**2/2/(n-0.5)**2/4
for n in [1] + [2]*3 + [3]*5 + [4]*8 + [5]*15]

elif dim == 3:
eigs = [-float(Z)**2/2/n**2 for n in [1] + [2]*2**2 + [3]*3**2]

return eigs

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def fun_v(ts, coor, mode=None, **kwargs):
if not mode == 'qp': return

out = {}
C = 0.5
r = norm_l2_along_axis(coor, axis=1)
V = - C * 5.0 / r

V.shape = (V.shape[0], 1, 1)
out['V'] = V
return out

def define(n_eigs=10, tau=-15):

l = common(fun_v, get_exact=get_exact, n_eigs=n_eigs, tau=tau)
return l

quantum/hydrogen.py

Description
Hydrogen atom.
See quantum/quantum_common.py.

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source code

"""
Hydrogen atom.

See :ref:`quantum-quantum_common`.
"""
from __future__ import absolute_import
from sfepy.linalg import norm_l2_along_axis

from sfepy.examples.quantum.quantum_common import common

def get_exact(n_eigs, box_size, dim):

Z = 1
if dim == 2:
eigs = [-float(Z)**2/2/(n-0.5)**2/4
for n in [1] + [2]*3 + [3]*5 + [4]*8 + [5]*15]

elif dim == 3:
eigs = [-float(Z)**2/2/n**2 for n in [1] + [2]*2**2 + [3]*3**2]

return eigs

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def fun_v(ts, coor, mode=None, **kwargs):
if not mode == 'qp': return

out = {}
C = 0.5
r = norm_l2_along_axis(coor, axis=1)
V = - C * 1.0 / r

V.shape = (V.shape[0], 1, 1)
out['V'] = V
return out

def define(n_eigs=5, tau=-1.0):

l = common(fun_v, get_exact=get_exact, n_eigs=n_eigs, tau=tau)
return l

quantum/oscillator.py

Description
Quantum oscillator.
See quantum/quantum_common.py.

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source code

"""
Quantum oscillator.

See :ref:`quantum-quantum_common`.
"""
from __future__ import absolute_import
from sfepy.linalg import norm_l2_along_axis

from sfepy.examples.quantum.quantum_common import common

def get_exact(n_eigs, box_size, dim):

if dim == 2:
eigs = [1] + [2]*2 + [3]*3 + [4]*4 + [5]*5 + [6]*6

elif dim == 3:
eigs = [float(1)/2 + x for x in [1] + [2]*3 + [3]*6 + [4]*10]

return eigs

def fun_v(ts, coor, mode=None, **kwargs):

if not mode == 'qp': return
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out = {}
C = 0.5
val = C * norm_l2_along_axis(coor, axis=1, squared=True)

val.shape = (val.shape[0], 1, 1)
out['V'] = val
return out

def define(n_eigs=20, tau=0.0):

l = common(fun_v, get_exact=get_exact, n_eigs=n_eigs, tau=tau)
return l

quantum/quantum_common.py

Description
Common code for basic electronic structure examples.
It covers only simple single electron problems, e.g. well, oscillator, hydrogen atom and boron atom with 1 electron -
see the corresponding files in this directory, where potentials (fun_v()) as well as exact solutions (get_exact()) for
those problems are defined.

Notes

The same code should work also with a 3D (box) mesh, but a very fine mesh would be required. Also in the 2D case,
finer mesh and/or higher approximation order means higher accuracy.
Try changing C, F and L parameters in meshes/quantum/square.geo and regenerate the mesh using gmsh:

gmsh -2 -format mesh meshes/quantum/square.geo -o meshes/quantum/square.mesh

./script/convert_mesh.py -2 meshes/quantum/square.mesh meshes/quantum/square.mesh

The script/convert_mesh.py call makes the mesh planar, as gmsh saves 2D medit meshes including the zero z
coordinates.
Also try changing approximation order (‘approx_order’) of the field below.

Usage Examples

The following examples are available and can be run using the simple.py script:

python simple.py examples/quantum/boron.py

python simple.py examples/quantum/hydrogen.py
python simple.py examples/quantum/oscillator.py
python simple.py examples/quantum/well.py

source code

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"""
Common code for basic electronic structure examples.

It covers only simple single electron problems, e.g. well, oscillator, hydrogen
atom and boron atom with 1 electron - see the corresponding files in this
directory, where potentials (:func:`fun_v()`) as well as exact solutions
(:func:`get_exact()`) for those problems are defined.

Notes
-----

The same code should work also with a 3D (box) mesh, but a very fine mesh would
be required. Also in the 2D case, finer mesh and/or higher approximation order
means higher accuracy.

Try changing C, F and L parameters in ``meshes/quantum/square.geo`` and

regenerate the mesh using gmsh::

gmsh -2 -format mesh meshes/quantum/square.geo -o meshes/quantum/square.mesh

./script/convert_mesh.py -2 meshes/quantum/square.mesh meshes/quantum/square.mesh

The ``script/convert_mesh.py`` call makes the mesh planar, as gmsh saves 2D

medit meshes including the zero z coordinates.

Also try changing approximation order ('approx_order') of the field below.

Usage Examples
--------------

The following examples are available and can be run using the `simple.py`
script::

python simple.py sfepy/examples/quantum/boron.py

python simple.py sfepy/examples/quantum/hydrogen.py
python simple.py sfepy/examples/quantum/oscillator.py
python simple.py sfepy/examples/quantum/well.py
"""
from __future__ import absolute_import
from sfepy.base.base import output
from sfepy import data_dir

def common(fun_v, get_exact=None, n_eigs=5, tau=0.0):

def report_eigs(pb, evp):

from numpy import NaN

bounding_box = pb.domain.mesh.get_bounding_box()
box_size = bounding_box[1][0] - bounding_box[0][0]
output('box_size: %f ' % box_size)
output('eigenvalues:')

if get_exact is not None:

eeigs = get_exact(n_eigs, box_size, pb.domain.shape.dim)
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output('n exact FEM error')

for ie, eig in enumerate(evp.eigs):
if ie < len(eeigs):
exact = eeigs[ie]
err = 100*abs((exact - eig)/exact)
else:
exact = NaN
err = NaN
output('%d: %.8f %.8f %7.4f %% ' % (ie, exact, eig, err))

else:
output('n FEM')
for ie, eig in enumerate(evp.eigs):
output('%d: %.8f ' % (ie, eig))

filename_mesh = data_dir + '/meshes/quantum/square.mesh'

options = {
'n_eigs' : n_eigs,
'eigs_only' : False,
'post_process_hook_final' : 'report_eigs',

'evps' : 'eig',
}

regions = {
'Omega' : 'all',
'Surface' : ('vertices of surface', 'facet'),
}

materials = {
'm' : ({'val' : 0.5},),
'mat_v' : 'fun_v',
}

functions = {
'fun_v' : (fun_v,),
}

approx_order = 2
fields = {
'field_Psi' : ('real', 'scalar', 'Omega', approx_order),
}

variables = {
'Psi' : ('unknown field', 'field_Psi', 0),
'v' : ('test field', 'field_Psi', 'Psi'),
}

ebcs = {
'ZeroSurface' : ('Surface', {'Psi.0' : 0.0}),
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}

integrals = {
'i' : 2 * approx_order,
}

equations = {
'lhs' : """dw_laplace.i.Omega(m.val, v, Psi)
+ dw_dot.i.Omega(mat_v.V, v, Psi)""",
'rhs' : """dw_dot.i.Omega(v, Psi)""",
}

solvers = {
'eig' : ('eig.scipy', {
'method' : 'eigsh',
'tol' : 1e-10,
'maxiter' : 150,

# Compute the eigenvalues near tau using the shift-invert mode.

'which' : 'LM',
'sigma' : tau,
}),
}

return locals()

quantum/well.py

Description
Quantum potential well.
See quantum/quantum_common.py.

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source code

"""
Quantum potential well.

See :ref:`quantum-quantum_common`.
"""
from __future__ import absolute_import

from sfepy.examples.quantum.quantum_common import common

def get_exact(n_eigs, box_size, dim):

from numpy import pi

if dim == 2:
eigs = [pi**2/(2*box_size**2)*x
for x in [2, 5, 5, 8, 10, 10, 13, 13, 17, 17, 18, 20, 20]]

elif dim == 3:
eigs = [pi**2/(2*box_size**2)*x
for x in [3, 6, 6, 6, 9, 9, 9, 11, 11, 11,
12, 14, 14, 14, 14, 14, 14, 17, 17, 17]]

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return eigs

def fun_v(ts, coor, mode=None, **kwargs):

from numpy import zeros_like

if not mode == 'qp': return

out = {}
val = zeros_like(coor[:,0])

val.shape = (val.shape[0], 1, 1)
out['V'] = val
return out

def define(n_eigs=10, tau=0.0):

l = common(fun_v, get_exact=get_exact, n_eigs=n_eigs, tau=tau)
return l

1.5.7 Example Applications

• Two-scale numerical simulation of a large deforming fluid-saturated porous structure (2021)

• Homogenization of the vibro-acoustic transmission on perforated plates with embedded resonators (2021)
• Multiscale numerical modelling of perfusion in deformable double porous media described by the Biot-Darcy-
Brinkman model (2020)
• Homogenization of piezoelectric porous media (2020)
• Numerical simulation of viscous flow in deformable double porous media (2020)
• Numerical simulations of large-deforming fluid-saturated porous media using an Eulerian incremental formula-
tion (2017)
• Fish heart model (2010)
• Phononic materials (2010)
Note that older examples do not reflect the current state of SfePy.

1.6 Useful Code Snippets and FAQ

1.6.1 Miscellaneous

1. No module named 'sfepy.discrete.common.extmods.mappings'.

When installing SfePy from sources or using the git version, its extension modules have to be compiled before
using the package, see Compilation of C Extension Modules.
2. The extension modules are compiled in place, but ModuleNotFoundError: No module named 'sfepy'
shows up when running some interactive examples/scripts/modules from the SfePy source directory.
On some platforms the current directory is not in the sys.path directory list. Add it using:

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export PYTHONPATH=.

or add the following code prior to sfepy imports into the module:

import sys
sys.path.append('.')

3. Finite element approximation (field) order and numerical quadrature order.

SfePy supports reading only straight-facet (linear approximation) meshes, nevertheless field orders higher than
one can be used, because internally, the mesh elements are enriched with the required additional nodes. The
calculation then occurs on such an augmented mesh with appropriate higher order elements.
The quadrature order equal to two-times the field order (used in many examples) works well for bilinear forms
with constant (on each element) material parameters. For example, a dot product involves integrating u * v, so
if the approximation order of u and v is 1, their product’s order is 2. Of course, there are terms that could use
a lower quadrature order, or higher, depending on the data. Increased quadrature order is required e.g. in terms
with highly oscillating material coefficients.
Example:

approx_order = 2
# The finite element approximation order.
fields = {
'displacement': ('real', 3, 'Omega', approx_order),
}
# The numerical quadrature order.
integrals = {
'i' : 2 * approx_order,
}

4. Higher order DOF visualization when using an approximation order greater than one.
By default, the additional, higher order DOFs, are not used in the VTK/HDF5 results files ('strip' lineariza-
tion kind). To see the influence of those DOFs, 'adaptive' linearization has to be used, see diffusion/sinbc.py
(declarative API) and diffusion/laplace_refine_interactive.py or multi_physics/biot_parallel_interactive.py (im-
perative API, search linearization).
5. Numbering of DOFs.
Locally (in a connectivity row), the DOFs are stored DOF-by-DOF (u_0 in all local nodes, u_1 in all local nodes,
. . . ).
Globally (in a state vector), the DOFs are stored node-by-node (u_0, u_1, ..., u_X in node 0, u_0, u_1,
..., u_X in node 1, . . . ).
See also create_adof_conn().
6. Visualization of various FEM-related information.
• Quadrature rules:

python3 script/plot_quadratures.py

• Facet orientations - run in the source code directory and make sure the current directory is in the Python’s
path list (see Miscellaneous):

python3 sfepy/postprocess/plot_facets.py

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• Global and local numberings of mesh topological entities (cells, faces, edges, vertices):

python3 script/plot_mesh.py meshes/elements/2_4_2.mesh

The global numbers serve as indices into connectivities. In the plot, the global numbers are on the entities,
the cell-local ones are inside the cells next to each entity towards the cell centroids.
7. How to work with solvers/preconditioners?
See multi_physics/biot_short_syntax.py (user-defined preconditioners) or navier_stokes/stokes_slip_bc.py (petsc
solver setup).
8. How to get the linear system components: the matrix and the right-hand side?
To get the residual vector r (see Implementation of Essential Boundary Conditions) and the tangent matrix K,
the imperative API can be used as follows:

# pb is a Problem instance,
pb.set_bcs(ebcs=Conditions([...])) # Set Dirichlet boundary conditions.
pb.set_ics(Conditions([...])) # Set initial conditions (if any).
variables = pb.get_initial_state()
pb.time_update()
variables.apply_ebc()
r = pb.equations.eval_residuals(variables())
K = pb.equations.eval_tangent_matrices(variables(), pb.mtx_a)

See also diffusion/poisson_parallel_interactive.py.

9. Where is the code that calculates the element (e.g. stiffness) matrix?
The code that computes the per element residuals and matrices is organized in terms, see Term Overview - click
on the term class name and then “source” link to see the code. The original terms are implemented in C, newer
terms tend to be implemented directly in Python. The structure and attributes of a term class are described in
How to Implement a New Term.
10. What structural elements (beams, shells, etc.) are available in SfePy?
The code is currently focused on solid elements. The only supported structural element is shell10x, see lin-
ear_elasticity/shell10x_cantilever.py.

1.6.2 Mesh-Related Tasks

1. Checking and fixing a mesh (double vertices, disconnected components, etc.).

• Show the mesh Euler characteristic, number of components and other information:

python3 script/show_mesh_info.py -d cylinder.mesh

• Fix double/disconnected vertices:

python3 script/convert_mesh.py -m bad.mesh maybe-good.mesh

2. Convert a mesh to another format (as supported by meshio).

• Simple conversion:

python3 script/convert_mesh.py mesh.format1 mesh.format2

• Scaling the mesh anisotropically:

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python3 script/convert_mesh.py -s 2,4,3 cylinder.mesh cylinder-scaled.mesh

3. Verify that regions are correctly defined.

• Using the problem description files (declarative API):

python3 simple.py sfepy/examples/diffusion/poisson_short_syntax.py --save-

˓→regions-as-groups --solve-not

python3 resview.py -e cylinder_regions.vtk

• In a script (imperative API):

problem.save_regions_as_groups('regions')

4. Remove lower-dimensional entities from a mesh (e.g. edges).

Use script/convert_mesh.py with the -d <dimension> option, where <dimension> is the topological
dimension of cells that should be in the mesh. For example, -d 2 stores only the 2D cells.
5. It is suggested to use msh22 format instead of the default msh4 when generating a mesh with gmsh:

gmsh -2 cylinder.geo -o cylinder.msh -format msh22

msh22 seems to be more reliable and foolproof when converting.

1.6.3 Regions

1. How to define a region using a function of coordinates in the interactive mode (imperative API)?
Examples:
• A facet region defined using a function of mesh vertex coordinates:

from sfepy.discrete import Function, Functions

def _get_region(coors, domain=None):

ii = np.nonzero(coors[:,0] < 0.5)[0]
return ii

get_region = Function('get_region', _get_region)

region = domain.create_region(
'Region', 'vertices by get_region', 'facet',
functions=Functions([get_region]),
)

• Analogously a cell region defined using the coordinates of cell centroids:

# ...
region = domain.create_region(
'Region', 'cells by get_region', 'cell',
functions=Functions([get_region]),
)

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1.6.4 Material Parameters

1. How to set material parameters per region in the interactive mode (imperative API)?
Example: define rho, D to have different values in regions omega1, omega2:

m = Material('m', values={'rho': {'omega1': 2700, 'omega2': 6000},

'D': {'omega1': D1, 'omega2': D2}})

2. How to implement state dependent materials?

Besides writing a custom solver, one can use pseudo-time-stepping for this purpose, as demonstrated in lin-
ear_elasticity/material_nonlinearity.py or diffusion/poisson_field_dependent_material.py. Note that the exam-
ples are contrived, and in practice care must be taken to ensure convergence.
3. Why are results of a 2D elasticity simulation not consistent with a properly constrained 3D elasticity simulation?
Possible reason: when using the Young’s modulus and Poisson’s ratio as input parameters, and then calling
stiffness_from_youngpoisson(), note that the default value of the plane argument is 'strain', corre-
sponding to the plane strain assumption, see also lame_from_youngpoisson(). Try setting plane='stress'.
4. How to set (time-dependent) material parameters by a function in the interactive mode (imperative API)?
Example (also showing the full material function signature):

from sfepy.discrete import Material, Function

def get_pars(ts, coors, mode=None,

equations=None, term=None, problem=None, **kwargs):
value1 = a_function(ts.t, coors)
value2 = another_function(ts.step, coors)
if mode == 'qp':
out = {
'value1' : value1.reshape(coors.shape[0], 1, 1),
'value2' : value2.reshape(coors.shape[0], 1, 1),
}
return out
m = Material('m', function=Function('get_pars', get_pars))

5. How to get cells corresponding to coordinates in a material function?

The full signature of the material function is:

def get_pars(ts, coors, mode=None,

equations=None, term=None, problem=None, **kwargs)

Thus it has access to term.region.cells, hence access to the cells that correspond to the coordinates. The
length of the coors is n_cell * n_qp, where n_qp is the number of quadrature points per cell, and n_cell =
len(term.region.cells), so that coors.reshape((n_cell, n_qp, -1)) can be used.

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1.7 Theoretical Background

This part introduces parts the theoretical mathematical background necessary to use SfePy effectively. It also discusses
some implementation choices done in SfePy.
Contents:

1.7.1 Notes on solving PDEs by the Finite Element Method

The Finite Element Method (FEM) is the numerical method for solving Partial Differential Equations (PDEs). FEM
was developed in the middle of XX. century and now it is widely used in different areas of science and engineering,
including mechanical and structural design, biomedicine, electrical and power design, fluid dynamics and other. FEM
is based on a very elegant mathematical theory of weak solution of PDEs. In this section we will briefly discuss basic
ideas underlying FEM.

Strong form of Poisson’s equation and its integration

Let us start our discussion about FEM with the strong form of Poisson’s equation

∆𝑇 = 𝑓 (𝑥), 𝑥 ∈ Ω, (1.11)

𝑇 = 𝑢(𝑥), 𝑥 ∈ Γ𝐷 , (1.12)

∇𝑇 · n = 𝑔(𝑥), 𝑥 ∈ Γ𝑁 , (1.13)
where Ω ⊂ R𝑛 is the solution domain with the boundary 𝜕Ω, Γ𝐷 is the part of the boundary where Dirichlet boundary
conditions are given, Γ𝑁 is the part of the boundary where Neumann boundary conditions are given, 𝑇 (𝑥) is the
unknown function to be found, 𝑓 (𝑥), 𝑢(𝑥), 𝑔(𝑥) are known functions.
FEM is based on a weak formulation. The weak form of the equation (1.11) is
∫︁
(∆𝑇 − 𝑓 ) · 𝑠 dΩ = 0,
Ω

where 𝑠 is a test function. Integrating this equation by parts

∫︁ ∫︁ ∫︁
0 = (∆𝑇 − 𝑓 ) · 𝑠 dΩ = ∇ · (∇𝑇 ) · 𝑠 dΩ − 𝑓 · 𝑠 dΩ =
Ω
Ω Ω
∫︁ ∫︁ ∫︁
=− ∇𝑇 · ∇𝑠 dΩ + ∇ · (∇𝑇 · 𝑠) dΩ − 𝑓 · 𝑠 dΩ
Ω Ω Ω

and applying Gauss theorem we obtain:

∫︁ ∫︁ ∫︁
0 = − ∇𝑇 · ∇𝑠 dΩ + 𝑠 · (∇𝑇 · n) dΓ − 𝑓 · 𝑠 dΩ
Ω Γ𝐷 ∪Γ𝑁 Ω

or
∫︁ ∫︁ ∫︁
∇𝑇 · ∇𝑠 dΩ = 𝑠 · (∇𝑇 · n) dΓ − 𝑓 · 𝑠 dΩ.
Ω Γ𝐷 ∪Γ𝑁 Ω

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The surface integral term can be split into two integrals, one over the Dirichlet part of the surface and second over the
Neumann part
∫︁ ∫︁ ∫︁ ∫︁
∇𝑇 · ∇𝑠 dΩ = 𝑠 · (∇𝑇 · n) dΓ + 𝑠 · (∇𝑇 · n) dΓ − 𝑓 · 𝑠 dΩ. (1.14)
Ω Γ𝐷 Γ𝑁 Ω

The equation (1.14) is the initial weak form of the Poisson’s problem (1.11)–(1.13). But we can not work with it without
applying the boundary conditions. So it is time to talk about the boundary conditions.

Dirichlet Boundary Conditions

On the Dirichlet part of the surface we have two restrictions. One is the Dirichlet boundary conditions 𝑇 (𝑥) = 𝑢(𝑥)
as they are, and the second is the integral term over Γ𝐷 in equation (1.14). To be consistent we have to use only the
Dirichlet conditions and avoid the integral term. To implement this we can take the function 𝑇 ∈ 𝑉 (Ω) and the test
function 𝑠 ∈ 𝑉0 (Ω), where

𝑉 (Ω) = {𝑣(𝑥) ∈ 𝐻 1 (Ω)},

𝑉0 (Ω) = {𝑣(𝑥) ∈ 𝐻 1 (Ω); 𝑣(𝑥) = 0, 𝑥 ∈ Γ𝐷 }.

In other words the unknown function 𝑇 must be continuous together with its gradient in the domain. In contrast the
test function 𝑠 must be also continuous together with its gradient in the domain but it should be zero on the surface Γ𝐷 .
With this requirement the integral term over Dirichlet part of the surface is vanishing and the weak form of the Poisson
equation for 𝑇 ∈ 𝑉 (Ω) and 𝑠 ∈ 𝑉0 (Ω) becomes
∫︁ ∫︁ ∫︁
∇𝑇 · ∇𝑠 dΩ = 𝑠 · (∇𝑇 · n) dΓ − 𝑓 · 𝑠 dΩ,
Ω Γ𝑁 Ω

𝑇 (𝑥) = 𝑢(𝑥), 𝑥 ∈ Γ𝐷 .

That is why Dirichlet conditions in FEM terminology are called Essential Boundary Conditions. These conditions
are not a part of the weak form and they are used as they are.

Neumann Boundary Conditions

The Neumann boundary conditions correspond to the known flux 𝑔(𝑥) = ∇𝑇 · n. The integral term over the Neumann
surface in the equation (1.14) contains exactly the same flux. So we can use the known function 𝑔(𝑥) in the integral
term:
∫︁ ∫︁ ∫︁
∇𝑇 · ∇𝑠 dΩ = 𝑔 · 𝑠 dΓ − 𝑓 · 𝑠 dΩ,
Ω Γ𝑁 Ω

where test function 𝑠 also belongs to the space 𝑉0 .

That is why Neumann conditions in FEM terminology are called Natural Boundary Conditions. These conditions
are a part of weak form terms.

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The weak form of the Poisson’s equation

Now we can write the resulting weak form for the Poisson’s problem (1.11)–(1.13). For any test function 𝑠 ∈ 𝑉0 (Ω)
find 𝑇 ∈ 𝑉 (Ω) such that
∫︁ ∫︁ ∫︁
∇𝑇 · ∇𝑠 dΩ = 𝑔 · 𝑠 dΓ − 𝑓 · 𝑠 dΩ, and
Ω Γ𝑁 Ω (1.15)
𝑇 (𝑥) = 𝑢(𝑥), 𝑥 ∈ Γ𝐷 .

Discussion of discretization and meshing

It is planned to have an example of the discretization based on the Poisson’s equation weak form (1.15). For now, please
refer to the wikipedia page Finite Element Method for a basic description of the disretization and meshing.

Numerical solution of the problem

To solve numerically given problem based on the weak form (1.15) we have to go through 5 steps:
1. Define geometry of the domain Ω and surfaces Γ𝐷 and Γ𝑁 .
2. Define the known functions 𝑓 , 𝑢 and 𝑔.
3. Define the unknown function 𝑇 and the test functions 𝑠.
4. Define essential boundary conditions (Dirichlet conditions) 𝑇 (𝑥) = 𝑢(𝑥), 𝑥 ∈ Γ𝐷 .
5. Define equation and natural boundary conditions (Neumann conditions) as the set of all integral terms ∇𝑇 ·
∫︀
∫︀ ∫︀ Ω
∇𝑠 dΩ, 𝑔 · 𝑠 dΓ, 𝑓 · 𝑠 dΩ.
Γ𝑁 Ω

1.7.2 Implementation of Essential Boundary Conditions

The essential boundary conditions can be applied in several ways. Here we describe the implementation used in SfePy.

Motivation

Let us solve a linear system 𝐴𝑥 = 𝑏 with 𝑛 × 𝑛 matrix 𝐴 with 𝑛𝑓 values in the 𝑥 vector known. The known values can
be for example EBC values on a boundary, if 𝐴 comes from a PDE discretization. If we put the known fixed values into
a vector 𝑥𝑓 , that has the same size as 𝑥, and has zeros in positions that are not fixed, we can easily construct a 𝑛 × 𝑛𝑟
matrix 𝑇 that maps the reduced vector 𝑥𝑟 of size 𝑛𝑟 = 𝑛 − 𝑛𝑓 , where the fixed values are removed, to the full vector
𝑥:
𝑥 = 𝑇 𝑥𝑟 + 𝑥𝑓 .
With that the reduced linear system with a 𝑛𝑟 × 𝑛𝑟 can be formed:
𝑇 𝑇 𝐴𝑇 𝑥𝑟 = 𝑇 𝑇 (𝑏 − 𝐴𝑥𝑓 )
that can be solved by a linear solver. We can see, that the (non-zero) known values are now on the right-hand side of
the linear system. When the known values are all zero, we have simply
𝑇 𝑇 𝐴𝑇 𝑥𝑟 = 𝑇 𝑇 𝑏 ,
which is convenient, as it allows simply throwing away the A and b entries corresponding to the known values already
during the finite element assembling.

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Implementation

All PDEs in SfePy are solved in a uniform way as a system of non-linear equations

𝑓 (𝑢) = 0 ,

where 𝑓 is the nonlinear function and 𝑢 the vector of unknown DOFs. This system is solved iteratively by the Newton
method
d𝑓 −1
𝑢𝑛𝑒𝑤 = 𝑢𝑜𝑙𝑑 − ( ) 𝑓 (𝑢𝑜𝑙𝑑 )
d𝑢𝑜𝑙𝑑
until a convergence criterion is met. Each iteration involves solution of the system of linear equations

𝐾∆𝑢 = 𝑟 ,

where the tangent matrix 𝐾 and the residual 𝑟 are

d𝑓
𝐾≡ ,
d𝑢𝑜𝑙𝑑
𝑟 ≡ 𝑓 (𝑢𝑜𝑙𝑑 ) .

Then

𝑢𝑛𝑒𝑤 = 𝑢𝑜𝑙𝑑 − ∆𝑢 .

If the initial (old) vector 𝑢𝑜𝑙𝑑 contains the values of EBCs at correct positions, the increment ∆𝑢 is zero at those
positions. This allows us to assemble directly the reduced matrix 𝑇 𝑇 𝐾𝑇 , the right-hand side 𝑇 𝑇 𝑟, and ignore the
values of EBCs during assembling. The EBCs are satisfied automatically by applying them to the initial guess 𝑢0 , that
is given to the Newton solver.

Linear Problems

For linear problems we have

𝑓 (𝑢) ≡ 𝐴𝑢 − 𝑏 = 0 ,
d𝑓
=𝐴,
d𝑢
and so the Newton method converges in a single iteration:

𝑢𝑛𝑒𝑤 = 𝑢𝑜𝑙𝑑 − 𝐴−1 (𝐴𝑢𝑜𝑙𝑑 − 𝑏) = 𝐴−1 𝑏 .

Evaluation of Residual and Tangent Matrix

The evaluation of the residual 𝑓 as well as the tangent matrix 𝐾 within the Newton solver proceeds in the following
steps:
• The EBCs are applied to the full DOF vector 𝑢.
• The reduced vector 𝑢𝑟 is passed to the Newton solver.
• Newton iteration loop:
– Evaluation of 𝑓𝑟 or 𝐾𝑟 :
1. 𝑢 is reconstructed from 𝑢𝑟 ;

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2. local element contributions are evaluated using 𝑢;

3. local element contributions are assembled into 𝑓𝑟 or 𝐾𝑟 - values corresponding to fixed DOF positions
are thrown away.
– The reduced system 𝐾𝑟 ∆𝑢𝑟 = 𝑟𝑟 is solved.
– Solution is updated: 𝑢𝑟 ← 𝑢𝑟 − ∆𝑢𝑟 .
– The loop is terminated if a stopping condition is satisfied, the solver returns the final 𝑢𝑟 .
• The final 𝑢 is reconstructed from 𝑢𝑟 .

1.8 Term Overview

1.8.1 Term Syntax

In general, the syntax of a term call is:

<term name>.<i>.<r>( <arg1>, <arg2>, ... ),
where <i> denotes an integral name (i.e. a name of numerical quadrature to use) and <r> marks a region (domain of
the integral).
The following notation is used:

Table 1: Notation.
symbol meaning
Ω volume (sub)domain
Γ surface (sub)domain
𝒟 volume or surface (sub)domain
𝑑 dimension of space
𝑡 time
𝑦 any function
𝑦 any vector function
𝑛 unit outward normal
𝑞, 𝑠 scalar test or parameter function
𝑝, 𝑟 scalar unknown or parameter function
𝑝¯ scalar parameter function
𝑣 vector test or parameter function
𝑤, 𝑢 vector unknown or parameter function
𝑏 vector parameter function
𝑒(𝑢) Cauchy strain tensor ( 21 ((∇𝑢) + (∇𝑢)𝑇 ))
𝐹 deformation gradient 𝐹𝑖𝑗 = 𝜕𝑋 𝜕𝑥𝑖
𝑗
𝐽 det(𝐹 )
𝐶 right Cauchy-Green deformation tensor 𝐶 = 𝐹 𝑇 𝐹
𝜕𝑢
𝐸(𝑢) Green strain tensor 𝐸𝑖𝑗 = 21 ( 𝜕𝑋
𝜕𝑢𝑖
𝑗
+ 𝜕𝑋𝑗𝑖 + 𝜕𝑢 𝑚 𝜕𝑢𝑚
𝜕𝑋𝑖 𝜕𝑋𝑗 )
𝑆 second Piola-Kirchhoff stress tensor
𝑓 vector volume forces
𝑓 scalar volume force (source)
𝜌 density
𝜈 kinematic viscosity
𝑐 any constant
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symbol meaning
𝛿𝑖𝑗 , 𝐼 Kronecker delta, identity matrix
∑︀𝑑
tr ∙ trace of a second order tensor ( 𝑖=1 ∙𝑖𝑖 )
dev ∙ deviator of a second order tensor (∙ − 𝑑1 tr ∙)
𝑇𝐾 ∈ 𝒯ℎ 𝐾-th element of triangulation (= mesh) 𝒯ℎ of domain Ω
𝐾 ← ℐℎ 𝐾 is assigned values from {0, 1, . . . , 𝑁ℎ − 1} ≡ ℐℎ in ascending order

The suffix “0 ” denotes a quantity related to a previous time step.

Term names are (usually) prefixed according to the following conventions:

Table 2: Term name prefixes.

pre- meaning evaluation modes meaning
fix
dw discrete weak ‘weak’ terms having a virtual (test) argument and zero or more
unknown arguments, used for FE assembling
ev evaluate ‘eval’, ‘el_eval’, ‘el_avg’, terms having all arguments known, modes ‘el_avg’, ‘qp’
‘qp’ are not supported by all ev_ terms
de discrete einsum any (work in progress) multi-linear terms defined using an enriched einsum no-
tation

1.8.2 Term Table

Below we list all the terms available in automatically generated tables. The first column lists the name, the second
column the argument lists and the third column the mathematical definition of each term. The terms are devided into
the following tables:
• Table of basic terms
• Table of large deformation terms (total/updated Lagrangian formulation)
• Table of sensitivity terms
• Table of special terms
• Table of multi-linear terms
The notation <virtual> corresponds to a test function, <state> to a unknown function and <parameter> to a known
function. By <material> we denote material (constitutive) parameters, or, in general, any given function of space and
time that parameterizes a term, for example a given traction force vector.

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Table of basic terms

Table 3: Basic terms

name/class argu- definition examples
ments
dw_advect_div_free <material>, tim.adv.dif
AdvectDivFreeTerm <virtual>, ∫︁ ∫︁
<state> ∇ · (𝑦𝑝)𝑞 = ((∇ · 𝑦) +𝑦 · ∇)𝑝)𝑞
Ω Ω ⏟ ⏞
≡0

dw_bc_newton <material_1>,
BCNewtonTerm <material_2>, ∫︁
<virtual>, 𝛼𝑞(𝑝 − 𝑝outer )
<state> Γ

dw_biot <material>, bio.npb, the.ela,

BiotTerm <virtual/ ∫︁ ∫︁ bio.npb.lag,
param_v>, 𝑝 𝛼𝑖𝑗 𝑒𝑖𝑗 (𝑣) , 𝑞 𝛼𝑖𝑗 𝑒𝑖𝑗 (𝑢) bio.sho.syn,
<state/ Ω Ω the.ela.ess, bio
param_s>
<material>,
<state>,
<virtual>
ev_biot_stress <material>,
BiotStressTerm <parameter> ∫︁
− 𝛼𝑖𝑗 𝑝¯
Ω
∫︁ ∫︁
vector for 𝐾 ← ℐℎ : − 𝛼𝑖𝑗 𝑝¯/ 1
𝑇𝐾 𝑇𝐾

−𝛼𝑖𝑗 𝑝¯|𝑞𝑝

ev_cauchy_strain <parameter>
CauchyStrainTerm ∫︁
𝑒(𝑤)
𝒟
∫︁ ∫︁
vector for 𝐾 ← ℐℎ : 𝑒(𝑤)/ 1
𝑇𝐾 𝑇𝐾

𝑒(𝑤)|𝑞𝑝

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name/class argu- definition examples
ments
ev_cauchy_stress <material>,
CauchyStressTerm<parameter> ∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑘𝑙 (𝑤)
𝒟
∫︁ ∫︁
vector for 𝐾 ← ℐℎ : 𝐷𝑖𝑗𝑘𝑙 𝑒𝑘𝑙 (𝑤)/ 1
𝑇𝐾 𝑇𝐾

𝐷𝑖𝑗𝑘𝑙 𝑒𝑘𝑙 (𝑤)|𝑞𝑝

dw_contact <material>, two.bod.con

ContactTerm <virtual>, ∫︁
<state> 𝜀𝑁 ⟨𝑔𝑁 (𝑢)⟩𝑛𝑣
Γ𝑐

dw_contact_plane <material_f>, ela.con.pla

ContactPlaneTerm<material_n>, ∫︁
<material_a>, 𝑣 · 𝑓 (𝑑(𝑢))𝑛
<material_b>, Γ

<virtual>,
<state>
dw_contact_sphere <material_f>, ela.con.sph
ContactSphereTerm <material_c>, ∫︁
<material_r>, 𝑣 · 𝑓 (𝑑(𝑢))𝑛(𝑢)
<virtual>, Γ

<state>
dw_convect <virtual>, nav.sto,
ConvectTerm <state> ∫︁ nav.sto.iga,
((𝑢 · ∇)𝑢) · 𝑣 nav.sto
Ω

dw_convect_v_grad_s
<virtual>, poi.fun
ConvectVGradSTerm<state_v>, ∫︁
<state_s> 𝑞(𝑢 · ∇𝑝)
Ω

ev_def_grad <parameter>
DeformationGradientTerm
𝜕𝑥 𝜕𝑢
𝐹 = |𝑞𝑝 = 𝐼 + |𝑞𝑝 ,
𝜕𝑋 𝜕𝑋
𝑥 = 𝑋 + 𝑢 , 𝐽 = det (𝐹 )

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name/class argu- definition examples
ments
dw_dg_advect_laxfrie_flux
<opt_material>, adv.2D, adv.1D,
AdvectionDGFluxTerm
<material_advelo>, ∫︁ adv.dif.2D
<virtual>, 𝑛 · 𝑓 * (𝑝𝑖𝑛 , 𝑝𝑜𝑢𝑡 )𝑞
<state> 𝜕𝑇𝐾

where
𝑝𝑖𝑛 + 𝑝𝑜𝑢𝑡 𝑝𝑖𝑛 − 𝑝𝑜𝑢𝑡
𝑓 * (𝑝𝑖𝑛 , 𝑝𝑜𝑢𝑡 ) = 𝑎 + (1 − 𝛼)𝑛𝐶 ,
2 2

dw_dg_diffusion_flux
<material>, adv.dif.2D,
DiffusionDGFluxTerm<state>, ∫︁ ∫︁ lap.2D, bur.2D
<virtual> 𝐷⟨∇𝑝⟩[𝑞] , 𝐷⟨∇𝑞⟩[𝑝]
<material>, 𝜕𝑇𝐾 𝜕𝑇𝐾

<virtual>, where
<state>
∇𝜑𝑖𝑛 + ∇𝜑𝑜𝑢𝑡
⟨∇𝜑⟩ =
2
[𝜑] = 𝜑𝑖𝑛 − 𝜑𝑜𝑢𝑡

dw_dg_interior_penalty
<material>, adv.dif.2D,
DiffusionInteriorPenaltyTerm
<material_Cw>, ∫︁ 2
lap.2D, bur.2D
<virtual>, ¯ 𝑤 𝑂𝑟𝑑 [𝑝][𝑞]
𝐷𝐶
<state> 𝜕𝑇𝐾 𝑑(𝜕𝑇𝐾 )

where

[𝜑] = 𝜑𝑖𝑛 − 𝜑𝑜𝑢𝑡

dw_dg_nonlinear_laxfrie_flux
<opt_material>, bur.2D
NonlinearHyperbolicDGFluxTerm
<fun>, ∫︁
<fun_d>, 𝑛 · 𝑓 * (𝑝𝑖𝑛 , 𝑝𝑜𝑢𝑡 )𝑞
<virtual>, 𝜕𝑇𝐾

<state> where
𝑓 (𝑝𝑖𝑛 ) + 𝑓 (𝑝𝑜𝑢𝑡 ) 𝑝𝑖𝑛 − 𝑝𝑜𝑢𝑡
𝑓 * (𝑝𝑖𝑛 , 𝑝𝑜𝑢𝑡 ) = + (1 − 𝛼)𝑛𝐶 ,
2 2

dw_diffusion <material>, bio.npb, poi.neu,

DiffusionTerm <virtual/ ∫︁ ∫︁ bio.npb.lag,
param_1>, 𝐾𝑖𝑗 ∇𝑖 𝑞∇𝑗 𝑝 , 𝐾𝑖𝑗 ∇𝑖 𝑝¯∇𝑗 𝑟 bio.sho.syn,
<state/ Ω Ω pie.ela,
param_2> dar.flo.mul,
bio
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name/class argu- definition examples
ments
dw_diffusion_coupling
<material>,
DiffusionCoupling <virtual/ ∫︁ ∫︁
param_1>, 𝑝𝐾𝑗 ∇𝑗 𝑞 , 𝑞𝐾𝑗 ∇𝑗 𝑝
<state/ Ω Ω

param_2>
<material>,
<state>,
<virtual>
dw_diffusion_r <material>,
DiffusionRTerm <virtual> ∫︁
𝐾𝑗 ∇𝑗 𝑞
Ω

ev_diffusion_velocity<material>,
DiffusionVelocityTerm<parameter> ∫︁
− 𝐾𝑖𝑗 ∇𝑗 𝑝¯
𝒟
∫︁ ∫︁
vector for 𝐾 ← ℐℎ : − 𝐾𝑖𝑗 ∇𝑗 𝑝¯/ 1
𝑇𝐾 𝑇𝐾

−𝐾𝑖𝑗 ∇𝑗 𝑝¯

ev_div <opt_material>,
DivTerm <parameter> ∫︁ ∫︁
∇·𝑢, 𝑐∇ · 𝑢
𝒟 𝒟
∫︁ ∫︁
vector for 𝐾 ← ℐℎ : ∇ · 𝑢/ 1
𝑇𝐾 𝑇𝐾

(∇ · 𝑢)|𝑞𝑝

dw_div <opt_material>,
DivOperatorTerm <virtual> ∫︁ ∫︁
∇ · 𝑣 or 𝑐∇ · 𝑣
Ω Ω

dw_div_grad <opt_material>, sto.sli.bc, nav.sto,

DivGradTerm <virtual/ ∫︁ ∫︁ sto, nav.sto,
param_1>, 𝜈 ∇𝑣 : ∇𝑢 , 𝜈 ∇𝑢 : ∇𝑤 nav.sto.iga,
<state/ Ω
∫︁ Ω
∫︁ sta.nav.sto
param_2> ∇𝑣 : ∇𝑢 , ∇𝑢 : ∇𝑤
Ω Ω

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name/class argu- definition examples
ments
dw_dot <opt_material>, sto.sli.bc,
DotProductTerm <virtual/ ∫︁ ∫︁ ∫︁ ∫︁ ∫︁ ∫︁ ∫︁ the.ele, aco,
param_1>, 𝑞𝑝 , 𝑣·𝑢, 𝑣 · 𝑛𝑝 , 𝑞𝑛 · 𝑢 , 𝑝𝑟 , 𝑢·𝑤, 𝑤 · 𝑛𝑝 bal, lin.ela.up,
<state/ 𝒟 𝒟 Γ
∫︁Γ ∫︁ 𝒟 𝒟
∫︁ ∫︁ Γ pie.ela,
param_2> 𝑐𝑞𝑝 , 𝑐𝑣 · 𝑢 , 𝑐𝑝𝑟 , 𝑐𝑢 · 𝑤 dar.flo.mul,
𝒟 𝒟 𝒟
∫︁ 𝒟 tim.poi.exp, hyd,
bor, tim.adv.dif ,
∫︁
𝑣·𝑀 ·𝑢, 𝑢·𝑀 ·𝑤
𝒟 𝒟 poi.fun,
lin.ela.dam,
bur.2D,
poi.per.bou.con,
wel, aco, osc, ela,
adv.2D, adv.1D,
vib.aco, tim.poi
dw_elastic_wave <material_1>,
ElasticWaveTerm <material_2>, ∫︁
<virtual>, 𝐷𝑖𝑗𝑘𝑙 𝑔𝑖𝑗 (𝑣)𝑔𝑘𝑙 (𝑢)
<state> Ω

dw_elastic_wave_cauchy
<material_1>,
ElasticWaveCauchyTerm
<material_2>, ∫︁ ∫︁
<virtual>, 𝐷𝑖𝑗𝑘𝑙 𝑔𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) , 𝐷𝑖𝑗𝑘𝑙 𝑔𝑖𝑗 (𝑢)𝑒𝑘𝑙 (𝑣)
<state> Ω Ω

<material_1>,
<material_2>,
<state>,
<virtual>
dw_electric_source <material>, the.ele
ElectricSourceTerm <virtual>, ∫︁
<parameter> 𝑐𝑠(∇𝜑)2
Ω

ev_grad <opt_material>,
GradTerm <parameter> ∫︁ ∫︁ ∫︁ ∫︁
∇𝑝 or ∇𝑤 , 𝑐∇𝑝 or 𝑐∇𝑤
𝒟 𝒟 𝒟 𝒟
∫︁ ∫︁ ∫︁ ∫︁
vector for 𝐾 ← ℐℎ : ∇𝑝/ 1 or ∇𝑤/ 1
𝑇𝐾 𝑇𝐾 𝑇𝐾 𝑇𝐾

(∇𝑝)|𝑞𝑝 or ∇𝑤|𝑞𝑝

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name/class argu- definition examples
ments
ev_integrate <opt_material>,
IntegrateTerm <parameter> ∫︁ ∫︁ ∫︁
𝑦, 𝑦, 𝑦·𝑛
∫︁ ∫︁ 𝒟 ∫︁𝒟 Γ

𝑐𝑦 , 𝑐𝑦 , 𝑐𝑦 · 𝑛 flux
𝒟 𝒟 Γ
∫︁ ∫︁ ∫︁ ∫︁ ∫︁ ∫︁
vector for 𝐾 ← ℐℎ : 𝑦/ 1, 𝑦/ 1, (𝑦 · 𝑛)/ 1
𝑇𝐾 𝑇𝐾 𝑇𝐾 𝑇 𝑇 𝑇
∫︁ ∫︁ ∫︁ ∫︁ 𝐾 ∫︁ 𝐾 ∫︁ 𝐾
vector for 𝐾 ← ℐℎ : 𝑐𝑦/ 1, 𝑐𝑦/ 1, (𝑐𝑦 · 𝑛)/ 1
𝑇𝐾 𝑇𝐾 𝑇𝐾 𝑇𝐾 𝑇𝐾 𝑇𝐾

𝑦|𝑞𝑝 , 𝑦|𝑞𝑝 , (𝑦 · 𝑛)|𝑞𝑝 flux

𝑐𝑦|𝑞𝑝 , 𝑐𝑦|𝑞𝑝 , (𝑐𝑦 · 𝑛)|𝑞𝑝 flux

dw_integrate <opt_material>, aco, aco,

IntegrateOperatorTerm
<virtual> ∫︁ ∫︁ poi.per.bou.con,
𝑞 or 𝑐𝑞 dar.flo.mul,
𝒟 𝒟 poi.neu, vib.aco

ev_integrate_mat <material>,
IntegrateMatTerm<parameter> ∫︁
𝑚
𝒟
∫︁ ∫︁
vector for 𝐾 ← ℐℎ : 𝑚/ 1
𝑇𝐾 𝑇𝐾

𝑚|𝑞𝑝

dw_jump <opt_material>, aco

SurfaceJumpTerm <virtual>, ∫︁
<state_1>, 𝑐 𝑞(𝑝1 − 𝑝2 )
<state_2> Γ

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name/class argu- definition examples
ments
dw_laplace <opt_material>, sto.sli.bc, the.ele,
LaplaceTerm <virtual/ ∫︁ ∫︁ aco, lap.flu.2d,
param_1>, 𝑐∇𝑞 · ∇𝑝 , 𝑝 · ∇𝑟
𝑐∇¯ sin, the.ela.ess,
<state/ Ω Ω tim.poi.exp, hyd,
param_2> bor, tim.adv.dif ,
poi.fun,
poi.iga, bur.2D,
poi.per.bou.con,
lap.tim.ebc,
lap.2D, wel,
aco, osc, cub,
poi.par.stu, poi,
lap.cou.lcb,
poi.sho.syn,
adv.dif.2D,
lap.1d,
poi.fie.dep.mat,
vib.aco, tim.poi
dw_lin_convect <virtual>, sta.nav.sto
LinearConvectTerm
<parameter>, ∫︁
<state> ((𝑏 · ∇)𝑢) · 𝑣
Ω

((𝑏 · ∇)𝑢)|𝑞𝑝

dw_lin_convect2 <material>,
LinearConvect2Term
<virtual>, ∫︁
<state> ((𝑏 · ∇)𝑢) · 𝑣
Ω

((𝑏 · ∇)𝑢)|𝑞𝑝

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name/class argu- definition examples
ments
dw_lin_elastic <material>, the.ela,
LinearElasticTerm
<virtual/ ∫︁ lin.ela.up, its.1,
param_1>, 𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) the.ela.ess,
<state/ Ω pie.ela,
param_2> pie.ela.mac,
com.ela.mat,
lin.ela.dam,
bio.npb.lag,
lin.ela.iga, bio,
bio.npb, its.2,
ela.con.pla, ela,
bio.sho.syn,
ela.shi.per,
mat.non,
pre.fib, nod.lcb,
ela.con.sph,
lin.ela,
lin.vis, its.4,
lin.ela.tra, its.3,
two.bod.con,
lin.ela.mM,
lin.ela.opt
dw_lin_elastic_iso <material_1>,
LinearElasticIsotropicTerm
<material_2>, ∫︁
<virtual/ 𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) with 𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙
param_1>, Ω

<state/
param_2>
dw_lin_prestress <material>, pre.fib,
LinearPrestressTerm<virtual/ ∫︁ pie.ela.mac,
param> 𝜎𝑖𝑗 𝑒𝑖𝑗 (𝑣) non.hyp.mM
Ω

dw_lin_strain_fib <material_1>, pre.fib

LinearStrainFiberTerm
<material_2>, ∫︁
<virtual> 𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣) (𝑑𝑘 𝑑𝑙 )
Ω

dw_non_penetration <opt_material>, bio.npb.lag

NonPenetrationTerm <virtual>, ∫︁ ∫︁
<state> 𝑐𝜆𝑛 · 𝑣 , ˆ ·𝑢
𝑐𝜆𝑛
<opt_material>, Γ Γ
∫︁ ∫︁
<state>, 𝜆𝑛 · 𝑣 , ˆ ·𝑢
𝜆𝑛
<virtual> Γ Γ

dw_non_penetration_p
<material>, bio.sho.syn
NonPenetrationPenaltyTerm
<virtual>, ∫︁
<state> 𝑐(𝑛 · 𝑣)(𝑛 · 𝑢)
Γ

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Table 3 – continued from previous page

name/class argu- definition examples
ments
dw_nonsym_elastic <material>, non.hyp.mM
NonsymElasticTerm <virtual/ ∫︁
param_1>, 𝐷∇𝑢 : ∇𝑣
<state/ Ω

param_2>
dw_ns_dot_grad_s <fun>, bur.2D
NonlinearScalarDotGradTerm
<fun_d>, ∫︁ ∫︁ ∫︁
<virtual>, 𝑞 · ∇ · 𝑓 (𝑝) = 𝑞 · div𝑓 (𝑝) , 𝑓 (𝑝) · ∇𝑞
<state> Ω Ω Ω

<fun>,
<fun_d>,
<state>,
<virtual>
dw_piezo_coupling <material>, pie.ela
PiezoCouplingTerm <virtual/ ∫︁ ∫︁
param_v>, 𝑔𝑘𝑖𝑗 𝑒𝑖𝑗 (𝑣)∇𝑘 𝑝 , 𝑔𝑘𝑖𝑗 𝑒𝑖𝑗 (𝑢)∇𝑘 𝑞
<state/ Ω Ω

param_s>
<material>,
<state>,
<virtual>
ev_piezo_strain <material>,
PiezoStrainTerm <parameter> ∫︁
𝑔𝑘𝑖𝑗 𝑒𝑖𝑗 (𝑢)
Ω

ev_piezo_stress <material>,
PiezoStressTerm <parameter> ∫︁
𝑔𝑘𝑖𝑗 ∇𝑘 𝑝
Ω

dw_point_load <material>, its.2, its.4, its.3,

ConcentratedPointLoadTerm
<virtual> she.can, its.1
𝑖
𝑓 𝑖 = 𝑓¯ ∀ FE node 𝑖 in a region

dw_point_lspring <material>,
LinearPointSpringTerm
<virtual>,
<state> 𝑓 𝑖 = −𝑘𝑢𝑖 ∀ FE node 𝑖 in a region

dw_s_dot_grad_i_s <material>,
ScalarDotGradIScalarTerm
<virtual>, ∫︁
<state> 𝑍𝑖 = 𝑞∇𝑖 𝑝
Ω

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Table 3 – continued from previous page

name/class argu- definition examples
ments
dw_s_dot_mgrad_s <material>, adv.2D, adv.1D,
ScalarDotMGradScalarTerm
<virtual>, ∫︁ ∫︁ adv.dif.2D
<state> 𝑞𝑦 · ∇𝑝 , 𝑝𝑦 · ∇𝑞
<material>, Ω Ω

<state>,
<virtual>
dw_shell10x <material_d>, she.can
Shell10XTerm <material_drill>, ∫︁
<virtual>, 𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢)
<state> Ω

dw_stokes <opt_material>, sto.sli.bc, nav.sto,

StokesTerm <virtual/ ∫︁ ∫︁ ∫︁ ∫︁ sto, lin.ela.up,
param_v>, 𝑝∇·𝑣, 𝑞 ∇ · 𝑢 or 𝑐𝑝∇·𝑣, 𝑐𝑞∇·𝑢 nav.sto,
<state/ Ω Ω Ω Ω nav.sto.iga,
param_s> sta.nav.sto
<opt_material>,
<state>,
<virtual>
dw_stokes_wave <material>,
StokesWaveTerm <virtual>, ∫︁
<state> (𝜅 · 𝑣)(𝜅 · 𝑢)
Ω

dw_stokes_wave_div<material>,
StokesWaveDivTerm <virtual>, ∫︁ ∫︁
<state> (𝜅 · 𝑣)(∇ · 𝑢) , (𝜅 · 𝑢)(∇ · 𝑣)
<material>, Ω Ω

<state>,
<virtual>
ev_sum_vals <parameter>
SumNodalValuesTerm
ev_surface_flux <material>,
SurfaceFluxTerm <parameter> ∫︁
𝑛 · 𝐾𝑖𝑗 ∇𝑗 𝑝¯
Γ
∫︁ ∫︁
vector for 𝐾 ← ℐℎ : 𝑛 · 𝐾𝑖𝑗 ∇𝑗 𝑝¯ / 1
𝑇𝐾 𝑇𝐾
∫︁
vector for 𝐾 ← ℐℎ : 𝑛 · 𝐾𝑖𝑗 ∇𝑗 𝑝¯
𝑇𝐾

dw_surface_flux <opt_material>,
SurfaceFluxOperatorTerm
<virtual>, ∫︁
<state> 𝑞𝑛 · 𝐾 · ∇𝑝
Γ

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Table 3 – continued from previous page

name/class argu- definition examples
ments
dw_surface_ltr <opt_material>, lin.vis,
LinearTractionTerm
<virtual/ ∫︁ ∫︁ com.ela.mat,
param> 𝑣 · 𝜎 · 𝑛, 𝑣 · 𝑛, lin.ela.tra,
Γ Γ ela.shi.per,
nod.lcb,
lin.ela.opt
ev_surface_moment <material>,
SurfaceMomentTerm <parameter> ∫︁
𝑛(𝑥 − 𝑥0 )
Γ

dw_surface_ndot <material>, lap.flu.2d

SufaceNormalDotTerm
<virtual/ ∫︁
param> 𝑞𝑐 · 𝑛
Γ

dw_v_dot_grad_s <opt_material>,
VectorDotGradScalarTerm
<virtual/ ∫︁ ∫︁
param_v>, 𝑣 · ∇𝑝 , 𝑢 · ∇𝑞
<state/ ∫︁ Ω ∫︁ Ω
param_s> 𝑐𝑣 · ∇𝑝 , 𝑐𝑢 · ∇𝑞
<opt_material>, ∫︁ Ω
∫︁ Ω
<state>,
𝑣 · (𝑀 ∇𝑝) , 𝑢 · (𝑀 ∇𝑞)
<virtual> Ω Ω

dw_vm_dot_s <material>,
VectorDotScalarTerm
<virtual/ ∫︁ ∫︁
param_v>, 𝑣 · 𝑚𝑝 , 𝑢 · 𝑚𝑞
<state/ Ω Ω

param_s>
<material>,
<state>,
<virtual>
ev_volume <parameter>
VolumeTerm ∫︁
1
𝒟

dw_volume_lvf <material>, poi.par.stu,

LinearVolumeForceTerm
<virtual> ∫︁ ∫︁ adv.dif.2D,
𝑓 · 𝑣 or 𝑓𝑞 bur.2D, poi.iga
Ω Ω

ev_volume_surface <parameter>
VolumeSurfaceTerm ∫︁
1/𝐷 𝑥·𝑛
Γ

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name/class argu- definition examples
ments
dw_zero <virtual>, ela
ZeroTerm <state>
0

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Table of sensitivity terms

Table 4: Sensitivity terms

name/class argu- definition examples
ments
dw_adj_convect1 <virtual>,
AdjConvect1Term <state>, ∫︁
<parameter> ((𝑣 · ∇)𝑢) · 𝑤
Ω

dw_adj_convect2 <virtual>,
AdjConvect2Term <state>, ∫︁
<parameter> ((𝑢 · ∇)𝑣) · 𝑤
Ω

dw_adj_div_grad <material_1>,
AdjDivGradTerm <material_2>,
<virtual>, 𝑤𝛿𝑢 Ψ(𝑢) ∘ 𝑣
<parameter>

ev_sd_convect <parameter_u>,
SDConvectTerm <parameter_w>, ∫︁
𝜕𝑢𝑖 𝜕𝒱𝑗 𝜕𝑢𝑖
<parameter_mv> [𝑢𝑘 𝑤𝑖 (∇ · 𝒱) − 𝑢𝑘 𝑤𝑖 ]
Ω 𝜕𝑥𝑘 𝜕𝑥𝑘 𝜕𝑥𝑗

ev_sd_diffusion <material>,
SDDiffusionTerm <parameter_q>, ∫︁
<parameter_p>, ˆ 𝑖𝑗 ∇𝑖 𝑞 ∇𝑗 𝑝
𝐾
<parameter_mv> Ω
(︂ )︂
ˆ 𝜕𝒱𝑗 𝜕𝒱𝑖
𝐾𝑖𝑗 = 𝐾𝑖𝑗 𝛿𝑖𝑘 𝛿𝑗𝑙 ∇ · 𝒱 − 𝛿𝑖𝑘 − 𝛿𝑗𝑙
𝜕𝑥𝑙 𝜕𝑥𝑘

de_sd_diffusion <material>,
ESDDiffusionTerm<virtual/ ∫︁
param_1>, ˆ 𝑖𝑗 ∇𝑖 𝑞 ∇𝑗 𝑝
𝐾
<state/ Ω

param_2>, (︂
𝜕𝒱𝑗 𝜕𝒱𝑖
)︂
<parameter_mv> ˆ
𝐾𝑖𝑗 = 𝐾𝑖𝑗 𝛿𝑖𝑘 𝛿𝑗𝑙 ∇ · 𝒱 − 𝛿𝑖𝑘 − 𝛿𝑗𝑙
𝜕𝑥𝑙 𝜕𝑥𝑘

ev_sd_div <parameter_u>,
SDDivTerm <parameter_p>, ∫︁
𝜕𝒱𝑘 𝜕𝑤𝑖
<parameter_mv> 𝑝[(∇ · 𝑤)(∇ · 𝒱) − ]
Ω 𝜕𝑥𝑖 𝜕𝑥𝑘

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Table 4 – continued from previous page

name/class argu- definition examples
ments
de_sd_div_grad <opt_material>,
ESDDivGradTerm <virtual/ ∫︁ ∫︁
param_1>, 𝐼∇𝑣 : ∇𝑢 ,
ˆ ˆ
𝜈 𝐼∇𝑣 : ∇𝑢
<state/ Ω Ω

param_2>, 𝜕𝒱𝑙 𝜕𝒱𝑘

<parameter_mv> 𝐼ˆ𝑖𝑗𝑘𝑙 = 𝛿𝑖𝑘 𝛿𝑗𝑙 ∇ · 𝒱 − 𝛿𝑖𝑘 𝛿𝑗𝑠 − 𝛿𝑖𝑠 𝛿𝑗𝑙
𝜕𝑥𝑠 𝜕𝑥𝑠

ev_sd_div_grad <opt_material>,
SDDivGradTerm <parameter_u>, ∫︁ ∫︁
<parameter_w>, ˆ
𝐼∇𝑣 : ∇𝑢 , ˆ
𝜈 𝐼∇𝑣 : ∇𝑢
<parameter_mv> Ω Ω

𝜕𝒱𝑙 𝜕𝒱𝑘
𝐼ˆ𝑖𝑗𝑘𝑙 = 𝛿𝑖𝑘 𝛿𝑗𝑙 ∇ · 𝒱 − 𝛿𝑖𝑘 𝛿𝑗𝑠 − 𝛿𝑖𝑠 𝛿𝑗𝑙
𝜕𝑥𝑠 𝜕𝑥𝑠

de_sd_dot <opt_material>,
ESDDotTerm <virtual/ ∫︁ ∫︁
param_1>, 𝑞𝑝(∇ · 𝒱) , (𝑣 · 𝑢)(∇ · 𝒱)
Ω
<state/ ∫︁ ∫︁ Ω
param_2>, 𝑐𝑞𝑝(∇ · 𝒱) , 𝑐(𝑣 · 𝑢)(∇ · 𝒱)
<parameter_mv> Ω
∫︁ Ω

𝑣 · (𝑀 𝑢)(∇ · 𝒱)
Ω

ev_sd_dot <parameter_1>,
SDDotTerm <parameter_2>, ∫︁ ∫︁
<parameter_mv> 𝑝𝑞(∇ · 𝒱) , (𝑢 · 𝑤)(∇ · 𝒱)
Ω Ω

de_sd_lin_elastic <material>,
ESDLinearElasticTerm
<virtual/ ∫︁
param_1>, ˆ 𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢)
𝐷
<state/ Ω

param_2>,
<parameter_mv> ˆ 𝑖𝑗𝑘𝑙 = 𝐷𝑖𝑗𝑘𝑙 (∇ · 𝒱) − 𝐷𝑖𝑗𝑘𝑞 𝜕𝒱𝑙 − 𝐷𝑖𝑞𝑘𝑙 𝜕𝒱𝑗
𝐷
𝜕𝑥𝑞 𝜕𝑥𝑞

ev_sd_lin_elastic <material>,
SDLinearElasticTerm
<parameter_w>, ∫︁
<parameter_u>, ˆ 𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢)
𝐷
<parameter_mv> Ω

ˆ 𝑖𝑗𝑘𝑙 = 𝐷𝑖𝑗𝑘𝑙 (∇ · 𝒱) − 𝐷𝑖𝑗𝑘𝑞 𝜕𝒱𝑙 − 𝐷𝑖𝑞𝑘𝑙 𝜕𝒱𝑗

𝐷
𝜕𝑥𝑞 𝜕𝑥𝑞

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Table 4 – continued from previous page

name/class argu- definition examples
ments
ev_sd_piezo_coupling
<material>,
SDPiezoCouplingTerm<parameter_u>, ∫︁
<parameter_p>, 𝑔ˆ𝑘𝑖𝑗 𝑒𝑖𝑗 (𝑢)∇𝑘 𝑝
<parameter_mv> Ω

𝜕𝒱𝑗 𝜕𝒱𝑘
𝑔ˆ𝑘𝑖𝑗 = 𝑔𝑘𝑖𝑗 (∇ · 𝒱) − 𝑔𝑘𝑖𝑙 − 𝑔𝑙𝑖𝑗
𝜕𝑥𝑙 𝜕𝑥𝑙

de_sd_piezo_coupling
<material>,
ESDPiezoCouplingTerm
<virtual/ ∫︁ ∫︁
param_v>, 𝑔ˆ𝑘𝑖𝑗 𝑒𝑖𝑗 (𝑣)∇𝑘 𝑝 , 𝑔ˆ𝑘𝑖𝑗 𝑒𝑖𝑗 (𝑢)∇𝑘 𝑞
<state/ Ω Ω

param_s>, 𝜕𝒱𝑗 𝜕𝒱𝑘

<parameter_mv> 𝑔ˆ𝑘𝑖𝑗 = 𝑔𝑘𝑖𝑗 (∇ · 𝒱) − 𝑔𝑘𝑖𝑙 − 𝑔𝑙𝑖𝑗
𝜕𝑥𝑙 𝜕𝑥𝑙
<material>,
<state>,
<virtual>,
<parameter_mv>
de_sd_stokes <opt_material>,
ESDStokesTerm <virtual/ ∫︁ ∫︁
𝜕𝑣𝑖 𝜕𝑢𝑖
param_v>, 𝑝 𝐼𝑖𝑗 , 𝑞 𝐼𝑖𝑗
<state/ Ω 𝜕𝑥𝑗 Ω 𝜕𝑥𝑗
param_s>, 𝜕𝒱𝑗
<parameter_mv> 𝐼ˆ𝑖𝑗 = 𝛿𝑖𝑗 ∇ · 𝒱 −
𝜕𝑥𝑖
<opt_material>,
<state>,
<virtual>,
<parameter_mv>
ev_sd_surface_integrate
<parameter>,
SDSufaceIntegrateTerm
<parameter_mv> ∫︁
𝑝∇ · 𝒱
Γ

de_sd_surface_ltr <opt_material>,
ESDLinearTractionTerm
<virtual/ ∫︁
[︀(︀ )︀ ]︀
param>, 𝑣· 𝜎ˆ∇·𝒱 −𝜎
ˆ ∇𝒱 𝑛
<parameter_mv> Γ

ˆ =𝐼 ,𝜎
𝜎 ˆ = 𝑐 𝐼 or 𝜎
ˆ=𝜎

ev_sd_surface_ltr <opt_material>,
SDLinearTractionTerm
<parameter>, ∫︁ ∫︁
<parameter_mv> 𝑣 · (𝜎 𝑛), 𝑣 · 𝑛,
Γ Γ

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Table of large deformation terms

Table 5: Large deformation terms

name/class argu- definition examples
ments
dw_tl_bulk_active <material>,
BulkActiveTLTerm<virtual>, ∫︁
<state> 𝑆𝑖𝑗 (𝑢)𝛿𝐸𝑖𝑗 (𝑢; 𝑣)
Ω

dw_tl_bulk_penalty <material>, act.fib, hyp,

BulkPenaltyTLTerm <virtual>, ∫︁ com.ela.mat
<state> 𝑆𝑖𝑗 (𝑢)𝛿𝐸𝑖𝑗 (𝑢; 𝑣)
Ω

dw_tl_bulk_pressure<virtual>, per.tl, bal

BulkPressureTLTerm <state>, ∫︁
<state_p> 𝑆𝑖𝑗 (𝑝)𝛿𝐸𝑖𝑗 (𝑢; 𝑣)
Ω

dw_tl_diffusion <material_1>, per.tl

DiffusionTLTerm <material_2>, ∫︁
𝜕𝑞 𝜕𝑝
<virtual>, 𝐾(𝑢(𝑛−1) ) :
<state>, Ω 𝜕𝑋 𝜕𝑋
<parameter>
dw_tl_fib_a <material_1>, act.fib
FibresActiveTLTerm
<material_2>, ∫︁
<material_3>, 𝑆𝑖𝑗 (𝑢)𝛿𝐸𝑖𝑗 (𝑢; 𝑣)
<material_4>, Ω

<material_5>,
<virtual>,
<state>
dw_tl_he_genyeoh <material>,
GenYeohTLTerm <virtual>, ∫︁
<state> 𝑆𝑖𝑗 (𝑢)𝛿𝐸𝑖𝑗 (𝑢; 𝑣)
Ω

dw_tl_he_mooney_rivlin
<material>, hyp, bal,
MooneyRivlinTLTerm
<virtual>, ∫︁ com.ela.mat
<state> 𝑆𝑖𝑗 (𝑢)𝛿𝐸𝑖𝑗 (𝑢; 𝑣)
Ω

dw_tl_he_neohook <material>, per.tl,

NeoHookeanTLTerm<virtual>, ∫︁ com.ela.mat,
<state> 𝑆𝑖𝑗 (𝑢)𝛿𝐸𝑖𝑗 (𝑢; 𝑣) act.fib, hyp, bal
Ω

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Table 5 – continued from previous page

name/class argu- definition examples
ments
dw_tl_he_ogden <material>,
OgdenTLTerm <virtual>, ∫︁
<state> 𝑆𝑖𝑗 (𝑢)𝛿𝐸𝑖𝑗 (𝑢; 𝑣)
Ω

dw_tl_membrane <material_a1>, bal

TLMembraneTerm <material_a2>,
<material_h0>,
<virtual>,
<state>
ev_tl_surface_flux <material_1>,
SurfaceFluxTLTerm <material_2>, ∫︁
𝜕𝑝
<parameter_1>, 𝜈 · 𝐾(𝑢(𝑛−1) )
<parameter_2> Γ 𝜕𝑋

dw_tl_surface_traction
<opt_material>, per.tl
SurfaceTractionTLTerm
<virtual>, ∫︁
<state> 𝜈 · 𝐹 −1 · 𝜎 · 𝑣𝐽
Γ

dw_tl_volume <virtual>, per.tl, bal

VolumeTLTerm <state> ∫︀
Ω
𝑞𝐽(𝑢)
volume mode: vector for 𝐾 ← ℐℎ : 𝑇𝐾 ∫︀𝐽(𝑢)
∫︀

rel_volume mode: vector for 𝐾 ← ℐℎ : 𝑇𝐾 𝐽(𝑢)/ 𝑇𝐾 1

∫︀

ev_tl_volume_surface
<parameter>
VolumeSurfaceTLTerm ∫︁
1/𝐷 𝜈 · 𝐹 −1 · 𝑥𝐽
Γ

dw_ul_bulk_penalty <material>, hyp.ul

BulkPenaltyULTerm <virtual>, ∫︁
<state> ℒ𝜏𝑖𝑗 (𝑢)𝑒𝑖𝑗 (𝛿𝑣)/𝐽
Ω

dw_ul_bulk_pressure<virtual>, hyp.ul.up
BulkPressureULTerm <state>, ∫︁
<state_p> ℒ𝜏𝑖𝑗 (𝑢)𝑒𝑖𝑗 (𝛿𝑣)/𝐽
Ω

dw_ul_compressible<material>, hyp.ul.up
CompressibilityULTerm
<virtual>, ∫︀
<state>, 1 Ω
<parameter_u> 𝛾𝑝 𝑞

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Table 5 – continued from previous page

name/class argu- definition examples
ments
dw_ul_he_mooney_rivlin
<material>, hyp.ul, hyp.ul.up
MooneyRivlinULTerm
<virtual>, ∫︁
<state> ℒ𝜏𝑖𝑗 (𝑢)𝑒𝑖𝑗 (𝛿𝑣)/𝐽
Ω

dw_ul_he_neohook <material>, hyp.ul, hyp.ul.up

NeoHookeanULTerm<virtual>, ∫︁
<state> ℒ𝜏𝑖𝑗 (𝑢)𝑒𝑖𝑗 (𝛿𝑣)/𝐽
Ω

dw_ul_volume <virtual>, hyp.ul.up

VolumeULTerm <state> ∫︀
Ω
𝑞𝐽(𝑢)
volume mode: vector for 𝐾 ← ℐℎ : 𝑇𝐾 ∫︀𝐽(𝑢)
∫︀

rel_volume mode: vector for 𝐾 ← ℐℎ : 𝑇𝐾 𝐽(𝑢)/ 𝑇𝐾 1

∫︀

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Table of special terms

Table 6: Special terms

name/class argu- definition examples
ments
dw_biot_eth <ts>,
BiotETHTerm <material_0>, ∫︀ [︁∫︀ 𝑡 ]︁
<material_1>, 𝛼 (𝑡 − 𝜏 ) 𝑝(𝜏 )) d𝜏 𝑒𝑖𝑗 (𝑣) ,
Ω [︁ 0 𝑖𝑗 ]︁
<virtual>, ∫︀ ∫︀ 𝑡
𝛼 (𝑡 − 𝜏 )𝑒 (𝑢(𝜏 )) d𝜏 𝑞
Ω 0 𝑖𝑗 𝑘𝑙
<state>
<ts>,
<material_0>,
<material_1>,
<state>,
<virtual>
dw_biot_th <ts>,
BiotTHTerm <material>, ∫︀ [︁∫︀ 𝑡 ]︁
<virtual>, 𝛼 (𝑡 − 𝜏 ) 𝑝(𝜏 )) d𝜏 𝑒𝑖𝑗 (𝑣) ,
Ω [︁ 0 𝑖𝑗 ]︁
<state> ∫︀ ∫︀ 𝑡
𝛼 (𝑡 − 𝜏 )𝑒 (𝑢(𝜏 )) d𝜏 𝑞
Ω 0 𝑖𝑗 𝑘𝑙
<ts>,
<material>,
<state>,
<virtual>
ev_cauchy_stress_eth<ts>,
CauchyStressETHTerm <material_0>, ∫︁ ∫︁ 𝑡
<material_1>, ℋ𝑖𝑗𝑘𝑙 (𝑡 − 𝜏 ) 𝑒𝑘𝑙 (𝑤(𝜏 )) d𝜏
<parameter> Ω 0
∫︁ ∫︁ 𝑡 ∫︁
vector for 𝐾 ← ℐℎ : ℋ𝑖𝑗𝑘𝑙 (𝑡 − 𝜏 ) 𝑒𝑘𝑙 (𝑤(𝜏 )) d𝜏 / 1
𝑇𝐾 0 𝑇𝐾
∫︁ 𝑡
ℋ𝑖𝑗𝑘𝑙 (𝑡 − 𝜏 ) 𝑒𝑘𝑙 (𝑤(𝜏 )) d𝜏 |𝑞𝑝
0

ev_cauchy_stress_th <ts>,
CauchyStressTHTerm <material>, ∫︁ ∫︁ 𝑡
<parameter> ℋ𝑖𝑗𝑘𝑙 (𝑡 − 𝜏 ) 𝑒𝑘𝑙 (𝑤(𝜏 )) d𝜏
Ω 0
∫︁ ∫︁ 𝑡 ∫︁
vector for 𝐾 ← ℐℎ : ℋ𝑖𝑗𝑘𝑙 (𝑡 − 𝜏 ) 𝑒𝑘𝑙 (𝑤(𝜏 )) d𝜏 / 1
𝑇𝐾 0 𝑇𝐾
∫︁ 𝑡
ℋ𝑖𝑗𝑘𝑙 (𝑡 − 𝜏 ) 𝑒𝑘𝑙 (𝑤(𝜏 )) d𝜏 |𝑞𝑝
0

dw_lin_elastic_eth <ts>, lin.vis

LinearElasticETHTerm
<material_0>, ∫︁ [︂∫︁ 𝑡 ]︂
<material_1>, ℋ𝑖𝑗𝑘𝑙 (𝑡 − 𝜏 ) 𝑒𝑘𝑙 (𝑢(𝜏 )) d𝜏 𝑒𝑖𝑗 (𝑣)
<virtual>, Ω 0
<state>
continues on next page

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Table 6 – continued from previous page

name/class argu- definition examples
ments
dw_lin_elastic_th <ts>,
LinearElasticTHTerm
<material>, ∫︁ [︂∫︁ 𝑡 ]︂
<virtual>, ℋ𝑖𝑗𝑘𝑙 (𝑡 − 𝜏 ) 𝑒𝑘𝑙 (𝑢(𝜏 )) d𝜏 𝑒𝑖𝑗 (𝑣)
<state> Ω 0

ev_of_ns_surf_min_d_press
<material_1>,
NSOFSurfMinDPressTerm
<material_2>, (︂∫︁ ∫︁ )︂
<parameter> 𝛿Ψ(𝑝) = 𝛿 𝑝− 𝑏𝑝𝑟𝑒𝑠𝑠
Γ𝑖𝑛 Γ𝑜𝑢𝑡

dw_of_ns_surf_min_d_press_diff
<material>,
NSOFSurfMinDPressDiffTerm
<virtual>
𝑤𝛿𝑝 Ψ(𝑝) ∘ 𝑞

ev_sd_st_grad_div <material>,
SDGradDivStabilizationTerm
<parameter_u>,∫︁
𝜕𝑢𝑖 𝜕𝒱𝑘 𝜕𝑤𝑖 𝜕𝒱𝑘
𝛾 [(∇ · 𝑢)(∇ · 𝑤)(∇ · 𝒱) −
<parameter_w>, (∇ · 𝑤) − (∇ · 𝑢) ]
<parameter_mv> Ω 𝜕𝑥𝑘 𝜕𝑥𝑖 𝜕𝑥𝑘 𝜕𝑥𝑖

ev_sd_st_pspg_c <material>,
SDPSPGCStabilizationTerm
<parameter_b>,
∑︁ ∫︁ 𝜕𝑟 𝜕𝑟 𝜕𝒱𝑘 𝜕𝑟 𝜕𝑢𝑖
<parameter_u>, 𝛿𝐾 [ (𝑏 · ∇𝑢𝑖 )(∇ · 𝒱) − (𝑏 · ∇𝑢𝑖 ) − (𝑏 · ∇𝒱𝑘 ) ]
𝜕𝑥𝑖 𝜕𝑥𝑘 𝜕𝑥𝑖 𝜕𝑥𝑘 𝜕𝑥𝑘
𝐾∈ℐℎ 𝑇𝐾
<parameter_r>,
<parameter_mv>
ev_sd_st_pspg_p <material>,
SDPSPGPStabilizationTerm
<parameter_r>,
∑︁ ∫︁ 𝜕𝑟 𝜕𝑝
<parameter_p>, 𝜏𝐾 [(∇𝑟 · ∇𝑝)(∇ · 𝒱) − (∇𝒱𝑘 · ∇𝑝) − (∇𝑟 · ∇𝒱𝑘 ) ]
𝜕𝑥𝑘 𝜕𝑥𝑘
𝐾∈ℐℎ 𝑇𝐾
<parameter_mv>

ev_sd_st_supg_c <material>,
SDSUPGCStabilizationTerm
<parameter_b>,
∑︁ ∫︁ 𝜕𝑢𝑘 𝜕𝑤𝑘
<parameter_u>, 𝛿𝐾 [(𝑏 · ∇𝑢𝑘 )(𝑏 · ∇𝑤𝑘 )(∇ · 𝒱) − (𝑏 · ∇𝒱𝑖 ) (𝑏 · ∇𝑤𝑘 ) − (𝑢 · ∇𝑢𝑘 )(𝑏 · ∇𝒱𝑖 ) ]
𝜕𝑥𝑖 𝜕𝑥𝑖
𝐾∈ℐℎ 𝑇𝐾
<parameter_w>,
<parameter_mv>
dw_st_adj1_supg_p <material>,
SUPGPAdj1StabilizationTerm
<virtual>, ∑︁ ∫︁
<state>, 𝛿𝐾 ∇𝑝(𝑣 · ∇𝑤)
<parameter> 𝐾∈ℐℎ 𝑇𝐾

dw_st_adj2_supg_p <material>,
SUPGPAdj2StabilizationTerm
<virtual>, ∑︁ ∫︁
<parameter>, 𝜏𝐾 ∇𝑟(𝑣 · ∇𝑢)
<state> 𝐾∈ℐℎ 𝑇𝐾

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Table 6 – continued from previous page

name/class argu- definition examples
ments
dw_st_adj_supg_c <material>,
SUPGCAdjStabilizationTerm
<virtual>, ∑︁ ∫︁
<parameter>, 𝛿𝐾 [((𝑣 · ∇)𝑢)((𝑢 · ∇)𝑤) + ((𝑢 · ∇)𝑢)((𝑣 · ∇)𝑤)]
<state> 𝐾∈ℐℎ 𝑇𝐾

dw_st_grad_div <material>, sta.nav.sto

GradDivStabilizationTerm
<virtual>, ∫︁
<state> 𝛾 (∇ · 𝑢) · (∇ · 𝑣)
Ω

dw_st_pspg_c <material>, sta.nav.sto

PSPGCStabilizationTerm
<virtual>, ∑︁ ∫︁
<parameter>, 𝜏𝐾 ((𝑏 · ∇)𝑢) · ∇𝑞
<state> 𝐾∈ℐℎ 𝑇𝐾

dw_st_pspg_p <opt_material>, sta.nav.sto

PSPGPStabilizationTerm
<virtual/ ∑︁ ∫︁
param_1>, 𝜏𝐾 ∇𝑝 · ∇𝑞
<state/ 𝐾∈ℐℎ 𝑇𝐾

param_2>
dw_st_supg_c <material>, sta.nav.sto
SUPGCStabilizationTerm
<virtual>, ∑︁ ∫︁
<parameter>, 𝛿𝐾 ((𝑏 · ∇)𝑢) · ((𝑏 · ∇)𝑣)
<state> 𝐾∈ℐℎ 𝑇𝐾

dw_st_supg_p <material>, sta.nav.sto

SUPGPStabilizationTerm
<virtual>, ∑︁ ∫︁
<parameter>, 𝛿𝐾 ∇𝑝 · ((𝑏 · ∇)𝑣)
<state> 𝐾∈ℐℎ 𝑇𝐾

dw_volume_dot_w_scalar_eth
<ts>,
DotSProductVolumeOperatorWETHTerm
<material_0>, ∫︁ [︂∫︁ 𝑡 ]︂
<material_1>, 𝒢(𝑡 − 𝜏 )𝑝(𝜏 ) d𝜏 𝑞
<virtual>, Ω 0
<state>
dw_volume_dot_w_scalar_th
<ts>,
DotSProductVolumeOperatorWTHTerm
<material>, ∫︁ [︂∫︁ 𝑡 ]︂
<virtual>, 𝒢(𝑡 − 𝜏 )𝑝(𝜏 ) d𝜏 𝑞
<state> Ω 0

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Table of multi-linear terms

Table 7: Multi-linear terms

name/class argu- definition examples
ments
de_cauchy_stress <material>,
ECauchyStressTerm<parameter> ∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑘𝑙 (𝑤)
Ω

de_convect <virtual/
EConvectTerm param_1>, ∫︁
<state/ ((𝑢 · ∇)𝑢) · 𝑣
param_2> Ω

de_diffusion <material>,
EDiffusionTerm <virtual/ ∫︁
param_1>, 𝐾𝑖𝑗 ∇𝑖 𝑞 ∇𝑗 𝑝
<state/ Ω

param_2>
de_div <opt_material>,
EDivTerm <virtual/ ∫︁ ∫︁
param> ∇·𝑣, 𝑐∇ · 𝑣
Ω Ω

de_div_grad <opt_material>,
EDivGradTerm <virtual/ ∫︁ ∫︁
param_1>, ∇𝑣 : ∇𝑢 , 𝜈 ∇𝑣 : ∇𝑢
<state/ Ω Ω

param_2>
de_dot <opt_material>,
EDotTerm <virtual/ ∫︁ ∫︁
param_1>, 𝑞𝑝 , 𝑣·𝑢
𝒟
<state/ ∫︁ ∫︁ 𝒟
param_2> 𝑐𝑞𝑝 , 𝑐𝑣 · 𝑢
𝒟 𝒟
∫︁
𝑣 · (𝑀 𝑢)
𝒟

de_grad <opt_material>,
EGradTerm <parameter> ∫︁ ∫︁
∇𝑣 , 𝑐∇𝑣
Ω Ω

de_integrate <opt_material>,
EIntegrateOperatorTerm
<virtual> ∫︁ ∫︁
𝑞 or 𝑐𝑞
𝒟 𝒟

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Table 7 – continued from previous page

name/class argu- definition examples
ments
de_laplace <opt_material>,
ELaplaceTerm <virtual/ ∫︁ ∫︁
param_1>, ∇𝑞 · ∇𝑝 , 𝑐∇𝑞 · ∇𝑝
<state/ Ω Ω

param_2>
de_lin_convect <virtual/
ELinearConvectTerm param_1>, ∫︁
<parameter>, ((𝑏 · ∇)𝑢) · 𝑣
<state/ Ω

param_3>
de_lin_elastic <material>,
ELinearElasticTerm <virtual/ ∫︁
param_1>, 𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢)
<state/ Ω

param_2>
de_non_penetration_p
<material>,
ENonPenetrationPenaltyTerm
<virtual>, ∫︁
<state> 𝑐(𝑛 · 𝑣)(𝑛 · 𝑢)
Γ

de_nonsym_elastic <material>,
ENonSymElasticTerm<virtual/ ∫︁
param_1>, 𝐷∇𝑣 : ∇𝑢
<state/ Ω

param_2>
de_s_dot_mgrad_s <material>,
EScalarDotMGradScalarTerm
<virtual>, ∫︁ ∫︁
<state> 𝑞𝑦 · ∇𝑝 , 𝑝𝑦 · ∇𝑞
<material>, Ω Ω

<state>,
<virtual>
de_stokes <opt_material>,
EStokesTerm <virtual/ ∫︁ ∫︁
param_v>, 𝑝∇ · 𝑣 , 𝑞∇·𝑢
Ω
<state/ ∫︁ ∫︁ Ω
param_s> 𝑐𝑝∇ · 𝑣 , 𝑐𝑞∇ · 𝑢
<opt_material>, Ω Ω
<state>,
<virtual>
de_surface_ltr <opt_material>,
ELinearTractionTerm
<virtual/ ∫︁ ∫︁
param> 𝑣·𝑛, 𝑐𝑣 · 𝑛
Γ Γ
∫︁ ∫︁
𝑣 · (𝜎 𝑛) , 𝑣·𝑓
Γ Γ

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 CHAPTER

TWO

DEVELOPMENT

The SfePy development takes place in the sfepy/sfepy repository on Github. The users and developers can also com-
municate using the mailing list.

2.1 General Information

We are interested in any contribution. There are many ways how you can contribute:
• You can report bugs using our mailing list. You can also add a bug report (or a comment) into the issues.
• You can contribute interesting examples/tutorials.
• You can blog about how you use SfePy (let us know!).
• You can help with improving our documentation and these pages.
• ...
To get acquainted with SfePy, you can start by reading the Tutorial and Primer sections of the documentation and trying
out the examples that come with the sources. Your first contribution could be pinpointing anything that is not clear in
the docs.
We also recommend reading the How to Contribute section of our Developer Guide.

2.2 Possible Topics

Several specific topics that we wish to address in the future are listed below. If you would like to contribute code/advice
to our project with respect to these topics, do not hesitate to contact us (either directly: cimrman3(at)ntc.zcu.cz, or on
our mailing list)
• finish/improve IGA implementation (see Isogeometric Analysis):
– support multiple patches
– efficient quadrature formulas
– local refinement?
• discretization methods:
– implement vector elements (Nedelec, Raviart-Thomas, . . . )
– implement the discontinuous Galerkin method
• material models: plasticity, viscoplasticity, damage, . . .
• improve parallelization (see Solving Problems in Parallel):

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– cluster installation with fast BLAS

– parallel code speed-up
– remove (some of) the serial parts
– preconditioning for multi-physics problems
• solvers:
– better defaults/recommendations for iterative solvers (PETSc) with respect to large problems
– dynamics/time-stepping solvers, interface PETSc time-steppers
– interface more sparse linear solvers (or enable via PETSc), for example BDDCML
– interface more eigenvalue problem solvers
• visualization of large data
• automatic differentiation:
– for tangent matrices
– for identification of (material) parameters
• core data structures & programming:
– using octree-based(?) mesh representation for local refinement
– continue with/improve the current hanging nodes implementation
– exploit lazy evaluation
See also the enhacement issues.

2.3 Developer Guide

This section purports to document the SfePy internals. It is mainly useful for those who wish to contribute to the
development of SfePy and understand the inner workings of the code.
We use git to track source code, documentation, examples, and other files related to the project.
It is not necessary to learn git in order to contribute to SfePy but we strongly suggest you do so as soon as possible - it
is an extremely useful tool not just for writing code, but also for tracking revisions of articles, Ph.D. theses, books, . . .
it will also look well in your CV :-) It is also much easier for us to integrate changes that are in form of a github pull
request than in another form.

2.3.1 Retrieving the Latest Code

The first step is to obtain the latest development version of the code from the SfePy git repository:

git clone git://github.com/sfepy/sfepy.git

For development, it is preferable to build the extension modules in place (see Compilation of C Extension Modules):

python setup.py build_ext --inplace

On Unix-like systems, you can simply type make in the top-level folder to build in-place.
After the initial compilation, or after making changes, do not forget to run the tests, see Testing Installation.

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2.3.2 SfePy Directory Structure

Here we list and describe the directories that are in the main sfepy directory.

Table 1: Top directory structure.

name description
build/ directory created by the build process (generated)
doc/ source files of this documentation
meshes/ finite element mesh files in various formats shared by the examples
output/ default output directory for storing results of the examples
script/ various small scripts (simple mesh generators, mesh format convertors etc.)
sfepy/ the source code including examples and tests

New users/developers (after going through the Tutorial) should explore the sfepy/examples/ directory. For developers,
the principal directory is sfepy/, which has the following contents:

Table 2: sfepy/ directory structure.

name description field-
specific
applica- top level application classes (e.g. PDESolverApp that implements all that simple.py script
tions/ does)
base/ common utilities and classes used by most of the other modules
dis- general classes and modules for describing a discrete problem, taking care of boundary con-
crete/ ditions, degrees of freedom, approximations, variables, equations, meshes, regions, quadra-
tures, etc.
Discretization-specific classes are in subdirectories:
• common/ - common parent classes for discretization-specific classes
• fem/ - finite element specific classes
• iga/ - isogeometric analysis specific classes

mesh/ some utilities to interface with tetgen and triangle mesh generators
homog- the homogenization engine and supporting modules - highly specialized code, one of the •
eniza- reasons of SfePy existence
tion/
linalg/ linear algebra functions not covered by NumPy and SciPy
mechan- modules for (continuum) mechanics: elastic constant conversions, tensor, units utilities, etc. •
ics/
opti- modules for shape optimization based on free-form deformation •
mize/
paral- modules supporting parallel assembling and solution of problems
lel/
postpro- Mayavi-based post-processing modules (postproc.py)
cess/
solvers/ interface classes to various internal/external solvers (linear, nonlinear, eigenvalue, optimiza-
tion, time stepping)
terms/ implementation of the terms (weak formulation integrals), see Term Overview

The directories in the “field-specific” column are mostly interesting for specialists working in the respective fields.
The fem/ is the heart of the code, while the terms/ contains the particular integral forms usable to build equations -
new term writers should look there.

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2.3.3 Exploring the Code

It is convenient to install IPython (see also Using IPython) to have the tab completion available. Moreover, all SfePy
classes can be easily examined by printing them:

1 In [1]: from sfepy.discrete.fem import Mesh

2

3 In [2]: mesh = Mesh.from_file('meshes/2d/rectangle_tri.mesh')

4 sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (meshes/2d/rectangle_tri.mesh)...
5 sfepy: ...done in 0.00 s
6

7 In [3]: print mesh

8 Mesh:meshes/2d/rectangle_tri
9 cmesh:
10 CMesh: n_coor: 258, dim 2, tdim: 2, n_el 454
11 descs:
12 list: ['2_3']
13 dim:
14 2
15 dims:
16 list: [2]
17 io:
18 None
19 n_el:
20 454
21 n_nod:
22 258
23 name:
24 meshes/2d/rectangle_tri
25 nodal_bcs:
26 dict with keys: []

We recommend going through the interactive example in the tutorial Interactive Example: Linear Elasticity in this way,
printing all the variables.
Another useful tool is the debug() function, that can be used as follows:

from sfepy.base.base import debug; debug()

Try to use it in the examples with user defined functions to explore their parameters etc. It works best with IPython
installed, as then the tab completion is available also when debugging.

2.3.4 How to Contribute

Read this section if you wish to contribute some work to the SfePy project - everyone is welcome to contribute. Con-
tributions can be made in a variety of forms, not just code. Reporting bugs and contributing to the documentation,
tutorials, and examples is in great need!
Below we describe
1. where to report problems or find existing issues and additional development suggestions
2. what to do to apply changes/fixes
3. what to do after you made your changes/fixes

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Reporting problems

Reporting a bug is the first way in which to contribute to an open source project
Short version: go to the main SfePy site and follow the links given there.
When you encounter a problem, try searching that site first - an answer may already be posted in the SfePy mailing
list (to which we suggest you subscribe. . . ), or the problem might have been added to the SfePy issues. As is true in
any open source project, doing your homework by searching for existing known problems greatly reduces the burden
on the developers by eliminating duplicate issues. If you find your problem already exists in the issue tracker, feel free
to gather more information and append it to the issue. In case the problem is not there, create a new issue with proper
labels for the issue type and priority, and/or ask us using the mailing list.
Note: A google account (e.g., gmail account) is needed to join the mailing list. A github account is needed for working
with the source code repository and issues.
Note: When reporting a problem, try to provide as much information as possible concerning the version of SfePy, the
OS / Linux distribution, and the versions of Python, NumPy and SciPy, and other prerequisites. The versions found on
your system can be printed by running:

python setup.py --help

If you are a new user, please let us know what difficulties you have with this documentation. We greatly welcome a
variety of contributions not limited to code only.

Contributing changes

Note: To avoid duplicating work, it is highly advised that you contact the developers on the mailing list or create an
enhancement issue before starting work on a non-trivial feature.
Before making any changes, read the Notes on commits and patches.

Using git and github

The preferred way to contribute to SfePy is to fork the main repository on github, then submit a “pull request” (PR):
1. Create a github account if you do not already have one.
2. Fork the project repository: click on the “Fork” button near the top of the sfepy git repository page. This creates
a copy of the repository under your account on the github server.
3. Clone your fork to your computer:

git clone [email protected]:YourLogin/sfepy.git

4. If you have never used git before, introduce yourself to git and make (optionally) some handy aliases either in
.gitconfig in your home directory (global settings for all your git projects), or directly in .git/config in the
repository:

1 [user]
2 email = [email protected]
3 name = Name Surname
4

5 [color]
6 ui = auto
7 interactive = true
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8

9 [alias]
10 ci = commit
11 di = diff --color-words
12 st = status
13 co = checkout

5. Create a feature branch to hold your changes:

git checkout -b my-feature

Then you can start to make your changes. Do not work in the master branch!
6. Modify some files and use git to track your local changes. The changed added/modified files can be listed using:

git status

and the changes can be reviewed using:

git diff

A more convenient way of achieving the above is to run:

gitk --all

in order to visualize of project history (all branches). There are other GUIs for this purpose, e.g. qgit. You may
need to install those tools, as they usually are not installed with git by default. Record a set of changes by:

1 # schedule some of the changed files for the next commit

2 git add file1 file2 ...
3 # an editor will pop up where you should describe the commit
4 git commit

We recommend git gui command in case you want to add and commit only some changes in a modified file.
Note: Do not be afraid to experiment - git works with your local copy of the repository, so it is not possible to
damage the master repository. It is always possible to re-clone a fresh copy, in case you do something that is
really bad.
7. The commit(s) now reflect changes, but only in your local git repository. To update your github repository with
your new commit(s), run:

git push origin my-feature:my-feature

8. Finally, when your feature is ready, and all tests pass, go to the github page of your sfepy repository fork, and
click “Pull request” to send your changes to the maintainers for review. It is recommended to check that your
contribution complies with the Notes on commits and patches.
In the above setup, your origin remote repository points to YourLogin/sfepy.git. If you wish to fetch/merge from
the main repository instead of your forked one, you will need to add another remote to use instead of origin. The main
repository is usually called “upstream”. To add it, type:

git remote add upstream https://github.com/sfepy/sfepy.git

To synchronize your repository with the upstream, proceed as follows:

1. Fetch the upstream changes:

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git fetch upstream

Never start with git pull upstream!

2. Check the changes of the upstream master branch. You can use gitk --all to visualize all your and remote
branches. The upstream master is named remotes/upstream/master.
3. Make sure all your local changes are either committed in a feature branch or stashed (see git stash). Then
reset your master to the upstream master:

git checkout master

git reset --hard upstream/master

Warning The above will remove all your local commits in the master branch that are not in upstream/master,
and also reset all the changes in your non-committed modified files!
Optionally, the reset command can be run conveniently in gitk by right-clicking on a commit you want to reset
the current branch onto.
4. Optionally, rebase your feature branch onto the upstream master:

git checkout my-feature

git rebase upstream/master

This is useful, for example, when the upstream master contains a change you need in your feature branch.
For additional information, see, for example, the gitwash git tutorial, or its incarnation NumPy gitwash.

Notes on commits and patches

• Follow our Coding style.

• Do not use lines longer than 79 characters (exception: tables of values, e.g., quadratures).
• Write descriptive docstrings in correct style, see Docstring standard.
• There should be one patch for one topic - do not mix unrelated things in one patch. For example, when you add
a new function, then notice a typo in docstring in a nearby function and correct it, create two patches: one fixing
the docstring, the other adding the new function.
• The commit message and description should clearly state what the patch does. Try to follow the style of other
commit messages. Some interesting notes can be found at tbaggery.com, namely that the commit message is
better to be written in the present tense: “fix bug” and not “fixed bug”.

Without using git

Without using git, send the modified files to the SfePy mailing list or attach them using gist to the corresponding issue
at the Issues web page. Do not forget to describe the changes properly, and to follow the spirit of Notes on commits and
patches and the Coding style.

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Coding style

All the code in SfePy should try to adhere to python style guidelines, see PEP-0008.
There are some additional recommendations:
• Prefer whole words to abbreviations in public APIs - there is completion after all. If some abbreviation is needed
(really too long name), try to make it as comprehensible as possible. Also check the code for similar names - try
to name things consistently with the existing code. Examples:
– yes: equation, transform_variables(), filename
– rather not: eq, transvar(), fname
• Functions have usually form <action>_<subject>() e.g.: save_data(), transform_variables(), do not
use data_save(), variable_transform() etc.
• Variables like V, c, A, b, x should be tolerated only locally when expressing mathematical ideas.
Really minor recommendations:
• Avoid single letter names, if you can:
– not even for loop variables - use e.g. ir, ic, . . . instead of i, j for rows and columns
– not even in generators, as they “leak” (this is fixed in Python 3.x)
These are recommendations only, we will not refuse code just on the ground that it uses slightly different formatting,
as long as it follows the PEP.
Note: some old parts of the code might not follow the PEP, yet. We fix them progressively as we update the code.

Docstring standard

We use sphinx with the numpydoc extension to generate this documentation. Refer to the sphinx site for the possible
markup constructs.
Basically (with a little tweak), we try to follow the NumPy/SciPy docstring standard as described in NumPy documen-
tation guide. See also the complete docstring example. It is exaggerated a bit to show all the possibilities. Use your
common sense here - the docstring should be sufficient for a new user to use the documented object. A good way to
remember the format is to type:

In [1]: import numpy as nm

In [2]: nm.sin?

in ipython. The little tweak mentioned above is the starting newline:

1 def function(arg1, arg2):

2 """
3 This is a function.
4

5 Parameters
6 ----------
7 arg1 : array
8 The coordinates of ...
9 arg2 : int
10 The dimension ...
11

12 Returns
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13 -------
14 out : array
15 The resulting array of shape ....
16 """

It seems visually better than:

1 def function(arg1, arg2):

2 """This is a function.
3

4 Parameters
5 ----------
6 arg1 : array
7 The coordinates of ...
8 arg2 : int
9 The dimension ...
10

11 Returns
12 -------
13 out : array
14 The resulting array of shape ....
15 """

When using LATEX in a docstring, use a raw string:

1 def function():
2 r"""
3 This is a function with :math:`\mbox{\LaTeX}` math:
4 :math:`\frac{1}{\pi}`.
5 """

to prevent Python from interpreting and consuming the backslashes in common escape sequences like ‘\n’, ‘\f’ etc.

2.3.5 How to Regenerate Documentation

The following steps summarize how to regenerate this documentation.

1. Install sphinx and numpydoc. Do not forget to set the path to numpydoc in site_cfg.py if it is not installed in a
standard location for Python packages on your platform. A recent LATEX distribution is required, too, for example
TeX Live. Depending on your OS/platform, it can be in the form of one or several packages.
2. Edit the rst files in doc/ directory using your favorite text editor - the ReST format is really simple, so nothing
fancy is needed. Follow the existing files in doc/ ; for reference also check reStructuredText Primer, Sphinx
Markup Constructs and docutils reStructuredText.
• When adding a new Python module, add a corresponding documentation file into doc/src/sfepy/<path>,
where <path> should reflect the location of the module in sfepy/.
• Figures belong to doc/images; subdirectories can be used.
3. (Re)generate the documentation (assuming GNU make is installed):

cd doc
make html

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4. View it (substitute your favorite browser):

firefox _build/html/index.html

2.3.6 How to Implement a New Term

Warning Implementing a new term usually involves C. As Cython is now supported by our build system, it should not
be that difficult. Python-only terms are possible as well.
Note There is an experimental way (newly from version 2021.1) of implementing multi-linear terms that is much easier
than what is described here, see Multi-linear Terms.

Notes on terminology

Volume refers to the whole domain (in space of dimension 𝑑), while surface to a subdomain of dimension 𝑑 − 1, for
example a part of the domain boundary. So in 3D problems volume = volume, surface = surface, while in 2D volume
= area, surface = curve.

Introduction

A term in SfePy usually corresponds to a single integral term in (weak) integral formulation of an equation. Both
volume and surface integrals are supported. There are three types of arguments a term can have:
• variables, i.e. the unknown, test or parameter variables declared by the variables keyword, see Problem Descrip-
tion File,
• materials, corresponding to material and other parameters (functions) that are known, declared by the materials
keyword,
• user data - anything, but user is responsible for passing them to the evaluation functions.
SfePy terms are subclasses of sfepy.terms.terms.Term. The purpose of a term is to implement a (vectorized)
function that evaluates the term contribution to residual/matrix and/or evaluates the term integral in elements of the
term region. Many such functions are currently implemented in C, but some terms are pure Python, vectorized using
NumPy.

Evaluation modes

A term can support several evaluation modes, as described in Term Evaluation.

Basic attributes

A term class should inherit from sfepy.terms.terms.Term base class. The simplest possible term with volume
integration and ‘weak’ evaluation mode needs to have the following attributes and methods:
• docstring (not really required per se, but we require it);
• name attribute - the name to be used in equations;
• arg_types attribute - the types of arguments the term accepts;
• integration attribute, optional - the kind of integral the term implements, one of ‘volume’ (the default, if not
given), ‘surface’, ‘surface_extra’ or ‘by_region’;
• function() static method - the assembling function;

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• get_fargs() method - the method that takes term arguments and converts them to arguments for function().

Argument types

The argument types can be (“[_*]” denotes an optional suffix):

• ‘material[_*]’ for a material parameter, i.e. any function that can be can evaluated in quadrature points and that
is not a variable;
• ‘opt_material[_*]’ for an optional material parameter, that can be left out - there can be only one in a term and
it must be the first argument;
• ‘virtual’ for a virtual (test) variable (no value defined), ‘weak’ evaluation mode;
• ‘state[_*]’ for state (unknown) variables (have value), ‘weak’ evaluation mode;
• ‘parameter[_*]’ for parameter variables (have known value), any evaluation mode.
Only one ‘virtual’ variable is allowed in a term.

Integration kinds

The integration kinds have the following meaning:

• ‘volume’ for volume integral over a region that contains elements; uses volume element connectivity for assem-
bling;
• ‘surface’ for surface integral over a region that contains faces; uses surface face connectivity for assembling;
• ‘surface_extra’ for surface integral over a region that contains faces; uses volume element connectivity for as-
sembling - this is needed if full gradients of a variable are required on the boundary;
• ‘by_region’ - the integration mode is determined by the region kind, The term attribute ‘surface_integration’
allows to set ‘surface_extra’ integration for surface regions.

function()

The function() static method has always the following arguments:

out, *args

where out is the already preallocated output array (change it in place!) and *args are any other arguments the function
requires. These function arguments have to be provided by the get_fargs() method. The function returns zero status on
success, nonzero on failure.
The out array has shape (n_el, 1, n_row, n_col), where n_el is the number of elements and n_row, n_col are matrix
dimensions of the value on a single element.

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get_fargs()

The get_fargs() method has always the same structure of arguments:

• positional arguments corresponding to arg_types attribute:
– example for a typical weak term:
∗ for:

arg_types = ('material', 'virtual', 'state')

the positional arguments are:

material, virtual, state

• keyword arguments common to all terms:

mode=None, term_mode=None, diff_var=None, **kwargs

here:
– mode is the actual evaluation mode, default is ‘eval’;
– term_mode is an optional term sub-mode influencing what the term should return (example:
dw_tl_he_neohook term has ‘strain’ and ‘stress’ evaluation sub-modes);
– diff_var is taken into account in the ‘weak’ evaluation mode. It is either None (residual mode) or a name
of variable with respect to differentiate to (matrix mode);
– **kwargs are any other arguments that the term supports.
The get_fargs() method returns arguments for function().

Additional attributes

These attributes are used mostly in connection with the tests/test_term_call_modes.py test for automatic testing of term
calls.
• arg_shapes attribute - the possible shapes of term arguments;
• geometries attribute - the list of reference element geometries that the term supports;
• mode attribute - the default evaluation mode.

Argument shapes

The argument shapes are specified using a dict of the following form:

arg_shapes = {'material' : 'D, D', 'virtual' : (1, 'state'),

'state' : 1, 'parameter_1' : 1, 'parameter_2' : 1}

The keys are the argument types listed in the arg_types attribute, for example:

arg_types = (('material', 'virtual', 'state'),

('material', 'parameter_1', 'parameter_2'))

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The values are the shapes containing either integers, or ‘D’ (for space dimension) or ‘S’ (symmetric storage size corre-
sponding to the space dimension). For materials, the shape is a string ‘nr, nc’ or a single value, denoting a special-valued
term, or None denoting an optional material that is left out. For state and parameter variables, the shape is a single
value. For virtual variables, the shape is a tuple of a single shape value and a name of the corresponding state variable;
the name can be None.
When several alternatives are possible, a list of dicts can be used. For convenience, only the shapes of arguments that
change w.r.t. a previous dict need to be included, as the values of the other shapes are taken from the previous dict. For
example, the following corresponds to a case, where an optional material has either the shape (1, 1) in each point, or is
left out:

1 arg_types = ('opt_material', 'parameter')

2 arg_shapes = [{'opt_material' : '1, 1', 'parameter' : 1},
3 {'opt_material' : None}]

Geometries

The default that most terms use is a list of all the geometries:

geometries = ['2_3', '2_4', '3_4', '3_8']

In that case, the attribute needs not to be define explicitly.

Examples

Let us now discuss the implementation of a simple weak term dw_integrate defined as 𝑐𝑞, where 𝑐 is a weight
∫︀
𝒟
(material parameter) and 𝑞 is a virtual variable. This term is implemented as follows:

1 class IntegrateOperatorTerm(Term):
2 r"""
3 Integral of a test function weighted by a scalar function
4 :math:`c`.
5

6 :Definition:
7

8 .. math::
9 \int_{\cal{D}} q \mbox{ or } \int_{\cal{D}} c q
10

11 :Arguments:
12 - material : :math:`c` (optional)
13 - virtual : :math:`q`
14 """
15 name = 'dw_integrate'
16 arg_types = ('opt_material', 'virtual')
17 arg_shapes = [{'opt_material' : '1, 1', 'virtual' : (1, None)},
18 {'opt_material' : None}]
19 integration = 'by_region'
20

21 @staticmethod
22 def function(out, material, bf, geo):
23 bf_t = nm.tile(bf.transpose((0, 1, 3, 2)), (out.shape[0], 1, 1, 1))
24 bf_t = nm.ascontiguousarray(bf_t)
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25 if material is not None:
26 status = geo.integrate(out, material * bf_t)
27 else:
28 status = geo.integrate(out, bf_t)
29 return status
30

31 def get_fargs(self, material, virtual,

32 mode=None, term_mode=None, diff_var=None, **kwargs):
33 assert_(virtual.n_components == 1)
34 geo, _ = self.get_mapping(virtual)
35

36 return material, geo.bf, geo

• lines 2-14: the docstring - always write one!

• line 15: the name of the term, that can be referred to in equations;
• line 16: the argument types - here the term takes a single material parameter, and a virtual variable;
• lines 17-18: the possible argument shapes
• line 19: the integration mode is choosen according to a given domain
• lines 21-29: the term function
– its arguments are:
∗ the output array out, already having the required shape,
∗ the material coefficient (array) mat evaluated in physical quadrature points of elements of the term
region,
∗ a base function (array) bf evaluated in the quadrature points of a reference element and
∗ a reference element (geometry) mapping geo.
– line 23: transpose the base function and tile it so that is has the correct shape - it is repeated for each
element;
– line 24: ensure C contiguous order;
– lines 25-28: perform numerical integration in C - geo.integrate() requires the C contiguous order;
– line 29: return the status.
• lines 31-36: prepare arguments for the function above:
– line 33: verify that the variable is scalar, as our implementation does not support vectors;
– line 34: get reference element mapping corresponding to the virtual variable;
– line 36: return the arguments for the function.

∫︀A more complex term that involves an ∫︀unknown variable and has two call modes, is dw_s_dot_mgrad_s, defined as
Ω
𝑞𝑦 · ∇𝑝 in the`’grad_state’` mode or Ω 𝑝𝑦 · ∇𝑞 in the ‘grad_virtual’ mode, where 𝑦 is a vector material parameter,
𝑞 is a virtual variable, and 𝑝 is a state variable:
1 class ScalarDotMGradScalarTerm(Term):
2 r"""
3 Volume dot product of a scalar gradient dotted with a material vector
4 with a scalar.
5
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6 :Definition:
7

8 .. math::
9 \int_{\Omega} q \ul{y} \cdot \nabla p \mbox{ , }
10 \int_{\Omega} p \ul{y} \cdot \nabla q
11

12 :Arguments 1:
13 - material : :math:`\ul{y}`
14 - virtual : :math:`q`
15 - state : :math:`p`
16

17 :Arguments 2:
18 - material : :math:`\ul{y}`
19 - state : :math:`p`
20 - virtual : :math:`q`
21 """
22 name = 'dw_s_dot_mgrad_s'
23 arg_types = (('material', 'virtual', 'state'),
24 ('material', 'state', 'virtual'))
25 arg_shapes = [{'material' : 'D, 1',
26 'virtual/grad_state' : (1, None),
27 'state/grad_state' : 1,
28 'virtual/grad_virtual' : (1, None),
29 'state/grad_virtual' : 1}]
30 modes = ('grad_state', 'grad_virtual')
31

32 @staticmethod
33 def function(out, out_qp, geo, fmode):
34 status = geo.integrate(out, out_qp)
35 return status
36

37 def get_fargs(self, mat, var1, var2,

38 mode=None, term_mode=None, diff_var=None, **kwargs):
39 vg1, _ = self.get_mapping(var1)
40 vg2, _ = self.get_mapping(var2)
41

42 if diff_var is None:
43 if self.mode == 'grad_state':
44 geo = vg1
45 bf_t = vg1.bf.transpose((0, 1, 3, 2))
46 val_qp = self.get(var2, 'grad')
47 out_qp = bf_t * dot_sequences(mat, val_qp, 'ATB')
48

49 else:
50 geo = vg2
51 val_qp = self.get(var1, 'val')
52 out_qp = dot_sequences(vg2.bfg, mat, 'ATB') * val_qp
53

54 fmode = 0
55

56 else:
57 if self.mode == 'grad_state':
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58 geo = vg1
59 bf_t = vg1.bf.transpose((0, 1, 3, 2))
60 out_qp = bf_t * dot_sequences(mat, vg2.bfg, 'ATB')
61

62 else:
63 geo = vg2
64 out_qp = dot_sequences(vg2.bfg, mat, 'ATB') * vg1.bf
65

66 fmode = 1
67

68 return out_qp, geo, fmode

Only interesting differences with respect to the previous example will by discussed:
• the argument types and shapes (lines 23-29) have to be specified for all the call modes (line 30)
• the term function (lines 32-35) just integrates the element contributions, as all the other calculations are done by
the get_fargs() function.
• the get_fargs() function (lines 37-68) contains:
– residual computation (lines 43-54) for both modes
– matrix computation (lines 57-66) for both modes

Concluding remarks

This is just a very basic introduction to the topic of new term implementation. Do not hesitate to ask the SfePy mailing
list, and look at the source code of the already implemented terms.

2.3.7 Multi-linear Terms

tentative documentation, the enriched einsum notation is still in flux

Multi-linear terms can be implemented simply by using the following enriched einsum notation:

Table 3: The enriched einsum notation for defining multi-linear terms.

symbol meaning example
0 scalar 𝑝
i 𝑖-th vector component 𝑢𝑖
i.j gradient: derivative of 𝑖-th vector component w.r.t. 𝑗-th coor- 𝜕𝑥
𝜕𝑢𝑖
𝑗
dinate component
𝜕𝑢𝑗
i:j symmetric gradient 1 𝜕𝑢𝑖
2 ( 𝜕𝑥𝑗 + 𝜕𝑥𝑖 )
s(i:j)->Ivector storage of symmetric second order tensor, 𝐼 is the vector Cauchy strain tensor 𝑒𝑖𝑗 (𝑢)
component

The examples below present the new way of implementing the terms shown in the original Examples, using sfepy.
terms.terms_multilinear.ETermBase.

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Examples

• de_integrate defined as 𝑐𝑞, where 𝑐 is a weight (material parameter) and 𝑞 is a virtual variable:
∫︀
Ω

1 class EIntegrateOperatorTerm(ETermBase):
2 r"""
3 Volume and surface integral of a test function weighted by a scalar
4 function :math:`c`.
5

6 :Definition:
7

8 .. math::
9 \int_{\cal{D}} q \mbox{ or } \int_{\cal{D}} c q
10

11 :Arguments:
12 - material : :math:`c` (optional)
13 - virtual : :math:`q`
14 """
15 name = 'de_integrate'
16 arg_types = ('opt_material', 'virtual')
17 arg_shapes = [{'opt_material' : '1, 1', 'virtual' : (1, None)},
18 {'opt_material' : None}]
19

20 def get_function(self, mat, virtual, mode=None, term_mode=None,

21 diff_var=None, **kwargs):
22 if mat is None:
23 fun = self.make_function(
24 '0', virtual, diff_var=diff_var,
25 )
26

27 else:
28 fun = self.make_function(
29 '00,0', mat, virtual, diff_var=diff_var,
30 )
31

32 return fun

• de_s_dot_mgrad_s defined as Ω 𝑞𝑦 · ∇𝑝 in the`’grad_state’` mode or Ω 𝑝𝑦 · ∇𝑞 in the ‘grad_virtual’ mode,

∫︀ ∫︀

where 𝑦 is a vector material parameter, 𝑞 is a virtual variable, and 𝑝 is a state variable:

1 class EScalarDotMGradScalarTerm(ETermBase):
2 r"""
3 Volume dot product of a scalar gradient dotted with a material vector with
4 a scalar.
5

6 :Definition:
7

8 .. math::
9 \int_{\Omega} q \ul{y} \cdot \nabla p \mbox{ , }
10 \int_{\Omega} p \ul{y} \cdot \nabla q
11

12 :Arguments 1:
13 - material : :math:`\ul{y}`
14 - virtual : :math:`q`
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15 - state : :math:`p`
16

17 :Arguments 2:
18 - material : :math:`\ul{y}`
19 - state : :math:`p`
20 - virtual : :math:`q`
21 """
22 name = 'de_s_dot_mgrad_s'
23 arg_types = (('material', 'virtual', 'state'),
24 ('material', 'state', 'virtual'))
25 arg_shapes = [{'material' : 'D, 1',
26 'virtual/grad_state' : (1, None),
27 'state/grad_state' : 1,
28 'virtual/grad_virtual' : (1, None),
29 'state/grad_virtual' : 1}]
30 modes = ('grad_state', 'grad_virtual')
31

32 def get_function(self, mat, var1, var2, mode=None, term_mode=None,

33 diff_var=None, **kwargs):
34 return self.make_function(
35 'i0,0,0.i', mat, var1, var2, diff_var=diff_var,
36 )

2.3.8 How To Make a Release

Release Tasks

A few notes on what to do during a release.

Things to check before a release

1. synchronize module documentation (dry run):

$ python3 script/sync_module_docs.py doc/src/ . -n

2. regenerate gallery page and examples:

$ rm -rf doc/examples/
$ python3 script/gen_gallery.py

3. create temporary/testing tarball:

$ python3 setup.py sdist

4. check in-place build:

$ # unpack the tarball

$ # cd into

$ python3 setup.py build_ext --inplace

$ python3 test_install.py

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5. check that documentation can be built:

$ # copy site_cfg.py
$ python3 setup.py htmldocs
$ firefox doc/_build/html/index.html

or use:

$ cd doc/
$ make html
$ firefox _build/html/index.html

try also:

$ python3 setup.py pdfdocs

6. check installed build:

$ python3 -m pip install . --user

$ cd
$ sfepy-run run_tests
$ rm -r output/

then remove the installed files so that they do not interfere with the local build
7. create final tarball
• update doc/release_notes.rst, with the help of:

$ python3 script/gen_release_notes.py 2019.2

• update doc/news.rst, doc/archived_news.rst

• change version number (sfepy/version.py) so that previous release tarball is not overwritten!
• set is_release = True in site_cfg.py
• update pdfdocs:

$ python3 setup.py pdfdocs

• create tarball:

$ python3 setup.py sdist

8. tag the release using:

$ git tag release_XXXX.X

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Useful Git commands

• log

git log --pretty=format:"%s%n%b%n" --topo-order --reverse release_2016.4..HEAD

• who has contributed since <date>:

git log --after=<date> | grep Author | sort | uniq

git log release_2012.1..HEAD | grep Author | sort -k3 | uniq
git shortlog -s -n release_2012.3..HEAD

git rev-list --committer="Name Surname" --since=6.months.ago HEAD | wc

git rev-list --author="Name Surname" --since=6.months.ago HEAD | wc
# ?no-merges

• misc:

git archive --format=tar HEAD | gzip > name.tar.gz

Web update and file uploading

• make a pull request with the updated version in sfepy-feedstock/recipe/meta.yaml from a fork (e.g. https:
//github.com/rc/sfepy-feedstock) of https://github.com/conda-forge/sfepy-feedstock.
• publish development docs also as new release docs
• send announcement to
– [email protected], [email protected], [email protected], [email protected],
[email protected]

2.3.9 Module Index

Main scripts

extractor.py script

Extract information from a SfePy multi-time-step results file (HDF5 format) and/or linearize results with stored higher
order DOFs.
For the linearization, the original input (problem description) file must be specified as the first argument. Use the
option –linearization below to override linearization parameters defined in the input file. The linearization forces
–dump option, i.e., output to VTK files.

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Examples

$ ./extractor.py -e “p e 0 1999” bone.h5 $ ./extractor.py -e “p e 0 1999” bone.h5 -a $ ./extractor.py -e “p e 0 1999”

bone.h5 -o extracted.h5 $ ./extractor.py -e “p e 0 1999” bone.h5 -o extracted.h5 -a
extractor.create_problem(filename)

extractor.main()

extractor.parse_linearization(linearization)

phonon.py script

phonon.main()

postproc.py script

This is a script for quick Mayavi-based visualizations of finite element computations results.

Examples

The examples assume that python -c "import sfepy; sfepy.test('--output-dir=output-tests')" has

been run successfully and the resulting data files are present.
• view data in output-tests/navier_stokes-navier_stokes.vtk
$ python postproc.py output-tests/navier_stokes-navier_stokes.vtk $ python postproc.py output-
tests/navier_stokes-navier_stokes.vtk –3d
• save a snapshot image and exit
$ python postproc.py output-tests/diffusion-poisson.vtk -o image.png -n
• save a snapshot image without off-screen rendering and exit
$ python postproc.py output-tests/diffusion-poisson.vtk -o image.png -n –no-offscreen
• create animation (forces offscreen rendering) from output-tests/diffusion-time_poisson.*.vtk
$ python postproc.py output-tests/diffusion-time_poisson.*.vtk -a mov
• create animation (forces offscreen rendering) from output-tests/test_hyperelastic_TL.*.vtk
The range specification for the displacements ‘u’ is required, as output-tests/test_hyperelastic_TL.00.vtk contains
only zero displacements which leads to invisible glyph size.
$ python postproc.py output-tests/test_hyperelastic_TL.*.vtk –ranges=u,0,0.02 -a mov
• same as above, but slower frame rate
$ python postproc.py output-tests/test_hyperelastic_TL.*.vtk –ranges=u,0,0.02 -a mov –ffmpeg-options=”-
framerate 2”

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class postproc.ParseDomainSpecific(option_strings, dest, nargs=None, const=None, default=None,

type=None, choices=None, required=False, help=None,
metavar=None)

class postproc.ParseGroupNames(option_strings, dest, nargs=None, const=None, default=None, type=None,

choices=None, required=False, help=None, metavar=None)

class postproc.ParseOpacity(option_strings, dest, nargs=None, const=None, default=None, type=None,

choices=None, required=False, help=None, metavar=None)

class postproc.ParseRanges(option_strings, dest, nargs=None, const=None, default=None, type=None,

choices=None, required=False, help=None, metavar=None)

class postproc.ParseResolution(option_strings, dest, nargs=None, const=None, default=None, type=None,

choices=None, required=False, help=None, metavar=None)

class postproc.ParseSubdomains(option_strings, dest, nargs=None, const=None, default=None, type=None,

choices=None, required=False, help=None, metavar=None)

class postproc.ParseView(option_strings, dest, nargs=None, const=None, default=None, type=None,

choices=None, required=False, help=None, metavar=None)

postproc.main()

postproc.view_file(filename, filter_names, options, view=None)

probe.py script

Probe finite element solutions in points defined by various geometrical probes.

Generation mode

python probe.py [generation options] <input file> <results file>

Probe the data in the results file corresponding to the problem defined in the input file. The input file options must
contain ‘gen_probes’ and ‘probe_hook’ keys, pointing to proper functions accessible from the input file scope.
For each probe returned by gen_probes() a data plot figure and a text file with the data plotted are saved, see the options
below.

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Generation options

-o, –auto-dir, –same-dir, -f, –only-names, -s

Postprocessing mode

python probe.py [postprocessing options] <probe file> <figure file>

Read a previously probed data from the probe text file, re-plot them, and integrate them along the probe.

Postprocessing options

–postprocess, –radial, –only-names

Notes

For extremely thin hexahedral elements the Newton’s iteration for finding the reference element coordinates might
converge to a spurious solution outside of the element. To obtain some values even in this case, try increasing the
–close-limit option value.
probe.generate_probes(filename_input, filename_results, options, conf=None, problem=None, probes=None,
labels=None, probe_hooks=None)
Generate probe figures and data files.
probe.integrate_along_line(x, y, is_radial=False)
Integrate numerically (trapezoidal rule) a function 𝑦 = 𝑦(𝑥).
If is_radial is True, multiply each 𝑦 by 4𝜋𝑥2 .
probe.main()

probe.postprocess(filename_input, filename_results, options)

Postprocess probe data files - replot, integrate data.

resview.py script

This is a script for quick VTK-based visualizations of finite element computations results.

Examples

The examples assume that python -c "import sfepy; sfepy.test('--output-dir=output-tests')" has

been run successfully and the resulting data files are present.
• View data in output-tests/test_navier_stokes.vtk:

$ python resview.py output-tests/navier_stokes-navier_stokes.vtk

• Customize the above output: plot0: field “p”, switch on edges, plot1: field “u”, surface with opacity 0.4, glyphs
scaled by factor 2e-2.
$ python resview.py output-tests/navier_stokes-navier_stokes.vtk -f p:e:p0 u:o.4:p1 u:g:f2e-2:p1

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• As above, but glyphs are scaled by the factor determined automatically as 20% of the minimum bounding box
size.
$ python resview.py output-tests/navier_stokes-navier_stokes.vtk -f p:e:p0 u:o.4:p1 u:g:f10%:p1
• View data and take a screenshot.
$ python resview.py output-tests/diffusion-poisson.vtk -o image.png
• Take a screenshot without a window popping up.
$ python resview.py output-tests/diffusion-poisson.vtk -o image.png –off-screen
• Create animation from output-tests/diffusion-time_poisson.*.vtk.
$ python resview.py output-tests/diffusion-time_poisson.*.vtk -a mov.mp4
• Create animation from output-tests/test_hyperelastic.*.vtk, set frame rate to 3, plot displacements and
mooney_rivlin_stress.
$ python resview.py output-tests/test_hyperelastic_TL.*.vtk -f u:wu:e:p0 mooney_rivlin_stress:p1 -a mov.mp4
-r 3
class resview.FieldOptsToListAction(option_strings, dest, nargs=None, const=None, default=None,
type=None, choices=None, required=False, help=None,
metavar=None)

separator = ':'
class resview.OptsToListAction(option_strings, dest, nargs=None, const=None, default=None, type=None,
choices=None, required=False, help=None, metavar=None)

separator = '='
class resview.StoreNumberAction(option_strings, dest, nargs=None, const=None, default=None, type=None,
choices=None, required=False, help=None, metavar=None)

resview.add_mat_id_to_grid(grid, cell_groups)

resview.get_camera_position(bounds, azimuth, elevation, distance=None, zoom=1.0)

resview.main()

resview.make_cells_from_conn(conns, convert_to_vtk_type)

resview.parse_options(opts, separator=':')

resview.pv_plot(filenames, options, plotter=None, step=None, scalar_bar_limits=None,

ret_scalar_bar_limits=False, step_inc=None, use_cache=True)

resview.read_mesh(filenames, step=None, print_info=True, ret_n_steps=False, use_cache=True)

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simple.py script

Solve partial differential equations given in a SfePy problem definition file.

Example problem definition files can be found in sfepy/examples/ directory of the SfePy top-level directory.
Both normal and parametric study runs are supported. A parametric study allows repeated runs for varying some of
the simulation parameters - see sfepy/examples/diffusion/poisson_parametric_study.py file.
simple.main()

simple.print_solvers()

simple.print_terms()

simple_homog_mpi.py script

Solve a coupled two-scale problem in parallel. One computational node is solving a macroscopic equation while the
others are solving local microscopic problems and homogenized coefficients.
Run this script as:

mpiexec -n 4 simple_homog_mpi.py sfepy/examples/homogenization/nonlinear_hyperelastic_mM.

˓→py

simple_homog_mpi.main()

Utility scripts

build_helpers.py script

Build helpers for setup.py.

Includes package dependency checks and monkey-patch to numpy.distutils to work with Cython.

Notes

The original version of this file was adapted from NiPy project [1].
[1] http://nipy.sourceforge.net/
class build_helpers.Clean(dist)
Distutils Command class to clean, enhanced to clean also files generated during python setup.py build_ext –in-
place.
run()
A command’s raison d’etre: carry out the action it exists to perform, controlled by the options initialized
in ‘initialize_options()’, customized by other commands, the setup script, the command-line, and config
files, and finalized in ‘finalize_options()’. All terminal output and filesystem interaction should be done by
‘run()’.
This method must be implemented by all command classes.

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class build_helpers.DoxygenDocs(dist)

description = 'generate docs by Doxygen'

run()
A command’s raison d’etre: carry out the action it exists to perform, controlled by the options initialized
in ‘initialize_options()’, customized by other commands, the setup script, the command-line, and config
files, and finalized in ‘finalize_options()’. All terminal output and filesystem interaction should be done by
‘run()’.
This method must be implemented by all command classes.
class build_helpers.NoOptionsDocs(dist)

finalize_options()
Set final values for all the options that this command supports. This is always called as late as possible, ie.
after any option assignments from the command-line or from other commands have been done. Thus, this
is the place to code option dependencies: if ‘foo’ depends on ‘bar’, then it is safe to set ‘foo’ from ‘bar’ as
long as ‘foo’ still has the same value it was assigned in ‘initialize_options()’.
This method must be implemented by all command classes.
initialize_options()
Set default values for all the options that this command supports. Note that these defaults may be overridden
by other commands, by the setup script, by config files, or by the command-line. Thus, this is not the place
to code dependencies between options; generally, ‘initialize_options()’ implementations are just a bunch
of “self.foo = None” assignments.
This method must be implemented by all command classes.
user_options = [('None', None, 'this command has no options')]
class build_helpers.SphinxHTMLDocs(dist)

description = 'generate html docs by Sphinx'

run()
A command’s raison d’etre: carry out the action it exists to perform, controlled by the options initialized
in ‘initialize_options()’, customized by other commands, the setup script, the command-line, and config
files, and finalized in ‘finalize_options()’. All terminal output and filesystem interaction should be done by
‘run()’.
This method must be implemented by all command classes.
class build_helpers.SphinxPDFDocs(dist)

description = 'generate pdf docs by Sphinx'

run()
A command’s raison d’etre: carry out the action it exists to perform, controlled by the options initialized
in ‘initialize_options()’, customized by other commands, the setup script, the command-line, and config
files, and finalized in ‘finalize_options()’. All terminal output and filesystem interaction should be done by
‘run()’.
This method must be implemented by all command classes.
build_helpers.generate_a_pyrex_source(self, base, ext_name, source, extension)
Monkey patch for numpy build_src.build_src method

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Uses Cython instead of Pyrex.

build_helpers.get_sphinx_make_command()

build_helpers.have_good_cython()

build_helpers.package_check(pkg_name, version=None, optional=False, checker=<function parse_version>,

version_getter=None, messages=None, show_only=False)
Check if package pkg_name is present, and in correct version.
Parameters
pkg_name [str or sequence of str] The name of the package as imported into python. Alternative
names (e.g. for different versions) may be given in a list.
version [str, optional] The minimum version of the package that is required. If not given, the
version is not checked.
optional [bool, optional] If False, raise error for absent package or wrong version; otherwise
warn
checker [callable, optional] If given, the callable with which to return a comparable thing from
a version string. The default is pkg_resources.parse_version.
version_getter [callable, optional:] If given, the callable that takes pkg_name as argument, and
returns the package version string - as in:

``version = version_getter(pkg_name)``

The default is equivalent to:

mod = __import__(pkg_name); version = mod.__version__``

messages [dict, optional] If given, the dictionary providing (some of) output messages.
show_only [bool] If True, do not raise exceptions, only show the package name and version
information.
build_helpers.recursive_glob(top_dir, pattern)
Utility function working like glob.glob(), but working recursively and returning generator.
Parameters
topdir [str] The top-level directory.
pattern [str or list of str] The pattern or list of patterns to match.

test_install.py script

Simple script for testing various SfePy functionality, examples not covered by tests, and running the tests.
The script just runs the commands specified in its main() using the subprocess module, captures the output and compares
one or more key words to the expected ones.
The output of failed commands is saved to ‘test_install.log’ file.
test_install.check_output(cmd)
Run the specified command and capture its outputs.
Returns

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out [tuple] The (stdout, stderr) output tuple.

test_install.main()

test_install.report(out, name, line, item, value, eps=None, return_item=False, match_numbers=False)

Check that item at line of the output string out is equal to value. If not, print the output.
test_install.report2(out, name, items, return_item=False)
Check that items are in the output string out. If not, print the output.
test_install.report_tests(out, return_item=False)
Check that all tests in the output string out passed. If not, print the output.

script/blockgen.py script

Block mesh generator.

blockgen.main()

script/convert_mesh.py script

Convert a mesh file from one SfePy-supported format to another.

Examples:

$ ./script/convert_mesh.py meshes/3d/cylinder.mesh new.vtk

$ ./script/convert_mesh.py meshes/3d/cylinder.mesh new.vtk -s2.5
$ ./script/convert_mesh.py meshes/3d/cylinder.mesh new.vtk -s0.5,2,1
$ ./script/convert_mesh.py meshes/3d/cylinder.mesh new.vtk -s0.5,2,1 -c 0
$ ./script/convert_mesh.py meshes/3d/cylinder.mesh new.mesh --remesh='q2/0 a1e-8 O9/7 V'
$ ./script/convert_mesh.py meshes/3d/cylinder.mesh new2.mesh --remesh='rq2/0 a1e-8 O9/7 V
˓→'

convert_mesh.main()

script/cylindergen.py script

Cylinder mesh generator.

cylindergen.main()

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script/dg_plot_1D.py script

Script for plotting 1D DG FEM data stored in VTK files

dg_plot_1D.load_and_plot_fun(folder, filename, t0, t1, tn, ic_fun=None, exact=None, compare=False,
polar=False)

Parameters
folder [str] folder where to look for files
filename [str] used in {name}.i.vtk, i = 0,1, . . . tns - 1
t0 [float] starting time
t1 [int] final time
tn [int] number of time steps
ic_fun [callable] initital condition
exact [callable] exact solution, for transient problems function of space ant time
compare [bool]
polar [bool]
dg_plot_1D.main(argv)

script/edit_identifiers.py script

Convert mixedCase identifiers to under_scores.

edit_identifiers.cw2us(x)

edit_identifiers.edit(line)

edit_identifiers.main()

edit_identifiers.match_candidate(/, string, pos=0, endpos=sys.maxsize)

Matches zero or more characters at the beginning of the string.
edit_identifiers.mc2us(x)

edit_identifiers.split_on(token, chars)

edit_identifiers.us2cw(x)

edit_identifiers.us2mc(x)

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script/eval_ns_forms.py script

Operators present in the FE discretization of (adjoint) Navier-Stokes terms.

eval_ns_forms.create_scalar(name, n_ep)

eval_ns_forms.create_scalar_base(name, n_ep)

eval_ns_forms.create_scalar_base_grad(name, phic, dim)

eval_ns_forms.create_scalar_var_data(name, phi, g, u)

eval_ns_forms.create_u_operator(u, transpose=False)

eval_ns_forms.create_vector(name, n_ep, dim)

ordering is DOF-by-DOF
eval_ns_forms.create_vector_base(name, phic, dim)

eval_ns_forms.create_vector_base_grad(name, gc, transpose=False)

eval_ns_forms.create_vector_var_data(name, phi, vindx, g, gt, vgindx, u)

eval_ns_forms.grad_vector_to_matrix(name, gv)

eval_ns_forms.main()

eval_ns_forms.substitute_continuous(expr, names, u, phi)

script/eval_tl_forms.py script

Operators present in the FE discretization of hyperelastic terms in the total Lagrangian formulation.
eval_tl_forms.main()

script/extract_edges.py script

Extract outline edges of a given mesh and save them into ‘<original path>/edge_<original mesh file name>.vtk’ or into
a user defined output file. The outline edge is an edge for which norm(nvec1 - nvec2) < eps, where nvec1 and nvec2
are the normal vectors of the incident facets.
extract_edges.extract_edges(mesh, eps=1e-16)
Extract outline edges of a given mesh. The outline edge is an edge for which norm(nvec_1 - nvec_2) < eps, where
nvec_1 and nvec_2 are the normal vectors of the incident facets.
Parameters
mesh [Mesh] The 3D or 2D mesh.

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eps [float] The tolerance parameter of the outline edge searching algorithm.
Returns
mesh_out [tuple] The data of the outline mesh, Mesh.from_data() format, i.e. (coors, ngroups,
ed_conns, mat_ids, descs).
extract_edges.main()

extract_edges.merge_lines(mesh, eps=1e-18)

script/extract_surface.py script

Given a mesh file, this script extracts its surface and prints it to stdout in form of a list where each row is [element, face,
component]. A component corresponds to a contiguous surface region - for example, a cubical mesh with a spherical
hole has two surface components. Two surface faces sharing a single node belong to one component.
With ‘-m’ option, a mesh of the surface is created and saved in ‘<original path>/surf_<original mesh file name>.mesh’.

extract_surface.get_surface_faces(domain)

extract_surface.main()

extract_surface.surface_components(gr_s, surf_faces)
Determine surface components given surface mesh connectivity graph.
extract_surface.surface_graph(surf_faces, n_nod)

script/gen_gallery.py script

Generate the images and rst files for gallery of SfePy examples.
The following steps need to be made to regenerate the documentation with the updated example files:
1. remove doc/examples/*:

$ rm -rf doc/examples/*

2. generate the files:

$ ./script/gen_gallery.py
3. regenerate the documentation:

$ python setup.py htmldocs

gen_gallery.apply_view_options(views, default)

gen_gallery.ebase2fbase(ebase)

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gen_gallery.generate_gallery(examples_dir, output_filename, doc_dir, rst_dir, thumbnails_dir, dir_map,

n_col=3)
Generate the gallery rst file with thumbnail images and links to examples.
Parameters
output_filename [str] The output rst file name.
doc_dir [str] The top level directory of gallery files.
rst_dir [str] The full path to rst files of examples within doc_dir.
thumbnails_dir [str] The full path to thumbnail images within doc_dir.
dir_map [dict] The directory mapping returned by generate_rst_files()
n_col [int] The number of columns in the gallery table.
gen_gallery.generate_images(images_dir, examples_dir)
Generate images from results of running examples found in examples_dir directory.
The generated images are stored to images_dir,
gen_gallery.generate_rst_files(rst_dir, examples_dir, images_dir)
Generate Sphinx rst files for examples in examples_dir with images in images_dir and put them into rst_dir.
Returns
dir_map [dict] The directory mapping of examples and corresponding rst files.
gen_gallery.generate_thumbnails(thumbnails_dir, images_dir, scale=0.3)
Generate thumbnails into thumbnails_dir corresponding to images in images_dir.
gen_gallery.main()

gen_gallery.resview_plot(filename, filename_out, options)

script/gen_iga_patch.py script

Generate a single IGA patch block in 2D or 3D of given degrees and continuity using igakit.
The grid has equally-spaced knot vectors.
gen_iga_patch.main()

script/gen_legendre_simplex_base.py script

Generate simplex legendre 2D basis coffecients and exponents matrices and save them to legendre2D_simplex_coefs.txt
and legendre2D_simplex_expos.txt
gen_legendre_simplex_base.main()

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script/gen_lobatto1d_c.py script

Generate lobatto1d.c and lobatto1h.c files.

gen_lobatto1d_c.append_declarations(out, cpolys, comment, cvar_name, shift=0)

gen_lobatto1d_c.append_lists(out, names, length)

gen_lobatto1d_c.append_polys(out, cpolys, comment, cvar_name, var_name='x', shift=0)

gen_lobatto1d_c.gen_lobatto(max_order)

gen_lobatto1d_c.main()

gen_lobatto1d_c.plot_polys(fig, polys, var_name='x')

script/gen_mesh_prev.py script

Mesh Preview Generator.

Examples

$ ./script/gen_mesh_prev.py meshes/2d/
gen_mesh_prev.gen_shot(vtk_filename, png_filename)
Generate PNG image of the FE mesh.
Parameters
vtk_filename [str] The input mesh filename (file in VTK format).
png_filename [str] The name of the output PNG file.
gen_mesh_prev.main()

script/gen_release_notes.py script

Generate release notes using git log starting from the given version.
gen_release_notes.main()

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script/gen_serendipity_basis.py script

python3 script/gen_serendipity_basis.py > sfepy/discrete/fem/_serendipity.py

gen_serendipity_basis.main()

script/gen_solver_table.py script

Generate available solvers table for ReST documentation.

gen_solver_table.gen_solver_table(app)

gen_solver_table.main()

gen_solver_table.setup(app)

gen_solver_table.trim(docstring)
Trim and split (doc)string.
gen_solver_table.typeset(fd)
Utility function called by Sphinx.
gen_solver_table.typeset_solvers_table(fd, solver_table)
Generate solvers table ReST output.

script/gen_term_table.py script

Generate the table of all terms for the sphinx documentation.

gen_term_table.create_parser(slist, current_section)

gen_term_table.format_next(text, new_text, pos, can_newline, width, ispaces)

gen_term_table.gen_term_table(app)

gen_term_table.get_examples(table)

gen_term_table.main()

gen_term_table.set_section(sec)

gen_term_table.setup(app)

gen_term_table.to_list(slist, sec)

gen_term_table.typeset(filename)
Utility function called by sphinx.

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gen_term_table.typeset_examples(term_class, term_use)

gen_term_table.typeset_term_syntax(term_class)

gen_term_table.typeset_term_table(fd, keys, table, title)

Terms are sorted by name without the d*_ prefix.
gen_term_table.typeset_term_tables(fd, table)
Generate tables: basic, sensitivity, special.
gen_term_table.typeset_to_indent(txt, indent0, indent, width)

script/plot_condition_numbers.py script

Plot conditions numbers w.r.t. polynomial approximation order of reference element matrices for various FE polynomial
spaces (bases).
plot_condition_numbers.main()

script/plot_logs.py script

Plot logs of variables saved in a text file by sfepy.base.log.Log class.

The plot should be almost the same as the plot that would be generated by the Log directly.
class plot_logs.ParseRc(option_strings, dest, nargs=None, const=None, default=None, type=None,
choices=None, required=False, help=None, metavar=None)

plot_logs.main()

script/plot_mesh.py script

Plot mesh connectivities, facet orientations, global and local DOF ids etc.
To switch off plotting some mesh entities, set the corresponding color to None.
plot_mesh.main()

script/plot_quadratures.py script

Plot quadrature points for the given geometry and integration order.
plot_quadratures.main()

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script/plot_times.py script

Plot time steps, times of time steps and time deltas in a HDF5 results file.
plot_times.main()

script/save_basis.py script

Save polynomial basis on reference elements or on a mesh for visualization into a given output directory.
save_basis.get_dofs(dofs, n_total)

save_basis.main()

save_basis.save_basis_on_mesh(mesh, options, output_dir, lin, permutations=None, suffix='')

script/show_authors.py script

show_authors.main()

script/show_mesh_info.py script

Print various information about a mesh.

show_mesh_info.main()

script/show_terms_use.py script

Show terms use in problem description files in the given directory.

show_terms_use.main()

script/sync_module_docs.py script

Synchronize the documentation files in a given directory doc_dir with the actual state of the SfePy sources in top_dir.
Missing files are created, files with no corresponding source file are removed, other files are left untouched.

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Notes

The developer guide needs to be edited manually to reflect the changes.

sync_module_docs.main()

script/tile_periodic_mesh.py script

The program scales a periodic input mesh (a rectangle or box) in filename_in by a scale factor and generates a new
mesh by repeating the scaled original mesh in a regular grid (scale x scale [x scale]) if repeat option is None, or in a
grid nx x ny x nz for repeat ‘nx,ny,nz’, producing again a periodic rectangle or box mesh.
class tile_periodic_mesh.ParseRepeat(option_strings, dest, nargs=None, const=None, default=None,
type=None, choices=None, required=False, help=None,
metavar=None)

tile_periodic_mesh.main()

sfepy package

sfepy.config module

class sfepy.config.Config

compile_flags()

debug_flags()

is_release()

link_flags()

numpydoc_path()

python_include()

python_version()

refmap_memory_factor()

system()

tetgen_path()

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sfepy.config.has_attr(obj, attr)

sfepy.version module

sfepy.version.get_basic_info(version='2022.1')
Return SfePy installation directory information. Append current git commit hash to version.

sfepy.applications package

sfepy.applications.application module

class sfepy.applications.application.Application(conf, options, output_prefix, **kwargs)

Base class for applications.
Subclasses should implement: __init__(), call().
Automates parametric studies, see parametrize().
call_basic(**kwargs)

call_parametrized(**kwargs)

parametrize(parametric_hook)
Add parametric_hook, set __call__() to call_parametrized().
restore()
Remove parametric_hook, restore __call__() to call_basic().
setup_options()

sfepy.applications.evp_solver_app module

Eigenvalue problem solver application.

class sfepy.applications.evp_solver_app.EVPSolverApp(conf, options, output_prefix, **kwargs)
Solve an eigenvalue problem.
call(status=None)

make_full(svecs)

static process_options(options)
Application options setup. Sets default values for missing non-compulsory options.
save_results(eigs, vecs, out=None, mesh_results_name=None, eig_results_name=None)

setup_options()

setup_output()
Setup various file names for the output directory given by self.problem.output_dir.

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solve_eigen_problem()

sfepy.applications.pde_solver_app module

class sfepy.applications.pde_solver_app.PDESolverApp(conf, options, output_prefix,

init_equations=True, **kwargs)

call(status=None)

load_dict(filename)
Utility function to load a dictionary data from a HDF5 file filename.
static process_options(options)
Application options setup. Sets default values for missing non-compulsory options.
save_dict(filename, data)
Utility function to save a dictionary data to a HDF5 file filename.
setup_options()

setup_output_info(problem, options)
Modifies both problem and options!
sfepy.applications.pde_solver_app.assign_standard_hooks(obj, get, conf )
Set standard hook function attributes from conf to obj using the get function.
sfepy.applications.pde_solver_app.save_only(conf, save_names, problem=None)
Save information available prior to setting equations and solving them.
sfepy.applications.pde_solver_app.solve_pde(conf, options=None, status=None, **app_options)
Solve a system of partial differential equations (PDEs).
This function is a convenience wrapper that creates and runs an instance of PDESolverApp.
Parameters
conf [str or ProblemConf instance] Either the name of the problem description file defining the
PDEs, or directly the ProblemConf instance.
options [options] The command-line options.
status [dict-like] The object for storing the solver return status.
app_options [kwargs] The keyword arguments that can override application-specific options.

sfepy.base package

sfepy.base.base module

sfepy.base.base.debug(frame=None, frames_back=1)
Start debugger on line where it is called, roughly equivalent to:

import pdb; pdb.set_trace()

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First, this function tries to start an IPython-enabled debugger using the IPython API.
When this fails, the plain old pdb is used instead.
With IPython, one can say in what frame the debugger can stop.
class sfepy.base.base.Container(objs=None, **kwargs)

append(obj)

as_dict()
Return stored objects in a dictionary with object names as keys.
extend(objs)
Extend the container items by the sequence objs.
get(ii, default=None, msg_if_none=None)
Get an item from Container - a wrapper around Container.__getitem__() with defaults and custom error
message.
Parameters
ii [int or str] The index or name of the item.
default [any, optional] The default value returned in case the item ii does not exist.
msg_if_none [str, optional] If not None, and if default is None and the item ii does not exist,
raise ValueError with this message.
get_names()

has_key(ii)

insert(ii, obj)

iteritems()

iterkeys()

itervalues()

print_names()

remove_name(name)

update(objs=None)
A dict-like update for Struct attributes.
class sfepy.base.base.IndexedStruct(**kwargs)

class sfepy.base.base.OneTypeList(item_class, seq=None)

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find(name, ret_indx=False)

get_names()

print_names()

class sfepy.base.base.Output(prefix, filename=None, quiet=False, combined=False, append=False,

**kwargs)
Factory class providing output (print) functions. All SfePy printing should be accomplished by this class.

Examples

>>> from sfepy.base.base import Output

>>> output = Output('sfepy:')
>>> output(1, 2, 3, 'hello')
sfepy: 1 2 3 hello
>>> output.prefix = 'my_cool_app:'
>>> output(1, 2, 3, 'hello')
my_cool_app: 1 2 3 hello

get_output_function()

get_output_prefix()

property prefix
set_output(filename=None, quiet=False, combined=False, append=False)
Set the output mode.
If quiet is True, no messages are printed to screen. If simultaneously filename is not None, the messages
are logged into the specified file.
If quiet is False, more combinations are possible. If filename is None, output is to screen only, otherwise it
is to the specified file. Moreover, if combined is True, both the ways are used.
Parameters
filename [str or file object] Print messages into the specified file.
quiet [bool] Do not print anything to screen.
combined [bool] Print both on screen and into the specified file.
append [bool] Append to an existing file instead of overwriting it. Use with filename.
set_output_prefix(prefix)

class sfepy.base.base.Struct(**kwargs)

copy(deep=False, name=None)
Make a (deep) copy of self.
Parameters:
deep [bool] Make a deep copy.

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name [str] Name of the copy, with default self.name + ‘_copy’.

get(key, default=None, msg_if_none=None)
A dict-like get() for Struct attributes.
set_default(key, default=None)
Behaves like dict.setdefault().
str_all()

str_class()
As __str__(), but for class attributes.
to_dict()

update(other, **kwargs)
A dict-like update for Struct attributes.
sfepy.base.base.as_float_or_complex(val)
Try to cast val to Python float, and if this fails, to Python complex type.
sfepy.base.base.assert_(condition, msg='assertion failed!')

sfepy.base.base.check_names(names1, names2, msg)

Check if all names in names1 are in names2, otherwise raise IndexError with the provided message msg.
sfepy.base.base.configure_output(options)
Configure the standard output() function using output_log_name and output_screen attributes of options.
Parameters
options [Struct or dict] The options with output_screen and output_log_name items. Defaults
are provided if missing.
sfepy.base.base.debug(frame=None, frames_back=1)
Start debugger on line where it is called, roughly equivalent to:

import pdb; pdb.set_trace()

First, this function tries to start an IPython-enabled debugger using the IPython API.
When this fails, the plain old pdb is used instead.
With IPython, one can say in what frame the debugger can stop.
sfepy.base.base.debug_on_error()
Start debugger at the line where an exception was raised.
sfepy.base.base.dict_extend(d1, d2)

sfepy.base.base.dict_from_keys_init(keys, seq_class=None)

sfepy.base.base.dict_to_array(adict)
Convert a dictionary of nD arrays of the same shapes with non-negative integer keys to a single (n+1)D array.
sfepy.base.base.dict_to_struct(*args, **kwargs)
Convert a dict instance to a Struct instance.

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sfepy.base.base.edit_dict_strings(str_dict, old, new, recur=False)

Replace substrings old with new in string values of dictionary str_dict. Both old and new can be lists of the same
length - items in old are replaced by items in new with the same index.
Parameters
str_dict [dict] The dictionary with string values or tuples containing strings.
old [str or list of str] The old substring or list of substrings.
new [str or list of str] The new substring or list of substrings.
recur [bool] If True, edit tuple values recursively.
Returns
new_dict [dict] The dictionary with edited strings.
sfepy.base.base.edit_tuple_strings(str_tuple, old, new, recur=False)
Replace substrings old with new in items of tuple str_tuple. Non-string items are just copied to the new tuple.
Parameters
str_tuple [tuple] The tuple with string values.
old [str] The old substring.
new [str] The new substring.
recur [bool] If True, edit items that are tuples recursively.
Returns
new_tuple [tuple] The tuple with edited strings.
sfepy.base.base.find_subclasses(context, classes, omit_unnamed=False, name_attr='name')
Find subclasses of the given classes in the given context.

Examples

>>> solver_table = find_subclasses(vars().items(),

[LinearSolver, NonlinearSolver,
TimeSteppingSolver, EigenvalueSolver,
OptimizationSolver])

sfepy.base.base.get_arguments(omit=None)
Get a calling function’s arguments.
Returns:
args [dict] The calling function’s arguments.
sfepy.base.base.get_debug()
Utility function providing debug() function.
sfepy.base.base.get_default(arg, default, msg_if_none=None)

sfepy.base.base.get_default_attr(obj, attr, default, msg_if_none=None)

sfepy.base.base.get_subdict(adict, keys)
Get a sub-dictionary of adict with given keys.

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sfepy.base.base.import_file(filename, package_name=None, can_reload=True)

Import a file as a module. The module is explicitly reloaded to prevent undesirable interactions.
sfepy.base.base.insert_as_static_method(cls, name, function)

sfepy.base.base.insert_method(instance, function)

sfepy.base.base.insert_static_method(cls, function)

sfepy.base.base.invert_dict(d, is_val_tuple=False, unique=True)

Invert a dictionary by making its values keys and vice versa.
Parameters
d [dict] The input dictionary.
is_val_tuple [bool] If True, the d values are tuples and new keys are the tuple items.
unique [bool] If True, the d values are unique and so the mapping is one to one. If False, the d
values (possibly) repeat, so the inverted dictionary will have as items lists of corresponding
keys.
Returns
di [dict] The inverted dictionary.
sfepy.base.base.ipython_shell(frame=0)

sfepy.base.base.is_derived_class(cls, parent)

sfepy.base.base.is_integer(var)

sfepy.base.base.is_sequence(var)

sfepy.base.base.is_string(var)

sfepy.base.base.iter_dict_of_lists(dol, return_keys=False)

sfepy.base.base.load_classes(filenames, classes, package_name=None, ignore_errors=False,

name_attr='name')
For each filename in filenames, load all subclasses of classes listed.
sfepy.base.base.ordered_iteritems(adict)

sfepy.base.base.pause(msg=None)
Prints the line number and waits for a keypress.
If you press: “q” . . . . . . . . . . . . . it will call sys.exit() any other key . . . it will continue execution of the program
This is useful for debugging.
sfepy.base.base.print_structs(objs)
Print Struct instances in a container, works recursively. Debugging utility function.

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sfepy.base.base.python_shell(frame=0)

sfepy.base.base.remap_dict(d, map)
Utility function to remap state dict keys according to var_map.
sfepy.base.base.select_by_names(objs_all, names, replace=None, simple=True)

sfepy.base.base.set_defaults(dict_, defaults)

sfepy.base.base.shell(frame=0)
Embed an IPython (if available) or regular Python shell in the given frame.
sfepy.base.base.spause(msg=None)
Waits for a keypress.
If you press: “q” . . . . . . . . . . . . . it will call sys.exit() any other key . . . it will continue execution of the program
This is useful for debugging. This function is called from pause().
sfepy.base.base.structify(obj)
Convert a (nested) dict obj into a (nested) Struct.
sfepy.base.base.try_imports(imports, fail_msg=None)
Try import statements until one succeeds.
Parameters
imports [list] The list of import statements.
fail_msg [str] If not None and no statement succeeds, a ValueError is raised with the given
message, appended to all failed messages.
Returns
locals [dict] The dictionary of imported modules.
sfepy.base.base.update_dict_recursively(dst, src, tuples_too=False, overwrite_by_none=True)
Update dst dictionary recursively using items in src dictionary.
Parameters
dst [dict] The destination dictionary.
src [dict] The source dictionary.
tuples_too [bool] If True, recurse also into dictionaries that are members of tuples.
overwrite_by_none [bool] If False, do not overwrite destination dictionary values by None.
Returns
dst [dict] The destination dictionary.
sfepy.base.base.use_method_with_name(instance, method, new_name)

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sfepy.base.compat module

This module contains functions that have different names or behavior depending on NumPy and Scipy versions.
sfepy.base.compat.in1d(ar1, ar2, assume_unique=False, invert=False)
Test whether each element of a 1-D array is also present in a second array.
Returns a boolean array the same length as ar1 that is True where an element of ar1 is in ar2 and False otherwise.
We recommend using isin() instead of in1d for new code.
Parameters
ar1 [(M,) array_like] Input array.
ar2 [array_like] The values against which to test each value of ar1.
assume_unique [bool, optional] If True, the input arrays are both assumed to be unique, which
can speed up the calculation. Default is False.
invert [bool, optional] If True, the values in the returned array are inverted (that is, False
where an element of ar1 is in ar2 and True otherwise). Default is False. np.in1d(a, b,
invert=True) is equivalent to (but is faster than) np.invert(in1d(a, b)).
New in version 1.8.0.
Returns
in1d [(M,) ndarray, bool] The values ar1[in1d] are in ar2.
See also:

isin Version of this function that preserves the shape of ar1.

numpy.lib.arraysetops Module with a number of other functions for performing set operations on arrays.

Notes

in1d can be considered as an element-wise function version of the python keyword in, for 1-D sequences.
in1d(a, b) is roughly equivalent to np.array([item in b for item in a]). However, this idea fails if
ar2 is a set, or similar (non-sequence) container: As ar2 is converted to an array, in those cases asarray(ar2)
is an object array rather than the expected array of contained values.
New in version 1.4.0.

Examples

>>> test = np.array([0, 1, 2, 5, 0])

>>> states = [0, 2]
>>> mask = np.in1d(test, states)
>>> mask
array([ True, False, True, False, True])
>>> test[mask]
array([0, 2, 0])
>>> mask = np.in1d(test, states, invert=True)
>>> mask
array([False, True, False, True, False])
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>>> test[mask]
array([1, 5])

sfepy.base.compat.unique(ar, return_index=False, return_inverse=False, return_counts=False, axis=None)

Find the unique elements of an array.
Returns the sorted unique elements of an array. There are three optional outputs in addition to the unique ele-
ments:
• the indices of the input array that give the unique values
• the indices of the unique array that reconstruct the input array
• the number of times each unique value comes up in the input array

Parameters
ar [array_like] Input array. Unless axis is specified, this will be flattened if it is not already 1-D.
return_index [bool, optional] If True, also return the indices of ar (along the specified axis, if
provided, or in the flattened array) that result in the unique array.
return_inverse [bool, optional] If True, also return the indices of the unique array (for the spec-
ified axis, if provided) that can be used to reconstruct ar.
return_counts [bool, optional] If True, also return the number of times each unique item appears
in ar.
New in version 1.9.0.
axis [int or None, optional] The axis to operate on. If None, ar will be flattened. If an integer,
the subarrays indexed by the given axis will be flattened and treated as the elements of a 1-D
array with the dimension of the given axis, see the notes for more details. Object arrays or
structured arrays that contain objects are not supported if the axis kwarg is used. The default
is None.
New in version 1.13.0.
Returns
unique [ndarray] The sorted unique values.
unique_indices [ndarray, optional] The indices of the first occurrences of the unique values in
the original array. Only provided if return_index is True.
unique_inverse [ndarray, optional] The indices to reconstruct the original array from the unique
array. Only provided if return_inverse is True.
unique_counts [ndarray, optional] The number of times each of the unique values comes up in
the original array. Only provided if return_counts is True.
New in version 1.9.0.

See also:

numpy.lib.arraysetops Module with a number of other functions for performing set operations on arrays.
repeat Repeat elements of an array.

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Notes

When an axis is specified the subarrays indexed by the axis are sorted. This is done by making the specified
axis the first dimension of the array (move the axis to the first dimension to keep the order of the other axes) and
then flattening the subarrays in C order. The flattened subarrays are then viewed as a structured type with each
element given a label, with the effect that we end up with a 1-D array of structured types that can be treated in
the same way as any other 1-D array. The result is that the flattened subarrays are sorted in lexicographic order
starting with the first element.

Examples

>>> np.unique([1, 1, 2, 2, 3, 3])

array([1, 2, 3])
>>> a = np.array([[1, 1], [2, 3]])
>>> np.unique(a)
array([1, 2, 3])

Return the unique rows of a 2D array

>>> a = np.array([[1, 0, 0], [1, 0, 0], [2, 3, 4]])

>>> np.unique(a, axis=0)
array([[1, 0, 0], [2, 3, 4]])

Return the indices of the original array that give the unique values:

>>> a = np.array(['a', 'b', 'b', 'c', 'a'])

>>> u, indices = np.unique(a, return_index=True)
>>> u
array(['a', 'b', 'c'], dtype='<U1')
>>> indices
array([0, 1, 3])
>>> a[indices]
array(['a', 'b', 'c'], dtype='<U1')

Reconstruct the input array from the unique values and inverse:

>>> a = np.array([1, 2, 6, 4, 2, 3, 2])

>>> u, indices = np.unique(a, return_inverse=True)
>>> u
array([1, 2, 3, 4, 6])
>>> indices
array([0, 1, 4, 3, 1, 2, 1])
>>> u[indices]
array([1, 2, 6, 4, 2, 3, 2])

Reconstruct the input values from the unique values and counts:

>>> a = np.array([1, 2, 6, 4, 2, 3, 2])

>>> values, counts = np.unique(a, return_counts=True)
>>> values
array([1, 2, 3, 4, 6])
>>> counts
array([1, 3, 1, 1, 1])
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>>> np.repeat(values, counts)
array([1, 2, 2, 2, 3, 4, 6]) # original order not preserved

sfepy.base.conf module

Problem description file handling.

Notes

Short syntax: key is suffixed with ‘__<number>’ to prevent collisions with long syntax keys -> both cases can be used
in a single input.
class sfepy.base.conf.ProblemConf(define_dict, funmod=None, filename=None, required=None,
other=None, verbose=True, override=None, setup=True)
Problem configuration, corresponding to an input (problem description file). It validates the input using lists
of required and other keywords that have to/can appear in the input. Default keyword lists can be obtained by
sfepy.base.conf.get_standard_keywords().
ProblemConf instance is used to construct a Problem instance via Problem.from_conf(conf).
add_missing(conf )
Add missing values from another problem configuration.
Missing keys/values are added also to values that are dictionaries.
Parameters
conf [ProblemConf instance] The other configuration.
edit(key, newval)

static from_dict(dict_, funmod, required=None, other=None, verbose=True, override=None,

setup=True)

static from_file(filename, required=None, other=None, verbose=True, define_args=None,

override=None, setup=True)
Loads the problem definition from a file.
The filename can either contain plain definitions, or it can contain the define() function, in which case it
will be called to return the input definitions.
The job of the define() function is to return a dictionary of parameters. How the dictionary is constructed
is not our business, but the usual way is to simply have a function define() along these lines in the input file:

def define():
options = {
'save_eig_vectors' : None,
'eigen_solver' : 'eigen1',
}
region_2 = {
'name' : 'Surface',
'select' : 'nodes of surface',
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(continued from previous page)

}
return locals()

Optionally, the define() function can accept additional arguments that should be defined using the de-
fine_args tuple or dictionary.
static from_file_and_options(filename, options, required=None, other=None, verbose=True,
define_args=None, setup=True)
Utility function, a wrapper around ProblemConf.from_file() with possible override taken from options.
static from_module(module, required=None, other=None, verbose=True, override=None, setup=True)

get_function(name)
Get a function object given its name.
It can be either in ProblemConf.funmod, or a ProblemConf attribute directly.
Parameters
name [str or function or None] The function name or directly the function.
Returns
fun [function or None] The required function, or None if name was None.
get_item_by_name(key, item_name)
Return item with name item_name in configuration group given by key.
get_raw(key=None)

setup(define_dict=None, funmod=None, filename=None, required=None, other=None)

transform_input()

transform_input_trivial()
Trivial input transformations.
update_conf(conf )
Update configuration by values in another problem configuration.
Values that are dictionaries are updated in-place by dict.update().
Parameters
conf [ProblemConf instance] The other configuration.
validate(required=None, other=None)

sfepy.base.conf.dict_from_options(options)
Return a dictionary that can be used to construct/override a ProblemConf instance based on options.
See --conf and --options options of the simple.py script.
sfepy.base.conf.dict_from_string(string, allow_tuple=False, free_word=False)
Parse string and return a dictionary that can be used to construct/override a ProblemConf instance.
sfepy.base.conf.get_standard_keywords()

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sfepy.base.conf.transform_conditions(adict, prefix)

sfepy.base.conf.transform_dgebcs(adict)

sfepy.base.conf.transform_dgepbcs(adict)

sfepy.base.conf.transform_ebcs(adict)

sfepy.base.conf.transform_epbcs(adict, prefix='epbc')

sfepy.base.conf.transform_fields(adict)

sfepy.base.conf.transform_functions(adict)

sfepy.base.conf.transform_ics(adict)

sfepy.base.conf.transform_integrals(adict)

sfepy.base.conf.transform_lcbcs(adict)

sfepy.base.conf.transform_materials(adict)

sfepy.base.conf.transform_regions(adict)

sfepy.base.conf.transform_solvers(adict)

sfepy.base.conf.transform_to_i_struct_1(adict)

sfepy.base.conf.transform_to_struct_01(adict)

sfepy.base.conf.transform_to_struct_1(adict)

sfepy.base.conf.transform_to_struct_10(adict)

sfepy.base.conf.transform_variables(adict)

sfepy.base.conf.tuple_to_conf(name, vals, order)

Convert a configuration tuple vals into a Struct named name, with attribute names given in and ordered by order.
Items in order at indices outside the length of vals are ignored.

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sfepy.base.getch module

getch()-like unbuffered character reading from stdin on both Windows and Unix
_Getch classes inspired by Danny Yoo, iskeydown() based on code by Zachary Pincus.

sfepy.base.goptions module

Various global options/parameters.

Notes

Inspired by rcParams of matplotlib.

class sfepy.base.goptions.ValidatedDict
A dictionary object including validation.
keys()
Return sorted list of keys.
validate = {'check_term_finiteness': <function validate_bool>, 'verbose':
<function validate_bool>}
values()
Return values in order of sorted keys.
sfepy.base.goptions.validate_bool(val)
Convert b to a boolean or raise a ValueError.

sfepy.base.ioutils module

class sfepy.base.ioutils.Cached(data)
The wrapper class that marks data, that should be checked during saving, whether it has been stored to the hdf5
file already and if so, a softlink to the already created instance is created instead of saving.
class sfepy.base.ioutils.DataMarker(data)
The Base class for classes for marking data to be handled in a special way during saving to a HDF5 file by
write_to_hdf5(). The usage is simple: just “decorate” the desired data element, e.g.:

data = [data1, Cached(data2)]

write_to_hdf5(... , ... , data)

unpack_data()
One can request unpacking of the wrappers during saving.
Returns
object The original object, if possible, or self.
class sfepy.base.ioutils.DataSoftLink(type, destination, cache=None)
This object is written to the HDF5 file as a softlink to the given path. The destination of the softlink should
contain only data, so the structure {type: type, data: softlink_to(destination)} is created in the place where the
softlink is written.
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unpack_data()
One can request unpacking of the wrappers during saving.
Returns
object The original object, if possible, or self.
write_data(fd, group, cache=None)
Create the softlink to the destination and handle the caching.
class sfepy.base.ioutils.HDF5BaseData
When storing values to HDF5, special classes can be used that wrap the stored data and modify the way the
storing is done. This class is the base of those.
unpack_data()
One can request unpacking of the wrappers during saving.
Returns
object The original object, if possible, or self.
class sfepy.base.ioutils.HDF5ContextManager(filename, *args, **kwargs)

class sfepy.base.ioutils.HDF5Data
Some data written to the HDF5 file can have a custom format. Descendants of this class should have the method
.write_data() or redefine the .write() method.
write(fd, group, name, cache=None)
Write a data structure to the HDF5 file.
Create the following structure in the HDF5 file: {type: self.get_type(), anything writed by self.write_data()}
Parameters
fd: tables.File The hdf5 file handle the data should be writed in.
group: tables.group.Group The group the data will be stored to
name: str Name of node that will be appended to group and will contain the data
cache: dict or None, optional Store for already cached objects with structs id(obj) : /path/to
Can be used for not storing the one object twice.
write_data(fd, group)
Write data to the HDF5 file. Redefine this function in sub-classes.
Parameters
fd: tables.File The hdf5 file handle the data should be writed to.
group: tables.group.Group The group the data should be stored to.
class sfepy.base.ioutils.InDir(filename)
Store the directory name a file is in, and prepend this name to other files.

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Examples

>>> indir = InDir('output/file1')

>>> print indir('file2')

class sfepy.base.ioutils.SoftLink(destination)
This object is written to the HDF5 file as a softlink to the given path.
write(fd, group, name, cache=None)
Create the softlink to the destination.
class sfepy.base.ioutils.Uncached(data)
The wrapper class that marks data, that should be always stored to the hdf5 file, even if the object has been already
stored at a different path in the file and so it would have been stored by a softlink otherwise (IGDomain, Mesh
and sparse matrices behave so).
sfepy.base.ioutils.dec(val, encoding='utf-8')
Decode given bytes using the specified encoding.
sfepy.base.ioutils.edit_filename(filename, prefix='', suffix='', new_ext=None)
Edit a file name by add a prefix, inserting a suffix in front of a file name extension or replacing the extension.
Parameters
filename [str] The file name.
prefix [str] The prefix to be added.
suffix [str] The suffix to be inserted.
new_ext [str, optional] If not None, it replaces the original file name extension.
Returns
new_filename [str] The new file name.
sfepy.base.ioutils.enc(string, encoding='utf-8')
Encode given string or bytes using the specified encoding.
sfepy.base.ioutils.ensure_path(filename)
Check if path to filename exists and if not, create the necessary intermediate directories.
sfepy.base.ioutils.get_or_create_hdf5_group(fd, path, from_group=None)

sfepy.base.ioutils.get_print_info(n_step, fill=None)
Returns the max. number of digits in range(n_step) and the corresponding format string.
Examples:

>>> get_print_info(11)
(2, '%2d')
>>> get_print_info(8)
(1, '%1d')
>>> get_print_info(100)
(2, '%2d')
>>> get_print_info(101)
(3, '%3d')
>>> get_print_info(101, fill='0')
(3, '%03d')

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sfepy.base.ioutils.get_trunk(filename)

sfepy.base.ioutils.locate_files(pattern, root_dir='.', **kwargs)

Locate all files matching fiven filename pattern in and below supplied root directory.
The **kwargs arguments are passed to os.walk().
sfepy.base.ioutils.look_ahead_line(fd)
Read and return a line from the given file object. Saves the current position in the file before the reading occurs
and then, after the reading, restores the saved (original) position.
sfepy.base.ioutils.path_of_hdf5_group(group)

sfepy.base.ioutils.read_array(fd, n_row, n_col, dtype)

Read a NumPy array of shape (n_row, n_col) from the given file object and cast it to type dtype. If n_col is None,
determine the number of columns automatically.
sfepy.base.ioutils.read_dict_hdf5(filename, level=0, group=None, fd=None)

sfepy.base.ioutils.read_from_hdf5(fd, group, cache=None)

Read custom data from a HDF5 file group saved by write_to_hdf5().
The data are stored in a general (possibly nested) structure: {
‘type’ : string type identificator ‘data’ : stored data ‘cache’: string, optional - another posible location
of object
}
Parameters
fd: tables.File The hdf5 file handle the data should be restored from.
group: tables.group.Group The group in the hdf5 file the data will be restored from.
cache: dict or None Some objects (e.g. Mesh instances) can be stored on more places in the
HDF5 file tree using softlinks, so when the data are restored, the restored objects are stored
and searched in cache so that they are created only once. The keys to cache are the (real)
paths of the created objects. Moreover, if some stored object has a ‘cache’ key (see e.g.
DataSoftLink class), and the object with a given ‘path’ has been already created, it is returned
instead of creating a new object. Otherwise, the newly created object is associated both with
its real path and with the cache key path.
The caching is not active for scalar data types.
Returns
data [object] The restored custom data.
sfepy.base.ioutils.read_list(fd, n_item, dtype)

sfepy.base.ioutils.read_sparse_matrix_from_hdf5(fd, group, output_format=None)

Read sparse matrix from given data group of hdf5 file
Parameters
fd: tables.File The hdf5 file handle the matrix will be read from.
group: tables.group.group The hdf5 file group of the file the matrix will be read from.

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output_format: {‘csr’, ‘csc’, None}, optional The resulting matrix will be in CSR or CSC for-
mat if this parameter is not None (which is default), otherwise it will be in the format the
matrix was stored.
Returns
scipy.sparse.base.spmatrix Readed matrix
sfepy.base.ioutils.read_sparse_matrix_hdf5(filename, output_format=None)

sfepy.base.ioutils.read_token(fd)
Read a single token (sequence of non-whitespace characters) from the given file object.

Notes

Consumes the first whitespace character after the token.

sfepy.base.ioutils.remove_files(root_dir, **kwargs)
Remove all files and directories in supplied root directory.
The **kwargs arguments are passed to os.walk().
sfepy.base.ioutils.remove_files_patterns(root_dir, patterns, ignores=None, verbose=False)
Remove files with names satisfying the given glob patterns in a supplied root directory. Files with patterns in
ignores are omitted.
sfepy.base.ioutils.save_options(filename, options_groups, save_command_line=True,
quote_command_line=False)
Save groups of options/parameters into a file.
Each option group has to be a sequence with two items: the group name and the options in {key : value}
form.
sfepy.base.ioutils.skip_read_line(fd, no_eof=False)
Read the first non-empty line (if any) from the given file object. Return an empty string at EOF, if no_eof is
False. If it is True, raise the EOFError instead.
sfepy.base.ioutils.write_dict_hdf5(filename, adict, level=0, group=None, fd=None)

sfepy.base.ioutils.write_sparse_matrix_hdf5(filename, mtx, name='a sparse matrix')

Assume CSR/CSC.
sfepy.base.ioutils.write_sparse_matrix_to_hdf5(fd, group, mtx)
Write sparse matrix to given data group of hdf5 file
Parameters
group: tables.group.group The hdf5 file group the matrix will be read from.
mtx: scipy.sparse.base.spmatrix The writed matrix
sfepy.base.ioutils.write_to_hdf5(fd, group, name, data, cache=None, unpack_markers=False)
Save custom data to a HDF5 file group to be restored by read_from_hdf5().
Allows saving lists, dicts, numpy arrays, scalars, sparse matrices, meshes and iga domains and all pickleable
objects.
Parameters
fd: tables.File The hdf5 file handle the data should be written in.
group: tables.group.Group The group the data will be stored to.

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name: str The name of the node that will be appended to the group and will contain the data.
data: object Data to be stored in the HDF5 file.
cache: dict or None The cache where the paths to stored objects (currently meshes and iga do-
mains) are stored, so subsequent attempts to store such objects create only softlinks to the
initially stored object. The id() of objects serve as the keys into the cache. Mark the object
with Cached() or Uncached() for (no) softlinking.
unpack_markers: If True, the input data is modified so that Cached and Uncached markers are
removed from all sub-elements of the data.
Returns
tables.group.Group The HDF5 group the data was stored to.

sfepy.base.log module

class sfepy.base.log.Log(data_names=None, plot_kwargs=None, xlabels=None, ylabels=None,

yscales=None, show_legends=True, is_plot=True, aggregate=100, sleep=1.0,
log_filename=None, formats=None)
Log data and (optionally) plot them in the second process via LogPlotter.
add_group(names, plot_kwargs=None, yscale=None, xlabel=None, ylabel=None, formats=None)
Add a new data group. Notify the plotting process if it is already running.
count = -1
static from_conf(conf, data_names)

Parameters
data_names [list of lists of str] The data names grouped by subplots: [[name1, name2, . . . ],
[name3, name4, . . . ], . . . ], where name<n> are strings to display in (sub)plot legends.
get_log_name()

plot_data(igs)

plot_vlines(igs=None, **kwargs)
Plot vertical lines in axes given by igs at current x locations to mark some events.
terminate()

sfepy.base.log.get_logging_conf(conf, log_name='log')
Check for a log configuration (‘log’ attribute by default) in conf. Supply default values if necessary.
Parameters
conf [Struct] The configuration object.
log_name [str, optional] The name of the log configuration attribute in conf.
Returns
log [dict] The dictionary {‘plot’ : <figure_file>, ‘text’ : <text_log_file>}. One or both values
can be None.

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sfepy.base.log.iter_names(data_names, igs=None)

sfepy.base.log.plot_log(axs, log, info, xticks=None, yticks=None, xnbins=None, ynbins=None, groups=None,

show_legends=True, swap_axes=False)
Plot log data returned by read_log() into a specified figure.
Parameters
axs [sequence of matplotlib.axes.Axes] The list of axes for the log data plots.
log [dict] The log with data names as keys and (xs, ys, vlines) as values.
info [dict] The log plot configuration with subplot numbers as keys.
xticks [list of arrays, optional] The list of x-axis ticks (array or None) for each subplot.
yticks [list of arrays, optional] The list of y-axis ticks (array or None) for each subplot.
xnbins [list, optional] The list of x-axis number of bins (int or None) for each subplot.
ynbins [list, optional] The list of y-axis number of bins (int or None) for each subplot.
groups [list, optional] The list of data groups subplots. If not given, all groups are plotted.
show_legends [bool] If True, show legends in plots.
swap_axes [bool] If True, swap the axes of the plots.
sfepy.base.log.read_log(filename)
Read data saved by Log into a text file.
Parameters
filename [str] The name of a text log file.
Returns
log [dict] The log with data names as keys and (xs, ys, vlines) as values.
info [dict] The log plot configuration with subplot numbers as keys.
sfepy.base.log.write_log(output, log, info)

sfepy.base.log_plotter module

Plotting class to be used by Log.

class sfepy.base.log_plotter.LogPlotter(aggregate=100, sleep=1.0)
LogPlotter to be used by sfepy.base.log.Log.
apply_commands()

make_axes()

output = Output
poll_draw()

process_command(command)

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terminate()

sfepy.base.log_plotter.draw_data(ax, xdata, ydata, label, plot_kwargs, swap_axes=False)

Draw log data to a given axes, obeying swap_axes.

sfepy.base.mem_usage module

Memory usage functions.

sfepy.base.mem_usage.get_mem_usage(obj, usage=None, name=None, traversal_order=None, level=0)
Get lower bound of memory usage of an object.
Takes into account strings, numpy arrays and scipy CSR sparse matrices, descends into sequences, mappings
and objects.
Parameters
obj [any object] The object to be measured.
usage [dict] The dict with memory usage records, serving also as a cache of already traversed
objects.
name [str] The name to be given to the object in its record.
traversal_order [list, internal] The traversal order of the object.
level [int, internal] The recurrence level.
Returns
usage [int] The object’s lower bound of memory usage.
sfepy.base.mem_usage.print_mem_usage(usage, order_by='usage', direction='up', print_key=False)
Print memory usage dictionary.
Parameters
usage [dict] The dict with memory usage records.
order_by [‘usage’, ‘name’, ‘kind’, ‘nrefs’, ‘traversal_order’, or ‘level’] The sorting field name.
direction [‘up’ or ‘down’] The sorting direction.
print_key [bool] If True, print also the record key (object’s id).
sfepy.base.mem_usage.raise_if_too_large(size, factor=1.0)
Raise MemoryError if the total system memory is lower than size times safety factor. Use factor=None for
skipping the memory check.

sfepy.base.multiproc module

Multiprocessing functions.
sfepy.base.multiproc.get_multiproc(mpi=False)

sfepy.base.multiproc.get_num_workers()
Get the number of slave nodes.
sfepy.base.multiproc.is_remote_dict(d)

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sfepy.base.multiproc_mpi module

Multiprocessing functions.
class sfepy.base.multiproc_mpi.MPIFileHandler(filename, mode=4, encoding=None, delay=0,
comm=<mpi4py.MPI.Intracomm object>)
MPI file class for logging process communication.
close()
Closes the stream.
class sfepy.base.multiproc_mpi.MPILogFile

write(*args, **kwargs)

class sfepy.base.multiproc_mpi.RemoteDict(name, mutable=False)

Remote dictionary class - slave side.
get(key, default=None)

keys()

update(other)

class sfepy.base.multiproc_mpi.RemoteDictMaster(name, mutable=False, soft_set=False, *args)

Remote dictionary class - master side.
remote_get(key, slave)

remote_get_in(key, slave)

remote_get_keys(slave)

remote_get_len(slave)

remote_set(data, slave, mutable=False)

class sfepy.base.multiproc_mpi.RemoteInt(remote_dict, value=None)

Remote intiger class, data saved in RemoteDict.
class IntDesc
value
class sfepy.base.multiproc_mpi.RemoteLock
Remote lock class - lock and unlock restricted access to the master.
acquire()

release()

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class sfepy.base.multiproc_mpi.RemoteQueue(name)
Remote queue class - slave side.
get()

put(value)

class sfepy.base.multiproc_mpi.RemoteQueueMaster(name, mode='fifo', *args)

Remote queue class - master side.
clean()

get()

static get_gdict_key(name)

put(value)

remote_get(slave)

remote_put(value, slave)

sfepy.base.multiproc_mpi.cpu_count()
Get the number of MPI nodes.
sfepy.base.multiproc_mpi.enum(*sequential)

sfepy.base.multiproc_mpi.get_dict(name, mutable=False, clear=False, soft_set=False)

Get the remote dictionary.
sfepy.base.multiproc_mpi.get_int_value(name, init_value=0)
Get the remote integer value.
sfepy.base.multiproc_mpi.get_logger(log_filename='multiproc_mpi.log')
Get the MPI logger which log information into a shared file.
sfepy.base.multiproc_mpi.get_queue(name)
Get the queue.
sfepy.base.multiproc_mpi.get_slaves()
Get the list of slave nodes
sfepy.base.multiproc_mpi.is_remote_dict(d)
Return True if ‘d’ is RemoteDict or RemoteDictMaster instance.
sfepy.base.multiproc_mpi.master_loop()
Run the master loop - wait for requests from slaves.
sfepy.base.multiproc_mpi.master_send_continue()
Send ‘continue’ to all slaves.
sfepy.base.multiproc_mpi.master_send_task(task, data)
Send task to all slaves.

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sfepy.base.multiproc_mpi.set_logging_level(log_level='info')

sfepy.base.multiproc_mpi.slave_get_task(name='')
Start the slave nodes.
sfepy.base.multiproc_mpi.slave_task_done(task='')
Stop the slave nodes.
sfepy.base.multiproc_mpi.tags
alias of sfepy.base.multiproc_mpi.Enum
sfepy.base.multiproc_mpi.wait_for_tag(wtag, num=1)

sfepy.base.multiproc_proc module

Multiprocessing functions - using multiprocessing (process based) module.

class sfepy.base.multiproc_proc.MyQueue

get()

put(value)

sfepy.base.multiproc_proc.get_dict(name, clear=False, **kwargs)

Get the remote dictionary.
sfepy.base.multiproc_proc.get_int_value(name, val0=0)
Get the remote integer value.
sfepy.base.multiproc_proc.get_list(name, clear=False)
Get the remote list.
sfepy.base.multiproc_proc.get_lock(name)
Get the global lock.
sfepy.base.multiproc_proc.get_manager()
Get the multiprocessing manager. If not in the global cache, create a new instance.
Returns
manager [manager] The multiprocessing manager.
sfepy.base.multiproc_proc.get_mpdict_value(mode, key, clear=False)
Get the item from the global multiprocessing cache.
Parameters
mode [str] The type of the required object.
key [immutable type] The key of the required object.
clear [bool] If True, clear the dictionary or list (for modes ‘dict’ and ‘list’).
Returns
value [remote object] The remote object.
sfepy.base.multiproc_proc.get_queue(name)
Get the global queue.

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sfepy.base.multiproc_proc.is_remote_dict(d)
Return True if ‘d’ is instance.

sfepy.base.parse_conf module

Create pyparsing grammar for problem configuration and options.

sfepy.base.parse_conf.create_bnf(allow_tuple=False, free_word=False)

sfepy.base.parse_conf.cvt_array_index(toks)

sfepy.base.parse_conf.cvt_cmplx(toks)

sfepy.base.parse_conf.cvt_int(toks)

sfepy.base.parse_conf.cvt_none(toks)

sfepy.base.parse_conf.cvt_real(toks)

sfepy.base.parse_conf.get_standard_type_defs(word={W:(ABCD...) [{{{Suppress:("{") Forward: None}

Suppress:("}")} Forward: None}]})
Return dict of the pyparsing base lexical elements.
The compound types (tuple, list, dict) can contain compound types or simple types such as integers, floats and
words.
Parameters
word [lexical element] A custom lexical element for word.
Returns
defs [dict] The dictionary with the following items:
• tuple: (. . . , . . . , . . . )
• list: [. . . , . . . ., . . . ]
• dict: {. . . :. . . , . . . :. . . , . . . .} or {. . . =. . . , . . . =. . . , . . . .}
• list_item: any of preceding compound types or simple types
sfepy.base.parse_conf.list_dict(word={W:(ABCD...) [{{{Suppress:("{") Forward: None} Suppress:("}")}
Forward: None}]})
Return the pyparsing lexical element, that parses a string either as a list or as a dictionary.
Parameters
word [lexical element] A custom lexical element for word.
Returns
ld [lexical element] The returned lexical element parses a string in the form ..., ..
., ... or key1:..., key2=..., key3: ... where ... is a list_item from
get_standard_type_defs() and interprets it as a list or a dictionary.

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sfepy.base.parse_conf.list_of(element, *elements)
Return lexical element that parses a list of items. The items can be a one or several lexical elements. For example,
result of list_of(real, integer) parses list of real or integer numbers.

sfepy.base.plotutils module

sfepy.base.plotutils.font_size(size)

sfepy.base.plotutils.iplot(*args, **kwargs)

sfepy.base.plotutils.plot_matrix_diff(mtx1, mtx2, delta, legend, mode)

sfepy.base.plotutils.print_matrix_diff(title, legend, mtx1, mtx2, mtx_da, mtx_dr, iis)

sfepy.base.plotutils.set_axes_font_size(ax, size)

sfepy.base.plotutils.spy(mtx, eps=None, color='b', **kwargs)

Show sparsity structure of a scipy.sparse matrix.
sfepy.base.plotutils.spy_and_show(mtx, **kwargs)

sfepy.base.reader module

class sfepy.base.reader.Reader(directory)
Reads and executes a Python file as a script with execfile(), storing its locals. Then sets the __dict__ of a new
instance of obj_class to the stored locals.
Example:

>>> class A:
>>> pass

>>> read = Reader( '.' )

>>> instance_of_a = read( A, 'file.py' )

It is equivalent to:

>>> mod = __import__( 'file' )

>>> instance_of_a = A()
>>> instance_of_a.__dict__.update( mod.__dict__ )

The first way does not create the ‘file.pyc’. . .

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sfepy.base.resolve_deps module

Functions for resolving dependencies.

sfepy.base.resolve_deps.get_nums(deps)
Get number of prerequisite names for each name in dependencies.
sfepy.base.resolve_deps.remove_known(deps, known)
Remove known names from dependencies.
sfepy.base.resolve_deps.resolve(deps)
Resolve dependencies among equations so that smaller blocks are solved first.
The dependencies are given in terms of variable names.
Parameters
deps [dict] The dependencies as a dictionary with names as keys and sets of prerequisite names
as values.
Returns
order [list] The list of blocks in the order of solving. Each block is a list of names.
sfepy.base.resolve_deps.solvable(deps, names)
Return True if names form a solvable block, i.e. the set of names equals to the set of their prerequisites.
sfepy.base.resolve_deps.try_block(deps, num)
Return generator of lists of solvable blocks of the length num.

sfepy.base.testing module

class sfepy.base.testing.NLSStatus(**kwargs)
Custom nonlinear solver status storing stopping condition of all time steps.
sfepy.base.testing.assert_equal(a, b, msg='assertion of equality failed!')

sfepy.base.testing.check_conditions(conditions)

sfepy.base.testing.compare_vectors(vec1, vec2, allowed_error=1e-08, label1='vec1', label2='vec2',

norm=None)

sfepy.base.testing.eval_coor_expression(expression, coor)

sfepy.base.testing.report(*argc)
All tests should print via this function.
sfepy.base.testing.run_declaratice_example(ex_filename, output_dir, ext='.vtk', remove_prefix='')
Run a declarative example in ex_filename given relatively to sfepy.base_dir.

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sfepy.base.timing module

Elapsed time measurement utilities.

class sfepy.base.timing.Timer(name='timer', start=False)

reset()

start(reset=False)

stop()

sfepy.discrete package

This package implements various PDE discretization schemes (FEM or IGA).

sfepy.discrete.conditions module

The Dirichlet, periodic and linear combination boundary condition classes, as well as the initial condition class.
class sfepy.discrete.conditions.Condition(name, **kwargs)
Common boundary condition methods.
canonize_dof_names(dofs)
Canonize the DOF names using the full list of DOFs of a variable.
Assumes single condition instance.
iter_single()
Create a single condition instance for each item in self.dofs and yield it.
class sfepy.discrete.conditions.Conditions(objs=None, **kwargs)
Container for various conditions.
canonize_dof_names(dofs)
Canonize the DOF names using the full list of DOFs of a variable.
static from_conf(conf, regions)

group_by_variables(groups=None)
Group boundary conditions of each variable. Each condition is a group is a single condition.
Parameters
groups [dict, optional] If present, update the groups dictionary.
Returns
out [dict] The dictionary with variable names as keys and lists of single condition instances
as values.
sort()
Sort boundary conditions by their key.
zero_dofs()
Set all boundary condition values to zero, if applicable.

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class sfepy.discrete.conditions.DGEssentialBC(*args, diff=0, **kwargs)

This class is empty, it serves the same purpose as EssentialBC, and is created only for branching in dof_info.py
class sfepy.discrete.conditions.DGPeriodicBC(name, regions, dofs, match, key='', times=None)
This class is empty, it serves the same purpose as PeriodicBC, and is created only for branching in dof_info.py
class sfepy.discrete.conditions.EssentialBC(name, region, dofs, key='', times=None)
Essential boundary condidion.
Parameters
name [str] The boundary condition name.
region [Region instance] The region where the boundary condition is applied.
dofs [dict] The boundary condition specification defining the constrained DOFs and their values.
key [str, optional] The sorting key.
times [list or str, optional] The list of time intervals or a function returning True at time steps,
when the condition applies.
zero_dofs()
Set all essential boundary condition values to zero.
class sfepy.discrete.conditions.InitialCondition(name, region, dofs, key='')
Initial condidion.
Parameters
name [str] The initial condition name.
region [Region instance] The region where the initial condition is applied.
dofs [dict] The initial condition specification defining the constrained DOFs and their values.
key [str, optional] The sorting key.
class sfepy.discrete.conditions.LinearCombinationBC(name, regions, dofs, dof_map_fun, kind, key='',
times=None, arguments=None)
Linear combination boundary condidion.
Parameters
name [str] The boundary condition name.
regions [list of two Region instances] The constrained (master) DOFs region and the new (slave)
DOFs region. The latter can be None if new DOFs are not field variable DOFs.
dofs [dict] The boundary condition specification defining the constrained DOFs and the new
DOFs (can be None).
dof_map_fun [str] The name of function for mapping the constrained DOFs to new DOFs (can
be None).
kind [str] The linear combination condition kind.
key [str, optional] The sorting key.
times [list or str, optional] The list of time intervals or a function returning True at time steps,
when the condition applies.
arguments: tuple, optional Additional arguments, depending on the condition kind.
canonize_dof_names(dofs0, dofs1=None)
Canonize the DOF names using the full list of DOFs of a variable.

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Assumes single condition instance.

get_var_names()
Get names of variables corresponding to the constrained and new DOFs.
class sfepy.discrete.conditions.PeriodicBC(name, regions, dofs, match, key='', times=None)
Periodic boundary condidion.
Parameters
name [str] The boundary condition name.
regions [list of two Region instances] The master region and the slave region where the DOFs
should match.
dofs [dict] The boundary condition specification defining the DOFs in the master region and the
corresponding DOFs in the slave region.
match [str] The name of function for matching corresponding nodes in the two regions.
key [str, optional] The sorting key.
times [list or str, optional] The list of time intervals or a function returning True at time steps,
when the condition applies.
canonize_dof_names(dofs)
Canonize the DOF names using the full list of DOFs of a variable.
Assumes single condition instance.
sfepy.discrete.conditions.get_condition_value(val, functions, kind, name)
Check a boundary/initial condition value type and return the value or corresponding function.

sfepy.discrete.equations module

Classes of equations composed of terms.

class sfepy.discrete.equations.Equation(name, terms)

collect_conn_info(conn_info)

collect_materials()
Collect materials present in the terms of the equation.
collect_variables()
Collect variables present in the terms of the equation.
Ensures that corresponding primary variables of test/parameter variables are always in the list, even if they
are not directly used in the terms.
evaluate(mode='eval', dw_mode='vector', term_mode=None, asm_obj=None)

Parameters
mode [one of ‘eval’, ‘el_eval’, ‘el_avg’, ‘qp’, ‘weak’] The evaluation mode.
static from_desc(name, desc, variables, regions, materials, integrals, user=None, eterm_options=None)

class sfepy.discrete.equations.Equations(equations)

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add_equation(equation)
Add a new equation.
Parameters
equation [Equation instance] The new equation.
advance(ts)

apply_ebc(vec=None, force_values=None)
Apply essential (Dirichlet) boundary conditions to equations’ variables, or a given vector.
apply_ic(vec=None, force_values=None)
Apply initial conditions to equations’ variables, or a given vector.
collect_conn_info()
Collect connectivity information as defined by the equations.
collect_materials()
Collect materials present in the terms of all equations.
collect_variables()
Collect variables present in the terms of all equations.
create_matrix_graph(any_dof_conn=False, rdcs=None, cdcs=None, shape=None, active_only=True,
verbose=True)
Create tangent matrix graph, i.e. preallocate and initialize the sparse storage needed for the tangent matrix.
Order of DOF connectivities is not important.
Parameters
any_dof_conn [bool] By default, only volume DOF connectivities are used, with the ex-
ception of trace surface DOF connectivities. If True, any kind of DOF connectivities is
allowed.
rdcs, cdcs [arrays, optional] Additional row and column DOF connectivities, corresponding
to the variables used in the equations.
shape [tuple, optional] The required shape, if it is different from the shape determined by the
equations variables. This may be needed if additional row and column DOF connectivities
are passed in.
active_only [bool] If True, the matrix graph has reduced size and is created with the reduced
(active DOFs only) numbering.
verbose [bool] If False, reduce verbosity.
Returns
matrix [csr_matrix] The matrix graph in the form of a CSR matrix with preallocated struc-
ture and zero data.
create_reduced_vec()

create_subequations(var_names, known_var_names=None)
Create sub-equations containing only terms with the given virtual variables.
Parameters
var_names [list] The list of names of virtual variables.
known_var_names [list] The list of names of (already) known state variables.

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Returns
subequations [Equations instance] The sub-equations.
create_vec()

eval_residuals(state, by_blocks=False, names=None)

Evaluate (assemble) residual vectors.
Parameters
state [array] The vector of DOF values. Note that it is needed only in nonlinear terms.
by_blocks [bool] If True, return the individual blocks composing the whole residual vec-
tor. Each equation should then correspond to one required block and should be named as
‘block_name, test_variable_name, unknown_variable_name’.
names [list of str, optional] Optionally, select only blocks with the given names, if by_blocks
is True.
Returns
out [array or dict of array] The assembled residual vector. If by_blocks is True, a dictionary
is returned instead, with keys given by block_name part of the individual equation names.
eval_tangent_matrices(state, tangent_matrix, by_blocks=False, names=None)
Evaluate (assemble) tangent matrices.
Parameters
state [array] The vector of DOF values. Note that it is needed only in nonlinear terms.
tangent_matrix [csr_matrix] The preallocated CSR matrix with zero data.
by_blocks [bool] If True, return the individual blocks composing the whole matrix.
Each equation should then correspond to one required block and should be named as
‘block_name, test_variable_name, unknown_variable_name’.
names [list of str, optional] Optionally, select only blocks with the given names, if by_blocks
is True.
Returns
out [csr_matrix or dict of csr_matrix] The assembled matrix. If by_blocks is True, a dic-
tionary is returned instead, with keys given by block_name part of the individual equation
names.
evaluate(names=None, mode='eval', dw_mode='vector', term_mode=None, asm_obj=None)
Evaluate the equations.
Parameters
mode [one of ‘eval’, ‘el_avg’, ‘qp’, ‘weak’] The evaluation mode.
names [str or sequence of str, optional] Evaluate only equations of the given name(s).
Returns
out [dict or result] The evaluation result. In ‘weak’ mode it is the asm_obj. Otherwise, it is
a dict of results with equation names as keys or a single result for a single equation.
static from_conf(conf, variables, regions, materials, integrals, user=None, eterm_options=None,
verbose=True)

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get_domain()

get_graph_conns(any_dof_conn=False, rdcs=None, cdcs=None, active_only=True)

Get DOF connectivities needed for creating tangent matrix graph.
Parameters
any_dof_conn [bool] By default, only volume DOF connectivities are used, with the ex-
ception of trace surface DOF connectivities. If True, any kind of DOF connectivities is
allowed.
rdcs, cdcs [arrays, optional] Additional row and column DOF connectivities, corresponding
to the variables used in the equations.
active_only [bool] If True, the active DOF connectivities have reduced size and are created
with the reduced (active DOFs only) numbering.
Returns
rdcs, cdcs [arrays] The row and column DOF connectivities defining the matrix graph
blocks.
get_lcbc_operator()

get_variable(name)

get_variable_dependencies()
For each virtual variable get names of state/parameter variables that are present in terms with that virtual
variable.
The virtual variables define the actual equations and their dependencies define the variables needed to
evaluate the equations.
Returns
deps [dict] The dependencies as a dictionary with virtual variable names as keys and sets of
state/parameter variables as values.
get_variable_names()
Return the list of names of all variables used in equations.
init_state(vec=None)

init_time(ts)

invalidate_term_caches()
Invalidate evaluate caches of variables present in equations.
make_full_vec(svec, force_value=None)
Make a full DOF vector satisfying E(P)BCs from a reduced DOF vector.
print_terms()
Print names of equations and their terms.
reduce_vec(vec, follow_epbc=False)
Get the reduced DOF vector, with EBC and PBC DOFs removed.

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Notes

If ‘follow_epbc’ is True, values of EPBC master dofs are not simply thrown away, but added to the corre-
sponding slave dofs, just like when assembling. For vectors with state (unknown) variables it should be set
to False, for assembled vectors it should be set to True.
reset_materials()
Clear material data so that next materials.time_update() is performed even for stationary materials.
set_data(data, step=0, ignore_unknown=False)
Set data (vectors of DOF values) of variables.
Parameters
data [dict] The dictionary of {variable_name : data vector}.
step [int, optional] The time history step, 0 (default) = current.
ignore_unknown [bool, optional] Ignore unknown variable names if data is a dict.
set_state(vec, reduced=False, force=False, preserve_caches=False)

setup_initial_conditions(ics, functions=None)

time_update(ts, ebcs=None, epbcs=None, lcbcs=None, functions=None, problem=None, active_only=True,

verbose=True)
Update the equations for current time step.
The update involves creating the mapping of active DOFs from/to all DOFs for all state variables, the setup
of linear combination boundary conditions operators and the setup of active DOF connectivities.
Parameters
ts [TimeStepper instance] The time stepper.
ebcs [Conditions instance, optional] The essential (Dirichlet) boundary conditions.
epbcs [Conditions instance, optional] The periodic boundary conditions.
lcbcs [Conditions instance, optional] The linear combination boundary conditions.
functions [Functions instance, optional] The user functions for boundary conditions, mate-
rials, etc.
problem [Problem instance, optional] The problem that can be passed to user functions as a
context.
active_only [bool] If True, the active DOF connectivities and matrix graph have reduced size
and are created with the reduced (active DOFs only) numbering.
verbose [bool] If False, reduce verbosity.
Returns
graph_changed [bool] The flag set to True if the current time step set of active boundary
conditions differs from the set of the previous time step.
time_update_materials(ts, mode='normal', problem=None, verbose=True)
Update data materials for current time and possibly also state.
Parameters
ts [TimeStepper instance] The time stepper.

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mode [‘normal’, ‘update’ or ‘force’] The update mode, see sfepy.discrete.materials.

Material.time_update().
problem [Problem instance, optional] The problem that can be passed to user functions as a
context.
verbose [bool] If False, reduce verbosity.
sfepy.discrete.equations.get_expression_arg_names(expression, strip_dots=True)
Parse expression and return set of all argument names. For arguments with attribute-like syntax (e.g. materials),
if strip_dots is True, only base argument names are returned.
sfepy.discrete.equations.parse_definition(equation_def )
Parse equation definition string to create term description list.

sfepy.discrete.evaluate module

class sfepy.discrete.evaluate.Evaluator(problem, matrix_hook=None)

This class provides the functions required by a nonlinear solver for a given problem.
eval_residual(vec, is_full=False)

eval_tangent_matrix(vec, mtx=None, is_full=False)

make_full_vec(vec)

static new_ulf_iteration(problem, nls, vec, it, err, err0)

sfepy.discrete.evaluate.apply_ebc_to_matrix(mtx, ebc_rows, epbc_rows=None)

Apply E(P)BC to matrix rows: put 1 to the diagonal for EBC DOFs, 1 to the diagonal for master EPBC DOFs,
-1 to the [master, slave] entries. It is assumed, that the matrix contains zeros in EBC and master EPBC DOFs
rows and columns.
sfepy.discrete.evaluate.assemble_by_blocks(conf_equations, problem, ebcs=None, epbcs=None,
dw_mode='matrix', active_only=True)
Instead of a global matrix, return its building blocks as defined in conf_equations. The name and row/column
variables of each block have to be encoded in the equation’s name, as in:

conf_equations = {
'A,v,u' : "dw_lin_elastic.i1.Y2( inclusion.D, v, u )",
}

Notes

ebcs, epbcs must be either lists of BC names, or BC configuration dictionaries.

sfepy.discrete.evaluate.create_evaluable(expression, fields, materials, variables, integrals,
regions=None, ebcs=None, epbcs=None, lcbcs=None,
ts=None, functions=None, auto_init=False, mode='eval',
extra_args=None, active_only=True, eterm_options=None,
verbose=True, kwargs=None)
Create evaluable object (equations and corresponding variables) from the expression string.
Parameters

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expression [str] The expression to evaluate.

fields [dict] The dictionary of fields used in variables.
materials [Materials instance] The materials used in the expression.
variables [Variables instance] The variables used in the expression.
integrals [Integrals instance] The integrals to be used.
regions [Region instance or list of Region instances] The region(s) to be used. If not given, the
regions defined within the fields domain are used.
ebcs [Conditions instance, optional] The essential (Dirichlet) boundary conditions for ‘weak’
mode.
epbcs [Conditions instance, optional] The periodic boundary conditions for ‘weak’ mode.
lcbcs [Conditions instance, optional] The linear combination boundary conditions for ‘weak’
mode.
ts [TimeStepper instance, optional] The time stepper.
functions [Functions instance, optional] The user functions for boundary conditions, materials
etc.
auto_init [bool] Set values of all variables to all zeros.
mode [one of ‘eval’, ‘el_avg’, ‘qp’, ‘weak’] The evaluation mode - ‘weak’ means the finite el-
ement assembling, ‘qp’ requests the values in quadrature points, ‘el_avg’ element averages
and ‘eval’ means integration over each term region.
extra_args [dict, optional] Extra arguments to be passed to terms in the expression.
active_only [bool] If True, in ‘weak’ mode, the (tangent) matrices and residual vectors (right-
hand sides) contain only active DOFs.
eterm_options [dict, optional] The einsum-based terms evaluation options.
verbose [bool] If False, reduce verbosity.
kwargs [dict, optional] The variables (dictionary of (variable name) : (Variable instance)) to be
used in the expression.
Returns
equation [Equation instance] The equation that is ready to be evaluated.
variables [Variables instance] The variables used in the equation.
sfepy.discrete.evaluate.eval_equations(equations, variables, names=None, preserve_caches=False,
mode='eval', dw_mode='vector', term_mode=None,
active_only=True, verbose=True)
Evaluate the equations.
Parameters
equations [Equations instance] The equations returned by create_evaluable().
variables [Variables instance] The variables returned by create_evaluable().
names [str or sequence of str, optional] Evaluate only equations of the given name(s).
preserve_caches [bool] If True, do not invalidate evaluate caches of variables.

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mode [one of ‘eval’, ‘el_avg’, ‘qp’, ‘weak’] The evaluation mode - ‘weak’ means the finite el-
ement assembling, ‘qp’ requests the values in quadrature points, ‘el_avg’ element averages
and ‘eval’ means integration over each term region.
dw_mode [‘vector’ or ‘matrix’] The assembling mode for ‘weak’ evaluation mode.
term_mode [str] The term call mode - some terms support different call modes and depending
on the call mode different values are returned.
active_only [bool] If True, in ‘weak’ mode, the (tangent) matrices and residual vectors (right-
hand sides) contain only active DOFs.
verbose [bool] If False, reduce verbosity.
Returns
out [dict or result] The evaluation result. In ‘weak’ mode it is the vector or sparse matrix, de-
pending on dw_mode. Otherwise, it is a dict of results with equation names as keys or a
single result for a single equation.
sfepy.discrete.evaluate.eval_in_els_and_qp(expression, iels, coors, fields, materials, variables,
functions=None, mode='eval', term_mode=None,
extra_args=None, active_only=True, verbose=True,
kwargs=None)
Evaluate an expression in given elements and points.
Parameters
expression [str] The expression to evaluate.
fields [dict] The dictionary of fields used in variables.
materials [Materials instance] The materials used in the expression.
variables [Variables instance] The variables used in the expression.
functions [Functions instance, optional] The user functions for materials etc.
mode [one of ‘eval’, ‘el_avg’, ‘qp’] The evaluation mode - ‘qp’ requests the values in quadrature
points, ‘el_avg’ element averages and ‘eval’ means integration over each term region.
term_mode [str] The term call mode - some terms support different call modes and depending
on the call mode different values are returned.
extra_args [dict, optional] Extra arguments to be passed to terms in the expression.
active_only [bool] If True, in ‘weak’ mode, the (tangent) matrices and residual vectors (right-
hand sides) contain only active DOFs.
verbose [bool] If False, reduce verbosity.
kwargs [dict, optional] The variables (dictionary of (variable name) : (Variable instance)) to be
used in the expression.
Returns
out [array] The result of the evaluation.

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sfepy.discrete.evaluate_variable module

sfepy.discrete.evaluate_variable.eval_complex(vec, conn, geo, mode, shape, bf=None)

Evaluate basic derived quantities of a complex variable given its DOF vector, connectivity and reference mapping.
sfepy.discrete.evaluate_variable.eval_real(vec, conn, geo, mode, shape, bf=None)
Evaluate basic derived quantities of a real variable given its DOF vector, connectivity and reference mapping.

sfepy.discrete.functions module

class sfepy.discrete.functions.ConstantFunction(values, no_tile=False)

Function with constant values.
class sfepy.discrete.functions.ConstantFunctionByRegion(values)
Function with constant values in regions.
class sfepy.discrete.functions.Function(name, function, is_constant=False, extra_args=None)
Base class for user-defined functions.
set_extra_args(**extra_args)

set_function(function, is_constant=False)

class sfepy.discrete.functions.Functions(objs=None, **kwargs)

Container to hold all user-defined functions.
static from_conf(conf )

sfepy.discrete.functions.make_sfepy_function(fun_or_name=None)
Convenience decorator to quickly create sfepy.discrete.functions.Function objects.
Has two modes of use either without parameter:

@make_sfepy_function
def my_function(...):
...

or with name:

@make_sfepy_function("new_name_for_my_function")
def my_function(...):
...

Parameters
fun_or_name [string, optional] Name to be saved within Function instance, if None name of
decorated function is used.
Returns
new_fun [sfepy.discrete.functions.Function] With attribute name set to provided name or origi-
nal function name.

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sfepy.discrete.integrals module

Classes for accessing quadrature points and weights for various reference element geometries.
class sfepy.discrete.integrals.Integral(name, order=1, coors=None, weights=None, bounds=None,
tp_fix=1.0, weight_fix=1.0, symmetric=False)
Wrapper class around quadratures.
get_qp(geometry)
Get quadrature point coordinates and corresponding weights for given geometry. For built-in quadratures,
the integration order is given by self.order.
Parameters
geometry [str] The geometry key describing the integration domain, see the keys of
sfepy.discrete.quadratures.quadrature_tables.
Returns
coors [array] The coordinates of quadrature points.
weights: array The quadrature weights.
integrate(function, order=1, geometry='1_2')
Integrate numerically a given scalar function.
Parameters
function [callable(coors)] The function of space coordinates to integrate.
order [int, optional] The integration order. For tensor product geometries, this is the 1D
(line) order.
geometry [str] The geometry key describing the integration domain. Default is
‘1_2’, i.e. a line integral in [0, 1]. For other values see the keys of
sfepy.discrete.quadratures.quadrature_tables.
Returns
val [float] The value of the integral.
class sfepy.discrete.integrals.Integrals(objs=None, **kwargs)
Container for instances of Integral.
static from_conf(conf )

get(name)
Return existing or new integral.
Parameters
name [str] The name can either be a non-negative integer, a string representation of a non-
negative integer (the integral order) or ‘a’ (automatic order) or a string beginning with ‘i’
(existing custom integral name).

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sfepy.discrete.materials module

class sfepy.discrete.materials.Material(name, kind='time-dependent', function=None, values=None,

flags=None, **kwargs)
A class holding constitutive and other material parameters.
Example input:

material_2 = {
'name' : 'm',
'values' : {'E' : 1.0},
}

Material parameters are passed to terms using the dot notation, i.e. ‘m.E’ in our example case.
static from_conf(conf, functions)
Construct Material instance from configuration.
get_constant_data(name)
Get constant data by name.
get_data(key, name)
name can be a dict - then a Struct instance with data as attributes named as the dict keys is returned.
get_keys(region_name=None)
Get all data keys.
Parameters
region_name [str] If not None, only keys with this region are returned.
iter_terms(equations, only_new=True)
Iterate terms for which the material data should be evaluated.
reduce_on_datas(reduce_fun, init=0.0)
For non-special values only!
reset()
Clear all data created by a call to time_update(), set self.mode to None.
set_all_data(datas)
Use the provided data, set mode to ‘user’.
set_data(key, qps, data)
Set the material data in quadrature points.
Parameters
key [tuple] The (region_name, integral_name) data key.
qps [Struct] Information about the quadrature points.
data [dict] The material data.
set_extra_args(**extra_args)
Extra arguments passed tu the material function.
set_function(function)

time_update(ts, equations, mode='normal', problem=None)

Evaluate material parameters in physical quadrature points.
Parameters

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ts [TimeStepper instance] The time stepper.

equations [Equations instance] The equations using the materials.
mode [‘normal’, ‘update’ or ‘force’] The update mode. In ‘force’ mode, self.datas is
cleared and all updates are redone. In ‘update’ mode, existing data are preserved and new
can be added. The ‘normal’ mode depends on other attributes: for stationary (self.kind
== 'stationary') materials and materials in ‘user’ mode, nothing is done if self.
datas is not empty. For time-dependent materials (self.kind == 'time-dependent',
the default) that are not constant, i.e., are given by a user function, ‘normal’ mode behaves
like ‘force’ mode. For constant materials it behaves like ‘update’ mode - existing data are
reused.
problem [Problem instance, optional] The problem that can be passed to user functions as a
context.
update_data(key, ts, equations, term, problem=None)
Update the material parameters in quadrature points.
Parameters
key [tuple] The (region_name, integral_name) data key.
ts [TimeStepper] The time stepper.
equations [Equations] The equations for which the update occurs.
term [Term] The term for which the update occurs.
problem [Problem, optional] The problem definition for which the update occurs.
update_special_constant_data(equations=None, problem=None)
Update the special constant material parameters.
Parameters
equations [Equations] The equations for which the update occurs.
problem [Problem, optional] The problem definition for which the update occurs.
update_special_data(ts, equations, problem=None)
Update the special material parameters.
Parameters
ts [TimeStepper] The time stepper.
equations [Equations] The equations for which the update occurs.
problem [Problem, optional] The problem definition for which the update occurs.
class sfepy.discrete.materials.Materials(objs=None, **kwargs)

static from_conf(conf, functions, wanted=None)

Construct Materials instance from configuration.
reset()
Clear material data so that next materials.time_update() is performed even for stationary materials.
time_update(ts, equations, mode='normal', problem=None, verbose=True)
Update material parameters for given time, problem, and equations.
Parameters
ts [TimeStepper instance] The time stepper.

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equations [Equations instance] The equations using the materials.

mode [‘normal’, ‘update’ or ‘force’] The update mode, see Material.time_update().
problem [Problem instance, optional] The problem that can be passed to user functions as a
context.
verbose [bool] If False, reduce verbosity.

sfepy.discrete.parse_equations module

class sfepy.discrete.parse_equations.TermParse
sfepy.discrete.parse_equations.collect_term(term_descs, lc)

sfepy.discrete.parse_equations.create_bnf(term_descs)
term_descs .. list of TermParse objects (sign, term_name, term_arg_names), where sign can be real or complex
multiplier
sfepy.discrete.parse_equations.rhs(lc)

sfepy.discrete.parse_regions module

Grammar for selecting regions of a domain.

Regions serve for selection of certain parts of the computational domain represented as a finite element mesh. They
are used to define the boundary conditions, the domains of terms and materials etc.

Notes

History: pre-git versions already from from 13.06.2006.

sfepy.discrete.parse_regions.create_bnf(stack)

sfepy.discrete.parse_regions.join_tokens(str, loc, toks)

sfepy.discrete.parse_regions.print_leaf(level, op)

sfepy.discrete.parse_regions.print_op(level, op, item1, item2)

sfepy.discrete.parse_regions.print_stack(stack)

sfepy.discrete.parse_regions.replace(what, keep=False)

sfepy.discrete.parse_regions.replace_with_region(what, r_index)

sfepy.discrete.parse_regions.to_stack(stack)

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sfepy.discrete.parse_regions.visit_stack(stack, op_visitor, leaf_visitor)

sfepy.discrete.probes module

Classes for probing values of Variables, for example, along a line.

class sfepy.discrete.probes.CircleProbe(centre, normal, radius, n_point, share_geometry=True)
Probe variables along a circle.
If n_point is positive, that number of evenly spaced points is used. If n_point is None or non-positive, an adap-
tive refinement based on element diameters is used and the number of points and their spacing are determined
automatically. If it is negative, -n_point is used as an initial guess.
get_points(refine_flag=None)
Get the probe points.
Returns
pars [array_like] The independent coordinate of the probe.
points [array_like] The probe points, parametrized by pars.
is_cyclic = True
report()
Report the probe parameters.
class sfepy.discrete.probes.IntegralProbe(name, problem, expressions, labels)
Evaluate integral expressions.
class sfepy.discrete.probes.LineProbe(p0, p1, n_point, share_geometry=True)
Probe variables along a line.
If n_point is positive, that number of evenly spaced points is used. If n_point is None or non-positive, an adap-
tive refinement based on element diameters is used and the number of points and their spacing are determined
automatically. If it is negative, -n_point is used as an initial guess.
get_points(refine_flag=None)
Get the probe points.
Returns
pars [array_like] The independent coordinate of the probe.
points [array_like] The probe points, parametrized by pars.
report()
Report the probe parameters.
class sfepy.discrete.probes.PointsProbe(points, share_geometry=True)
Probe variables in given points.
get_points(refine_flag=None)
Get the probe points.
Returns
pars [array_like] The independent coordinate of the probe.
points [array_like] The probe points, parametrized by pars.
refine_points(variable, points, cache)
No refinement for this probe.

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report()
Report the probe parameters.
class sfepy.discrete.probes.Probe(name, share_geometry=True, n_point=None, **kwargs)
Base class for all point probes. Enforces two points minimum.
cache = Struct:probe_shared_evaluate_cache
get_actual_cache(pars, cache, hash_chunk_size=100000)
Return the actual evaluate cache, which is a combination of the (mesh-based) evaluate cache and probe-
specific data, like the reference element coordinates. The reference element coordinates are reused, if the
sha1 hash of the probe parameter vector does not change.
get_evaluate_cache()
Return the evaluate cache for domain-related data given by self.share_geometry.
is_cyclic = False
probe(variable, mode='val', ret_points=False)
Probe the given variable.
Parameters
variable [Variable instance] The variable to be sampled along the probe.
mode [{‘val’, ‘grad’}, optional] The evaluation mode: the variable value (default) or the
variable value gradient.
ret_points [bool] If True, return also the probe points.
Returns
pars [array] The parametrization of the probe points.
points [array, optional] If ret_points is True, the coordinates of points corresponding to pars,
where the variable is evaluated.
vals [array] The probed values.
static refine_pars(pars, refine_flag, cyclic_val=None)
Refine the probe parametrization based on the refine_flag.
refine_points(variable, points, cells)
Mark intervals between points for a refinement, based on element sizes at those points. Assumes the points
to be ordered.
Returns
refine_flag [bool array] True at places corresponding to intervals between subsequent points
that need to be refined.
report()
Report the probe parameters.
reset_refinement()
Reset the probe refinement state.
set_n_point(n_point)
Set the number of probe points.
Parameters
n_point [int] The (fixed) number of probe points, when positive. When non-positive, the
number of points is adaptively increased starting from -n_point, until the neighboring point

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distance is less than the diameter of the elements enclosing the points. When None, it is
set to -10.
set_options(close_limit=None, size_hint=None)
Set the probe options.
Parameters
close_limit [float] The maximum limit distance of a point from the closest element allowed
for extrapolation.
size_hint [float] Element size hint for the refinement of probe parametrization.
class sfepy.discrete.probes.RayProbe(p0, dirvec, p_fun, n_point, both_dirs, share_geometry=True)
Probe variables along a ray. The points are parametrized by a function of radial coordinates from a given point
in a given direction.
gen_points(sign)
Generate the probe points and their parametrization.
get_points(refine_flag=None)
Get the probe points.
Returns
pars [array_like] The independent coordinate of the probe.
points [array_like] The probe points, parametrized by pars.
refine_points(variable, points, cache)
No refinement for this probe.
report()
Report the probe parameters.
sfepy.discrete.probes.get_data_name(fd)
Try to read next data name in file fd.
Returns
name [str] The data name.
nc [int] The number of data columns.
sfepy.discrete.probes.read_header(fd)
Read the probe data header from file descriptor fd.
Returns
header [Struct instance] The probe data header.
sfepy.discrete.probes.read_results(filename, only_names=None)
Read probing results from a file.
Parameters
filename [str or file object] The probe results file name.
Returns
header [Struct instance] The probe data header.
results [dict] The dictionary of probing results. Keys are data names, values are the probed
values.
sfepy.discrete.probes.write_results(filename, probe, results)
Write probing results into a file.

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Parameters
filename [str or file object] The output file name.
probe [Probe subclass instance] The probe used to obtain the results.
results [dict] The dictionary of probing results. Keys are data names, values are the probed
values.

sfepy.discrete.problem module

class sfepy.discrete.problem.Problem(name, conf=None, functions=None, domain=None, fields=None,

equations=None, auto_conf=True, active_only=True)
Problem definition, the top-level class holding all data necessary to solve a problem.
It can be constructed from a ProblemConf instance using Problem.from_conf() or directly from a problem
description file using Problem.from_conf_file()
For interactive use, the constructor requires only the equations, nls and ls keyword arguments, see below.
Parameters
name [str] The problem name.
conf [ProblemConf instance, optional] The ProblemConf describing the problem.
functions [Functions instance, optional] The user functions for boundary conditions, materials,
etc.
domain [Domain instance, optional] The solution Domain.
fields [dict, optional] The dictionary of Field instances.
equations [Equations instance, optional] The Equations to solve. This argument is required
when auto_conf is True.
auto_conf [bool] If True, fields and domain are determined by equations.
active_only [bool] If True, the (tangent) matrices and residual vectors (right-hand sides) contain
only active DOFs, see below.

Notes

The Problem is by default created with active_only set to True. Then the (tangent) matrices and residual vectors
(right-hand sides) have reduced sizes and contain only the active DOFs, i.e., DOFs not constrained by EBCs or
EPBCs.
Setting active_only to False results in full-size vectors and matrices. Then the matrix size non-zeros structure
does not depend on the actual E(P)BCs applied. It must be False when using parallel PETSc solvers.
The active DOF connectivities contain all DOFs, with the E(P)BC-constrained ones stored as -1 - <DOF num-
ber>, so that the full connectivities can be reconstructed for the matrix graph creation. However, the negative
entries mean that the assembled matrices/residuals have zero values at positions corresponding to constrained
DOFs.
The resulting linear system then provides a solution increment, that has to be added to the initial guess used to
compute the residual, just like in the Newton iterations. The increment of the constrained DOFs is automatically
zero.

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When solving with a direct solver, the diagonal entries of a matrix at positions corresponding to con-
strained DOFs has to be set to ones, so that the matrix is not singular, see sfepy.discrete.evaluate.
apply_ebc_to_matrix(), which is called automatically in sfepy.discrete.evaluate.Evaluator.
eval_tangent_matrix(). It is not called automatically in Problem.evaluate(). Note that setting the diag-
onal entries to one might not be necessary with iterative solvers, as the zero matrix rows match the zero residual
rows, i.e. if the reduced matrix would be regular, then the right-hand side (the residual) is orthogonal to the
kernel of the matrix.
advance(ts=None)

block_solve(state0=None, status=None, save_results=True, step_hook=None, post_process_hook=None,

verbose=True)
Call Problem.solve() sequentially for the individual matrix blocks of a block-triangular matrix. It is
called by Problem.solve() if the ‘block_solve’ option is set to True.
clear_equations()

copy(name=None)
Make a copy of Problem.
create_evaluable(expression, try_equations=True, auto_init=False, preserve_caches=False,
copy_materials=True, integrals=None, ebcs=None, epbcs=None, lcbcs=None, ts=None,
functions=None, mode='eval', var_dict=None, strip_variables=True, extra_args=None,
active_only=True, eterm_options=None, verbose=True, **kwargs)
Create evaluable object (equations and corresponding variables) from the expression string. Convenience
function calling create_evaluable() with defaults provided by the Problem instance self.
The evaluable can be repeatedly evaluated by calling eval_equations(), e.g. for different values of
variables.
Parameters
expression [str] The expression to evaluate.
try_equations [bool] Try to get variables from self.equations. If this fails, variables can ei-
ther be provided in var_dict, as keyword arguments, or are created automatically according
to the expression.
auto_init [bool] Set values of all variables to all zeros.
preserve_caches [bool] If True, do not invalidate evaluate caches of variables.
copy_materials [bool] Work with a copy of self.equations.materials instead of reusing them.
Safe but can be slow.
integrals [Integrals instance, optional] The integrals to be used. Automatically created as
needed if not given.
ebcs [Conditions instance, optional] The essential (Dirichlet) boundary conditions for ‘weak’
mode. If not given, self.ebcs are used.
epbcs [Conditions instance, optional] The periodic boundary conditions for ‘weak’ mode. If
not given, self.epbcs are used.
lcbcs [Conditions instance, optional] The linear combination boundary conditions for ‘weak’
mode. If not given, self.lcbcs are used.
ts [TimeStepper instance, optional] The time stepper. If not given, self.ts is used.
functions [Functions instance, optional] The user functions for boundary conditions, mate-
rials etc. If not given, self.functions are used.

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mode [one of ‘eval’, ‘el_avg’, ‘qp’, ‘weak’] The evaluation mode - ‘weak’ means the finite el-
ement assembling, ‘qp’ requests the values in quadrature points, ‘el_avg’ element averages
and ‘eval’ means integration over each term region.
var_dict [dict, optional] The variables (dictionary of (variable name) : (Variable instance))
to be used in the expression. Use this if the name of a variable conflicts with one of the
parameters of this method.
strip_variables [bool] If False, the variables in var_dict or kwargs not present in the expres-
sion are added to the actual variables as a context.
extra_args [dict, optional] Extra arguments to be passed to terms in the expression.
active_only [bool] If True, in ‘weak’ mode, the (tangent) matrices and residual vectors (right-
hand sides) contain only active DOFs.
eterm_options [dict, optional] The einsum-based terms evaluation options.
verbose [bool] If False, reduce verbosity.
**kwargs [keyword arguments] Additional variables can be passed as keyword arguments,
see var_dict.
Returns
equations [Equations instance] The equations that can be evaluated.
variables [Variables instance] The corresponding variables. Set their values and use
eval_equations().

Examples

problem is Problem instance.

>>> out = problem.create_evaluable('ev_integrate.i1.Omega(u)')

>>> equations, variables = out

vec is a vector of coefficients compatible with the field of ‘u’ - let’s use all ones.

>>> vec = nm.ones((variables['u'].n_dof,), dtype=nm.float64)

>>> variables['u'].set_data(vec)
>>> vec_qp = eval_equations(equations, variables, mode='qp')

Try another vector:

>>> vec = 3 * nm.ones((variables['u'].n_dof,), dtype=nm.float64)

>>> variables['u'].set_data(vec)
>>> vec_qp = eval_equations(equations, variables, mode='qp')

create_materials(mat_names=None)
Create materials with names in mat_names. Their definitions have to be present in self.conf.materials.

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Notes

This method does not change self.equations, so it should not have any side effects.
create_state()

create_subproblem(var_names, known_var_names)
Create a sub-problem with equations containing only terms with the given virtual variables.
Parameters
var_names [list] The list of names of virtual variables.
known_var_names [list] The list of names of (already) known state variables.
Returns
subpb [Problem instance] The sub-problem.
create_variables(var_names=None)
Create variables with names in var_names. Their definitions have to be present in self.conf.variables.

Notes

This method does not change self.equations, so it should not have any side effects.
eval_equations(names=None, preserve_caches=False, mode='eval', dw_mode='vector', term_mode=None,
active_only=True, verbose=True)
Evaluate (some of) the problem’s equations, convenience wrapper of eval_equations().
Parameters
names [str or sequence of str, optional] Evaluate only equations of the given name(s).
preserve_caches [bool] If True, do not invalidate evaluate caches of variables.
mode [one of ‘eval’, ‘el_avg’, ‘qp’, ‘weak’] The evaluation mode - ‘weak’ means the finite el-
ement assembling, ‘qp’ requests the values in quadrature points, ‘el_avg’ element averages
and ‘eval’ means integration over each term region.
dw_mode [‘vector’ or ‘matrix’] The assembling mode for ‘weak’ evaluation mode.
term_mode [str] The term call mode - some terms support different call modes and depend-
ing on the call mode different values are returned.
verbose [bool] If False, reduce verbosity.
Returns
out [dict or result] The evaluation result. In ‘weak’ mode it is the vector or sparse matrix,
depending on dw_mode. Otherwise, it is a dict of results with equation names as keys or a
single result for a single equation.
evaluate(expression, try_equations=True, auto_init=False, preserve_caches=False, copy_materials=True,
integrals=None, ebcs=None, epbcs=None, lcbcs=None, ts=None, functions=None, mode='eval',
dw_mode='vector', term_mode=None, var_dict=None, strip_variables=True, ret_variables=False,
active_only=True, eterm_options=None, verbose=True, extra_args=None, **kwargs)
Evaluate an expression, convenience wrapper of Problem.create_evaluable() and
eval_equations().
Parameters
dw_mode [‘vector’ or ‘matrix’] The assembling mode for ‘weak’ evaluation mode.

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term_mode [str] The term call mode - some terms support different call modes and depend-
ing on the call mode different values are returned.
ret_variables [bool] If True, return the variables that were created to evaluate the expression.
other [arguments] See docstrings of Problem.create_evaluable().
Returns
out [array] The result of the evaluation.
variables [Variables instance] The variables that were created to evaluate the expression.
Only provided if ret_variables is True.
static from_conf(conf, init_fields=True, init_equations=True, init_solvers=True)

static from_conf_file(conf_filename, required=None, other=None, init_fields=True,

init_equations=True, init_solvers=True)

get_default_ts(t0=None, t1=None, dt=None, n_step=None, step=None)

get_dim(get_sym=False)
Returns mesh dimension, symmetric tensor dimension (if get_sym is True).
get_ebc_indices()
Get indices of E(P)BC-constrained DOFs in the full global state vector.
get_evaluator(reuse=False)
Either create a new Evaluator instance (reuse == False), or return an existing instance, created in a preceding
call to Problem.init_solvers().
get_initial_state(vec=None)
Create a zero state and apply initial conditions.
get_integrals(names=None)
Get integrals, initialized from problem configuration if available.
Parameters
names [list, optional] If given, only the named integrals are returned.
Returns
integrals [Integrals instance] The requested integrals.
get_ls()

get_materials()

get_mesh_coors(actual=False)

get_nls()

get_nls_functions()
Returns functions to be used by a nonlinear solver to evaluate the nonlinear function value (the residual)
and its gradient (the tangent matrix) corresponding to the problem equations.
Returns

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fun [function] The function fun(x) for computing the residual.

fun_grad [function] The function fun_grad(x) for computing the tangent matrix.
iter_hook [function] The optional (user-defined) function to be called before each nonlinear
solver iteration iteration.
get_output_name(suffix=None, extra=None, mode=None)
Return default output file name, based on the output directory, output format, step suffix and mode. If
present, the extra string is put just before the output format suffix.
get_restart_filename(ts=None)
If restarts are allowed in problem definition options, return the restart file name, based on the output direc-
tory and time step.
get_solver()

get_solver_conf(name)

get_timestepper()

get_tss()

get_tss_functions(update_bcs=True, update_materials=True, save_results=True, step_hook=None,

post_process_hook=None)
Get the problem-dependent functions required by the time-stepping solver during the solution process.
Parameters
update_bcs [bool, optional] If True, update the boundary conditions in each prestep_fun
call.
update_materials [bool, optional] If True, update the values of material parameters in each
prestep_fun call.
save_results [bool, optional] If True, save the results in each poststep_fun call.
step_hook [callable, optional] The optional user-defined function that is called in each post-
step_fun call before saving the results.
post_process_hook [callable, optional] The optional user-defined function that is passed in
each poststep_fun to Problem.save_state().
Returns
init_fun [callable] The initialization function called before the actual time-stepping.
prestep_fun [callable] The function called in each time (sub-)step prior to the nonlinear
solver call.
poststep_fun [callable] The function called at the end of each time step.
get_variables(auto_create=False)

init_solvers(status=None, ls_conf=None, nls_conf=None, ts_conf=None, force=False)

Create and initialize solver instances.
Parameters

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status [dict-like, IndexedStruct, optional] The user-supplied object to hold the time-
stepping/nonlinear solver convergence statistics.
ls_conf [Struct, optional] The linear solver options.
nls_conf [Struct, optional] The nonlinear solver options.
force [bool] If True, re-create the solver instances even if they already exist in self.nls at-
tribute.
init_time(ts)

is_linear()

load_restart(filename, ts=None)
Load the current state and time step from a restart file.
Alternatively, a regular output file in the HDF5 format can be used in place of the restart file. In that case
the restart is only approximate, because higher order field DOFs (if any) were stripped out. Files with the
adaptive linearization are not supported. Use with caution!
Parameters
filename [str] The restart file name.
ts [TimeStepper instance, optional] The time stepper. If not given, a default one is created.
Otherwise, it is modified in place.
Returns
variables [Variables instance] The loaded variables.
refine_uniformly(level)
Refine the mesh uniformly level-times.

Notes

This operation resets almost everything (fields, equations, . . . ) - it is roughly equivalent to creating a new
Problem instance with the refined mesh.
remove_bcs()
Convenience function to remove boundary conditions.
reset()

save_ebc(filename, ebcs=None, epbcs=None, force=True, default=0.0)

Save essential boundary conditions as state variables.
Parameters
filename [str] The output file name.
ebcs [Conditions instance, optional] The essential (Dirichlet) boundary conditions. If not
given, self.conf.ebcs are used.
epbcs [Conditions instance, optional] The periodic boundary conditions. If not given,
self.conf.epbcs are used.
force [bool] If True, sequential nonzero values are forced to individual ebcs so that the con-
ditions are visible even when zero.

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default [float] The default constant value of state vector.

save_field_meshes(filename_trunk)

save_regions(filename_trunk, region_names=None)
Save regions as meshes.
Parameters
filename_trunk [str] The output filename without suffix.
region_names [list, optional] If given, only the listed regions are saved.
save_regions_as_groups(filename_trunk, region_names=None)
Save regions in a single mesh but mark them by using different element/node group numbers.
See Domain.save_regions_as_groups() for more details.
Parameters
filename_trunk [str] The output filename without suffix.
region_names [list, optional] If given, only the listed regions are saved.
save_restart(filename, ts=None)
Save the current state and time step to a restart file.
Parameters
filename [str] The restart file name.
ts [TimeStepper instance, optional] The time stepper. If not given, a default one is created.

Notes

Does not support terms with internal state.

save_state(filename, state=None, out=None, fill_value=None, post_process_hook=None,
linearization=None, file_per_var=False, **kwargs)

Parameters
file_per_var [bool or None] If True, data of each variable are stored in a separate file. If
None, it is set to the application option value.
linearization [Struct or None] The linearization configuration for higher order approxima-
tions. If its kind is ‘adaptive’, file_per_var is assumed True.
select_bcs(ebc_names=None, epbc_names=None, lcbc_names=None, create_matrix=False)

select_materials(material_names, only_conf=False)

select_variables(variable_names, only_conf=False)

set_bcs(ebcs=None, epbcs=None, lcbcs=None)

Update boundary conditions.
set_conf_solvers(conf_solvers=None, options=None)
Choose which solvers should be used. If solvers are not set in options, use the ones named ls, nls or ts. If
such solver names do not exist, use the first of each required solver kind listed in conf_solvers.

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set_default_state(vec=None)
Return variables with an initialized state.
A convenience function that obtains the problem equations’ variables, initializes the state ones with zeros
(default) or using vec and then returns the variables.
set_equations(conf_equations=None, user=None, keep_solvers=False, make_virtual=False)
Set equations of the problem using the equations problem description entry.
Fields and Regions have to be already set.
set_equations_instance(equations, keep_solvers=False)
Set equations of the problem to equations.
set_fields(conf_fields=None)

set_ics(ics=None)
Set the initial conditions to use.
set_linear(is_linear)

set_materials(conf_materials=None)
Set definition of materials.
set_mesh_coors(coors, update_fields=False, actual=False, clear_all=True, extra_dofs=False)
Set mesh coordinates.
Parameters
coors [array] The new coordinates.
update_fields [bool] If True, update also coordinates of fields.
actual [bool] If True, update the actual configuration coordinates, otherwise the undeformed
configuration ones.
set_output_dir(output_dir=None)
Set the directory for output files.
The directory is created if it does not exist.
set_regions(conf_regions=None, conf_materials=None, functions=None, allow_empty=False)

set_solver(solver, status=None)
Set a time-stepping or nonlinear solver to be used in Problem.solve() call.
Parameters
solver [NonlinearSolver or TimeSteppingSolver instance] The nonlinear or time-stepping
solver.

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Notes

A copy of the solver is used, and the nonlinear solver functions are set to those returned by Problem.
get_nls_functions(), if not set already. If a nonlinear solver is set, a default StationarySolver instance
is created automatically as the time-stepping solver. Also sets self.ts attribute.
set_variables(conf_variables=None)
Set definition of variables.
setup_default_output(conf=None, options=None)
Provide default values to Problem.setup_output() from conf.options and options.
setup_hooks(options=None)
Setup various hooks (user-defined functions), as given in options.
Supported hooks:
• matrix_hook
– check/modify tangent matrix in each nonlinear solver iteration
• nls_iter_hook
– called prior to every iteration of nonlinear solver, if the solver supports that
– takes the Problem instance (self ) as the first argument
setup_output(output_filename_trunk=None, output_dir=None, output_format=None, file_format=None,
float_format=None, file_per_var=None, linearization=None)
Sets output options to given values, or uses the defaults for each argument that is None.
solve(state0=None, status=None, force_values=None, var_data=None, update_bcs=True,
update_materials=True, save_results=True, step_hook=None, post_process_hook=None,
post_process_hook_final=None, verbose=True)
Solve the problem equations by calling the top-level solver.
Before calling this function the top-level solver has to be set, see Problem.set_solver(). Also, the
boundary conditions and the initial conditions (for time-dependent problems) has to be set, see Problem.
set_bcs(), Problem.set_ics().
Parameters
state0 [array, optional] If given, the initial state - then the initial conditions stored in the Prob-
lem instance are ignored. By default, the initial state is created and the initial conditions
are applied automatically.
status [dict-like, optional] The user-supplied object to hold the solver convergence statistics.
force_values [dict of floats or float, optional] If given, the supplied values override the values
of the essential boundary conditions.
var_data [dict, optional] A dictionary of {variable_name : data vector} used to initialize
parameter variables.
update_bcs [bool, optional] If True, update the boundary conditions in each prestep_fun
call. See Problem.get_tss_functions().
update_materials [bool, optional] If True, update the values of material parameters in each
prestep_fun call. See Problem.get_tss_functions().
save_results [bool, optional] If True, save the results in each poststep_fun call. See
Problem.get_tss_functions().

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step_hook [callable, optional] The optional user-defined function that is called in each post-
step_fun call before saving the results. See Problem.get_tss_functions().
post_process_hook [callable, optional] The optional user-defined function that is passed in
each poststep_fun to Problem.save_state(). See Problem.get_tss_functions().
post_process_hook_final [callable, optional] The optional user-defined function that is
called after the top-level solver returns.
Returns
variables [Variables] The variables with the final time step state.
time_update(ts=None, ebcs=None, epbcs=None, lcbcs=None, functions=None, create_matrix=False,
is_matrix=True)

try_presolve(mtx)

update_equations(ts=None, ebcs=None, epbcs=None, lcbcs=None, functions=None, create_matrix=False,

is_matrix=True)
Update equations for current time step.
The tangent matrix graph is automatically recomputed if the set of active essential or periodic boundary
conditions changed w.r.t. the previous time step.
Parameters
ts [TimeStepper instance, optional] The time stepper. If not given, self.ts is used.
ebcs [Conditions instance, optional] The essential (Dirichlet) boundary conditions. If not
given, self.ebcs are used.
epbcs [Conditions instance, optional] The periodic boundary conditions. If not given,
self.epbcs are used.
lcbcs [Conditions instance, optional] The linear combination boundary conditions. If not
given, self.lcbcs are used.
functions [Functions instance, optional] The user functions for boundary conditions, mate-
rials, etc. If not given, self.functions are used.
create_matrix [bool] If True, force the matrix graph computation.
is_matrix [bool] If False, the matrix is not created. Has precedence over create_matrix.
update_materials(ts=None, mode='normal', verbose=True)
Update materials used in equations.
Parameters
ts [TimeStepper instance] The time stepper.
mode [‘normal’, ‘update’ or ‘force’] The update mode, see Material.time_update().
verbose [bool] If False, reduce verbosity.
update_time_stepper(ts)

sfepy.discrete.problem.make_is_save(options)
Given problem options, return a callable that determines whether to save results of a time step.
sfepy.discrete.problem.prepare_matrix(problem, state)
Pre-assemble tangent system matrix.

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sfepy.discrete.projections module

Construct projections between FE spaces.

sfepy.discrete.projections.create_mass_matrix(field)
Create scalar mass matrix corresponding to the given field.
Returns
mtx [csr_matrix] The mass matrix in CSR format.
sfepy.discrete.projections.make_h1_projection_data(target, eval_data)
Project scalar data given by a material-like eval_data() function to a scalar target field variable using the 𝐻 1 dot
product.
sfepy.discrete.projections.make_l2_projection(target, source, ls=None, nls_options=None)
Project a scalar source field variable to a scalar target field variable using the 𝐿2 dot product.
sfepy.discrete.projections.make_l2_projection_data(target, eval_data, order=None, ls=None,
nls_options=None)
Project scalar data to a scalar target field variable using the 𝐿2 dot product.
Parameters
target [FieldVariable instance] The target variable.
eval_data [callable or array] Either a material-like function eval_data(), or an array of values in
quadrature points that has to be reshapable to the shape required by order.
order [int, optional] The quadrature order. If not given, it is set to 2 * target.field.approx_order.
sfepy.discrete.projections.project_by_component(tensor, tensor_qp, component, order, ls=None,
nls_options=None)
Wrapper around make_l2_projection_data() for non-scalar fields.
sfepy.discrete.projections.project_to_facets(region, fun, dpn, field)
Project a function fun to the field in facets of the given region.

sfepy.discrete.quadratures module

quadrature_tables are organized as follows:

quadrature_tables = {
'<geometry1>' : {
order1 : QuadraturePoints(args1),
order2 : QuadraturePoints(args2),
...
},
'<geometry2>' : {
order1 : QuadraturePoints(args1),
order2 : QuadraturePoints(args2),
...
},
...
}

Note The order for quadratures on tensor product domains (‘2_4’, ‘3_8’ geometries) in case of composite Gauss quadra-
tures (products of 1D quadratures) holds for each component separately, so the actual polynomial order may be much
higher (up to order * dimension).

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Naming conventions in problem description files:

`<family>_<order>_<dimension>`

Integral ‘family’ is just an arbitrary name given by user.

Low order quadrature coordinates and weights copied from The Finite Element Method Displayed by Gouri Dhatt and
Gilbert Touzat, Wiley-Interscience Production, 1984.
The line integral (geometry ‘1_2’) coordinates and weights are from Abramowitz, M. and Stegun, I.A., Handbook of
Mathematical Functions, Dover Publications, New York, 1972. The triangle (geometry ‘2_3’) coordinates and weights
are from Dunavant, D.A., High Degree Efficient Symmetrical Gaussian Quadrature Rules for the Triangle, Int. J. Num.
Meth. Eng., 21 (1985) pp 1129-1148 - only rules with points inside the reference triangle are used. The actual values
were copied from PHAML (http://math.nist.gov/phaml/), see also Mitchell, W.F., PHAML User’s Guide, NISTIR
7374, 2006.
Quadrature rules for the quadrilateral (geometry ‘2_4’) and hexahedron (geometry ‘3_8’) of order higher than 5 are
computed as the tensor product of the line (geometry ‘1_2’) rules.
Quadrature rules for the triangle (geometry ‘2_3’) and tetrahedron (geometry ‘3_4’) of order higher than 19 and 6,
respectively follow A. Grundmann and H.M. Moeller, Invariant integration formulas for the n-simplex by combinatorial
methods, SIAM J. Numer. Anal. 15 (1978), 282–290. The generating function was adapted from pytools/hegde codes
(http://mathema.tician.de/software/hedge) by Andreas Kloeckner.
class sfepy.discrete.quadratures.QuadraturePoints(data, coors=None, weights=None, bounds=None,
tp_fix=1.0, weight_fix=1.0, symmetric=False)
Representation of a set of quadrature points.
Parameters
data [array_like] The array of shape (n_point, dim + 1) of quadrature point coordinates (first
dim columns) and weights (the last column).
coors [array_like, optional] Optionally, instead of using data, the coordinates and weights can
be provided separately - data are then ignored.
weights [array_like, optional] Optionally, instead of using data, the coordinates and weights can
be provided separately - data are then ignored.
bounds [(float, float), optional] The coordinates and weights should correspond to a reference
element in [0, 1] x dim. Provide the correct bounds if this is not the case.
tp_fix [float, optional] The value that is used to multiply the tensor product element volume (=
1.0) to get the correct volume.
weight_fix [float, optional] The value that is used to multiply the weights to get the correct
values.
symmetric [bool] If True, the integral is 1D and the given coordinates and weights are symmetric
w.r.t. the centre of bounds; only the non-negative coordinates are given.
static from_table(geometry, order)
Create a new QuadraturePoints instance, given reference element geometry name and polynomial order.
For tensor product geometries, the polynomial order is the 1D (line) order.
sfepy.discrete.quadratures.get_actual_order(geometry, order)
Return the actual integration order for given geometry.
Parameters
geometry [str] The geometry key describing the integration domain, see the keys of quadra-
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Returns
order [int] If order is in quadrature tables it is this value. Otherwise it is the closest higher order.
If no higher order is available, a warning is printed and the highest available order is used.

sfepy.discrete.simplex_cubature module

Generate simplex quadrature points. Code taken and adapted from pytools/hedge by Andreas Kloeckner.
sfepy.discrete.simplex_cubature.factorial(n)

sfepy.discrete.simplex_cubature.generate_decreasing_nonnegative_tuples_summing_to(n, length,
min=0,
max=None)

sfepy.discrete.simplex_cubature.generate_permutations(original)
Generate all permutations of the list `original’.
Nicked from http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/252178
sfepy.discrete.simplex_cubature.generate_unique_permutations(original)
Generate all unique permutations of the list `original’.
sfepy.discrete.simplex_cubature.get_simplex_cubature(order, dimension)
Cubature on an M{n}-simplex.
cf. A. Grundmann and H.M. Moeller, Invariant integration formulas for the n-simplex by combinatorial methods,
SIAM J. Numer. Anal. 15 (1978), 282–290.
This cubature rule has both negative and positive weights. It is exact for polynomials up to order 2𝑠 + 1, where
𝑠 is given as order. The integration domain is the unit simplex
∑︁
𝑇𝑛 := {(𝑥1 , . . . , 𝑥𝑛 ) : 𝑥𝑖 ≥ −1, 𝑥𝑖 ≤ −1}
𝑖

sfepy.discrete.simplex_cubature.wandering_element(length, wanderer=1, landscape=0)

sfepy.discrete.variables module

Classes of variables for equations/terms.

class sfepy.discrete.variables.DGFieldVariable(name, kind, field, order=None,
primary_var_name=None, special=None, flags=None,
history=None, **kwargs)
Fieald variable specificaly intended for use with DGFields, bypasses application of EBC and EPBC as this is
done in DGField.
Is instance checked in create_adof_conns.
apply_ebc(vec, offset=0, force_values=None)
Apply essential (Dirichlet) and periodic boundary conditions to vector vec, starting at offset.
get_full(r_vec, r_offset=0, force_value=None, vec=None, offset=0)
Get the full DOF vector satisfying E(P)BCs from a reduced DOF vector.

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Notes

The reduced vector starts in r_vec at r_offset. Passing a force_value overrides the EBC values. Optionally,
vec argument can be provided to store the full vector (in place) starting at offset.
class sfepy.discrete.variables.FieldVariable(name, kind, field, order=None, primary_var_name=None,
special=None, flags=None, history=None, **kwargs)
A finite element field variable.
field .. field description of variable (borrowed)
apply_ebc(vec, offset=0, force_values=None)
Apply essential (Dirichlet) and periodic boundary conditions to vector vec, starting at offset.
apply_ic(vec, offset=0, force_values=None)
Apply initial conditions conditions to vector vec, starting at offset.
clear_evaluate_cache()
Clear current evaluate cache.
create_output(vec=None, key=None, extend=True, fill_value=None, linearization=None)
Convert the DOF vector to a dictionary of output data usable by Mesh.write().
Parameters
vec [array, optional] An alternative DOF vector to be used instead of the variable DOF vector.
key [str, optional] The key to be used in the output dictionary instead of the variable name.
extend [bool] Extend the DOF values to cover the whole domain.
fill_value [float or complex] The value used to fill the missing DOF values if extend is True.
linearization [Struct or None] The linearization configuration for higher order approxima-
tions.
equation_mapping(bcs, var_di, ts, functions, problem=None, warn=False)
Create the mapping of active DOFs from/to all DOFs.
Sets n_adof.
Returns
active_bcs [set] The set of boundary conditions active in the current time.
evaluate(mode='val', region=None, integral=None, integration=None, step=0, time_derivative=None,
is_trace=False, trace_region=None, dt=None, bf=None)
Evaluate various quantities related to the variable according to mode in quadrature points defined by inte-
gral.
The evaluated data are cached in the variable instance in evaluate_cache attribute.
Parameters
mode [one of ‘val’, ‘grad’, ‘div’, ‘cauchy_strain’] The evaluation mode.
region [Region instance, optional] The region where the evaluation occurs. If None, the
underlying field region is used.
integral [Integral instance, optional] The integral defining quadrature points in which the
evaluation occurs. If None, the first order volume integral is created. Must not be None for
surface integrations.
integration [‘volume’, ‘surface’, ‘surface_extra’, or ‘point’] The term integration type. If
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step [int, default 0] The time step (0 means current, -1 previous, . . . ).

time_derivative [None or ‘dt’] If not None, return time derivative of the data, approximated
by the backward finite difference.
is_trace [bool, default False] Indicate evaluation of trace of the variable on a boundary re-
gion.
dt [float, optional] The time step to be used if derivative is ‘dt’. If None, the dt attribute of
the variable is used.
bf [Base function, optional] The base function to be used in ‘val’ mode.
Returns
out [array] The 4-dimensional array of shape (n_el, n_qp, n_row, n_col) with the requested
data, where n_row, n_col depend on mode.
evaluate_at(coors, mode='val', strategy='general', close_limit=0.1, get_cells_fun=None, cache=None,
ret_cells=False, ret_status=False, ret_ref_coors=False, verbose=False)
Evaluate the variable in the given physical coordinates. Convenience wrapper around Field.
evaluate_at(), see its docstring for more details.
get_data_shape(integral, integration='volume', region_name=None)
Get element data dimensions for given approximation.
Parameters
integral [Integral instance] The integral describing used numerical quadrature.
integration [‘volume’, ‘surface’, ‘surface_extra’, ‘point’ or ‘custom’] The term integration
type.
region_name [str] The name of the region of the integral.
Returns
data_shape [5 ints] The (n_el, n_qp, dim, n_en, n_comp) for volume shape kind, (n_fa, n_qp,
dim, n_fn, n_comp) for surface shape kind and (n_nod, 0, 0, 1, n_comp) for point shape
kind.

Notes

• n_el, n_fa = number of elements/facets

• n_qp = number of quadrature points per element/facet
• dim = spatial dimension
• n_en, n_fn = number of element/facet nodes
• n_comp = number of variable components in a point/node
• n_nod = number of element nodes

get_dof_conn(dc_type, is_trace=False, trace_region=None)

Get active dof connectivity of a variable.

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Notes

The primary and dual variables must have the same Region.
get_dof_info(active=False)

get_element_diameters(cells, mode, square=False)

Get diameters of selected elements.
get_field()

get_full(r_vec, r_offset=0, force_value=None, vec=None, offset=0)

Get the full DOF vector satisfying E(P)BCs from a reduced DOF vector.

Notes

The reduced vector starts in r_vec at r_offset. Passing a force_value overrides the EBC values. Optionally,
vec argument can be provided to store the full vector (in place) starting at offset.
get_interp_coors(strategy='interpolation', interp_term=None)
Get the physical coordinates to interpolate into, based on the strategy used.
get_mapping(region, integral, integration, get_saved=False, return_key=False)
Get the reference element mapping of the underlying field.
See also:

sfepy.discrete.common.fields.Field.get_mapping

get_reduced(vec, offset=0, follow_epbc=False)

Get the reduced DOF vector, with EBC and PBC DOFs removed.

Notes

The full vector starts in vec at offset. If ‘follow_epbc’ is True, values of EPBC master DOFs are not simply
thrown away, but added to the corresponding slave DOFs, just like when assembling. For vectors with state
(unknown) variables it should be set to False, for assembled vectors it should be set to True.
get_state_in_region(region, reshape=True, step=0)
Get DOFs of the variable in the given region.
Parameters
region [Region] The selected region.
reshape [bool] If True, reshape the DOF vector to a 2D array with the individual components
as columns. Otherwise a 1D DOF array of the form [all DOFs in region node 0, all DOFs
in region node 1, . . . ] is returned.
step [int, default 0] The time step (0 means current, -1 previous, . . . ).
Returns
out [array] The selected DOFs.
has_same_mesh(other)

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Returns
flag [int] The flag can be either ‘different’ (different meshes), ‘deformed’ (slightly deformed
same mesh), or ‘same’ (same).
invalidate_evaluate_cache(step=0)
Invalidate variable data in evaluate cache for time step given by step (0 is current, -1 previous, . . . ).
This should be done, for example, prior to every nonlinear solver iteration.
save_as_mesh(filename)
Save the field mesh and the variable values into a file for visualization. Only the vertex values are stored.
set_from_function(fun, step=0)
Set the variable data (the vector of DOF values) using a function of space coordinates.
Parameters
fun [callable] The function of coordinates returning DOF values of shape (n_coor,
n_components).
step [int, optional] The time history step, 0 (default) = current.
set_from_mesh_vertices(data)
Set the variable using values at the mesh vertices.
set_from_other(other, strategy='projection', close_limit=0.1)
Set the variable using another variable. Undefined values (e.g. outside the other mesh) are set to numpy.nan,
or extrapolated.
Parameters
strategy [‘projection’ or ‘interpolation’] The strategy to set the values: the L^2 orthogonal
projection (not implemented!), or a direct interpolation to the nodes (nodal elements only!)

Notes

If the other variable uses the same field mesh, the coefficients are set directly.
set_from_qp(data_qp, integral, step=0)
Set DOFs of variable using values in quadrature points corresponding to the given integral.
setup_initial_conditions(ics, di, functions, warn=False)
Setup of initial conditions.
time_update(ts, functions)
Store time step, set variable data for variables with the setter function.
class sfepy.discrete.variables.Variable(name, kind, order=None, primary_var_name=None,
special=None, flags=None, **kwargs)

advance(ts)
Advance in time the DOF state history. A copy of the DOF vector is made to prevent history modification.
static from_conf(key, conf, fields)

get_dual()
Get the dual variable.
Returns

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var [Variable instance] The primary variable for non-state variables, or the dual variable for
state variables.
get_initial_condition()

get_primary()
Get the corresponding primary variable.
Returns
var [Variable instance] The primary variable, or self for state variables or if pri-
mary_var_name is None, or None if no other variables are defined.
get_primary_name()

init_data(step=0)
Initialize the dof vector data of time step step to zeros.
init_history()
Initialize data of variables with history.
is_complex()

is_finite(step=0, derivative=None, dt=None)

is_kind(kind)

is_parameter()

is_real()

is_state()

is_state_or_parameter()

is_virtual()

static reset()

set_constant(val=0.0, step=0)
Set the variable dof vector data of time step step to a scalar val.
set_data(data=None, indx=None, step=0, preserve_caches=False)
Set data (vector of DOF values) of the variable.
Parameters
data [array] The vector of DOF values.
indx [int, optional] If given, data[indx] is used.
step [int, optional] The time history step, 0 (default) = current.
preserve_caches [bool] If True, do not invalidate evaluate caches of the variable.

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time_update(ts, functions)
Implemented in subclasses.
class sfepy.discrete.variables.Variables(variables=None)
Container holding instances of Variable.
advance(ts)

apply_ebc(vec=None, force_values=None)
Apply essential (Dirichlet) and periodic boundary conditions to state all variables or the given vector vec.
apply_ic(vec=None, force_values=None)
Apply initial conditions to all state variables or the given vector vec.
check_vec_size(vec, reduced=False)
Check whether the shape of the DOF vector corresponds to the total number of DOFs of the state variables.
Parameters
vec [array] The vector of DOF values.
reduced [bool] If True, the size of the DOF vector should be reduced, i.e. without DOFs
fixed by boundary conditions.
create_output(vec=None, fill_value=None, var_info=None, extend=True, linearization=None)
Creates an output dictionary with state variables data, that can be passed as ‘out’ kwarg to Mesh.write().
Then the dictionary entries are formed by components of the state vector corresponding to unknown vari-
ables according to kind of linearization given by linearization.
create_reduced_vec()

create_vec()

equation_mapping(ebcs, epbcs, ts, functions, problem=None, active_only=True)

Create the mapping of active DOFs from/to all DOFs for all state variables.
Parameters
ebcs [Conditions instance] The essential (Dirichlet) boundary conditions.
epbcs [Conditions instance] The periodic boundary conditions.
ts [TimeStepper instance] The time stepper.
functions [Functions instance] The user functions for boundary conditions.
problem [Problem instance, optional] The problem that can be passed to user functions as a
context.
active_only [bool] If True, the active DOF info self.adi uses the reduced (active DOFs
only) numbering. Otherwise it is the same as self.di.
Returns
active_bcs [set] The set of boundary conditions active in the current time.
fill_state(value)
Fill the DOF vector with given value.
static from_conf(conf, fields)
This method resets the variable counters for automatic order!

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get_dual_names()
Get names of pairs of dual variables.
Returns
duals [dict] The dual names as virtual name : state name pairs.
get_indx(var_name, reduced=False, allow_dual=False)

get_lcbc_operator()

get_matrix_shape()

get_reduced_state(follow_epbc=False, force=False)
Get the reduced DOF vector, with EBC and PBC DOFs removed.
get_state(reduced=False, follow_epbc=False, force=False)

get_state_parts(vec=None)
Return parts of a state vector corresponding to individual state variables.
Parameters
vec [array, optional] The state vector. If not given, then the data stored in the variables are
returned instead.
Returns
out [dict] The dictionary of the state parts.
get_vec_part(vec, var_name, reduced=False)

has_ebc(vec=None, force_values=None)

has_virtuals()

init_history()

init_state(vec=None)

invalidate_evaluate_caches(step=0)

iter_state(ordered=True)

link_duals()
Link state variables with corresponding virtual variables, and assign link to self to each variable instance.
Usually, when solving a PDE in the weak form, each state variable has a corresponding virtual variable.
make_full_vec(svec, force_value=None, vec=None)
Make a full DOF vector satisfying E(P)BCs from a reduced DOF vector.
Parameters
svec [array] The reduced DOF vector.

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force_value [float, optional] Passing a force_value overrides the EBC values.

vec [array, optional] If given, the buffer for storing the result (zeroed).
Returns
vec [array] The full DOF vector.
reduce_vec(vec, follow_epbc=False, svec=None)
Get the reduced DOF vector, with EBC and PBC DOFs removed.

Notes

If ‘follow_epbc’ is True, values of EPBC master dofs are not simply thrown away, but added to the corre-
sponding slave dofs, just like when assembling. For vectors with state (unknown) variables it should be set
to False, for assembled vectors it should be set to True.
set_adof_conns(adof_conns)
Set all active DOF connectivities to self as well as relevant sub-dicts to the individual variables.
set_data(data, step=0, ignore_unknown=False, preserve_caches=False)
Set data (vectors of DOF values) of variables.
Parameters
data [array] The state vector or dictionary of {variable_name : data vector}.
step [int, optional] The time history step, 0 (default) = current.
ignore_unknown [bool, optional] Ignore unknown variable names if data is a dict.
preserve_caches [bool] If True, do not invalidate evaluate caches of variables.
set_full_state(vec, force=False, preserve_caches=False)
Set the full DOF vector (including EBC and PBC DOFs). If var_name is given, set only the DOF sub-vector
corresponding to the given variable. If force is True, setting variables with LCBC DOFs is allowed.
set_reduced_state(r_vec, preserve_caches=False)
Set the reduced DOF vector, with EBC and PBC DOFs removed.
Parameters
r_vec [array] The reduced DOF vector corresponding to the variables.
preserve_caches [bool] If True, do not invalidate evaluate caches of variables.
set_state(vec, reduced=False, force=False, preserve_caches=False)

set_state_parts(parts, vec=None, force=False)

Set parts of the DOF vector corresponding to individual state variables.
Parameters
parts [dict] The dictionary of the DOF vector parts.
force [bool] If True, proceed even with LCBCs present.
set_vec_part(vec, var_name, part, reduced=False)

setup_dof_info(make_virtual=False)
Setup global DOF information.

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setup_dtype()
Setup data types of state variables - all have to be of the same data type, one of nm.float64 or
nm.complex128.
setup_initial_conditions(ics, functions)

setup_lcbc_operators(lcbcs, ts=None, functions=None)

Prepare linear combination BC operator matrix and right-hand side vector.
setup_ordering()
Setup ordering of variables.
time_update(ts, functions, verbose=True)

sfepy.discrete.variables.create_adof_conn(eq, conn, dpn, offset)

Given a node connectivity, number of DOFs per node and equation mapping, create the active dof connectivity.
Locally (in a connectivity row), the DOFs are stored DOF-by-DOF (u_0 in all local nodes, u_1 in all local nodes,
. . . ).
Globally (in a state vector), the DOFs are stored node-by-node (u_0, u_1, . . . , u_X in node 0, u_0, u_1, . . . , u_X
in node 1, . . . ).
sfepy.discrete.variables.create_adof_conns(conn_info, var_indx=None, active_only=True,
verbose=True)
Create active DOF connectivities for all variables referenced in conn_info.
If a variable has not the equation mapping, a trivial mapping is assumed and connectivity with all DOFs active
is created.
DOF connectivity key is a tuple (primary variable name, region name, type, is_trace flag).

Notes

If active_only is False, the DOF connectivities contain all DOFs, with the E(P)BC-constrained ones stored as -1
- <DOF number>, so that the full connectivities can be reconstructed for the matrix graph creation.
sfepy.discrete.variables.expand_basis(basis, dpn)
Expand basis for variables with several components (DOFs per node), in a way compatible with
create_adof_conn(), according to dpn (DOF-per-node count).

sfepy.discrete.common sub-package

Common lower-level code and parent classes for FEM and IGA.

sfepy.discrete.common.dof_info module

Classes holding information on global DOFs and mapping of all DOFs - equations (active DOFs).
Helper functions for the equation mapping.
class sfepy.discrete.common.dof_info.DofInfo(name)
Global DOF information, i.e. ordering of DOFs of the state (unknown) variables in the global state vector.
append_raw(name, n_dof )
Append raw DOFs.

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Parameters
name [str] The name of variable the DOFs correspond to.
n_dof [int] The number of DOFs.
append_variable(var, active=False)
Append DOFs of the given variable.
Parameters
var [Variable instance] The variable to append.
active [bool, optional] When True, only active (non-constrained) DOFs are considered.
get_info(var_name)
Return information on DOFs of the given variable.
Parameters
var_name [str] The name of the variable.
get_n_dof_total()
Return the total number of DOFs of all state variables.
get_subset_info(var_names)
Return global DOF information for selected variables only. Silently ignores non-existing variable names.
Parameters
var_names [list] The names of the selected variables.
update(name, n_dof )
Set the number of DOFs of the given variable.
Parameters
name [str] The name of variable the DOFs correspond to.
n_dof [int] The number of DOFs.
class sfepy.discrete.common.dof_info.EquationMap(name, dof_names, var_di)
Map all DOFs to equations for active DOFs.
get_operator()
Get the matrix operator 𝑅 corresponding to the equation mapping, such that the restricted matrix 𝐴𝑟 can
be obtained from the full matrix 𝐴 by 𝐴𝑟 = 𝑅𝑇 𝐴𝑅. All the matrices are w.r.t. a single variables that uses
this mapping.
Returns
mtx [coo_matrix] The matrix 𝑅.
map_equations(bcs, field, ts, functions, problem=None, warn=False)
Create the mapping of active DOFs from/to all DOFs.
Parameters
bcs [Conditions instance] The Dirichlet or periodic boundary conditions (single condition
instances). The dof names in the conditions must already be canonized.
field [Field instance] The field of the variable holding the DOFs.
ts [TimeStepper instance] The time stepper.
functions [Functions instance] The registered functions.

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problem [Problem instance, optional] The problem that can be passed to user functions as a
context.
warn [bool, optional] If True, warn about BC on non-existent nodes.
Returns
active_bcs [set] The set of boundary conditions active in the current time.

Notes

• Periodic bc: master and slave DOFs must belong to the same field (variables can differ, though).

sfepy.discrete.common.dof_info.expand_nodes_to_dofs(nods, n_dof_per_node)
Expand DOF node indices into DOFs given a constant number of DOFs per node.
sfepy.discrete.common.dof_info.expand_nodes_to_equations(nods, dof_names, all_dof_names)
Expand vector of node indices to equations (DOF indices) based on the DOF-per-node count.
DOF names must be already canonized.
Returns
eq [array] The equations/DOF indices in the node-by-node order.
sfepy.discrete.common.dof_info.group_chains(chain_list)
Group EPBC chains.
sfepy.discrete.common.dof_info.is_active_bc(bc, ts=None, functions=None)
Check whether the given boundary condition is active in the current time.
Returns
active [bool] True if the condition bc is active.
sfepy.discrete.common.dof_info.resolve_chains(master_slave, chains)
Resolve EPBC chains - e.g. in corner nodes.

sfepy.discrete.common.domain module

class sfepy.discrete.common.domain.Domain(name, mesh=None, nurbs=None, bmesh=None,

regions=None, verbose=False)

create_region(name, select, kind='cell', parent=None, check_parents=True, extra_options=None,

functions=None, add_to_regions=True, allow_empty=False)
Region factory constructor. Append the new region to self.regions list.
create_regions(region_defs, functions=None, allow_empty=False)

get_centroids(dim)
Return the coordinates of centroids of mesh entities with dimension dim.
has_faces()

reset_regions()
Reset the list of regions associated with the domain.

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save_regions(filename, region_names=None)
Save regions as individual meshes.
Parameters
filename [str] The output filename.
region_names [list, optional] If given, only the listed regions are saved.
save_regions_as_groups(filename, region_names=None)
Save regions in a single mesh but mark them by using different element/node group numbers.
If regions overlap, the result is undetermined, with exception of the whole domain region, which is marked
by group id 0.
Region masks are also saved as scalar point data for output formats that support this.
Parameters
filename [str] The output filename.
region_names [list, optional] If given, only the listed regions are saved.
sfepy.discrete.common.domain.region_leaf(domain, regions, rdef, functions)
Create/setup a region instance according to rdef.
sfepy.discrete.common.domain.region_op(level, op_code, item1, item2)

sfepy.discrete.common.extmods._fmfield module

sfepy.discrete.common.extmods._geommech module

Low level functions.

sfepy.discrete.common.extmods._geommech.geme_mulAVSB3py()

sfepy.discrete.common.extmods.assemble module

Low level finite element assembling functions.

sfepy.discrete.common.extmods.assemble.assemble_matrix()

sfepy.discrete.common.extmods.assemble.assemble_matrix_complex()

sfepy.discrete.common.extmods.assemble.assemble_vector()

sfepy.discrete.common.extmods.assemble.assemble_vector_complex()

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sfepy.discrete.common.extmods.cmesh module

C Mesh data structures and functions.

class sfepy.discrete.common.extmods.cmesh.CConnectivity

Notes

The memory is allocated/freed in C - this class just wraps NumPy arrays around that data without copying.
cprint()

indices
n_incident
num
offset
offsets
class sfepy.discrete.common.extmods.cmesh.CMesh

cell_groups
cell_types
conns
coors
cprint()

create_new()
Create a new CMesh instance, with cells corresponding to the given entities of dimension dent.
Parameters
entities [array, optional] The selected topological entities of the mesh to be in the new mesh.
If not given, a copy of the mesh based on the cell-vertex connectivity is returned.
dent [int, optional] The topological dimension of the entities.
localize [bool] If True, strip the vertices not used in the the resulting sub-mesh cells and
renumber the connectivity.
Returns
cmesh [CMesh] The new mesh with the cell-vertex connectivity. Other connectivities have
to be created and local entities need to be set manually.
dim
edge_oris
entities
face_oris
facet_oris

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free_connectivity()

from_data()
Fill CMesh data using Python data.
get_cell_conn()

get_centroids()
Return the coordinates of centroids of mesh entities with dimension dim.
get_complete()
Get entities of dimension dim that are completely given by entities of dimension dent listed in entities.
get_conn()

get_conn_as_graph()
Get d1 -> d2 connectivity as a sparse matrix graph (values = ones).
For safety, creates a copy of the connectivity arrays. The connectivity is created if necessary.
get_facet_normals()
Return the normals of facets for each mesh cell. The normals can be accessed using the cell-facet connec-
tivity.
If which is -1, two normals of each quadrilateral face are averaged. If it is 0 or 1, the corresponding normal
is used.
get_incident()
Get non-unique entities indices of dimension dim that are contained in entities of dimension dent listed in
entities. As each of entities can be in several entities of dimension dent, offsets array is returned optionally.
get_local_entities()

get_local_ids()
Get local ids of entities of dimension dent in non-unique entities incident of dimension dim (with given
offsets per entities) incident to entities, see mesh_get_incident().
The function searches entities in incident -> entities connectivity for each non-unique entity in incident.
get_orientations()
Get orientations of entities of dimension dim. Alternatively, co-dimension can be specified using codim
argument.
get_surface_facets()
Get facets (edges in 2D, faces in 3D) on the mesh surface.
get_volumes()
Return the volumes of mesh entities with dimension dim > 0.
key_to_index
n_coor
n_el
num
set_local_entities()

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setup_connectivity()

setup_entities()
Set up mesh edge (2D and 3D) and face connectivities (3D only) as well as their orientations.
tdim
vertex_groups
sfepy.discrete.common.extmods.cmesh.cmem_statistics()

sfepy.discrete.common.extmods.cmesh.create_mesh_graph()
Create sparse (CSR) graph corresponding to given row and column connectivities.
Parameters
n_row [int] The number of row connectivity nodes.
n_col [int] The number of column connectivity nodes.
n_gr [int] The number of element groups.
rconns [list of arrays] The list of length n_gr of row connectivities.
cconns [list of arrays] The list of length n_gr of column connectivities.
Returns
nnz [int] The number of graph nonzeros.
prow [array] The array of CSR row pointers.
icol [array] The array of CSR column indices.
sfepy.discrete.common.extmods.cmesh.get_cmem_usage()

sfepy.discrete.common.extmods.cmesh.graph_components()
Determine connected compoments of a compressed sparse graph.
Returns
n_comp [int] The number of components.
flag [array] The flag marking for each node its component.
sfepy.discrete.common.extmods.cmesh.orient_elements()
Swap element nodes so that its volume is positive.

sfepy.discrete.common.extmods.crefcoors module

class sfepy.discrete.common.extmods.crefcoors.CBasisContext
sfepy.discrete.common.extmods.crefcoors.evaluate_in_rc()
Evaluate source field DOF values or gradients in the given reference element coordinates using the given inter-
polation.
1. Evaluate basis functions or gradients of basis functions in the reference coordinates. For gradients, tranform
the values to the material coordinates. 2. Interpolate source values using the basis functions/gradients.
Interpolation uses field approximation connectivity.

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sfepy.discrete.common.extmods.crefcoors.find_ref_coors()

sfepy.discrete.common.extmods.crefcoors.find_ref_coors_convex()

sfepy.discrete.common.extmods.mappings module

Low level reference mapping functionality.

class sfepy.discrete.common.extmods.mappings.CMapping

alloc_extra_data()

bf
bfg
cprint()

describe()
Describe the element geometry - compute the reference element mapping.
det
dim
evaluate_bfbgm()
Evaluate volume base function gradients in surface quadrature points.
get_element_diameters()
Compute diameters of selected elements.
integral
integrate()
Integrate arr over the domain of the mapping into out.
mode
mtx_t
n_el
n_ep
n_qp
normal
ps
qp
shape
volume

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sfepy.discrete.common.fields module

class sfepy.discrete.common.fields.Field(**kwargs)
Base class for fields.
clear_mappings(clear_all=False)
Clear current reference mappings.
create_eval_mesh()
Create a mesh for evaluating the field. The default implementation returns None, because this mesh is for
most fields the same as the one created by Field.create_mesh().
evaluate_at(coors, source_vals, mode='val', strategy='general', close_limit=0.1, get_cells_fun=None,
cache=None, ret_cells=False, ret_status=False, ret_ref_coors=False, verbose=False)
Evaluate source DOF values corresponding to the field in the given coordinates using the field interpolation.
Parameters
coors [array, shape (n_coor, dim)] The coordinates the source values should be interpo-
lated into.
source_vals [array, shape (n_nod, n_components)] The source DOF values correspond-
ing to the field.
mode [{‘val’, ‘grad’}, optional] The evaluation mode: the field value (default) or the field
value gradient.
strategy [{‘general’, ‘convex’}, optional] The strategy for finding the elements that contain
the coordinates. For convex meshes, the ‘convex’ strategy might be faster than the ‘general’
one.
close_limit [float, optional] The maximum limit distance of a point from the closest element
allowed for extrapolation.
get_cells_fun [callable, optional] If given, a function with signature
get_cells_fun(coors, cmesh, **kwargs) returning cells and offsets that po-
tentially contain points with the coordinates coors. Applicable only when strategy is
‘general’. When not given, get_potential_cells() is used.
cache [Struct, optional] To speed up a sequence of evaluations, the field mesh and other
data can be cached. Optionally, the cache can also contain the reference element coor-
dinates as cache.ref_coors, cache.cells and cache.status, if the evaluation occurs in the
same coordinates repeatedly. In that case the mesh related data are ignored. See Field.
get_evaluate_cache().
ret_ref_coors [bool, optional] If True, return also the found reference element coordinates.
ret_status [bool, optional] If True, return also the enclosing cell status for each point.
ret_cells [bool, optional] If True, return also the cell indices the coordinates are in.
verbose [bool] If False, reduce verbosity.
Returns
vals [array] The interpolated values with shape (n_coor, n_components) or gradients
with shape (n_coor, n_components, dim) according to the mode. If ret_status is
False, the values where the status is greater than one are set to numpy.nan.
ref_coors [array] The found reference element coordinates, if ret_ref_coors is True.
cells [array] The cell indices, if ret_ref_coors or ret_cells or ret_status are True.

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status [array] The status, if ret_ref_coors or ret_status are True, with the following meaning:
0 is success, 1 is extrapolation within close_limit, 2 is extrapolation outside close_limit, 3 is
failure, 4 is failure due to non-convergence of the Newton iteration in tensor product cells.
If close_limit is 0, then for the ‘general’ strategy the status 5 indicates points outside of the
field domain that had no potential cells.
static from_args(name, dtype, shape, region, approx_order=1, space='H1', poly_space_base='lagrange')
Create a Field subclass instance corresponding to a given space.
Parameters
name [str] The field name.
dtype [numpy.dtype] The field data type: float64 or complex128.
shape [int/tuple/str] The field shape: 1 or (1,) or ‘scalar’, space dimension (2, or (2,) or 3 or
(3,)) or ‘vector’, or a tuple. The field shape determines the shape of the FE base functions
and is related to the number of components of variables and to the DOF per node count,
depending on the field kind.
region [Region] The region where the field is defined.
approx_order [int/str] The FE approximation order, e.g. 0, 1, 2, ‘1B’ (1 with bubble).
space [str] The function space name.
poly_space_base [str] The name of polynomial space base.

Notes

Assumes one cell type for the whole region!

static from_conf(conf, regions)
Create a Field subclass instance based on the configuration.
get_mapping(region, integral, integration, get_saved=False, return_key=False)
For given region, integral and integration type, get a reference mapping, i.e. jacobians, element volumes and
base function derivatives for Volume-type geometries, and jacobians, normals and base function derivatives
for Surface-type geometries corresponding to the field approximation.
The mappings are cached in the field instance in mappings attribute. The mappings can be saved to map-
pings0 using Field.save_mappings. The saved mapping can be retrieved by passing get_saved=True. If the
required (saved) mapping is not in cache, a new one is created.
Returns
geo [CMapping instance] The reference mapping.
mapping [VolumeMapping or SurfaceMapping instance] The mapping.
key [tuple] The key of the mapping in mappings or mappings0.
save_mappings()
Save current reference mappings to mappings0 attribute.
set_dofs(fun=0.0, region=None, dpn=None, warn=None)
Set the values of DOFs in a given region using a function of space coordinates or value fun.
If fun is a function, the l2 projection that is global for all region facets is used to set the DOFs.
If dpn > 1, and fun is a function, it has to return the values point-by-point, i.e. all components in the first
point, in the second point etc., concatenated to an array that is reshapable to the shape (n_point, dpn).
Parameters

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fun [float or array of length dpn or callable] The DOF values.

region [Region] The region containing the DOFs.
dpn [int, optional] The DOF-per-node count. If not given, the number of field components
is used.
warn [str, optional] The warning message printed when the region selects no DOFs.
Returns
nods [array, shape (n_dof,)] The field DOFs (or node indices) given by the region.
vals [array, shape (n_dof, dpn)] The values of the DOFs, node-by-node when raveled in C
(row-major) order.

Notes

The nodal basis fields (lagrange) reimplement this function to set DOFs directly.
The hierarchical basis field (lobatto) do not support surface mappings, so also reimplement this function.
sfepy.discrete.common.fields.fields_from_conf(conf, regions)

sfepy.discrete.common.fields.parse_approx_order(approx_order)
Parse the uniform approximation order value (str or int).
sfepy.discrete.common.fields.parse_shape(shape, dim)

sfepy.discrete.common.fields.setup_extra_data(conn_info)
Setup extra data required for non-volume integration.

sfepy.discrete.common.global_interp module

Global interpolation functions.

sfepy.discrete.common.global_interp.get_potential_cells(coors, cmesh, centroids=None,
extrapolate=True)
Get cells that potentially contain points with the given physical coordinates.
Parameters
coors [array] The physical coordinates.
cmesh [CMesh instance] The cmesh defining the cells.
centroids [array, optional] The centroids of the cells.
extrapolate [bool] If True, even the points that are surely outside of the cmesh are considered
and assigned potential cells.
Returns
potential_cells [array] The indices of the cells that potentially contain the points.
offsets [array] The offsets into potential_cells for each point: a point ip is potentially in cells
potential_cells[offsets[ip]:offsets[ip+1]].
sfepy.discrete.common.global_interp.get_ref_coors(field, coors, strategy='general', close_limit=0.1,
get_cells_fun=None, cache=None, verbose=False)
Get reference element coordinates and elements corresponding to given physical coordinates.

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Parameters
field [Field instance] The field defining the approximation.
coors [array] The physical coordinates.
strategy [{‘general’, ‘convex’}, optional] The strategy for finding the elements that contain the
coordinates. For convex meshes, the ‘convex’ strategy might be faster than the ‘general’ one.
close_limit [float, optional] The maximum limit distance of a point from the closest element
allowed for extrapolation.
get_cells_fun [callable, optional] If given, a function with signature get_cells_fun(coors,
cmesh, **kwargs) returning cells and offsets that potentially contain points with the
coordinates coors. Applicable only when strategy is ‘general’. When not given,
get_potential_cells() is used.
cache [Struct, optional] To speed up a sequence of evaluations, the field mesh and other data
can be cached. Optionally, the cache can also contain the reference element coordinates as
cache.ref_coors, cache.cells and cache.status, if the evaluation occurs in the same coordi-
nates repeatedly. In that case the mesh related data are ignored.
verbose [bool] If False, reduce verbosity.
Returns
ref_coors [array] The reference coordinates.
cells [array] The cell indices corresponding to the reference coordinates.
status [array] The status: 0 is success, 1 is extrapolation within close_limit, 2 is extrapolation
outside close_limit, 3 is failure, 4 is failure due to non-convergence of the Newton iteration
in tensor product cells. If close_limit is 0, then for the ‘general’ strategy the status 5 indicates
points outside of the field domain that had no potential cells.
sfepy.discrete.common.global_interp.get_ref_coors_convex(field, coors, close_limit=0.1, cache=None,
verbose=False)
Get reference element coordinates and elements corresponding to given physical coordinates.
Parameters
field [Field instance] The field defining the approximation.
coors [array] The physical coordinates.
close_limit [float, optional] The maximum limit distance of a point from the closest element
allowed for extrapolation.
cache [Struct, optional] To speed up a sequence of evaluations, the field mesh and other data
can be cached. Optionally, the cache can also contain the reference element coordinates as
cache.ref_coors, cache.cells and cache.status, if the evaluation occurs in the same coordi-
nates repeatedly. In that case the mesh related data are ignored.
verbose [bool] If False, reduce verbosity.
Returns
ref_coors [array] The reference coordinates.
cells [array] The cell indices corresponding to the reference coordinates.
status [array] The status: 0 is success, 1 is extrapolation within close_limit, 2 is extrapolation
outside close_limit, 3 is failure, 4 is failure due to non-convergence of the Newton iteration
in tensor product cells.

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Notes

Outline of the algorithm for finding xi such that X(xi) = P:

1. make inverse connectivity - for each vertex have cells it is in.
2. find the closest vertex V.
3. choose initial cell: i0 = first from cells incident to V.
4. while not P in C_i, change C_i towards P, check if P in new C_i.
sfepy.discrete.common.global_interp.get_ref_coors_general(field, coors, close_limit=0.1,
get_cells_fun=None, cache=None,
verbose=False)
Get reference element coordinates and elements corresponding to given physical coordinates.
Parameters
field [Field instance] The field defining the approximation.
coors [array] The physical coordinates.
close_limit [float, optional] The maximum limit distance of a point from the closest element
allowed for extrapolation.
get_cells_fun [callable, optional] If given, a function with signature get_cells_fun(coors,
cmesh, **kwargs) returning cells and offsets that potentially contain points with the co-
ordinates coors. When not given, get_potential_cells() is used.
cache [Struct, optional] To speed up a sequence of evaluations, the field mesh and other data
can be cached. Optionally, the cache can also contain the reference element coordinates as
cache.ref_coors, cache.cells and cache.status, if the evaluation occurs in the same coordi-
nates repeatedly. In that case the mesh related data are ignored.
verbose [bool] If False, reduce verbosity.
Returns
ref_coors [array] The reference coordinates.
cells [array] The cell indices corresponding to the reference coordinates.
status [array] The status: 0 is success, 1 is extrapolation within close_limit, 2 is extrapolation
outside close_limit, 3 is failure, 4 is failure due to non-convergence of the Newton iteration
in tensor product cells. If close_limit is 0, then status 5 indicates points outside of the field
domain that had no potential cells.

sfepy.discrete.common.mappings module

Reference-physical domain mappings.

class sfepy.discrete.common.mappings.Mapping(**kwargs)
Base class for mappings.
static from_args(region, kind='v')
Create mapping from reference to physical entities in a given region, given the integration kind (‘v’ or ‘s’).
This mapping can be used to compute the physical quadrature points.
Parameters
region [Region instance] The region defining the entities.

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kind [‘v’ or ‘s’] The kind of the entities: ‘v’ - cells, ‘s’ - facets.
Returns
mapping [VolumeMapping or SurfaceMapping instance] The requested mapping.
class sfepy.discrete.common.mappings.PhysicalQPs(num=0)
Physical quadrature points in a region.
get_shape(rshape)
Get shape from raveled shape.
sfepy.discrete.common.mappings.get_jacobian(field, integral, region=None, integration='volume')
Get the jacobian of reference mapping corresponding to field.
Parameters
field [Field instance] The field defining the reference mapping.
integral [Integral instance] The integral defining quadrature points.
region [Region instance, optional] If given, use the given region instead of field region.
integration [one of (‘volume’, ‘surface’, ‘surface_extra’)] The integration type.
Returns
jac [array] The jacobian merged for all element groups.
See also:

get_mapping_data

Notes

Assumes the same element geometry in all element groups of the field!
sfepy.discrete.common.mappings.get_mapping_data(name, field, integral, region=None,
integration='volume')
General helper function for accessing reference mapping data.
Get data attribute name from reference mapping corresponding to field in region in quadrature points of the given
integral and integration type.
Parameters
name [str] The reference mapping attribute name.
field [Field instance] The field defining the reference mapping.
integral [Integral instance] The integral defining quadrature points.
region [Region instance, optional] If given, use the given region instead of field region.
integration [one of (‘volume’, ‘surface’, ‘surface_extra’)] The integration type.
Returns
data [array] The required data merged for all element groups.

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Notes

Assumes the same element geometry in all element groups of the field!
sfepy.discrete.common.mappings.get_normals(field, integral, region)
Get the normals of element faces in region.
Parameters
field [Field instance] The field defining the reference mapping.
integral [Integral instance] The integral defining quadrature points.
region [Region instance] The given of the element faces.
Returns
normals [array] The normals merged for all element groups.
See also:

get_mapping_data

Notes

Assumes the same element geometry in all element groups of the field!
sfepy.discrete.common.mappings.get_physical_qps(region, integral, map_kind=None)
Get physical quadrature points corresponding to the given region and integral.

sfepy.discrete.common.poly_spaces module

class sfepy.discrete.common.poly_spaces.PolySpace(name, geometry, order)

Abstract polynomial space class.
static any_from_args(name, geometry, order, base='lagrange', force_bubble=False)
Construct a particular polynomial space classes according to the arguments passed in.
eval_base(coors, diff=0, ori=None, force_axis=False, transform=None, suppress_errors=False, eps=1e-15)
Evaluate the basis or its first or second derivatives in points given by coordinates. The real work is done in
_eval_base() implemented in subclasses.
Note that the second derivative code is a work-in-progress and only coors and transform arguments are
used.
Parameters
coors [array_like] The coordinates of points where the basis is evaluated. See Notes.
diff [0, 1 or 2] If nonzero, return the given derivative.
ori [array_like, optional] Optional orientation of element facets for per element basis.
force_axis [bool] If True, force the resulting array shape to have one more axis even when
ori is None.
transform [array_like, optional] The basis transform array.
suppress_errors [bool] If True, do not report points outside the reference domain.
eps [float] Accuracy for comparing coordinates.
Returns

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base [array] The basis (shape (n_coor, 1, n_base)) or its first derivative (shape (n_coor, dim,
n_base)) or its second derivative (shape (n_coor, dim, dim, n_base)) evaluated in the given
points. An additional axis is pre-pended of length n_cell, if ori is given, or of length 1, if
force_axis is True.

Notes

If coors.ndim == 3, several point sets are assumed, with equal number of points in each of them. This is
the case, for example, of the values of the volume base functions on the element facets. The indexing (of
bf_b(g)) is then (ifa,iqp,:,n_ep), so that the facet can be set in C using FMF_SetCell.
keys = {(0, 1): 'simplex', (1, 2): 'simplex', (2, 3): 'simplex', (2, 4):
'tensor_product', (3, 4): 'simplex', (3, 8): 'tensor_product'}
static suggest_name(geometry, order, base='lagrange', force_bubble=False)
Suggest the polynomial space name given its constructor parameters.
sfepy.discrete.common.poly_spaces.transform_basis(transform, bf )
Transform a basis bf using transform array of matrices.

sfepy.discrete.common.region module

class sfepy.discrete.common.region.Region(name, definition, domain, parse_def, kind='cell',

parent=None)
Region defines a subset of a FE domain.
Region kinds:
• cell_only, facet_only, face_only, edge_only, vertex_only - only the specified entities are included, others
are empty sets (so that the operators are still defined)
• cell, facet, face, edge, vertex - entities of higher dimension are not included
The ‘cell’ kind is the most general and it is the default.
Region set-like operators: + (union), - (difference), * (intersection), followed by one of (‘v’, ‘e’, ‘f’, ‘c’, and ‘s’)
for vertices, edges, faces, cells, and facets.
Created: 31.10.2005
property cells
contains(other)
Return True in the region contains the other region.
The check is performed using entities corresponding to the other region kind.
copy()
Vertices-based copy.
delete_zero_faces(eps=1e-14)

property edges
eval_op_cells(other, op)

eval_op_edges(other, op)

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eval_op_faces(other, op)

eval_op_facets(other, op)

eval_op_vertices(other, op)

property faces
property facets
finalize(allow_empty=False)
Initialize the entities corresponding to the region kind and regenerate all already existing (accessed) entities
of lower topological dimension from the kind entities.
static from_cells(cells, domain, name='region', kind='cell', parent=None)
Create a new region containing given cells.
Parameters
cells [array] The array of cells.
domain [Domain instance] The domain containing the facets.
name [str, optional] The name of the region.
kind [str, optional] The kind of the region.
parent [str, optional] The name of the parent region.
Returns
obj [Region instance] The new region.
static from_facets(facets, domain, name='region', kind='facet', parent=None)
Create a new region containing given facets.
Parameters
facets [array] The array with indices to unique facets.
domain [Domain instance] The domain containing the facets.
name [str, optional] The name of the region.
kind [str, optional] The kind of the region.
parent [str, optional] The name of the parent region.
Returns
obj [Region instance] The new region.
static from_vertices(vertices, domain, name='region', kind='cell')
Create a new region containing given vertices.
Parameters
vertices [array] The array of vertices.
domain [Domain instance] The domain containing the vertices.
name [str, optional] The name of the region.
kind [str, optional] The kind of the region.
Returns

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obj [Region instance] The new region.

get_cell_indices(cells, true_cells_only=True)
Return indices of cells in the region cells.
Raises ValueError if true_cells_only is True and the region kind does not allow cells. For true_cells_only
equal to False, cells incident to facets are returned if the region itself contains no cells.

Notes

If the number of unique values in cells is smaller or equal to the number of cells in the region, all cells
has to be also the region cells (self is a superset of cells). The region cells are considered depending on
true_cells_only.
Otherwise, indices of all cells in self that are in cells are returned.
get_cells(true_cells_only=True)
Get cells of the region.
Raises ValueError if true_cells_only is True and the region kind does not allow cells. For true_cells_only
equal to False, cells incident to facets are returned if the region itself contains no cells. Obeys parent region,
if given.
get_charfun(by_cell=False, val_by_id=False)
Return the characteristic function of the region as a vector of values defined either in the mesh vertices
(by_cell == False) or cells. The values are either 1 (val_by_id == False) or sequential id + 1.
get_edge_graph()
Return the graph of region edges as a sparse matrix having uid(k) + 1 at (i, j) if vertex[i] is connected with
vertex[j] by the edge k.
Degenerate edges are ignored.
get_entities(dim)
Return mesh entities of dimension dim.
get_facet_indices()
Return an array (per group) of (iel, ifa) for each facet. A facet can be in 1 (surface) or 2 (inner) cells.
get_mirror_region(name)

get_n_cells(is_surface=False)
Get number of region cells.
Parameters
is_surface [bool] If True, number of edges or faces according to domain dimension is re-
turned instead.
Returns
n_cells [int] The number of cells.
has_cells()

light_copy(name, parse_def )

set_kind(kind)

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set_kind_tdim()

setup_from_highest(dim, allow_lower=True, allow_empty=False)

Setup entities of topological dimension dim using the available entities of the highest topological dimension.
setup_from_vertices(dim)
Setup entities of topological dimension dim using the region vertices.
setup_mirror_region(mirror_name=None, ret_name=False)
Find the corresponding mirror region, set up element mapping.
update_shape()
Update shape of each group according to region vertices, edges, faces and cells.
property vertices
sfepy.discrete.common.region.are_disjoint(r1, r2)
Check if the regions r1 and r2 are disjoint.
Uses vertices for the check - *_only regions not allowed.
sfepy.discrete.common.region.get_dependency_graph(region_defs)
Return a dependency graph and a name-sort name mapping for given region definitions.
sfepy.discrete.common.region.get_parents(selector)
Given a region selector, return names of regions it is based on.
sfepy.discrete.common.region.sort_by_dependency(graph)

sfepy.discrete.fem sub-package

sfepy.discrete.fem.domain module

Computational domain, consisting of the mesh and regions.

class sfepy.discrete.fem.domain.FEDomain(name, mesh, verbose=False, **kwargs)
Domain is divided into groups, whose purpose is to have homogeneous data shapes.
clear_surface_groups()
Remove surface group data.
create_surface_group(region)
Create a new surface group corresponding to region if it does not exist yet.

Notes

Surface groups define surface facet connectivity that is needed for sfepy.discrete.fem.mappings.
SurfaceMapping.
fix_element_orientation()
Ensure element vertices ordering giving positive cell volumes.
get_conn(ret_gel=False)
Get the cell-vertex connectivity and, if ret_gel is True, also the corresponding reference geometry element.
get_diameter()
Return the diameter of the domain.

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Notes

The diameter corresponds to the Friedrichs constant.

get_element_diameters(cells, vg, mode, square=True)

get_mesh_bounding_box()
Return the bounding box of the underlying mesh.
Returns
bbox [ndarray (2, dim)] The bounding box with min. values in the first row and max. values
in the second row.
get_mesh_coors(actual=False)
Return the coordinates of the underlying mesh vertices.
refine()
Uniformly refine the domain mesh.
Returns
domain [FEDomain instance] The new domain with the refined mesh.

Notes

Works only for meshes with single element type! Does not preserve node groups!

sfepy.discrete.fem.extmods.bases module

Polynomial base functions and related utilities.

class sfepy.discrete.fem.extmods.bases.CLagrangeContext

base1d
cprint()

e_coors_max
evaluate()

geo_ctx
iel
is_bubble
mbfg
mesh_conn
mesh_coors

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sfepy.discrete.fem.extmods.lobatto_bases module

Interface to Lobatto bases.

sfepy.discrete.fem.extmods.lobatto_bases.eval_lobatto1d()
Evaluate 1D Lobatto functions of the given order in given points.
sfepy.discrete.fem.extmods.lobatto_bases.eval_lobatto_tensor_product()
Evaluate tensor product Lobatto functions of the given order in given points.
Base functions are addressed using the nodes array with rows corresponding to individual functions and columns
to 1D indices (= orders when >= 1) into lobatto[] and d_lobatto[] lists for each axis.

sfepy.discrete.fem.facets module

Helper functions related to mesh facets and Lagrange FE approximation.

Line: ori - iter:
0 - iter0 1 - iter1
Triangle: ori - iter:
0 - iter21 1 - iter12 3 - iter02 4 - iter20 6 - iter10 7 - iter01
Possible couples:
1, 4, 7 <-> 0, 3, 6
Square: ori - iter:
0 - iter10x01y 7 - iter10y01x
11 - iter01y01x 30 - iter01x10y 33 - iter10x10y 52 - iter01y10x 56 - iter10y10x 63 - iter01x01y
Possible couples:
7, 33, 52, 63 <-> 0, 11, 30, 56
_quad_ori_groups:
i<j<k<l
all faces are permuted to
l—k||||i—j
ijkl
which is the same as
l—j||||i—k
ikjl
k—l||||i—j
ijlk
• start at one vertex and go around clock-wise or anticlock-wise
-> 8 groups of 3 -> same face nodes order in ijkl (63), ikjl (59), ijlk (31) ilkj (11), iklj (15), iljk (43) jkli ( 7), jlki ( 3),
kjli ( 6) kjil (56), jkil (57), ljik (48) lijk (52), likj (20), kijl (60) lkji ( 0), ljki ( 4), klji ( 1) klij (33), lkij (32), jlik (41)
jilk (30), kilj (22), jikl (62)

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sfepy.discrete.fem.facets.build_orientation_map(n_fp)
The keys are binary masks of the lexicographical ordering of facet vertices. A bit i set to one means v[i] < v[i+1].
The values are [original_order, permutation], where permutation can be used to sort facet vertices lexicograph-
ically. Hence permuted_facet = facet[permutation].
sfepy.discrete.fem.facets.get_facet_dof_permutations(n_fp, order)
Prepare DOF permutation vector for each possible facet orientation.
sfepy.discrete.fem.facets.iter0(num)

sfepy.discrete.fem.facets.iter01(num)

sfepy.discrete.fem.facets.iter01x01y(num)

sfepy.discrete.fem.facets.iter01x10y(num)

sfepy.discrete.fem.facets.iter01y01x(num)

sfepy.discrete.fem.facets.iter01y10x(num)

sfepy.discrete.fem.facets.iter02(num)

sfepy.discrete.fem.facets.iter1(num)

sfepy.discrete.fem.facets.iter10(num)

sfepy.discrete.fem.facets.iter10x01y(num)

sfepy.discrete.fem.facets.iter10x10y(num)

sfepy.discrete.fem.facets.iter10y01x(num)

sfepy.discrete.fem.facets.iter10y10x(num)

sfepy.discrete.fem.facets.iter12(num)

sfepy.discrete.fem.facets.iter20(num)

sfepy.discrete.fem.facets.iter21(num)

sfepy.discrete.fem.facets.make_line_matrix(order)

sfepy.discrete.fem.facets.make_square_matrix(order)

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sfepy.discrete.fem.facets.make_triangle_matrix(order)

sfepy.discrete.fem.fe_surface module

class sfepy.discrete.fem.fe_surface.FESurface(name, region, efaces, volume_econn,

volume_region=None)
Description of a surface of a finite element domain.
get_connectivity(local=False, is_trace=False)
Return the surface element connectivity.
Parameters
local [bool] If True, return local connectivity w.r.t. surface nodes, otherwise return global
connectivity w.r.t. all mesh nodes.
is_trace [bool] If True, return mirror connectivity according to local.
setup_mirror_connectivity(region, mirror_name)
Setup mirror surface connectivity required to integrate over a mirror region.
1. Get orientation of the faces: a) for own elements -> ooris b) for mirror elements -> moris
2. orientation -> permutation.

sfepy.discrete.fem.fields_base module

Notes

Important attributes of continuous (order > 0) Field and SurfaceField instances:

• vertex_remap : econn[:, :n_vertex] = vertex_remap[conn]
• vertex_remap_i : conn = vertex_remap_i[econn[:, :n_vertex]]
where conn is the mesh vertex connectivity, econn is the region-local field connectivity.
class sfepy.discrete.fem.fields_base.FEField(name, dtype, shape, region, approx_order=1)
Base class for finite element fields.

Notes

• interps and hence node_descs are per region (must have single geometry!)

Field shape information:

• shape - the shape of the base functions in a point
• n_components - the number of DOFs per FE node
• val_shape - the shape of field value (the product of DOFs and base functions) in a point
clear_qp_base()
Remove cached quadrature points and base functions.
create_bqp(region_name, integral)

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create_mapping(region, integral, integration, return_mapping=True)

Create a new reference mapping.
Compute jacobians, element volumes and base function derivatives for Volume-type geometries (volume
mappings), and jacobians, normals and base function derivatives for Surface-type geometries (surface map-
pings).

Notes

• surface mappings are defined on the surface region

• surface mappings require field order to be > 0

create_mesh(extra_nodes=True)
Create a mesh from the field region, optionally including the field extra nodes.
create_output(dofs, var_name, dof_names=None, key=None, extend=True, fill_value=None,
linearization=None)
Convert the DOFs corresponding to the field to a dictionary of output data usable by Mesh.write().
Parameters
dofs [array, shape (n_nod, n_component)] The array of DOFs reshaped so that each column
corresponds to one component.
var_name [str] The variable name corresponding to dofs.
dof_names [tuple of str] The names of DOF components.
key [str, optional] The key to be used in the output dictionary instead of the variable name.
extend [bool] Extend the DOF values to cover the whole domain.
fill_value [float or complex] The value used to fill the missing DOF values if extend is True.
linearization [Struct or None] The linearization configuration for higher order approxima-
tions.
Returns
out [dict] The output dictionary.
extend_dofs(dofs, fill_value=None)
Extend DOFs to the whole domain using the fill_value, or the smallest value in dofs if fill_value is None.
get_base(key, derivative, integral, iels=None, from_geometry=False, base_only=True)

get_connectivity(region, integration, is_trace=False)

Convenience alias to Field.get_econn(), that is used in some terms.
get_coor(nods=None)
Get coordinates of the field nodes.
Parameters
nods [array, optional] The indices of the required nodes. If not given, the coordinates of all
the nodes are returned.
get_data_shape(integral, integration='volume', region_name=None)
Get element data dimensions.
Parameters

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integral [Integral instance] The integral describing used numerical quadrature.

integration [‘volume’, ‘surface’, ‘surface_extra’, ‘point’ or ‘custom’] The term integration
type.
region_name [str] The name of the region of the integral.
Returns
data_shape [4 ints] The (n_el, n_qp, dim, n_en) for volume shape kind, (n_fa, n_qp, dim,
n_fn) for surface shape kind and (n_nod, 0, 0, 1) for point shape kind.

Notes

• n_el, n_fa = number of elements/facets

• n_qp = number of quadrature points per element/facet
• dim = spatial dimension
• n_en, n_fn = number of element/facet nodes
• n_nod = number of element nodes

get_dofs_in_region(region, merge=True)
Return indices of DOFs that belong to the given region and group.
get_evaluate_cache(cache=None, share_geometry=False, verbose=False)
Get the evaluate cache for Variable.evaluate_at().
Parameters
cache [Struct instance, optional] Optionally, use the provided instance to store the cache data.
share_geometry [bool] Set to True to indicate that all the evaluations will work on the same
region. Certain data are then computed only for the first probe and cached.
verbose [bool] If False, reduce verbosity.
Returns
cache [Struct instance] The evaluate cache.
get_output_approx_order()
Get the approximation order used in the output file.
get_qp(key, integral)
Get quadrature points and weights corresponding to the given key and integral. The key is ‘v’ or ‘s#’, where
# is the number of face vertices.
get_true_order()
Get the true approximation order depending on the reference element geometry.
For example, for P1 (linear) approximation the true order is 1, while for Q1 (bilinear) approximation in 2D
the true order is 2.
get_vertices()
Return indices of vertices belonging to the field region.
interp_to_qp(dofs)
Interpolate DOFs into quadrature points.
The quadrature order is given by the field approximation order.
Parameters

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dofs [array] The array of DOF values of shape (n_nod, n_component).

Returns
data_qp [array] The values interpolated into the quadrature points.
integral [Integral] The corresponding integral defining the quadrature points.
is_higher_order()
Return True, if the field’s approximation order is greater than one.
linearize(dofs, min_level=0, max_level=1, eps=0.0001)
Linearize the solution for post-processing.
Parameters
dofs [array, shape (n_nod, n_component)] The array of DOFs reshaped so that each column
corresponds to one component.
min_level [int] The minimum required level of mesh refinement.
max_level [int] The maximum level of mesh refinement.
eps [float] The relative tolerance parameter of mesh adaptivity.
Returns
mesh [Mesh instance] The adapted, nonconforming, mesh.
vdofs [array] The DOFs defined in vertices of mesh.
levels [array of ints] The refinement level used for each element group.
remove_extra_dofs(dofs)
Remove DOFs defined in higher order nodes (order > 1).
restore_dofs(store=False)
Undoes the effect of FEField.substitute_dofs().
restore_substituted(vec)
Restore values of the unused DOFs using the transpose of the applied basis transformation.
set_basis_transform(transform)
Set local element basis transformation.
The basis transformation is applied in FEField.get_base() and FEField.create_mapping().
Parameters
transform [array, shape (n_cell, n_ep, n_ep)] The array with (n_ep, n_ep) transformation
matrices for each cell in the field’s region, where n_ep is the number of element DOFs.
set_coors(coors, extra_dofs=False)
Set coordinates of field nodes.
setup_coors()
Setup coordinates of field nodes.
substitute_dofs(subs, restore=False)
Perform facet DOF substitutions according to subs.
Modifies self.econn in-place and sets self.econn0, self.unused_dofs and self.basis_transform.
class sfepy.discrete.fem.fields_base.H1Mixin(**kwargs)
Methods of fields specific to H1 space.

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class sfepy.discrete.fem.fields_base.SurfaceField(name, dtype, shape, region, approx_order=1)

Finite element field base class over surface (element dimension is one less than space dimension).
average_qp_to_vertices(data_qp, integral)
Average data given in quadrature points in region elements into region vertices.
∑︁ ∑︁ ∑︁ ∫︁ ∑︁
𝑢𝑛 = (𝑢𝑒,𝑎𝑣𝑔 * 𝑎𝑟𝑒𝑎𝑒 )/ 𝑎𝑟𝑒𝑎𝑒 = 𝑢/ 𝑎𝑟𝑒𝑎𝑒
𝑒 𝑒 𝑒 𝑎𝑟𝑒𝑎𝑒

get_econn(conn_type, region, is_trace=False, integration=None)

Get extended connectivity of the given type in the given region.
setup_extra_data(geometry, info, is_trace)

class sfepy.discrete.fem.fields_base.VolumeField(name, dtype, shape, region, approx_order=1)

Finite element field base class over volume elements (element dimension equals space dimension).
average_qp_to_vertices(data_qp, integral)
Average data given in quadrature points in region elements into region vertices.
∑︁ ∑︁ ∑︁ ∫︁ ∑︁
𝑢𝑛 = (𝑢𝑒,𝑎𝑣𝑔 * 𝑣𝑜𝑙𝑢𝑚𝑒𝑒 )/ 𝑣𝑜𝑙𝑢𝑚𝑒𝑒 = 𝑢/ 𝑣𝑜𝑙𝑢𝑚𝑒𝑒
𝑒 𝑒 𝑒 𝑣𝑜𝑙𝑢𝑚𝑒𝑒

get_econn(conn_type, region, is_trace=False, integration=None, local=False)

Get extended connectivity of the given type in the given region.
setup_extra_data(geometry, info, is_trace)

setup_point_data(field, region)

setup_surface_data(region, is_trace=False, trace_region=None)

nodes[leconn] == econn
sfepy.discrete.fem.fields_base.create_expression_output(expression, name, primary_field_name,
fields, materials, variables,
functions=None, mode='eval',
term_mode=None, extra_args=None,
verbose=True, kwargs=None, min_level=0,
max_level=1, eps=0.0001)
Create output mesh and data for the expression using the adaptive linearizer.
Parameters
expression [str] The expression to evaluate.
name [str] The name of the data.
primary_field_name [str] The name of field that defines the element groups and polynomial
spaces.
fields [dict] The dictionary of fields used in variables.
materials [Materials instance] The materials used in the expression.
variables [Variables instance] The variables used in the expression.
functions [Functions instance, optional] The user functions for materials etc.

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mode [one of ‘eval’, ‘el_avg’, ‘qp’] The evaluation mode - ‘qp’ requests the values in quadrature
points, ‘el_avg’ element averages and ‘eval’ means integration over each term region.
term_mode [str] The term call mode - some terms support different call modes and depending
on the call mode different values are returned.
extra_args [dict, optional] Extra arguments to be passed to terms in the expression.
verbose [bool] If False, reduce verbosity.
kwargs [dict, optional] The variables (dictionary of (variable name) : (Variable instance)) to be
used in the expression.
min_level [int] The minimum required level of mesh refinement.
max_level [int] The maximum level of mesh refinement.
eps [float] The relative tolerance parameter of mesh adaptivity.
Returns
out [dict] The output dictionary.
sfepy.discrete.fem.fields_base.eval_nodal_coors(coors, mesh_coors, region, poly_space,
geom_poly_space, econn, only_extra=True)
Compute coordinates of nodes corresponding to poly_space, given mesh coordinates and geom_poly_space.
sfepy.discrete.fem.fields_base.get_eval_expression(expression, fields, materials, variables,
functions=None, mode='eval', term_mode=None,
extra_args=None, verbose=True, kwargs=None)
Get the function for evaluating an expression given a list of elements, and reference element coordinates.
sfepy.discrete.fem.fields_base.set_mesh_coors(domain, fields, coors, update_fields=False,
actual=False, clear_all=True, extra_dofs=False)

sfepy.discrete.fem.fields_hierarchic module

class sfepy.discrete.fem.fields_hierarchic.H1HierarchicVolumeField(name, dtype, shape, region,

approx_order=1)

create_basis_context()
Create the context required for evaluating the field basis.
family_name = 'volume_H1_lobatto'
set_dofs(fun=0.0, region=None, dpn=None, warn=None)
Set the values of DOFs in a given region using a function of space coordinates or value fun.

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sfepy.discrete.fem.fields_nodal module

Notes

Important attributes of continuous (order > 0) Field and SurfaceField instances:

• vertex_remap : econn[:, :n_vertex] = vertex_remap[conn]
• vertex_remap_i : conn = vertex_remap_i[econn[:, :n_vertex]]
where conn is the mesh vertex connectivity, econn is the region-local field connectivity.
class sfepy.discrete.fem.fields_nodal.GlobalNodalLikeBasis(**kwargs)

get_surface_basis(region)
Get basis for projections to region’s facets.

Notes

Cannot be uses for all fields because IGA does not support surface mappings.
class sfepy.discrete.fem.fields_nodal.H1DiscontinuousField(name, dtype, shape, region,
approx_order=1)

average_to_vertices(dofs)
Average DOFs of the discontinuous field into the field region vertices.
extend_dofs(dofs, fill_value=None)
Extend DOFs to the whole domain using the fill_value, or the smallest value in dofs if fill_value is None.
family_name = 'volume_H1_lagrange_discontinuous'
remove_extra_dofs(dofs)
Remove DOFs defined in higher order nodes (order > 1).
class sfepy.discrete.fem.fields_nodal.H1NodalMixin(**kwargs)

create_basis_context()
Create the context required for evaluating the field basis.
set_dofs(fun=0.0, region=None, dpn=None, warn=None)
Set the values of DOFs in a given region using a function of space coordinates or value fun.
class sfepy.discrete.fem.fields_nodal.H1NodalSurfaceField(name, dtype, shape, region,
approx_order=1)
A field defined on a surface region.
family_name = 'surface_H1_lagrange'
interp_v_vals_to_n_vals(vec)
Interpolate a function defined by vertex DOF values using the FE surface geometry base (P1 or Q1) into
the extra nodes, i.e. define the extra DOF values.
class sfepy.discrete.fem.fields_nodal.H1NodalVolumeField(name, dtype, shape, region,
approx_order=1)

family_name = 'volume_H1_lagrange'

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interp_v_vals_to_n_vals(vec)
Interpolate a function defined by vertex DOF values using the FE geometry base (P1 or Q1) into the extra
nodes, i.e. define the extra DOF values.
class sfepy.discrete.fem.fields_nodal.H1SNodalSurfaceField(name, dtype, shape, region,
approx_order=1)

family_name = 'surface_H1_serendipity'
class sfepy.discrete.fem.fields_nodal.H1SNodalVolumeField(name, dtype, shape, region,
approx_order=1)

create_basis_context()
Create the context required for evaluating the field basis.
family_name = 'volume_H1_serendipity'

sfepy.discrete.fem.fields_positive module

class sfepy.discrete.fem.fields_positive.H1BernsteinSurfaceField(name, dtype, shape, region,

approx_order=1)

family_name = 'surface_H1_bernstein'
class sfepy.discrete.fem.fields_positive.H1BernsteinVolumeField(name, dtype, shape, region,
approx_order=1)

create_basis_context()
Create the context required for evaluating the field basis.
family_name = 'volume_H1_bernstein'

sfepy.discrete.fem.geometry_element module

GeometryElement describes the geometric entities of a finite element mesh.

Notes

• geometry_data: surface facets are assumed to be of the same kind for each geometry element - wedges or pyra-
mides are not supported.
• the orientation is a tuple: (root1, vertices of direction vectors, swap from, swap to, root2, . . . )
class sfepy.discrete.fem.geometry_element.GeometryElement(name)
The geometric entities of a finite element mesh.
create_surface_facet()
Create a GeometryElement instance corresponding to this instance surface facet.
get_conn_permutations()
Get all possible connectivity permutations corresponding to different spatial orientations of the geometry
element.

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get_edges_per_face()
Return the indices into self.edges per face.
get_grid(n_nod)
Get a grid of n_nod interpolation points, including the geometry element vertices. The number of points
must correspond to a valid number of FE nodes for each geometry.
get_interpolation_name()
Get the name of corresponding linear interpolant.
get_surface_entities()
Return self.vertices in 1D, self.edges in 2D and self.faces in 3D.
sfepy.discrete.fem.geometry_element.create_geometry_elements(names=None)
Utility function to create GeometryElement instances.
Parameters
names [str, optional] The names of the entity, one of the keys in geometry_data dictionary. If
None, all keys of geometry_data are used.
Returns
gels [dict] The dictionary of geometry elements with names as keys.
sfepy.discrete.fem.geometry_element.setup_orientation(vecs_tuple)

sfepy.discrete.fem.history module

class sfepy.discrete.fem.history.Histories(objs=None, **kwargs)

static from_file_hdf5(filename, var_names)

TODO: do not read entire file, provide data on demand.
class sfepy.discrete.fem.history.History(name, th=None, steps=None, times=None)

append(item, step, time)

static from_sequence(seq, name)

sfepy.discrete.fem.lcbc_operators module

Operators for enforcing linear combination boundary conditions in nodal FEM setting.
class sfepy.discrete.fem.lcbc_operators.EdgeDirectionOperator(name, regions, dof_names,
dof_map_fun, filename, variables,
ts=None, functions=None)
Transformation matrix operator for edges direction LCBCs.
The substitution (in 3D) is:

[𝑢1 , 𝑢2 , 𝑢3 ]𝑇 = [𝑑1 , 𝑑2 , 𝑑3 ]𝑇 𝑤,

where 𝑑 is an edge direction vector averaged into a node. The new DOF is 𝑤.

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get_vectors(nodes, region, field, filename=None)

kind = 'edge_direction'
class sfepy.discrete.fem.lcbc_operators.IntegralMeanValueOperator(name, regions, dof_names,
dof_map_fun, variables,
ts=None, functions=None)
Transformation matrix operator for integral mean value LCBCs. All DOFs in a region are summed to form a
single new DOF.
kind = 'integral_mean_value'
class sfepy.discrete.fem.lcbc_operators.LCBCOperator(name, regions, dof_names, dof_map_fun,
variables, functions=None)
Base class for LCBC operators.
setup()

class sfepy.discrete.fem.lcbc_operators.LCBCOperators(name, variables, functions=None)

Container holding instances of LCBCOperator subclasses for a single variable.
add_from_bc(bc, ts)
Create a new LCBC operator described by bc, and add it to the container.
Parameters
bc [LinearCombinationBC instance] The LCBC condition description.
ts [TimeStepper instance] The time stepper.
append(op)

finalize()
Call this after all LCBCs of the variable have been added.
Initializes the global column indices and DOF counts.
make_global_operator(adi, new_only=False)
Assemble all LCBC operators into a single matrix.
Parameters
adi [DofInfo] The active DOF information.
new_only [bool] If True, the operator columns will contain only new DOFs.
Returns
mtx_lc [csr_matrix] The global LCBC operator in the form of a CSR matrix.
rhs_lc [array] The right-hand side for non-homogeneous LCBCs.
lcdi [DofInfo] The global active LCBC-constrained DOF information.
class sfepy.discrete.fem.lcbc_operators.MRLCBCOperator(name, regions, dof_names, dof_map_fun,
variables, functions=None)
Base class for model-reduction type LCBC operators.
These operators are applied to a single field, and replace its DOFs in a given region by new DOFs. In case some
field DOFs are to be preserved, those have to be “copied” explicitly, by setting the corresponding row of the
operator matrix to a single value one (see, for example, NoPenetrationOperator).

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setup()

treat_pbcs(dofs, master)
Treat dofs with periodic BC.
class sfepy.discrete.fem.lcbc_operators.NoPenetrationOperator(name, regions, dof_names,
dof_map_fun, filename, variables,
ts=None, functions=None)
Transformation matrix operator for no-penetration LCBCs.
kind = 'no_penetration'
class sfepy.discrete.fem.lcbc_operators.NodalLCOperator(name, regions, dof_names, dof_map_fun,
constraints, variables, ts=None,
functions=None)
Transformation matrix operator for the general linear combination of DOFs in each node of a field in the given
region.
The DOFs can be fully constrained - then the operator corresponds to enforcing Dirichlet boundary conditions.
The linear combination is given by:
𝑛
∑︁
𝐴𝑖𝑗 𝑢𝑗 = 𝑏𝑖 , ∀𝑖 ,
𝑗=1

where 𝑢𝑗 , 𝑗 = 1, . . . , 𝑛 are the DOFs in the node and 𝑖 = 1, . . . , 𝑚, 𝑚 < 𝑛, are the linear constraint indices.
SymPy is used to solve the constraint linear system in each node for the dependent DOF(s).
kind = 'nodal_combination'
class sfepy.discrete.fem.lcbc_operators.NormalDirectionOperator(name, regions, dof_names,
dof_map_fun, filename,
variables, ts=None,
functions=None)
Transformation matrix operator for normal direction LCBCs.
The substitution (in 3D) is:
[𝑢1 , 𝑢2 , 𝑢3 ]𝑇 = [𝑛1 , 𝑛2 , 𝑛3 ]𝑇 𝑤
The new DOF is 𝑤.
get_vectors(nodes, region, field, filename=None)

kind = 'normal_direction'
class sfepy.discrete.fem.lcbc_operators.RigidOperator(name, regions, dof_names, dof_map_fun,
variables, ts=None, functions=None)
Transformation matrix operator for rigid LCBCs.
kind = 'rigid'
class sfepy.discrete.fem.lcbc_operators.ShiftedPeriodicOperator(name, regions, dof_names,
dof_map_fun, shift_fun,
variables, ts, functions)
Transformation matrix operator for shifted periodic boundary conditions.
This operator ties existing DOFs of two fields in two disjoint regions together. Unlike MRLCBCOperator sub-
classes, it does not create any new DOFs.
kind = 'shifted_periodic'

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sfepy.discrete.fem.linearizer module

Linearization of higher order solutions for the purposes of visualization.

sfepy.discrete.fem.linearizer.create_output(eval_dofs, eval_coors, n_el, ps, min_level=0, max_level=2,
eps=0.0001)
Create mesh with linear elements that approximates DOFs returned by eval_dofs() corresponding to a higher
order approximation with a relative precision given by eps. The DOFs are evaluated in physical coordinates
returned by eval_coors().
sfepy.discrete.fem.linearizer.get_eval_coors(coors, conn, ps)
Get default function for evaluating physical coordinates given a list of elements and reference element coordi-
nates.
sfepy.discrete.fem.linearizer.get_eval_dofs(dofs, dof_conn, ps, ori=None)
Get default function for evaluating field DOFs given a list of elements and reference element coordinates.

sfepy.discrete.fem.mappings module

Finite element reference mappings.

class sfepy.discrete.fem.mappings.FEMapping(coors, conn, poly_space=None, gel=None, order=1)
Base class for finite element mappings.
get_base(coors, diff=False)
Get base functions or their gradient evaluated in given coordinates.
get_geometry()
Return reference element geometry as a GeometryElement instance.
get_physical_qps(qp_coors)
Get physical quadrature points corresponding to given reference element quadrature points.
Returns
qps [array] The physical quadrature points ordered element by element, i.e. with shape (n_el,
n_qp, dim).
class sfepy.discrete.fem.mappings.SurfaceMapping(coors, conn, poly_space=None, gel=None, order=1)
Mapping from reference domain to physical domain of the space dimension higher by one.
get_base(coors, diff=False)
Get base functions or their gradient evaluated in given coordinates.
get_mapping(qp_coors, weights, poly_space=None, mode='surface')
Get the mapping for given quadrature points, weights, and polynomial space.
Returns
cmap [CMapping instance] The surface mapping.
set_basis_indices(indices)
Set indices to cell-based basis that give the facet-based basis.
class sfepy.discrete.fem.mappings.VolumeMapping(coors, conn, poly_space=None, gel=None, order=1)
Mapping from reference domain to physical domain of the same space dimension.
get_mapping(qp_coors, weights, poly_space=None, ori=None, transform=None)
Get the mapping for given quadrature points, weights, and polynomial space.
Returns

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cmap [CMapping instance] The volume mapping.

sfepy.discrete.fem.mesh module

class sfepy.discrete.fem.mesh.Mesh(name='mesh', cmesh=None)

The Mesh class is a light proxy to CMesh.
Input and output is handled by the MeshIO class and subclasses.
property coors
copy(name=None)
Make a deep copy of the mesh.
Parameters
name [str] Name of the copied mesh.
create_conn_graph(verbose=True)
Create a graph of mesh connectivity.
Returns
graph [csr_matrix] The mesh connectivity graph as a SciPy CSR matrix.
static from_data(name, coors, ngroups, conns, mat_ids, descs, nodal_bcs=None)
Create a mesh from mesh IO data.
static from_file(filename=None, io='auto', prefix_dir=None, omit_facets=False, file_format=None)
Read a mesh from a file.
Parameters
filename [string or function or MeshIO instance or Mesh instance] The name of file to read
the mesh from. For convenience, a mesh creation function or a MeshIO instance or directly
a Mesh instance can be passed in place of the file name.
io [*MeshIO instance] Passing *MeshIO instance has precedence over filename.
prefix_dir [str] If not None, the filename is relative to that directory.
omit_facets [bool] If True, do not read cells of lower dimension than the space dimension
(faces and/or edges). Only some MeshIO subclasses support this!
static from_region(region, mesh_in, localize=False, is_surface=False)
Create a mesh corresponding to cells, or, if is_surface is True, to facets, of a given region.
get_bounding_box()

get_conn(desc, ret_cells=False)
Get the rectangular cell-vertex connectivity corresponding to desc. If ret_cells is True, the corresponding
cells are returned as well.
transform_coors(mtx_t, ref_coors=None)
Transform coordinates of the mesh by the given transformation matrix.
Parameters
mtx_t [array] The transformation matrix T (2D array). It is applied depending on its shape:
• (dim, dim): x = T * x
• (dim, dim + 1): x = T[:, :-1] * x + T[:, -1]

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ref_coors [array, optional] Alternative coordinates to use for the transformation instead of
the mesh coordinates, with the same shape as self.coors.
write(filename=None, io=None, out=None, float_format=None, file_format=None, **kwargs)
Write mesh + optional results in out to a file.
Parameters
filename [str, optional] The file name. If None, the mesh name is used instead.
io [MeshIO instance or ‘auto’, optional] Passing ‘auto’ respects the extension of filename.
out [dict, optional] The output data attached to the mesh vertices and/or cells.
float_format [str, optional] The format string used to print floats in case of a text file format.
**kwargs [dict, optional] Additional arguments that can be passed to the MeshIO instance.
sfepy.discrete.fem.mesh.find_map(x1, x2, allow_double=False, join=True)
Find a mapping between common coordinates in x1 and x2, such that x1[cmap[:,0]] == x2[cmap[:,1]]
sfepy.discrete.fem.mesh.fix_double_nodes(coor, ngroups, conns)
Detect and attempt fixing double nodes in a mesh.
The double nodes are nodes having the same coordinates w.r.t. precision given by eps.
sfepy.discrete.fem.mesh.get_min_vertex_distance(coor, guess)
Can miss the minimum, but is enough for our purposes.
sfepy.discrete.fem.mesh.get_min_vertex_distance_naive(coor)

sfepy.discrete.fem.mesh.make_mesh(coor, ngroups, conns, mesh_in)

Create a mesh reusing mat_ids and descs of mesh_in.
sfepy.discrete.fem.mesh.merge_mesh(x1, ngroups1, conn1, mat_ids1, x2, ngroups2, conn2, mat_ids2, cmap)
Merge two meshes in common coordinates found in x1, x2.

Notes

Assumes the same number and kind of element groups in both meshes!
sfepy.discrete.fem.mesh.set_accuracy(eps)

sfepy.discrete.fem.meshio module

class sfepy.discrete.fem.meshio.ANSYSCDBMeshIO(filename, **kwargs)

format = 'ansys_cdb'
static guess(filename)

static make_format(format, nchar=1000)

read(mesh, **kwargs)

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read_bounding_box()

read_dimension(ret_fd=False)

write(filename, mesh, out=None, **kwargs)

class sfepy.discrete.fem.meshio.ComsolMeshIO(filename, **kwargs)

format = 'comsol'
read(mesh, **kwargs)

write(filename, mesh, out=None, **kwargs)

class sfepy.discrete.fem.meshio.GmshIO(filename, file_format=None, **kwargs)

Used to read and write data in .msh format when file_format gmsh-dg is specified. Tailored for use with Dis-
continous galerking methods, mesh and ElementNodeData with InterpolationScheme can be written and read.
It however omits mat_ids and node_groups.
For details on format see [1].
For details on representing and visualization of DG FEM data using gmsh see [2].
[1] http://gmsh.info/doc/texinfo/gmsh.html#File-formats
[2] Remacle, J.-F., Chevaugeon, N., Marchandise, E., & Geuzaine, C. (2007). Efficient visualization of high-
order finite elements. International Journal for Numerical Methods in Engineering, 69(4), 750-771. https://doi.
org/10.1002/nme.1787
format = 'gmshio'
load_slices = {'all': slice(0, None, None), 'first': slice(0, 1, None), 'last':
slice(-1, None, None)}
read_data(step=None, filename=None, cache=None)
Reads file or files with basename filename or self.filename. Considers all files to contain data from time
steps of solution of single transient problem i.e. all data have the same shape, mesh and same interpolation
scheme in case of ElementNodeData. Does not read mulitple NodeData or ElementData. For stationary
problems just reads one file with time 0.0 and time step 0.
Providing filename allows reading multiple files of format basename.*[0-9].msh
Parameters
step [String, int, optional] “all”, “last”, “first” or number of step to read: if “all” read all
files with the basename and varying step, if “last” read only last step of all files with the
filename, if “first” reads step=0, if None reads file with filename provided or specified in
object.
filename [string, optional] Filename of the files to use, if None filename from object is used.
Basename is extracted as basename.*[0-9].msh
cache [has no effect]
Returns
out [dictionary] Keys represent name of data, values are Structs with attributes:

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data [list, array] For ElementNodeData with shape (n_cell, n_cell_dof) contains for each
time step. For other contains array of data from last time step.
time [list] Contains times.
time_n [list] Contains time step numbers.
scheme [Struct] Interpolation scheme used in data, only one interpolation scheme is al-
lowed.
scheme_name [str] Name of the interpolation scheme, repeated fo convenience.
mode [str] Represents of type of data. cell_nodes : for ElementNodeData; vertex or cell :
Note that for vertex and cell data reading multiple time steps does not work yet.

Notes

The interpolation scheme Struct contains the following items:

name [string] Name of the scheme.
F [array] Coefficients matrix as defined in [1] and [2].
P [array] Exponents matrix as defined in [1] and [2].

write(filename, mesh, out=None, ts=None, **kwargs)

Writes mesh and data, handles cell DOFs data from DGField as ElementNodeData.
Omits gmsh:ref for cells and vertices i.e. mat_ids and node_groups to prevent cluttering the GMSH post-
processing.
Parameters
filename [string] Path to file.
mesh [sfepy.discrete.fem.mesh.Mesh] Computational mesh to write.
out [dictionary] Keys represent name of the data, values are Structs with attributes:
data [array] For ElementNodeData shape is (n_cell, n_cell_dof)
mode [str] Represents type of data, cell_nodes for ElementNodeData.
For ElementNodeData:
scheme [Struct] Interpolation scheme used in data, only one interpolation scheme is al-
lowed.
scheme_name [str] Name of the interpolation scheme, associated with data, repeated fo
convenience.
ts [sfepy.solvers.ts.TimeStepper instance, optional] Provides data to write time step.

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Notes

The interpolation scheme Struct contains the following items:

name [string] Name of the scheme.
F [array] Coefficients matrix as defined in [1] and [2].
P [array] Exponents matrix as defined in [1] and [2].

class sfepy.discrete.fem.meshio.HDF5MeshIO(filename, **kwargs)

format = 'hdf5'
read(mesh=None, **kwargs)

read_bounding_box(ret_fd=False, ret_dim=False)

read_data(step, filename=None, cache=None)

read_data_header(dname, step=None, filename=None)

read_dimension(ret_fd=False)

read_last_step(filename=None)
The default implementation: just return 0 as the last step.
static read_mesh_from_hdf5(filename, group=None, mesh=None)
Read the mesh from a HDF5 file.
filename: str or tables.File The HDF5 file to read the mesh from.
group: tables.group.Group or str, optional The HDF5 file group to read the mesh from. If None, the
root group is used.
mesh: sfepy.dicrete.fem.Mesh or None If None, the new mesh is created and returned, otherwise content
of this argument is replaced by the read mesh.

Returns
sfepy.dicrete.fem.Mesh readed mesh

read_time_history(node_name, indx, filename=None)

read_time_stepper(filename=None)

read_times(filename=None)
Read true time step data from individual time steps.
Returns
steps [array] The time steps.
times [array] The times of the time steps.
nts [array] The normalized times of the time steps, in [0, 1].

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read_variables_time_history(var_names, ts, filename=None)

string = <module 'string' from '/usr/lib/python3.8/string.py'>

write(filename, mesh, out=None, ts=None, cache=None, xdmf=False, **kwargs)

static write_mesh_to_hdf5(filename, group, mesh, force_3d=False)

Write mesh to a hdf5 file.
filename: str or tables.File The HDF5 file to write the mesh to.
group: tables.group.Group or None or str The HDF5 file group to write the mesh to. If None, the root
group is used. The group can be given as a path from root, e.g. /path/to/mesh
mesh: sfepy.dicrete.fem.Mesh The mesh to write.
static write_xdmf_file(filename, **kwargs)

class sfepy.discrete.fem.meshio.HDF5XdmfMeshIO(filename, **kwargs)

format = 'hdf5-xdmf'
write(filename, mesh, out=None, ts=None, cache=None, **kwargs)

class sfepy.discrete.fem.meshio.HypermeshAsciiMeshIO(filename, **kwargs)

format = 'hmascii'
read(mesh, **kwargs)

read_dimension()

write(filename, mesh, out=None, **kwargs)

class sfepy.discrete.fem.meshio.Mesh3DMeshIO(filename, **kwargs)

format = 'mesh3d'
read(mesh, **kwargs)

read_dimension()

class sfepy.discrete.fem.meshio.MeshIO(filename, **kwargs)

The abstract class for importing and exporting meshes.
Read the docstring of the Mesh() class. Basically all you need to do is to implement the read() method:

def read(self, mesh, **kwargs):

nodes = ...
ngroups = ...
conns = ...
mat_ids = ...
(continues on next page)

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(continued from previous page)

descs = ...
mesh._set_io_data(nodes, ngroups, conns, mat_ids, descs)
return mesh

See the Mesh class’ docstring how the nodes, ngroups, conns, mat_ids and descs should look like. You just need
to read them from your specific format from disk.
To write a mesh to disk, just implement the write() method and use the information from the mesh instance (e.g.
nodes, conns, mat_ids and descs) to construct your specific format.
Optionally, subclasses can implement read_data() to read also computation results. This concerns mainly the
subclasses with implemented write() supporting the ‘out’ kwarg.
The default implementation od read_last_step() just returns 0. It should be reimplemented in subclasses capable
of storing several steps.
static any_from_filename(filename, prefix_dir=None, file_format=None, mode='r')
Create a MeshIO instance according to the kind of filename.
Parameters
filename [str, function or MeshIO subclass instance] The name of the mesh file. It can be
also a user-supplied function accepting two arguments: mesh, mode, where mesh is a Mesh
instance and mode is one of ‘read’,’write’, or a MeshIO subclass instance.
prefix_dir [str] The directory name to prepend to filename.
Returns
io [MeshIO subclass instance] The MeshIO subclass instance corresponding to the kind of
filename.
call_msg = 'called an abstract MeshIO instance!'
format = None
get_filename_trunk()

get_vector_format(dim)

read(mesh, omit_facets=False, **kwargs)

read_data(step, filename=None, cache=None)

read_last_step()
The default implementation: just return 0 as the last step.
read_times(filename=None)
Read true time step data from individual time steps.
Returns
steps [array] The time steps.
times [array] The times of the time steps.
nts [array] The normalized times of the time steps, in [0, 1].

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Notes

The default implementation returns empty arrays.

set_float_format(format=None)

write(filename, mesh, **kwargs)

class sfepy.discrete.fem.meshio.MeshioLibIO(filename, file_format=None, **kwargs)

cell_types = {('hexahedron', 3): '3_8', ('line', 1): '1_2', ('line', 2): '1_2',
('line', 3): '1_2', ('quad', 2): '2_4', ('quad', 3): '2_4', ('tetra', 3): '3_4',
('triangle', 2): '2_3', ('triangle', 3): '2_3'}
format = 'meshio'
read(mesh, omit_facets=False, **kwargs)

read_bounding_box(ret_dim=False)

read_data(step, filename=None, cache=None)

Renames cell resp. vertex data with name “*:ref” to mat_id resp. node_groups
Parameters
step: has no effect
filename [string, optional] The file name to use instead of self.filename.
cache: has no effect
Returns
out [dictionary] Data loaded from file, keys are names. values are Structs with name re-
peated, mode (‘vertex’ or ‘cell’) and the data itself.
read_dimension()

write(filename, mesh, out=None, ts=None, **kwargs)

class sfepy.discrete.fem.meshio.NEUMeshIO(filename, **kwargs)

format = 'gambit'
read(mesh, **kwargs)

read_dimension(ret_fd=False)

write(filename, mesh, out=None, **kwargs)

class sfepy.discrete.fem.meshio.UserMeshIO(filename, **kwargs)

Special MeshIO subclass that enables reading and writing a mesh using a user-supplied function.
format = 'function'

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get_filename_trunk()

read(mesh, *args, **kwargs)

write(filename, mesh, *args, **kwargs)

class sfepy.discrete.fem.meshio.XYZMeshIO(filename, **kwargs)

Trivial XYZ format working only with coordinates (in a .XYZ file) and the connectivity stored in another file
with the same base name and .IEN suffix.
format = 'xyz'
read(mesh, omit_facets=False, **kwargs)

read_bounding_box(ret_fd=False, ret_dim=False)

read_dimension(ret_fd=False)

write(filename, mesh, out=None, **kwargs)

sfepy.discrete.fem.meshio.check_format_suffix(file_format, suffix)
Check compatibility of a mesh file format and a mesh file suffix.
sfepy.discrete.fem.meshio.convert_complex_output(out_in)
Convert complex values in the output dictionary out_in to pairs of real and imaginary parts.
sfepy.discrete.fem.meshio.mesh_from_groups(mesh, ids, coors, ngroups, tris, mat_tris, quads, mat_quads,
tetras, mat_tetras, hexas, mat_hexas, remap=None)

sfepy.discrete.fem.meshio.output_mesh_formats(mode='r')

sfepy.discrete.fem.meshio.split_conns_mat_ids(conns_in)
Split connectivities (columns except the last ones in conns_in) from cell groups (the last columns of conns_in).
sfepy.discrete.fem.meshio.update_supported_formats(formats)

sfepy.discrete.fem.meshio.var
alias of sfepy.discrete.fem.meshio.XYZMeshIO

sfepy.discrete.fem.periodic module

sfepy.discrete.fem.periodic.get_grid_plane(idim)

sfepy.discrete.fem.periodic.match_coors(coors1, coors2, get_saved=True)

sfepy.discrete.fem.periodic.match_grid_line(coors1, coors2, which, get_saved=True)

Match coordinates coors1 with coors2 along the axis which.
sfepy.discrete.fem.periodic.match_grid_plane(coors1, coors2, idim, get_saved=True)

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sfepy.discrete.fem.periodic.match_plane_by_dir(coors1, coors2, direction, get_saved=True)

Match coordinates coors1 with coors2 in a given direction.
sfepy.discrete.fem.periodic.match_x_line(coors1, coors2, get_saved=True)

sfepy.discrete.fem.periodic.match_x_plane(coors1, coors2, get_saved=True)

sfepy.discrete.fem.periodic.match_y_line(coors1, coors2, get_saved=True)

sfepy.discrete.fem.periodic.match_y_plane(coors1, coors2, get_saved=True)

sfepy.discrete.fem.periodic.match_z_line(coors1, coors2, get_saved=True)

sfepy.discrete.fem.periodic.match_z_plane(coors1, coors2, get_saved=True)

sfepy.discrete.fem.periodic.set_accuracy(eps)

sfepy.discrete.fem.poly_spaces module

class sfepy.discrete.fem.poly_spaces.BernsteinSimplexPolySpace(name, geometry, order)

Bernstein polynomial space on simplex domains.

Notes

Naive proof-of-concept implementation, does not use recurrent formulas or Duffy transformation to obtain tensor
product structure.
name = 'bernstein_simplex'
class sfepy.discrete.fem.poly_spaces.BernsteinTensorProductPolySpace(name, geometry, order)
Bernstein polynomial space.
Each row of the nodes attribute defines indices of 1D Bernstein basis functions that need to be multiplied together
to evaluate the corresponding shape function. This defines the ordering of basis functions on the reference
element.
name = 'bernstein_tensor_product'
class sfepy.discrete.fem.poly_spaces.FEPolySpace(name, geometry, order)
Base for FE polynomial space classes.
describe_nodes()

get_mtx_i()

class sfepy.discrete.fem.poly_spaces.LagrangeNodes(**kwargs)
Helper class for defining nodes of Lagrange elements.
static append_bubbles(nodes, nts, iseq, nt, order)

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static append_edges(nodes, nts, iseq, nt, edges, order)

static append_faces(nodes, nts, iseq, nt, faces, order)

static append_tp_bubbles(nodes, nts, iseq, nt, ao)

static append_tp_edges(nodes, nts, iseq, nt, edges, ao)

static append_tp_faces(nodes, nts, iseq, nt, faces, ao)

class sfepy.discrete.fem.poly_spaces.LagrangePolySpace(name, geometry, order)

create_context(cmesh, eps, check_errors, i_max, newton_eps, tdim=None)

class sfepy.discrete.fem.poly_spaces.LagrangeSimplexBPolySpace(name, geometry, order,

init_context=True)
Lagrange polynomial space with forced bubble function on a simplex domain.
create_context(*args, **kwargs)

name = 'lagrange_simplex_bubble'
class sfepy.discrete.fem.poly_spaces.LagrangeSimplexPolySpace(name, geometry, order,
init_context=True)
Lagrange polynomial space on a simplex domain.
name = 'lagrange_simplex'
class sfepy.discrete.fem.poly_spaces.LagrangeTensorProductPolySpace(name, geometry, order,
init_context=True)
Lagrange polynomial space on a tensor product domain.
get_mtx_i()

name = 'lagrange_tensor_product'
class sfepy.discrete.fem.poly_spaces.LobattoTensorProductPolySpace(name, geometry, order)
Hierarchical polynomial space using Lobatto functions.
Each row of the nodes attribute defines indices of Lobatto functions that need to be multiplied together to evaluate
the corresponding shape function. This defines the ordering of basis functions on the reference element.
name = 'lobatto_tensor_product'
class sfepy.discrete.fem.poly_spaces.NodeDescription(node_types, nodes)
Describe FE nodes defined on different parts of a reference element.
has_extra_nodes()
Return True if the element has some edge, face or bubble nodes.
class sfepy.discrete.fem.poly_spaces.SerendipityTensorProductPolySpace(name, geometry, order)
Serendipity polynomial space using Lagrange functions.

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Notes

• Orders >= 4 (with bubble functions) are not supported.

• Does not use CLagrangeContext, basis functions are hardcoded.
• self.nodes, self.node_coors are not used for basis evaluation and assembling.

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all_bfs = {2: {1: [[x*(y - 1.0) - y + 1.0, x*(1.0 - y), x*y, -x*y + y], [[y - 1.0,
x - 1.0], [1.0 - y, -x], [y, x], [-y, 1.0 - x]]], 2: [[x*(x*(2.0 - 2.0*y) + y*(5.0
- 2.0*y) - 3.0) + y*(2.0*y - 3.0) + 1.0, x*(x*(2.0 - 2.0*y) + y*(2.0*y - 1.0) -
1.0), x*(2.0*x*y + y*(2.0*y - 3.0)), x*(2.0*x*y + y*(-2.0*y - 1.0)) + y*(2.0*y -
1.0), x*(x*(4*y - 4) - 4*y + 4), x*y*(4.0 - 4.0*y), x*(-4.0*x*y + 4.0*y), x*y*(4.0*y
- 4.0) + y*(4.0 - 4.0*y)], [[x*(4.0 - 4.0*y) + y*(5.0 - 2.0*y) - 3.0, x*(-2.0*x -
4.0*y + 5.0) + 4.0*y - 3.0], [x*(4.0 - 4.0*y) + y*(2.0*y - 1.0) - 1.0, x*(-2.0*x +
4.0*y - 1.0)], [4.0*x*y + y*(2.0*y - 3.0), x*(2.0*x + 4.0*y - 3.0)], [4.0*x*y +
y*(-2.0*y - 1.0), x*(2.0*x - 4.0*y - 1.0) + 4.0*y - 1.0], [x*(8*y - 8) - 4*y + 4,
x*(4*x - 4)], [y*(4.0 - 4.0*y), x*(4.0 - 8.0*y)], [-8.0*x*y + 4.0*y, x*(4.0 -
4.0*x)], [y*(4.0*y - 4.0), x*(8.0*y - 4.0) - 8.0*y + 4.0]]], 3: [[x*(x*(x*(4.5*y -
4.5) - 9.0*y + 9.0) + y*(y*(4.5*y - 9.0) + 10.0) - 5.5) + y*(y*(9.0 - 4.5*y) - 5.5)
+ 1.0, x*(x*(x*(4.5 - 4.5*y) + 4.5*y - 4.5) + y*(y*(9.0 - 4.5*y) - 5.5) + 1.0),
x*(x*(4.5*x*y - 4.5*y) + y*(y*(4.5*y - 4.5) + 1.0)), x*(x*(-4.5*x*y + 9.0*y) +
y*(y*(4.5 - 4.5*y) - 5.5)) + y*(y*(4.5*y - 4.5) + 1.0), x*(x*(x*(13.5 - 13.5*y) +
22.5*y - 22.5) - 9.0*y + 9.0), x*(x*(x*(13.5*y - 13.5) - 18.0*y + 18.0) + 4.5*y -
4.5), x*y*(y*(13.5*y - 22.5) + 9.0), x*y*(y*(18.0 - 13.5*y) - 4.5), x*(x*(-13.5*x*y
+ 18.0*y) - 4.5*y), x*(x*(13.5*x*y - 22.5*y) + 9.0*y), x*y*(y*(13.5*y - 18.0) + 4.5)
+ y*(y*(18.0 - 13.5*y) - 4.5), x*y*(y*(22.5 - 13.5*y) - 9.0) + y*(y*(13.5*y - 22.5)
+ 9.0)], [[x*(x*(13.5*y - 13.5) - 18.0*y + 18.0) + y*(y*(4.5*y - 9.0) + 10.0) - 5.5,
x*(x*(4.5*x - 9.0) + y*(13.5*y - 18.0) + 10.0) + y*(18.0 - 13.5*y) - 5.5],
[x*(x*(13.5 - 13.5*y) + 9.0*y - 9.0) + y*(y*(9.0 - 4.5*y) - 5.5) + 1.0, x*(x*(4.5 -
4.5*x) + y*(18.0 - 13.5*y) - 5.5)], [x*(13.5*x*y - 9.0*y) + y*(y*(4.5*y - 4.5) +
1.0), x*(x*(4.5*x - 4.5) + y*(13.5*y - 9.0) + 1.0)], [x*(-13.5*x*y + 18.0*y) +
y*(y*(4.5 - 4.5*y) - 5.5), x*(x*(9.0 - 4.5*x) + y*(9.0 - 13.5*y) - 5.5) + y*(13.5*y
- 9.0) + 1.0], [x*(x*(40.5 - 40.5*y) + 45.0*y - 45.0) - 9.0*y + 9.0, x*(x*(22.5 -
13.5*x) - 9.0)], [x*(x*(40.5*y - 40.5) - 36.0*y + 36.0) + 4.5*y - 4.5, x*(x*(13.5*x
- 18.0) + 4.5)], [y*(y*(13.5*y - 22.5) + 9.0), x*(y*(40.5*y - 45.0) + 9.0)],
[y*(y*(18.0 - 13.5*y) - 4.5), x*(y*(36.0 - 40.5*y) - 4.5)], [x*(-40.5*x*y + 36.0*y)
- 4.5*y, x*(x*(18.0 - 13.5*x) - 4.5)], [x*(40.5*x*y - 45.0*y) + 9.0*y, x*(x*(13.5*x
- 22.5) + 9.0)], [y*(y*(13.5*y - 18.0) + 4.5), x*(y*(40.5*y - 36.0) + 4.5) + y*(36.0
- 40.5*y) - 4.5], [y*(y*(22.5 - 13.5*y) - 9.0), x*(y*(45.0 - 40.5*y) - 9.0) +
y*(40.5*y - 45.0) + 9.0]]]}, 3: {1: [[x*(y*(1.0 - z) + z - 1.0) + y*(z - 1.0) - z
+ 1.0, x*(y*(z - 1.0) - z + 1.0), x*y*(1.0 - z), x*y*(z - 1.0) + y*(1.0 - z), x*(y*z
- z) - y*z + z, x*(-y*z + z), x*y*z, -x*y*z + y*z], [[y*(1.0 - z) + z - 1.0, x*(1.0
- z) + z - 1.0, x*(1.0 - y) + y - 1.0], [y*(z - 1.0) - z + 1.0, x*(z - 1.0), x*(y -
1.0)], [y*(1.0 - z), x*(1.0 - z), -x*y], [y*(z - 1.0), x*(z - 1.0) - z + 1.0, x*y -
y], [y*z - z, x*z - z, x*(y - 1.0) - y + 1.0], [-y*z + z, -x*z, x*(1.0 - y)], [y*z,
x*z, x*y], [-y*z, -x*z + z, -x*y + y]]], 2: [[x*(x*(y*(2.0*z - 2.0) - 2.0*z + 2.0)
+ y*(y*(2.0*z - 2.0) + z*(2.0*z - 7.0) + 5.0) + z*(5.0 - 2.0*z) - 3.0) + y*(y*(2.0 -
2.0*z) + z*(5.0 - 2.0*z) - 3.0) + z*(2.0*z - 3.0) + 1.0, x*(x*(y*(2.0*z - 2.0) -
2.0*z + 2.0) + y*(y*(2.0 - 2.0*z) + z*(3.0 - 2.0*z) - 1.0) + z*(2.0*z - 1.0) - 1.0),
x*(x*y*(2.0 - 2.0*z) + y*(y*(2.0 - 2.0*z) + z*(2.0*z + 1.0) - 3.0)), x*(x*y*(2.0 -
2.0*z) + y*(y*(2.0*z - 2.0) + z*(3.0 - 2.0*z) - 1.0)) + y*(y*(2.0 - 2.0*z) +
z*(2.0*z - 1.0) - 1.0), x*(x*(-2.0*y*z + 2.0*z) + y*(-2.0*y*z + z*(2.0*z + 3.0)) +
z*(-2.0*z - 1.0)) + y*(2.0*y*z + z*(-2.0*z - 1.0)) + z*(2.0*z - 1.0), x*(x*(-2.0*y*z
+ 2.0*z) + y*(2.0*y*z + z*(1.0 - 2.0*z)) + z*(2.0*z - 3.0)), x*(2.0*x*y*z +
y*(2.0*y*z + z*(2.0*z - 5.0))), x*(2.0*x*y*z + y*(-2.0*y*z + z*(1.0 - 2.0*z))) +
y*(2.0*y*z + z*(2.0*z - 3.0)), x*(x*(y*(4.0 - 4.0*z) + 4.0*z - 4.0) + y*(4.0*z -
4.0) - 4.0*z + 4.0), x*y*(y*(4.0*z - 4.0) - 4.0*z + 4.0), x*(x*y*(4.0*z - 4.0) +
y*(4.0 - 4.0*z)), x*y*(y*(4.0 - 4.0*z) + 4.0*z - 4.0) + y*(y*(4.0*z - 4.0) - 4.0*z +
4.0), x*(x*(4.0*y*z - 4.0*z) - 4.0*y*z + 4.0*z), x*y*(-4.0*y*z + 4.0*z),
x*(-4.0*x*y*z + 4.0*y*z), x*y*(4.0*y*z - 4.0*z) + y*(-4.0*y*z + 4.0*z), x*(y*z*(4.0
- 4.0*z) + z*(4.0*z - 4.0)) + y*z*(4.0*z - 4.0) + z*(4.0 - 4.0*z), x*(y*z*(4.0*z -
4.0) + z*(4.0 - 4.0*z)), x*y*z*(4.0 - 4.0*z), x*y*z*(4.0*z - 4.0) + y*z*(4.0 -
4.0*z)], [[x*(y*(4.0*z - 4.0) - 4.0*z + 4.0) + y*(y*(2.0*z - 2.0) + z*(2.0*z - 7.0)
772 + 5.0) + z*(5.0 - 2.0*z) - 3.0, x*(x*(2.0*z - 2.0) + y*(4.0*z -Chapter
4.0) +2.z*(2.0*z
Development
-
7.0) + 5.0) + y*(4.0 - 4.0*z) + z*(5.0 - 2.0*z) - 3.0, x*(x*(2.0*y - 2.0) + y*(2.0*y
+ 4.0*z - 7.0) - 4.0*z + 5.0) + y*(-2.0*y - 4.0*z + 5.0) + 4.0*z - 3.0],
[x*(y*(4.0*z - 4.0) - 4.0*z + 4.0) + y*(y*(2.0 - 2.0*z) + z*(3.0 - 2.0*z) - 1.0) +
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create_context(cmesh, eps, check_errors, i_max, newton_eps, tdim=None)

name = 'serendipity_tensor_product'
supported_orders = {1, 2, 3}

sfepy.discrete.fem.refine module

Basic uniform mesh refinement functions.

sfepy.discrete.fem.refine.refine_1_2(mesh_in)
Refines 1D mesh by cutting each element in half
sfepy.discrete.fem.refine.refine_2_3(mesh_in)
Refines mesh out of triangles by cutting cutting each edge in half and making 4 new finer triangles out of one
coarser one.
sfepy.discrete.fem.refine.refine_2_4(mesh_in)
Refines mesh out of quadrilaterals by cutting cutting each edge in half and making 4 new finer quadrilaterals out
of one coarser one.
sfepy.discrete.fem.refine.refine_3_4(mesh_in)
Refines tetrahedra by cutting each edge in half and making 8 new finer tetrahedra out of one coarser one. Old
nodal coordinates come first in coors, then the new ones. The new tetrahedra are similar to the old one, no
degeneration is supposed to occur as at most 3 congruence classes of tetrahedra appear, even when re-applied
iteratively (provided that conns are not modified between two applications - ordering of vertices in tetrahedra
matters not only for positivity of volumes).
References:
• Juergen Bey: Simplicial grid refinement: on Freudenthal s algorithm and the optimal number of congruence
classes, Numer.Math. 85 (2000), no. 1, 1–29, or
• Juergen Bey: Tetrahedral grid refinement, Computing 55 (1995), no. 4, 355–378, or http://citeseer.ist.psu.
edu/bey95tetrahedral.html
sfepy.discrete.fem.refine.refine_3_8(mesh_in)
Refines hexahedral mesh by cutting cutting each edge in half and making 8 new finer hexahedrons out of one
coarser one.
sfepy.discrete.fem.refine.refine_reference(geometry, level)
Refine reference element given by geometry.

Notes

The error edges must be generated in the order of the connectivity of the previous (lower) level.

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sfepy.discrete.fem.refine_hanging module

Functions for a mesh refinement with hanging nodes.

Notes

Using LCBCs with hanging nodes is not supported.

sfepy.discrete.fem.refine_hanging.find_facet_substitutions(facets, cells, sub_cells, refine_facets)
Find facet substitutions in connectivity.
sub = [coarse cell, coarse facet, fine1 cell, fine1 facet, fine2 cell, fine2 facet]
sfepy.discrete.fem.refine_hanging.find_level_interface(domain, refine_flag)
Find facets of the coarse mesh that are on the coarse-refined cell boundary.
ids w.r.t. current mesh: - facets: global, local w.r.t. cells[:, 0], local w.r.t. cells[:, 1]
• interface cells: - cells[:, 0] - cells to refine - cells[:, 1] - their facet sharing neighbors (w.r.t. both meshes) -
cells[:, 2] - facet kind: 0 = face, 1 = edge
sfepy.discrete.fem.refine_hanging.refine(domain0, refine, subs=None, ret_sub_cells=False)

sfepy.discrete.fem.refine_hanging.refine_region(domain0, region0, region1)

Coarse cell sub_cells[ii, 0] in mesh0 is split into sub_cells[ii, 1:] in mesh1.
The new fine cells are interleaved among the original coarse cells so that the indices of the coarse cells do not
change.
The cell groups are preserved. The vertex groups are preserved only in the coarse (non-refined) cells.

sfepy.discrete.fem._serendipity module

sfepy.discrete.fem.utils module

sfepy.discrete.fem.utils.compute_nodal_edge_dirs(nodes, region, field, return_imap=False)

Nodal edge directions are computed by simple averaging of direction vectors of edges a node is contained in.
Edges are assumed to be straight and a node must be on a single edge (a border node) or shared by exactly two
edges.
sfepy.discrete.fem.utils.compute_nodal_normals(nodes, region, field, return_imap=False)
Nodal normals are computed by simple averaging of element normals of elements every node is contained in.
sfepy.discrete.fem.utils.extend_cell_data(data, domain, rname, val=None, is_surface=False,
average_surface=True)
Extend cell data defined in a region to the whole domain.
Parameters
data [array] The data defined in the region.
domain [FEDomain instance] The FE domain.
rname [str] The region name.
val [float, optional] The value for filling cells not covered by the region. If not given, the smallest
value in data is used.

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is_surface [bool] If True, the data are defined on a surface region. In that case the values are
averaged or summed into the cells containing the region surface faces (a cell can have several
faces of the surface), see average_surface.
average_surface [bool] If True, the data defined on a surface region are averaged, otherwise the
data are summed.
Returns
edata [array] The data extended to all domain elements.
sfepy.discrete.fem.utils.get_edge_paths(graph, mask)
Get all edge paths in a graph with non-masked vertices. The mask is updated.
sfepy.discrete.fem.utils.get_min_value(dofs)
Get a reasonable minimal value of DOFs suitable for extending over a whole domain.
sfepy.discrete.fem.utils.invert_remap(remap)
Return the inverse of remap, i.e. a mapping from a sub-range indices to a full range, see prepare_remap().
sfepy.discrete.fem.utils.prepare_remap(indices, n_full)
Prepare vector for remapping range [0, n_full] to its subset given by indices.
sfepy.discrete.fem.utils.prepare_translate(old_indices, new_indices)
Prepare vector for translating old_indices to new_indices.
Returns
translate [array] The translation vector. Then new_ar = translate[old_ar].
sfepy.discrete.fem.utils.refine_mesh(filename, level)
Uniformly refine level-times a mesh given by filename.
The refined mesh is saved to a file with name constructed from base name of filename and level-times appended
‘_r’ suffix.
Parameters
filename [str] The mesh file name.
level [int] The refinement level.

sfepy.discrete.dg sub-package

sfepy.discrete.dg.dg_1D_vizualizer module

Module for animating solutions in 1D. Can also save them but requieres ffmpeg package see save_animation method.
sfepy.discrete.dg.dg_1D_vizualizer.animate1D_dgsol(Y, X, T, ax=None, fig=None, ylims=None,
labs=None, plott=None, delay=None)
Animates solution of 1D problem into current figure. Keep reference to returned animation object otherwise it
is discarded
Parameters
Y : solution, array |T| x |X| x n, where n is dimension of the solution
X : space interval discetization
T : time interval discretization
ax : specify axes to plot to (Default value = None)
fig : specifiy figure to plot to (Default value = None)

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ylims : limits for y axis, default are 10% offsets of Y extremes

labs : labels to use for parts of the solution (Default value = None)
plott : plot type - how to plot data: tested plot, step (Default value = None)
delay : (Default value = None)
Returns
anim the animation object, keep it to see the animation, used for savig too
sfepy.discrete.dg.dg_1D_vizualizer.animate_1D_DG_sol(coors, t0, t1, u, tn=None, dt=None,
ic=<function <lambda>>, exact=<function
<lambda>>, delay=None, polar=False)

Animates solution to 1D problem produced by DG:

1. animates DOF values in elements as steps
2. animates reconstructed solution with discontinuities

Parameters
coors : coordinates of the mesh
t0 [float] starting time
t1 [float] final time
u : vectors of DOFs, for each order one, shape(u) = (order, nspace_steps, ntime_steps, 1)
ic : analytical initial condition, optional (Default value = lambda x: 0.0)
tn : number of time steps to plot, starting at 0, if None and dt is not None run animation through
all time steps, spaced dt within [t0, tn] (Default value = None)
dt : time step size, if None and tn is not None computed as (t1- t0) / tn otherwise set to 1 if
dt and tn are both None, t0 and t1 are ignored and solution is animated as if in time 0 . . .
ntime_steps (Default value = None)
exact : (Default value = lambda x)
t: 0 :
delay : (Default value = None)
polar : (Default value = False)
Returns
anim_dofs [animation object of DOFs,]
anim_recon [animation object of reconstructed solution]

sfepy.discrete.dg.dg_1D_vizualizer.head(l)
Maybe get head of the list.
Parameters
l [indexable]
Returns
head [first element in l or None is l is empty]

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sfepy.discrete.dg.dg_1D_vizualizer.load_1D_vtks(fold, name)
Reads series of .vtk files and crunches them into form suitable for plot10_DG_sol.
Attempts to read modal cell data for variable mod_data. i.e.
?_modal{i}, where i is number of modal DOF
Resulting solution data have shape: (order, nspace_steps, ntime_steps, 1)
Parameters
fold : folder where to look for files
name : used in {name}.i.vtk, i = 0,1, ... tns - 1
Returns
coors [ndarray]
mod_data [ndarray] solution data
sfepy.discrete.dg.dg_1D_vizualizer.load_state_1D_vtk(name)
Load one VTK file containing state in time
Parameters
name [str]
Returns
coors [ndarray]
u [ndarray]
sfepy.discrete.dg.dg_1D_vizualizer.plot1D_legendre_dofs(coors, dofss, fun=None)
Plots values of DOFs as steps
Parameters
coors : coordinates of nodes of the mesh
dofss : iterable of different projections’ DOFs into legendre space
fun : analytical function to plot (Default value = None)
sfepy.discrete.dg.dg_1D_vizualizer.plotsXT(Y1, Y2, YE, extent, lab1=None, lab2=None, lab3=None)
Plots Y1 and Y2 to one axes and YE to the second axes, Y1 and Y2 are presumed to be two solutions and YE
their error
Parameters
Y1 : solution 1, shape = (space nodes, time nodes)
Y2 : solution 2, shape = (space nodes, time nodes)
YE : soulutio 1 - soulution 2||
extent : imshow extent
lab1 : (Default value = None)
lab2 : (Default value = None)
lab3 : (Default value = None)
sfepy.discrete.dg.dg_1D_vizualizer.reconstruct_legendre_dofs(coors, tn, u)
Creates solution and coordinates vector which when plotted as
plot(xx, ww)

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represent solution reconstructed from DOFs in Legendre poly space at cell borders.
Works only as linear interpolation between cell boundary points
Parameters
coors : coors of nodes of the mesh
u : vectors of DOFs, for each order one, shape(u) = (order, nspace_steps, ntime_steps, 1)
tn : number of time steps to reconstruct, if None all steps are reconstructed
Returns
ww [ndarray] solution values vector, shape is (3 * nspace_steps - 1, ntime_steps, 1),
xx [ndarray] corresponding coordinates vector, shape is (3 * nspace_steps - 1, 1)
sfepy.discrete.dg.dg_1D_vizualizer.save_animation(anim, filename)
Saves animation as .mp4, requires ffmeg package
Parameters
anim : animation object
filename : name of the file, without the .mp4 ending
sfepy.discrete.dg.dg_1D_vizualizer.save_sol_snap(Y, X, T, t0=0.5, filename=None, name=None,
ylims=None, labs=None, plott=None)
Wrapper for sol_frame, saves the frame to file specified.
Parameters
name : name of the solution e.g. name of the solver used (Default value = None)
filename : name of the file, overrides automatic generation (Default value = None)
Y : solution, array |T| x |X| x n, where n is dimension of the solution
X : space interval discetization
T : time interval discretization
t0 : time to take snap at (Default value = .5)
ylims : limits for y axis, default are 10% offsets of Y extremes
labs : labels to use for parts of the solution (Default value = None)
plott : plot type - how to plot data: tested plot, step (Default value = None)
Returns
fig
sfepy.discrete.dg.dg_1D_vizualizer.setup_axis(X, Y, ax=None, fig=None, ylims=None)
Setup axis, including timer for animation or snaps
Parameters
X : space disctretization to get limits
Y : solution to get limits
ax : ax where to put everything, if None current axes are used (Default value = None)
fig : fig where to put everything, if None current figure is used (Default value = None)
ylims : custom ylims, if None y axis limits are calculated from Y (Default value = None)

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Returns
ax
fig
time_text object to fill in text
sfepy.discrete.dg.dg_1D_vizualizer.setup_lines(ax, Yshape, labs, plott)
Sets up artist for animation or solution snaps
Parameters
ax : axes to use for artist
Yshape [tuple] shape of the solution array
labs [list] labels for the solution
plott [str (“steps” or “plot”)] type of plot to use
Returns
lines
sfepy.discrete.dg.dg_1D_vizualizer.sol_frame(Y, X, T, t0=0.5, ax=None, fig=None, ylims=None,
labs=None, plott=None)
Creates snap of solution at specified time frame t0, basically gets one frame from animate1D_dgsol, but colors
wont be the same :-(
Parameters
Y : solution, array |T| x |X| x n, where n is dimension of the solution
X : space interval discetization
T : time interval discretization
t0 : time to take snap at (Default value = .5)
ax : specify axes to plot to (Default value = None)
fig : specifiy figure to plot to (Default value = None)
ylims : limits for y axis, default are 10% offsets of Y extremes
labs : labels to use for parts of the solution (Default value = None)
plott : plot type - how to plot data: tested plot, step (Default value = None)
Returns
fig

sfepy.discrete.dg.fields module

Fields for Discontinous Galerkin method

class sfepy.discrete.dg.fields.DGField(name, dtype, shape, region, space='H1',
poly_space_base='legendre', approx_order=1, integral=None)
Class for usage with DG terms, provides functionality for Discontinous Galerkin method like neighbour look up,
projection to discontinuous basis and correct DOF treatment.
clear_facet_neighbour_idx_cache(region=None)
If region is None clear all!

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Parameters
region [sfepy.discrete.common.region.Region] If None clear all.
clear_facet_qp_base()
Clears facet_qp_base cache
clear_facet_vols_cache(region=None)
Clears facet volume cache for given region or all regions.
Parameters
region [sfepy.discrete.common.region.Region] region to clear cache or None to clear all
clear_normals_cache(region=None)
Clears normals cache for given region or all regions.
Parameters
region [sfepy.discrete.common.region.Region] region to clear cache or None to clear all
create_mapping(region, integral, integration, return_mapping=True)
Creates and returns mapping
Parameters
region [sfepy.discrete.common.region.Region]
integral [Integral]
integration [str] ‘volume’ is only accepted option
return_mapping [default True] (Default value = True)
Returns
mapping [VolumeMapping]
create_output(dofs, var_name, dof_names=None, key=None, extend=True, fill_value=None,
linearization=None)
Converts the DOFs corresponding to the field to a dictionary of output data usable by Mesh.write().
For 1D puts DOFs into vairables u_modal{0} . . . u_modal{n}, where n = approx_order and marks them
for writing as cell data.
For 2+D puts dofs into name_cell_nodes and creates sturct with: mode = “cell_nodes”, data and iterpolation
scheme.
Also get node values and adds them to dictionary as cell_nodes
Parameters
dofs [ndarray, shape (n_nod, n_component)] The array of DOFs reshaped so that each col-
umn corresponds to one component.
var_name [str] The variable name corresponding to dofs.
dof_names [tuple of str] The names of DOF components. (Default value = None)
key [str, optional] The key to be used in the output dictionary instead of the variable name.
(Default value = None)
extend [bool, not used] Extend the DOF values to cover the whole domain. (Default value =
True)
fill_value [float or complex, not used] The value used to fill the missing DOF values if extend
is True. (Default value = None)

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linearization [Struct or None, not used] The linearization configuration for higher order ap-
proximations. (Default value = None)
Returns
out [dict]
family_name = 'volume_DG_legendre_discontinuous'
get_bc_facet_idx(region)
Caches results in self.boundary_facet_local_idx
Parameters
region [sfepy.discrete.common.region.Region] surface region defining BCs
Returns
bc2bfi [ndarray] index of cells on boundary along with corresponding facets
get_bc_facet_values(fun, region, ret_coors=False, diff=0)
Returns values of fun in facet QPs of the region
Parameters
diff: derivative 0 or 1 supported
fun: Function value or values to set qps values to
region [sfepy.discrete.common.region.Region] boundary region
ret_coors: default False, Return physical coors of qps in shape (n_cell, n_qp, dim).
Returns
vals [ndarray] In shape (n_cell,) + (self.dim,) * diff + (n_qp,)
get_both_facet_base_vals(state, region, derivative=None)
Returns values of the basis function in quadrature points on facets broadcasted to all cells inner to the
element as well as outer ones along with weights for the qps broadcasted and transformed to elements.
Contains quick fix to flip facet QPs for right integration order.
Parameters
state [used to get EPBC info]
region [sfepy.discrete.common.region.Region for connectivity]
derivative [if u need derivative] (Default value = None)
Returns
outer_facet_base_vals:
inner_facet_base_vals:
shape (n_cell, n_el_nod, n_el_facet, n_qp) or (n_cell, n_el_nod, n_el_facet, dim, n_qp)
when derivative is True or 1
whs: shape (n_cell, n_el_facet, n_qp)
get_both_facet_state_vals(state, region, derivative=None, reduce_nod=True)
Computes values of the variable represented by dofs in quadrature points located at facets, returns both
values - inner and outer, along with weights.
Parameters

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state [state variable containing BC info]

region [sfepy.discrete.common.region.Region]
derivative [compute derivative if truthy,] compute n-th derivative if a number (Default value
= None)
reduce_nod [if False DOES NOT sum nodes into values at QPs] (Default value = True)
Returns
inner_facet_values (n_cell, n_el_facets, n_qp), outer facet values (n_cell, n_el_facets,
n_qp), weights, if derivative is True:
inner_facet_values (n_cell, n_el_facets, dim, n_qp), outer_facet values (n_cell,
n_el_facets, dim, n_qp)
get_cell_normals_per_facet(region)
Caches results, use clear_normals_cache to clear the cache.
Parameters
region: sfepy.discrete.common.region.Region Main region, must contain cells.
Returns
normals: ndarray normals of facets in array of shape (n_cell, n_el_facets, dim)
get_coor(nods=None)
Returns coors for matching nodes # TODO revise DG_EPBC and EPBC matching?
Parameters
nods : if None use all nodes (Default value = None)
Returns
coors [ndarray] coors on surface
get_data_shape(integral, integration='volume', region_name=None)
Returns data shape (n_nod, n_qp, self.gel.dim, self.n_el_nod)
Parameters
integral [integral used]
integration : ‘volume’ is only supported value (Default value = ‘volume’)
region_name [not used] (Default value = None)
Returns
data_shape [tuple]
get_dofs_in_region(region, merge=True)
Return indices of DOFs that belong to the given region.
Not Used in BC treatment
Parameters
region [sfepy.discrete.common.region.Region]
merge [bool] merge dof tuple into one numpy array, default True
Returns
dofs [ndarray]

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get_econn(conn_type, region, is_trace=False, integration=None)

Getter for econn
Parameters
conn_type [string or Struct] ‘volume’ is only supported
region [sfepy.discrete.common.region.Region]
is_trace [ignored] (Default value = False)
integration [ignored] (Default value = None)
Returns
econn [ndarray] connectivity information
get_facet_base(derivative=False, base_only=False)
Returns values of base in facets quadrature points, data shape is a bit crazy right now:
(number of qps, 1, n_el_facets, 1, n_el_nod)

end for derivatine: (1, number of qps, (dim,) * derivative, n_el_facets, 1, n_el_nod)

Parameters
derivative: truthy or integer
base_only: do not return weights
Returns
facet_bf [ndarray] values of basis functions in facet qps
weights [ndarray, optionally] weights of qps

get_facet_neighbor_idx(region=None, eq_map=None)
Returns index of cell neighbours sharing facet, along with local index of the facet within neighbour, also
treats periodic boundary conditions i.e. plugs correct neighbours for cell on periodic boundary. Where
there are no neighbours specified puts -1 instead of neighbour and facet id
Cashes neighbour index in self.facet_neighbours
Parameters
region [sfepy.discrete.common.region.Region] Main region, must contain cells.
eq_map : eq_map from state variable containing information on EPBC and DG EPBC. (De-
fault value = None)
Returns
facet_neighbours [ndarray]
Shape is (n_cell, n_el_facet, 2),
first value is index of the neighbouring cell, the second is index of the facet in said nb. cell.
get_facet_qp()
Returns quadrature points on all facets of the reference element in array of shape (n_qp, 1 , n_el_facets,
dim)
Returns
qps [ndarray] quadrature points
weights [ndarray] Still needs to be transformed to actual facets!

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get_facet_vols(region)
Caches results, use clear_facet_vols_cache to clear the cache
Parameters
region [sfepy.discrete.common.region.Region]
Returns
vols_out: ndarray volumes of the facets by cells shape (n_cell, n_el_facets, 1)
get_nodal_values(dofs, region, ref_nodes=None)
Computes nodal representation of the DOFs
dofs [array_like] dofs to transform to nodes
region : ignored
ref_nodes: reference node to use instead of default qps

Parameters
dofs [array_like]
region [Region]
ref_nodes [array_like] (Default value = None)
Returns
nodes [ndarray]
nodal_vals [ndarray]

static get_region_info(region)
Extracts information about region needed in various methods of DGField
Parameters
region [sfepy.discrete.common.region.Region]
Returns
dim, n_cell, n_el_facets
is_surface = False
set_cell_dofs(fun=0.0, region=None, dpn=None, warn=None)
Compute projection of fun onto the basis, in main region, alternatively set DOFs directly to provided value
or values
Parameters
fun [callable, scallar or array corresponding to dofs] (Default value = 0.0)
region [sfepy.discrete.common.region.Region] region to set DOFs on (Default value = None)
dpn [number of dofs per element] (Default value = None)
warn [not used] (Default value = None)
Returns
nods [ndarray]
vals [ndarray]

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set_dofs(fun=0.0, region=None, dpn=None, warn=None)

Compute projection of fun into the basis, alternatively set DOFs directly to provided value or values either
in main volume region or in boundary region.
Parameters
fun [callable, scalar or array corresponding to dofs] (Default value = 0.0)
region [sfepy.discrete.common.region.Region] region to set DOFs on (Default value = None)
dpn [number of dofs per element] (Default value = None)
warn : (Default value = None)
Returns
nods [ndarray]
vals [ndarray]
set_facet_dofs(fun, region, dpn, warn)
Compute projection of fun onto the basis on facets, alternatively set DOFs directly to provided value or
values
Parameters
fun [callable, scalar or array corresponding to dofs]
region [sfepy.discrete.common.region.Region] region to set DOFs on
dpn [int] number of dofs per element
warn : not used
Returns
nods [ndarray]
vals [ndarray]
setup_extra_data(geometry, info, is_trace)

This is called in create_adof_conns(conn_info, var_indx=None, active_only=True, verbose=True)

for each variable but has no effect.
Parameters
geometry : ignored
info : set to self.info
is_trace : set to self.trace
sfepy.discrete.dg.fields.get_gel(region)

Parameters
region [sfepy.discrete.common.region.Region]
Returns
gel : base geometry element of the region

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sfepy.discrete.dg.fields.get_raveler(n_el_nod, n_cell)
Returns function for raveling i.e. packing dof data from two dimensional array of shape (n_cell, n_el_nod, 1) to
(n_el_nod*n_cell, 1)
The raveler returns view into the input array.
Parameters
n_el_nod : param n_el_nod, n_cell: expected dimensions of dofs array
n_cell [int]
Returns
ravel [callable]
sfepy.discrete.dg.fields.get_unraveler(n_el_nod, n_cell)
Returns function for unraveling i.e. unpacking dof data from serialized array from shape (n_el_nod*n_cell, 1)
to (n_cell, n_el_nod, 1).
The unraveler returns non-writeable view into the input array.
Parameters
n_el_nod [int] expected dimensions of dofs array
n_cell [int]
Returns
unravel [callable]

sfepy.discrete.dg.poly_spaces module

class sfepy.discrete.dg.poly_spaces.LegendrePolySpace(name, geometry, order, extended)

Legendre hierarchical polynomials basis, over [0, 1] domain.
get_interpol_scheme()
For dim > 1 returns F and P matrices according to gmsh basis specification [1]: Let us assume that the
approximation of the view’s value over an element is written as a linear combination of d basis functions
𝑓𝑖 , 𝑖 = 0, ..., 𝑛 − 1 (the coefficients being stored in list-of-values).
Defining
𝑑−1
∑︁
𝑓𝑖 = 𝐹𝑖𝑗 · 𝑝𝑗 ,
𝑗=0

with
(0) (1) (2)
𝑝𝑗 (𝑢, 𝑣, 𝑤) = 𝑢𝑃𝑗 · 𝑣 𝑃𝑗 · 𝑤𝑃𝑗 (u, v and w being the coordinates in the element’s parameter space),
then val-coef-matrix denotes the n x n matrix F and val-exp-matrix denotes the n x 3 matrix P where n is
number of basis functions as calculated by get_n_el_nod.
Expects matrices to be saved in atributes coefM and expoM!
Returns
interp_scheme_struct [Struct] Struct with name of the scheme, geometry desc and P and F
get_nth_fun(n)
Uses shifted Legendre polynomials formula on interval [0, 1].
Convenience function for testing

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Parameters
n [int]
Returns
fun [callable] n-th function of the legendre basis
get_nth_fun_der(n, diff=1)
Returns diff derivative of nth function. Uses shifted legendre polynomials formula on interval [0, 1].
Useful for testing.
Parameters
n [int]
diff [int] (Default value = 1)
Returns
fun [callable] derivative of n-th function of the 1D legendre basis
gradjacobiP(coors, alpha, beta, diff=1)
diff derivative of the jacobi polynomials on interval [-1, 1] up to self.order + 1 at coors
Parameters
coors :
alpha [float]
beta [float]
diff [int] (Default value = 1)
Returns
values [ndarray] output shape is shape(coor) + (self.order + 1,)
gradlegendreP(coors, diff=1)

Parameters
diff [int] default 1
coors [array_like] coordinates, preferably in interval [-1, 1] for which this basis is intented
Returns
values [ndarray] values at coors of all the legendre polynomials up to self.order
jacobiP(coors, alpha, beta)
Values of the jacobi polynomials on interval [-1, 1] up to self.order + 1 at coors
Parameters
coors [array_like]
beta [float]
alpha [float]
Returns
values [ndarray] output shape is shape(coor) + (self.order + 1,)
legendreP(coors)

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Parameters
coors [array_like] coordinates, preferably in interval [-1, 1] for which this basis is intented
Returns
values [ndarray] values at coors of all the legendre polynomials up to self.order
legendre_funs = [<function LegendrePolySpace.<lambda>>, <function
LegendrePolySpace.<lambda>>, <function LegendrePolySpace.<lambda>>, <function
LegendrePolySpace.<lambda>>, <function LegendrePolySpace.<lambda>>, <function
LegendrePolySpace.<lambda>>]
class sfepy.discrete.dg.poly_spaces.LegendreSimplexPolySpace(name, geometry, order,
extended=False)

name = 'legendre_simplex'
class sfepy.discrete.dg.poly_spaces.LegendreTensorProductPolySpace(name, geometry, order)

build_interpol_scheme()
Builds F and P matrices returned by self.get_interpol_scheme.
Note that this function returns coeficients according to gmsh parametrization of Quadrangle i.e. [-1, 1] x [-1,
1] and hence the form of basis function is not the same as exhibited by the LegendreTensorProductPolySpace
object which acts on parametrization [0, 1] x [0, 1].
Returns
F [ndarray] coefficient matrix
P [ndarray] exponent matrix
name = 'legendre_tensor_product'
sfepy.discrete.dg.poly_spaces.get_n_el_nod(order, dim, extended=False)
Number of nodes per element for discontinuous legendre basis, i.e. number of iterations yielded by iter_by_order
When extended is False
(𝑛 + 1) · (𝑛 + 2) · ... · (𝑛 + 𝑑)
𝑁𝑝 =
𝑑!
where n is the order and d the dimension. When extended is True

𝑁𝑝 = (𝑛 + 1)𝑑

where n is the order and d the dimension.

Parameters
order [int] desired order of multidimensional basis
dim [int] dimension of the basis
extended [bool] iterate over extended tensor product basis (Default value = False)
Returns
n_el_nod [int] number of basis functions in basis
sfepy.discrete.dg.poly_spaces.iter_by_order(order, dim, extended=False)
Iterates over all combinations of basis functions indexes needed to create multidimensional basis in a way that
creates hierarchical basis

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Parameters
order [int] desired order of multidimensional basis
dim [int] dimension of the basis
extended [bool] iterate over extended tensor product basis (Default value = False)
Yields
idx [tuple] containing basis function indexes, used in _combine_polyvals and
_combine_polyvals_der

sfepy.discrete.dg.limiters module

Limiters for high order DG methods

class sfepy.discrete.dg.limiters.ComposedLimiter(fields, limiters, verbose=False)

class sfepy.discrete.dg.limiters.DGLimiter(field, verbose=False)

name = 'abstract DG limiter'

class sfepy.discrete.dg.limiters.IdentityLimiter(field, verbose=False)
Neutral limiter returning unchanged solution.
name = 'identity'
class sfepy.discrete.dg.limiters.MomentLimiter1D(field, verbose=False)
Moment limiter for 1D based on [1]
name = 'moment_1D_limiter'
class sfepy.discrete.dg.limiters.MomentLimiter2D(field, verbose=False)
Moment limiter for 2D based on [R31316dc91f1d-1] .. [R31316dc91f1d-1] Krivodonova (2007):
Limiters for high-order discontinuous Galerkin methods
name = 'moment_limiter_2D'
sfepy.discrete.dg.limiters.minmod(a, b, c)
Minmod function of three variables, returns:
0 , where sign(a) != sign(b) != sign(c)
min(a,b,c) , elsewhere
Parameters
a [array_like]
c [array_like]
b [array_like]
Returns
out [ndarray]
sfepy.discrete.dg.limiters.minmod_seq(abc)
Minmod function of n variables, returns:
0 , where sign(a_1) != sign(a_2) != . . . != sign(a_n)

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min(a_1, a_2, a_3, . . . , a_n) , elsewhere

Parameters
abc [sequence of array_like]
Returns
out [ndarray]

sfepy.solvers.ts_dg_solvers module

Explicit time stepping solvers for use with DG FEM

class sfepy.solvers.ts_dg_solvers.DGMultiStageTSS(conf, nls=None, context=None, **kwargs)
Explicit time stepping solver with multistage solve_step method
Kind: ‘ts.multistaged’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
t0 [float (default: 0.0)] The initial time.
t1 [float (default: 1.0)] The final time.
dt [float] The time step. Used if n_step is not given.
n_step [int (default: 10)] The number of time steps. Has precedence over dt.
quasistatic [bool (default: False)] If True, assume a quasistatic time-stepping. Then the non-
linear solver is invoked also for the initial time.
limiters [dictionary] Limiters for DGFields, keys: field name, values: limiter class
name = 'ts.multistaged'
output_step_info(ts)

solve_step(ts, nls, vec, prestep_fun=None, poststep_fun=None, status=None)

solve_step0(nls, vec0)

class sfepy.solvers.ts_dg_solvers.EulerStepSolver(conf, nls=None, context=None, **kwargs)

Simple forward euler method
Kind: ‘ts.euler’
For common configuration parameters, see Solver.
Specific configuration parameters:
name = 'ts.euler'
solve_step(ts, nls, vec_x0, status=None, prestep_fun=None, poststep_fun=None)

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class sfepy.solvers.ts_dg_solvers.RK4StepSolver(conf, nls=None, context=None, **kwargs)

Classical 4th order Runge-Kutta method, implemetantions is based on [1]
Kind: ‘ts.runge_kutta_4’
For common configuration parameters, see Solver.
Specific configuration parameters:
name = 'ts.runge_kutta_4'
solve_step(ts, nls, vec_x0, status=None, prestep_fun=None, poststep_fun=None)

stage_updates = (<function RK4StepSolver.<lambda>>, <function

RK4StepSolver.<lambda>>, <function RK4StepSolver.<lambda>>, <function
RK4StepSolver.<lambda>>)
class sfepy.solvers.ts_dg_solvers.TVDRK3StepSolver(conf, nls=None, context=None, **kwargs)
3rd order Total Variation Diminishing Runge-Kutta method based on [1]

p(1) = p𝑛 − ∆𝑡ℒ̄(p𝑛 ),
3 1 1
p(2) = p𝑛 + p(1) − ∆𝑡ℒ̄(p(1) ),
4 4 4
1 2 2
p(𝑛+1) = p𝑛 + p(2) − ∆𝑡ℒ̄(p(2) ).
3 3 3
Kind: ‘ts.tvd_runge_kutta_3’
For common configuration parameters, see Solver.
Specific configuration parameters:
name = 'ts.tvd_runge_kutta_3'
solve_step(ts, nls, vec_x0, status=None, prestep_fun=None, poststep_fun=None)

sfepy.discrete.iga sub-package

sfepy.discrete.iga.domain module

Computational domain for isogeometric analysis.

class sfepy.discrete.iga.domain.IGDomain(name, nurbs, bmesh, regions=None, **kwargs)
Bezier extraction based NURBS domain for isogeometric analysis.
static from_data(knots, degrees, cps, weights, cs, conn, bcps, bweights, bconn, regions,
name='iga_domain_from_data')
Create the IGA domain from the given data.
static from_file(filename)

filename [str] The name of the IGA domain file.

static read_domain_from_hdf5(fd, group)
Create a domain from the given hdf5 data group.
fd: tables.File HDF5 file handle to read the mesh from.
group: tables.group.Group HDF5 data group (of file fd) to read the mesh from.

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write_domain_to_hdf5(fd, group)
Save the domain to a hdf5 file.
fd: tables.File HDF5 file handle to write the mesh to.
group: tables.group.Group HDF5 data group (of file fd) to write the mesh to.
class sfepy.discrete.iga.domain.NurbsPatch(knots, degrees, cps, weights, cs, conn)
Single NURBS patch data.
elevate(times=0)
Elevate the patch degrees several times by one.
Returns
nurbs [NurbsPatch instance] Either self if times is zero, or a new instance.
evaluate(field, u=None, v=None, w=None)
Igakit-like interface for NURBS evaluation.

sfepy.discrete.iga.domain_generators module

IGA domain generators.

sfepy.discrete.iga.domain_generators.create_from_igakit(inurbs, verbose=False)
Create IGDomain data from a given igakit NURBS object.
Parameters
inurbs [igakit.nurbs.NURBS instance] The igakit NURBS object.
Returns
nurbs [NurbsPatch instance] The NURBS data. The igakit NURBS object is stored as nurbs
attribute.
bmesh [Struct instance] The Bezier mesh data.
regions [dict] The patch surface regions.
sfepy.discrete.iga.domain_generators.gen_patch_block_domain(dims, shape, centre, degrees,
continuity=None, cp_mode='greville',
name='block', verbose=True)
Generate a single IGA patch block in 2D or 3D of given degrees and continuity using igakit.
Parameters
dims [array of D floats] Dimensions of the block.
shape [array of D ints] Numbers of unique knot values along each axis.
centre [array of D floats] Centre of the block.
degrees [array of D floats] NURBS degrees along each axis.
continuity [array of D ints, optional] NURBS continuity along each axis. If None, degrees-1 is
used.
cp_mode [‘greville’ or ‘uniform’] The control points mode. The default ‘greville’ results in a
uniform Bezier mesh, while the ‘uniform’ mode results in a uniform grid of control points a
finer Bezier mesh inside the block and a coarser Bezier mesh near the block boundary.
name [string] Domain name.
verbose [bool] If True, report progress of the domain generation.

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Returns
nurbs [NurbsPatch instance] The NURBS data. The igakit NURBS object is stored as nurbs
attribute.
bmesh [Struct instance] The Bezier mesh data.
regions [dict] The patch surface regions.

sfepy.discrete.iga.extmods.igac module

class sfepy.discrete.iga.extmods.igac.CNURBSContext

R
bf
bfg
bufBN
cprint()

dR_dx
dR_dxi
e_coors_max
evaluate()

iel
sfepy.discrete.iga.extmods.igac.eval_bernstein_basis()

sfepy.discrete.iga.extmods.igac.eval_in_tp_coors()
Evaluate a field variable (if given) or the NURBS geometry in the given tensor-product reference coordinates.
The field variable is defined by its DOFs - the coefficients of the NURBS basis.
Parameters
variable [array] The DOF values of the variable with n_c components, shape (:, n_c).
indices [list of arrays] The indices of knot spans for each axis, defining the Bezier element num-
bers.
ref_coors [list of arrays] The reference coordinates in [0, 1] for each knot span for each axis,
defining the reference coordinates in the Bezier elements given by indices.
control_points [array] The NURBS control points.
weights [array] The NURBS weights.
degrees [sequence of ints or int] The basis degrees in each parametric dimension.
cs [list of lists of 2D arrays] The element extraction operators in each parametric dimension.
conn [array] The connectivity of the global NURBS basis.
Returns

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out [array] The field variable values or NURBS geometry coordinates for the given reference
coordinates.
sfepy.discrete.iga.extmods.igac.eval_mapping_data_in_qp()
Evaluate data required for the isogeometric domain reference mapping in the given quadrature points. The
quadrature points are the same for all Bezier elements and should correspond to the Bernstein basis degree.
Parameters
qps [array] The quadrature points coordinates with components in [0, 1] reference element do-
main.
control_points [array] The NURBS control points.
weights [array] The NURBS weights.
degrees [sequence of ints or int] The basis degrees in each parametric dimension.
cs [list of lists of 2D arrays] The element extraction operators in each parametric dimension.
conn [array] The connectivity of the global NURBS basis.
cells [array, optional] If given, use only the given Bezier elements.
Returns
bfs [array] The NURBS shape functions in the physical quadrature points of all elements.
bfgs [array] The NURBS shape functions derivatives w.r.t. the physical coordinates in the phys-
ical quadrature points of all elements.
dets [array] The Jacobians of the mapping to the unit reference element in the physical quadra-
ture points of all elements.
sfepy.discrete.iga.extmods.igac.eval_variable_in_qp()
Evaluate a field variable in the given quadrature points. The quadrature points are the same for all Bezier elements
and should correspond to the Bernstein basis degree. The field variable is defined by its DOFs - the coefficients
of the NURBS basis.
Parameters
variable [array] The DOF values of the variable with n_c components, shape (:, n_c).
qps [array] The quadrature points coordinates with components in [0, 1] reference element do-
main.
control_points [array] The NURBS control points.
weights [array] The NURBS weights.
degrees [sequence of ints or int] The basis degrees in each parametric dimension.
cs [list of lists of 2D arrays] The element extraction operators in each parametric dimension.
conn [array] The connectivity of the global NURBS basis.
cells [array, optional] If given, use only the given Bezier elements.
Returns
coors [array] The physical coordinates of the quadrature points of all elements.
vals [array] The field variable values in the physical quadrature points.
dets [array] The Jacobians of the mapping to the unit reference element in the physical quadra-
ture points.

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sfepy.discrete.iga.extmods.igac.is_nurbs()
Return True if some weights are not one.

sfepy.discrete.iga.fields module

Fields for isogeometric analysis.

class sfepy.discrete.iga.fields.IGField(name, dtype, shape, region, approx_order=None, **kwargs)
Bezier extraction based NURBS field for isogeometric analysis.

Notes

The field has to cover the whole IGA domain. The field’s NURBS basis can have higher degree than the domain
NURBS basis.
create_basis_context()
Create the context required for evaluating the field basis.
create_eval_mesh()
Create a mesh with the original NURBS connectivity for evaluating the field. The mesh coordinates are
the NURBS control points.
create_mapping(region, integral, integration)
Create a new reference mapping.
create_mesh(extra_nodes=True)
Create a mesh corresponding to the field region. For IGA fields, this is directly the topological mesh. The
extra_nodes argument is ignored.
create_output(dofs, var_name, dof_names=None, key=None, **kwargs)
Convert the DOFs corresponding to the field to a dictionary of output data usable by Mesh.write().
Parameters
dofs [array, shape (n_nod, n_component)] The array of DOFs reshaped so that each column
corresponds to one component.
var_name [str] The variable name corresponding to dofs.
dof_names [tuple of str] The names of DOF components.
key [str, optional] The key to be used in the output dictionary instead of the variable name.
Returns
out [dict] The output dictionary.
family_name = 'volume_H1_iga'
get_data_shape(integral, integration='volume', region_name=None)
Get element data dimensions.
Parameters
integral [Integral instance] The integral describing used numerical quadrature.
integration [‘volume’] The term integration type. Only ‘volume’ type is implemented.
region_name [str] The name of the region of the integral.
Returns
data_shape [4 ints] The (n_el, n_qp, dim, n_en) for volume shape kind.

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Notes

• n_el = number of elements

• n_qp = number of quadrature points per element/facet
• dim = spatial dimension
• n_en = number of element nodes

get_dofs_in_region(region, merge=True)
Return indices of DOFs that belong to the given region and group.

Notes

merge is not used.

get_econn(conn_type, region, is_trace=False, integration=None, local=False)
Get DOF connectivity of the given type in the given region.
get_surface_basis(region)

get_true_order()

is_higher_order()
Return True, if the field’s approximation order is greater than one.
setup_extra_data(geometry, info, is_trace)

sfepy.discrete.iga.fields.parse_approx_order(approx_order)

sfepy.discrete.iga.iga module

Isogeometric analysis utilities.

Notes

The functions compute_bezier_extraction_1d() and eval_nurbs_basis_tp() implement the algorithms de-

scribed in [1].
[1] Michael J. Borden, Michael A. Scott, John A. Evans, Thomas J. R. Hughes: Isogeometric finite element data
structures based on Bezier extraction of NURBS, Institute for Computational Engineering and Sciences, The
University of Texas at Austin, Austin, Texas, March 2010.
sfepy.discrete.iga.iga.combine_bezier_extraction(cs)
For a nD B-spline parametric domain, combine the 1D element extraction operators in each parametric dimension
into a single operator for each nD element.
Parameters
cs [list of lists of 2D arrays] The element extraction operators in each parametric dimension.
Returns
ccs [list of 2D arrays] The combined element extraction operators.

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sfepy.discrete.iga.iga.compute_bezier_control(control_points, weights, ccs, conn, bconn)

Compute the control points and weights of the Bezier mesh.
Parameters
control_points [array] The NURBS control points.
weights [array] The NURBS weights.
ccs [list of 2D arrays] The combined element extraction operators.
conn [array] The connectivity of the global NURBS basis.
bconn [array] The connectivity of the Bezier basis.
Returns
bezier_control_points [array] The control points of the Bezier mesh.
bezier_weights [array] The weights of the Bezier mesh.
sfepy.discrete.iga.iga.compute_bezier_extraction(knots, degrees)
Compute local (element) Bezier extraction operators for a nD B-spline parametric domain.
Parameters
knots [sequence of array or array] The knot vectors.
degrees [sequence of ints or int] Polynomial degrees in each parametric dimension.
Returns
cs [list of lists of 2D arrays] The element extraction operators in each parametric dimension.
sfepy.discrete.iga.iga.compute_bezier_extraction_1d(knots, degree)
Compute local (element) Bezier extraction operators for a 1D B-spline parametric domain.
Parameters
knots [array] The knot vector.
degree [int] The curve degree.
Returns
cs [array of 2D arrays (3D array)] The element extraction operators.
sfepy.discrete.iga.iga.create_boundary_qp(coors, dim)
Create boundary quadrature points from the surface quadrature points.
Uses the Bezier element tensor product structure.
Parameters
coors [array, shape (n_qp, d)] The coordinates of the surface quadrature points.
dim [int] The topological dimension.
Returns
bcoors [array, shape (n_qp, d + 1)] The coordinates of the boundary quadrature points.
sfepy.discrete.iga.iga.create_connectivity(n_els, knots, degrees)
Create connectivity arrays of nD Bezier elements.
Parameters
n_els [sequence of ints] The number of elements in each parametric dimension.
knots [sequence of array or array] The knot vectors.

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degrees [sequence of ints or int] The basis degrees in each parametric dimension.
Returns
conn [array] The connectivity of the global NURBS basis.
bconn [array] The connectivity of the Bezier basis.
sfepy.discrete.iga.iga.create_connectivity_1d(n_el, knots, degree)
Create connectivity arrays of 1D Bezier elements.
Parameters
n_el [int] The number of elements.
knots [array] The knot vector.
degree [int] The basis degree.
Returns
conn [array] The connectivity of the global NURBS basis.
bconn [array] The connectivity of the Bezier basis.
sfepy.discrete.iga.iga.eval_bernstein_basis(x, degree)
Evaluate the Bernstein polynomial basis of the given degree, and its derivatives, in a point x in [0, 1].
Parameters
x [float] The point in [0, 1].
degree [int] The basis degree.
Returns
funs [array] The degree + 1 values of the Bernstein polynomial basis.
ders [array] The degree + 1 values of the Bernstein polynomial basis derivatives.
sfepy.discrete.iga.iga.eval_mapping_data_in_qp(qps, control_points, weights, degrees, cs, conn,
cells=None)
Evaluate data required for the isogeometric domain reference mapping in the given quadrature points. The
quadrature points are the same for all Bezier elements and should correspond to the Bernstein basis degree.
Parameters
qps [array] The quadrature points coordinates with components in [0, 1] reference element do-
main.
control_points [array] The NURBS control points.
weights [array] The NURBS weights.
degrees [sequence of ints or int] The basis degrees in each parametric dimension.
cs [list of lists of 2D arrays] The element extraction operators in each parametric dimension.
conn [array] The connectivity of the global NURBS basis.
cells [array, optional] If given, use only the given Bezier elements.
Returns
bfs [array] The NURBS shape functions in the physical quadrature points of all elements.
bfgs [array] The NURBS shape functions derivatives w.r.t. the physical coordinates in the phys-
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dets [array] The Jacobians of the mapping to the unit reference element in the physical quadra-
ture points of all elements.
sfepy.discrete.iga.iga.eval_nurbs_basis_tp(qp, ie, control_points, weights, degrees, cs, conn)
Evaluate the tensor-product NURBS shape functions in a quadrature point for a given Bezier element.
Parameters
qp [array] The quadrature point coordinates with components in [0, 1] reference element do-
main.
ie [int] The Bezier element index.
control_points [array] The NURBS control points.
weights [array] The NURBS weights.
degrees [sequence of ints or int] The basis degrees in each parametric dimension.
cs [list of lists of 2D arrays] The element extraction operators in each parametric dimension.
conn [array] The connectivity of the global NURBS basis.
Returns
R [array] The NURBS shape functions.
dR_dx [array] The NURBS shape functions derivatives w.r.t. the physical coordinates.
det [array] The Jacobian of the mapping to the unit reference element.
sfepy.discrete.iga.iga.eval_variable_in_qp(variable, qps, control_points, weights, degrees, cs, conn,
cells=None)
Evaluate a field variable in the given quadrature points. The quadrature points are the same for all Bezier elements
and should correspond to the Bernstein basis degree. The field variable is defined by its DOFs - the coefficients
of the NURBS basis.
Parameters
variable [array] The DOF values of the variable with n_c components, shape (:, n_c).
qps [array] The quadrature points coordinates with components in [0, 1] reference element do-
main.
control_points [array] The NURBS control points.
weights [array] The NURBS weights.
degrees [sequence of ints or int] The basis degrees in each parametric dimension.
cs [list of lists of 2D arrays] The element extraction operators in each parametric dimension.
conn [array] The connectivity of the global NURBS basis.
cells [array, optional] If given, use only the given Bezier elements.
Returns
coors [array] The physical coordinates of the quadrature points of all elements.
vals [array] The field variable values in the physical quadrature points.
dets [array] The Jacobians of the mapping to the unit reference element in the physical quadra-
ture points.
sfepy.discrete.iga.iga.get_bezier_element_entities(degrees)
Get faces and edges of a Bezier mesh element in terms of indices into the element’s connectivity (reference
Bezier element entities).

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Parameters
degrees [sequence of ints or int] Polynomial degrees in each parametric dimension.
Returns
faces [list of arrays] The indices for each face or None if not 3D.
edges [list of arrays] The indices for each edge or None if not at least 2D.
vertices [list of arrays] The indices for each vertex.

Notes

The ordering of faces and edges has to be the same as in sfepy.discrete.fem.geometry_element.

geometry_data.
sfepy.discrete.iga.iga.get_bezier_topology(bconn, degrees)
Get a topology connectivity corresponding to the Bezier mesh connectivity.
In the referenced Bezier control points the Bezier mesh is interpolatory.
Parameters
bconn [array] The connectivity of the Bezier basis.
degrees [sequence of ints or int] The basis degrees in each parametric dimension.
Returns
tconn [array] The topology connectivity (corner nodes, or vertices, of Bezier elements) with
vertex ordering suitable for a FE mesh.
sfepy.discrete.iga.iga.get_facet_axes(dim)
For each reference Bezier element facet return the facet axes followed by the remaining (perpendicular) axis, as
well as the remaining axis coordinate of the facet.
Parameters
dim [int] The topological dimension.
Returns
axes [array] The axes of the reference element facets.
coors [array] The remaining coordinate of the reference element facets.
sfepy.discrete.iga.iga.get_patch_box_regions(n_els, degrees)
Get box regions of Bezier topological mesh in terms of element corner vertices of Bezier mesh.
Parameters
n_els [sequence of ints] The number of elements in each parametric dimension.
degrees [sequence of ints or int] Polynomial degrees in each parametric dimension.
Returns
regions [dict] The Bezier mesh vertices of box regions.
sfepy.discrete.iga.iga.get_raveled_index(indices, shape)
Get a global raveled index corresponding to nD indices into an array of the given shape.
sfepy.discrete.iga.iga.get_surface_degrees(degrees)
Get degrees of the NURBS patch surfaces.
Parameters

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degrees [sequence of ints or int] Polynomial degrees in each parametric dimension.

Returns
sdegrees [list of arrays] The degrees of the patch surfaces, in the order of the reference Bezier
element facets.
sfepy.discrete.iga.iga.get_unraveled_indices(index, shape)
Get nD indices into an array of the given shape corresponding to a global raveled index.
sfepy.discrete.iga.iga.tensor_product(a, b)
Compute tensor product of two 2D arrays with possibly different shapes. The result has the form:

c = [[a00 b, a01 b, ...],

[a10 b, a11 b, ...],
...
... ]

sfepy.discrete.iga.io module

IO for NURBS and Bezier extraction data.

sfepy.discrete.iga.io.read_iga_data(filename, group=None)
Read IGA-related data from a HDF5 file using pytables.
filename: str or tables.File File to read the hdf5 mesh to.
group: tables.group.Group or None HDF5 file group to read the mesh from. If it’s None, the root of file is
used.

Returns
tuple Data for restoring IGA domain.

sfepy.discrete.iga.io.write_iga_data(filename, group, knots, degrees, control_points, weights, cs, conn,

bezier_control_points, bezier_weights, bezier_conn, regions,
name=None)
Write IGA-related data into a HDF5 file using pytables.
filename: str or tables.File File to read the hdf5 mesh to.
group: tables.group.Group, optional HDF5 file group to read the data from. If None, the root of file is used.

Returns
tuple Data for restoring IGA domain.

sfepy.discrete.iga.mappings module

Reference mappings for isogeometric analysis.

class sfepy.discrete.iga.mappings.IGMapping(domain, cells, nurbs=None)
Reference mapping for isogeometric analysis based on Bezier extraction.
Parameters
domain [IGDomain instance] The mapping domain.
cells [array] The mapping region cells. (All domain cells required.)

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nurbs [NurbsPatch instance, optional] If given, the nurbs is used instead of domain.nurbs. The
nurbs has to be obtained by degree elevation of domain.nurbs.
get_geometry()
Return reference element geometry as a GeometryElement instance.
get_mapping(qp_coors, weights)
Get the mapping for given quadrature points and weights.
Returns
cmap [CMapping instance] The reference mapping.

Notes

Does not set total volume of the C mapping structure!

get_physical_qps(qp_coors)
Get physical quadrature points corresponding to given reference Bezier element quadrature points.
Returns
qps [array] The physical quadrature points ordered element by element, i.e. with shape (n_el,
n_qp, dim).

sfepy.discrete.iga.plot_nurbs module

sfepy.discrete.iga.plot_nurbs.plot_bezier_mesh(ax, control_points, conn, degrees, label=False)

Plot the Bezier mesh of a NURBS given by its control points and connectivity.
sfepy.discrete.iga.plot_nurbs.plot_bezier_nurbs_basis_1d(ax, control_points, weights, degrees, cs,
conn, n_points=20)
Plot a 1D NURBS basis using the Bezier extraction and local Bernstein basis.
sfepy.discrete.iga.plot_nurbs.plot_control_mesh(ax, control_points, label=False)
Plot the control mesh of a NURBS given by its control points.
sfepy.discrete.iga.plot_nurbs.plot_iso_lines(ax, nurbs, color='b', n_points=100)
Plot the NURBS object using iso-lines in Greville abscissae coordinates.
sfepy.discrete.iga.plot_nurbs.plot_nurbs_basis_1d(ax, nurbs, n_points=100, x_axis='parametric',
legend=False)
Plot a 1D NURBS basis.
sfepy.discrete.iga.plot_nurbs.plot_parametric_mesh(ax, knots)
Plot the parametric mesh of a NURBS given by its knots.

sfepy.discrete.iga.utils module

Utility functions based on igakit.

sfepy.discrete.iga.utils.create_linear_fe_mesh(nurbs, pars=None)
Convert a NURBS object into a nD-linear tensor product FE mesh.
Parameters
nurbs [igakit.nurbs.NURBS instance] The NURBS object.

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pars [sequence of array, optional] The values of parameters in each parametric dimension. If
not given, the values are set so that the resulting mesh has the same number of vertices as
the number of control points/basis functions of the NURBS object.
Returns
coors [array] The coordinates of mesh vertices.
conn [array] The vertex connectivity array.
desc [str] The cell kind.
sfepy.discrete.iga.utils.create_mesh_and_output(nurbs, pars=None, **kwargs)
Create a nD-linear tensor product FE mesh using create_linear_fe_mesh(), evaluate field variables given
as keyword arguments in the mesh vertices and create a dictionary of output data usable by Mesh.write().
Parameters
nurbs [igakit.nurbs.NURBS instance] The NURBS object.
pars [sequence of array, optional] The values of parameters in each parametric dimension. If
not given, the values are set so that the resulting mesh has the same number of vertices as
the number of control points/basis functions of the NURBS object.
**kwargs [kwargs] The field variables as keyword arguments. Their names serve as keys in the
output dictionary.
Returns
mesh [Mesh instance] The finite element mesh.
out [dict] The output dictionary.
sfepy.discrete.iga.utils.save_basis(nurbs, pars)
Save a NURBS object basis on a FE mesh corresponding to the given parametrization in VTK files.
Parameters
nurbs [igakit.nurbs.NURBS instance] The NURBS object.
pars [sequence of array, optional] The values of parameters in each parametric dimension.

sfepy.discrete.structural sub-package

sfepy.discrete.structural.fields module

Fields corresponding to structural elements.

class sfepy.discrete.structural.fields.Shell10XField(name, dtype, shape, region, approx_order=1)
The field for the shell10x element.
create_mapping(region, integral, integration, return_mapping=True)
Create a new reference mapping.
create_output(dofs, var_name, dof_names=None, key=None, thickness=None, **kwargs)
Convert the DOFs corresponding to the field to a dictionary of output data usable by Mesh.write().
Parameters
dofs [array, shape (n_nod, n_component)] The array of DOFs reshaped so that each column
corresponds to one component.
var_name [str] The variable name corresponding to dofs.

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dof_names [tuple of str] The names of DOF components.

key [str, optional] The key to be used in the output dictionary instead of the variable name.
Returns
out [dict] The output dictionary.
family_name = 'volume_H1_shell10x'

sfepy.discrete.structural.mappings module

Finite element reference mappings for structural elements.

class sfepy.discrete.structural.mappings.Shell10XMapping(region, field)
The reference mapping for the shell10x element.
get_mapping(qp_coors, weights)
Get the mapping for given quadrature points and weights.
get_physical_qps(qp_coors)
Get physical quadrature points corresponding the given reference element quadrature points.
Returns
qps [array] The physical quadrature points ordered element by element, i.e. with shape (n_el,
n_qp, dim).

sfepy.homogenization package

sfepy.homogenization.band_gaps_app module

class sfepy.homogenization.band_gaps_app.AcousticBandGapsApp(conf, options, output_prefix,

**kwargs)
Application for computing acoustic band gaps.
call()
Construct and call the homogenization engine accoring to options.
plot_band_gaps(coefs)

plot_dispersion(coefs)

static process_options(options)
Application options setup. Sets default values for missing non-compulsory options.
static process_options_pv(options)
Application options setup for phase velocity computation. Sets default values for missing non-compulsory
options.
setup_options()

sfepy.homogenization.band_gaps_app.plot_eigs(fig_num, plot_rsc, plot_labels, valid, freq_range,

plot_range, show=False, clear=False, new_axes=False)
Plot resonance/eigen-frequencies.
valid must correspond to freq_range

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resonances : red masked resonances: dotted red

sfepy.homogenization.band_gaps_app.plot_gap(ax, ranges, kind, kind_desc, plot_range, plot_rsc)
Plot single band gap frequency ranges as rectangles.
sfepy.homogenization.band_gaps_app.plot_gaps(fig_num, plot_rsc, gaps, kinds, gap_ranges, freq_range,
plot_range, show=False, clear=False, new_axes=False)
Plot band gaps as rectangles.
sfepy.homogenization.band_gaps_app.plot_logs(fig_num, plot_rsc, plot_labels, freqs, logs, valid,
freq_range, plot_range, draw_eigs=True,
show_legend=True, show=False, clear=False,
new_axes=False)
Plot logs of min/middle/max eigs of a mass matrix.
sfepy.homogenization.band_gaps_app.save_raw_bg_logs(filename, logs)
Save raw band gaps logs into the filename file.
sfepy.homogenization.band_gaps_app.transform_plot_data(datas, plot_transform, conf )

sfepy.homogenization.band_gaps_app.try_set_defaults(obj, attr, defaults, recur=False)

sfepy.homogenization.coefficients module

class sfepy.homogenization.coefficients.Coefficients(**kwargs)
Class for storing (homogenized) material coefficients.
static from_file_hdf5(filename)

to_file_hdf5(filename)

to_file_latex(filename, names, format='%.2e', cdot=False, filter=None, idx=None)

Save the coefficients to a file in LaTeX format.
Parameters
filename [str] The name of the output file.
names [dict] Mapping of attribute names to LaTeX names.
format [str] Format string for numbers.
cdot [bool] For ‘%.e’ formats only. If True, replace ‘e’ by LaTeX ‘cdot 10^{exponent}’
format.
filter [int] For ‘%.e’ formats only. Typeset as 0, if exponent is less than filter.
idx [int] For multi-coefficients, set the coefficient index.
to_file_txt(filename, names, format)

to_latex(attr_name, dim, style='table', format='%f', step=None)

sfepy.homogenization.coefficients.coef_arrays_to_dicts(idict, format='%s/%d')

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sfepy.homogenization.coefs_base module

class sfepy.homogenization.coefs_base.CoefDim(name, problem, kwargs)

class sfepy.homogenization.coefs_base.CoefDimDim(name, problem, kwargs)

class sfepy.homogenization.coefs_base.CoefDimSym(name, problem, kwargs)

class sfepy.homogenization.coefs_base.CoefDummy(name, problem, kwargs)

Dummy class serving for computing and returning its requirements.
class sfepy.homogenization.coefs_base.CoefEval(name, problem, kwargs)
Evaluate expression.
class sfepy.homogenization.coefs_base.CoefExprPar(name, problem, kwargs)
The coefficient which expression can be parametrized via ‘expr_pars’, the dimension is given by the number of
parameters.
Example:
‘expression’: ‘dw_surface_ndot.5.Ys(mat_norm.k%d, corr1)’, ‘expr_pars’: [ii for ii in range(dim)],
‘class’: cb.CoefExprPar,
static set_variables_default(variables, ir, set_var, data)

class sfepy.homogenization.coefs_base.CoefMN(name, problem, kwargs)

get_coef(row, col, volume, problem, data)

static set_variables_default(variables, ir, ic, mode, set_var, data, dtype)

class sfepy.homogenization.coefs_base.CoefN(name, problem, kwargs)

get_coef(row, volume, problem, data)

static set_variables_default(variables, ir, ic, mode, set_var, data, dtype)

class sfepy.homogenization.coefs_base.CoefNonSym(name, problem, kwargs)

is_sym = False
static iter_sym(dim)

class sfepy.homogenization.coefs_base.CoefNonSymNonSym(name, problem, kwargs)

is_sym = False
static iter_sym(dim)

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class sfepy.homogenization.coefs_base.CoefNone(name, problem, kwargs)

class sfepy.homogenization.coefs_base.CoefOne(name, problem, kwargs)

static set_variables_default(variables, set_var, data, dtype)

class sfepy.homogenization.coefs_base.CoefSum(name, problem, kwargs)

class sfepy.homogenization.coefs_base.CoefSym(name, problem, kwargs)

is_sym = True
static iter_sym(dim)

class sfepy.homogenization.coefs_base.CoefSymSym(name, problem, kwargs)

is_sym = True
static iter_sym(dim)

class sfepy.homogenization.coefs_base.CorrDim(name, problem, kwargs)

class sfepy.homogenization.coefs_base.CorrDimDim(name, problem, kwargs)

class sfepy.homogenization.coefs_base.CorrEqPar(name, problem, kwargs)

The corrector which equation can be parametrized via ‘eq_pars’, the dimension is given by the number of pa-
rameters.
Example:
‘equations’: ‘dw_diffusion.5.Y(mat.k, q, p) = dw_integrate.5.%s(q)’,
‘eq_pars’: (‘bYMp’, ‘bYMm’), ‘class’: cb.CorrEqPar,
class sfepy.homogenization.coefs_base.CorrEval(name, problem, kwargs)

class sfepy.homogenization.coefs_base.CorrMiniApp(name, problem, kwargs)

get_output(corr_sol, is_dump=False, extend=True, variables=None, var_map=None)

get_save_name(save_format='.h5', stamp='')

get_save_name_base()

save(state, problem, variables=None, ts=None, var_map=None)

setup_output(save_formats=None, post_process_hook=None, file_per_var=None)

Instance attributes have precedence!

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class sfepy.homogenization.coefs_base.CorrN(name, problem, kwargs)

static set_variables_default(variables, ir, set_var, data)

class sfepy.homogenization.coefs_base.CorrNN(name, problem, kwargs)

__init__() kwargs: {
‘ebcs’ : [], ‘epbcs’ : [], ‘equations’ : {}, ‘set_variables’ : None,
},
static set_variables_default(variables, ir, ic, set_var, data)

class sfepy.homogenization.coefs_base.CorrOne(name, problem, kwargs)

static set_variables_default(variables, set_var, data)

class sfepy.homogenization.coefs_base.CorrSetBCS(name, problem, kwargs)

class sfepy.homogenization.coefs_base.CorrSolution(**kwargs)
Class for holding solutions of corrector problems.
get_ts_val(step)

iter_solutions()

iter_time_steps()

class sfepy.homogenization.coefs_base.MiniAppBase(name, problem, kwargs)

static any_from_conf(name, problem, kwargs)

init_solvers(problem)
Setup solvers. Use local options if these are defined, otherwise use the global ones.
For linear problems, assemble the matrix and try to presolve the linear system.
process_options()
Setup application-specific options.
Subclasses should implement this method as needed.
Returns
app_options [Struct instance] The application options.
class sfepy.homogenization.coefs_base.OnesDim(name, problem, kwargs)

class sfepy.homogenization.coefs_base.PressureEigenvalueProblem(name, problem, kwargs)

Pressure eigenvalue problem solver for time-dependent correctors.
presolve(mtx)
Prepare A^{-1} B^T for the Schur complement.

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solve_pressure_eigenproblem(mtx, eig_problem=None, n_eigs=0, check=False)

G = B*AI*BT or B*AI*BT+D
class sfepy.homogenization.coefs_base.ShapeDim(name, problem, kwargs)

class sfepy.homogenization.coefs_base.ShapeDimDim(name, problem, kwargs)

class sfepy.homogenization.coefs_base.TCorrectorsViaPressureEVP(name, problem, kwargs)

Time correctors via the pressure eigenvalue problem.
compute_correctors(evp, sign, state0, ts, problem=None, vec_g=None)

save(corrs, problem, ts)

setup_equations(equations, problem=None)
Set equations, update boundary conditions and materials.
class sfepy.homogenization.coefs_base.TSTimes(name, problem, kwargs)
Coefficient-like class, returns times of the time stepper.
class sfepy.homogenization.coefs_base.VolumeFractions(name, problem, kwargs)
Coefficient-like class, returns volume fractions of given regions within the whole domain.
sfepy.homogenization.coefs_base.create_ts_coef(cls)
Define a new class with modified call method which accepts time dependent data (correctors).

sfepy.homogenization.coefs_elastic module

class sfepy.homogenization.coefs_elastic.PressureRHSVector(name, problem, kwargs)

class sfepy.homogenization.coefs_elastic.TCorrectorsPressureViaPressureEVP(name, problem,

kwargs)

class sfepy.homogenization.coefs_elastic.TCorrectorsRSViaPressureEVP(name, problem, kwargs)

sfepy.homogenization.coefs_perfusion module

class sfepy.homogenization.coefs_perfusion.CoefRegion(name, problem, kwargs)

get_variables(problem, ir, data)

class sfepy.homogenization.coefs_perfusion.CorrRegion(name, problem, kwargs)

get_variables(ir, data)

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sfepy.homogenization.coefs_phononic module

class sfepy.homogenization.coefs_phononic.AcousticMassLiquidTensor(name, problem, kwargs)

get_coefs(freq)
Get frequency-dependent coefficients.
class sfepy.homogenization.coefs_phononic.AcousticMassTensor(name, problem, kwargs)
The acoustic mass tensor for a given frequency.
Returns
self [AcousticMassTensor instance] This class instance whose evaluate() method computes for
a given frequency the required tensor.

Notes

eigenmomenta, eigs should contain only valid resonances.

evaluate(freq)

get_coefs(freq)
Get frequency-dependent coefficients.
to_file_txt = None
class sfepy.homogenization.coefs_phononic.AppliedLoadTensor(name, problem, kwargs)
The applied load tensor for a given frequency.
Returns
self [AppliedLoadTensor instance] This class instance whose evaluate() method computes for a
given frequency the required tensor.

Notes

eigenmomenta, ueigenmomenta, eigs should contain only valid resonances.

evaluate(freq)

to_file_txt = None
class sfepy.homogenization.coefs_phononic.BandGaps(name, problem, kwargs)
Band gaps detection.
Parameters
eigensolver [str] The name of the eigensolver for mass matrix eigenvalues.
eig_range [(int, int)] The eigenvalues range (squared frequency) to consider.
freq_margins [(float, float)] Margins in percents of initial frequency range given by eig_range
by which the range is increased.
fixed_freq_range [(float, float)] The frequency range to consider. Has precedence over
eig_range and freq_margins.
freq_step [float] The frequency step for tracing, in percent of the frequency range.

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freq_eps [float] The frequency difference smaller than freq_eps is considered zero.
zero_eps [float] The tolerance for finding zeros of mass matrix eigenvalues.
detect_fun [callable] The function for detecting the band gaps. Default is
detect_band_gaps().
log_save_name [str] If not None, the band gaps log is to be saved under the given name.
raw_log_save_name [str] If not None, the raw band gaps log is to be saved under the given
name.
fix_eig_range(n_eigs)

process_options()
Setup application-specific options.
Subclasses should implement this method as needed.
Returns
app_options [Struct instance] The application options.
static save_log(filename, float_format, bg)
Save band gaps, valid flags and eigenfrequencies.
static to_file_txt(fd, float_format, bg)

class sfepy.homogenization.coefs_phononic.ChristoffelAcousticTensor(name, problem, kwargs)

process_options()
Setup application-specific options.
Subclasses should implement this method as needed.
Returns
app_options [Struct instance] The application options.
class sfepy.homogenization.coefs_phononic.DensityVolumeInfo(name, problem, kwargs)
Determine densities of regions specified in region_to_material, and compute average density based on region
volumes.
static to_file_txt(fd, float_format, dv_info)

class sfepy.homogenization.coefs_phononic.Eigenmomenta(name, problem, kwargs)

Eigenmomenta corresponding to eigenvectors.
Parameters
var_name [str] The name of the variable used in the integral.
threshold [float] The threshold under which an eigenmomentum is considered zero.
threshold_is_relative [bool] If True, the threshold is relative w.r.t. max. norm of eigenmo-
menta.
transform [callable, optional] Optional function for transforming the eigenvectors before com-
puting the eigenmomenta.
Returns

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eigenmomenta [Struct] The resulting eigenmomenta. An eigenmomentum above threshold is

marked by the attribute ‘valid’ set to True.
process_options()
Setup application-specific options.
Subclasses should implement this method as needed.
Returns
app_options [Struct instance] The application options.
class sfepy.homogenization.coefs_phononic.PhaseVelocity(name, problem, kwargs)
Compute phase velocity.
process_options()
Setup application-specific options.
Subclasses should implement this method as needed.
Returns
app_options [Struct instance] The application options.
class sfepy.homogenization.coefs_phononic.PolarizationAngles(name, problem, kwargs)
Compute polarization angles, i.e., angles between incident wave direction and wave vectors. Vector length does
not matter - eigenvectors are used directly.
process_options()
Setup application-specific options.
Subclasses should implement this method as needed.
Returns
app_options [Struct instance] The application options.
class sfepy.homogenization.coefs_phononic.SchurEVP(name, problem, kwargs)
Schur complement eigenvalue problem.
post_process(eigs, mtx_s_phi, mtx_dib, problem)

prepare_matrices(problem)
A = K + B^T D^{-1} B
class sfepy.homogenization.coefs_phononic.SimpleEVP(name, problem, kwargs)
Simple eigenvalue problem.
post_process(eigs, mtx_s_phi, data, problem)

prepare_matrices(problem)

process_options()
Setup application-specific options.
Subclasses should implement this method as needed.
Returns
app_options [Struct instance] The application options.
save(eigs, mtx_phi, problem)

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sfepy.homogenization.coefs_phononic.compute_cat_dim_dim(coef, iw_dir)
Christoffel acoustic tensor part of dielectric tensor dimension.
sfepy.homogenization.coefs_phononic.compute_cat_dim_sym(coef, iw_dir)
Christoffel acoustic tensor part of piezo-coupling tensor dimension.
sfepy.homogenization.coefs_phononic.compute_cat_sym_sym(coef, iw_dir)
Christoffel acoustic tensor (part) of elasticity tensor dimension.
sfepy.homogenization.coefs_phononic.compute_eigenmomenta(em_equation, var_name, problem,
eig_vectors, transform=None)
Compute the eigenmomenta corresponding to given eigenvectors.
sfepy.homogenization.coefs_phononic.cut_freq_range(freq_range, eigs, valid, freq_margins, eig_range,
fixed_freq_range, freq_eps)
Cut off masked resonance frequencies. Margins are preserved, like no resonances were cut.
Returns
freq_range [array] The new range of frequencies.
freq_range_margins [array] The range of frequencies with prepended/appended margins equal
to fixed_freq_range if it is not None.
sfepy.homogenization.coefs_phononic.describe_gaps(gaps)

sfepy.homogenization.coefs_phononic.detect_band_gaps(mass, freq_info, opts, gap_kind='normal',

mtx_b=None)
Detect band gaps given solution to eigenproblem (eigs, eig_vectors). Only valid resonance frequencies (e.i. those
for which corresponding eigenmomenta are above a given threshold) are taken into account.

Notes

• make freq_eps relative to ]f0, f1[ size?

sfepy.homogenization.coefs_phononic.find_zero(f0, f1, callback, freq_eps, zero_eps, mode)

For f in ]f0, f1[ find frequency f for which either the smallest (mode = 0) or the largest (mode = 1) eigenvalue of
problem P given by callback is zero.
Returns
flag [0, 1, or 2] The flag, see Notes below.
frequency [float] The found frequency.
eigenvalue [float] The eigenvalue corresponding to the found frequency.

Notes

Meaning of the return value combinations:

mode flag meaning

0, 1 0 eigenvalue -> 0 for f in ]f0, f1[
0 1 f -> f1, smallest eigenvalue < 0
0 2 f -> f0, smallest eigenvalue > 0 and -> -infty
1 1 f -> f1, largest eigenvalue < 0 and -> +infty
1 2 f -> f0, largest eigenvalue > 0

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sfepy.homogenization.coefs_phononic.get_callback(mass, method, mtx_b=None, mode='trace')

Return callback to solve band gaps or dispersion eigenproblem P.

Notes

Find zero callbacks return: eigenvalues

Trace callbacks return: (eigenvalues,)
or (eigenvalues, eigenvectors) (in full (dispoersion) mode)
If mtx_b is None, the problem P is M w = lambda w,
otherwise it is omega^2 M w = eta B w

sfepy.homogenization.coefs_phononic.get_gap_ranges(freq_range, gaps, kinds)

For each (potential) band gap in gaps, return the frequency ranges of its parts according to kinds.
sfepy.homogenization.coefs_phononic.get_log_freqs(f0, f1, df, freq_eps, n_point_min, n_point_max)
Get logging frequencies.
The frequencies get denser towards the interval boundaries.
sfepy.homogenization.coefs_phononic.get_ranges(freq_range, eigs)
Get an eigenvalue range slice and a corresponding initial frequency range within a given frequency range.
sfepy.homogenization.coefs_phononic.split_chunks(indx)
Split index vector to chunks of consecutive numbers.

sfepy.homogenization.convolutions module

class sfepy.homogenization.convolutions.ConvolutionKernel(name, times, kernel, decay=None,

exp_coefs=None, exp_decay=None)
The convolution kernel with exponential synchronous decay approximation approximating the original kernel
represented by the array 𝑐[𝑖], 𝑖 = 0, 1, . . ..

𝑐0 ≡ 𝑐[0] , 𝑐𝑒0 ≡ 𝑐0 𝑐𝑒0 ,

𝑐(𝑡) ≈ 𝑐0 𝑑(𝑡) ≈ 𝑐0 𝑒(𝑡) = 𝑐𝑒0 𝑒𝑛 (𝑡) ,

where 𝑑(0) = 𝑒𝑛 (0) = 1, 𝑑 is the synchronous decay and 𝑒 its exponential approximation, 𝑒 = 𝑐𝑒0 𝑒𝑥𝑝(−𝑐𝑒1 𝑡).
diff_dt(use_exp=False)
The derivative of the kernel w.r.t. time.
get_exp()
Get the exponential synchronous decay kernel approximation.
get_full()
Get the original (full) kernel.
int_dt(use_exp=False)
The integral of the kernel in time.
sfepy.homogenization.convolutions.approximate_exponential(x, y)
Approximate 𝑦 = 𝑓 (𝑥) by 𝑦𝑎 = 𝑐1 𝑒𝑥𝑝(−𝑐2 𝑥).
Initial guess is given by assuming y has already the required exponential form.
sfepy.homogenization.convolutions.compute_mean_decay(coef )
Compute mean decay approximation of a non-scalar fading memory coefficient.

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sfepy.homogenization.convolutions.eval_exponential(coefs, x)

sfepy.homogenization.convolutions.fit_exponential(x, y, return_coefs=False)
Evaluate 𝑦 = 𝑓 (𝑥) after approximating 𝑓 by an exponential.

sfepy.homogenization.engine module

class sfepy.homogenization.engine.CoefVolume(name, problem, kwargs)

class sfepy.homogenization.engine.HomogenizationEngine(problem, options, app_options=None,

volumes=None, output_prefix='he:',
**kwargs)

call(ret_all=False, time_tag='')

static define_volume_coef(coef_info, volumes)

Define volume coefficients and make all other dependent on them.
Parameters
coef_info [dict] The coefficient definitions.
volumes [dict] The definitions of volumes.
Returns
coef_info [dict] The coefficient definitions extended by the volume coefficients.
static process_options(options)
Application options setup. Sets default values for missing non-compulsory options.
set_micro_states(states)

setup_options(app_options=None)

class sfepy.homogenization.engine.HomogenizationWorker

static calculate(mini_app, problem, dependencies, dep_requires, save_names, micro_states, chunk_tab,

mode, proc_id)

static calculate_req(problem, opts, post_process_hook, name, req_info, coef_info, save_names,

dependencies, micro_states, time_tag='', chunk_tab=None, proc_id='0')
Calculate a requirement, i.e. correctors or coefficients.
Parameters
problem [problem] The problem definition related to the microstructure.
opts [struct] The options of the homogenization application.
post_process_hook [function] The postprocessing hook.
name [str] The name of the requirement.
req_info [dict] The definition of correctors.

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coef_info [dict] The definition of homogenized coefficients.

save_names [dict] The dictionary containing names of saved correctors.
dependencies [dict] The dependencies required by the correctors/coefficients.
micro_states [array] The configurations of multiple microstructures.
time_tag [str] The label corresponding to the actual time step and iteration, used in the cor-
rector file names.
chunk_tab [list] In the case of multiprocessing the requirements are divided into several
chunks that are solved in parallel.
proc_id [int] The id number of the processor (core) which is solving the actual chunk.
Returns
val [coefficient/corrector or list of coefficients/correctors] The resulting homogenized coef-
ficients or correctors.
static get_sorted_dependencies(req_info, coef_info, compute_only)
Make corrs and coefs list sorted according to the dependencies.
class sfepy.homogenization.engine.HomogenizationWorkerMulti(num_workers)

static calculate_req_multi(tasks, lock, remaining, numdeps, inverse_deps, problem, opts,

post_process_hook, req_info, coef_info, save_names, dependencies,
micro_states, time_tag, chunk_tab, proc_id)
Calculate a requirement in parallel.
Parameters
tasks [queue] The queue of requirements to be solved.
lock [lock] The multiprocessing lock used to ensure save access to the global variables.
remaining [int] The number of remaining requirements.
numdeps [dict] The number of dependencies for the each requirement.
inverse_deps [dict] The inverse dependencies - which requirements depend on a given one.
For the definition of other parameters see ‘calculate_req’.
static chunk_micro_tasks(num_workers, num_micro, reqs, coefs, chunks_per_worker=1,
store_micro_idxs=[])
Split multiple microproblems into several chunks that can be processed in parallel.
Parameters
num_workers [int] The number of available CPUs.
num_micro [int] The number of microstructures.
reqs [dict] The requirement definitions.
coefs [dict] The coefficient definitions.
chunks_per_worker [int] The number of chunks per one worker.
store_micro_idxs [list of int] The indices of microstructures whose results are to be stored.
Returns
micro_tab [list of slices] The indices of microproblems contained in each chunk.

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new_reqs [dict] The new requirement definitions.

new_coefs [dict] The new coefficient definitions.
static dechunk_reqs_coefs(deps, num_chunks)
Merge the results related to the multiple microproblems.
Parameters
deps [dict] The calculated dependencies.
num_chunks [int] The number of chunks.
Returns
new_deps [dict] The merged dependencies.
static process_reqs_coefs(old, num_workers, store_idxs=[])

class sfepy.homogenization.engine.HomogenizationWorkerMultiMPI(num_workers)

sfepy.homogenization.engine.get_dict_idxval(dict_array, idx)

sfepy.homogenization.engine.insert_sub_reqs(reqs, levels, req_info)

Recursively build all requirements in correct order.

sfepy.homogenization.homogen_app module

class sfepy.homogenization.homogen_app.HomogenizationApp(conf, options, output_prefix, **kwargs)

call(verbose=False, ret_all=None, itime=None, iiter=None)

Call the homogenization engine and compute the homogenized coefficients.
Parameters
verbose [bool] If True, print the computed coefficients.
ret_all [bool or None] If not None, it can be used to override the ‘return_all’ option. If True,
also the dependencies are returned.
time_tag: str The time tag used in file names.
Returns
coefs [Coefficients instance] The homogenized coefficients.
dependencies [dict] The dependencies, if ret_all is True.
get_micro_cache_key(key, icoor, itime)

static process_options(options)
Application options setup. Sets default values for missing non-compulsory options.
setup_macro_data(data)
Setup macroscopic deformation gradient.
setup_options()

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update_micro_states()
Update microstructures state according to the macroscopic data and corrector functions.

sfepy.homogenization.micmac module

sfepy.homogenization.micmac.get_correctors_from_file_hdf5(coefs_filename='coefs.h5',
dump_names=None)

sfepy.homogenization.micmac.get_homog_coefs_linear(ts, coor, mode, micro_filename=None,

regenerate=False, coefs_filename=None,
define_args=None, output_dir=None)

sfepy.homogenization.micmac.get_homog_coefs_nonlinear(ts, coor, mode, macro_data=None,

term=None, problem=None, iteration=None,
define_args=None, output_dir=None,
**kwargs)

sfepy.homogenization.recovery module

sfepy.homogenization.recovery.add_strain_rs(corrs_rs, strain, vu, dim, iel, out=None)

sfepy.homogenization.recovery.add_stress_p(out, pb, integral, region, vp, data)

sfepy.homogenization.recovery.combine_scalar_grad(corrs, grad, vn, ii, shift_coors=None)

𝜂𝑘 𝜕𝑘𝑥 𝑝

or

(𝑦𝑘 + 𝜂𝑘 )𝜕𝑘𝑥 𝑝

sfepy.homogenization.recovery.compute_mac_stress_part(pb, integral, region, material, vu, mac_strain)

sfepy.homogenization.recovery.compute_micro_u(corrs, strain, vu, dim, out=None)

Micro displacements.

𝑢1 = 𝜒𝑖𝑗 𝑒𝑥𝑖𝑗 (𝑢0 )

sfepy.homogenization.recovery.compute_p_corr_steady(corrs_pressure, pressure, vp, iel)

̃︀𝑃 𝑝
𝜋

sfepy.homogenization.recovery.compute_p_corr_time(corrs_rs, dstrains, corrs_pressure, pressures, vdp,

dim, iel, ts)

∑︁ ∫︁ 𝑡 ∫︁ 𝑡
d 𝑖𝑗 d d 𝑃
̃︀ (𝑡 − 𝑠) 𝑒𝑖𝑗 (𝑢(𝑠)) 𝑑𝑠 +
𝜋 ̃︀ (𝑡 − 𝑠) 𝑝(𝑠) 𝑑𝑠
𝜋
𝑖𝑗 0 d𝑡 d𝑠 0 d𝑡

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sfepy.homogenization.recovery.compute_p_from_macro(p_grad, coor, iel, centre=None, extdim=0)

Macro-induced pressure.

𝜕𝑗𝑥 𝑝 (𝑦𝑗 − 𝑦𝑗𝑐 )

sfepy.homogenization.recovery.compute_stress_strain_u(pb, integral, region, material, vu, data)

sfepy.homogenization.recovery.compute_u_corr_steady(corrs_rs, strain, vu, dim, iel)

∑︁
𝜔 𝑖𝑗 𝑒𝑖𝑗 (𝑢)
𝑖𝑗

Notes

• iel = element number

sfepy.homogenization.recovery.compute_u_corr_time(corrs_rs, dstrains, corrs_pressure, pressures, vu,

dim, iel, ts)

∑︁ [︂∫︁ 𝑡 ]︂ ∫︁ 𝑡
d
𝜔 𝑖𝑗 (𝑡 − 𝑠) 𝑒𝑖𝑗 (𝑢(𝑠)) 𝑑𝑠 + ̃︀ 𝑃 (𝑡 − 𝑠) 𝑝(𝑠) 𝑑𝑠
𝜔
𝑖𝑗 0 d𝑠 0

sfepy.homogenization.recovery.compute_u_from_macro(strain, coor, iel, centre=None)

Macro-induced displacements.

𝑒𝑥𝑖𝑗 (𝑢) (𝑦𝑗 − 𝑦𝑗𝑐 )

sfepy.homogenization.recovery.convolve_field_scalar(fvars, pvars, iel, ts)

∫︁ 𝑡
𝑓 (𝑡 − 𝑠)𝑝(𝑠)𝑑𝑠
0

Notes

• t is given by step
• f: fvars scalar field variables, defined in a micro domain, have shape [step][fmf dims]
• p: pvars scalar point variables, a scalar in a point of macro-domain, FMField style have shape [n_step][var
dims]

sfepy.homogenization.recovery.convolve_field_sym_tensor(fvars, pvars, var_name, dim, iel, ts)

∫︁ 𝑡
𝑓 𝑖𝑗 (𝑡 − 𝑠)𝑝𝑖𝑗 (𝑠)𝑑𝑠
0

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Notes

• t is given by step
• f: fvars field variables, defined in a micro domain, have shape [step][fmf dims]
• p: pvars sym. tensor point variables, a scalar in a point of macro-domain, FMField style, have shape [dim,
dim][var_name][n_step][var dims]

sfepy.homogenization.recovery.destroy_pool()

sfepy.homogenization.recovery.get_output_suffix(iel, ts, naming_scheme, format, output_format)

sfepy.homogenization.recovery.recover_bones(problem, micro_problem, region, eps0, ts, strain, dstrains,

p_grad, pressures, corrs_permeability, corrs_rs,
corrs_time_rs, corrs_pressure, corrs_time_pressure,
var_names, naming_scheme='step_iel')

Notes

• note that

̃︀𝑃
𝜋

is in corrs_pressure -> from time correctors only ‘u’, ‘dp’ are needed.

sfepy.homogenization.recovery.recover_micro_hook(micro_filename, region, macro,

naming_scheme='step_iel', recovery_file_tag='',
define_args=None, output_dir=None,
verbose=False)

sfepy.homogenization.recovery.recover_micro_hook_eps(micro_filename, region, eval_var,

nodal_values, const_values, eps0,
recovery_file_tag='', define_args=None,
output_dir=None, verbose=False)

sfepy.homogenization.recovery.recover_micro_hook_init(micro_filename, define_args,
output_dir=None)

sfepy.homogenization.recovery.recover_paraflow(problem, micro_problem, region, ts, strain, dstrains,

pressures1, pressures2, corrs_rs, corrs_time_rs,
corrs_alpha1, corrs_time_alpha1, corrs_alpha2,
corrs_time_alpha2, var_names,
naming_scheme='step_iel')

sfepy.homogenization.recovery.save_recovery_region(mac_pb, rname, filename=None)

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sfepy.homogenization.utils module

sfepy.homogenization.utils.build_op_pi(var, ir, ic)

Pi_i^{rs} = y_s delta_{ir} for r = ir, s = ic.
sfepy.homogenization.utils.coor_to_sym(ir, ic, dim)

sfepy.homogenization.utils.create_pis(problem, var_name)
Pi_i^{rs} = y_s delta_{ir}, ul{y} in Y coordinates.
sfepy.homogenization.utils.create_scalar_pis(problem, var_name)
Pi^k = y_k, ul{y} in Y coordinates.
sfepy.homogenization.utils.define_box_regions(dim, lbn, rtf=None, eps=0.001, kind='facet')
Define sides and corner regions for a box aligned with coordinate axes.
Parameters
dim [int] Space dimension
lbn [tuple] Left bottom near point coordinates if rtf is not None. If rtf is None, lbn are the
(positive) distances from the origin.
rtf [tuple] Right top far point coordinates.
eps [float] A parameter, that should be smaller than the smallest mesh node distance.
kind [bool, optional] The region kind.
Returns
regions [dict] The box regions.
sfepy.homogenization.utils.get_box_volume(dim, lbn, rtf=None)
Volume of a box aligned with coordinate axes.
Parameters:
dim [int] Space dimension
lbn [tuple] Left bottom near point coordinates if rtf is not None. If rtf is None, lbn are the (positive) distances
from the origin.
rtf [tuple] Right top far point coordinates.
Returns:
volume [float] The box volume.
sfepy.homogenization.utils.get_lattice_volume(axes)
Volume of a periodic cell in a rectangular 3D (or 2D) lattice.
Parameters
axes [array] The array with the periodic cell axes 𝑎1 , . . . , 𝑎3 as rows.
Returns
volume [float] The periodic cell volume 𝑉 = (𝑎1 × 𝑎2 ) · 𝑎3 . In 2D 𝑉 = |(𝑎1 × 𝑎2 )| with zeros
as the third components of vectors 𝑎1 , 𝑎2 .
sfepy.homogenization.utils.get_volume(problem, field_name, region_name, quad_order=1)
Get volume of a given region using integration defined by a given field. Both the region and the field have to be
defined in problem.

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sfepy.homogenization.utils.integrate_in_time(coef, ts, scheme='forward')

Forward difference or trapezoidal rule. ‘ts’ can be anything with ‘times’ attribute.
sfepy.homogenization.utils.interp_conv_mat(mat, ts, tdiff )

sfepy.homogenization.utils.iter_nonsym(dim)

sfepy.homogenization.utils.iter_sym(dim)

sfepy.homogenization.utils.rm_multi(s)

sfepy.homogenization.utils.set_nonlin_states(variables, nl_state, problem)

Setup reference state for nonlinear homogenization
Parameters
variables [dict] All problem variables
nl_state [reference state]
problem [problem description]

sfepy.linalg package

sfepy.linalg.check_derivatives module

Utilities for checking derivatives of functions.

sfepy.linalg.check_derivatives.check_fx(x0, fx, fx_args, dfx, dfx_args=None, delta=1e-05)
Check derivatives of a (vectorized) scalar function of a scalar variable.
sfepy.linalg.check_derivatives.check_vfvx(x0, fx, fx_args, dfx, dfx_args=None, delta=1e-05)
Check derivatives of a (vectorized) vector or scalar function of a vector variable.

sfepy.linalg.eigen module

sfepy.linalg.eigen.cg_eigs(mtx, rhs=None, precond=None, i_max=None, eps_r=1e-10, shift=None,

select_indices=None, verbose=False, report_step=10)
Make several iterations of the conjugate gradients and estimate so the eigenvalues of a (sparse SPD) matrix
(Lanczos algorithm).
Parameters
mtx [spmatrix or array] The sparse matrix 𝐴.
precond [spmatrix or array, optional] The preconditioner matrix. Any object that can be multi-
plied by vector can be passed.
i_max [int] The maximum number of the Lanczos algorithm iterations.
eps_r [float] The relative stopping tolerance.
shift [float, optional] Eigenvalue shift for non-SPD matrices. If negative, the shift is computed
as |𝑠ℎ𝑖𝑓 𝑡|||𝐴||∞ .
select_indices [(min, max), optional] If given, computed only the eigenvalues with indices min
<= i <= max.

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verbose [bool] Verbosity control.

report_step [int] If verbose is True, report in every report_step-th step.
Returns
vec [array] The approximate solution to the linear system.
n_it [int] The number of CG iterations used.
norm_rs [array] Convergence history of residual norms.
eigs [array] The approximate eigenvalues sorted in ascending order.
sfepy.linalg.eigen.sym_tri_eigen(diags, select_indices=None)
Compute eigenvalues of a symmetric tridiagonal matrix using scipy.linalg.eigvals_banded().

sfepy.linalg.geometry module

sfepy.linalg.geometry.barycentric_coors(coors, s_coors)
Get barycentric (area in 2D, volume in 3D) coordinates of points with coordinates coors w.r.t. the simplex given
by s_coors.
Returns
bc [array] The barycentric coordinates. Then reference element coordinates xi = dot(bc.T,
ref_coors).
sfepy.linalg.geometry.flag_points_in_polygon2d(polygon, coors)
Test if points are in a 2D polygon.
Parameters
polygon [array, (:, 2)] The polygon coordinates.
coors: array, (:, 2) The coordinates of points.
Returns
flag [bool array] The flag that is True for points that are in the polygon.

Notes

This is a semi-vectorized version of [1].

[1] PNPOLY - Point Inclusion in Polygon Test, W. Randolph Franklin (WRF)
sfepy.linalg.geometry.get_coors_in_ball(coors, centre, radius, inside=True)
Return indices of coordinates inside or outside a ball given by centre and radius.

Notes

All float comparisons are done using <= or >= operators, i.e. the points on the boundaries are taken into account.
sfepy.linalg.geometry.get_coors_in_tube(coors, centre, axis, radius_in, radius_out, length,
inside_radii=True)
Return indices of coordinates inside a tube given by centre, axis vector, inner and outer radii and length.
Parameters
inside_radii [bool, optional] If False, select points outside the radii, but within the tube length.

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Notes

All float comparisons are done using <= or >= operators, i.e. the points on the boundaries are taken into account.
sfepy.linalg.geometry.get_face_areas(faces, coors)
Get areas of planar convex faces in 2D and 3D.
Parameters
faces [array, shape (n, m)] The indices of n faces with m vertices into coors.
coors [array] The coordinates of face vertices.
Returns
areas [array] The areas of the faces.
sfepy.linalg.geometry.get_perpendiculars(vec)
For a given vector, get a unit vector perpendicular to it in 2D, or get two mutually perpendicular unit vectors
perpendicular to it in 3D.
sfepy.linalg.geometry.get_simplex_circumcentres(coors, force_inside_eps=None)
Compute the circumcentres of n_s simplices in 1D, 2D and 3D.
Parameters
coors [array] The coordinates of the simplices with n_v vertices given in an array of shape (n_s,
n_v, dim), where dim is the space dimension and 2 <= n_v <= (dim + 1).
force_inside_eps [float, optional] If not None, move the circumcentres that are outside of their
simplices or closer to their boundary then force_inside_eps so that they are inside the sim-
plices at the distance given by force_inside_eps. It is ignored for edges.
Returns
centres [array] The circumcentre coordinates as an array of shape (n_s, dim).
sfepy.linalg.geometry.get_simplex_volumes(cells, coors)
Get volumes of simplices in nD.
Parameters
cells [array, shape (n, d)] The indices of n simplices with d vertices into coors.
coors [array] The coordinates of simplex vertices.
Returns
volumes [array] The volumes of the simplices.
sfepy.linalg.geometry.inverse_element_mapping(coors, e_coors, eval_base, ref_coors,
suppress_errors=False)
Given spatial element coordinates, find the inverse mapping for points with coordinats X = X(xi), i.e. xi = xi(X).
Returns
xi [array] The reference element coordinates.
sfepy.linalg.geometry.make_axis_rotation_matrix(direction, angle)
Create a rotation matrix 𝑅 corresponding to the rotation around a general axis 𝑑 by a specified angle 𝛼.

𝑅 = 𝑑𝑑𝑇 + cos(𝛼)(𝐼 − 𝑑𝑑𝑇 ) + sin(𝛼) skew(𝑑)

Parameters
direction [array] The rotation axis direction vector 𝑑.

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angle [float] The rotation angle 𝛼.

Returns
mtx [array] The rotation matrix 𝑅.

Notes

The matrix follows the right hand rule: if the right hand thumb points along the axis vector 𝑑 the fingers show
the positive angle rotation direction.

Examples

Make transformation matrix for rotation of coordinate system by 90 degrees around ‘z’ axis.

>>> mtx = make_axis_rotation_matrix([0., 0., 1.], nm.pi/2)

>>> mtx
array([[ 0., 1., 0.],
[-1., 0., 0.],
[ 0., 0., 1.]])

Coordinates of vector [1, 0, 0]𝑇 w.r.t. the original system in the rotated system. (Or rotation of the vector by -90
degrees in the original system.)

>>> nm.dot(mtx, [1., 0., 0.])

>>> array([ 0., -1., 0.])

Coordinates of vector [1, 0, 0]𝑇 w.r.t. the rotated system in the original system. (Or rotation of the vector by +90
degrees in the original system.)

>>> nm.dot(mtx.T, [1., 0., 0.])

>>> array([ 0., 1., 0.])

sfepy.linalg.geometry.points_in_simplex(coors, s_coors, eps=1e-08)

Test if points with coordinates coors are in the simplex given by s_coors.
sfepy.linalg.geometry.rotation_matrix2d(angle)
Construct a 2D (plane) rotation matrix corresponding to angle.
sfepy.linalg.geometry.transform_bar_to_space_coors(bar_coors, coors)
Transform barycentric coordinates bar_coors within simplices with vertex coordinates coors to space coordi-
nates.

sfepy.linalg.sparse module

Some sparse matrix utilities missing in scipy.

sfepy.linalg.sparse.compose_sparse(blocks, row_sizes=None, col_sizes=None)
Compose sparse matrices into a global sparse matrix.
Parameters
blocks [sequence of sequences] The sequence of sequences of equal lengths - the individual
sparse matrix blocks. The integer 0 can be used to mark an all-zero block, if its size can be
determined from the other blocks.

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row_sizes [sequence, optional] The required row sizes of the blocks. It can be either a sequence
of non-negative integers, or a sequence of slices with non-negative limits. In any case the
sizes have to be compatible with the true block sizes. This allows to extend the matrix shape
as needed and to specify sizes of all-zero blocks.
col_sizes [sequence, optional] The required column sizes of the blocks. See row_sizes.
Returns
mtx [coo_matrix] The sparse matrix (COO format) composed from the given blocks.

Examples

Stokes-like problem matrix.

>>> import scipy.sparse as sp

>>> A = sp.csr_matrix([[1, 0], [0, 1]])
>>> B = sp.coo_matrix([[1, 1]])
>>> K = compose_sparse([[A, B.T], [B, 0]])
>>> print K.todense()
[[1 0 1]
[0 1 1]
[1 1 0]]

sfepy.linalg.sparse.infinity_norm(mtx)
Infinity norm of a sparse matrix (maximum absolute row sum).
Parameters
mtx [spmatrix or array] The sparse matrix.
Returns
norm [float] Infinity norm of the matrix.
See also:

scipy.linalg.norm dense matrix norms

Notes

• This serves as an upper bound on spectral radius.

• CSR and CSC avoid copying indices and indptr arrays.
• inspired by PyAMG

sfepy.linalg.sparse.insert_sparse_to_csr(mtx1, mtx2, irs, ics)

Insert a sparse matrix mtx2 into a CSR sparse matrix mtx1 at rows irs and columns ics. The submatrix
mtx1[irs,ics] must already be preallocated and have the same structure as mtx2.
sfepy.linalg.sparse.save_sparse_txt(filename, mtx, fmt='%d %d %f\n')
Save a CSR/CSC sparse matrix into a text file

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sfepy.linalg.sympy_operators module

sfepy.linalg.sympy_operators.boundary(f, variables)

sfepy.linalg.sympy_operators.default_space_variables(variables)

sfepy.linalg.sympy_operators.div(field, variables=None)

sfepy.linalg.sympy_operators.grad(f, variables=None)

sfepy.linalg.sympy_operators.grad_v(f, variables=None)

sfepy.linalg.sympy_operators.laplace(f, variables=None)

sfepy.linalg.sympy_operators.set_dim(dim)

sfepy.linalg.utils module

class sfepy.linalg.utils.MatrixAction(**kwargs)

static from_array(arr)

static from_function(fun, expected_shape, dtype)

to_array()

sfepy.linalg.utils.apply_to_sequence(seq, fun, ndim, out_item_shape)

Applies function fun() to each item of the sequence seq. An item corresponds to the last ndim dimensions of seq.
Parameters
seq [array] The sequence array with shape (n_1, . . . , n_r, m_1, . . . , m_{ndim}).
fun [function] The function taking an array argument of shape of length ndim.
ndim [int] The number of dimensions of an item in seq.
out_item_shape [tuple] The shape an output item.
Returns
out [array] The resulting array of shape (n_1, . . . , n_r) + out_item_shape. The out_item_shape
must be compatible with the fun.
sfepy.linalg.utils.argsort_rows(seq)
Returns an index array that sorts the sequence seq. Works along rows if seq is two-dimensional.
sfepy.linalg.utils.assemble1d(ar_out, indx, ar_in)
Perform ar_out[indx] += ar_in, where items of ar_in corresponding to duplicate indices in indx are summed
together.

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sfepy.linalg.utils.combine(seqs)
Same as cycle, but with general sequences.
Example:
In [19]: c = combine( [[‘a’, ‘x’], [‘b’, ‘c’], [‘dd’]] )
In [20]: list(c) Out[20]: [[‘a’, ‘b’, ‘dd’], [‘a’, ‘c’, ‘dd’], [‘x’, ‘b’, ‘dd’], [‘x’, ‘c’, ‘dd’]]
sfepy.linalg.utils.cycle(bounds)
Cycles through all combinations of bounds, returns a generator.
More specifically, let bounds=[a, b, c, . . . ], so cycle returns all combinations of lists [0<=i<a, 0<=j<b, 0<=k<c,
. . . ] for all i,j,k,. . .
Examples: In [9]: list(cycle([3, 2])) Out[9]: [[0, 0], [0, 1], [1, 0], [1, 1], [2, 0], [2, 1]]
In [14]: list(cycle([3, 4])) [[0, 0], [0, 1], [0, 2], [0, 3], [1, 0], [1, 1], [1, 2], [1, 3], [2, 0], [2, 1], [2, 2], [2, 3]]
sfepy.linalg.utils.dets_fast(a)
Fast determinant calculation of 3-dimensional array.
Parameters
a [array] The input array with shape (m, n, n).
Returns
out [array] The output array with shape (m,): out[i] = det(a[i, :, :]).
sfepy.linalg.utils.dot_sequences(mtx, vec, mode='AB')
Computes dot product for each pair of items in the two sequences.
Equivalent to

>>> out = nm.empty((vec.shape[0], mtx.shape[1], vec.shape[2]),

>>> dtype=vec.dtype)
>>> for ir in range(mtx.shape[0]):
>>> out[ir] = nm.dot(mtx[ir], vec[ir])

Parameters
mtx [array] The array of matrices with shape (n_item, m, n).
vec [array] The array of vectors with shape (n_item, a) or matrices with shape (n_item, a, b).
mode [one of ‘AB’, ‘ATB’, ‘ABT’, ‘ATBT’] The mode of the dot product - the corresponding
axes are dotted together:
‘AB’ : a = n ‘ATB’ : a = m ‘ABT’ : b = n (*) ‘ATBT’ : b = m (*)
(*) The ‘BT’ part is ignored for the vector second argument.
Returns
out [array] The resulting array.

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Notes

Uses numpy.matmul() via the @ operator.

sfepy.linalg.utils.insert_strided_axis(ar, axis, length)
Insert a new axis of given length into an array using numpy stride tricks, i.e. no copy is made.
Parameters
ar [array] The input array.
axis [int] The axis before which the new axis will be inserted.
length [int] The length of the inserted axis.
Returns
out [array] The output array sharing data with ar.

Examples

>>> import numpy as nm

>>> from sfepy.linalg import insert_strided_axis
>>> ar = nm.random.rand(2, 1, 2)
>>> ar
array([[[ 0.18905119, 0.44552425]],

[[ 0.78593989, 0.71852473]]])

>>> ar.shape
(2, 1, 2)
>>> ar2 = insert_strided_axis(ar, 1, 3)
>>> ar2
array([[[[ 0.18905119, 0.44552425]],

[[ 0.18905119, 0.44552425]],
[[ 0.18905119, 0.44552425]]],
[[[ 0.78593989, 0.71852473]],
[[ 0.78593989, 0.71852473]],
[[ 0.78593989, 0.71852473]]]])

>>> ar2.shape
(2, 3, 1, 2)

sfepy.linalg.utils.map_permutations(seq1, seq2, check_same_items=False)

Returns an index array imap such that seq1[imap] == seq2, if both sequences have the same items - this is not
checked by default!
In other words, finds the indices of items of seq2 in seq1.
sfepy.linalg.utils.max_diff_csr(mtx1, mtx2)

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sfepy.linalg.utils.mini_newton(fun, x0, dfun, i_max=100, eps=1e-08)

sfepy.linalg.utils.norm_l2_along_axis(ar, axis=1, n_item=None, squared=False)

Compute l2 norm of rows (axis=1) or columns (axis=0) of a 2D array.
n_item . . . use only the first n_item columns/rows squared . . . if True, return the norm squared
sfepy.linalg.utils.normalize_vectors(vecs, eps=1e-08)
Normalize an array of vectors in place.
Parameters
vecs [array] The 2D array of vectors in rows.
eps [float] The tolerance for considering a vector to have zero norm. Such vectors are left un-
changed.
sfepy.linalg.utils.output_array_stats(ar, name, verbose=True)

sfepy.linalg.utils.permutations(seq)

sfepy.linalg.utils.print_array_info(ar)
Print array shape and other basic information.
sfepy.linalg.utils.split_range(n_item, step)

sfepy.linalg.utils.unique_rows(ar, return_index=False, return_inverse=False)

Return unique rows of a two-dimensional array ar. The arguments follow numpy.unique().

sfepy.mechanics package

sfepy.mechanics.contact_bodies module

class sfepy.mechanics.contact_bodies.ContactPlane(anchor, normal, bounds)

get_distance(points)

mask_points(points)

class sfepy.mechanics.contact_bodies.ContactSphere(centre, radius)

get_distance(points)
Get the penetration distance and normals of points w.r.t. the sphere surface.
Returns
d [array] The penetration distance.
normals [array] The normals from the points to the sphere centre.
mask_points(points, eps)

sfepy.mechanics.contact_bodies.plot_points(ax, points, marker, **kwargs)

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sfepy.mechanics.contact_bodies.plot_polygon(ax, polygon)

sfepy.mechanics.elastic_constants module

sfepy.mechanics.matcoefs module

Conversion of material parameters and other utilities.

class sfepy.mechanics.matcoefs.ElasticConstants(young=None, poisson=None, bulk=None, lam=None,
mu=None, p_wave=None,
_regenerate_relations=False)
Conversion formulas for various groups of elastic constants. The elastic constants supported are:
• 𝐸 : Young’s modulus
• 𝜈 : Poisson’s ratio
• 𝐾 : bulk modulus
• 𝜆 : Lamé’s first parameter
• 𝜇, 𝐺 : shear modulus, Lamé’s second parameter
• 𝑀 : P-wave modulus, longitudinal wave modulus
The elastic constants are referred to by the following keyword arguments: young, poisson, bulk, lam, mu, p_wave.
Exactly two of them must be provided to the __init__() method.

Examples

• basic usage:

>>> from sfepy.mechanics.matcoefs import ElasticConstants

>>> ec = ElasticConstants(lam=1.0, mu=1.5)
>>> ec.young
3.6000000000000001
>>> ec.poisson
0.20000000000000001
>>> ec.bulk
2.0
>>> ec.p_wave
4.0
>>> ec.get(['bulk', 'lam', 'mu', 'young', 'poisson', 'p_wave'])
[2.0, 1.0, 1.5, 3.6000000000000001, 0.20000000000000001, 4.0]

• reinitialize existing instance:

>>> ec.init(p_wave=4.0, bulk=2.0)

>>> ec.get(['bulk', 'lam', 'mu', 'young', 'poisson', 'p_wave'])
[2.0, 1.0, 1.5, 3.6000000000000001, 0.20000000000000001, 4.0]

get(names)
Get the named elastic constants.

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init(young=None, poisson=None, bulk=None, lam=None, mu=None, p_wave=None)

Set exactly two of the elastic constants, and compute the remaining. (Re)-initializes the existing instance
of ElasticConstants.
class sfepy.mechanics.matcoefs.TransformToPlane(iplane=None)
Transformations of constitutive law coefficients of 3D problems to 2D.
tensor_plane_stress(c3=None, d3=None, b3=None)
Transforms all coefficients of the piezoelectric constitutive law from 3D to plane stress problem in 2D:
strain/stress ordering: 11 22 33 12 13 23. If d3 is None, uses only the stiffness tensor c3.
Parameters
c3 [array] The stiffness tensor.
d3 [array] The dielectric tensor.
b3 [array] The piezoelectric coupling tensor.
sfepy.mechanics.matcoefs.bulk_from_lame(lam, mu)
Compute bulk modulus from Lamé parameters.
2
𝛾 =𝜆+ 𝜇
3

sfepy.mechanics.matcoefs.bulk_from_youngpoisson(young, poisson, plane='strain')

Compute bulk modulus corresponding to Young’s modulus and Poisson’s ratio.
sfepy.mechanics.matcoefs.lame_from_stiffness(stiffness, plane='strain')
Compute Lamé parameters from an isotropic stiffness tensor.
sfepy.mechanics.matcoefs.lame_from_youngpoisson(young, poisson, plane='strain')
Compute Lamé parameters from Young’s modulus and Poisson’s ratio.
The relationship between Lamé parameters and Young’s modulus, Poisson’s ratio (see [1],[2]):
𝜈𝐸 𝐸
𝜆= , 𝜇=
(1 + 𝜈)(1 − 2𝜈) 2(1 + 𝜈)

The plain stress hypothesis:

¯= 2𝜆𝜇
𝜆
𝜆 + 2𝜇
[1] I.S. Sokolnikoff: Mathematical Theory of Elasticity. New York, 1956.
[2] T.J.R. Hughes: The Finite Element Method, Linear Static and Dynamic Finite Element Analysis. New Jersey,
1987.
sfepy.mechanics.matcoefs.stiffness_from_lame(dim, lam, mu)
Compute stiffness tensor corresponding to Lamé parameters.
⎡ ⎤
𝜆 + 2𝜇 𝜆 0
𝐷(2𝐷) = ⎣ 𝜆 𝜆 + 2𝜇 0⎦
0 0 𝜇
⎡ ⎤
𝜆 + 2𝜇 𝜆 𝜆 0 0 0
⎢ 𝜆 𝜆 + 2𝜇 𝜆 0 0 0⎥
⎢ ⎥
⎢ 𝜆 𝜆 𝜆 + 2𝜇 0 0 0⎥
𝐷(3𝐷) = ⎢⎢ 0
⎥
⎢ 0 0 𝜇 0 0⎥⎥
⎣ 0 0 0 0 𝜇 0⎦
0 0 0 0 0 𝜇

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sfepy.mechanics.matcoefs.stiffness_from_lame_mixed(dim, lam, mu)

Compute stiffness tensor corresponding to Lamé parameters for mixed formulation.
⎡ ⎤
𝜆̃︀ + 2𝜇 𝜆
̃︀ 0
𝐷(2𝐷) =⎣ 𝜆 ̃︀ 𝜆
̃︀ + 2𝜇 0 ⎦
0 0 𝜇
⎡̃︀ ⎤
𝜆 + 2𝜇 𝜆
̃︀ 𝜆
̃︀ 0 0 0
⎢ 𝜆 ̃︀ 𝜆
̃︀ + 2𝜇 𝜆
̃︀ 0 0 0⎥
⎢ ⎥
⎢ 𝜆 𝜆 𝜆 + 2𝜇 0 0 0 ⎥
𝐷(3𝐷) =⎢
⎢ ̃︀ ̃︀ ̃︀ ⎥
⎢ 0 0 0 𝜇 0 0⎥⎥
⎣ 0 0 0 0 𝜇 0⎦
0 0 0 0 0 𝜇
where

̃︀ = − 2 𝜇
𝜆
3

sfepy.mechanics.matcoefs.stiffness_from_youngpoisson(dim, young, poisson, plane='strain')

Compute stiffness tensor corresponding to Young’s modulus and Poisson’s ratio.
sfepy.mechanics.matcoefs.stiffness_from_youngpoisson_mixed(dim, young, poisson, plane='strain')
Compute stiffness tensor corresponding to Young’s modulus and Poisson’s ratio for mixed formulation.
sfepy.mechanics.matcoefs.youngpoisson_from_stiffness(stiffness, plane='strain')
Compute Young’s modulus and Poisson’s ratio from an isotropic stiffness tensor.

sfepy.mechanics.membranes module

sfepy.mechanics.membranes.create_mapping(coors, gel, order)

Create mapping from transformed (in x-y plane) element faces to reference element faces.
Parameters
coors [array] The transformed coordinates of element nodes, shape (n_el, n_ep, dim). The func-
tion verifies that the all z components are zero.
gel [GeometryElement instance] The geometry element corresponding to the faces.
order [int] The polynomial order of the mapping.
Returns
mapping [VolumeMapping instance] The reference element face mapping.
sfepy.mechanics.membranes.create_transformation_matrix(coors)
Create a transposed coordinate transformation matrix, that transforms 3D coordinates of element face nodes so
that the transformed nodes are in the x-y plane. The rotation is performed w.r.t. the first node of each face.
Parameters
coors [array] The coordinates of element nodes, shape (n_el, n_ep, dim).
Returns
mtx_t [array] The transposed transformation matrix 𝑇 , i.e. 𝑋𝑖𝑛𝑝𝑙𝑎𝑛𝑒 = 𝑇 𝑇 𝑋3𝐷 .

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Notes

𝑇 = [𝑡1 , 𝑡2 , 𝑛], where 𝑡1 , 𝑡2 , are unit in-plane (column) vectors and 𝑛 is the unit normal vector, all mutually
orthonormal.
sfepy.mechanics.membranes.describe_deformation(el_disps, bfg)
Describe deformation of a thin incompressible 2D membrane in 3D space, composed of flat finite element faces.
The coordinate system of each element (face), i.e. the membrane mid-surface, should coincide with the x, y axes
of the x-y plane.
Parameters
el_disps [array] The displacements of element nodes, shape (n_el, n_ep, dim).
bfg [array] The in-plane base function gradients, shape (n_el, n_qp, dim-1, n_ep).
Returns
mtx_c ; array The in-plane right Cauchy-Green deformation tensor 𝐶𝑖𝑗 , 𝑖, 𝑗 = 1, 2.
c33 [array] The component 𝐶33 computed from the incompressibility condition.
mtx_b [array] The discrete Green strain variation operator.
sfepy.mechanics.membranes.describe_geometry(field, region, integral)
Describe membrane geometry in a given region.
Parameters
field [Field instance] The field defining the FE approximation.
region [Region instance] The surface region to describe.
integral [Integral instance] The integral defining the quadrature points.
Returns
mtx_t [array] The transposed transformation matrix 𝑇, see
create_transformation_matrix().
membrane_geo [CMapping instance] The mapping from transformed elements to a reference
elements.
sfepy.mechanics.membranes.get_green_strain_sym3d(mtx_c, c33)
Get the 3D Green strain tensor in symmetric storage.
Parameters
mtx_c ; array The in-plane right Cauchy-Green deformation tensor 𝐶𝑖𝑗 , 𝑖, 𝑗 = 1, 2, shape (n_el,
n_qp, dim-1, dim-1).
c33 [array] The component 𝐶33 computed from the incompressibility condition, shape (n_el,
n_qp).
Returns
mtx_e [array] The membrane Green strain 𝐸𝑖𝑗 = 21 (𝐶𝑖𝑗 ) − 𝛿𝑖𝑗 , symmetric storage: items (11,
22, 33, 12, 13, 23), shape (n_el, n_qp, sym, 1).
sfepy.mechanics.membranes.get_invariants(mtx_c, c33)
Get the first and second invariants of the right Cauchy-Green deformation tensor describing deformation of an
incompressible membrane.
Parameters

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mtx_c ; array The in-plane right Cauchy-Green deformation tensor 𝐶𝑖𝑗 , 𝑖, 𝑗 = 1, 2, shape (n_el,
n_qp, dim-1, dim-1).
c33 [array] The component 𝐶33 computed from the incompressibility condition, shape (n_el,
n_qp).
Returns
i1 [array] The first invariant of 𝐶𝑖𝑗 .
i2 [array] The second invariant of 𝐶𝑖𝑗 .
sfepy.mechanics.membranes.get_tangent_stress_matrix(stress, bfg)
Get the tangent stress matrix of a thin incompressible 2D membrane in 3D space, given a stress.
Parameters
stress [array] The components 11, 22, 12 of the second Piola-Kirchhoff stress tensor, shape
(n_el, n_qp, 3, 1).
bfg [array] The in-plane base function gradients, shape (n_el, n_qp, dim-1, n_ep).
Returns
mtx [array] The tangent stress matrix, shape (n_el, n_qp, dim*n_ep, dim*n_ep).
sfepy.mechanics.membranes.transform_asm_matrices(out, mtx_t)
Transform matrix assembling contributions to global coordinate system, one node at a time.
Parameters
out [array] The array of matrices, transformed in-place.
mtx_t [array] The transposed transformation matrix 𝑇, see
create_transformation_matrix().
sfepy.mechanics.membranes.transform_asm_vectors(out, mtx_t)
Transform vector assembling contributions to global coordinate system, one node at a time.
Parameters
out [array] The array of vectors, transformed in-place.
mtx_t [array] The transposed transformation matrix 𝑇, see
create_transformation_matrix().

sfepy.mechanics.shell10x module

Functions implementing the shell10x element.

sfepy.mechanics.shell10x.add_eas_dofs(mtx_b, qp_coors, det, det0, dxidx0)
Add additional strain components [Andelfinger and Ramm] (7 parameters to be condensed out).
sfepy.mechanics.shell10x.create_drl_transform(ebs)
Create the transformation matrix for locking of the drilling rotations.
sfepy.mechanics.shell10x.create_elastic_tensor(young, poisson, shear_correction=True)
Create the elastic tensor with the applied shear correction (the default) for the shell10x element.
sfepy.mechanics.shell10x.create_local_bases(coors)
Create local orthonormal bases in each vertex of quadrilateral cells.
Parameters
coors [array] The coordinates of cell vertices, shape (n_el, 4, 3).

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Returns
ebs [array] The local bases, shape (n_el, 4, 3, 3). The basis vectors are rows of the (. . . , 3, 3)
blocks.
sfepy.mechanics.shell10x.create_rotation_ops(ebs)
Create operators associated to rotation DOFs.
Parameters
ebs [array] The local bases, shape (n_el, 4, 3, 3).
Returns
rops [array] The rotation operators, shape (n_el, 4, 3, 3).
sfepy.mechanics.shell10x.create_strain_matrix(bfgm, dxidx, dsg)
Create the strain operator matrix.
sfepy.mechanics.shell10x.create_strain_transform(mtx_ts)
Create strain tensor transformation matrices, given coordinate transformation matrices.

Notes

Expresses 𝑇 𝐸𝑇 𝑇 in terms of symmetrix storage as 𝑄𝑒, with the ordering of components: 𝑒 =

[𝑒11 , 𝑒22 , 𝑒33 , 2𝑒12 , 2𝑒13 , 2𝑒23 ].
sfepy.mechanics.shell10x.create_transformation_matrix(coors)
Create a transposed coordinate transformation matrix, that transforms 3D coordinates of quadrilateral cell ver-
tices so that the transformed vertices of a plane cell are in the 𝑥 − 𝑦 plane. The rotation is performed w.r.t. the
centres of quadrilaterals.
Parameters
coors [array] The coordinates of cell vertices, shape (n_el, 4, 3).
Returns
mtx_t [array] The transposed transformation matrix 𝑇 , i.e. 𝑋𝑖𝑛𝑝𝑙𝑎𝑛𝑒 = 𝑇 𝑇 𝑋3𝐷 .

Notes

𝑇 = [𝑡1 , 𝑡2 , 𝑛], where 𝑡1 , 𝑡2 , are unit in-plane (column) vectors and 𝑛 is the unit normal vector, all mutually
orthonormal.
sfepy.mechanics.shell10x.get_dsg_strain(coors_loc, qp_coors)
Compute DSG strain components.
Returns
dsg [array] The strain matrix components corresponding to 𝑒13 , 𝑒23 , shape (n_el, n_qp, 2, 24).

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Notes

Involves 𝑤, 𝛼, 𝛽 DOFs.
sfepy.mechanics.shell10x.get_mapping_data(ebs, rops, ps, coors_loc, qp_coors, qp_weights,
special_dx3=False)
Compute reference element mapping data for shell10x elements.

Notes

The code assumes that the quadrature points are w.r.t. (𝑡 = thickness of the shell) [0, 1] × [0, 1] × [−𝑡/2, 𝑡/2]
reference cell and the quadrature weights are multiplied by 𝑡.
sfepy.mechanics.shell10x.lock_drilling_rotations(mtx, ebs, coefs)
Lock the drilling rotations in the stiffness matrix.
sfepy.mechanics.shell10x.rotate_elastic_tensor(mtx_d, bfu, ebs)
Rotate the elastic tensor into the local coordinate system of each cell. The local coordinate system results from
interpolation of ebs with the bilinear basis.
sfepy.mechanics.shell10x.transform_asm_matrices(out, mtx_t, blocks)
Transform matrix assembling contributions to global coordinate system, one node at a time.
Parameters
out [array] The array of matrices, transformed in-place.
mtx_t [array] The array of transposed transformation matrices 𝑇, see
create_transformation_matrix().
blocks [array] The DOF blocks that are

sfepy.mechanics.tensors module

Functions to compute some tensor-related quantities usual in continuum mechanics.

class sfepy.mechanics.tensors.StressTransform(def_grad, jacobian=None)
Encapsulates functions to convert various stress tensors in the symmetric storage given the deformation state.
get_cauchy_from_2pk(stress_in)
Get the Cauchy stress given the second Piola-Kirchhoff stress.

𝜎𝑖𝑗 = 𝐽 −1 𝐹𝑖𝑘 𝑆𝑘𝑙 𝐹𝑗𝑙

sfepy.mechanics.tensors.dim2sym(dim)
Given the space dimension, return the symmetric storage size.
sfepy.mechanics.tensors.get_deviator(tensor, sym_storage=True)
The deviatoric part (deviator) of a tensor.
sfepy.mechanics.tensors.get_full_indices(dim)
The indices for converting the symmetric storage to the full storage.
sfepy.mechanics.tensors.get_non_diagonal_indices(dim)
The non_diagonal indices for the full vector storage.
sfepy.mechanics.tensors.get_sym_indices(dim)
The indices for converting the full storage to the symmetric storage.

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sfepy.mechanics.tensors.get_t4_from_t2s(t2s)
Get the full 4D tensor with major/minor symmetries from its 2D matrix representation.
Parameters
t2s [array] The symmetrically-stored tensor of shape (S, S), where S it the symmetric storage
size.
Returns
t4 [array] The full 4D tensor of shape (D, D, D, D), where D is the space dimension.
sfepy.mechanics.tensors.get_trace(tensor, sym_storage=True)
The trace of a tensor.
sfepy.mechanics.tensors.get_volumetric_tensor(tensor, sym_storage=True)
The volumetric part of a tensor.
sfepy.mechanics.tensors.get_von_mises_stress(stress, sym_storage=True)
Given a symmetric stress tensor, compute the von Mises stress (also known as Equivalent tensile stress).

Notes
√︂
2 + 𝜎2 + 𝜎2 )
(𝜎11 − 𝜎22 )2 + (𝜎22 − 𝜎33 )2 + (𝜎11 − 𝜎33 )2 + 6(𝜎12 13 23
𝜎𝑉 =
2

sfepy.mechanics.tensors.prepare_cylindrical_transform(coors, origin, mode='axes')

Prepare matrices for transforming tensors into cylindrical coordinates with the axis ‘z’ in a given origin.
Parameters
coors [array] The Cartesian coordinates.
origin [array of length 3] The origin.
mode [‘axes’ or ‘data’] In ‘axes’ (default) mode the matrix transforms data to different coordinate
system, while in ‘data’ mode the matrix transforms the data in the same coordinate system
and is transpose of the matrix in the ‘axes’ mode.
Returns
mtx [array] The array of transformation matrices for each coordinate in coors.
sfepy.mechanics.tensors.sym2dim(sym)
Given the symmetric storage size, return the space dimension.

Notes

This function works for any space dimension.

sfepy.mechanics.tensors.transform_data(data, coors=None, mode='cylindrical', mtx=None)
Transform vector or tensor data components between orthogonal coordinate systems in 3D using transformation
matrix 𝑀 , that should express rotation of the original coordinate system to the new system denoted by ∙′ below.
For vectors:

𝑣′ = 𝑀 · 𝑣

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For second order tensors:

𝑡′ = 𝑀 · 𝑡 · 𝑀 𝑇
or
𝑡′𝑖𝑗 = 𝑀𝑖𝑝 𝑀𝑗𝑞 𝑡𝑝𝑞

For fourth order tensors:

𝑡′𝑖𝑗𝑘𝑙 = 𝑀𝑖𝑝 𝑀𝑗𝑞 𝑀𝑘𝑟 𝑀𝑙𝑠 𝑡𝑝𝑞𝑟𝑠

Parameters
data [array, shape (num, n_r) or (num, n_r, n_c)] The vectors (n_r is 3) or tensors (symmetric
storage, n_r is 6, n_c, if available, is 1 or 6) to be transformed.
coors [array] The Cartesian coordinates of the data. Not needed when mtx argument is given.
mode [one of [‘cylindrical’]] The requested coordinate system. Not needed when mtx argument
is given.
mtx [array] The array of transformation matrices 𝑀 for each data row.
Returns
new_data [array] The transformed data.

sfepy.mechanics.units module

Some utilities for work with units of physical quantities.

class sfepy.mechanics.units.Quantity(name, unit_set)
A physical quantity in a given set of basic units.

Examples

Construct the stress quantity:

>>> from sfepy.mechanics.units import Unit, Quantity

>>> units = ['m', 's', 'kg', 'C']
>>> unit_set = [Unit(key) for key in units]
>>> q1 = Quantity('stress', unit_set)
>>> q1()
'1.0 Pa'

Show its unit using various prefixes:

>>> q1('m')
'1000.0 mPa'
>>> q1('')
'1.0 Pa'
>>> q1('k')
'0.001 kPa'
>>> q1('M')
'1e-06 MPa'

Construct the stress quantity in another unit set:

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>>> units = ['mm', 's', 'kg', 'C']

>>> unit_set = [Unit(key) for key in units]
>>> q2 = Quantity('stress', unit_set)
>>> q2()
'1.0 kPa'

Show its unit using various prefixes:

>>> q2('m')
'1000000.0 mPa'
>>> q2('')
'1000.0 Pa'
>>> q2('k')
'1.0 kPa'
>>> q2('M')
'0.001 MPa'

class sfepy.mechanics.units.Unit(name)
A unit of a physical quantity. The prefix and coefficient of the unit are determined from to its name.

Examples

Construct some units:

>>> from sfepy.mechanics.units import Unit

>>> unit = Unit('mm')
>>> print unit
Unit:mm
coef:
0.001
name:
mm
prefix:
m
prefix_length:
1
unit:
m
>>> unit = Unit('kg')
>>> print unit
Unit:kg
coef:
1000.0
name:
kg
prefix:
k
prefix_length:
1
unit:
g

Get prefixes for a coefficient:

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>>> Unit.get_prefix(100.0)
('d', 10.0)
>>> Unit.get_prefix(100.0, omit=('d',))
('k', 0.10000000000000001)

static get_prefix(coef, bias=0.1, omit=None)

Get the prefix and numerical multiplier corresponding to a numerical coefficient, omitting prefixes in omit
tuple.
sfepy.mechanics.units.apply_unit_multipliers(values, unit_kinds, unit_multipliers)
Apply time, length and mass unit multipliers to given values with units corresponding to unit kinds.
Returns
new_values [list] The new values with applied unit multipliers
sfepy.mechanics.units.apply_units_to_pars(pars, pars_kinds, unit_multipliers)
Apply units in unit_multipliers to pars according to their kinds.
Parameters
pars [dict] The input parameters given as name : value items.
pars_kinds [dict] The kinds of the parameters given as name : kind items, with kinds defined
in apply_unit_multipliers().
unit_multipliers [tuple] The time, length and mass unit multipliers.
Returns
new_pars [dict] The output parameters.
sfepy.mechanics.units.get_consistent_unit_set(length=None, time=None, mass=None,
temperature=None)
Given a set of basic units, return a consistent set of derived units for quantities listed in the units_of_quantities
dictionary.

sfepy.mechanics.extmods.ccontres module

sfepy.mechanics.extmods.ccontres.assemble_contact_residual_and_stiffness()

sfepy.mechanics.extmods.ccontres.evaluate_contact_constraints()

sfepy.mechanics.extmods.ccontres.get_AABB()

sfepy.mechanics.extmods.ccontres.get_longest_edge_and_gps()

sfepy.mechanics.extmods.ccontres.init_global_search()
The linked list initialization. The head array contains, at the position Ic, the index of the first point that belongs
to the cell Ic, the second point index is then next[head[Ic]], the third point index is next[next[head[Ic]]] etc. - the
next array points from the i-th point in each cell to the (i+1)-th point, until -1 is reached.

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sfepy.mesh package

sfepy.mesh.bspline module

class sfepy.mesh.bspline.BSpline(degree=3, is_cyclic=False, ncp=0)

B-spline curve representation
approximate(coors, ncp=None, knot_type='clamped', knots=None, alpha=0.5, do_eval=False,
do_param_correction=False)
Approximate set of points by the B-spline curve.
Parameters
coors [array] The coordinates of the approximated points.
ncp [int] The number of control points.
knot_type [str] The knot vector type.
knots [array] The knot vector.
alpha [float]
The parameter vector distribution: 1.0 = chordal 0.5 = centripetal
do_eval [bool] Evaluate the curve coordinates?
do_param_correction [bool] Perform parametric corrections to improve the approxima-
tion?
static basis_function_dg(degree, t, knots, n)
B-spline basis functions.
Parameters
degree [int] The degree of the spline function.
t [array] The parametric vector.
knots [array] The knot vector.
n [int] The number of intervals.
Returns
bfun [array] The spline basis function evaluated for given values.
static basis_function_dg0(t, knots, n)
Basis function: degree = 0
Parameters
t [array] The parametric vector.
knots [array] The knot vector.
n [int] The number of intervals.
Returns
bfun [array] The spline basis function evaluated for given values.
draw(ret_ax=False, ax=None, color='r', cp_id=True)
Draw B-spline curve.
Parameters

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ret_ax [bool] Return an axes object?

ax [axes object] The axes to which will be drawn.
color [str] Line color.
cp_id [bool] If True, label control points.
draw_basis()
Draw B-spline curve.
eval(t=None, cp_coors=None)
Evaluate the coordinates of the bpsline curve.
Parameters
t [array] The parameter vector of the B-spline.
cp_coors [array] The coordinates of the control points.
eval_basis(t=None, return_val=False)
Evaluate the basis of the bpsline.
Parameters
t [array] The parameter vector of the B-spline.
get_control_points()
Get the B-spline control points.
Returns
coors [array] The coordinates of control points.
get_knot_vector()
Return the knot vector.
Returns
knots [array] The knot vector.
insert_knot(new)
Insert a new knot into the knot vector.
Parameters
new [float] The new knot value.
make_knot_vector(knot_type='clamped', knot_data=None, knot_range=(0.0, 1.0))
Create a knot vector of the requested type.
Parameters
knot_type [str] The knot vector type: clamped/cyclic/userdef.
knot_data : The extra knot data.
set_approx_points(coors)
Set the coordinates of approximated points.
Parameters
coors [array] The coordinates of approximated points.
set_control_points(coors, cyclic_form=False)
Set the B-spline control points.
Parameters

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coors [array] The coordinates of unique control points.

cyclic_form [bool] Are the control points in the cyclic form?
set_knot_vector(knots)
Set the knot vector.
Parameters
knots [array] The knot vector.
set_param(t)
Set the B-spline parametric vector.
Parameters
t [array] The parameter vector of the B-spline.
set_param_n(n=100, knot_range=(0.0, 1.0))
Generate the B-spline parametric vector using the number of steps.
Parameters
n [array] The number of steps in the B-spline parametric vector.
class sfepy.mesh.bspline.BSplineSurf(degree=(3, 3), is_cyclic=(False, False))
B-spline surface representation
approximate(coors, ncp, do_eval=False)
Approximate set of points by the B-spline surface.
Parameters
coors [array] The coordinates of the approximated points.
ncp [tuple of int] The number of control points.
draw(ret_ax=False, ax=None)
Draw B-spline surface.
Parameters
ret_ax [bool] Return an axes object?
ax [axes object] The axes to which will be drawn.
eval(t=(None, None), cp_coors=None)
Evaluate the coordinates of the bpsline curve.
Parameters
t [tuple of array] The parametric vector of the B-splines.
cp_coors [array] The coordinates of the control points.
get_control_points()
Get the B-spline surface control points.
Returns
coors [array] The coordinates of control points.
make_knot_vector(knot_type=('clamped', 'clamped'), knot_data=(None, None))
Create a knot vector of the requested type.
Parameters
knot_type [tuple of str] The knot vector types.

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knot_data [tuple of ANY] The extra knot data.

set_approx_points(coors)
Set the coordinates of approximated points.
Parameters
coors [array] The coordinates of approximated points.
set_control_points(coors, cyclic_form=False)
Set the B-spline control points.
Parameters
coors [array] The coordinates of unique control points.
cyclic_form [bool] Are the control points in the cyclic form?
set_param_n(n=(100, 100))
Generate the B-spline parametric vector using the number of steps.
Parameters
n [tuple of array] The number of steps in the B-spline parametric vectors.
write_control_polygon_vtk(filename, float_format='%.6f')
Write the control polygon to VTK file.
Parameters
filename: str Name of the VTK file.
float_format: str Float formating.
write_surface_vtk(filename, float_format='%.6f')
Write the spline surface to VTK file.
Parameters
filename: str Name of the VTK file.
float_format: str Float formating.
sfepy.mesh.bspline.approximation_example()
The example of using BSplineSurf for approximation of the surface given by the set of points.
sfepy.mesh.bspline.get_2d_points(is3d=False)
Returns the set of points.
Parameters
is3d [bool] 3D coordinates?
sfepy.mesh.bspline.main(argv)

sfepy.mesh.bspline.simple_example()
The example of using B-spline class.
sfepy.mesh.bspline.to_ndarray(a)

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sfepy.mesh.geom_tools module

class sfepy.mesh.geom_tools.geometry(dim=3)
The geometry is given by a sets of points (d0), lines (d1), surfaces (d2) and volumes (d3). A lines are constructed
from 2 points, a surface from any number of lines, a volume from any number of surfaces.
Physical volumes are contruted from any number of volumes.
The self.d0, self.d1, self.d2 and self.d3 are dictionaries holding a map
geometry element number -> instance of point,line,surface of volume

Examples

To get all the points which define a surface 5, use:

self.d2[5].getpoints()
This would give you a list [..] of point() instances.
addline(n, l)
l=[p1,p2]
addlines(ls, off=1)
ls=[l1, l2, . . . ]
addphysicalsurface(n, surfacelist)
surfacelist=[s1,s2,s3,. . . ]
addphysicalvolume(n, volumelist)
volumelist=[v1,v2,v3,. . . ]
addpoint(n, p)
p=[x,y,z]
addpoints(ps, off=1)
ps=[p1, p2, . . . ]
addsurface(n, s, is_hole=False)
s=[l1,l2,l3,. . . ]
addsurfaces(ss, off=1)
s=[s1,s2,s3,. . . ]
addvolume(n, v)
v=[s1,s2,s3,. . . ]
addvolumes(vs, off=1)
v=[v1,v2,v3,. . . ]
static from_gmsh_file(filename)
Import geometry - Gmsh geometry format.
Parameters
filename [string] file name
Returns
geo [geometry] geometry description
getBCnum(snum)

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leaveonlyphysicalsurfaces()

leaveonlyphysicalvolumes()

printinfo(verbose=False)

splitlines(ls, n)

to_poly_file(filename)
Export geometry to poly format (tetgen and triangle geometry format).
Parameters
geo [geometry] geometry description
filename [string] file name
class sfepy.mesh.geom_tools.geomobject

getn()

class sfepy.mesh.geom_tools.line(g, n, l)

getpoints()

class sfepy.mesh.geom_tools.physicalsurface(g, n, s)

getsurfaces()

class sfepy.mesh.geom_tools.physicalvolume(g, n, v)

getvolumes()

class sfepy.mesh.geom_tools.point(g, n, p)

getstr()

getxyz()

class sfepy.mesh.geom_tools.surface(g, n, s, is_hole=False)

getcenterpoint()

getholepoints()

getinsidepoint()

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getlines()

getpoints()

separate(s)

class sfepy.mesh.geom_tools.volume(g, n, v)

getinsidepoint()

getsurfaces()

sfepy.mesh.mesh_generators module

sfepy.mesh.mesh_generators.gen_block_mesh(dims, shape, centre, mat_id=0, name='block', coors=None,

verbose=True)
Generate a 2D or 3D block mesh. The dimension is determined by the lenght of the shape argument.
Parameters
dims [array of 2 or 3 floats] Dimensions of the block.
shape [array of 2 or 3 ints] Shape (counts of nodes in x, y, z) of the block mesh.
centre [array of 2 or 3 floats] Centre of the block.
mat_id [int, optional] The material id of all elements.
name [string] Mesh name.
verbose [bool] If True, show progress of the mesh generation.
Returns
mesh [Mesh instance]
sfepy.mesh.mesh_generators.gen_cylinder_mesh(dims, shape, centre, axis='x', force_hollow=False,
is_open=False, open_angle=0.0, non_uniform=False,
name='cylinder', verbose=True)
Generate a cylindrical mesh along an axis. Its cross-section can be ellipsoidal.
Parameters
dims [array of 5 floats] Dimensions of the cylinder: inner surface semi-axes a1, b1, outer surface
semi-axes a2, b2, length.
shape [array of 3 ints] Shape (counts of nodes in radial, circumferential and longitudinal direc-
tions) of the cylinder mesh.
centre [array of 3 floats] Centre of the cylinder.
axis: one of ‘x’, ‘y’, ‘z’ The axis of the cylinder.
force_hollow [boolean] Force hollow mesh even if inner radii a1 = b1 = 0.
is_open [boolean] Generate an open cylinder segment.
open_angle [float] Opening angle in radians.

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non_uniform [boolean] If True, space the mesh nodes in radial direction so that the element
volumes are (approximately) the same, making thus the elements towards the outer surface
thinner.
name [string] Mesh name.
verbose [bool] If True, show progress of the mesh generation.
Returns
mesh [Mesh instance]
sfepy.mesh.mesh_generators.gen_extended_block_mesh(b_dims, b_shape, e_dims, e_shape, centre,
grading_fun=None, name=None)
Generate a 3D mesh with a central block and (coarse) extending side meshes.
The resulting mesh is again a block. Each of the components has a different material id.
Parameters
b_dims [array of 3 floats] The dimensions of the central block.
b_shape [array of 3 ints] The shape (counts of nodes in x, y, z) of the central block mesh.
e_dims [array of 3 floats] The dimensions of the complete block (central block + extensions).
e_shape [int] The count of nodes of extending blocks in the direction from the central block.
centre [array of 3 floats] The centre of the mesh.
grading_fun [callable, optional] A function of 𝑥 ∈ [0, 1] that can be used to shift nodes in
the extension axis directions to allow smooth grading of element sizes from the centre. The
default function is 𝑥 * *𝑝 with 𝑝 determined so that the element sizes next to the central block
have the size of the shortest edge of the central block.
name [string, optional] The mesh name.
Returns
mesh [Mesh instance]
sfepy.mesh.mesh_generators.gen_mesh_from_geom(geo, a=None, verbose=False, refine=False)
Runs mesh generator - tetgen for 3D or triangle for 2D meshes.
Parameters
geo [geometry] geometry description
a [int, optional] a maximum area/volume constraint
verbose [bool, optional] detailed information
refine [bool, optional] refines mesh
Returns
mesh [Mesh instance] triangular or tetrahedral mesh
sfepy.mesh.mesh_generators.gen_mesh_from_string(mesh_name, mesh_dir)

sfepy.mesh.mesh_generators.gen_mesh_from_voxels(voxels, dims, etype='q')

Generate FE mesh from voxels (volumetric data).
Parameters
voxels [array] Voxel matrix, 1=material.

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dims [array] Size of one voxel.

etype [integer, optional] ‘q’ - quadrilateral or hexahedral elements ‘t’ - triangular or tetrahedral
elements
Returns
——-
mesh [Mesh instance] Finite element mesh.
sfepy.mesh.mesh_generators.gen_misc_mesh(mesh_dir, force_create, kind, args, suffix='.mesh',
verbose=False)
Create sphere or cube mesh according to kind in the given directory if it does not exist and return path to it.
sfepy.mesh.mesh_generators.gen_tiled_mesh(mesh, grid=None, scale=1.0, eps=1e-06, ret_ndmap=False)
Generate a new mesh by repeating a given periodic element along each axis.
Parameters
mesh [Mesh instance] The input periodic FE mesh.
grid [array] Number of repetition along each axis.
scale [float, optional] Scaling factor.
eps [float, optional] Tolerance for boundary detection.
ret_ndmap [bool, optional] If True, return global node map.
Returns
mesh_out [Mesh instance] FE mesh.
ndmap [array] Maps: actual node id –> node id in the reference cell.
sfepy.mesh.mesh_generators.get_tensor_product_conn(shape)
Generate vertex connectivity for cells of a tensor-product mesh of the given shape.
Parameters
shape [array of 2 or 3 ints] Shape (counts of nodes in x, y, z) of the mesh.
Returns
conn [array] The vertex connectivity array.
desc [str] The cell kind.
sfepy.mesh.mesh_generators.main()

sfepy.mesh.mesh_generators.tiled_mesh1d(conn, coors, ngrps, idim, n_rep, bb, eps=1e-06, ndmap=False)

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sfepy.mesh.mesh_tools module

sfepy.mesh.mesh_tools.elems_q2t(el)

sfepy.mesh.mesh_tools.expand2d(mesh2d, dist, rep)

Expand 2D planar mesh into 3D volume, convert triangular/quad mesh to tetrahedrons/hexahedrons.
Parameters
mesh2d [Mesh] The 2D mesh.
dist [float] The elements size in the 3rd direction.
rep [int] The number of elements in the 3rd direction.
Returns
mesh3d [Mesh] The 3D mesh.
sfepy.mesh.mesh_tools.smooth_mesh(mesh, n_iter=4, lam=0.6307, mu=- 0.6347, weights=None,
bconstr=True, volume_corr=False)
FE mesh smoothing.
Based on:
[1] Steven K. Boyd, Ralph Muller, Smooth surface meshing for automated finite element model generation
from 3D image data, Journal of Biomechanics, Volume 39, Issue 7, 2006, Pages 1287-1295, ISSN 0021-9290,
10.1016/j.jbiomech.2005.03.006. (http://www.sciencedirect.com/science/article/pii/S0021929005001442)
Parameters
mesh [mesh] FE mesh.
n_iter [integer, optional] Number of iteration steps.
lam [float, optional] Smoothing factor, see [1].
mu [float, optional] Unshrinking factor, see [1].
weights [array, optional] Edge weights, see [1].
bconstr: logical, optional Boundary constraints, if True only surface smoothing performed.
volume_corr: logical, optional Correct volume after smoothing process.
Returns
coors [array] Coordinates of mesh nodes.
sfepy.mesh.mesh_tools.triangulate(mesh, verbose=False)
Triangulate a 2D or 3D tensor product mesh: quadrilaterals->triangles, hexahedrons->tetrahedrons.
Parameters
mesh [Mesh] The input mesh.
Returns
mesh [Mesh] The triangulated mesh.

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sfepy.mesh.splinebox module

class sfepy.mesh.splinebox.SplineBox(bbox, coors, nsg=None, field=None)

B-spline geometry parametrization. The geometry can be modified by moving spline control points.
static create_spb(bbox, coors, degree=3, nsg=None)

evaluate(cp_values=None, outside=True)
Evaluate the new position of the mesh coordinates.
Parameters
cp_values [array] The actual control point values. If None, use self.control_values.
outside [bool] If True, return also the coordinates outside the spline box.
Returns
new_coors [array] The new position of the mesh coordinates.
evaluate_derivative(cpoint, dirvec)
Evaluate derivative of the spline in a given control point and direction.
Parameters
cpoint [int, list] The position (index or grid indicies) of the spline control point.
dirvec [array] The directional vector.
Returns
diff [array] The derivative field.
static gen_cp_idxs(ncp)

get_box_matrix()

Returns:
mtx [2D array] The matrix containing the coefficients of b-spline basis functions.
get_control_points(init=False)
Get the spline control points coordinates.
Returns
cpt_coors [array] The coordinates of the spline control points.
init [bool] If True, return the initial state.
get_coors_shape()
Get the shape of the coordinates.
move_control_point(cpoint, val)
Change shape of spline parametrization.
Parameters
cpoint [int, list] The position (index or grid indicies) of the spline control point.
val [array] Displacement.
set_control_points(cpt_coors, add=False)
Set the spline control points position.

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Parameters
cpt_coors [array] The coordinates of the spline control points.
add [bool] If True, coors += cpt_coors
write_control_net(filename, deform_by_values=True)
Write the SplineBox shape to the VTK file.
Parameters
filename [str] The VTK file name.
class sfepy.mesh.splinebox.SplineRegion2D(spl_bnd, coors, rho=1000.0)
B-spline geometry parametrization. The boundary of the SplineRegion2D is defined by BSpline curves.
static create_spb(spl_bnd, coors, rho=10)
Initialize SplineBox knots, control points, base functions, . . .
static define_control_points(cp_bnd_coors, ncp)
Find positions of “inner” control points depending on boundary splines.
find_ts(coors)
Function finds parameters (t, s) corresponding to given points (coors).
static points_in_poly(points, poly, tol=1e-06)
Find which points are located inside the polygon.

sfepy.parallel package

sfepy.parallel.evaluate module

PETSc-related parallel evaluation of problem equations.

class sfepy.parallel.evaluate.PETScParallelEvaluator(problem, pdofs, drange, is_overlap, psol, comm,
matrix_hook=None, verbose=False)
The parallel evaluator of the problem equations for PETScNonlinearSolver.
Its methods can be used as the function and Jacobian callbacks of the PETSc SNES (Scalable Nonlinear Equations
Solvers).

Notes

Assumes problem.active_only == False.

eval_residual(snes, psol, prhs)

eval_tangent_matrix(snes, psol, pmtx, ppmtx)

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sfepy.parallel.parallel module

Functions for a high-level PETSc-based parallelization.

sfepy.parallel.parallel.assemble_mtx_to_petsc(pmtx, mtx, pdofs, drange, is_overlap=True, comm=None,
verbose=False)
Assemble a local CSR matrix to a global PETSc matrix.
sfepy.parallel.parallel.assemble_rhs_to_petsc(prhs, rhs, pdofs, drange, is_overlap=True, comm=None,
verbose=False)
Assemble a local right-hand side vector to a global PETSc vector.
sfepy.parallel.parallel.call_in_rank_order(fun, comm=None)
Call a function fun task by task in the task rank order.
sfepy.parallel.parallel.create_gather_scatter(pdofs, pvec_i, pvec, comm=None)
Create the gather() function for updating a global PETSc vector from local ones and the scatter() function
for updating local PETSc vectors from the global one.
sfepy.parallel.parallel.create_gather_to_zero(pvec)
Create the gather_to_zero() function for collecting the global PETSc vector on the task of rank zero.
sfepy.parallel.parallel.create_local_petsc_vector(pdofs)
Create a local PETSc vector with the size corresponding to pdofs.
sfepy.parallel.parallel.create_petsc_matrix(sizes, mtx_prealloc=None, comm=None)
Create and allocate a PETSc matrix.
sfepy.parallel.parallel.create_petsc_system(mtx, sizes, pdofs, drange, is_overlap=True, comm=None,
verbose=False)
Create and pre-allocate (if is_overlap is True) a PETSc matrix and related solution and right-hand side vectors.
sfepy.parallel.parallel.create_prealloc_data(mtx, pdofs, drange, verbose=False)
Create CSR preallocation data for a PETSc matrix based on the owned PETSc DOFs and a local matrix with
EBCs not applied.
sfepy.parallel.parallel.create_task_dof_maps(field, cell_tasks, inter_facets, is_overlap=True,
use_expand_dofs=False, save_inter_regions=False,
output_dir=None)
For each task list its inner and interface DOFs of the given field and create PETSc numbering that is consecutive
in each subdomain.
For each task, the DOF map has the following structure:

[inner,
[own_inter1, own_inter2, ...],
[overlap_cells1, overlap_cells2, ...],
n_task_total, task_offset]

The overlapping cells are defined so that the system matrix corresponding to each task can be assembled inde-
pendently, see [1]. TODO: Some “corner” cells may be added even if not needed - filter them out by using the
PETSc DOFs range.
When debugging domain partitioning problems, it is advisable to set save_inter_regions to True to save the task
interfaces as meshes as well as vertex-based markers - to be used only with moderate problems and small numbers
of tasks.
[1] J. Sistek and F. Cirak. Parallel iterative solution of the incompressible Navier-Stokes equations with applica-
tion to rotating wings. Submitted for publication, 2015

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sfepy.parallel.parallel.distribute_field_dofs(field, gfd, use_expand_dofs=False, comm=None,

verbose=False)
Distribute the owned cells and DOFs of the given field to all tasks.
The DOFs use the PETSc ordering and are in form of a connectivity, so that each task can easily identify them
with the DOFs of the original global ordering or local ordering.
sfepy.parallel.parallel.distribute_fields_dofs(fields, cell_tasks, is_overlap=True,
use_expand_dofs=False, save_inter_regions=False,
output_dir=None, comm=None, verbose=False)
Distribute the owned cells and DOFs of the given field to all tasks.
Uses interleaved PETSc numbering in each task, i.e., the PETSc DOFs of each tasks are consecutive and corre-
spond to the first field DOFs block followed by the second etc.
Expand DOFs to equations if use_expand_dofs is True.
sfepy.parallel.parallel.expand_dofs(dofs, n_components)
Expand DOFs to equation numbers.
sfepy.parallel.parallel.get_composite_sizes(lfds)
Get (local, total) sizes of a vector and local equation range for a composite matrix built from field blocks described
by lfds local field distributions information.
sfepy.parallel.parallel.get_inter_facets(domain, cell_tasks)
For each couple of neighboring task subdomains get the common boundary (interface) facets.
sfepy.parallel.parallel.get_local_ordering(field_i, petsc_dofs_conn, use_expand_dofs=False)
Get PETSc DOFs in the order of local DOFs of the localized field field_i.
Expand DOFs to equations if use_expand_dofs is True.
sfepy.parallel.parallel.get_sizes(petsc_dofs_range, n_dof, n_components)
Get (local, total) sizes of a vector and local equation range.
sfepy.parallel.parallel.init_petsc_args()

sfepy.parallel.parallel.partition_mesh(mesh, n_parts, use_metis=True, verbose=False)

Partition the mesh cells into n_parts subdomains, using metis, if available.
sfepy.parallel.parallel.setup_composite_dofs(lfds, fields, local_variables, verbose=False)
Setup composite DOFs built from field blocks described by lfds local field distributions information.
Returns (local, total) sizes of a vector, local equation range for a composite matrix, and the local ordering of
composite PETSc DOFs, corresponding to local_variables (must be in the order of fields!).
sfepy.parallel.parallel.verify_task_dof_maps(dof_maps, id_map, field, use_expand_dofs=False,
verbose=False)
Verify the counts and values of DOFs in dof_maps and id_map corresponding to field.
Returns the vector with a task number for each DOF.
sfepy.parallel.parallel.view_petsc_local(data, name='data', viewer=None, comm=None)
View local PETSc data called name. The data object has to have .view() method.

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sfepy.parallel.plot_parallel_dofs module

Functions to visualize the partitioning of a domain and a field DOFs.

sfepy.parallel.plot_parallel_dofs.label_dofs(ax, coors, dofs, colors)
Label DOFs using the given colors.
sfepy.parallel.plot_parallel_dofs.mark_subdomains(ax, cmesh, cell_tasks, size=None, icolor=0,
alpha=1.0, mask=False)
Mark cells of subdomains corresponding to each task by a different color. Plots nothing in 3D.
sfepy.parallel.plot_parallel_dofs.plot_local_dofs(axs, field, field_i, omega_gi, output_dir, rank)
Plot the local ang global field DOFs local to the subdomain on the task with the given rank.
sfepy.parallel.plot_parallel_dofs.plot_partitioning(axs, field, cell_tasks, gfd, output_dir, size)
Plot the partitioning of the domain and field DOFs.

sfepy.postprocess package

sfepy.postprocess.domain_specific module

Domain-specific plot functions.

All the plot functions accept the following parameters:
• source : Mayavi source
• ctp : Mayavi cell-to-point filter
• position : (x, y, z)
• family : ‘point’ or ‘cell’
• kind : ‘scalars’, ‘vectors’ or ‘tensors’
• name : name of a variable
All the plot functions return: - kind : ‘scalars’, ‘vectors’ or ‘tensors’ - name : name of a variable - active : Mayavi
module
class sfepy.postprocess.domain_specific.DomainSpecificPlot(fun_name, args)
Class holding domain-specific plot function and its parameters.
sfepy.postprocess.domain_specific.plot_displacements(source, ctp, bbox, position, family, kind, name,
rel_scaling=1.0, color_kind=None,
color_name=None, opacity=1.0)
Show displacements by displaying a colormap given by quantity color_name on the deformed mesh.
Parameters
rel_scaling [float] The relative scaling of displacements.
color_kind [str, optional] The kind of data determining the colormap.
color_name [str, optional] The name of data determining the colormap.
opacity [float] The surface plot opacity.

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sfepy.postprocess.domain_specific.plot_velocity(source, ctp, bbox, position, family, kind, name,

seed='sphere', type='ribbon',
integration_direction='both', seed_scale=1.0,
seed_resolution=20, widget_enabled=True,
color_kind=None, color_name=None, opacity=1.0,
**kwargs)
Show velocity field by displaying streamlines and optionally a surface plot given by quantity color_name.
Parameters
seed [one of (‘sphere’, ‘point’, ‘line’, ‘plane’)] The streamline seed name.
type [one of (‘line’, ‘ribbon’, ‘tube’)] The streamline seed line type.
integration_direction [one of (‘forward’, ‘backward’, ‘both’)] The stream tracer integration di-
rection.
seed_scale [float] The seed size scale.
seed_resolution [int] The number of seed points in a direction (depends on seed).
widget_enabled [bool] It True, the seed widget is visible and can be interacted with.
color_kind [str, optional] The kind of data determining the colormap.
color_name [str, optional] The name of data determining the colormap.
opacity [float] The surface plot opacity.
**kwargs [dict] Additional keyword arguments for attributes of streamline.seed.widget.
sfepy.postprocess.domain_specific.plot_warp_scalar(source, ctp, bbox, position, family, kind, name,
rel_scaling=1.0, color_kind=None,
color_name=None, opacity=1.0)
Show a 2D scalar field by displaying a colormap given by quantity color_name on the deformed mesh deformed
by the scalar in the third dimension.
Parameters
rel_scaling [float] The relative scaling of scalar warp.
color_kind [str, optional] The kind of data determining the colormap.
color_name [str, optional] The name of data determining the colormap.
opacity [float] The surface plot opacity.

sfepy.postprocess.plot_cmesh module

Functions to visualize the CMesh geometry and topology.

sfepy.postprocess.plot_cmesh.label_global_entities(ax, cmesh, edim, color='b', fontsize=10,
**kwargs)
Label mesh topology entities using global ids.
sfepy.postprocess.plot_cmesh.label_local_entities(ax, cmesh, edim, color='b', fontsize=10, **kwargs)
Label mesh topology entities using cell-local ids.
sfepy.postprocess.plot_cmesh.plot_cmesh(ax, cmesh, wireframe_opts=None, entities_opts=None)
Convenience function for plotting all entities of a finite element mesh.
Pass plot() arguments to wireframe_opts dict.

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Pass ‘color’, ‘label_global’, ‘label_global’ for text() color and font sizes arguments and ‘size’ for scatter() to
each dict for topological entities in entities_opts list.

Examples

>>> # 2D mesh.
>>> plot_cmesh(None, cmesh,
wireframe_opts = {'color' : 'k', 'linewidth' : 2},
entities_opts=[
{'color' : 'k', 'label_local' : 8, 'size' : 20},
{'color' : 'b', 'label_global' : 12, 'label_local' : 8, 'size' : 10},
{'color' : 'r', 'label_global' : 12, 'size' : 20},
])

sfepy.postprocess.plot_cmesh.plot_entities(ax, cmesh, edim, color='b', size=10, **kwargs)

Plot mesh topology entities using scatter plot.
sfepy.postprocess.plot_cmesh.plot_wireframe(ax, cmesh, color='k', **kwargs)
Plot a finite element mesh as a wireframe using edges connectivity.

sfepy.postprocess.plot_dofs module

Functions to visualize the mesh connectivity with global and local DOF numberings.
sfepy.postprocess.plot_dofs.plot_global_dofs(ax, coors, econn)
Plot global DOF numbers given in an extended connectivity.
The DOF numbers are plotted for each element, so on common facets they are plotted several times - this can be
used to check the consistency of the global DOF connectivity.
sfepy.postprocess.plot_dofs.plot_local_dofs(ax, coors, econn)
Plot local DOF numbers corresponding to an extended connectivity.
sfepy.postprocess.plot_dofs.plot_mesh(ax, coors, conn, edges, color='k', **plot_kwargs)
Plot a finite element mesh as a wireframe.
sfepy.postprocess.plot_dofs.plot_nodes(ax, coors, econn, ref_nodes, dofs)
Plot Lagrange reference element nodes corresponding to global DOF numbers given in an extended connectivity.
sfepy.postprocess.plot_dofs.plot_points(ax, coors, vals=None, point_size=20, show_colorbar=False)
Plot points with given coordinates, optionally colored using vals values.

sfepy.postprocess.plot_facets module

Functions to visualize the geometry elements and numbering and orientation of their facets (edges and faces).
The standard geometry elements can be plotted by running:

$ python sfepy/postprocess/plot_facets.py

sfepy.postprocess.plot_facets.draw_arrow(ax, coors, angle=20.0, length=0.3, **kwargs)

Draw a line ended with an arrow head, in 2D or 3D.
sfepy.postprocess.plot_facets.plot_edges(ax, gel, length)
Plot edges of a geometry element as numbered arrows.

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sfepy.postprocess.plot_facets.plot_faces(ax, gel, radius, n_point)

Plot faces of a 3D geometry element as numbered oriented arcs. An arc centre corresponds to the first node of a
face. It points from the first edge towards the last edge of the face.
sfepy.postprocess.plot_facets.plot_geometry(ax, gel)
Plot a geometry element as a wireframe.

sfepy.postprocess.plot_quadrature module

Functions to visualize quadrature points in reference elements.

sfepy.postprocess.plot_quadrature.label_points(ax, coors)
Label points with their indices.
sfepy.postprocess.plot_quadrature.plot_quadrature(ax, geometry, order, boundary=False,
min_radius=10, max_radius=50,
show_colorbar=False, show_labels=False)
Plot quadrature points for the given geometry and integration order.
The points are plotted as circles/spheres with radii given by quadrature weights - the weights are mapped to
[min_radius, max_radius] interval.
sfepy.postprocess.plot_quadrature.plot_weighted_points(ax, coors, weights, min_radius=10,
max_radius=50, show_colorbar=False)
Plot points with given coordinates as circles/spheres with radii given by weights.

sfepy.postprocess.probes_vtk module

Classes for probing values of Variables, for example, along a line, using PyVTK library
class sfepy.postprocess.probes_vtk.Probe(data, mesh, **kwargs)
Probe class.
add_circle_probe(name, centre, normal, radius, n_point)
Create the ray (line) probe - VTK object.
Parameters
name [str] The probe name.
centre [array] The coordinates of the circle center point.
normal [array] The normal vector perpendicular to the circle plane.
radius [float] The radius of the circle.
n_point [int] The number of probe points.
add_line_probe(name, p0, p1, n_point)
Create the line probe - VTK object.
Parameters
name [str] The probe name.
p0 [array_like] The coordinates of the start point.
p1 [array_like] The coordinates of the end point.
n_point [int] The number of probe points.

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add_points_probe(name, coors)
Create the point probe - VTK object.
Parameters
name [str] The probe name.
coors [array] The coordinates of the probe points.
add_ray_probe(name, p0, dirvec, p_fun, n_point)
Create the ray (line) probe - VTK object.
Parameters
name [str] The probe name.
p0 [array] The coordinates of the start point.
dirvec [array] The probe direction vector.
p_fun [function] The function returning the probe parametrization along the dirvec direction.
n_point [int] The number of probe points.
gen_mesh_probe_png(probe, png_filename)
Generate PNG image of the FE mesh.
Parameters
probe [VTK objectstr] The probe, VTKPolyData or VTKSource.
png_filename [str] The name of the output PNG file.
new_vtk_polyline(points, closed=False)
Create the VTKPolyData object and store the line data.
Parameters
points [array] The line points.
Returns
vtkpd [VTK object] VTKPolyData with the polyline.
class sfepy.postprocess.probes_vtk.ProbeFromFile(filename, **kwargs)
Probe class - read a given VTK file.

sfepy.postprocess.sources module

class sfepy.postprocess.sources.FileSource(filename, watch=False, offscreen=True)

General file source.
file_changed()

get_mat_id(mat_id_name='mat_id')
Get material ID numbers of the underlying mesh elements.
get_step_time(step=None, time=None)
Set current step and time to the values closest greater or equal to either step or time. Return the found
values.
get_ts_info()

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poll_file()
Check the source file’s time stamp and notify the self.notify_obj in case it changed. Subclasses should
implement the file_changed() method.
reset()
Reset.
setup_mat_id(mat_id_name='mat_id', single_color=False)

setup_notification(obj, attr)
The attribute ‘attr’ of the object ‘obj’ will be set to True when the source file is watched and changes.
class sfepy.postprocess.sources.GenericFileSource(*args, **kwargs)
File source usable with any format supported by MeshIO classes.
add_data_to_dataset(dataset, data)
Add point and cell data to the dataset.
create_dataset()
Create a tvtk.UnstructuredGrid dataset from the Mesh instance of the file source.
create_source()
Create a VTK source from data in a SfePy-supported file.

Notes

All data need to be set here, otherwise time stepping will not work properly - data added by user later will
be thrown away on time step change.
file_changed()

get_bounding_box()

get_mat_id(mat_id_name='mat_id')
Get material ID numbers of the underlying mesh elements.
read_common(filename)

set_filename(filename, vis_source)

class sfepy.postprocess.sources.GenericSequenceFileSource(*args, **kwargs)

File source usable with any format supported by MeshIO classes, with exception of HDF5 (.h5), for file sequences.

file_changed()

read_common(filename)

set_filename(filename, vis_source)

class sfepy.postprocess.sources.VTKFileSource(filename, watch=False, offscreen=True)

A thin wrapper around mlab.pipeline.open().

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create_source()
Create a VTK file source
get_bounding_box()

set_filename(filename, vis_source)

class sfepy.postprocess.sources.VTKSequenceFileSource(*args, **kwargs)

A thin wrapper around mlab.pipeline.open() for VTK file sequences.
create_source()
Create a VTK file source
set_filename(filename, vis_source)

sfepy.postprocess.sources.create_file_source(filename, watch=False, offscreen=True)

Factory function to create a file source corresponding to the given file format.

sfepy.postprocess.time_history module

sfepy.postprocess.time_history.average_vertex_var_in_cells(ths_in)
Average histories in the element nodes for each nodal variable originally requested in elements.
sfepy.postprocess.time_history.dump_to_vtk(filename, output_filename_trunk=None, step0=0,
steps=None, fields=None, linearization=None)
Dump a multi-time-step results file into a sequence of VTK files.
sfepy.postprocess.time_history.extract_time_history(filename, extract, verbose=True)
Extract time history of a variable from a multi-time-step results file.
Parameters
filename [str] The name of file to extract from.
extract [str] The description of what to extract in a string of comma-separated description items.
A description item consists of: name of the variable to extract, mode (‘e’ for elements, ‘n’
for nodes), ids of the nodes or elements (given by the mode). Example: ‘u n 10 15, p e 0’
means variable ‘u’ in nodes 10, 15 and variable ‘p’ in element 0.
verbose [bool] Verbosity control.
Returns
ths [dict] The time histories in a dict with variable names as keys. If a nodal variable is requested
in elements, its value is a dict of histories in the element nodes.
ts [TimeStepper instance] The time stepping information.
sfepy.postprocess.time_history.extract_times(filename)
Read true time step data from individual time steps.
Returns
steps [array] The time steps.
times [array] The times of the time steps.
nts [array] The normalized times of the time steps, in [0, 1].
dts [array] The true time deltas.

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sfepy.postprocess.time_history.guess_time_units(times)
Given a vector of times in seconds, return suitable time units and new vector of times suitable for plotting.
Parameters
times [array] The vector of times in seconds.
Returns
new_times [array] The vector of times in units.
units [str] The time units.
sfepy.postprocess.time_history.save_time_history(ths, ts, filename_out)
Save time history and time-stepping information in a HDF5 file.

sfepy.postprocess.utils module

sfepy.postprocess.utils.get_data_ranges(obj, return_only=False, use_names=None, filter_names=None)

Collect and print information on ranges of data in a dataset.
Parameters
obj [a mayavi pipeline object] The object to probe for data.
return_only [boolean] If True, do not print the information, just return it to the caller.
use_names [list of strings] Consider only data with names in the list.
filter_names [list of strings] Consider only data with names not in the list.
Returns
ranges [dict] The requested data ranges.

sfepy.postprocess.utils_vtk module

Postprocessing utils based on VTK library

sfepy.postprocess.utils_vtk.get_vtk_by_group(vtkdata, group_lower, group_upper=None)
Get submesh by material group id.
Parameters
vtkdata [VTK object] Mesh, scalar, vector and tensor data.
group_lower [int] The lower material id.
group_lower [int] The Upper material id.
Returns
slection [VTK object] Mesh, scalar, vector and tensor data.
sfepy.postprocess.utils_vtk.get_vtk_edges(vtkdata)
Get mesh edges.
Parameters
vtkdata [VTK object] Mesh, scalar, vector and tensor data.
Returns
edges [VTK object] Mesh, scalar, vector and tensor data.

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sfepy.postprocess.utils_vtk.get_vtk_from_file(filename)
Read VTK file.
Parameters
filename [str] Name of the VTK file.
Returns
vtkdata [VTK object] Mesh, scalar, vector and tensor data.
sfepy.postprocess.utils_vtk.get_vtk_from_mesh(mesh, data, prefix='')

sfepy.postprocess.utils_vtk.get_vtk_surface(vtkdata)
Get mesh surface.
Parameters
vtkdata [VTK object] Mesh, scalar, vector and tensor data.
Returns
surface [VTK object] Mesh, scalar, vector and tensor data.
sfepy.postprocess.utils_vtk.tetrahedralize_vtk_mesh(vtkdata)
3D cells are converted to tetrahedral meshes, 2D cells to triangles.
Parameters
vtkdata [VTK object] Mesh, scalar, vector and tensor data.
Returns
tetra [VTK object] Mesh, scalar, vector and tensor data.
sfepy.postprocess.utils_vtk.write_vtk_to_file(filename, vtkdata)
Write VTK file.
Parameters
filename [str] Name of the VTK file.
vtkdata [VTK object] Mesh, scalar, vector and tensor data.

sfepy.postprocess.viewer module

class sfepy.postprocess.viewer.ClosingHandler

object_button_quit_changed(info)

class sfepy.postprocess.viewer.ReloadSource
class sfepy.postprocess.viewer.SetStep

init_seq_selection(name, new)

is_adjust = False
step = None
time = None

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class sfepy.postprocess.viewer.Viewer(filename, watch=False, ffmpeg_options=None, output_dir='.',

offscreen=False)
Class to automate visualization of various data using Mayavi.
It can use any format that mlab.pipeline.open() handles, e.g. a VTK format. After opening a data file, all data
(point, cell, scalars, vectors, tensors) are plotted in a grid layout.
Parameters:
watch [bool] If True, watch the file for changes and update the mayavi pipeline automatically.
ffmpeg_options [str] The ffmpeg animation encoding options.
output_dir [str] The output directory, where view snapshots will be saved.
Examples:

>>> view = Viewer('file.vtk')

>>> view() # view with default parameters
>>> view(layout='col') # use column layout

build_mlab_pipeline(file_source=None, is_3d=False, layout='rowcol', scalar_mode='iso_surface',

vector_mode='arrows_norm', rel_scaling=None, clamping=False, ranges=None,
is_scalar_bar=False, is_wireframe=False, opacity=None, subdomains_args=None,
rel_text_width=None, filter_names=None, group_names=None, only_names=None,
domain_specific=None, **kwargs)
Sets self.source, self.is_3d_data
call_empty(*args, **kwargs)

call_mlab(scene=None, show=True, is_3d=False, view=None, roll=None, parallel_projection=False,

fgcolor=(0.0, 0.0, 0.0), bgcolor=(1.0, 1.0, 1.0), colormap='blue-red', layout='rowcol',
scalar_mode='iso_surface', vector_mode='arrows_norm', rel_scaling=None, clamping=False,
ranges=None, is_scalar_bar=False, is_wireframe=False, opacity=None,
subdomains_args=None, rel_text_width=None, fig_filename='view.png', resolution=None,
filter_names=None, only_names=None, group_names=None, step=None, time=None,
anti_aliasing=None, domain_specific=None)
By default, all data (point, cell, scalars, vectors, tensors) are plotted in a grid layout, except data named
‘node_groups’, ‘mat_id’ which are usually not interesting.
Parameters
show [bool] Call mlab.show().
is_3d [bool] If True, use scalar cut planes instead of surface for certain datasets. Also sets
3D view mode.
view [tuple] Azimuth, elevation angles, distance and focal point as in mlab.view().
roll [float] Roll angle tuple as in mlab.roll().
parallel_projection: bool If True, use parallel projection.
fgcolor [tuple of floats (R, G, B)] The foreground color, that is the color of all text annotation
labels (axes, orientation axes, scalar bar labels).
bgcolor [tuple of floats (R, G, B)] The background color.
colormap [str] The colormap name.
layout [str] Grid layout for placing the datasets. Possible values are: ‘row’, ‘col’, ‘rowcol’,
‘colrow’.

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scalar_mode [str] Mode for plotting scalars and tensor magnitudes, one of ‘cut_plane’,
‘iso_surface’, ‘both’.
vector_mode [str] Mode for plotting vectors, one of ‘arrows’, ‘norm’, ‘arrows_norm’,
‘warp_norm’.
rel_scaling [float] Relative scaling of glyphs for vector datasets.
clamping [bool] Clamping for vector datasets.
ranges [dict] List of data ranges in the form {name : (min, max), . . . }.
is_scalar_bar [bool] If True, show a scalar bar for each data.
is_wireframe [bool] If True, show a wireframe of mesh surface bar for each data.
opacity [float] Global surface and wireframe opacity setting in [0.0, 1.0],
subdomains_args [tuple] Tuple of (mat_id_name, threshold_limits, single_color), see
add_subdomains_surface(), or None.
rel_text_width [float] Relative text width.
fig_filename [str] File name for saving the resulting scene figure.
resolution [tuple] Scene and figure resolution. If None, it is set automatically according to
the layout.
filter_names [list of strings] Omit the listed datasets. If None, it is initialized to
[‘node_groups’, ‘mat_id’]. Pass [] if you need no filtering.
only_names [list of strings] Draw only the listed datasets. If None, it is initialized all names
besides those in filter_names.
group_names [list of tuples] List of data names in the form [(name1, . . . , nameN), (. . . )].
Plots of data named in each group are superimposed. Repetitions of names are possible.
step [int, optional] If not None, the time step to display. The closest higher step is used if the
desired one is not available. Has precedence over time.
time [float, optional] If not None, the time of the time step to display. The closest higher
time is used if the desired one is not available.
anti_aliasing [int] Value of anti-aliasing.
domain_specific [dict] Domain-specific drawing functions and configurations.
encode_animation(filename, format, ffmpeg_options=None)

get_animation_info(filename, add_output_dir=True, last_step=None)

get_data_names(source=None, detailed=False)

get_size_hint(layout, resolution=None)

render_scene(scene, options)
Render the scene, preferably after it has been activated.
reset_view()

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save_animation(filename, steps=None, times=None)

Animate the current scene view for the selected time steps or times and save a snapshot of each view.
save_image(filename)
Save a snapshot of the current scene.
set_source_filename(filename)

show_scalar_bars(scalar_bars)

class sfepy.postprocess.viewer.ViewerGUI(fgcolor=(0.0, 0.0, 0.0), bgcolor=(1.0, 1.0, 1.0), **traits)

sfepy.postprocess.viewer.add_glyphs(obj, position, bbox, rel_scaling=None, scale_factor='auto',

clamping=False, color=None)

sfepy.postprocess.viewer.add_iso_surface(obj, position, contours=10, opacity=1.0)

sfepy.postprocess.viewer.add_scalar_cut_plane(obj, position, normal, opacity=1.0)

sfepy.postprocess.viewer.add_subdomains_surface(obj, position, mat_id_name='mat_id',

threshold_limits=(None, None), **kwargs)

sfepy.postprocess.viewer.add_surf(obj, position, opacity=1.0)

sfepy.postprocess.viewer.add_text(obj, position, text, width=None, color=(0, 0, 0))

sfepy.postprocess.viewer.add_vector_cut_plane(obj, position, normal, bbox, rel_scaling=None,

scale_factor='auto', clamping=False, opacity=1.0)

sfepy.postprocess.viewer.get_glyphs_scale_factor(rng, rel_scaling, bbox)

sfepy.postprocess.viewer.get_opacities(opacity)
Provide defaults for all supported opacity settings.
sfepy.postprocess.viewer.get_position_counts(n_data, layout)

sfepy.postprocess.viewer.make_animation(filename, view, roll, anim_format, options, steps=None,

times=None, reuse_viewer=None)

sfepy.postprocess.viewer.set_colormap(source, colormap_name)
Set the given colormap to all look-up tables depending on the given source.

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sfepy.solvers package

sfepy.solvers.auto_fallback module

class sfepy.solvers.auto_fallback.AutoDirect(conf, **kwargs)

The automatically selected linear direct solver.
The first available solver from the following list is used: ls.mumps <sfepy.solvers.ls.MUMPSSolver>,
ls.scipy_umfpack <sfepy.solvers.ls.ScipyUmfpack> and ls.scipy_superlu <sfepy.solvers.ls.ScipySuperLU>.
Kind: ‘ls.auto_direct’
For common configuration parameters, see Solver.
Specific configuration parameters:
name = 'ls.auto_direct'
class sfepy.solvers.auto_fallback.AutoFallbackSolver(conf, **kwargs)
Base class for virtual solvers with the automatic fallback.
class sfepy.solvers.auto_fallback.AutoIterative(conf, **kwargs)
The automatically selected linear iterative solver.
The first available solver from the following list is used: ls.petsc <sfepy.solvers.ls.PETScKrylovSolver> and
ls.scipy_iterative <sfepy.solvers.ls.ScipyIterative>
Kind: ‘ls.auto_iterative’
For common configuration parameters, see Solver.
Specific configuration parameters:
name = 'ls.auto_iterative'

sfepy.solvers.eigen module

class sfepy.solvers.eigen.LOBPCGEigenvalueSolver(conf, **kwargs)

SciPy-based LOBPCG solver for sparse symmetric problems.
Kind: ‘eig.scipy_lobpcg’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
i_max [int (default: 20)] The maximum number of iterations.
eps_a [float] The absolute tolerance for the convergence.
largest [bool (default: True)] If True, solve for the largest eigenvalues, otherwise the smallest.
precond [{dense matrix, sparse matrix, LinearOperator}] The preconditioner.
name = 'eig.scipy_lobpcg'
class sfepy.solvers.eigen.MatlabEigenvalueSolver(conf, comm=None, context=None, **kwargs)
Matlab eigenvalue problem solver.
Kind: ‘eig.matlab’
For common configuration parameters, see Solver.

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Specific configuration parameters:

Parameters
method [{‘eig’, ‘eigs’, None} (default: ‘eigs’)] The solution method. Note that eig() function
cannot be used for all inputs. If n_eigs is not None, eigs() is used regardless of this parameter.
balance [{‘balance’, ‘nobalance’} (default: ‘balance’)] The balance option for eig().
algorithm [{‘chol’, ‘qz’} (default: ‘chol’)] The algorithm option for eig().
which [{‘lm’, ‘sm’, ‘la’, ‘sa’, ‘be’ ‘lr’, ‘sr’, ‘li’, ‘si’, sigma} (default: ‘lm’)] Which eigenvectors
and eigenvalues to find with eigs().
* [*] Additional parameters supported by eigs().
name = 'eig.matlab'
class sfepy.solvers.eigen.SLEPcEigenvalueSolver(conf, comm=None, context=None, **kwargs)
General SLEPc eigenvalue problem solver.
Kind: ‘eig.slepc’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
method [str (default: ‘krylovschur’)] The actual solver to use.
problem [str (default: ‘gnhep’)] The problem type: Hermitian (hep), non-Hermitian (nhep),
generalized Hermitian (ghep), generalized non-Hermitian (gnhep), generalized non-
Hermitian with positive semi-definite B (pgnhep), and generalized Hermitian-indefinite
(ghiep).
i_max [int (default: 20)] The maximum number of iterations.
eps [float] The convergence tolerance.
conv_test [{“abs”, “rel”, “norm”, “user”}, (default: ‘abs’)] The type of convergence test.
which [{‘largest_magnitude’, ‘smallest_magnitude’,] ‘largest_real’, ‘smallest_real’,
‘largest_imaginary’, ‘smallest_imaginary’, ‘target_magnitude’, ‘target_real’, ‘tar-
get_imaginary’, ‘all’, ‘which_user’} (default: ‘largest_magnitude’) Which eigenvectors and
eigenvalues to find.
* [*] Additional parameters supported by the method.
create_eps(options=None, comm=None)

create_petsc_matrix(mtx, comm=None)

name = 'eig.slepc'
class sfepy.solvers.eigen.ScipyEigenvalueSolver(conf, **kwargs)
SciPy-based solver for both dense and sparse problems.
The problem is consirered sparse if n_eigs argument is not None.
Kind: ‘eig.scipy’
For common configuration parameters, see Solver.
Specific configuration parameters:

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Parameters
method [{‘eig’, ‘eigh’, ‘eigs’, ‘eigsh’} (default: ‘eigs’)] The method for solving general or sym-
metric eigenvalue problems: for dense problems eig() or eigh() can be used, for sparse
problems eigs() or eigsh() should be used.
which [‘LM’ | ‘SM’ | ‘LR’ | ‘SR’ | ‘LI’ | ‘SI’ (default: ‘SM’)] Which eigenvectors and eigen-
values to find, see scipy.sparse.linalg.eigs() or scipy.sparse.linalg.eigsh().
For dense problmes, only ‘LM’ and ‘SM’ can be used
* [*] Additional parameters supported by the method.
name = 'eig.scipy'
class sfepy.solvers.eigen.ScipySGEigenvalueSolver(conf, **kwargs)
SciPy-based solver for dense symmetric problems.
Kind: ‘eig.sgscipy’
For common configuration parameters, see Solver.
Specific configuration parameters:
name = 'eig.sgscipy'
sfepy.solvers.eigen.eig(mtx_a, mtx_b=None, n_eigs=None, eigenvectors=True, return_time=None,
method='eig.scipy', **ckwargs)
Utility function that constructs an eigenvalue solver given by method, calls it and returns solution.
sfepy.solvers.eigen.init_slepc_args()

sfepy.solvers.eigen.standard_call(call)
Decorator handling argument preparation and timing for eigensolvers.

sfepy.solvers.ls module

class sfepy.solvers.ls.MUMPSParallelSolver(conf, **kwargs)

Interface to MUMPS parallel solver.
Kind: ‘ls.mumps_par’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
memory_relaxation [int (default: 20)] The percentage increase in the estimated working space.
name = 'ls.mumps_par'
class sfepy.solvers.ls.MUMPSSolver(conf, **kwargs)
Interface to MUMPS solver.
Kind: ‘ls.mumps’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
use_presolve [bool (default: False)] If True, pre-factorize the matrix.

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memory_relaxation [int (default: 20)] The percentage increase in the estimated working space.
name = 'ls.mumps'
presolve(mtx, presolve_flag=False)

class sfepy.solvers.ls.MultiProblem(conf, context=None, **kwargs)

Conjugate multiple problems.
Allows to define conjugate multiple problems.
Kind: ‘ls.cm_pb’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
method [{‘auto’, ‘umfpack’, ‘superlu’} (default: ‘auto’)] The actual solver to use.
use_presolve [bool (default: False)] If True, pre-factorize the matrix.
others [list] The list of auxiliary problem definition files.
coupling_variables [list] The list of coupling variables.
init_subproblems(conf, **kwargs)

name = 'ls.cm_pb'
sparse_submat(Ad, Ar, Ac, gr, gc, S)
A[gr,gc] = S
class sfepy.solvers.ls.PETScKrylovSolver(conf, comm=None, context=None, **kwargs)
PETSc Krylov subspace solver.
The solver supports parallel use with a given MPI communicator (see comm argument of PETScKrylovSolver.
__init__()) and allows passing in PETSc matrices and vectors. Returns a (global) PETSc solution vector
instead of a (local) numpy array, when given a PETSc right-hand side vector.
The solver and preconditioner types are set upon the solver object creation. Tolerances can be overridden when
called by passing a conf object.
Convergence is reached when rnorm < max(eps_r * rnorm_0, eps_a), where, in PETSc, rnorm is by default the
norm of preconditioned residual.
Kind: ‘ls.petsc’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
method [str (default: ‘cg’)] The actual solver to use.
setup_precond [callable] User-supplied function for the preconditioner initialization/setup. It
is called as setup_precond(mtx, context), where mtx is the matrix, context is a user-supplied
context, and should return an object with setUp(self, pc) and apply(self, pc, x, y) methods.
Has precedence over the precond/sub_precond parameters.
precond [str (default: ‘icc’)] The preconditioner.
sub_precond [str (default: ‘none’)] The preconditioner for matrix blocks (in parallel runs).

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precond_side [{‘left’, ‘right’, ‘symmetric’, None}] The preconditioner side.

i_max [int (default: 100)] The maximum number of iterations.
eps_a [float (default: 1e-08)] The absolute tolerance for the residual.
eps_r [float (default: 1e-08)] The relative tolerance for the residual.
eps_d [float (default: 100000.0)] The divergence tolerance for the residual.
force_reuse [bool (default: False)] If True, skip the check whether the KSP solver object corre-
sponds to the mtx argument: it is always reused.
* [*] Additional parameters supported by the method. Can be used to pass all PETSc options
supported by petsc.Options().
create_ksp(options=None, comm=None)

create_petsc_matrix(mtx, comm=None)

name = 'ls.petsc'
set_field_split(field_ranges, comm=None)
Setup local PETSc ranges for fields to be used with ‘fieldsplit’ preconditioner.
This function must be called before solving the linear system.
class sfepy.solvers.ls.PyAMGKrylovSolver(conf, context=None, **kwargs)
Interface to PyAMG Krylov solvers.
Kind: ‘ls.pyamg_krylov’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
method [str (default: ‘cg’)] The actual solver to use.
setup_precond [callable (default: <function PyAMGKrylovSolver.<lambda> at
0x7f90e875eaf0>)] User-supplied function for the preconditioner initialization/setup.
It is called as setup_precond(mtx, context), where mtx is the matrix, context is a user-
supplied context, and should return one of {sparse matrix, dense matrix, LinearOperator}.
callback [callable] User-supplied function to call after each iteration. It is called as callback(xk),
where xk is the current solution vector, except the gmres method, where the argument is the
residual norm.
i_max [int (default: 100)] The maximum number of iterations.
eps_r [float (default: 1e-08)] The relative tolerance for the residual.
* [*] Additional parameters supported by the method.
name = 'ls.pyamg_krylov'
class sfepy.solvers.ls.PyAMGSolver(conf, **kwargs)
Interface to PyAMG solvers.
The method parameter can be one of: ‘smoothed_aggregation_solver’, ‘ruge_stuben_solver’. The accel param-
eter specifies the Krylov solver name, that is used as an accelerator for the multigrid solver.
Kind: ‘ls.pyamg’

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For common configuration parameters, see Solver.

Specific configuration parameters:
Parameters
method [str (default: ‘smoothed_aggregation_solver’)] The actual solver to use.
accel [str] The accelerator.
callback [callable] User-supplied function to call after each iteration. It is called as callback(xk),
where xk is the current solution vector, except the gmres accelerator, where the argument is
the residual norm.
i_max [int (default: 100)] The maximum number of iterations.
eps_r [float (default: 1e-08)] The relative tolerance for the residual.
force_reuse [bool (default: False)] If True, skip the check whether the MG solver object corre-
sponds to the mtx argument: it is always reused.
* [*] Additional parameters supported by the method. Use the ‘method:’ prefix for arguments
of the method construction function (e.g. ‘method:max_levels’ : 5), and the ‘solve:’ prefix
for the subsequent solver call.
name = 'ls.pyamg'
class sfepy.solvers.ls.SchurMumps(conf, **kwargs)
Mumps Schur complement solver.
Kind: ‘ls.schur_mumps’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
use_presolve [bool (default: False)] If True, pre-factorize the matrix.
memory_relaxation [int (default: 20)] The percentage increase in the estimated working space.
schur_variables [list] The list of Schur variables.
name = 'ls.schur_mumps'
class sfepy.solvers.ls.ScipyDirect(conf, method=None, **kwargs)
Direct sparse solver from SciPy.
Kind: ‘ls.scipy_direct’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
method [{‘auto’, ‘umfpack’, ‘superlu’} (default: ‘auto’)] The actual solver to use.
use_presolve [bool (default: False)] If True, pre-factorize the matrix.
name = 'ls.scipy_direct'
presolve(mtx)

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class sfepy.solvers.ls.ScipyIterative(conf, context=None, **kwargs)

Interface to SciPy iterative solvers.
The eps_r tolerance is both absolute and relative - the solvers stop when either the relative or the absolute residual
is below it.
Kind: ‘ls.scipy_iterative’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
method [str (default: ‘cg’)] The actual solver to use.
setup_precond [callable (default: <function ScipyIterative.<lambda> at 0x7f90e875e700>)]
User-supplied function for the preconditioner initialization/setup. It is called as
setup_precond(mtx, context), where mtx is the matrix, context is a user-supplied context,
and should return one of {sparse matrix, dense matrix, LinearOperator}.
callback [callable] User-supplied function to call after each iteration. It is called as callback(xk),
where xk is the current solution vector, except the gmres method, where the argument is the
residual.
i_max [int (default: 100)] The maximum number of iterations.
eps_a [float (default: 1e-08)] The absolute tolerance for the residual.
eps_r [float (default: 1e-08)] The relative tolerance for the residual.
* [*] Additional parameters supported by the method.
name = 'ls.scipy_iterative'
class sfepy.solvers.ls.ScipySuperLU(conf, **kwargs)
SuperLU - direct sparse solver from SciPy.
Kind: ‘ls.scipy_superlu’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
use_presolve [bool (default: False)] If True, pre-factorize the matrix.
name = 'ls.scipy_superlu'
class sfepy.solvers.ls.ScipyUmfpack(conf, **kwargs)
UMFPACK - direct sparse solver from SciPy.
Kind: ‘ls.scipy_umfpack’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
use_presolve [bool (default: False)] If True, pre-factorize the matrix.
name = 'ls.scipy_umfpack'
sfepy.solvers.ls.petsc_call(call)
Decorator handling argument preparation and timing for PETSc-based linear solvers.

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sfepy.solvers.ls.solve(mtx, rhs, solver_class=None, solver_conf=None)

Solve the linear system with the matrix mtx and the right-hand side rhs.
Convenience wrapper around the linear solver classes below.
sfepy.solvers.ls.standard_call(call)
Decorator handling argument preparation and timing for linear solvers.

sfepy.solvers.ls_mumps module

class sfepy.solvers.ls_mumps.MumpsSolver(is_sym=False, mpi_comm=None, system='real', silent=True,

mem_relax=20)
MUMPS object.
expand_schur(x2)
Expand the Schur local solution on the complete solution.
Parameters
x2 [array] The local Schur solution.
Returns
x [array] The global solution.
get_schur(schur_list)
Get the Schur matrix and the condensed right-hand side vector.
Parameters
schur_list [array] The list of the Schur DOFs (indexing starts with 1).
Returns
schur_arr [array] The Schur matrix of order ‘schur_size’.
schur_rhs [array] The reduced right-hand side vector.
set_mtx_centralized(mtx)
Set the sparse matrix.
Parameters
mtx [scipy sparse martix] The sparse matrix in COO format.
set_rcd_centralized(ir, ic, data, n)
Set the matrix by row and column indicies and data vector. The matrix shape is determined by the maximal
values of row and column indicies. The indices start with 1.
Parameters
ir [array] The row idicies.
ic [array] The column idicies.
data [array] The matrix entries.
n [int] The matrix dimension.
set_rhs(rhs)
Set the right hand side of the linear system.
set_silent()

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set_verbose()

sfepy.solvers.ls_mumps.coo_is_symmetric(mtx, tol=1e-06)

sfepy.solvers.ls_mumps.dec(val, encoding='utf-8')
Decode given bytes using the specified encoding.
sfepy.solvers.ls_mumps.load_library(libname)
Load shared library in a system dependent way.
sfepy.solvers.ls_mumps.load_mumps_libraries()

sfepy.solvers.ls_mumps.mumps_pcomplex
alias of sfepy.solvers.ls_mumps.LP_c_double
sfepy.solvers.ls_mumps.mumps_preal
alias of sfepy.solvers.ls_mumps.LP_c_double
class sfepy.solvers.ls_mumps.mumps_struc_c_4

a
Structure/Union member
a_elt
Structure/Union member
a_loc
Structure/Union member
cntl
Structure/Union member
colsca
Structure/Union member
comm_fortran
Structure/Union member
deficiency
Structure/Union member
eltptr
Structure/Union member
eltvar
Structure/Union member
icntl
Structure/Union member
info
Structure/Union member
infog
Structure/Union member
instance_number
Structure/Union member

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irhs_ptr
Structure/Union member
irhs_sparse
Structure/Union member
irn
Structure/Union member
irn_loc
Structure/Union member
isol_loc
Structure/Union member
jcn
Structure/Union member
jcn_loc
Structure/Union member
job
Structure/Union member
listvar_schur
Structure/Union member
lredrhs
Structure/Union member
lrhs
Structure/Union member
lsol_loc
Structure/Union member
lwk_user
Structure/Union member
mapping
Structure/Union member
mblock
Structure/Union member
n
Structure/Union member
nblock
Structure/Union member
nelt
Structure/Union member
npcol
Structure/Union member
nprow
Structure/Union member
nrhs
Structure/Union member

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nz
Structure/Union member
nz_alloc
Structure/Union member
nz_loc
Structure/Union member
nz_rhs
Structure/Union member
ooc_prefix
Structure/Union member
ooc_tmpdir
Structure/Union member
par
Structure/Union member
perm_in
Structure/Union member
pivnul_list
Structure/Union member
redrhs
Structure/Union member
rhs
Structure/Union member
rhs_sparse
Structure/Union member
rinfo
Structure/Union member
rinfog
Structure/Union member
rowsca
Structure/Union member
schur
Structure/Union member
schur_lld
Structure/Union member
schur_mloc
Structure/Union member
schur_nloc
Structure/Union member
size_schur
Structure/Union member
sol_loc
Structure/Union member

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sym
Structure/Union member
sym_perm
Structure/Union member
uns_perm
Structure/Union member
version_number
Structure/Union member
wk_user
Structure/Union member
write_problem
Structure/Union member
class sfepy.solvers.ls_mumps.mumps_struc_c_5_0

a
Structure/Union member
a_elt
Structure/Union member
a_loc
Structure/Union member
cntl
Structure/Union member
colsca
Structure/Union member
colsca_from_mumps
Structure/Union member
comm_fortran
Structure/Union member
deficiency
Structure/Union member
dkeep
Structure/Union member
eltptr
Structure/Union member
eltvar
Structure/Union member
icntl
Structure/Union member
info
Structure/Union member
infog
Structure/Union member

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instance_number
Structure/Union member
irhs_ptr
Structure/Union member
irhs_sparse
Structure/Union member
irn
Structure/Union member
irn_loc
Structure/Union member
isol_loc
Structure/Union member
jcn
Structure/Union member
jcn_loc
Structure/Union member
job
Structure/Union member
keep
Structure/Union member
keep8
Structure/Union member
listvar_schur
Structure/Union member
lredrhs
Structure/Union member
lrhs
Structure/Union member
lsol_loc
Structure/Union member
lwk_user
Structure/Union member
mapping
Structure/Union member
mblock
Structure/Union member
n
Structure/Union member
nblock
Structure/Union member
nelt
Structure/Union member

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npcol
Structure/Union member
nprow
Structure/Union member
nrhs
Structure/Union member
nz
Structure/Union member
nz_alloc
Structure/Union member
nz_loc
Structure/Union member
nz_rhs
Structure/Union member
ooc_prefix
Structure/Union member
ooc_tmpdir
Structure/Union member
par
Structure/Union member
perm_in
Structure/Union member
pivnul_list
Structure/Union member
redrhs
Structure/Union member
rhs
Structure/Union member
rhs_sparse
Structure/Union member
rinfo
Structure/Union member
rinfog
Structure/Union member
rowsca
Structure/Union member
rowsca_from_mumps
Structure/Union member
schur
Structure/Union member
schur_lld
Structure/Union member

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schur_mloc
Structure/Union member
schur_nloc
Structure/Union member
size_schur
Structure/Union member
sol_loc
Structure/Union member
sym
Structure/Union member
sym_perm
Structure/Union member
uns_perm
Structure/Union member
version_number
Structure/Union member
wk_user
Structure/Union member
write_problem
Structure/Union member
class sfepy.solvers.ls_mumps.mumps_struc_c_5_1

a
Structure/Union member
a_elt
Structure/Union member
a_loc
Structure/Union member
cntl
Structure/Union member
colsca
Structure/Union member
colsca_from_mumps
Structure/Union member
comm_fortran
Structure/Union member
deficiency
Structure/Union member
dkeep
Structure/Union member
eltptr
Structure/Union member

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eltvar
Structure/Union member
icntl
Structure/Union member
info
Structure/Union member
infog
Structure/Union member
instance_number
Structure/Union member
irhs_ptr
Structure/Union member
irhs_sparse
Structure/Union member
irn
Structure/Union member
irn_loc
Structure/Union member
isol_loc
Structure/Union member
jcn
Structure/Union member
jcn_loc
Structure/Union member
job
Structure/Union member
keep
Structure/Union member
keep8
Structure/Union member
listvar_schur
Structure/Union member
lredrhs
Structure/Union member
lrhs
Structure/Union member
lsol_loc
Structure/Union member
lwk_user
Structure/Union member
mapping
Structure/Union member

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mblock
Structure/Union member
n
Structure/Union member
nblock
Structure/Union member
nelt
Structure/Union member
nnz
Structure/Union member
nnz_loc
Structure/Union member
npcol
Structure/Union member
nprow
Structure/Union member
nrhs
Structure/Union member
nz
Structure/Union member
nz_alloc
Structure/Union member
nz_loc
Structure/Union member
nz_rhs
Structure/Union member
ooc_prefix
Structure/Union member
ooc_tmpdir
Structure/Union member
par
Structure/Union member
perm_in
Structure/Union member
pivnul_list
Structure/Union member
redrhs
Structure/Union member
rhs
Structure/Union member
rhs_sparse
Structure/Union member

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rinfo
Structure/Union member
rinfog
Structure/Union member
rowsca
Structure/Union member
rowsca_from_mumps
Structure/Union member
save_dir
Structure/Union member
save_prefix
Structure/Union member
schur
Structure/Union member
schur_lld
Structure/Union member
schur_mloc
Structure/Union member
schur_nloc
Structure/Union member
size_schur
Structure/Union member
sol_loc
Structure/Union member
sym
Structure/Union member
sym_perm
Structure/Union member
uns_perm
Structure/Union member
version_number
Structure/Union member
wk_user
Structure/Union member
write_problem
Structure/Union member
class sfepy.solvers.ls_mumps.mumps_struc_c_5_2

a
Structure/Union member
a_elt
Structure/Union member

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a_loc
Structure/Union member
cntl
Structure/Union member
colsca
Structure/Union member
colsca_from_mumps
Structure/Union member
comm_fortran
Structure/Union member
deficiency
Structure/Union member
dkeep
Structure/Union member
eltptr
Structure/Union member
eltvar
Structure/Union member
icntl
Structure/Union member
info
Structure/Union member
infog
Structure/Union member
instance_number
Structure/Union member
irhs_loc
Structure/Union member
irhs_ptr
Structure/Union member
irhs_sparse
Structure/Union member
irn
Structure/Union member
irn_loc
Structure/Union member
isol_loc
Structure/Union member
jcn
Structure/Union member
jcn_loc
Structure/Union member

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job
Structure/Union member
keep
Structure/Union member
keep8
Structure/Union member
listvar_schur
Structure/Union member
lredrhs
Structure/Union member
lrhs
Structure/Union member
lrhs_loc
Structure/Union member
lsol_loc
Structure/Union member
lwk_user
Structure/Union member
mapping
Structure/Union member
mblock
Structure/Union member
metis_options
Structure/Union member
n
Structure/Union member
nblock
Structure/Union member
nelt
Structure/Union member
nloc_rhs
Structure/Union member
nnz
Structure/Union member
nnz_loc
Structure/Union member
npcol
Structure/Union member
nprow
Structure/Union member
nrhs
Structure/Union member

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nz
Structure/Union member
nz_alloc
Structure/Union member
nz_loc
Structure/Union member
nz_rhs
Structure/Union member
ooc_prefix
Structure/Union member
ooc_tmpdir
Structure/Union member
par
Structure/Union member
perm_in
Structure/Union member
pivnul_list
Structure/Union member
redrhs
Structure/Union member
rhs
Structure/Union member
rhs_loc
Structure/Union member
rhs_sparse
Structure/Union member
rinfo
Structure/Union member
rinfog
Structure/Union member
rowsca
Structure/Union member
rowsca_from_mumps
Structure/Union member
save_dir
Structure/Union member
save_prefix
Structure/Union member
schur
Structure/Union member
schur_lld
Structure/Union member

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schur_mloc
Structure/Union member
schur_nloc
Structure/Union member
size_schur
Structure/Union member
sol_loc
Structure/Union member
sym
Structure/Union member
sym_perm
Structure/Union member
uns_perm
Structure/Union member
version_number
Structure/Union member
wk_user
Structure/Union member
write_problem
Structure/Union member
class sfepy.solvers.ls_mumps.mumps_struc_c_x

aux
Structure/Union member
comm_fortran
Structure/Union member
icntl
Structure/Union member
job
Structure/Union member
par
Structure/Union member
sym
Structure/Union member

sfepy.solvers.ls_mumps_parallel module

sfepy.solvers.ls_mumps_parallel.mumps_parallel_solve()

sfepy.solvers.ls_mumps_parallel.tmpfile(fname)

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sfepy.solvers.nls module

Nonlinear solvers.
class sfepy.solvers.nls.Newton(conf, **kwargs)
Solves a nonlinear system 𝑓 (𝑥) = 0 using the Newton method.
The solver uses a backtracking line-search on divergence.
Kind: ‘nls.newton’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
i_max [int (default: 1)] The maximum number of iterations.
eps_a [float (default: 1e-10)] The absolute tolerance for the residual, i.e. ||𝑓 (𝑥𝑖 )||.
eps_r [float (default: 1.0)] The relative tolerance for the residual, i.e. ||𝑓 (𝑥𝑖 )||/||𝑓 (𝑥0 )||.
eps_mode [‘and’ or ‘or’ (default: ‘and’)] The logical operator to use for combining the absolute
and relative tolerances.
macheps [float (default: 2.220446049250313e-16)] The float considered to be machine “zero”.
lin_red [float (default: 1.0)] The linear system solution error should be smaller than (eps_a *
lin_red), otherwise a warning is printed.
lin_precision [float or None] If not None, the linear system solution tolerances are set in each
nonlinear iteration relative to the current residual norm by the lin_precision factor. Ignored
for direct linear solvers.
step_red [0.0 < float <= 1.0 (default: 1.0)] Step reduction factor. Equivalent to the mixing
parameter 𝑎: (1 − 𝑎)𝑥 + 𝑎(𝑥 + 𝑑𝑥) = 𝑥 + 𝑎𝑑𝑥
ls_on [float (default: 0.99999)] Start the backtracking line-search by reducing the step, if
||𝑓 (𝑥𝑖 )||/||𝑓 (𝑥𝑖−1 )|| is larger than ls_on.
ls_red [0.0 < float < 1.0 (default: 0.1)] The step reduction factor in case of correct residual
assembling.
ls_red_warp [0.0 < float < 1.0 (default: 0.001)] The step reduction factor in case of failed resid-
ual assembling (e.g. the “warp violation” error caused by a negative volume element result-
ing from too large deformations).
ls_min [0.0 < float < 1.0 (default: 1e-05)] The minimum step reduction factor.
give_up_warp [bool (default: False)] If True, abort on the “warp violation” error.
check [0, 1 or 2 (default: 0)] If >= 1, check the tangent matrix using finite differences. If 2, plot
the resulting sparsity patterns.
delta [float (default: 1e-06)] If check >= 1, the finite difference matrix is taken as 𝐴𝑖𝑗 =
𝑓𝑖 (𝑥𝑗 +𝛿)−𝑓𝑖 (𝑥𝑗 −𝛿)
2𝛿 .
log [dict or None] If not None, log the convergence according to the configuration in the follow-
ing form: {'text' : 'log.txt', 'plot' : 'log.pdf'}. Each of the dict items
can be None.
is_linear [bool (default: False)] If True, the problem is considered to be linear.

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__call__(vec_x0, conf=None, fun=None, fun_grad=None, lin_solver=None, iter_hook=None, status=None)

Nonlinear system solver call.
Solves a nonlinear system 𝑓 (𝑥) = 0 using the Newton method with backtracking line-search, starting with
an initial guess 𝑥0 .
Parameters
vec_x0 [array] The initial guess vector 𝑥0 .
conf [Struct instance, optional] The solver configuration parameters,
fun [function, optional] The function 𝑓 (𝑥) whose zero is sought - the residual.
fun_grad [function, optional] The gradient of 𝑓 (𝑥) - the tangent matrix.
lin_solver [LinearSolver instance, optional] The linear solver for each nonlinear iteration.
iter_hook [function, optional] User-supplied function to call before each iteration.
status [dict-like, optional] The user-supplied object to hold convergence statistics.

Notes

• The optional parameters except iter_hook and status need to be given either here or upon Newton
construction.
• Setting conf.is_linear == True means a pre-assembled and possibly pre-solved matrix. This is mostly
useful for linear time-dependent problems.

__init__(conf, **kwargs)

__module__ = 'sfepy.solvers.nls'
name = 'nls.newton'
class sfepy.solvers.nls.PETScNonlinearSolver(conf, pmtx=None, prhs=None, comm=None, **kwargs)
Interface to PETSc SNES (Scalable Nonlinear Equations Solvers).
The solver supports parallel use with a given MPI communicator (see comm argument of
PETScNonlinearSolver.__init__()). Returns a (global) PETSc solution vector instead of a (local)
numpy array, when given a PETSc initial guess vector.
For parallel use, the fun and fun_grad callbacks should be provided by PETScParallelEvaluator.
Kind: ‘nls.petsc’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
method [str (default: ‘newtonls’)] The SNES type.
i_max [int (default: 10)] The maximum number of iterations.
if_max [int (default: 100)] The maximum number of function evaluations.
eps_a [float (default: 1e-10)] The absolute tolerance for the residual, i.e. ||𝑓 (𝑥𝑖 )||.
eps_r [float (default: 1.0)] The relative tolerance for the residual, i.e. ||𝑓 (𝑥𝑖 )||/||𝑓 (𝑥0 )||.
eps_s [float (default: 0.0)] The convergence tolerance in terms of the norm of the change in the
solution between steps, i.e. $||delta x|| < epsilon_s ||x||$

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__call__(vec_x0, conf=None, fun=None, fun_grad=None, lin_solver=None, iter_hook=None, status=None,

pmtx=None, prhs=None, comm=None)
Call self as a function.
__init__(conf, pmtx=None, prhs=None, comm=None, **kwargs)

__module__ = 'sfepy.solvers.nls'
name = 'nls.petsc'
class sfepy.solvers.nls.ScipyBroyden(conf, **kwargs)
Interface to Broyden and Anderson solvers from scipy.optimize.
Kind: ‘nls.scipy_broyden_like’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
method [str (default: ‘anderson’)] The name of the solver in scipy.optimize.
i_max [int (default: 10)] The maximum number of iterations.
alpha [float (default: 0.9)] See scipy.optimize.
M [float (default: 5)] See scipy.optimize.
f_tol [float (default: 1e-06)] See scipy.optimize.
w0 [float (default: 0.1)] See scipy.optimize.
__call__(vec_x0, conf=None, fun=None, fun_grad=None, lin_solver=None, iter_hook=None, status=None)
Call self as a function.
__init__(conf, **kwargs)

__module__ = 'sfepy.solvers.nls'
name = 'nls.scipy_broyden_like'
set_method(conf )

sfepy.solvers.nls.check_tangent_matrix(conf, vec_x0, fun, fun_grad)

Verify the correctness of the tangent matrix as computed by fun_grad() by comparing it with its finite difference
approximation evaluated by repeatedly calling fun() with vec_x0 items perturbed by a small delta.
sfepy.solvers.nls.conv_test(conf, it, err, err0)
Nonlinear solver convergence test.
Parameters
conf [Struct instance] The nonlinear solver configuration.
it [int] The current iteration.
err [float] The current iteration error.
err0 [float] The initial error.
Returns
status [int] The convergence status: -1 = no convergence (yet), 0 = solver converged - tolerances
were met, 1 = max. number of iterations reached.

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sfepy.solvers.optimize module

class sfepy.solvers.optimize.FMinSteepestDescent(conf, **kwargs)

Steepest descent optimization solver.
Kind: ‘opt.fmin_sd’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
i_max [int (default: 10)] The maximum number of iterations.
eps_rd [float (default: 1e-05)] The relative delta of the objective function.
eps_of [float (default: 0.0001)] The tolerance for the objective function.
eps_ofg [float (default: 1e-08)] The tolerance for the objective function gradient.
norm [numpy norm (default: inf)] The norm to be used.
ls [bool (default: True)] If True, use a line-search.
ls_method [{‘backtracking’, ‘full’} (default: ‘backtracking’)] The line-search method.
ls_on [float (default: 0.99999)] Start the backtracking line-search by reducing the step, if
||𝑓 (𝑥𝑖 )||/||𝑓 (𝑥𝑖−1 )|| is larger than ls_on.
ls0 [0.0 < float < 1.0 (default: 1.0)] The initial step.
ls_red [0.0 < float < 1.0 (default: 0.5)] The step reduction factor in case of correct residual
assembling.
ls_red_warp [0.0 < float < 1.0 (default: 0.1)] The step reduction factor in case of failed residual
assembling (e.g. the “warp violation” error caused by a negative volume element resulting
from too large deformations).
ls_min [0.0 < float < 1.0 (default: 1e-05)] The minimum step reduction factor.
check [0, 1 or 2 (default: 0)] If >= 1, check the tangent matrix using finite differences. If 2, plot
the resulting sparsity patterns.
delta [float (default: 1e-06)] If check >= 1, the finite difference matrix is taken as 𝐴𝑖𝑗 =
𝑓𝑖 (𝑥𝑗 +𝛿)−𝑓𝑖 (𝑥𝑗 −𝛿)
2𝛿 .
output [function] If given, use it instead of output() function.
yscales [list of str (default: [‘linear’, ‘log’, ‘log’, ‘linear’])] The list of four convergence log
subplot scales.
log [dict or None] If not None, log the convergence according to the configuration in the follow-
ing form: {'text' : 'log.txt', 'plot' : 'log.pdf'}. Each of the dict items
can be None.
name = 'opt.fmin_sd'
class sfepy.solvers.optimize.ScipyFMinSolver(conf, **kwargs)
Interface to SciPy optimization solvers scipy.optimize.fmin_*.
Kind: ‘nls.scipy_fmin_like’
For common configuration parameters, see Solver.
Specific configuration parameters:

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Parameters
method [{‘fmin’, ‘fmin_bfgs’, ‘fmin_cg’, ‘fmin_cobyla’, ‘fmin_l_bfgs_b’, ‘fmin_ncg’,
‘fmin_powell’, ‘fmin_slsqp’, ‘fmin_tnc’} (default: ‘fmin’)] The actual optimization method
to use.
i_max [int (default: 10)] The maximum number of iterations.
* [*] Additional parameters supported by the method.
name = 'nls.scipy_fmin_like'
set_method(conf )

sfepy.solvers.optimize.check_gradient(xit, aofg, fn_of, delta, check)

sfepy.solvers.optimize.conv_test(conf, it, of, of0, ofg_norm=None)

Returns
flag [int]
• -1 . . . continue
• 0 . . . small OF -> stop
• 1 . . . i_max reached -> stop
• 2 . . . small OFG -> stop
• 3 . . . small relative decrase of OF
sfepy.solvers.optimize.wrap_function(function, args)

sfepy.solvers.oseen module

class sfepy.solvers.oseen.Oseen(conf, context=None, **kwargs)

The Oseen solver for Navier-Stokes equations.
Kind: ‘nls.oseen’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
stabil_mat [str] The name of stabilization material.
adimensionalize [bool (default: False)] If True, adimensionalize the problem (not imple-
mented!).
check_navier_stokes_residual [bool (default: False)] If True, check the Navier-Stokes residual
after the nonlinear loop.
i_max [int (default: 1)] The maximum number of iterations.
eps_a [float (default: 1e-10)] The absolute tolerance for the residual, i.e. ||𝑓 (𝑥𝑖 )||.
eps_r [float (default: 1.0)] The relative tolerance for the residual, i.e. ||𝑓 (𝑥𝑖 )||/||𝑓 (𝑥0 )||.
macheps [float (default: 2.220446049250313e-16)] The float considered to be machine “zero”.

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lin_red [float (default: 1.0)] The linear system solution error should be smaller than (eps_a *
lin_red), otherwise a warning is printed.
lin_precision [float or None] If not None, the linear system solution tolerances are set in each
nonlinear iteration relative to the current residual norm by the lin_precision factor. Ignored
for direct linear solvers.
name = 'nls.oseen'
class sfepy.solvers.oseen.StabilizationFunction(name_map, gamma=None, delta=None, tau=None,
tau_red=1.0, tau_mul=1.0, delta_mul=1.0,
gamma_mul=1.0, diameter_mode='max')
Definition of stabilization material function for the Oseen solver.

Notes

• tau_red <= 1.0; if tau is None: tau = tau_red * delta

• diameter mode: ‘edge’: longest edge ‘volume’: volume-based, ‘max’: max. of previous

get_maps()
Get the maps of names and indices of variables in state vector.
setup(problem)
Setup common problem-dependent data.
sfepy.solvers.oseen.are_close(a, b, rtol=0.2, atol=1e-08)

sfepy.solvers.oseen.scale_matrix(mtx, indx, factor)

sfepy.solvers.qeigen module

Quadratic eigenvalue problem solvers.

class sfepy.solvers.qeigen.LQuadraticEVPSolver(conf, mtx_m=None, mtx_d=None, mtx_k=None,
n_eigs=None, eigenvectors=None, status=None,
context=None, **kwargs)
Quadratic eigenvalue problem solver based on the problem linearization.
(w^2 M + w D + K) x = 0.
Kind: ‘eig.qevp’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
method [{‘companion’, ‘cholesky’} (default: ‘companion’)] The linearization method.
solver [dict (default: {‘kind’: ‘eig.scipy’, ‘method’: ‘eig’})] The configuration of an eigenvalue
solver for the linearized problem (A - w B) x = 0.
mode [{‘normal’, ‘inverted’} (default: ‘normal’)] Solve either A - w B (normal), or B - 1/w A
(inverted).
debug [bool (default: False)] If True, print debugging information.

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name = 'eig.qevp'
sfepy.solvers.qeigen.standard_call(call)
Decorator handling argument preparation and timing for quadratic eigensolvers.

sfepy.solvers.semismooth_newton module

class sfepy.solvers.semismooth_newton.SemismoothNewton(conf, **kwargs)

The semi-smooth Newton method.
This method is suitable for solving problems of the following structure:

𝐹 (𝑦) = 0
𝐴(𝑦) ≥ 0 , 𝐵(𝑦) ≥ 0 , ⟨𝐴(𝑦), 𝐵(𝑦)⟩ = 0

The function 𝐹 (𝑦) represents the smooth part of the problem.

Regular step: 𝑦 ← 𝑦 − 𝐽(𝑦)−1 Φ(𝑦)
Steepest descent step: 𝑦 ← 𝑦 − 𝛽𝐽(𝑦)Φ(𝑦)
Although fun_smooth_grad() computes the gradient of the smooth part only, it should return the global matrix,
where the non-smooth part is uninitialized, but pre-allocated.
Kind: ‘nls.semismooth_newton’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
semismooth [bool (default: True)] If True, use the semi-smooth algorithm. Otherwise a non-
smooth equation is assumed (use a brute force).
i_max [int (default: 1)] The maximum number of iterations.
eps_a [float (default: 1e-10)] The absolute tolerance for the residual, i.e. ||𝑓 (𝑥𝑖 )||.
eps_r [float (default: 1.0)] The relative tolerance for the residual, i.e. ||𝑓 (𝑥𝑖 )||/||𝑓 (𝑥0 )||.
macheps [float (default: 2.220446049250313e-16)] The float considered to be machine “zero”.
lin_red [float (default: 1.0)] The linear system solution error should be smaller than (eps_a *
lin_red), otherwise a warning is printed.
ls_on [float (default: 0.99999)] Start the backtracking line-search by reducing the step, if
||𝑓 (𝑥𝑖 )||/||𝑓 (𝑥𝑖−1 )|| is larger than ls_on.
ls_red [dict (default: {‘regular’: 0.1, ‘steepest_descent’: 0.01})] The step reduction factor in
case of correct residual assembling for regular and steepest descent modes.
ls_red_warp [0.0 < float < 1.0 (default: 0.001)] The step reduction factor in case of failed resid-
ual assembling (e.g. the “warp violation” error caused by a negative volume element result-
ing from too large deformations).
ls_min [0.0 < float < 1.0 (default: 1e-05)] The minimum step reduction factor.
compute_jacobian(vec_x, fun_smooth_grad, fun_a_grad, fun_b_grad, vec_smooth_r, vec_a_r, vec_b_r)

name = 'nls.semismooth_newton'

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sfepy.solvers.solvers module

Base (abstract) solver classes.

class sfepy.solvers.solvers.EigenvalueSolver(conf, mtx_a=None, mtx_b=None, n_eigs=None,
eigenvectors=None, status=None, context=None,
**kwargs)
Abstract eigenvalue solver class.
class sfepy.solvers.solvers.LinearSolver(conf, mtx=None, status=None, context=None, **kwargs)
Abstract linear solver class.
get_tolerance()
Return tuple (eps_a, eps_r) of absolute and relative tolerance settings. Either value can be None, meaning
that the solver does not use that setting.
presolve(mtx)

class sfepy.solvers.solvers.NonlinearSolver(conf, fun=None, fun_grad=None, lin_solver=None,

iter_hook=None, status=None, context=None, **kwargs)
Abstract nonlinear solver class.
class sfepy.solvers.solvers.OptimizationSolver(conf, obj_fun=None, obj_fun_grad=None,
status=None, obj_args=None, context=None,
**kwargs)
Abstract optimization solver class.
class sfepy.solvers.solvers.QuadraticEVPSolver(conf, mtx_m=None, mtx_d=None, mtx_k=None,
n_eigs=None, eigenvectors=None, status=None,
context=None, **kwargs)
Abstract quadratic eigenvalue problem solver class.
class sfepy.solvers.solvers.Solver(conf=None, context=None, **kwargs)
Base class for all solver kinds. Takes care of processing of common configuration options.
The factory method any_from_conf() can be used to create an instance of any subclass.
The subclasses have to reimplement __init__() and __call__().
All solvers use the following configuration parameters:
Parameters
name [str] The name referred to in problem description options.
kind [str] The solver kind, as given by the name class attribute of the Solver subclasses.
verbose [bool (default: False)] If True, the solver can print more information about the solution.
static any_from_conf(conf, **kwargs)
Create an instance of a solver class according to the configuration.
build_solver_kwargs(conf )
Build the kwargs dict for the underlying solver function using the extra options (marked by ‘*’ in
_parameters) in conf. The declared parameters are omitted.
classmethod process_conf(conf, kwargs)
Process configuration parameters.
set_field_split(field_ranges, **kwargs)

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class sfepy.solvers.solvers.SolverMeta(name, bases, ndict)

Metaclass for solver classes that automatically adds configuration parameters to the solver class docstring from
the _parameters class attribute.
class sfepy.solvers.solvers.TimeSteppingSolver(conf, nls=None, status=None, context=None,
**kwargs)
Abstract time stepping solver class.
sfepy.solvers.solvers.format_next(text, new_text, pos, can_newline, width, ispaces)

sfepy.solvers.solvers.make_get_conf(conf, kwargs)

sfepy.solvers.solvers.make_option_docstring(name, kind, default, required, doc)

sfepy.solvers.solvers.typeset_to_indent(txt, indent, width)

sfepy.solvers.solvers.use_first_available(solver_list, context=None, **kwargs)

Use the first available solver from solver_list.
Parameters
solver_list [list of str or Struct] The list of solver names or configuration objects.
context [object, optional] An optional solver context to pass to the solver.
**kwargs [keyword arguments] Additional solver options, see the particular __init__() methods.
Returns
out [Solver] The first available solver.

sfepy.solvers.ts module

class sfepy.solvers.ts.TimeStepper(t0, t1, dt=None, n_step=None, step=None, is_quasistatic=False)

Time stepper class.
advance()

static from_conf(conf )

get_state()

iter_from(step)

normalize_time()

restore_step_time()

set_from_data(t0, t1, dt=None, n_step=None, step=None)

set_from_ts(ts, step=None)

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set_state(step=0, **kwargs)

set_step(step=0, nt=0.0)

set_substep_time(sub_dt)

class sfepy.solvers.ts.VariableTimeStepper(t0, t1, dt=None, n_step=None, step=None,

is_quasistatic=False)
Time stepper class with a variable time step.
advance()

static from_conf(conf )

get_default_time_step()

get_state()

iter_from(step)

iter_from_current()
ts.step, ts.time is consistent with step, time returned here ts.nt is normalized time in [0, 1].
set_from_data(t0, t1, dt=None, n_step=None, step=None)

set_from_ts(ts, step=None)

set_n_digit_from_min_dt(dt)

set_state(step=0, dts=None, times=None, **kwargs)

set_step(step=0, nt=0.0)

set_time_step(dt, update_time=False)

sfepy.solvers.ts.get_print_info(n_step)

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sfepy.solvers.ts_solvers module

Time stepping solvers.

class sfepy.solvers.ts_solvers.AdaptiveTimeSteppingSolver(conf, nls=None, context=None,
**kwargs)
Implicit time stepping solver with an adaptive time step.
Either the built-in or user supplied function can be used to adapt the time step.
Kind: ‘ts.adaptive’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
t0 [float (default: 0.0)] The initial time.
t1 [float (default: 1.0)] The final time.
dt [float] The time step. Used if n_step is not given.
n_step [int (default: 10)] The number of time steps. Has precedence over dt.
quasistatic [bool (default: False)] If True, assume a quasistatic time-stepping. Then the non-
linear solver is invoked also for the initial time.
adapt_fun [callable(ts, status, adt, context, verbose)] If given, use this function to set the time
step in ts. The function return value is a bool - if True, the adaptivity loop should stop. The
other parameters below are collected in adt, status is the nonlinear solver status, context is
a user-defined context and verbose is a verbosity flag. Solvers created by Problem use the
Problem instance as the context.
dt_red_factor [float (default: 0.2)] The time step reduction factor.
dt_red_max [float (default: 0.001)] The maximum time step reduction factor.
dt_inc_factor [float (default: 1.25)] The time step increase factor.
dt_inc_on_iter [int (default: 4)] Increase the time step if the nonlinear solver converged in less
than this amount of iterations for dt_inc_wait consecutive time steps.
dt_inc_wait [int (default: 5)] The number of consecutive time steps, see dt_inc_on_iter.
name = 'ts.adaptive'
output_step_info(ts)

solve_step(ts, nls, vec, prestep_fun)

Solve a single time step.
class sfepy.solvers.ts_solvers.BatheTS(conf, nls=None, context=None, **kwargs)
Solve elastodynamics problems by the Bathe method.
The method was introduced in [1].
[1] Klaus-Juergen Bathe, Conserving energy and momentum in nonlinear dynamics: A simple implicit time
integration scheme, Computers & Structures, Volume 85, Issues 7-8, 2007, Pages 437-445, ISSN 0045-7949,
https://doi.org/10.1016/j.compstruc.2006.09.004.
Kind: ‘ts.bathe’
For common configuration parameters, see Solver.

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Specific configuration parameters:

Parameters
t0 [float (default: 0.0)] The initial time.
t1 [float (default: 1.0)] The final time.
dt [float] The time step. Used if n_step is not given.
n_step [int (default: 10)] The number of time steps. Has precedence over dt.
is_linear [bool (default: False)] If True, the problem is considered to be linear.
create_nlst1(nls, dt, u0, v0, a0)
The first sub-step: the trapezoidal rule.
create_nlst2(nls, dt, u0, u1, v0, v1)
The second sub-step: the three-point Euler backward method.
name = 'ts.bathe'
class sfepy.solvers.ts_solvers.ElastodynamicsBaseTS(conf, nls=None, context=None, **kwargs)
Base class for elastodynamics solvers.
Assumes block-diagonal matrix in u, v, a.
get_a0(nls, u0, v0)

get_initial_vec(nls, vec0, init_fun, prestep_fun, poststep_fun)

get_matrices(nls, vec)

class sfepy.solvers.ts_solvers.GeneralizedAlphaTS(conf, nls=None, context=None, **kwargs)

Solve elastodynamics problems by the generalized 𝛼 method.
• The method was introduced in [1].
• The method is unconditionally stable provided 𝛼𝑚 ≤ 𝛼𝑓 ≤ 12 , 𝛽 >= 1
4 + 12 (𝛼𝑓 − 𝛼𝑚 ).
• The method is second-order accurate provided 𝛾 = 1
2 − 𝛼𝑚 + 𝛼𝑓 . This is used when gamma is None.
• High frequency dissipation is maximized for 𝛽 = 1
4 (1 − 𝛼𝑚 + 𝛼𝑓 )2 . This is used when beta is None.
• The default values of 𝛼𝑚 , 𝛼𝑓 (if alpha_m or alpha_f are None) are based on the user specified high-
frequency dissipation parameter rho_inf.
Special settings:
• 𝛼𝑚 = 0 corresponds to the HHT-𝛼 method.
• 𝛼𝑓 = 0 corresponds to the WBZ-𝛼 method.
• 𝛼𝑚 = 0, 𝛼𝑓 = 0 produces the Newmark method.
[1] J. Chung, G.M.Hubert. “A Time Integration Algorithm for Structural Dynamics with Improved Numerical
Dissipation: The Generalized-𝛼 Method” ASME Journal of Applied Mechanics, 60, 371:375, 1993.
Kind: ‘ts.generalized_alpha’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters

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t0 [float (default: 0.0)] The initial time.

t1 [float (default: 1.0)] The final time.
dt [float] The time step. Used if n_step is not given.
n_step [int (default: 10)] The number of time steps. Has precedence over dt.
is_linear [bool (default: False)] If True, the problem is considered to be linear.
rho_inf [float (default: 0.5)] The spectral radius in the high frequency limit (user specified high-
frequency dissipation) in [0, 1]: 1 = no dissipation, 0 = asymptotic annihilation.
alpha_m [float] The parameter 𝛼𝑚 .
alpha_f [float] The parameter 𝛼𝑓 .
beta [float] The Newmark-like parameter 𝛽.
gamma [float] The Newmark-like parameter 𝛾.
create_nlst(nls, dt, alpha_m, alpha_f, gamma, beta, u0, v0, a0)

name = 'ts.generalized_alpha'
class sfepy.solvers.ts_solvers.NewmarkTS(conf, nls=None, context=None, **kwargs)
Solve elastodynamics problems by the Newmark method.
The method was introduced in [1]. Common settings [2]:

name kind beta gamma Omega_crit

trapezoidal rule: implicit 1/4 1/2 unconditional
√
linear acceleration: implicit 1/6 1/2 2√ 3
Fox-Goodwin: implicit 1/12 1/2 6
central difference: explicit 0 1/2 2

All of these methods are 2-order of accuracy.

[1] Newmark, N. M. (1959) A method of computation for structural dynamics. Journal of Engineering Mechan-
ics, ASCE, 85 (EM3) 67-94.
[2] Arnaud Delaplace, David Ryckelynck: Solvers for Computational Mechanics
Kind: ‘ts.newmark’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
t0 [float (default: 0.0)] The initial time.
t1 [float (default: 1.0)] The final time.
dt [float] The time step. Used if n_step is not given.
n_step [int (default: 10)] The number of time steps. Has precedence over dt.
is_linear [bool (default: False)] If True, the problem is considered to be linear.
beta [float (default: 0.25)] The Newmark method parameter beta.
gamma [float (default: 0.5)] The Newmark method parameter gamma.

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create_nlst(nls, dt, gamma, beta, u0, v0, a0)

name = 'ts.newmark'
class sfepy.solvers.ts_solvers.SimpleTimeSteppingSolver(conf, nls=None, context=None, **kwargs)
Implicit time stepping solver with a fixed time step.
Kind: ‘ts.simple’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters
t0 [float (default: 0.0)] The initial time.
t1 [float (default: 1.0)] The final time.
dt [float] The time step. Used if n_step is not given.
n_step [int (default: 10)] The number of time steps. Has precedence over dt.
quasistatic [bool (default: False)] If True, assume a quasistatic time-stepping. Then the non-
linear solver is invoked also for the initial time.
name = 'ts.simple'
output_step_info(ts)

solve_step(ts, nls, vec, prestep_fun=None)

solve_step0(nls, vec0)

class sfepy.solvers.ts_solvers.StationarySolver(conf, nls=None, context=None, **kwargs)

Solver for stationary problems without time stepping.
This class is provided to have a unified interface of the time stepping solvers also for stationary problems.
Kind: ‘ts.stationary’
For common configuration parameters, see Solver.
Specific configuration parameters:
name = 'ts.stationary'
class sfepy.solvers.ts_solvers.VelocityVerletTS(conf, nls=None, context=None, **kwargs)
Solve elastodynamics problems by the velocity-Verlet method.
The algorithm can be found in [1].
[1] Swope, William C.; H. C. Andersen; P. H. Berens; K. R. Wilson (1 January 1982). “A computer simulation
method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Applica-
tion to small water clusters”. The Journal of Chemical Physics. 76 (1): 648 (Appendix). doi:10.1063/1.442716
Kind: ‘ts.velocity_verlet’
For common configuration parameters, see Solver.
Specific configuration parameters:
Parameters

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t0 [float (default: 0.0)] The initial time.

t1 [float (default: 1.0)] The final time.
dt [float] The time step. Used if n_step is not given.
n_step [int (default: 10)] The number of time steps. Has precedence over dt.
is_linear [bool (default: False)] If True, the problem is considered to be linear.
create_nlst(nls, dt, u0, v0, a0)

name = 'ts.velocity_verlet'
sfepy.solvers.ts_solvers.adapt_time_step(ts, status, adt, context=None, verbose=False)
Adapt the time step of ts according to the exit status of the nonlinear solver.
The time step dt is reduced, if the nonlinear solver did not converge. If it converged in less then a specified number
of iterations for several time steps, the time step is increased. This is governed by the following parameters:
• red_factor : time step reduction factor
• red_max : maximum time step reduction factor
• inc_factor : time step increase factor
• inc_on_iter : increase time step if the nonlinear solver converged in less than this amount of iterations. . .
• inc_wait : . . . for this number of consecutive time steps

Parameters
ts [VariableTimeStepper instance] The time stepper.
status [IndexedStruct instance] The nonlinear solver exit status.
adt [Struct instance] The object with the adaptivity parameters of the time-stepping solver such
as red_factor (see above) as attributes.
context [object, optional] The context can be used in user-defined adaptivity functions. Not used
here.
Returns
is_break [bool] If True, the adaptivity loop should stop.

sfepy.solvers.ts_solvers.gen_multi_vec_packing(size, num)

sfepy.solvers.ts_solvers.get_min_dt(adt)

sfepy.solvers.ts_solvers.standard_ts_call(call)
Decorator handling argument preparation and timing for time-stepping solvers.

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sfepy.terms package

sfepy.terms.terms module

class sfepy.terms.terms.ConnInfo(**kwargs)

get_region(can_trace=True)

get_region_name(can_trace=True)

class sfepy.terms.terms.Term(name, arg_str, integral, region, **kwargs)

advance(ts)
Advance to the next time step. Implemented in subclasses.
arg_shapes = {}
arg_types = ()
assemble_to(asm_obj, val, iels, mode='vector', diff_var=None)
Assemble the results of term evaluation.
For standard terms, assemble the values in val corresponding to elements/cells iels into a vector or a CSR
sparse matrix asm_obj, depending on mode.
For terms with a dynamic connectivity (e.g. contact terms), in ‘matrix’ mode, return the extra COO sparse
matrix instead. The extra matrix has to be added to the global matrix by the caller. By default, this is done
in Equations.evaluate().
assign_args(variables, materials, user=None)
Check term argument existence in variables, materials, user data and assign the arguments to terms. Also
check compatibility of field and term regions.
call_function(out, fargs)

call_get_fargs(args, kwargs)

check_args()
Common checking to all terms.
Check compatibility of field and term regions.
check_shapes(*args, **kwargs)
Check term argument shapes at run-time.
classify_args()
Classify types of the term arguments and find matching call signature.
A state variable can be in place of a parameter variable and vice versa.
eval_complex(shape, fargs, mode='eval', term_mode=None, diff_var=None, **kwargs)

eval_real(shape, fargs, mode='eval', term_mode=None, diff_var=None, **kwargs)

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evaluate(mode='eval', diff_var=None, standalone=True, ret_status=False, **kwargs)

Evaluate the term.
Parameters
mode [‘eval’ (default), or ‘weak’] The term evaluation mode.
Returns
val [float or array] In ‘eval’ mode, the term returns a single value (the integral, it does not
need to be a scalar), while in ‘weak’ mode it returns an array for each element.
status [int, optional] The flag indicating evaluation success (0) or failure (nonzero). Only
provided if ret_status is True.
iels [array of ints, optional] The local elements indices in ‘weak’ mode. Only provided in
non-‘eval’ modes.
static from_desc(constructor, desc, region, integrals=None)

geometries = ['1_2', '2_3', '2_4', '3_4', '3_8']

get(variable, quantity_name, bf=None, integration=None, step=None, time_derivative=None)
Get the named quantity related to the variable.

Notes

This is a convenience wrapper of Variable.evaluate() that initializes the arguments using the term data.
get_arg_name(arg_type, full=False, join=None)
Get the name of the argument specified by arg_type.
Parameters
arg_type [str] The argument type string.
full [bool] If True, return the full name. For example, if the name of a variable argument is
‘u’ and its time derivative is requested, the full name is ‘du/dt’.
join [str, optional] Optionally, the material argument name tuple can be joined to a single
string using the join string.
Returns
name [str] The argument name.
get_args(arg_types=None, **kwargs)
Return arguments by type as specified in arg_types (or self.ats). Arguments in **kwargs can override the
ones assigned at the term construction - this is useful for passing user data.
get_args_by_name(arg_names)
Return arguments by name.
get_assembling_cells(shape=None)
Return the assembling cell indices into a DOF connectivity.
get_conn_info()

get_conn_key()
The key to be used in DOF connectivity information.

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get_data_shape(variable)
Get data shape information from variable.

Notes

This is a convenience wrapper of FieldVariable.get_data_shape() that initializes the arguments using the
term data.
get_dof_conn_type()

get_geometry_types()

Returns
out [dict] The required geometry types for each variable argument.
get_kwargs(keys, **kwargs)
Extract arguments from **kwargs listed in keys (default is None).
get_mapping(variable, get_saved=False, return_key=False)
Get the reference mapping from a variable.

Notes

This is a convenience wrapper of Field.get_mapping() that initializes the arguments using the term data.
get_material_names()

get_materials(join=False)

get_parameter_names()

get_parameter_variables()

get_physical_qps()
Get physical quadrature points corresponding to the term region and integral.
get_qp_key()
Return a key identifying uniquely the term quadrature points.
get_region()

get_state_names()
If variables are given, return only true unknowns whose data are of the current time step (0).
get_state_variables(unknown_only=False)

get_str()

get_user_names()

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get_variable_names()

get_variables(as_list=True)

get_vector(variable)
Get the vector stored in variable according to self.arg_steps and self.arg_derivatives. Supports only the
backward difference w.r.t. time.
get_virtual_name()

get_virtual_variable()

integration = 'volume'
name = ''
static new(name, integral, region, **kwargs)

set_arg_types()

set_integral(integral)
Set the term integral.
setup()

setup_args(**kwargs)

setup_formal_args()

setup_integration()

standalone_setup()

static tile_mat(mat, nel)

time_update(ts)

class sfepy.terms.terms.Terms(objs=None)

append(obj)

assign_args(variables, materials, user=None)

Assign all term arguments.
static from_desc(term_descs, regions, integrals=None)
Create terms, assign each term its region.
get_material_names()

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get_user_names()

get_variable_names()

insert(ii, obj)

setup()

update_expression()

sfepy.terms.terms.create_arg_parser()

sfepy.terms.terms.get_arg_kinds(arg_types)
Translate arg_types of a Term to a canonical form.
Parameters
arg_types [tuple of strings] The term argument types, as given in the arg_types attribute.
Returns
arg_kinds [list of strings] The argument kinds - one of ‘virtual_variable’, ‘state_variable’, ‘pa-
rameter_variable’, ‘opt_material’, ‘ts’, ‘user’.
sfepy.terms.terms.get_shape_kind(integration)
Get data shape kind for given integration type.
sfepy.terms.terms.split_complex_args(args)
Split complex arguments to real and imaginary parts.
Returns
newargs [dictionary] Dictionary with lists corresponding to args such that each argument of
numpy.complex128 data type is split to its real and imaginary part. The output depends on
the number of complex arguments in ‘args’:
• 0: list (key ‘r’) identical to input one
• 1: two lists with keys ‘r’, ‘i’ corresponding to real and imaginary parts
• 2: output dictionary contains four lists:
– ‘r’ - real(arg1), real(arg2)
– ‘i’ - imag(arg1), imag(arg2)
– ‘ri’ - real(arg1), imag(arg2)
– ‘ir’ - imag(arg1), real(arg2)

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sfepy.terms.terms_adj_navier_stokes module

class sfepy.terms.terms_adj_navier_stokes.AdjConvect1Term(name, arg_str, integral, region,

**kwargs)
The first adjoint term to nonlinear convective term dw_convect.
Definition
∫︁
((𝑣 · ∇)𝑢) · 𝑤
Ω
Call signature

dw_adj_convect1 (virtual, state, parameter)

Arguments
• virtual : 𝑣
• state : 𝑤
• parameter : 𝑢

arg_shapes = {'parameter': 'D', 'state': 'D', 'virtual': ('D', 'state')}

arg_types = ('virtual', 'state', 'parameter')
static function()

get_fargs(virtual, state, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_adj_convect1'
class sfepy.terms.terms_adj_navier_stokes.AdjConvect2Term(name, arg_str, integral, region,
**kwargs)
The second adjoint term to nonlinear convective term dw_convect.
Definition
∫︁
((𝑢 · ∇)𝑣) · 𝑤
Ω
Call signature

dw_adj_convect2 (virtual, state, parameter)

Arguments
• virtual : 𝑣
• state : 𝑤
• parameter : 𝑢

arg_shapes = {'parameter': 'D', 'state': 'D', 'virtual': ('D', 'state')}

arg_types = ('virtual', 'state', 'parameter')
static function()

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get_fargs(virtual, state, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_adj_convect2'
class sfepy.terms.terms_adj_navier_stokes.AdjDivGradTerm(name, arg_str, integral, region,
**kwargs)
Gateaux differential of Ψ(𝑢) = Ω 𝜈 ∇𝑣 : ∇𝑢 w.r.t. 𝑢 in the direction 𝑣 or adjoint term to dw_div_grad.
∫︀

Definition
𝑤𝛿𝑢 Ψ(𝑢) ∘ 𝑣
Call signature

dw_adj_div_grad (material_1, material_2, virtual, parameter)

Arguments
• material_1 : 𝑤 (weight)
• material_2 : 𝜈 (viscosity)
• virtual : 𝑣
• state : 𝑢

arg_shapes = {'material_1': '1, 1', 'material_2': '1, 1', 'parameter': 'D',

'virtual': ('D', None)}
arg_types = ('material_1', 'material_2', 'virtual', 'parameter')
static function()

get_fargs(mat1, mat2, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_adj_div_grad'
class sfepy.terms.terms_adj_navier_stokes.NSOFMinGradTerm(name, arg_str, integral, region,
**kwargs)

Call signature

d_of_ns_min_grad (material_1, material_2, parameter)

arg_shapes = {'material_1': '1, 1', 'material_2': '1, 1', 'parameter': 1}

arg_types = ('material_1', 'material_2', 'parameter')
static function()

get_eval_shape(weight, mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(weight, mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'd_of_ns_min_grad'

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class sfepy.terms.terms_adj_navier_stokes.NSOFSurfMinDPressDiffTerm(name, arg_str, integral,

region, **kwargs)
Gateaux differential of Ψ(𝑝) w.r.t. 𝑝 in the direction 𝑞.
Definition
𝑤𝛿𝑝 Ψ(𝑝) ∘ 𝑞
Call signature

dw_of_ns_surf_min_d_press_diff (material, virtual)

Arguments
• material : 𝑤 (weight)
• virtual : 𝑞

arg_shapes = {'material': 1, 'virtual': (1, None)}

arg_types = ('material', 'virtual')
get_fargs(weight, virtual, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_of_ns_surf_min_d_press_diff'
class sfepy.terms.terms_adj_navier_stokes.NSOFSurfMinDPressTerm(name, arg_str, integral, region,
**kwargs)
Sensitivity of Ψ(𝑝).
Definition
(︂∫︁ ∫︁ )︂
𝛿Ψ(𝑝) = 𝛿 𝑝− 𝑏𝑝𝑟𝑒𝑠𝑠
Γ𝑖𝑛 Γ𝑜𝑢𝑡

Call signature

ev_of_ns_surf_min_d_press (material_1, material_2, parameter)

Arguments
• material_1 : 𝑤 (weight)
• material_2 : 𝑏𝑝𝑟𝑒𝑠𝑠 (given pressure)
• parameter : 𝑝

arg_shapes = {'material_1': 1, 'material_2': 1, 'parameter': 1}

arg_types = ('material_1', 'material_2', 'parameter')
static function()

get_eval_shape(weight, bpress, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(weight, bpress, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'surface'

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name = 'ev_of_ns_surf_min_d_press'
class sfepy.terms.terms_adj_navier_stokes.SDConvectTerm(name, arg_str, integral, region, **kwargs)
Sensitivity (shape derivative) of convective term dw_convect.
Supports the following term modes: 1 (sensitivity) or 0 (original term value).
Definition
∫︁
𝜕𝑢𝑖 𝜕𝒱𝑗 𝜕𝑢𝑖
[𝑢𝑘 𝑤𝑖 (∇ · 𝒱) − 𝑢𝑘 𝑤𝑖 ]
Ω 𝜕𝑥𝑘 𝜕𝑥𝑘 𝜕𝑥𝑗
Call signature

ev_sd_convect (parameter_u, parameter_w, parameter_mv)

Arguments
• parameter_u : 𝑢
• parameter_w : 𝑤
• parameter_mv : 𝒱

arg_shapes = {'parameter_mv': 'D', 'parameter_u': 'D', 'parameter_w': 'D'}

arg_types = ('parameter_u', 'parameter_w', 'parameter_mv')
static function()

get_eval_shape(par_u, par_w, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(par_u, par_w, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'ev_sd_convect'
class sfepy.terms.terms_adj_navier_stokes.SDDivGradTerm(name, arg_str, integral, region, **kwargs)
Sensitivity (shape derivative) of diffusion term dw_div_grad.
Supports the following term modes: 1 (sensitivity) or 0 (original term value).
Definition
∫︁ ∫︁
ˆ
𝐼∇𝑣 : ∇𝑢 , ˆ
𝜈 𝐼∇𝑣 : ∇𝑢
Ω Ω
𝜕𝒱𝑙 𝜕𝒱𝑘
𝐼ˆ𝑖𝑗𝑘𝑙 = 𝛿𝑖𝑘 𝛿𝑗𝑙 ∇ · 𝒱 − 𝛿𝑖𝑘 𝛿𝑗𝑠 − 𝛿𝑖𝑠 𝛿𝑗𝑙
𝜕𝑥𝑠 𝜕𝑥𝑠
Call signature

ev_sd_div_grad (opt_material, parameter_u, parameter_w, parameter_mv)

Arguments
• material : 𝜈 (viscosity, optional)
• parameter_u : 𝑢
• parameter_w : 𝑤
• parameter_mv : 𝒱

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arg_shapes = [{'opt_material': '1, 1', 'parameter_u': 'D', 'parameter_w': 'D',

'parameter_mv': 'D'}, {'opt_material': None}]
arg_types = ('opt_material', 'parameter_u', 'parameter_w', 'parameter_mv')
static function()

get_eval_shape(mat, par_u, par_w, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, par_u, par_w, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'ev_sd_div_grad'
class sfepy.terms.terms_adj_navier_stokes.SDDivTerm(name, arg_str, integral, region, **kwargs)
Sensitivity (shape derivative) of Stokes term dw_stokes in ‘div’ mode.
Supports the following term modes: 1 (sensitivity) or 0 (original term value).
Definition
∫︁
𝜕𝒱𝑘 𝜕𝑤𝑖
𝑝[(∇ · 𝑤)(∇ · 𝒱) − ]
Ω 𝜕𝑥𝑖 𝜕𝑥𝑘
Call signature

ev_sd_div (parameter_u, parameter_p, parameter_mv)

Arguments
• parameter_u : 𝑢
• parameter_p : 𝑝
• parameter_mv : 𝒱

arg_shapes = {'parameter_mv': 'D', 'parameter_p': 1, 'parameter_u': 'D'}

arg_types = ('parameter_u', 'parameter_p', 'parameter_mv')
static function()

get_eval_shape(par_u, par_p, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(par_u, par_p, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'ev_sd_div'
class sfepy.terms.terms_adj_navier_stokes.SDDotTerm(name, arg_str, integral, region, **kwargs)
Sensitivity (shape derivative) of dot product of scalars or vectors.
Definition
∫︁ ∫︁
𝑝𝑞(∇ · 𝒱) , (𝑢 · 𝑤)(∇ · 𝒱)
Ω Ω
Call signature

ev_sd_dot (parameter_1, parameter_2, parameter_mv)

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Arguments
• parameter_1 : 𝑝 or 𝑢
• parameter_2 : 𝑞 or 𝑤
• parameter_mv : 𝒱

arg_shapes = [{'parameter_1': 'D', 'parameter_2': 'D', 'parameter_mv': 'D'},

{'parameter_1': 1, 'parameter_2': 1}]
arg_types = ('parameter_1', 'parameter_2', 'parameter_mv')
static function()

get_eval_shape(par1, par2, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(par1, par2, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'ev_sd_dot'
class sfepy.terms.terms_adj_navier_stokes.SDGradDivStabilizationTerm(name, arg_str, integral,
region, **kwargs)
Sensitivity (shape derivative) of stabilization term dw_st_grad_div.
Definition
∫︁
𝜕𝑢𝑖 𝜕𝒱𝑘 𝜕𝑤𝑖 𝜕𝒱𝑘
𝛾 [(∇ · 𝑢)(∇ · 𝑤)(∇ · 𝒱) − (∇ · 𝑤) − (∇ · 𝑢) ]
Ω 𝜕𝑥𝑘 𝜕𝑥𝑖 𝜕𝑥𝑘 𝜕𝑥𝑖
Call signature

ev_sd_st_grad_div (material, parameter_u, parameter_w, parameter_mv)

Arguments
• material : 𝛾
• parameter_u : 𝑢
• parameter_w : 𝑤
• parameter_mv : 𝒱
• mode : 1 (sensitivity) or 0 (original term value)

arg_shapes = {'material': '1, 1', 'parameter_mv': 'D', 'parameter_u': 'D',

'parameter_w': 'D'}
arg_types = ('material', 'parameter_u', 'parameter_w', 'parameter_mv')
static function()

get_eval_shape(mat, par_u, par_w, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, par_u, par_w, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'ev_sd_st_grad_div'

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class sfepy.terms.terms_adj_navier_stokes.SDPSPGCStabilizationTerm(name, arg_str, integral,

region, **kwargs)
Sensitivity (shape derivative) of stabilization terms dw_st_supg_p or dw_st_pspg_c.
Definition
∑︁ ∫︁ 𝜕𝑟 𝜕𝑟 𝜕𝒱𝑘 𝜕𝑟 𝜕𝑢𝑖
𝛿𝐾 [ (𝑏 · ∇𝑢𝑖 )(∇ · 𝒱) − (𝑏 · ∇𝑢𝑖 ) − (𝑏 · ∇𝒱𝑘 ) ]
𝑇𝐾 𝜕𝑥𝑖 𝜕𝑥𝑘 𝜕𝑥𝑖 𝜕𝑥𝑘 𝜕𝑥𝑘
𝐾∈ℐℎ

Call signature

ev_sd_st_pspg_c (material, parameter_b, parameter_u, parameter_r, parameter_mv)

Arguments
• material : 𝛿𝐾
• parameter_b : 𝑏
• parameter_u : 𝑢
• parameter_r : 𝑟
• parameter_mv : 𝒱
• mode : 1 (sensitivity) or 0 (original term value)

arg_shapes = {'material': '1, 1', 'parameter_b': 'D', 'parameter_mv': 'D',

'parameter_r': 1, 'parameter_u': 'D'}
arg_types = ('material', 'parameter_b', 'parameter_u', 'parameter_r',
'parameter_mv')
static function()

get_eval_shape(mat, par_b, par_u, par_r, par_mv, mode=None, term_mode=None, diff_var=None,

**kwargs)

get_fargs(mat, par_b, par_u, par_r, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'ev_sd_st_pspg_c'
class sfepy.terms.terms_adj_navier_stokes.SDPSPGPStabilizationTerm(name, arg_str, integral,
region, **kwargs)
Sensitivity (shape derivative) of stabilization term dw_st_pspg_p.
Definition
∑︁ ∫︁ 𝜕𝑟 𝜕𝑝
𝜏𝐾 [(∇𝑟 · ∇𝑝)(∇ · 𝒱) − (∇𝒱𝑘 · ∇𝑝) − (∇𝑟 · ∇𝒱𝑘 ) ]
𝑇𝐾 𝜕𝑥𝑘 𝜕𝑥𝑘
𝐾∈ℐℎ

Call signature

ev_sd_st_pspg_p (material, parameter_r, parameter_p, parameter_mv)

Arguments
• material : 𝜏𝐾
• parameter_r : 𝑟

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• parameter_p : 𝑝
• parameter_mv : 𝒱
• mode : 1 (sensitivity) or 0 (original term value)

arg_shapes = {'material': '1, 1', 'parameter_mv': 'D', 'parameter_p': 1,

'parameter_r': 1}
arg_types = ('material', 'parameter_r', 'parameter_p', 'parameter_mv')
static function()

get_eval_shape(mat, par_r, par_p, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, par_r, par_p, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'ev_sd_st_pspg_p'
class sfepy.terms.terms_adj_navier_stokes.SDSUPGCStabilizationTerm(name, arg_str, integral,
region, **kwargs)
Sensitivity (shape derivative) of stabilization term dw_st_supg_c.
Definition
∑︁ ∫︁ 𝜕𝑢𝑘 𝜕𝑤𝑘
𝛿𝐾 [(𝑏 · ∇𝑢𝑘 )(𝑏 · ∇𝑤𝑘 )(∇ · 𝒱) − (𝑏 · ∇𝒱𝑖 ) (𝑏 · ∇𝑤𝑘 ) − (𝑢 · ∇𝑢𝑘 )(𝑏 · ∇𝒱𝑖 ) ]
𝑇𝐾 𝜕𝑥𝑖 𝜕𝑥𝑖
𝐾∈ℐℎ

Call signature

ev_sd_st_supg_c (material, parameter_b, parameter_u, parameter_w, parameter_mv)

Arguments
• material : 𝛿𝐾
• parameter_b : 𝑏
• parameter_u : 𝑢
• parameter_w : 𝑤
• parameter_mv : 𝒱
• mode : 1 (sensitivity) or 0 (original term value)

arg_shapes = {'material': '1, 1', 'parameter_b': 'D', 'parameter_mv': 'D',

'parameter_u': 'D', 'parameter_w': 'D'}
arg_types = ('material', 'parameter_b', 'parameter_u', 'parameter_w',
'parameter_mv')
static function()

get_eval_shape(mat, par_b, par_u, par_w, par_mv, mode=None, term_mode=None, diff_var=None,

**kwargs)

get_fargs(mat, par_b, par_u, par_w, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

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name = 'ev_sd_st_supg_c'
class sfepy.terms.terms_adj_navier_stokes.SUPGCAdjStabilizationTerm(name, arg_str, integral,
region, **kwargs)
Adjoint term to SUPG stabilization term dw_st_supg_c.
Definition
∑︁ ∫︁
𝛿𝐾 [((𝑣 · ∇)𝑢)((𝑢 · ∇)𝑤) + ((𝑢 · ∇)𝑢)((𝑣 · ∇)𝑤)]
𝐾∈ℐℎ 𝑇𝐾

Call signature

dw_st_adj_supg_c (material, virtual, parameter, state)

Arguments
• material : 𝛿𝐾
• virtual : 𝑣
• state : 𝑤
• parameter : 𝑢

arg_shapes = {'material': '1, 1', 'parameter': 'D', 'state': 'D', 'virtual':

('D', 'state')}
arg_types = ('material', 'virtual', 'parameter', 'state')
static function()

get_fargs(mat, virtual, state, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_st_adj_supg_c'
class sfepy.terms.terms_adj_navier_stokes.SUPGPAdj1StabilizationTerm(name, arg_str, integral,
region, **kwargs)
The first adjoint term to SUPG stabilization term dw_st_supg_p.
Definition
∑︁ ∫︁
𝛿𝐾 ∇𝑝(𝑣 · ∇𝑤)
𝐾∈ℐℎ 𝑇𝐾

Call signature

dw_st_adj1_supg_p (material, virtual, state, parameter)

Arguments
• material : 𝛿𝐾
• virtual : 𝑣
• state : 𝑤
• parameter : 𝑝

arg_shapes = {'material': '1, 1', 'parameter': 1, 'state': 'D', 'virtual': ('D',

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arg_types = ('material', 'virtual', 'state', 'parameter')

static function()

get_fargs(mat, virtual, state, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_st_adj1_supg_p'
class sfepy.terms.terms_adj_navier_stokes.SUPGPAdj2StabilizationTerm(name, arg_str, integral,
region, **kwargs)
The second adjoint term to SUPG stabilization term dw_st_supg_p as well as adjoint term to PSPG stabilization
term dw_st_pspg_c.
Definition
∑︁ ∫︁
𝜏𝐾 ∇𝑟(𝑣 · ∇𝑢)
𝐾∈ℐℎ 𝑇𝐾

Call signature

dw_st_adj2_supg_p (material, virtual, parameter, state)

Arguments
• material : 𝜏𝐾
• virtual : 𝑣
• parameter : 𝑢
• state : 𝑟

arg_shapes = {'material': '1, 1', 'parameter': 'D', 'state': 1, 'virtual': ('D',

'state')}
arg_types = ('material', 'virtual', 'parameter', 'state')
static function()

get_fargs(mat, virtual, parameter, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_st_adj2_supg_p'
sfepy.terms.terms_adj_navier_stokes.grad_as_vector(grad)

sfepy.terms.terms_basic module

class sfepy.terms.terms_basic.IntegrateMatTerm(name, arg_str, integral, region, **kwargs)

Evaluate material parameter 𝑚 in a volume region.
Depending on evaluation mode, integrate a material parameter over a volume region (‘eval’), average it in ele-
ments (‘el_avg’) or interpolate it into volume quadrature points (‘qp’).
Uses reference mapping of 𝑦 variable.
Supports ‘eval’, ‘el_avg’ and ‘qp’ evaluation modes.

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Definition
∫︁
𝑚
𝒟
∫︁ ∫︁
vector for 𝐾 ← ℐℎ : 𝑚/ 1
𝑇𝐾 𝑇𝐾

𝑚|𝑞𝑝
Call signature

ev_integrate_mat (material, parameter)

Arguments
• material : 𝑚 (can have up to two dimensions)
• parameter : 𝑦

arg_shapes = [{'material': 'N, N', 'parameter': 'N'}]

arg_types = ('material', 'parameter')
static function(out, mat, geo, fmode)

get_eval_shape(mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'by_region'
name = 'ev_integrate_mat'
class sfepy.terms.terms_basic.IntegrateOperatorTerm(name, arg_str, integral, region, **kwargs)
Integral of a test function weighted by a scalar function 𝑐.
Definition
∫︁ ∫︁
𝑞 or 𝑐𝑞
𝒟 𝒟
Call signature

dw_integrate (opt_material, virtual)

Arguments
• material : 𝑐 (optional)
• virtual : 𝑞

arg_shapes = [{'opt_material': '1, 1', 'virtual': (1, None)}, {'opt_material':

None}]
arg_types = ('opt_material', 'virtual')
static function(out, material, bf, geo)

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get_fargs(material, virtual, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'by_region'
name = 'dw_integrate'
class sfepy.terms.terms_basic.IntegrateTerm(name, arg_str, integral, region, **kwargs)
Evaluate (weighted) variable in a region.
Depending on evaluation mode, integrate a variable over a region (‘eval’), average it in elements (‘el_avg’) or
interpolate it into quadrature points (‘qp’). For a surface region and vector variables, setting term_mode to ‘flux’
leads to computing corresponding fluxes for the three modes instead.
Supports ‘eval’, ‘el_avg’ and ‘qp’ evaluation modes.
Definition
∫︁ ∫︁ ∫︁
𝑦, 𝑦, 𝑦·𝑛
∫︁ ∫︁ 𝒟 ∫︁𝒟 Γ

𝑐𝑦 , 𝑐𝑦 , 𝑐𝑦 · 𝑛 flux
𝒟 𝒟 Γ
∫︁ ∫︁ ∫︁ ∫︁ ∫︁ ∫︁
vector for 𝐾 ← ℐℎ : 𝑦/ 1, 𝑦/ 1, (𝑦 · 𝑛)/ 1
𝑇𝐾 𝑇𝐾 𝑇𝐾 𝑇𝐾 𝑇𝐾 𝑇𝐾
∫︁ ∫︁ ∫︁ ∫︁ ∫︁ ∫︁
vector for 𝐾 ← ℐℎ : 𝑐𝑦/ 1, 𝑐𝑦/ 1, (𝑐𝑦 · 𝑛)/ 1
𝑇𝐾 𝑇𝐾 𝑇𝐾 𝑇𝐾 𝑇𝐾 𝑇𝐾

𝑦|𝑞𝑝 , 𝑦|𝑞𝑝 , (𝑦 · 𝑛)|𝑞𝑝 flux

𝑐𝑦|𝑞𝑝 , 𝑐𝑦|𝑞𝑝 , (𝑐𝑦 · 𝑛)|𝑞𝑝 flux
Call signature

ev_integrate (opt_material, parameter)

Arguments
• material : 𝑐 (optional)
• parameter : 𝑦 or 𝑦

arg_shapes = [{'opt_material': '1, 1', 'parameter': 'N'}, {'opt_material': None}]

arg_types = ('opt_material', 'parameter')
static function(out, val_qp, vg, fmode)

get_eval_shape(material, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(material, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'by_region'
name = 'ev_integrate'
class sfepy.terms.terms_basic.SumNodalValuesTerm(name, arg_str, integral, region, **kwargs)
Sum nodal values.
Call signature

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ev_sum_vals (parameter)

Arguments
• parameter : 𝑝 or 𝑢

arg_shapes = {'parameter': 'N'}

arg_types = ('parameter',)
static function(out, vec)

get_eval_shape(parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'ev_sum_vals'
class sfepy.terms.terms_basic.SurfaceMomentTerm(name, arg_str, integral, region, **kwargs)
Surface integral of the outer product of the unit outward normal 𝑛 and the coordinate 𝑥 shifted by 𝑥0
Definition
∫︁
𝑛(𝑥 − 𝑥0 )
Γ
Call signature

ev_surface_moment (material, parameter)

Arguments
• material : 𝑥0 (special)
• parameter : any variable

arg_shapes = {'material': '.: D', 'parameter': 'N'}

arg_types = ('material', 'parameter')
static function()

get_eval_shape(material, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(material, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'surface'
name = 'ev_surface_moment'
class sfepy.terms.terms_basic.VolumeSurfaceTerm(name, arg_str, integral, region, **kwargs)
Volume of a 𝐷-dimensional domain, using a surface integral. Uses approximation of the parameter variable.
Definition
∫︁
1/𝐷 𝑥·𝑛
Γ

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Call signature

ev_volume_surface (parameter)

Arguments
• parameter : any variable

arg_shapes = {'parameter': 'N'}

arg_types = ('parameter',)
static function()

get_eval_shape(parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'surface'
name = 'ev_volume_surface'
class sfepy.terms.terms_basic.VolumeTerm(name, arg_str, integral, region, **kwargs)
Volume or surface of a domain. Uses approximation of the parameter variable.
Definition
∫︁
1
𝒟
Call signature

ev_volume (parameter)

Arguments
• parameter : any variable

arg_shapes = [{'parameter': 'N'}]

arg_types = ('parameter',)
static function(out, geo)

get_eval_shape(parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'by_region'
name = 'ev_volume'
class sfepy.terms.terms_basic.ZeroTerm(name, arg_str, integral, region, **kwargs)
A do-nothing term useful for introducing additional variables into the equations.
Definition
0

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Call signature

dw_zero (virtual, state)

Arguments
• virtual : 𝑞 or 𝑣
• state : 𝑝 or 𝑢

arg_shapes = {'state': 'N', 'virtual': ('N', None)}

arg_types = ('virtual', 'state')
static function(out)

get_fargs(vvar, svar, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_zero'

sfepy.terms.terms_biot module

class sfepy.terms.terms_biot.BiotETHTerm(name, arg_str, integral, region, **kwargs)

This term has the same definition as dw_biot_th, but assumes an exponential approximation of the convolution
kernel resulting in much higher efficiency. Can use derivatives.
Definition
∫︀ [︁∫︀ 𝑡 ]︁
𝛼 (𝑡 − 𝜏 ) 𝑝(𝜏 )) d𝜏 𝑒𝑖𝑗 (𝑣) ,
Ω [︁ 0 𝑖𝑗
∫︀ ∫︀ 𝑡 ]︁
Ω 0
𝛼𝑖𝑗 (𝑡 − 𝜏 )𝑒 𝑘𝑙 (𝑢(𝜏 )) d𝜏 𝑞

Call signature

dw_biot_eth (ts, material_0, material_1, virtual, state)

(ts, material_0, material_1, state, virtual)

Arguments 1
• ts : TimeStepper instance
• material_0 : 𝛼𝑖𝑗 (0)
• material_1 : exp(−𝜆∆𝑡) (decay at 𝑡1 )
• virtual : 𝑣
• state : 𝑝
Arguments 2
• ts : TimeStepper instance
• material_0 : 𝛼𝑖𝑗 (0)
• material_1 : exp(−𝜆∆𝑡) (decay at 𝑡1 )
• state : 𝑢
• virtual : 𝑞

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arg_shapes = {'material_0': 'S, 1', 'material_1': '1, 1', 'state/div': 'D',

'state/grad': 1, 'virtual/div': (1, None), 'virtual/grad': ('D', None)}
arg_types = (('ts', 'material_0', 'material_1', 'virtual', 'state'), ('ts',
'material_0', 'material_1', 'state', 'virtual'))
get_fargs(ts, mat0, mat1, vvar, svar, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('grad', 'div')

name = 'dw_biot_eth'
class sfepy.terms.terms_biot.BiotStressTerm(name, arg_str, integral, region, **kwargs)
Evaluate Biot stress tensor.
It is given in the usual vector form exploiting symmetry: in 3D it has 6 components with the indices ordered as
[11, 22, 33, 12, 13, 23], in 2D it has 3 components with the indices ordered as [11, 22, 12].
Supports ‘eval’, ‘el_avg’ and ‘qp’ evaluation modes.
Definition
∫︁
− 𝛼𝑖𝑗 𝑝¯
Ω
∫︁ ∫︁
vector for 𝐾 ← ℐℎ : − 𝛼𝑖𝑗 𝑝¯/ 1
𝑇𝐾 𝑇𝐾

−𝛼𝑖𝑗 𝑝¯|𝑞𝑝
Call signature

ev_biot_stress (material, parameter)

Arguments
• material : 𝛼𝑖𝑗
• parameter : 𝑝¯

arg_shapes = {'material': 'S, 1', 'parameter': 1}

arg_types = ('material', 'parameter')
static function(out, val_qp, mat, vg, fmode)

get_fargs(mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'volume'
name = 'ev_biot_stress'
class sfepy.terms.terms_biot.BiotTHTerm(name, arg_str, integral, region, **kwargs)
Fading memory Biot term. Can use derivatives.
Definition
∫︀ [︁∫︀ 𝑡 ]︁
Ω
𝛼
0 𝑖𝑗
(𝑡 − 𝜏 ) 𝑝(𝜏 )) d𝜏 𝑒𝑖𝑗 (𝑣) ,
∫︀ [︁∫︀ 𝑡 ]︁
Ω 0
𝛼𝑖𝑗 (𝑡 − 𝜏 )𝑒 𝑘𝑙 (𝑢(𝜏 )) d𝜏 𝑞

Call signature

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dw_biot_th (ts, material, virtual, state)

(ts, material, state, virtual)

Arguments 1
• ts : TimeStepper instance
• material : 𝛼𝑖𝑗 (𝜏 )
• virtual : 𝑣
• state : 𝑝
Arguments 2
• ts : TimeStepper instance
• material : 𝛼𝑖𝑗 (𝜏 )
• state : 𝑢
• virtual : 𝑞

arg_shapes = {'material': '.: N, S, 1', 'state/div': 'D', 'state/grad': 1,

'virtual/div': (1, None), 'virtual/grad': ('D', None)}
arg_types = (('ts', 'material', 'virtual', 'state'), ('ts', 'material', 'state',
'virtual'))
get_fargs(ts, mats, vvar, svar, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('grad', 'div')

name = 'dw_biot_th'
class sfepy.terms.terms_biot.BiotTerm(name, arg_str, integral, region, **kwargs)
Biot coupling term with 𝛼𝑖𝑗 given in:
• vector form exploiting symmetry - in 3D it has the indices ordered as [11, 22, 33, 12, 13, 23], in 2D it has
the indices ordered as [11, 22, 12],
• matrix form - non-symmetric coupling parameter.
Corresponds to weak forms of Biot gradient and divergence terms. Can be evaluated. Can use derivatives.
Definition
∫︁ ∫︁
𝑝 𝛼𝑖𝑗 𝑒𝑖𝑗 (𝑣) , 𝑞 𝛼𝑖𝑗 𝑒𝑖𝑗 (𝑢)
Ω Ω
Call signature

dw_biot (material, virtual, state)

(material, state, virtual)
(material, parameter_v, parameter_s)

Arguments 1
• material : 𝛼𝑖𝑗
• virtual : 𝑣
• state : 𝑝

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Arguments 2
• material : 𝛼𝑖𝑗
• state : 𝑢
• virtual : 𝑞
Arguments 3
• material : 𝛼𝑖𝑗
• parameter_v : 𝑢
• parameter_s : 𝑝

arg_shapes = [{'material': 'S, 1', 'virtual/grad': ('D', None), 'state/grad': 1,

'virtual/div': (1, None), 'state/div': 'D', 'parameter_v': 'D', 'parameter_s':
1}, {'material': 'D, D'}]
arg_types = (('material', 'virtual', 'state'), ('material', 'state', 'virtual'),
('material', 'parameter_v', 'parameter_s'))
get_eval_shape(mat, vvar, svar, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, vvar, svar, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('grad', 'div', 'eval')

name = 'dw_biot'
set_arg_types()

sfepy.terms.terms_compat module

class sfepy.terms.terms_compat.CauchyStrainSTerm(name, arg_str, integral, region, **kwargs)

Call signature

ev_cauchy_strain_s (parameter)

name = 'ev_cauchy_strain_s'
class sfepy.terms.terms_compat.DSumNodalValuesTerm(name, arg_str, integral, region, **kwargs)

Call signature

d_sum_vals (parameter)

name = 'd_sum_vals'
class sfepy.terms.terms_compat.DSurfaceFluxTerm(name, arg_str, integral, region, **kwargs)

Call signature

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d_surface_flux (material, parameter)

name = 'd_surface_flux'
class sfepy.terms.terms_compat.DSurfaceMomentTerm(name, arg_str, integral, region, **kwargs)

Call signature

d_surface_moment (material, parameter)

name = 'd_surface_moment'
class sfepy.terms.terms_compat.DVolumeSurfaceTerm(name, arg_str, integral, region, **kwargs)

Call signature

d_volume_surface (parameter)

name = 'd_volume_surface'
class sfepy.terms.terms_compat.DotSurfaceProductTerm(name, arg_str, integral, region, **kwargs)

Call signature

dw_surface_dot (opt_material, virtual, state)

(opt_material, parameter_1, parameter_2)

name = 'dw_surface_dot'
class sfepy.terms.terms_compat.DotVolumeProductTerm(name, arg_str, integral, region, **kwargs)

Call signature

dw_volume_dot (opt_material, virtual, state)

(opt_material, parameter_1, parameter_2)

name = 'dw_volume_dot'
class sfepy.terms.terms_compat.IntegrateSurfaceMatTerm(name, arg_str, integral, region, **kwargs)

Call signature

ev_surface_integrate_mat (material, parameter)

name = 'ev_surface_integrate_mat'
class sfepy.terms.terms_compat.IntegrateSurfaceOperatorTerm(name, arg_str, integral, region,
**kwargs)

Call signature

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dw_surface_integrate (opt_material, virtual)

name = 'dw_surface_integrate'
class sfepy.terms.terms_compat.IntegrateSurfaceTerm(name, arg_str, integral, region, **kwargs)

Call signature

ev_surface_integrate (opt_material, parameter)

name = 'ev_surface_integrate'
class sfepy.terms.terms_compat.IntegrateVolumeMatTerm(name, arg_str, integral, region, **kwargs)

Call signature

ev_volume_integrate_mat (material, parameter)

name = 'ev_volume_integrate_mat'
class sfepy.terms.terms_compat.IntegrateVolumeOperatorTerm(name, arg_str, integral, region,
**kwargs)

Call signature

dw_volume_integrate (opt_material, virtual)

name = 'dw_volume_integrate'
class sfepy.terms.terms_compat.IntegrateVolumeTerm(name, arg_str, integral, region, **kwargs)

Call signature

ev_volume_integrate (opt_material, parameter)

name = 'ev_volume_integrate'
class sfepy.terms.terms_compat.SDVolumeDotTerm(name, arg_str, integral, region, **kwargs)

Call signature

ev_sd_volume_dot (parameter_1, parameter_2, parameter_mv)

name = 'ev_sd_volume_dot'
class sfepy.terms.terms_compat.SurfaceDivTerm(name, arg_str, integral, region, **kwargs)

Call signature

ev_surface_div (opt_material, parameter)

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name = 'ev_surface_div'
class sfepy.terms.terms_compat.SurfaceGradTerm(name, arg_str, integral, region, **kwargs)

Call signature

ev_surface_grad (opt_material, parameter)

name = 'ev_surface_grad'
class sfepy.terms.terms_compat.SurfaceTerm(name, arg_str, integral, region, **kwargs)

Call signature

d_surface (parameter)

name = 'd_surface'
class sfepy.terms.terms_compat.VolumeXTerm(name, arg_str, integral, region, **kwargs)

Call signature

d_volume (parameter)

name = 'd_volume'

sfepy.terms.terms_constraints module

class sfepy.terms.terms_constraints.NonPenetrationPenaltyTerm(name, arg_str, integral, region,

**kwargs)
Non-penetration condition in the weak sense using a penalty.
Definition
∫︁
𝑐(𝑛 · 𝑣)(𝑛 · 𝑢)
Γ
Call signature

dw_non_penetration_p (material, virtual, state)

Arguments
• material : 𝑐
• virtual : 𝑣
• state : 𝑢

arg_shapes = {'material': '1, 1', 'state': 'D', 'virtual': ('D', 'state')}

arg_types = ('material', 'virtual', 'state')
static function(out, val_qp, ebf, mat, sg, diff_var)

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get_fargs(mat, vvar, svar, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'surface'
name = 'dw_non_penetration_p'
class sfepy.terms.terms_constraints.NonPenetrationTerm(name, arg_str, integral, region, **kwargs)
Non-penetration condition in the weak sense.
Definition
∫︁ ∫︁
𝑐𝜆𝑛 · 𝑣 , ˆ ·𝑢
𝑐𝜆𝑛
Γ Γ
∫︁ ∫︁
𝜆𝑛 · 𝑣 , ˆ ·𝑢
𝜆𝑛
Γ Γ
Call signature

dw_non_penetration (opt_material, virtual, state)

(opt_material, state, virtual)

Arguments 1
• material : 𝑐 (optional)
• virtual : 𝑣
• state : 𝜆
Arguments 2
• material : 𝑐 (optional)
• state : 𝑢
ˆ
• virtual : 𝜆

arg_shapes = [{'opt_material': '1, 1', 'virtual/grad': ('D', None), 'state/grad':

1, 'virtual/div': (1, None), 'state/div': 'D'}, {'opt_material': None}]
arg_types = (('opt_material', 'virtual', 'state'), ('opt_material', 'state',
'virtual'))
static function(out, val_qp, ebf, bf, mat, sg, diff_var, mode)
ebf belongs to vector variable, bf to scalar variable.
get_fargs(mat, vvar, svar, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'surface'
modes = ('grad', 'div')
name = 'dw_non_penetration'

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sfepy.terms.terms_contact module

class sfepy.terms.terms_contact.ContactInfo(region, integral, geo, state)

Various contact-related data of contact terms.
update(xx)
A dict-like update for Struct attributes.
class sfepy.terms.terms_contact.ContactTerm(*args, **kwargs)
Contact term with a penalty function.
The penalty function is defined as 𝜀𝑁 ⟨𝑔𝑁 (𝑢)⟩, where 𝜀𝑁 is the normal penalty parameter and ⟨𝑔𝑁 (𝑢)⟩ are the
Macaulay’s brackets of the gap function 𝑔𝑁 (𝑢).
This term has a dynamic connectivity of DOFs in its region.
Definition
∫︁
𝜀𝑁 ⟨𝑔𝑁 (𝑢)⟩𝑛𝑣
Γ𝑐

Call signature

dw_contact (material, virtual, state)

Arguments
• material : 𝜀𝑁
• virtual : 𝑣
• state : 𝑢

arg_shapes = {'material': '.: 1', 'state': 'D', 'virtual': ('D', 'state')}

arg_types = ('material', 'virtual', 'state')
call_function(out, fargs)

eval_real(shape, fargs, mode='eval', term_mode=None, diff_var=None, **kwargs)

static function(out, fun, *args)

static function_weak(out, out_cc)

get_contact_info(geo, state, init_gps=False)

get_eval_shape(epss, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(epss, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

static integrate(out, val_qp, geo, fmode)

integration = 'surface'
name = 'dw_contact'

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sfepy.terms.terms_dg module

Discontinous Galekrin method specific terms

Note

In einsum calls the following convention is used:

i represents iterating over all cells of a region;
n represents iterating over selected cells of a region, for example over cells on boundary;
b represents iterating over basis functions of state variable;
d represents iterating over basis functions of test variable;
k, l , m represent iterating over geometric dimensions, for example coordinates of velocity or facet normal
vector or rows and columns of diffusion tensor;
q represents iterating over quadrature points;
f represents iterating over facets of cell;
class sfepy.terms.terms_dg.AdvectionDGFluxTerm(name, arg_str, integral, region, **kwargs)
Lax-Friedrichs flux term for advection of scalar quantity 𝑝 with the advection velocity 𝑎 given as a material
parameter (a known function of space and time).
Definition
∫︁
𝑛 · 𝑓 * (𝑝𝑖𝑛 , 𝑝𝑜𝑢𝑡 )𝑞
𝜕𝑇𝐾

where
𝑝𝑖𝑛 + 𝑝𝑜𝑢𝑡 𝑝𝑖𝑛 − 𝑝𝑜𝑢𝑡
𝑓 * (𝑝𝑖𝑛 , 𝑝𝑜𝑢𝑡 ) = 𝑎 + (1 − 𝛼)𝑛𝐶 ,
2 2
𝛼 ∈ [0, 1]; 𝛼 = 0 for upwind scheme, 𝛼 = 1 for central scheme, and

𝐶 = max |𝑛𝑥 𝑎1 + 𝑛𝑦 𝑎2 | = max |𝑛 · 𝑎|

𝑝∈[?,?] 𝑝∈[?,?]

the 𝑝𝑖𝑛 resp. 𝑝𝑜𝑢𝑡 is solution on the boundary of the element provided by element itself resp. its neighbor and 𝑎
is advection velocity.
Call signature

dw_dg_advect_laxfrie_flux (opt_material, material_advelo, virtual, state)

Arguments 1
• material : 𝑎
• virtual : 𝑞
• state : 𝑝
Arguments 3
• material : 𝑎
• virtual : 𝑞
• state : 𝑝

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• opt_material : 𝛼

alpha = 0
arg_shapes = [{'opt_material': '.: 1', 'material_advelo': 'D, 1', 'virtual': (1,
'state'), 'state': 1}, {'opt_material': None}]
arg_types = ('opt_material', 'material_advelo', 'virtual', 'state')
function(out, state, diff_var, field, region, advelo)

get_fargs(alpha, advelo, test, state, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'volume'
modes = ('weak',)
name = 'dw_dg_advect_laxfrie_flux'
symbolic = {'expression': 'div(a*p)*w', 'map': {'a': 'material', 'p': 'state',
'v': 'virtual'}}
class sfepy.terms.terms_dg.DGTerm(name, arg_str, integral, region, **kwargs)
Abstract base class for DG terms, provides alternative call_function and eval_real methods to accommodate
returning iels and vals.
call_function(out, fargs)

eval_real(shape, fargs, mode='eval', term_mode=None, diff_var=None, **kwargs)

poly_space_base = 'legendre'
class sfepy.terms.terms_dg.DiffusionDGFluxTerm(name, arg_str, integral, region, **kwargs)
Basic DG diffusion flux term for scalar quantity.
Definition
∫︁ ∫︁
𝐷⟨∇𝑝⟩[𝑞] , 𝐷⟨∇𝑞⟩[𝑝]
𝜕𝑇𝐾 𝜕𝑇𝐾

where
∇𝜑𝑖𝑛 + ∇𝜑𝑜𝑢𝑡
⟨∇𝜑⟩ =
2
[𝜑] = 𝜑𝑖𝑛 − 𝜑𝑜𝑢𝑡
Math
The 𝑝𝑖𝑛 resp. 𝑝𝑜𝑢𝑡 is solution on the boundary of the element provided by element itself resp. its neighbour.
Call signature

dw_dg_diffusion_flux (material, state, virtual)

(material, virtual, state)

Arguments 1
• material : 𝐷
• state : 𝑝

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• virtual : 𝑞
Arguments 2
• material : 𝐷
• virtual : 𝑞
• state : 𝑝

arg_shapes = [{'material': '1, 1', 'virtual/avg_state': (1, None),

'state/avg_state': 1, 'virtual/avg_virtual': (1, None), 'state/avg_virtual': 1}]
arg_types = (('material', 'state', 'virtual'), ('material', 'virtual', 'state'))
function(out, state, diff_var, field, region, D)

get_fargs(diff_tensor, test, state, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'volume'
modes = ('avg_state', 'avg_virtual')
name = 'dw_dg_diffusion_flux'
class sfepy.terms.terms_dg.DiffusionInteriorPenaltyTerm(name, arg_str, integral, region, **kwargs)
Penalty term used to counteract discontinuity arising when modeling diffusion using Discontinuous Galerkin
schemes.
Definition
∫︁ 2
¯ 𝑤 𝑂𝑟𝑑 [𝑝][𝑞]
𝐷𝐶
𝜕𝑇𝐾 𝑑(𝜕𝑇𝐾 )
where

[𝜑] = 𝜑𝑖𝑛 − 𝜑𝑜𝑢𝑡

Math
the 𝑝𝑖𝑛 resp. 𝑝𝑜𝑢𝑡 is solution on the boundary of the element provided by element itself resp. its neighbour.
Call signature

dw_dg_interior_penalty (material, material_Cw, virtual, state)

Arguments
• material : 𝐷
• material : 𝐶𝑤
• state : 𝑝
• virtual : 𝑞

arg_shapes = [{'material': '1, 1', 'material_Cw': '.: 1', 'virtual': (1,

'state'), 'state': 1}]
arg_types = ('material', 'material_Cw', 'virtual', 'state')
function(out, state, diff_var, field, region, Cw, diff_tensor)

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get_fargs(diff_tensor, Cw, test, state, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('weak',)
name = 'dw_dg_interior_penalty'
class sfepy.terms.terms_dg.NonlinearHyperbolicDGFluxTerm(name, arg_str, integral, region,
**kwargs)

Lax-Friedrichs flux term for nonlinear hyperpolic term of scalar quantity 𝑝 with the vector function
𝑓 given as a material parameter.

Definition
∫︁
𝑛 · 𝑓 * (𝑝𝑖𝑛 , 𝑝𝑜𝑢𝑡 )𝑞
𝜕𝑇𝐾

where
𝑓 (𝑝𝑖𝑛 ) + 𝑓 (𝑝𝑜𝑢𝑡 ) 𝑝𝑖𝑛 − 𝑝𝑜𝑢𝑡
𝑓 * (𝑝𝑖𝑛 , 𝑝𝑜𝑢𝑡 ) = + (1 − 𝛼)𝑛𝐶 ,
2 2
𝛼 ∈ [0, 1]; 𝛼 = 0 for upwind scheme, 𝛼 = 1 for central scheme, and
⃒ ⃒
⃒ 𝑑𝑓1 𝑑𝑓2 ⃒
𝐶 = max ⃒𝑛𝑥 ⃒ + 𝑛𝑦 + · · · ⃒⃒ =
𝑝∈[?,?] 𝑑𝑝 𝑑𝑝
⃒ ⃒
⃒ 𝑑𝑓 ⃒
max ⃒⃗𝑛 ·
⃒ (𝑝)⃒⃒
𝑝∈[?,?] 𝑑𝑝

the 𝑝𝑖𝑛 resp. 𝑝𝑜𝑢𝑡 is solution on the boundary of the element provided by element itself resp. its neighbor.
Call signature

dw_dg_nonlinear_laxfrie_flux (opt_material, fun, fun_d, virtual, state)

Arguments 1
• material : 𝑓
𝑑𝑓
• material : 𝑑𝑝

• virtual : 𝑞
• state : 𝑝
Arguments 3
• material : 𝑓
𝑑𝑓
• material : 𝑑𝑝

• virtual : 𝑞
• state : 𝑝
• opt_material : 𝛼

alf = 0
arg_shapes = [{'opt_material': '.: 1', 'material_fun': '.: 1', 'material_fun_d':
'.: 1', 'virtual': (1, 'state'), 'state': 1}, {'opt_material': None}]

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arg_types = ('opt_material', 'fun', 'fun_d', 'virtual', 'state')

function(out, state, field, region, f, df )

get_fargs(alpha, fun, dfun, test, state, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'volume'
modes = ('weak',)
name = 'dw_dg_nonlinear_laxfrie_flux'
symbolic = {'expression': 'div(f(p))*w', 'map': {'f': 'function', 'p': 'state',
'v': 'virtual'}}
class sfepy.terms.terms_dg.NonlinearScalarDotGradTerm(name, arg_str, integral, region, **kwargs)

Product of virtual and divergence of vector function of state or volume dot product of vector function
of state and gradient of scalar virtual.

Definition
∫︁ ∫︁ ∫︁
𝑞 · ∇ · 𝑓 (𝑝) = 𝑞 · div𝑓 (𝑝) , 𝑓 (𝑝) · ∇𝑞
Ω Ω Ω
Call signature

dw_ns_dot_grad_s (fun, fun_d, virtual, state)

(fun, fun_d, state, virtual)

Arguments 1
• function : 𝑓
• virtual : 𝑞
• state : 𝑝
Arguments 2
• function : 𝑓
• state : 𝑝
• virtual : 𝑞

TODO maybe this term would fit better to terms_dot?

arg_shapes = [{'material_fun': '.: 1', 'material_fun_d': '.: 1',
'virtual/grad_state': (1, None), 'state/grad_state': 1, 'virtual/grad_virtual':
(1, None), 'state/grad_virtual': 1}]
arg_types = (('fun', 'fun_d', 'virtual', 'state'), ('fun', 'fun_d', 'state',
'virtual'))
static function(out, out_qp, geo, fmode)

get_fargs(fun, dfun, var1, var2, mode=None, term_mode=None, diff_var=None, **kwargs)

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modes = ('grad_state', 'grad_virtual')

name = 'dw_ns_dot_grad_s'

sfepy.terms.terms_diffusion module

class sfepy.terms.terms_diffusion.AdvectDivFreeTerm(name, arg_str, integral, region, **kwargs)

Advection of a scalar quantity 𝑝 with the advection velocity 𝑦 given as a material parameter (a known function
of space and time).
The advection velocity has to be divergence-free!
Definition
∫︁ ∫︁
∇ · (𝑦𝑝)𝑞 = ((∇ · 𝑦) +𝑦 · ∇)𝑝)𝑞
Ω Ω ⏟ ⏞
≡0

Call signature

dw_advect_div_free (material, virtual, state)

Arguments
• material : 𝑦
• virtual : 𝑞
• state : 𝑝

arg_shapes = {'material': 'D, 1', 'state': '1', 'virtual': ('1', 'state')}

arg_types = ('material', 'virtual', 'state')
mode = 'grad_state'
name = 'dw_advect_div_free'
class sfepy.terms.terms_diffusion.ConvectVGradSTerm(name, arg_str, integral, region, **kwargs)
Scalar gradient term with convective velocity.
Definition
∫︁
𝑞(𝑢 · ∇𝑝)
Ω
Call signature

dw_convect_v_grad_s (virtual, state_v, state_s)

Arguments
• virtual : 𝑞
• state_v : 𝑢
• state_s : 𝑝

arg_shapes = [{'virtual': (1, 'state_s'), 'state_v': 'D', 'state_s': 1}]

arg_types = ('virtual', 'state_v', 'state_s')

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function()

get_fargs(virtual, state_v, state_s, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_convect_v_grad_s'
class sfepy.terms.terms_diffusion.DiffusionCoupling(name, arg_str, integral, region, **kwargs)
Diffusion copupling term with material parameter 𝐾𝑗 .
Definition
∫︁ ∫︁
𝑝𝐾𝑗 ∇𝑗 𝑞 , 𝑞𝐾𝑗 ∇𝑗 𝑝
Ω Ω
Call signature

dw_diffusion_coupling (material, virtual, state)

(material, state, virtual)
(material, parameter_1, parameter_2)

Arguments
• material : 𝐾𝑗
• virtual : 𝑞
• state : 𝑝

arg_shapes = {'material': 'D, 1', 'parameter_1': 1, 'parameter_2': 1, 'state':

1, 'virtual': (1, 'state')}
arg_types = (('material', 'virtual', 'state'), ('material', 'state', 'virtual'),
('material', 'parameter_1', 'parameter_2'))
static d_fun(out, mat, val, grad, vg)

static dw_fun(out, val, mat, bf, vg, fmode)

get_eval_shape(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('weak0', 'weak1', 'eval')

name = 'dw_diffusion_coupling'
set_arg_types()

class sfepy.terms.terms_diffusion.DiffusionRTerm(name, arg_str, integral, region, **kwargs)

Diffusion-like term with material parameter 𝐾𝑗 (to use on the right-hand side).
Definition
∫︁
𝐾𝑗 ∇𝑗 𝑞
Ω
Call signature

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dw_diffusion_r (material, virtual)

Arguments
• material : 𝐾𝑗
• virtual : 𝑞

arg_shapes = {'material': 'D, 1', 'virtual': (1, None)}

arg_types = ('material', 'virtual')
static function()

get_fargs(mat, virtual, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_diffusion_r'
class sfepy.terms.terms_diffusion.DiffusionTerm(name, arg_str, integral, region, **kwargs)
General diffusion term with permeability 𝐾𝑖𝑗 . Can be evaluated. Can use derivatives.
Definition
∫︁ ∫︁
𝐾𝑖𝑗 ∇𝑖 𝑞∇𝑗 𝑝 , 𝐾𝑖𝑗 ∇𝑖 𝑝¯∇𝑗 𝑟
Ω Ω
Call signature

dw_diffusion (material, virtual, state)

(material, parameter_1, parameter_2)

Arguments 1
• material : 𝐾𝑖𝑗
• virtual : 𝑞
• state : 𝑝
Arguments 2
• material : 𝐾𝑖𝑗
• parameter_1 : 𝑝¯
• parameter_2 : 𝑟

arg_shapes = {'material': 'D, D', 'parameter_1': 1, 'parameter_2': 1, 'state':

1, 'virtual': (1, 'state')}
arg_types = (('material', 'virtual', 'state'), ('material', 'parameter_1',
'parameter_2'))
get_eval_shape(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('weak', 'eval')

name = 'dw_diffusion'

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set_arg_types()

symbolic = {'expression': 'div( K * grad( u ) )', 'map': {'K': 'material', 'u':

'state'}}
class sfepy.terms.terms_diffusion.DiffusionVelocityTerm(name, arg_str, integral, region, **kwargs)
Evaluate diffusion velocity.
Supports ‘eval’, ‘el_avg’ and ‘qp’ evaluation modes.
Definition
∫︁
− 𝐾𝑖𝑗 ∇𝑗 𝑝¯
𝒟
∫︁ ∫︁
vector for 𝐾 ← ℐℎ : − 𝐾𝑖𝑗 ∇𝑗 𝑝¯/ 1
𝑇𝐾 𝑇𝐾

−𝐾𝑖𝑗 ∇𝑗 𝑝¯
Call signature

ev_diffusion_velocity (material, parameter)

Arguments
• material : 𝐾𝑖𝑗
• parameter : 𝑝¯

arg_shapes = {'material': 'D, D', 'parameter': 1}

arg_types = ('material', 'parameter')
static function(out, grad, mat, vg, fmode)

get_eval_shape(mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'by_region'
name = 'ev_diffusion_velocity'
surface_integration = 'surface_extra'
class sfepy.terms.terms_diffusion.LaplaceTerm(name, arg_str, integral, region, **kwargs)
Laplace term with 𝑐 coefficient. Can be evaluated. Can use derivatives.
Definition
∫︁ ∫︁
𝑐∇𝑞 · ∇𝑝 , 𝑝 · ∇𝑟
𝑐∇¯
Ω Ω
Call signature

dw_laplace (opt_material, virtual, state)

(opt_material, parameter_1, parameter_2)

Arguments 1

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• material : 𝑐
• virtual : 𝑞
• state : 𝑝
Arguments 2
• material : 𝑐
• parameter_1 : 𝑝¯
• parameter_2 : 𝑟

arg_shapes = [{'opt_material': '1, 1', 'virtual': (1, 'state'), 'state': 1,

'parameter_1': 1, 'parameter_2': 1}, {'opt_material': None}]
arg_types = (('opt_material', 'virtual', 'state'), ('opt_material', 'parameter_1',
'parameter_2'))
modes = ('weak', 'eval')
name = 'dw_laplace'
set_arg_types()

symbolic = {'expression': 'c * div( grad( u ) )', 'map': {'c': 'opt_material',

'u': 'state'}}
class sfepy.terms.terms_diffusion.SDDiffusionTerm(name, arg_str, integral, region, **kwargs)
Diffusion sensitivity analysis term.
Definition
∫︁
ˆ 𝑖𝑗 ∇𝑖 𝑞 ∇𝑗 𝑝
𝐾
Ω
(︂ )︂
ˆ 𝑖𝑗 = 𝐾𝑖𝑗 𝛿𝑖𝑘 𝛿𝑗𝑙 ∇ · 𝒱 − 𝛿𝑖𝑘 𝜕𝒱𝑗 − 𝛿𝑗𝑙 𝜕𝒱𝑖
𝐾
𝜕𝑥𝑙 𝜕𝑥𝑘
Call signature

ev_sd_diffusion (material, parameter_q, parameter_p, parameter_mv)

Arguments
• material: 𝐾𝑖𝑗
• parameter_q: 𝑞
• parameter_p: 𝑝
• parameter_mv: 𝒱

arg_shapes = {'material': 'D, D', 'parameter_mv': 'D', 'parameter_p': 1,

'parameter_q': 1}
arg_types = ('material', 'parameter_q', 'parameter_p', 'parameter_mv')
static function()

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get_eval_shape(mat, parameter_q, parameter_p, parameter_mv, mode=None, term_mode=None,

diff_var=None, **kwargs)

get_fargs(mat, parameter_q, parameter_p, parameter_mv, mode=None, term_mode=None, diff_var=None,

**kwargs)

name = 'ev_sd_diffusion'
class sfepy.terms.terms_diffusion.SurfaceFluxOperatorTerm(name, arg_str, integral, region,
**kwargs)
Surface flux operator term.
Definition
∫︁
𝑞𝑛 · 𝐾 · ∇𝑝
Γ
Call signature

dw_surface_flux (opt_material, virtual, state)

Arguments
• material : 𝐾
• virtual : 𝑞
• state : 𝑝

arg_shapes = [{'opt_material': 'D, D', 'virtual': (1, 'state'), 'state': 1},

{'opt_material': None}]
arg_types = ('opt_material', 'virtual', 'state')
function()

get_fargs(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'surface_extra'
name = 'dw_surface_flux'
class sfepy.terms.terms_diffusion.SurfaceFluxTerm(name, arg_str, integral, region, **kwargs)
Surface flux term.
Supports ‘eval’, ‘el_eval’ and ‘el_avg’ evaluation modes.
Definition
∫︁
𝑛 · 𝐾𝑖𝑗 ∇𝑗 𝑝¯
Γ
∫︁ ∫︁
vector for 𝐾 ← ℐℎ : 𝑛 · 𝐾𝑖𝑗 ∇𝑗 𝑝¯ / 1
𝑇𝐾 𝑇𝐾
∫︁
vector for 𝐾 ← ℐℎ : 𝑛 · 𝐾𝑖𝑗 ∇𝑗 𝑝¯
𝑇𝐾

Call signature

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ev_surface_flux (material, parameter)

Arguments
• material: 𝐾
• parameter: 𝑝¯,

arg_shapes = {'material': 'D, D', 'parameter': 1}

arg_types = ('material', 'parameter')
static function()

get_eval_shape(mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'surface_extra'
name = 'ev_surface_flux'

sfepy.terms.terms_dot module

class sfepy.terms.terms_dot.BCNewtonTerm(name, arg_str, integral, region, **kwargs)

Newton boundary condition term.
Definition
∫︁
𝛼𝑞(𝑝 − 𝑝outer )
Γ
Call signature

dw_bc_newton (material_1, material_2, virtual, state)

Arguments
• material_1 : 𝛼
• material_2 : 𝑝outer
• virtual : 𝑞
• state : 𝑝

arg_shapes = {'material_1': '1, 1', 'material_2': '1, 1', 'state': 1, 'virtual':

(1, 'state')}
arg_shapes_dict = None
arg_types = ('material_1', 'material_2', 'virtual', 'state')
get_fargs(alpha, p_outer, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'surface'
mode = 'weak'

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name = 'dw_bc_newton'
class sfepy.terms.terms_dot.DotProductTerm(name, arg_str, integral, region, **kwargs)
Volume and surface 𝐿2 () weighted dot product for both scalar and vector fields. If the region is a surface and
either virtual or state variable is a vector, the orientation of the normal vectors is outwards to the parent region
of the virtual variable. Can be evaluated. Can use derivatives.
Definition
∫︁ ∫︁ ∫︁ ∫︁ ∫︁ ∫︁ ∫︁
𝑞𝑝 , 𝑣·𝑢, 𝑣 · 𝑛𝑝 , 𝑞𝑛 · 𝑢 , 𝑝𝑟 , 𝑢·𝑤, 𝑤 · 𝑛𝑝
𝒟 𝒟 Γ
∫︁Γ ∫︁ 𝒟 𝒟
∫︁ ∫︁ Γ
𝑐𝑞𝑝 , 𝑐𝑣 · 𝑢 , 𝑐𝑝𝑟 , 𝑐𝑢 · 𝑤
𝒟 𝒟 𝒟
∫︁ ∫︁ 𝒟
𝑣·𝑀 ·𝑢, 𝑢·𝑀 ·𝑤
𝒟 𝒟
Call signature

dw_dot (opt_material, virtual, state)

(opt_material, parameter_1, parameter_2)

Arguments 1
• material : 𝑐 or 𝑀 (optional)
• virtual : 𝑞 or 𝑣
• state : 𝑝 or 𝑢
Arguments 2
• material : 𝑐 or 𝑀 (optional)
• parameter_1 : 𝑝 or 𝑢
• parameter_2 : 𝑟 or 𝑤

arg_shapes_dict = {'surface': [{'opt_material': '1, 1', 'virtual': (1, 'state'),

'state': 1, 'parameter_1': 1, 'parameter_2': 1}, {'opt_material': None},
{'opt_material': '1, 1', 'virtual': (1, None), 'state': 'D'}, {'opt_material':
None}, {'opt_material': '1, 1', 'virtual': ('D', None), 'state': 1},
{'opt_material': None}, {'opt_material': '1, 1', 'virtual': ('D', 'state'),
'state': 'D', 'parameter_1': 'D', 'parameter_2': 'D'}, {'opt_material': 'D, D'},
{'opt_material': None}], 'volume': [{'opt_material': '1, 1', 'virtual': (1,
'state'), 'state': 1, 'parameter_1': 1, 'parameter_2': 1}, {'opt_material':
None}, {'opt_material': '1, 1', 'virtual': ('D', 'state'), 'state': 'D',
'parameter_1': 'D', 'parameter_2': 'D'}, {'opt_material': 'D, D'},
{'opt_material': None}]}
arg_types = (('opt_material', 'virtual', 'state'), ('opt_material', 'parameter_1',
'parameter_2'))
static d_dot(out, mat, val1_qp, val2_qp, geo)

static dw_dot(out, mat, val_qp, vgeo, sgeo, fun, fmode)

get_eval_shape(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

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get_fargs(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'by_region'
modes = ('weak', 'eval')
name = 'dw_dot'
set_arg_types()

class sfepy.terms.terms_dot.DotSProductVolumeOperatorWETHTerm(name, arg_str, integral, region,

**kwargs)
Fading memory volume 𝐿2 (Ω) weighted dot product for scalar fields. This term has the same definition as
dw_volume_dot_w_scalar_th, but assumes an exponential approximation of the convolution kernel resulting in
much higher efficiency. Can use derivatives.
Definition
∫︁ [︂∫︁ 𝑡 ]︂
𝒢(𝑡 − 𝜏 )𝑝(𝜏 ) d𝜏 𝑞
Ω 0

Call signature

dw_volume_dot_w_scalar_eth (ts, material_0, material_1, virtual, state)

Arguments
• ts : TimeStepper instance
• material_0 : 𝒢(0)
• material_1 : exp(−𝜆∆𝑡) (decay at 𝑡1 )
• virtual : 𝑞
• state : 𝑝

arg_shapes = {'material_0': '1, 1', 'material_1': '1, 1', 'state': 1, 'virtual':

(1, 'state')}
arg_types = ('ts', 'material_0', 'material_1', 'virtual', 'state')
static function()

get_fargs(ts, mat0, mat1, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_volume_dot_w_scalar_eth'
class sfepy.terms.terms_dot.DotSProductVolumeOperatorWTHTerm(name, arg_str, integral, region,
**kwargs)
Fading memory volume 𝐿2 (Ω) weighted dot product for scalar fields. Can use derivatives.
Definition
∫︁ [︂∫︁ 𝑡 ]︂
𝒢(𝑡 − 𝜏 )𝑝(𝜏 ) d𝜏 𝑞
Ω 0

Call signature

dw_volume_dot_w_scalar_th (ts, material, virtual, state)

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Arguments
• ts : TimeStepper instance
• material : 𝒢(𝜏 )
• virtual : 𝑞
• state : 𝑝

arg_shapes = {'material': '.: N, 1, 1', 'state': 1, 'virtual': (1, 'state')}

arg_types = ('ts', 'material', 'virtual', 'state')
static function()

get_fargs(ts, mats, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_volume_dot_w_scalar_th'
class sfepy.terms.terms_dot.ScalarDotGradIScalarTerm(name, arg_str, integral, region, **kwargs)
Dot product of a scalar and the 𝑖-th component of gradient of a scalar. The index should be given as a ‘spe-
cial_constant’ material parameter.
Definition
∫︁
𝑖
𝑍 = 𝑞∇𝑖 𝑝
Ω
Call signature

dw_s_dot_grad_i_s (material, virtual, state)

Arguments
• material : 𝑖
• virtual : 𝑞
• state : 𝑝

arg_shapes = {'material': '.: 1, 1', 'state': 1, 'virtual': (1, 'state')}

arg_types = ('material', 'virtual', 'state')
static dw_fun(out, bf, vg, grad, idx, fmode)

get_fargs(material, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_s_dot_grad_i_s'
set_arg_types()

class sfepy.terms.terms_dot.ScalarDotMGradScalarTerm(name, arg_str, integral, region, **kwargs)

Volume dot product of a scalar gradient dotted with a material vector with a scalar.
Definition
∫︁ ∫︁
𝑞𝑦 · ∇𝑝 , 𝑝𝑦 · ∇𝑞
Ω Ω

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Call signature

dw_s_dot_mgrad_s (material, virtual, state)

(material, state, virtual)

Arguments 1
• material : 𝑦
• virtual : 𝑞
• state : 𝑝
Arguments 2
• material : 𝑦
• state : 𝑝
• virtual : 𝑞

arg_shapes = [{'material': 'D, 1', 'virtual/grad_state': (1, None),

'state/grad_state': 1, 'virtual/grad_virtual': (1, None), 'state/grad_virtual':
1}]
arg_types = (('material', 'virtual', 'state'), ('material', 'state', 'virtual'))
static function(out, out_qp, geo, fmode)

get_fargs(mat, var1, var2, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('grad_state', 'grad_virtual')

name = 'dw_s_dot_mgrad_s'
class sfepy.terms.terms_dot.VectorDotGradScalarTerm(name, arg_str, integral, region, **kwargs)
Volume dot product of a vector and a gradient of scalar. Can be evaluated.
Definition
∫︁ ∫︁
𝑣 · ∇𝑝 , 𝑢 · ∇𝑞
Ω
∫︁ ∫︁ Ω
𝑐𝑣 · ∇𝑝 , 𝑐𝑢 · ∇𝑞
Ω Ω
∫︁ ∫︁
𝑣 · (𝑀 ∇𝑝) , 𝑢 · (𝑀 ∇𝑞)
Ω Ω
Call signature

dw_v_dot_grad_s (opt_material, virtual, state)

(opt_material, state, virtual)
(opt_material, parameter_v, parameter_s)

Arguments 1
• material : 𝑐 or 𝑀 (optional)
• virtual : 𝑣
• state : 𝑝

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Arguments 2
• material : 𝑐 or 𝑀 (optional)
• state : 𝑢
• virtual : 𝑞
Arguments 3
• material : 𝑐 or 𝑀 (optional)
• parameter_v : 𝑢
• parameter_s : 𝑝

arg_shapes = [{'opt_material': '1, 1', 'virtual/v_weak': ('D', None),

'state/v_weak': 1, 'virtual/s_weak': (1, None), 'state/s_weak': 'D',
'parameter_v': 'D', 'parameter_s': 1}, {'opt_material': 'D, D'}, {'opt_material':
None}]
arg_types = (('opt_material', 'virtual', 'state'), ('opt_material', 'state',
'virtual'), ('opt_material', 'parameter_v', 'parameter_s'))
get_eval_shape(coef, vvar, svar, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(coef, vvar, svar, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('v_weak', 's_weak', 'eval')

name = 'dw_v_dot_grad_s'
set_arg_types()

class sfepy.terms.terms_dot.VectorDotScalarTerm(name, arg_str, integral, region, **kwargs)

Volume dot product of a vector and a scalar. Can be evaluated.
Definition
∫︁ ∫︁
𝑣 · 𝑚𝑝 , 𝑢 · 𝑚𝑞
Ω Ω
Call signature

dw_vm_dot_s (material, virtual, state)

(material, state, virtual)
(material, parameter_v, parameter_s)

Arguments 1
• material : 𝑚
• virtual : 𝑣
• state : 𝑝
Arguments 2
• material : 𝑚
• state : 𝑢
• virtual : 𝑞

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Arguments 3
• material : 𝑚
• parameter_v : 𝑢
• parameter_s : 𝑝

arg_shapes = [{'material': 'D, 1', 'virtual/v_weak': ('D', None), 'state/v_weak':

1, 'virtual/s_weak': (1, None), 'state/s_weak': 'D', 'parameter_v': 'D',
'parameter_s': 1}]
arg_types = (('material', 'virtual', 'state'), ('material', 'state', 'virtual'),
('material', 'parameter_v', 'parameter_s'))
static d_dot(out, mat, val1_qp, val2_qp, geo)

static dw_dot(out, mat, val_qp, bfve, bfsc, geo, fmode)

get_eval_shape(coef, vvar, svar, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(coef, vvar, svar, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('v_weak', 's_weak', 'eval')

name = 'dw_vm_dot_s'
set_arg_types()

sfepy.terms.terms_elastic module

class sfepy.terms.terms_elastic.CauchyStrainTerm(name, arg_str, integral, region, **kwargs)

Evaluate Cauchy strain tensor.
It is given in the usual vector form exploiting symmetry: in 3D it has 6 components with the indices ordered as
[11, 22, 33, 12, 13, 23], in 2D it has 3 components with the indices ordered as [11, 22, 12]. The last three (non-
diagonal) components are doubled so that it is energetically conjugate to the Cauchy stress tensor with the same
storage.
Supports ‘eval’, ‘el_avg’ and ‘qp’ evaluation modes.
Definition
∫︁
𝑒(𝑤)
𝒟
∫︁ ∫︁
vector for 𝐾 ← ℐℎ : 𝑒(𝑤)/ 1
𝑇𝐾 𝑇𝐾

𝑒(𝑤)|𝑞𝑝
Call signature

ev_cauchy_strain (parameter)

Arguments

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• parameter : 𝑤

arg_shapes = {'parameter': 'D'}

arg_types = ('parameter',)
static function(out, strain, vg, fmode)

get_eval_shape(parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'by_region'
name = 'ev_cauchy_strain'
surface_integration = 'surface_extra'
class sfepy.terms.terms_elastic.CauchyStressETHTerm(name, arg_str, integral, region, **kwargs)
Evaluate fading memory Cauchy stress tensor.
It is given in the usual vector form exploiting symmetry: in 3D it has 6 components with the indices ordered as
[11, 22, 33, 12, 13, 23], in 2D it has 3 components with the indices ordered as [11, 22, 12].
Assumes an exponential approximation of the convolution kernel resulting in much higher efficiency.
Supports ‘eval’, ‘el_avg’ and ‘qp’ evaluation modes.
Definition
∫︁ ∫︁ 𝑡
ℋ𝑖𝑗𝑘𝑙 (𝑡 − 𝜏 ) 𝑒𝑘𝑙 (𝑤(𝜏 )) d𝜏
Ω 0
∫︁ ∫︁ 𝑡 ∫︁
vector for 𝐾 ← ℐℎ : ℋ𝑖𝑗𝑘𝑙 (𝑡 − 𝜏 ) 𝑒𝑘𝑙 (𝑤(𝜏 )) d𝜏 / 1
𝑇𝐾 0 𝑇𝐾
∫︁ 𝑡
ℋ𝑖𝑗𝑘𝑙 (𝑡 − 𝜏 ) 𝑒𝑘𝑙 (𝑤(𝜏 )) d𝜏 |𝑞𝑝
0
Call signature

ev_cauchy_stress_eth (ts, material_0, material_1, parameter)

Arguments
• ts : TimeStepper instance
• material_0 : ℋ𝑖𝑗𝑘𝑙 (0)
• material_1 : exp(−𝜆∆𝑡) (decay at 𝑡1 )
• parameter : 𝑤

arg_shapes = {'material_0': 'S, S', 'material_1': '1, 1', 'parameter': 'D'}

arg_types = ('ts', 'material_0', 'material_1', 'parameter')
get_eval_shape(ts, mat0, mat1, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(ts, mat0, mat1, state, mode=None, term_mode=None, diff_var=None, **kwargs)

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name = 'ev_cauchy_stress_eth'
class sfepy.terms.terms_elastic.CauchyStressTHTerm(name, arg_str, integral, region, **kwargs)
Evaluate fading memory Cauchy stress tensor.
It is given in the usual vector form exploiting symmetry: in 3D it has 6 components with the indices ordered as
[11, 22, 33, 12, 13, 23], in 2D it has 3 components with the indices ordered as [11, 22, 12].
Supports ‘eval’, ‘el_avg’ and ‘qp’ evaluation modes.
Definition
∫︁ ∫︁ 𝑡
ℋ𝑖𝑗𝑘𝑙 (𝑡 − 𝜏 ) 𝑒𝑘𝑙 (𝑤(𝜏 )) d𝜏
Ω 0
∫︁ ∫︁ 𝑡 ∫︁
vector for 𝐾 ← ℐℎ : ℋ𝑖𝑗𝑘𝑙 (𝑡 − 𝜏 ) 𝑒𝑘𝑙 (𝑤(𝜏 )) d𝜏 / 1
𝑇𝐾 0 𝑇𝐾
∫︁ 𝑡
ℋ𝑖𝑗𝑘𝑙 (𝑡 − 𝜏 ) 𝑒𝑘𝑙 (𝑤(𝜏 )) d𝜏 |𝑞𝑝
0
Call signature

ev_cauchy_stress_th (ts, material, parameter)

Arguments
• ts : TimeStepper instance
• material : ℋ𝑖𝑗𝑘𝑙 (𝜏 )
• parameter : 𝑤

arg_shapes = {'material': '.: N, S, S', 'parameter': 'D'}

arg_types = ('ts', 'material', 'parameter')
get_eval_shape(ts, mats, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(ts, mats, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'ev_cauchy_stress_th'
class sfepy.terms.terms_elastic.CauchyStressTerm(name, arg_str, integral, region, **kwargs)
Evaluate Cauchy stress tensor.
It is given in the usual vector form exploiting symmetry: in 3D it has 6 components with the indices ordered as
[11, 22, 33, 12, 13, 23], in 2D it has 3 components with the indices ordered as [11, 22, 12].
Supports ‘eval’, ‘el_avg’ and ‘qp’ evaluation modes.
Definition
∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑘𝑙 (𝑤)
𝒟
∫︁ ∫︁
vector for 𝐾 ← ℐℎ : 𝐷𝑖𝑗𝑘𝑙 𝑒𝑘𝑙 (𝑤)/ 1
𝑇𝐾 𝑇𝐾

𝐷𝑖𝑗𝑘𝑙 𝑒𝑘𝑙 (𝑤)|𝑞𝑝

Call signature

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ev_cauchy_stress (material, parameter)

Arguments
• material : 𝐷𝑖𝑗𝑘𝑙
• parameter : 𝑤

arg_shapes = {'material': 'S, S', 'parameter': 'D'}

arg_types = ('material', 'parameter')
static function(out, coef, strain, mat, vg, fmode)

get_eval_shape(mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'by_region'
name = 'ev_cauchy_stress'
surface_integration = 'surface_extra'
class sfepy.terms.terms_elastic.ElasticWaveCauchyTerm(name, arg_str, integral, region, **kwargs)
Elastic dispersion term involving the wave strain 𝑔𝑖𝑗 , 𝑔𝑖𝑗 (𝑢) = 12 (𝑢𝑖 𝜅𝑗 + 𝜅𝑖 𝑢𝑗 ), with the wave vector 𝜅 and the
elastic strain 𝑒𝑖𝑗 . 𝐷𝑖𝑗𝑘𝑙 is given in the usual matrix form exploiting symmetry: in 3D it is 6 × 6 with the indices
ordered as [11, 22, 33, 12, 13, 23], in 2D it is 3 × 3 with the indices ordered as [11, 22, 12].
Definition
∫︁ ∫︁
𝐷𝑖𝑗𝑘𝑙 𝑔𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) , 𝐷𝑖𝑗𝑘𝑙 𝑔𝑖𝑗 (𝑢)𝑒𝑘𝑙 (𝑣)
Ω Ω
Call signature

dw_elastic_wave_cauchy (material_1, material_2, virtual, state)

(material_1, material_2, state, virtual)

Arguments 1
• material_1 : 𝐷𝑖𝑗𝑘𝑙
• material_2 : 𝜅
• virtual : 𝑣
• state : 𝑢
Arguments 2
• material_1 : 𝐷𝑖𝑗𝑘𝑙
• material_2 : 𝜅
• state : 𝑢
• virtual : 𝑣

arg_shapes = {'material_1': 'S, S', 'material_2': '.: D', 'state': 'D',

'virtual': ('D', 'state')}

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arg_types = (('material_1', 'material_2', 'virtual', 'state'), ('material_1',

'material_2', 'state', 'virtual'))
static function(out, out_qp, geo, fmode)

geometries = ['2_3', '2_4', '3_4', '3_8']

get_fargs(mat, kappa, gvar, evar, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('ge', 'eg')

name = 'dw_elastic_wave_cauchy'
class sfepy.terms.terms_elastic.ElasticWaveTerm(name, arg_str, integral, region, **kwargs)
Elastic dispersion term involving the wave strain 𝑔𝑖𝑗 , 𝑔𝑖𝑗 (𝑢) = 12 (𝑢𝑖 𝜅𝑗 + 𝜅𝑖 𝑢𝑗 ), with the wave vector 𝜅.
𝐷𝑖𝑗𝑘𝑙 is given in the usual matrix form exploiting symmetry: in 3D it is 6 × 6 with the indices ordered as
[11, 22, 33, 12, 13, 23], in 2D it is 3 × 3 with the indices ordered as [11, 22, 12].
Definition
∫︁
𝐷𝑖𝑗𝑘𝑙 𝑔𝑖𝑗 (𝑣)𝑔𝑘𝑙 (𝑢)
Ω
Call signature

dw_elastic_wave (material_1, material_2, virtual, state)

Arguments
• material_1 : 𝐷𝑖𝑗𝑘𝑙
• material_2 : 𝜅
• virtual : 𝑣
• state : 𝑢

arg_shapes = {'material_1': 'S, S', 'material_2': '.: D', 'state': 'D',

'virtual': ('D', 'state')}
arg_types = ('material_1', 'material_2', 'virtual', 'state')
static function(out, out_qp, geo, fmode)

geometries = ['2_3', '2_4', '3_4', '3_8']

get_fargs(mat, kappa, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_elastic_wave'
class sfepy.terms.terms_elastic.LinearElasticETHTerm(name, arg_str, integral, region, **kwargs)
This term has the same definition as dw_lin_elastic_th, but assumes an exponential approximation of the convo-
lution kernel resulting in much higher efficiency. Can use derivatives.
Definition
∫︁ [︂∫︁ 𝑡 ]︂
ℋ𝑖𝑗𝑘𝑙 (𝑡 − 𝜏 ) 𝑒𝑘𝑙 (𝑢(𝜏 )) d𝜏 𝑒𝑖𝑗 (𝑣)
Ω 0

Call signature

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dw_lin_elastic_eth (ts, material_0, material_1, virtual, state)

Arguments
• ts : TimeStepper instance
• material_0 : ℋ𝑖𝑗𝑘𝑙 (0)
• material_1 : exp(−𝜆∆𝑡) (decay at 𝑡1 )
• virtual : 𝑣
• state : 𝑢

arg_shapes = {'material_0': 'S, S', 'material_1': '1, 1', 'state': 'D',

'virtual': ('D', 'state')}
arg_types = ('ts', 'material_0', 'material_1', 'virtual', 'state')
static function()

get_fargs(ts, mat0, mat1, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_lin_elastic_eth'
class sfepy.terms.terms_elastic.LinearElasticIsotropicTerm(name, arg_str, integral, region,
**kwargs)
Isotropic linear elasticity term.
Definition
∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢) with 𝐷𝑖𝑗𝑘𝑙 = 𝜇(𝛿𝑖𝑘 𝛿𝑗𝑙 + 𝛿𝑖𝑙 𝛿𝑗𝑘 ) + 𝜆 𝛿𝑖𝑗 𝛿𝑘𝑙
Ω
Call signature

dw_lin_elastic_iso (material_1, material_2, virtual, state)

(material_1, material_2, parameter_1, parameter_2)

Arguments
• material_1 : 𝜆
• material_2 : 𝜇
• virtual : 𝑣
• state : 𝑢
Arguments 2
• material : 𝐷𝑖𝑗𝑘𝑙
• parameter_1 : 𝑤
• parameter_2 : 𝑢

arg_shapes = {'material_1': '1, 1', 'material_2': '1, 1', 'parameter_1': 'D',

'parameter_2': 'D', 'state': 'D', 'virtual': ('D', 'state')}
arg_types = (('material_1', 'material_2', 'virtual', 'state'), ('material_1',
'material_2', 'parameter_1', 'parameter_2'))

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geometries = ['2_3', '2_4', '3_4', '3_8']

get_eval_shape(mat1, mat2, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(lam, mu, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_lin_elastic_iso'
class sfepy.terms.terms_elastic.LinearElasticTHTerm(name, arg_str, integral, region, **kwargs)
Fading memory linear elastic (viscous) term. Can use derivatives.
Definition
∫︁ [︂∫︁ 𝑡 ]︂
ℋ𝑖𝑗𝑘𝑙 (𝑡 − 𝜏 ) 𝑒𝑘𝑙 (𝑢(𝜏 )) d𝜏 𝑒𝑖𝑗 (𝑣)
Ω 0

Call signature

dw_lin_elastic_th (ts, material, virtual, state)

Arguments
• ts : TimeStepper instance
• material : ℋ𝑖𝑗𝑘𝑙 (𝜏 )
• virtual : 𝑣
• state : 𝑢

arg_shapes = {'material': '.: N, S, S', 'state': 'D', 'virtual': ('D', 'state')}

arg_types = ('ts', 'material', 'virtual', 'state')
static function()

get_fargs(ts, mats, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_lin_elastic_th'
class sfepy.terms.terms_elastic.LinearElasticTerm(name, arg_str, integral, region, **kwargs)
General linear elasticity term, with 𝐷𝑖𝑗𝑘𝑙 given in the usual matrix form exploiting symmetry: in 3D it is 6 × 6
with the indices ordered as [11, 22, 33, 12, 13, 23], in 2D it is 3 × 3 with the indices ordered as [11, 22, 12]. Can
be evaluated. Can use derivatives.
Definition
∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢)
Ω
Call signature

dw_lin_elastic (material, virtual, state)

(material, parameter_1, parameter_2)

Arguments 1
• material : 𝐷𝑖𝑗𝑘𝑙
• virtual : 𝑣

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• state : 𝑢
Arguments 2
• material : 𝐷𝑖𝑗𝑘𝑙
• parameter_1 : 𝑤
• parameter_2 : 𝑢

arg_shapes = {'material': 'S, S', 'parameter_1': 'D', 'parameter_2': 'D',

'state': 'D', 'virtual': ('D', 'state')}
arg_types = (('material', 'virtual', 'state'), ('material', 'parameter_1',
'parameter_2'))
get_eval_shape(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('weak', 'eval')

name = 'dw_lin_elastic'
set_arg_types()

class sfepy.terms.terms_elastic.LinearPrestressTerm(name, arg_str, integral, region, **kwargs)

Linear prestress term, with the prestress 𝜎𝑖𝑗 given either in the usual vector form exploiting symmetry: in 3D it
has 6 components with the indices ordered as [11, 22, 33, 12, 13, 23], in 2D it has 3 components with the indices
ordered as [11, 22, 12], or in the matrix (possibly non-symmetric) form. Can be evaluated.
Definition
∫︁
𝜎𝑖𝑗 𝑒𝑖𝑗 (𝑣)
Ω
Call signature

dw_lin_prestress (material, virtual)

(material, parameter)

Arguments 1
• material : 𝜎𝑖𝑗
• virtual : 𝑣
Arguments 2
• material : 𝜎𝑖𝑗
• parameter : 𝑢

arg_shapes = [{'material': 'S, 1', 'virtual': ('D', None), 'parameter': 'D'},

{'material': 'D, D'}]
arg_types = (('material', 'virtual'), ('material', 'parameter'))
d_lin_prestress(out, strain, mat, vg, fmode)

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get_eval_shape(mat, virtual, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, virtual, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('weak', 'eval')

name = 'dw_lin_prestress'
set_arg_types()

class sfepy.terms.terms_elastic.LinearStrainFiberTerm(name, arg_str, integral, region, **kwargs)

Linear (pre)strain fiber term with the unit direction vector 𝑑.
Definition
∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣) (𝑑𝑘 𝑑𝑙 )
Ω
Call signature

dw_lin_strain_fib (material_1, material_2, virtual)

Arguments
• material_1 : 𝐷𝑖𝑗𝑘𝑙
• material_2 : 𝑑
• virtual : 𝑣

arg_shapes = {'material_1': 'S, S', 'material_2': 'D, 1', 'virtual': ('D', None)}
arg_types = ('material_1', 'material_2', 'virtual')
static function()

get_fargs(mat1, mat2, virtual, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_lin_strain_fib'
class sfepy.terms.terms_elastic.NonsymElasticTerm(name, arg_str, integral, region, **kwargs)
Elasticity term with non-symmetric gradient. The indices of matrix 𝐷𝑖𝑗𝑘𝑙 are ordered as
[11, 12, 13, 21, 22, 23, 31, 32, 33] in 3D and as [11, 12, 21, 22] in 2D.
Definition
∫︁
𝐷∇𝑢 : ∇𝑣
Ω
Call signature

dw_nonsym_elastic (material, virtual, state)

(material, parameter_1, parameter_2)

Arguments 1
• material : 𝐷
• virtual : 𝑣

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• state : 𝑢
Arguments 2
• material : 𝐷
• parameter_1 : 𝑤
• parameter_2 : 𝑢

arg_shapes = {'material': 'D2, D2', 'parameter_1': 'D', 'parameter_2': 'D',

'state': 'D', 'virtual': ('D', 'state')}
arg_types = (('material', 'virtual', 'state'), ('material', 'parameter_1',
'parameter_2'))
geometries = ['2_3', '2_4', '3_4', '3_8']
get_eval_shape(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('weak', 'eval')

name = 'dw_nonsym_elastic'
set_arg_types()

class sfepy.terms.terms_elastic.SDLinearElasticTerm(name, arg_str, integral, region, **kwargs)

Sensitivity analysis of the linear elastic term.
Definition
∫︁
ˆ 𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢)
𝐷
Ω

ˆ 𝑖𝑗𝑘𝑙 = 𝐷𝑖𝑗𝑘𝑙 (∇ · 𝒱) − 𝐷𝑖𝑗𝑘𝑞 𝜕𝒱𝑙 − 𝐷𝑖𝑞𝑘𝑙 𝜕𝒱𝑗

𝐷
𝜕𝑥𝑞 𝜕𝑥𝑞
Call signature

ev_sd_lin_elastic (material, parameter_w, parameter_u, parameter_mv)

Arguments
• material : 𝐷𝑖𝑗𝑘𝑙
• parameter_w : 𝑤
• parameter_u : 𝑢
• parameter_mv : 𝒱

arg_shapes = {'material': 'S, S', 'parameter_mv': 'D', 'parameter_u': 'D',

'parameter_w': 'D'}
arg_types = ('material', 'parameter_w', 'parameter_u', 'parameter_mv')
function()

geometries = ['2_3', '2_4', '3_4', '3_8']

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get_eval_shape(mat, par_w, par_u, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, par_w, par_u, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'ev_sd_lin_elastic'

sfepy.terms.terms_electric module

class sfepy.terms.terms_electric.ElectricSourceTerm(name, arg_str, integral, region, **kwargs)

Electric source term.
Definition
∫︁
𝑐𝑠(∇𝜑)2
Ω
Call signature

dw_electric_source (material, virtual, parameter)

Arguments
• material : 𝑐 (electric conductivity)
• virtual : 𝑠 (test function)
• parameter : 𝜑 (given electric potential)

arg_shapes = {'material': '1, 1', 'parameter': 1, 'virtual': (1, None)}

arg_types = ('material', 'virtual', 'parameter')
static function()

get_fargs(mat, virtual, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_electric_source'

sfepy.terms.terms_fibres module

class sfepy.terms.terms_fibres.FibresActiveTLTerm(*args,{︁**kwargs) }︁
𝜖−𝜀
Hyperelastic active fibres term. Effective stress 𝑆𝑖𝑗 = 𝐴𝑓max exp −( 𝑠opt )2 𝑑𝑖 𝑑𝑗 , where 𝜖 = 𝐸𝑖𝑗 𝑑𝑖 𝑑𝑗 is the
Green strain 𝐸 projected to the fibre direction 𝑑.
Definition
∫︁
𝑆𝑖𝑗 (𝑢)𝛿𝐸𝑖𝑗 (𝑢; 𝑣)
Ω
Call signature

dw_tl_fib_a (material_1, material_2, material_3, material_4, material_5, virtual,

state)

Arguments

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• material_1 : 𝑓max
• material_2 : 𝜀opt
• material_3 : 𝑠
• material_4 : 𝑑
• material_5 : 𝐴
• virtual : 𝑣
• state : 𝑢

arg_shapes = {'material_1': '1, 1', 'material_2': '1, 1', 'material_3': '1, 1',
'material_4': 'D, 1', 'material_5': '1, 1', 'state': 'D', 'virtual': ('D',
'state')}
arg_types = ('material_1', 'material_2', 'material_3', 'material_4', 'material_5',
'virtual', 'state')
family_data_names = ['green_strain']
get_eval_shape(mat1, mat2, mat3, mat4, mat5, virtual, state, mode=None, term_mode=None,
diff_var=None, **kwargs)

get_fargs(mat1, mat2, mat3, mat4, mat5, virtual, state, mode=None, term_mode=None, diff_var=None,
**kwargs)

name = 'dw_tl_fib_a'
static stress_function(out, pars, green_strain, fibre_data=None)

static tan_mod_function(out, pars, green_strain, fibre_data=None)

sfepy.terms.terms_fibres.compute_fibre_strain(green_strain, omega)
Compute the Green strain projected to the fibre direction.
sfepy.terms.terms_fibres.create_omega(fdir)
Create the fibre direction tensor 𝜔𝑖𝑗 = 𝑑𝑖 𝑑𝑗 .

sfepy.terms.terms_hyperelastic_base module

class sfepy.terms.terms_hyperelastic_base.DeformationGradientTerm(name, arg_str, integral,

region, **kwargs)
Deformation gradient 𝐹 in quadrature points for term_mode=’def_grad’ (default) or the jacobian 𝐽 if
term_mode=’jacobian’.
Supports ‘eval’, ‘el_avg’ and ‘qp’ evaluation modes.
Definition
𝜕𝑥 𝜕𝑢
𝐹 = |𝑞𝑝 = 𝐼 + |𝑞𝑝 ,
𝜕𝑋 𝜕𝑋
𝑥 = 𝑋 + 𝑢 , 𝐽 = det (𝐹 )
Call signature

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ev_def_grad (parameter)

Arguments
• parameter : 𝑢

arg_shapes = {'parameter': 'D'}

arg_types = ('parameter',)
static function(out, vec, vg, econn, term_mode, fmode)

get_eval_shape(parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'ev_def_grad'
class sfepy.terms.terms_hyperelastic_base.HyperElasticBase(*args, **kwargs)
Base class for all hyperelastic terms in TL/UL formulation.
HyperElasticBase.__call__() computes element contributions given either stress (-> residual) or tangent modulus
(-> tangent sitffnes matrix), i.e. constitutive relation type (CRT) related data. The CRT data are computed in
subclasses implementing particular CRT (e.g. neo-Hookean material), in self.compute_crt_data().
Modes:
• 0: total formulation
• 1: updated formulation

Notes

This is not a proper Term!

arg_shapes = {'material': '1, 1', 'state': 'D', 'virtual': ('D', 'state')}
arg_types = ('material', 'virtual', 'state')
compute_stress(mat, family_data, **kwargs)

compute_tan_mod(mat, family_data, **kwargs)

static function(out, fun, *args)

get_eval_shape(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

static integrate(out, val_qp, vg, fmode)

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class sfepy.terms.terms_hyperelastic_base.HyperElasticFamilyData(**kwargs)
Base class for hyperelastic family data.
The common (family) data are cached in the evaluate cache of state variable.
data_shapes = {'det_f': ('n_el', 'n_qp', 1, 1), 'green_strain': ('n_el', 'n_qp',
'sym', 1), 'in2_b': ('n_el', 'n_qp', 1, 1), 'in2_c': ('n_el', 'n_qp', 1, 1),
'inv_f': ('n_el', 'n_qp', 'dim', 'dim'), 'mtx_f': ('n_el', 'n_qp', 'dim', 'dim'),
'sym_b': ('n_el', 'n_qp', 'sym', 1), 'sym_c': ('n_el', 'n_qp', 'sym', 1),
'sym_inv_c': ('n_el', 'n_qp', 'sym', 1), 'tr_b': ('n_el', 'n_qp', 1, 1), 'tr_c':
('n_el', 'n_qp', 1, 1)}
init_data_struct(state_shape, name='family_data')

sfepy.terms.terms_hyperelastic_tl module

class sfepy.terms.terms_hyperelastic_tl.BulkActiveTLTerm(*args, **kwargs)

−1
Hyperelastic bulk active term. Stress 𝑆𝑖𝑗 = 𝐴𝐽𝐶𝑖𝑗 , where 𝐴 is the activation in [0, 𝐹max ].
Definition
∫︁
𝑆𝑖𝑗 (𝑢)𝛿𝐸𝑖𝑗 (𝑢; 𝑣)
Ω
Call signature

dw_tl_bulk_active (material, virtual, state)

Arguments
• material : 𝐴
• virtual : 𝑣
• state : 𝑢

family_data_names = ['det_f', 'sym_inv_c']

name = 'dw_tl_bulk_active'
static stress_function()

static tan_mod_function()

class sfepy.terms.terms_hyperelastic_tl.BulkPenaltyTLTerm(*args, **kwargs)

−1
Hyperelastic bulk penalty term. Stress 𝑆𝑖𝑗 = 𝐾(𝐽 − 1) 𝐽𝐶𝑖𝑗 .
Definition
∫︁
𝑆𝑖𝑗 (𝑢)𝛿𝐸𝑖𝑗 (𝑢; 𝑣)
Ω
Call signature

dw_tl_bulk_penalty (material, virtual, state)

Arguments

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• material : 𝐾
• virtual : 𝑣
• state : 𝑢

family_data_names = ['det_f', 'sym_inv_c']

name = 'dw_tl_bulk_penalty'
static stress_function()

static tan_mod_function()

class sfepy.terms.terms_hyperelastic_tl.BulkPressureTLTerm(*args, **kwargs)

−1
Hyperelastic bulk pressure term. Stress 𝑆𝑖𝑗 = −𝑝𝐽𝐶𝑖𝑗 .
Definition
∫︁
𝑆𝑖𝑗 (𝑝)𝛿𝐸𝑖𝑗 (𝑢; 𝑣)
Ω
Call signature

dw_tl_bulk_pressure (virtual, state, state_p)

Arguments
• virtual : 𝑣
• state : 𝑢
• state_p : 𝑝

arg_shapes = {'state': 'D', 'state_p': 1, 'virtual': ('D', 'state')}

arg_types = ('virtual', 'state', 'state_p')
compute_data(family_data, mode, **kwargs)

family_data_names = ['det_f', 'sym_inv_c']

get_eval_shape(virtual, state, state_p, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(virtual, state, state_p, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_tl_bulk_pressure'
static stress_function()

static tan_mod_u_function()

static weak_dp_function()

static weak_function()

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class sfepy.terms.terms_hyperelastic_tl.DiffusionTLTerm(*args, **kwargs)

Diffusion term in the total Lagrangian formulation with linearized deformation-dependent permeability 𝐾(𝑢) =
(︁ (︁ )︁)︁2
𝐽𝐹 −1 𝑘𝑓 (𝐽)𝐹 −𝑇 , where 𝑢 relates to the previous time step (𝑛 − 1) and 𝑓 (𝐽) = max 0, 1 + (𝐽−1) 𝑁𝑓
expresses the dependence on volume compression/expansion.
Definition
∫︁
𝜕𝑞 𝜕𝑝
𝐾(𝑢(𝑛−1) ) :
Ω 𝜕𝑋 𝜕𝑋
Call signature

dw_tl_diffusion (material_1, material_2, virtual, state, parameter)

Arguments
• material_1 : 𝑘
• material_2 : 𝑁𝑓
• virtual : 𝑞
• state : 𝑝
• parameter : 𝑢(𝑛−1)

arg_shapes = {'material_1': 'D, D', 'material_2': '1, 1', 'parameter': 'D',

'state': 1, 'virtual': (1, 'state')}
arg_types = ('material_1', 'material_2', 'virtual', 'state', 'parameter')
family_data_names = ['mtx_f', 'det_f']
static function()

get_eval_shape(perm, ref_porosity, virtual, state, parameter, mode=None, term_mode=None,

diff_var=None, **kwargs)

get_fargs(perm, ref_porosity, virtual, state, parameter, mode=None, term_mode=None, diff_var=None,

**kwargs)

name = 'dw_tl_diffusion'
class sfepy.terms.terms_hyperelastic_tl.GenYeohTLTerm(*args, **kwargs)
2
Hyperelastic generalized Yeoh term [1]. Effective stress 𝑆𝑖𝑗 = 2𝑝𝐾(𝐼1 − 3)𝑝−1 𝐽 − 3 (𝛿𝑖𝑗 − 31 𝐶𝑘𝑘 𝐶𝑖𝑗 −1 ).
Definition
∫︁
𝑆𝑖𝑗 (𝑢)𝛿𝐸𝑖𝑗 (𝑢; 𝑣)
Ω
Call signature

dw_tl_he_genyeoh (material, virtual, state)

Arguments
• material : 𝑝, 𝐾
• virtual : 𝑣

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• state : 𝑢

[1] Travis W. Hohenberger, Richard J. Windslow, Nicola M. Pugno, James J. C. Busfield. Aconstitutive Model
For Both Lowand High Strain Nonlinearities In Highly Filled Elastomers And Implementation With User-Defined
Material Subroutines In Abaqus. Rubber Chemistry And Technology, Vol. 92, No. 4, Pp. 653-686 (2019)
arg_shapes = {'material': '1, 2', 'state': 'D', 'virtual': ('D', 'state')}
family_data_names = ['det_f', 'tr_c', 'sym_inv_c']
geometries = ['3_4', '3_8']
name = 'dw_tl_he_genyeoh'
stress_function(out, mat, *fargs, **kwargs)

tan_mod_function(out, mat, *fargs, **kwargs)

class sfepy.terms.terms_hyperelastic_tl.HyperElasticSurfaceTLBase(*args, **kwargs)

Base class for all hyperelastic surface terms in TL formulation family.
get_family_data = HyperElasticSurfaceTLFamilyData
class sfepy.terms.terms_hyperelastic_tl.HyperElasticSurfaceTLFamilyData(**kwargs)
Family data for TL formulation applicable for surface terms.
cache_name = 'tl_surface_common'
data_names = ('mtx_f', 'det_f', 'inv_f')
static family_function()

class sfepy.terms.terms_hyperelastic_tl.HyperElasticTLBase(*args, **kwargs)

Base class for all hyperelastic terms in TL formulation family.
The subclasses should have the following static method attributes: - stress_function() (the stress) -
tan_mod_function() (the tangent modulus)
The common (family) data are cached in the evaluate cache of state variable.
get_family_data = HyperElasticTLFamilyData
hyperelastic_mode = 0
static weak_function()

class sfepy.terms.terms_hyperelastic_tl.HyperElasticTLFamilyData(**kwargs)
Family data for TL formulation.
cache_name = 'tl_common'
data_names = ('mtx_f', 'det_f', 'sym_c', 'tr_c', 'in2_c', 'sym_inv_c',
'green_strain')
static family_function()

class sfepy.terms.terms_hyperelastic_tl.MooneyRivlinTLTerm(*args, **kwargs)

4 −1
Hyperelastic Mooney-Rivlin term. Effective stress 𝑆𝑖𝑗 = 𝜅𝐽 − 3 (𝐶𝑘𝑘 𝛿𝑖𝑗 − 𝐶𝑖𝑗 − 32 𝐼2 𝐶𝑖𝑗 ).
Definition

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∫︁
𝑆𝑖𝑗 (𝑢)𝛿𝐸𝑖𝑗 (𝑢; 𝑣)
Ω
Call signature

dw_tl_he_mooney_rivlin (material, virtual, state)

Arguments
• material : 𝜅
• virtual : 𝑣
• state : 𝑢

family_data_names = ['det_f', 'tr_c', 'sym_inv_c', 'sym_c', 'in2_c']

name = 'dw_tl_he_mooney_rivlin'
static stress_function()

static tan_mod_function()

class sfepy.terms.terms_hyperelastic_tl.NeoHookeanTLTerm(*args, **kwargs)

2 −1
Hyperelastic neo-Hookean term. Effective stress 𝑆𝑖𝑗 = 𝜇𝐽 − 3 (𝛿𝑖𝑗 − 31 𝐶𝑘𝑘 𝐶𝑖𝑗 ).
Definition
∫︁
𝑆𝑖𝑗 (𝑢)𝛿𝐸𝑖𝑗 (𝑢; 𝑣)
Ω
Call signature

dw_tl_he_neohook (material, virtual, state)

Arguments
• material : 𝜇
• virtual : 𝑣
• state : 𝑢

family_data_names = ['det_f', 'tr_c', 'sym_inv_c']

name = 'dw_tl_he_neohook'
static stress_function()

static tan_mod_function()

class sfepy.terms.terms_hyperelastic_tl.OgdenTLTerm(*args, **kwargs)

Single term of the hyperelastic Ogden model [1] with the strain energy density
𝜇 𝛼
𝑊 = (𝜆 + 𝜆𝛼 𝛼
2 + 𝜆3 − 3) ,
𝛼 1
where 𝜆𝑘 , 𝑘 = 1, 2, 3 are the principal stretches, whose squares are the principal values of the right Cauchy-Green
deformation tensor C.

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Effective stress (2nd Piola-Kirchhoff) is [2]

3
𝜕𝑊 ∑︁ (𝑘) (𝑘)
𝑆𝑖𝑗 = 2 = 𝑆 (𝑘) 𝑁𝑖 𝑁𝑗 ,
𝜕𝐶𝑖𝑗
𝑘=1

where the principal stresses are

⎛ ⎞
3
¯ 𝛼−2 −
∑︁ 𝜇 𝜆𝛼
𝑗
𝑆 (𝑘) = 𝐽 −2/3 ⎝𝜇 𝜆 ⎠ , 𝑘 = 1, 2, 3 .
𝑗=1
3 𝜆2𝑘

and N(𝑘) , 𝑘 = 1, 2, 3 are the eigenvectors of C.

Definition
∫︁
𝑆𝑖𝑗 (𝑢)𝛿𝐸𝑖𝑗 (𝑢; 𝑣)
Ω
Call signature

dw_tl_he_ogden (material, virtual, state)

Arguments
• material : 𝑝, 𝐾
• virtual : 𝑣
• state : 𝑢

[1] Ogden, R. W. Large deformation isotropic elasticity - on the correlation of theory and experiment for incom-
pressible rubberlike solids. Proceedings of the Royal Society A, Vol. 326, No. 1567, Pp. 565-584 (1972), DOI
10.1098/rspa.1972.0026.
[2] Steinmann, P., Hossain, M., Possart, G. Hyperelastic models for rubber-like materials: Consistent tangent
operators and suitability for Treloar’s data. Archive of Applied Mechanics, Vol. 82, No. 9, Pp. 1183-1217
(2012), DOI 10.1007/s00419-012-0610-z.
arg_shapes = {'material': '1, 2', 'state': 'D', 'virtual': ('D', 'state')}
family_data_names = ['det_f', 'sym_c', 'tr_c', 'sym_inv_c']
geometries = ['3_4', '3_8']
name = 'dw_tl_he_ogden'
stress_function(out, mat, *fargs, **kwargs)

tan_mod_function(out, mat, *fargs, **kwargs)

class sfepy.terms.terms_hyperelastic_tl.SurfaceFluxTLTerm(*args, **kwargs)

Surface flux term in the total Lagrangian formulation, consistent with DiffusionTLTerm.
Definition
∫︁
𝜕𝑝
𝜈 · 𝐾(𝑢(𝑛−1) )
Γ 𝜕𝑋
Call signature

ev_tl_surface_flux (material_1, material_2, parameter_1, parameter_2)

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Arguments
• material_1 : 𝑘
• material_2 : 𝑁𝑓
• parameter_1 : 𝑝
• parameter_2 : 𝑢(𝑛−1)

arg_shapes = {'material_1': 'D, D', 'material_2': '1, 1', 'parameter_1': 1,

'parameter_2': 'D'}
arg_types = ('material_1', 'material_2', 'parameter_1', 'parameter_2')
family_data_names = ['det_f', 'inv_f']
static function()

get_eval_shape(perm, ref_porosity, pressure, displacement, mode=None, term_mode=None,

diff_var=None, **kwargs)

get_fargs(perm, ref_porosity, pressure, displacement, mode=None, term_mode=None, diff_var=None,

**kwargs)

integration = 'surface_extra'
name = 'ev_tl_surface_flux'
class sfepy.terms.terms_hyperelastic_tl.SurfaceTractionTLTerm(*args, **kwargs)
Surface traction term in the total Lagrangian formulation, expressed using 𝜈, the outward unit normal vector
w.r.t. the undeformed surface, 𝐹 (𝑢), the deformation gradient, 𝐽 = det(𝐹 ), and 𝜎 a given traction, often equal
to a given pressure, i.e. 𝜎 = 𝜋𝐼.
Definition
∫︁
𝜈 · 𝐹 −1 · 𝜎 · 𝑣𝐽
Γ
Call signature

dw_tl_surface_traction (opt_material, virtual, state)

Arguments
• material : 𝜎
• virtual : 𝑣
• state : 𝑢

arg_shapes = [{'opt_material': 'D, D', 'virtual': ('D', 'state'), 'state': 'D'},

{'opt_material': None}]
arg_types = ('opt_material', 'virtual', 'state')
family_data_names = ['det_f', 'inv_f']
static function()

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get_fargs(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'surface_extra'
name = 'dw_tl_surface_traction'
class sfepy.terms.terms_hyperelastic_tl.VolumeSurfaceTLTerm(*args, **kwargs)
Volume of a 𝐷-dimensional domain, using a surface integral in the total Lagrangian formulation, expressed
using 𝜈, the outward unit normal vector w.r.t. the undeformed surface, 𝐹 (𝑢), the deformation gradient, and
𝐽 = det(𝐹 ). Uses the approximation of 𝑢 for the deformed surface coordinates 𝑥.
Definition
∫︁
1/𝐷 𝜈 · 𝐹 −1 · 𝑥𝐽
Γ
Call signature

ev_tl_volume_surface (parameter)

Arguments
• parameter : 𝑢

arg_shapes = {'parameter': 'D'}

arg_types = ('parameter',)
family_data_names = ['det_f', 'inv_f']
static function()

get_eval_shape(parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'surface_extra'
name = 'ev_tl_volume_surface'
class sfepy.terms.terms_hyperelastic_tl.VolumeTLTerm(*args, **kwargs)
Volume term (weak form) in the total Lagrangian formulation.
Definition
∫︀
Ω
𝑞𝐽(𝑢)
volume mode: vector for 𝐾 ← ℐℎ : 𝑇𝐾 ∫︀𝐽(𝑢)
∫︀

rel_volume mode: vector for 𝐾 ← ℐℎ : 𝑇𝐾 𝐽(𝑢)/ 𝑇𝐾 1

∫︀

Call signature

dw_tl_volume (virtual, state)

Arguments
• virtual : 𝑞
• state : 𝑢

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arg_shapes = {'state': 'D', 'virtual': (1, None)}

arg_types = ('virtual', 'state')
family_data_names = ['mtx_f', 'det_f', 'sym_inv_c']
static function()

get_eval_shape(virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_tl_volume'

sfepy.terms.terms_hyperelastic_ul module

class sfepy.terms.terms_hyperelastic_ul.BulkPenaltyULTerm(*args, **kwargs)

Hyperelastic bulk penalty term. Stress 𝜏𝑖𝑗 = 𝐾(𝐽 − 1) 𝐽𝛿𝑖𝑗 .
Definition
∫︁
ℒ𝜏𝑖𝑗 (𝑢)𝑒𝑖𝑗 (𝛿𝑣)/𝐽
Ω
Call signature

dw_ul_bulk_penalty (material, virtual, state)

Arguments
• material : 𝐾
• virtual : 𝑣
• state : 𝑢

family_data_names = ['det_f']
name = 'dw_ul_bulk_penalty'
static stress_function()

static tan_mod_function()

class sfepy.terms.terms_hyperelastic_ul.BulkPressureULTerm(*args, **kwargs)

Hyperelastic bulk pressure term. Stress 𝑆𝑖𝑗 = −𝑝𝐽𝛿𝑖𝑗 .
Definition
∫︁
ℒ𝜏𝑖𝑗 (𝑢)𝑒𝑖𝑗 (𝛿𝑣)/𝐽
Ω
Call signature

dw_ul_bulk_pressure (virtual, state, state_p)

Arguments

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• virtual : 𝑣
• state : 𝑢
• state_p : 𝑝

arg_shapes = {'state': 'D', 'state_p': 1, 'virtual': ('D', 'state')}

arg_types = ('virtual', 'state', 'state_p')
compute_data(family_data, mode, **kwargs)

family_data_names = ['det_f', 'sym_b']

static family_function()

get_eval_shape(virtual, state, state_p, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(virtual, state, state_p, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_ul_bulk_pressure'
static stress_function()

static tan_mod_u_function()

static weak_dp_function()

static weak_function()

class sfepy.terms.terms_hyperelastic_ul.CompressibilityULTerm(*args, **kwargs)

Compressibility term for the updated Lagrangian formulation
Definition
∫︀
Ω
1
𝛾𝑝 𝑞
Call signature

dw_ul_compressible (material, virtual, state, parameter_u)

Arguments
• material : 𝛾
• virtual : 𝑞
• state : 𝑝
• parameter_u : (𝑢)

arg_shapes = {'material': '1, 1', 'parameter_u': 'D', 'state': 1, 'virtual': (1,

'state')}
arg_types = ('material', 'virtual', 'state', 'parameter_u')

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family_data_names = ['mtx_f', 'det_f']

static function()

get_fargs(bulk, virtual, state, parameter_u, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_ul_compressible'
class sfepy.terms.terms_hyperelastic_ul.HyperElasticULBase(*args, **kwargs)
Base class for all hyperelastic terms in UL formulation family.
The subclasses should have the following static method attributes: - stress_function() (the stress) -
tan_mod_function() (the tangent modulus)
get_family_data = HyperElasticULFamilyData
hyperelastic_mode = 1
static weak_function()

class sfepy.terms.terms_hyperelastic_ul.HyperElasticULFamilyData(**kwargs)
Family data for UL formulation.
cache_name = 'ul_common'
data_names = ('mtx_f', 'det_f', 'sym_b', 'tr_b', 'in2_b', 'green_strain')
static family_function()

class sfepy.terms.terms_hyperelastic_ul.MooneyRivlinULTerm(*args, **kwargs)

Hyperelastic Mooney-Rivlin term.
Definition
∫︁
ℒ𝜏𝑖𝑗 (𝑢)𝑒𝑖𝑗 (𝛿𝑣)/𝐽
Ω
Call signature

dw_ul_he_mooney_rivlin (material, virtual, state)

Arguments
• material : 𝜅
• virtual : 𝑣
• state : 𝑢

family_data_names = ['det_f', 'tr_b', 'sym_b', 'in2_b']

name = 'dw_ul_he_mooney_rivlin'
static stress_function()

static tan_mod_function()

class sfepy.terms.terms_hyperelastic_ul.NeoHookeanULTerm(*args, **kwargs)

2
Hyperelastic neo-Hookean term. Effective stress 𝜏𝑖𝑗 = 𝜇𝐽 − 3 (𝑏𝑖𝑗 − 31 𝑏𝑘𝑘 𝛿𝑖𝑗 ).

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Definition
∫︁
ℒ𝜏𝑖𝑗 (𝑢)𝑒𝑖𝑗 (𝛿𝑣)/𝐽
Ω
Call signature

dw_ul_he_neohook (material, virtual, state)

Arguments
• material : 𝜇
• virtual : 𝑣
• state : 𝑢

family_data_names = ['det_f', 'tr_b', 'sym_b']

name = 'dw_ul_he_neohook'
static stress_function()

static tan_mod_function()

class sfepy.terms.terms_hyperelastic_ul.VolumeULTerm(*args, **kwargs)

Volume term (weak form) in the updated Lagrangian formulation.
Definition
∫︀
Ω
𝑞𝐽(𝑢)
volume mode: vector for 𝐾 ← ℐℎ : 𝑇𝐾 ∫︀𝐽(𝑢)
∫︀

rel_volume mode: vector for 𝐾 ← ℐℎ : 𝑇𝐾 𝐽(𝑢)/ 𝑇𝐾 1

∫︀

Call signature

dw_ul_volume (virtual, state)

Arguments
• virtual : 𝑞
• state : 𝑢

arg_shapes = {'state': 'D', 'virtual': (1, None)}

arg_types = ('virtual', 'state')
family_data_names = ['mtx_f', 'det_f']
static function()

get_eval_shape(virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_ul_volume'

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sfepy.terms.terms_membrane module

class sfepy.terms.terms_membrane.TLMembraneTerm(*args, **kwargs)

Mooney-Rivlin membrane with plain stress assumption.
The membrane has a uniform initial thickness ℎ0 and obeys a hyperelastic material law with strain energy by
Mooney-Rivlin: Ψ = 𝑎1 (𝐼1 − 3) + 𝑎2 (𝐼2 − 3).
Call signature

dw_tl_membrane (material_a1, material_a2, material_h0, virtual, state)

Arguments
• material_a1 : 𝑎1
• material_a2 : 𝑎2
• material_h0 : ℎ0
• virtual : 𝑣
• state : 𝑢

arg_shapes = {'material_a1': '1, 1', 'material_a2': '1, 1', 'material_h0': '1,

1', 'state': 'D', 'virtual': ('D', 'state')}
arg_types = ('material_a1', 'material_a2', 'material_h0', 'virtual', 'state')
static eval_function(out, a1, a2, h0, mtx_c, c33, mtx_b, mtx_t, geo, term_mode, fmode)

static function(out, fun, *args)

Notes

fun is either weak_function or eval_function according to evaluation mode.

geometries = ['3_4', '3_8']
get_eval_shape(a1, a2, h0, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(a1, a2, h0, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'surface'
name = 'dw_tl_membrane'
static weak_function(out, a1, a2, h0, mtx_c, c33, mtx_b, mtx_t, bfg, geo, fmode)

sfepy.terms.terms_membrane.eval_membrane_mooney_rivlin(a1, a2, mtx_c, c33, mode)

Evaluate stress or tangent stiffness of the Mooney-Rivlin membrane.
[1] Baoguo Wu, Xingwen Du and Huifeng Tan: A three-dimensional FE nonlinear analysis of membranes, Com-
puters & Structures 59 (1996), no. 4, 601–605.

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sfepy.terms.terms_multilinear module

class sfepy.terms.terms_multilinear.ECauchyStressTerm(*args, **kwargs)

Evaluate Cauchy stress tensor.
It is given in the usual vector form exploiting symmetry: in 3D it has 6 components with the indices ordered as
[11, 22, 33, 12, 13, 23], in 2D it has 3 components with the indices ordered as [11, 22, 12].
Definition
∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑘𝑙 (𝑤)
Ω
Call signature

de_cauchy_stress (material, parameter)

Arguments
• material : 𝐷𝑖𝑗𝑘𝑙
• parameter : 𝑤

arg_shapes = {'material': 'S, S', 'parameter': 'D'}

arg_types = ('material', 'parameter')
get_function(mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'de_cauchy_stress'
class sfepy.terms.terms_multilinear.EConvectTerm(*args, **kwargs)
Nonlinear convective term.
Definition
∫︁
((𝑢 · ∇)𝑢) · 𝑣
Ω
Call signature

de_convect (virtual, state)

(parameter_1, parameter_2)

Arguments
• virtual/parameter_1: 𝑣
• state/parameter_2: 𝑢

arg_shapes = {'parameter_1': 'D', 'parameter_2': 'D', 'state': 'D', 'virtual':

('D', 'state')}
arg_types = (('virtual', 'state'), ('parameter_1', 'parameter_2'))
get_function(virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('weak', 'eval')

name = 'de_convect'

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class sfepy.terms.terms_multilinear.EDiffusionTerm(*args, **kwargs)

General diffusion term.
Definition
∫︁
𝐾𝑖𝑗 ∇𝑖 𝑞 ∇𝑗 𝑝
Ω
Call signature

de_diffusion (material, virtual, state)

(material, parameter_1, parameter_2)

Arguments
• material: 𝐾𝑖𝑗
• virtual/parameter_1: 𝑞
• state/parameter_2: 𝑝

arg_shapes = {'material': 'D, D', 'parameter_1': 1, 'parameter_2': 1, 'state':

1, 'virtual': (1, 'state')}
arg_types = (('material', 'virtual', 'state'), ('material', 'parameter_1',
'parameter_2'))
get_function(mat, vvar, svar, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('weak', 'eval')

name = 'de_diffusion'
class sfepy.terms.terms_multilinear.EDivGradTerm(*args, **kwargs)
Vector field diffusion term.
Definition
∫︁ ∫︁
∇𝑣 : ∇𝑢 , 𝜈 ∇𝑣 : ∇𝑢
Ω Ω
Call signature

de_div_grad (opt_material, virtual, state)

(opt_material, parameter_1, parameter_2)

Arguments
• material: 𝜈 (viscosity, optional)
• virtual/parameter_1: 𝑣
• state/parameter_2: 𝑢

arg_shapes = [{'opt_material': '1, 1', 'virtual': ('D', 'state'), 'state': 'D',

'parameter_1': 'D', 'parameter_2': 'D'}, {'opt_material': None}]
arg_types = (('opt_material', 'virtual', 'state'), ('opt_material', 'parameter_1',
'parameter_2'))
get_function(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

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modes = ('weak', 'eval')

name = 'de_div_grad'
class sfepy.terms.terms_multilinear.EDivTerm(*args, **kwargs)
Weighted divergence term.
Definition
∫︁ ∫︁
∇·𝑣, 𝑐∇ · 𝑣
Ω Ω
Call signature

de_div (opt_material, virtual)

(opt_material, parameter)

Arguments
• material: 𝑐 (optional)
• virtual/parameter: 𝑣

arg_shapes = [{'opt_material': '1, 1', 'virtual': ('D', None), 'parameter': 'D'},

{'opt_material': None}]
arg_types = (('opt_material', 'virtual'), ('opt_material', 'parameter'))
get_function(mat, virtual, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('weak', 'eval')

name = 'de_div'
class sfepy.terms.terms_multilinear.EDotTerm(*args, **kwargs)
Volume and surface 𝐿2 (Ω) weighted dot product for both scalar and vector fields. Can be evaluated. Can use
derivatives.
Definition
∫︁ ∫︁
𝑞𝑝 , 𝑣·𝑢
∫︁ 𝒟 ∫︁ 𝒟
𝑐𝑞𝑝 , 𝑐𝑣 · 𝑢
𝒟 𝒟
∫︁
𝑣 · (𝑀 𝑢)
𝒟
Call signature

de_dot (opt_material, virtual, state)

(opt_material, parameter_1, parameter_2)

Arguments
• material: 𝑐 or 𝑀 (optional)
• virtual/parameter_1: 𝑞 or 𝑣
• state/parameter_2: 𝑝 or 𝑢

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arg_shapes = [{'opt_material': '1, 1', 'virtual': (1, 'state'), 'state': 1,

'parameter_1': 1, 'parameter_2': 1}, {'opt_material': None}, {'opt_material':
'1, 1', 'virtual': ('D', 'state'), 'state': 'D', 'parameter_1': 'D',
'parameter_2': 'D'}, {'opt_material': 'D, D'}, {'opt_material': None}]
arg_types = (('opt_material', 'virtual', 'state'), ('opt_material', 'parameter_1',
'parameter_2'))
get_function(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'by_region'
modes = ('weak', 'eval')
name = 'de_dot'
class sfepy.terms.terms_multilinear.EGradTerm(*args, **kwargs)
Weighted gradient term.
Definition
∫︁ ∫︁
∇𝑣 , 𝑐∇𝑣
Ω Ω
Call signature

de_grad (opt_material, parameter)

Arguments
• material: 𝑐 (optional)
• virtual/parameter: 𝑣

arg_shapes = [{'opt_material': '1, 1', 'parameter': 'N'}, {'opt_material': None}]

arg_types = ('opt_material', 'parameter')
get_function(mat, virtual, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'de_grad'
class sfepy.terms.terms_multilinear.EIntegrateOperatorTerm(*args, **kwargs)
Volume and surface integral of a test function weighted by a scalar function 𝑐.
Definition
∫︁ ∫︁
𝑞 or 𝑐𝑞
𝒟 𝒟
Call signature

de_integrate (opt_material, virtual)

Arguments
• material : 𝑐 (optional)
• virtual : 𝑞

arg_shapes = [{'opt_material': '1, 1', 'virtual': (1, None)}, {'opt_material':

None}]

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arg_types = ('opt_material', 'virtual')

get_function(mat, virtual, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'by_region'
name = 'de_integrate'
class sfepy.terms.terms_multilinear.ELaplaceTerm(*args, **kwargs)
Laplace term with 𝑐 coefficient. Can be evaluated. Can use derivatives.
Definition
∫︁ ∫︁
∇𝑞 · ∇𝑝 , 𝑐∇𝑞 · ∇𝑝
Ω Ω
Call signature

de_laplace (opt_material, virtual, state)

(opt_material, parameter_1, parameter_2)

Arguments
• material: 𝑐
• virtual/parameter_1: 𝑞
• state/parameter_2: 𝑝

arg_shapes = [{'opt_material': '1, 1', 'virtual': (1, 'state'), 'state': 1,

'parameter_1': 1, 'parameter_2': 1}, {'opt_material': None}]
arg_types = (('opt_material', 'virtual', 'state'), ('opt_material', 'parameter_1',
'parameter_2'))
get_function(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('weak', 'eval')

name = 'de_laplace'
class sfepy.terms.terms_multilinear.ELinearConvectTerm(*args, **kwargs)
Linearized convective term.
Definition
∫︁
((𝑏 · ∇)𝑢) · 𝑣
Ω
Call signature

de_lin_convect (virtual, parameter, state)

(parameter_1, parameter_2, parameter_3)

Arguments
• virtual/parameter_1: 𝑣
• parameter/parameter_2: 𝑏
• state/parameter_3: 𝑢

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arg_shapes = {'parameter': 'D', 'parameter_1': 'D', 'parameter_2': 'D',

'parameter_3': 'D', 'state': 'D', 'virtual': ('D', 'state')}
arg_types = (('virtual', 'parameter', 'state'), ('parameter_1', 'parameter_2',
'parameter_3'))
get_function(virtual, parameter, state, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('weak', 'eval')

name = 'de_lin_convect'
class sfepy.terms.terms_multilinear.ELinearElasticTerm(*args, **kwargs)
General linear elasticity term, with 𝐷𝑖𝑗𝑘𝑙 given in the usual matrix form exploiting symmetry: in 3D it is 6 × 6
with the indices ordered as [11, 22, 33, 12, 13, 23], in 2D it is 3 × 3 with the indices ordered as [11, 22, 12].
Definition
∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢)
Ω
Call signature

de_lin_elastic (material, virtual, state)

(material, parameter_1, parameter_2)

Arguments
• material: 𝐷𝑖𝑗𝑘𝑙
• virtual/parameter_1: 𝑣
• state/parameter_2: 𝑢

arg_shapes = {'material': 'S, S', 'parameter_1': 'D', 'parameter_2': 'D',

'state': 'D', 'virtual': ('D', 'state')}
arg_types = (('material', 'virtual', 'state'), ('material', 'parameter_1',
'parameter_2'))
get_function(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('weak', 'eval')

name = 'de_lin_elastic'
class sfepy.terms.terms_multilinear.ELinearTractionTerm(*args, **kwargs)
Linear traction term. The material parameter can have one of the following shapes:
• 1 or (1, 1) - a given scalar pressure
• (D, 1) - a traction vector
• (S, 1) or (D, D) - a given stress in symmetric or non-symmetric tensor storage (in symmetric storage indicies
are order as follows: 2D: [11, 22, 12], 3D: [11, 22, 33, 12, 13, 23])

Definition
∫︁ ∫︁
𝑣·𝑛, 𝑐𝑣 · 𝑛
Γ Γ
∫︁ ∫︁
𝑣 · (𝜎 𝑛) , 𝑣·𝑓
Γ Γ

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Call signature

de_surface_ltr (opt_material, virtual)

(opt_material, parameter)

Arguments
• material: 𝑐, 𝑓 , 𝜎 or 𝜎
• virtual/parameter: 𝑣

arg_shapes = [{'opt_material': 'S, 1', 'virtual': ('D', None), 'parameter': 'D'},

{'opt_material': None}, {'opt_material': '1, 1'}, {'opt_material': 'D, 1'},
{'opt_material': 'D, D'}]
arg_types = (('opt_material', 'virtual'), ('opt_material', 'parameter'))
get_function(traction, vvar, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'surface'
modes = ('weak', 'eval')
name = 'de_surface_ltr'
class sfepy.terms.terms_multilinear.ENonPenetrationPenaltyTerm(*args, **kwargs)
Non-penetration condition in the weak sense using a penalty.
Definition
∫︁
𝑐(𝑛 · 𝑣)(𝑛 · 𝑢)
Γ
Call signature

de_non_penetration_p (material, virtual, state)

Arguments
• material : 𝑐
• virtual : 𝑣
• state : 𝑢

arg_shapes = {'material': '1, 1', 'state': 'D', 'virtual': ('D', 'state')}

arg_types = ('material', 'virtual', 'state')
get_function(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'surface'
name = 'de_non_penetration_p'
class sfepy.terms.terms_multilinear.ENonSymElasticTerm(*args, **kwargs)
Elasticity term with non-symmetric gradient. The indices of matrix 𝐷𝑖𝑗𝑘𝑙 are ordered as
[11, 12, 13, 21, 22, 23, 31, 32, 33] in 3D and as [11, 12, 21, 22] in 2D.
Definition

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∫︁
𝐷∇𝑣 : ∇𝑢
Ω
Call signature

de_nonsym_elastic (material, virtual, state)

(material, parameter_1, parameter_2)

Arguments
• material: 𝐷
• virtual/parameter_1: 𝑣
• state/parameter_2: 𝑢

arg_shapes = {'material': 'D2, D2', 'parameter_1': 'D', 'parameter_2': 'D',

'state': 'D', 'virtual': ('D', 'state')}
arg_types = (('material', 'virtual', 'state'), ('material', 'parameter_1',
'parameter_2'))
get_function(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('weak', 'eval')

name = 'de_nonsym_elastic'
class sfepy.terms.terms_multilinear.EScalarDotMGradScalarTerm(*args, **kwargs)
Volume dot product of a scalar gradient dotted with a material vector with a scalar.
Definition
∫︁ ∫︁
𝑞𝑦 · ∇𝑝 , 𝑝𝑦 · ∇𝑞
Ω Ω
Call signature

de_s_dot_mgrad_s (material, virtual, state)

(material, state, virtual)

Arguments 1
• material : 𝑦
• virtual : 𝑞
• state : 𝑝
Arguments 2
• material : 𝑦
• state : 𝑝
• virtual : 𝑞

arg_shapes = [{'material': 'D, 1', 'virtual/grad_state': (1, None),

'state/grad_state': 1, 'virtual/grad_virtual': (1, None), 'state/grad_virtual':
1}]
arg_types = (('material', 'virtual', 'state'), ('material', 'state', 'virtual'))

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get_function(mat, var1, var2, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('grad_state', 'grad_virtual')

name = 'de_s_dot_mgrad_s'
class sfepy.terms.terms_multilinear.EStokesTerm(*args, **kwargs)
Stokes problem coupling term. Corresponds to weak forms of gradient and divergence terms.
Definition
∫︁ ∫︁
𝑝∇ · 𝑣 , 𝑞∇·𝑢
∫︁ Ω ∫︁ Ω
𝑐𝑝∇ · 𝑣 , 𝑐𝑞∇ · 𝑢
Ω Ω
Call signature

de_stokes (opt_material, virtual, state)

(opt_material, state, virtual)
(opt_material, parameter_v, parameter_s)

Arguments 1
• material: 𝑐 (optional)
• virtual/parameter_v: 𝑣
• state/parameter_s: 𝑝
Arguments 2
• material : 𝑐 (optional)
• state : 𝑢
• virtual : 𝑞

arg_shapes = [{'opt_material': '1, 1', 'virtual/grad': ('D', None), 'state/grad':

1, 'virtual/div': (1, None), 'state/div': 'D', 'parameter_v': 'D', 'parameter_s':
1}, {'opt_material': None}]
arg_types = (('opt_material', 'virtual', 'state'), ('opt_material', 'state',
'virtual'), ('opt_material', 'parameter_v', 'parameter_s'))
get_function(coef, vvar, svar, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('grad', 'div', 'eval')

name = 'de_stokes'
class sfepy.terms.terms_multilinear.ETermBase(*args, **kwargs)
Reserved letters:
c .. cells q .. quadrature points d-h .. DOFs axes r-z .. auxiliary axes
Layout specification letters:
c .. cells q .. quadrature points v .. variable component - matrix form (v, d) -> vector v*d g .. gradient component
d .. local DOF (basis, node) 0 .. all material axes

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build_expression(texpr, *eargs, diff_var=None)

can_backend = {'dask_single': <module 'dask.array' from

'/home/eldaran/.local/lib/python3.8/site-packages/dask/array/__init__.py'>,
'dask_threads': <module 'dask.array' from
'/home/eldaran/.local/lib/python3.8/site-packages/dask/array/__init__.py'>, 'jax':
<module 'jax.numpy' from
'/home/eldaran/.local/lib/python3.8/site-packages/jax/numpy/__init__.py'>,
'jax_vmap': <module 'jax.numpy' from
'/home/eldaran/.local/lib/python3.8/site-packages/jax/numpy/__init__.py'>, 'numpy':
<module 'numpy' from
'/home/eldaran/.local/lib/python3.8/site-packages/numpy/__init__.py'>, 'numpy_loop':
<module 'numpy' from
'/home/eldaran/.local/lib/python3.8/site-packages/numpy/__init__.py'>,
'numpy_qloop': <module 'numpy' from
'/home/eldaran/.local/lib/python3.8/site-packages/numpy/__init__.py'>, 'opt_einsum':
<module 'opt_einsum' from
'/home/eldaran/.local/lib/python3.8/site-packages/opt_einsum/__init__.py'>,
'opt_einsum_dask_single': <module 'dask.array' from
'/home/eldaran/.local/lib/python3.8/site-packages/dask/array/__init__.py'>,
'opt_einsum_dask_threads': <module 'dask.array' from
'/home/eldaran/.local/lib/python3.8/site-packages/dask/array/__init__.py'>,
'opt_einsum_loop': <module 'opt_einsum' from
'/home/eldaran/.local/lib/python3.8/site-packages/opt_einsum/__init__.py'>,
'opt_einsum_qloop': <module 'opt_einsum' from
'/home/eldaran/.local/lib/python3.8/site-packages/opt_einsum/__init__.py'>}
clear_cache()

static function_silent(out, eval_einsum, *args)

static function_timer(out, eval_einsum, *args)

get_eval_shape(*args, **kwargs)

get_fargs(*args, **kwargs)

get_normals(arg)

get_operands(diff_var)

get_paths(expressions, operands)

layout_letters = 'cqgvd0'
make_function(texpr, *args, diff_var=None)

set_backend(backend='numpy', optimize=True, layout=None, **kwargs)

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set_verbosity(verbosity=None)

verbosity = 0
class sfepy.terms.terms_multilinear.ExpressionArg(**kwargs)

static from_term_arg(arg, term)

get_bf(expr_cache)

get_dofs(cache, expr_cache, oname)

class sfepy.terms.terms_multilinear.ExpressionBuilder(n_add, cache)

add_arg_dofs(iin, ein, name, n_components, iia=None)

add_bf(iin, ein, name, cell_dependent=False)

add_bfg(iin, ein, name)

add_constant(name, cname)

add_eye(iic, ein, name, iia=None)

add_material_arg(arg, ii, ein)

add_psg(iic, ein, name, iia=None)

add_pvg(iic, ein, name, iia=None)

add_state_arg(arg, ii, ein, modifier, diff_var)

add_virtual_arg(arg, ii, ein, modifier)

apply_layout(layout, operands, defaults=None, verbosity=0)

build(texpr, *args, diff_var=None)

get_expressions(subscripts=None)

static join_subscripts(subscripts, out_subscripts)

letters = 'defgh'

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make_eye(size)

make_psg(dim)

make_pvg(dim)

print_shapes(subscripts, operands)

transform(subscripts, operands, transformation='loop', **kwargs)

sfepy.terms.terms_multilinear.append_all(seqs, item, ii=None)

sfepy.terms.terms_multilinear.collect_modifiers(modifiers)

sfepy.terms.terms_multilinear.find_free_indices(indices)

sfepy.terms.terms_multilinear.get_einsum_ops(eargs, ebuilder, expr_cache)

sfepy.terms.terms_multilinear.get_loop_indices(subs, loop_index)

sfepy.terms.terms_multilinear.get_output_shape(out_subscripts, subscripts, operands)

sfepy.terms.terms_multilinear.get_sizes(indices, operands)

sfepy.terms.terms_multilinear.get_slice_ops(subs, ops, loop_index)

sfepy.terms.terms_multilinear.parse_term_expression(texpr)

sfepy.terms.terms_multilinear.sym2nonsym(sym_obj, axes=[3])

sfepy.terms.terms_navier_stokes module

class sfepy.terms.terms_navier_stokes.ConvectTerm(name, arg_str, integral, region, **kwargs)

Nonlinear convective term.
Definition
∫︁
((𝑢 · ∇)𝑢) · 𝑣
Ω
Call signature

dw_convect (virtual, state)

Arguments
• virtual : 𝑣

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• state : 𝑢

arg_shapes = {'state': 'D', 'virtual': ('D', 'state')}

arg_types = ('virtual', 'state')
static function()

get_fargs(virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_convect'
class sfepy.terms.terms_navier_stokes.DivGradTerm(name, arg_str, integral, region, **kwargs)
Diffusion term.
Definition
∫︁ ∫︁
𝜈 ∇𝑣 : ∇𝑢 , 𝜈 ∇𝑢 : ∇𝑤
Ω Ω
∫︁ ∫︁
∇𝑣 : ∇𝑢 , ∇𝑢 : ∇𝑤
Ω Ω
Call signature

dw_div_grad (opt_material, virtual, state)

(opt_material, parameter_1, parameter_2)

Arguments 1
• material : 𝜈 (viscosity, optional)
• virtual : 𝑣
• state : 𝑢
Arguments 2
• material : 𝜈 (viscosity, optional)
• parameter_1 : 𝑢
• parameter_2 : 𝑤

arg_shapes = [{'opt_material': '1, 1', 'virtual': ('D', 'state'), 'state': 'D',

'parameter_1': 'D', 'parameter_2': 'D'}, {'opt_material': None}]
arg_types = (('opt_material', 'virtual', 'state'), ('opt_material', 'parameter_1',
'parameter_2'))
d_div_grad(out, grad1, grad2, mat, vg, fmode)

static function()

get_eval_shape(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('weak', 'eval')

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name = 'dw_div_grad'
set_arg_types()

class sfepy.terms.terms_navier_stokes.DivOperatorTerm(name, arg_str, integral, region, **kwargs)

Weighted divergence term of a test function.
Definition
∫︁ ∫︁
∇ · 𝑣 or 𝑐∇ · 𝑣
Ω Ω
Call signature

dw_div (opt_material, virtual)

Arguments
• material : 𝑐 (optional)
• virtual : 𝑣

arg_shapes = [{'opt_material': '1, 1', 'virtual': ('D', None)}, {'opt_material':

None}]
arg_types = ('opt_material', 'virtual')
static function(out, mat, vg)

get_fargs(mat, virtual, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_div'
class sfepy.terms.terms_navier_stokes.DivTerm(name, arg_str, integral, region, **kwargs)
Evaluate divergence of a vector field.
Supports ‘eval’, ‘el_avg’ and ‘qp’ evaluation modes.
Definition
∫︁ ∫︁
∇·𝑢, 𝑐∇ · 𝑢
𝒟 𝒟
∫︁ ∫︁
vector for 𝐾 ← ℐℎ : ∇ · 𝑢/ 1
𝑇𝐾 𝑇𝐾

(∇ · 𝑢)|𝑞𝑝
Call signature

ev_div (opt_material, parameter)

Arguments
• parameter : 𝑢

arg_shapes = [{'opt_material': '1, 1', 'parameter': 'D'}, {'opt_material': None}]

arg_types = ('opt_material', 'parameter')

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static function(out, mat, div, vg, fmode)

get_eval_shape(mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'by_region'
name = 'ev_div'
surface_integration = 'surface_extra'
class sfepy.terms.terms_navier_stokes.GradDivStabilizationTerm(name, arg_str, integral, region,
**kwargs)
Grad-div stabilization term ( 𝛾 is a global stabilization parameter).
Definition
∫︁
𝛾 (∇ · 𝑢) · (∇ · 𝑣)
Ω
Call signature

dw_st_grad_div (material, virtual, state)

Arguments
• material : 𝛾
• virtual : 𝑣
• state : 𝑢

arg_shapes = {'material': '1, 1', 'state': 'D', 'virtual': ('D', 'state')}

arg_types = ('material', 'virtual', 'state')
static function()

get_fargs(gamma, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_st_grad_div'
class sfepy.terms.terms_navier_stokes.GradTerm(name, arg_str, integral, region, **kwargs)
Evaluate gradient of a scalar or vector field.
Supports ‘eval’, ‘el_avg’ and ‘qp’ evaluation modes.
Definition
∫︁ ∫︁ ∫︁ ∫︁
∇𝑝 or ∇𝑤 , 𝑐∇𝑝 or 𝑐∇𝑤
𝒟 𝒟 𝒟 𝒟
∫︁ ∫︁ ∫︁ ∫︁
vector for 𝐾 ← ℐℎ : ∇𝑝/ 1 or ∇𝑤/ 1
𝑇𝐾 𝑇𝐾 𝑇𝐾 𝑇𝐾

(∇𝑝)|𝑞𝑝 or ∇𝑤|𝑞𝑝
Call signature

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ev_grad (opt_material, parameter)

Arguments
• parameter : 𝑝 or 𝑤

arg_shapes = [{'opt_material': '1, 1', 'parameter': 'N'}, {'opt_material': None}]

arg_types = ('opt_material', 'parameter')
static function(out, mat, grad, vg, fmode)

get_eval_shape(mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'by_region'
name = 'ev_grad'
surface_integration = 'surface_extra'
class sfepy.terms.terms_navier_stokes.LinearConvect2Term(name, arg_str, integral, region,
**kwargs)
Linearized convective term with the convection velocity given as a material parameter.
Definition
∫︁
((𝑏 · ∇)𝑢) · 𝑣
Ω

((𝑏 · ∇)𝑢)|𝑞𝑝
Call signature

dw_lin_convect2 (material, virtual, state)

Arguments
• material : 𝑏
• virtual : 𝑣
• state : 𝑢

arg_shapes = {'material': 'D, 1', 'state': 'D', 'virtual': ('D', 'state')}

arg_types = ('material', 'virtual', 'state')
static function()

get_fargs(material, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_lin_convect2'
class sfepy.terms.terms_navier_stokes.LinearConvectTerm(name, arg_str, integral, region, **kwargs)
Linearized convective term.
Definition

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∫︁
((𝑏 · ∇)𝑢) · 𝑣
Ω

((𝑏 · ∇)𝑢)|𝑞𝑝
Call signature

dw_lin_convect (virtual, parameter, state)

Arguments
• virtual : 𝑣
• parameter : 𝑏
• state : 𝑢

arg_shapes = {'parameter': 'D', 'state': 'D', 'virtual': ('D', 'state')}

arg_types = ('virtual', 'parameter', 'state')
static function()

get_fargs(virtual, parameter, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_lin_convect'
class sfepy.terms.terms_navier_stokes.PSPGCStabilizationTerm(name, arg_str, integral, region,
**kwargs)
PSPG stabilization term, convective part ( 𝜏 is a local stabilization parameter).
Definition
∑︁ ∫︁
𝜏𝐾 ((𝑏 · ∇)𝑢) · ∇𝑞
𝐾∈ℐℎ 𝑇𝐾

Call signature

dw_st_pspg_c (material, virtual, parameter, state)

Arguments
• material : 𝜏𝐾
• virtual : 𝑞
• parameter : 𝑏
• state : 𝑢

arg_shapes = {'material': '1, 1', 'parameter': 'D', 'state': 'D', 'virtual': (1,
None)}
arg_types = ('material', 'virtual', 'parameter', 'state')
static function()

get_fargs(tau, virtual, parameter, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_st_pspg_c'

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class sfepy.terms.terms_navier_stokes.PSPGPStabilizationTerm(name, arg_str, integral, region,

**kwargs)
PSPG stabilization term, pressure part ( 𝜏 is a local stabilization parameter), alias to Laplace term dw_laplace.
Definition
∑︁ ∫︁
𝜏𝐾 ∇𝑝 · ∇𝑞
𝐾∈ℐℎ 𝑇𝐾

Call signature

dw_st_pspg_p (opt_material, virtual, state)

(opt_material, parameter_1, parameter_2)

Arguments
• material : 𝜏𝐾
• virtual : 𝑞
• state : 𝑝

name = 'dw_st_pspg_p'
class sfepy.terms.terms_navier_stokes.SUPGCStabilizationTerm(name, arg_str, integral, region,
**kwargs)
SUPG stabilization term, convective part ( 𝛿 is a local stabilization parameter).
Definition
∑︁ ∫︁
𝛿𝐾 ((𝑏 · ∇)𝑢) · ((𝑏 · ∇)𝑣)
𝐾∈ℐℎ 𝑇𝐾

Call signature

dw_st_supg_c (material, virtual, parameter, state)

Arguments
• material : 𝛿𝐾
• virtual : 𝑣
• parameter : 𝑏
• state : 𝑢

arg_shapes = {'material': '1, 1', 'parameter': 'D', 'state': 'D', 'virtual':

('D', 'state')}
arg_types = ('material', 'virtual', 'parameter', 'state')
static function()

get_fargs(delta, virtual, parameter, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_st_supg_c'

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class sfepy.terms.terms_navier_stokes.SUPGPStabilizationTerm(name, arg_str, integral, region,

**kwargs)
SUPG stabilization term, pressure part ( 𝛿 is a local stabilization parameter).
Definition
∑︁ ∫︁
𝛿𝐾 ∇𝑝 · ((𝑏 · ∇)𝑣)
𝐾∈ℐℎ 𝑇𝐾

Call signature

dw_st_supg_p (material, virtual, parameter, state)

Arguments
• material : 𝛿𝐾
• virtual : 𝑣
• parameter : 𝑏
• state : 𝑝

arg_shapes = {'material': '1, 1', 'parameter': 'D', 'state': 1, 'virtual': ('D',

None)}
arg_types = ('material', 'virtual', 'parameter', 'state')
static function()

get_fargs(delta, virtual, parameter, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_st_supg_p'
class sfepy.terms.terms_navier_stokes.StokesTerm(name, arg_str, integral, region, **kwargs)
Stokes problem coupling term. Corresponds to weak forms of gradient and divergence terms. Can be evaluated.
Definition
∫︁ ∫︁ ∫︁ ∫︁
𝑝∇·𝑣, 𝑞 ∇ · 𝑢 or 𝑐𝑝∇·𝑣, 𝑐𝑞∇·𝑢
Ω Ω Ω Ω
Call signature

dw_stokes (opt_material, virtual, state)

(opt_material, state, virtual)
(opt_material, parameter_v, parameter_s)

Arguments 1
• material : 𝑐 (optional)
• virtual : 𝑣
• state : 𝑝
Arguments 2
• material : 𝑐 (optional)
• state : 𝑢

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• virtual : 𝑞
Arguments 3
• material : 𝑐 (optional)
• parameter_v : 𝑢
• parameter_s : 𝑝

arg_shapes = [{'opt_material': '1, 1', 'virtual/grad': ('D', None), 'state/grad':

1, 'virtual/div': (1, None), 'state/div': 'D', 'parameter_v': 'D', 'parameter_s':
1}, {'opt_material': None}]
arg_types = (('opt_material', 'virtual', 'state'), ('opt_material', 'state',
'virtual'), ('opt_material', 'parameter_v', 'parameter_s'))
static d_eval(out, coef, vec_qp, div, vvg)

get_eval_shape(coef, vvar, svar, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(coef, vvar, svar, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('grad', 'div', 'eval')

name = 'dw_stokes'
set_arg_types()

class sfepy.terms.terms_navier_stokes.StokesWaveDivTerm(name, arg_str, integral, region, **kwargs)

Stokes dispersion term with the wave vector 𝜅 and the divergence operator.
Definition
∫︁ ∫︁
(𝜅 · 𝑣)(∇ · 𝑢) , (𝜅 · 𝑢)(∇ · 𝑣)
Ω Ω
Call signature

dw_stokes_wave_div (material, virtual, state)

(material, state, virtual)

Arguments 1
• material : 𝜅
• virtual : 𝑣
• state : 𝑢
Arguments 2
• material : 𝜅
• state : 𝑢
• virtual : 𝑣

arg_shapes = {'material': '.: D', 'state': 'D', 'virtual': ('D', 'state')}

arg_types = (('material', 'virtual', 'state'), ('material', 'state', 'virtual'))

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static function(out, out_qp, geo, fmode)

geometries = ['2_3', '2_4', '3_4', '3_8']

get_fargs(kappa, kvar, dvar, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('kd', 'dk')

name = 'dw_stokes_wave_div'
class sfepy.terms.terms_navier_stokes.StokesWaveTerm(name, arg_str, integral, region, **kwargs)
Stokes dispersion term with the wave vector 𝜅.
Definition
∫︁
(𝜅 · 𝑣)(𝜅 · 𝑢)
Ω
Call signature

dw_stokes_wave (material, virtual, state)

Arguments
• material : 𝜅
• virtual : 𝑣
• statee : 𝑢

arg_shapes = {'material': '.: D', 'state': 'D', 'virtual': ('D', 'state')}

arg_types = ('material', 'virtual', 'state')
static function(out, out_qp, geo, fmode)

geometries = ['2_3', '2_4', '3_4', '3_8']

get_fargs(kappa, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_stokes_wave'

sfepy.terms.terms_piezo module

class sfepy.terms.terms_piezo.PiezoCouplingTerm(name, arg_str, integral, region, **kwargs)

Piezoelectric coupling term. Can be evaluated.
Definition
∫︁ ∫︁
𝑔𝑘𝑖𝑗 𝑒𝑖𝑗 (𝑣)∇𝑘 𝑝 , 𝑔𝑘𝑖𝑗 𝑒𝑖𝑗 (𝑢)∇𝑘 𝑞
Ω Ω
Call signature

dw_piezo_coupling (material, virtual, state)

(material, state, virtual)
(material, parameter_v, parameter_s)

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Arguments 1
• material : 𝑔𝑘𝑖𝑗
• virtual : 𝑣
• state : 𝑝
Arguments 2
• material : 𝑔𝑘𝑖𝑗
• state : 𝑢
• virtual : 𝑞
Arguments 3
• material : 𝑔𝑘𝑖𝑗
• parameter_v : 𝑢
• parameter_s : 𝑝

arg_shapes = {'material': 'D, S', 'parameter_s': 1, 'parameter_v': 'D',

'state/div': 'D', 'state/grad': 1, 'virtual/div': (1, None), 'virtual/grad':
('D', None)}
arg_types = (('material', 'virtual', 'state'), ('material', 'state', 'virtual'),
('material', 'parameter_v', 'parameter_s'))
get_eval_shape(mat, vvar, svar, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, vvar, svar, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('grad', 'div', 'eval')

name = 'dw_piezo_coupling'
set_arg_types()

class sfepy.terms.terms_piezo.PiezoStrainTerm(name, arg_str, integral, region, **kwargs)

Evaluate piezoelectric strain tensor.
It is given in the usual vector form exploiting symmetry: in 3D it has 6 components with the indices ordered as
[11, 22, 33, 12, 13, 23], in 2D it has 3 components with the indices ordered as [11, 22, 12].
Supports ‘eval’, ‘el_avg’ and ‘qp’ evaluation modes.
Definition
∫︁
𝑔𝑘𝑖𝑗 𝑒𝑖𝑗 (𝑢)
Ω
Call signature

ev_piezo_strain (material, parameter)

Arguments
• material : 𝑔𝑘𝑖𝑗
• parameter : 𝑢

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arg_shapes = {'material': 'D, S', 'parameter': 'D'}

get_eval_shape(mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'ev_piezo_strain'
class sfepy.terms.terms_piezo.PiezoStressTerm(name, arg_str, integral, region, **kwargs)
Evaluate piezoelectric stress tensor.
It is given in the usual vector form exploiting symmetry: in 3D it has 6 components with the indices ordered as
[11, 22, 33, 12, 13, 23], in 2D it has 3 components with the indices ordered as [11, 22, 12].
Supports ‘eval’, ‘el_avg’ and ‘qp’ evaluation modes.
Definition
∫︁
𝑔𝑘𝑖𝑗 ∇𝑘 𝑝
Ω
Call signature

ev_piezo_stress (material, parameter)

Arguments
• material : 𝑔𝑘𝑖𝑗
• parameter : 𝑝

arg_shapes = {'material': 'D, S', 'parameter': '1'}

arg_types = ('material', 'parameter')
static function(out, val_qp, vg, fmode)

get_eval_shape(mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, parameter, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'ev_piezo_stress'
class sfepy.terms.terms_piezo.SDPiezoCouplingTerm(*args, **kwargs)
Sensitivity (shape derivative) of the piezoelectric coupling term.
Definition
∫︁
𝑔ˆ𝑘𝑖𝑗 𝑒𝑖𝑗 (𝑢)∇𝑘 𝑝
Ω
𝜕𝒱𝑗 𝜕𝒱𝑘
𝑔ˆ𝑘𝑖𝑗 = 𝑔𝑘𝑖𝑗 (∇ · 𝒱) − 𝑔𝑘𝑖𝑙 − 𝑔𝑙𝑖𝑗
𝜕𝑥𝑙 𝜕𝑥𝑙
Call signature

ev_sd_piezo_coupling (material, parameter_u, parameter_p, parameter_mv)

Arguments

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• material : 𝑔𝑘𝑖𝑗
• parameter_u : 𝑢
• parameter_p : 𝑝
• parameter_mv : 𝒱

arg_shapes = {'material': 'D, S', 'parameter_mv': 'D', 'parameter_p': 1,

'parameter_u': 'D'}
arg_types = ('material', 'parameter_u', 'parameter_p', 'parameter_mv')
geometries = ['2_3', '2_4', '3_4', '3_8']
get_function(mat, par_u, par_p, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'ev_sd_piezo_coupling'

sfepy.terms.terms_point module

class sfepy.terms.terms_point.ConcentratedPointLoadTerm(name, arg_str, integral, region, **kwargs)

Concentrated point load term.
The load value must be given in form of a special material parameter (name prefixed with ‘.’), e.g. (in 2D):

'load' : ({'.val' : [0.0, 1.0]},)

This term should be used with special care, as it bypasses the usual evaluation in quadrature points. It should
only be used with nodal FE basis. The number of rows of the load must be equal to the number of nodes in the
region and the number of columns equal to the field dimension.
Definition
𝑖
𝑓 𝑖 = 𝑓¯ ∀ FE node 𝑖 in a region
Call signature

dw_point_load (material, virtual)

Arguments
𝑖
• material : 𝑓¯
• virtual : 𝑣,

arg_shapes = {'material': '.: N', 'virtual': ('N', None)}

arg_types = ('material', 'virtual')
static function(out, mat)

get_fargs(mat, virtual, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'point'
name = 'dw_point_load'

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class sfepy.terms.terms_point.LinearPointSpringTerm(name, arg_str, integral, region, **kwargs)

Linear springs constraining movement of FE nodes in a region; to use as a relaxed Dirichlet boundary conditions.
Definition
𝑓 𝑖 = −𝑘𝑢𝑖 ∀ FE node 𝑖 in a region
Call signature

dw_point_lspring (material, virtual, state)

Arguments
• material : 𝑘
• virtual : 𝑣
• state : 𝑢

arg_shapes = {'material': '.: 1', 'state': 'D', 'virtual': ('D', 'state')}

arg_types = ('material', 'virtual', 'state')
static function(out, stiffness, vec, diff_var)

get_fargs(mat, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'point'
name = 'dw_point_lspring'

sfepy.terms.terms_sensitivity module

class sfepy.terms.terms_sensitivity.ESDDiffusionTerm(*args, **kwargs)

Diffusion sensitivity analysis term.
Definition
∫︁
ˆ 𝑖𝑗 ∇𝑖 𝑞 ∇𝑗 𝑝
𝐾
Ω
(︂ )︂
ˆ 𝜕𝒱𝑗 𝜕𝒱𝑖
𝐾𝑖𝑗 = 𝐾𝑖𝑗 𝛿𝑖𝑘 𝛿𝑗𝑙 ∇ · 𝒱 − 𝛿𝑖𝑘 − 𝛿𝑗𝑙
𝜕𝑥𝑙 𝜕𝑥𝑘
Call signature

de_sd_diffusion (material, virtual, state, parameter_mv)

(material, parameter_1, parameter_2, parameter_mv)

Arguments
• material: 𝐾𝑖𝑗
• virtual/parameter_1: 𝑞
• state/parameter_2: 𝑝
• parameter_mv: 𝒱

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arg_shapes = {'material': 'D, D', 'parameter_1': 1, 'parameter_2': 1,

'parameter_mv': 'D', 'state': 1, 'virtual': (1, 'state')}
arg_types = (('material', 'virtual', 'state', 'parameter_mv'), ('material',
'parameter_1', 'parameter_2', 'parameter_mv'))
get_function(mat, vvar, svar, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('weak', 'eval')

name = 'de_sd_diffusion'
class sfepy.terms.terms_sensitivity.ESDDivGradTerm(*args, **kwargs)

Sensitivity (shape derivative) of diffusion term de_div_grad.

Definition
∫︁ ∫︁
ˆ
𝐼∇𝑣 : ∇𝑢 , ˆ
𝜈 𝐼∇𝑣 : ∇𝑢
Ω Ω
𝜕𝒱𝑙 𝜕𝒱𝑘
𝐼ˆ𝑖𝑗𝑘𝑙 = 𝛿𝑖𝑘 𝛿𝑗𝑙 ∇ · 𝒱 − 𝛿𝑖𝑘 𝛿𝑗𝑠 − 𝛿𝑖𝑠 𝛿𝑗𝑙
𝜕𝑥𝑠 𝜕𝑥𝑠
Call signature

de_sd_div_grad (opt_material, virtual, state, parameter_mv)

(opt_material, parameter_1, parameter_2, parameter_mv)

Arguments
• material: 𝜈 (viscosity, optional)
• virtual/parameter_1: 𝑣
• state/parameter_2: 𝑢
• parameter_mv: 𝒱

arg_shapes = [{'opt_material': '1, 1', 'virtual': ('D', 'state'), 'state': 'D',

'parameter_1': 'D', 'parameter_2': 'D', 'parameter_mv': 'D'}, {'opt_material':
None}]
arg_types = (('opt_material', 'virtual', 'state', 'parameter_mv'), ('opt_material',
'parameter_1', 'parameter_2', 'parameter_mv'))
get_function(mat, vvar, svar, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('weak', 'eval')

name = 'de_sd_div_grad'
class sfepy.terms.terms_sensitivity.ESDDotTerm(*args, **kwargs)
Sensitivity (shape derivative) of dot product of scalars or vectors.
Definition

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∫︁ ∫︁
𝑞𝑝(∇ · 𝒱) , (𝑣 · 𝑢)(∇ · 𝒱)
∫︁ Ω ∫︁ Ω
𝑐𝑞𝑝(∇ · 𝒱) , 𝑐(𝑣 · 𝑢)(∇ · 𝒱)
Ω
∫︁ Ω
𝑣 · (𝑀 𝑢)(∇ · 𝒱)
Ω
Call signature

de_sd_dot (opt_material, virtual, state, parameter_mv)

(opt_material, parameter_1, parameter_2, parameter_mv)

Arguments
• material: 𝑐 or 𝑀 (optional)
• virtual/parameter_1: 𝑞 or 𝑣
• state/parameter_2: 𝑝 or 𝑢
• parameter_mv : 𝒱

arg_shapes = [{'opt_material': '1, 1', 'virtual': (1, 'state'), 'state': 1,

'parameter_1': 1, 'parameter_2': 1, 'parameter_mv': 'D'}, {'opt_material':
None}, {'opt_material': '1, 1', 'virtual': ('D', 'state'), 'state': 'D',
'parameter_1': 'D', 'parameter_2': 'D', 'parameter_mv': 'D'}, {'opt_material':
'D, D'}, {'opt_material': None}]
arg_types = (('opt_material', 'virtual', 'state', 'parameter_mv'), ('opt_material',
'parameter_1', 'parameter_2', 'parameter_mv'))
get_function(mat, vvar, svar, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('weak', 'eval')

name = 'de_sd_dot'
class sfepy.terms.terms_sensitivity.ESDLinearElasticTerm(*args, **kwargs)
Sensitivity analysis of the linear elastic term.
Definition
∫︁
ˆ 𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢)
𝐷
Ω

ˆ 𝑖𝑗𝑘𝑙 = 𝐷𝑖𝑗𝑘𝑙 (∇ · 𝒱) − 𝐷𝑖𝑗𝑘𝑞 𝜕𝒱𝑙 − 𝐷𝑖𝑞𝑘𝑙 𝜕𝒱𝑗

𝐷
𝜕𝑥𝑞 𝜕𝑥𝑞
Call signature

de_sd_lin_elastic (material, virtual, state, parameter_mv)

(material, parameter_1, parameter_2, parameter_mv)

Arguments 1
• material : 𝐷
• virtual/parameter_v : 𝑣
• state/parameter_s : 𝑢

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• parameter_mv : 𝒱

arg_shapes = {'material': 'S, S', 'parameter_1': 'D', 'parameter_2': 'D',

'parameter_mv': 'D', 'state': 'D', 'virtual': ('D', 'state')}
arg_types = (('material', 'virtual', 'state', 'parameter_mv'), ('material',
'parameter_1', 'parameter_2', 'parameter_mv'))
geometries = ['2_3', '2_4', '3_4', '3_8']
get_function(mat, vvar, svar, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('weak', 'eval')

name = 'de_sd_lin_elastic'
class sfepy.terms.terms_sensitivity.ESDLinearTractionTerm(*args, **kwargs)
Sensitivity of the linear traction term.
Definition
∫︁
[︀(︀ )︀ ]︀
𝑣· 𝜎ˆ∇·𝒱 −𝜎
ˆ ∇𝒱 𝑛
Γ

ˆ =𝐼 ,𝜎
𝜎 ˆ = 𝑐 𝐼 or 𝜎
ˆ=𝜎
Call signature

de_sd_surface_ltr (opt_material, virtual, parameter_mv)

(opt_material, parameter, parameter_mv)

Arguments
• material: 𝑐, 𝜎, 𝜎
• virtual/parameter: 𝑣
• parameter_mv: 𝒱

arg_shapes = [{'opt_material': 'S, 1', 'virtual': ('D', None), 'parameter_mv':

'D', 'parameter': 'D'}, {'opt_material': None}, {'opt_material': '1, 1'},
{'opt_material': 'D, D'}]
arg_types = (('opt_material', 'virtual', 'parameter_mv'), ('opt_material',
'parameter', 'parameter_mv'))
get_function(traction, vvar, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'surface'
modes = ('weak', 'eval')
name = 'de_sd_surface_ltr'
class sfepy.terms.terms_sensitivity.ESDPiezoCouplingTerm(*args, **kwargs)
Sensitivity (shape derivative) of the piezoelectric coupling term.
Definition

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∫︁ ∫︁
𝑔ˆ𝑘𝑖𝑗 𝑒𝑖𝑗 (𝑣)∇𝑘 𝑝 , 𝑔ˆ𝑘𝑖𝑗 𝑒𝑖𝑗 (𝑢)∇𝑘 𝑞
Ω Ω
𝜕𝒱𝑗 𝜕𝒱𝑘
𝑔ˆ𝑘𝑖𝑗 = 𝑔𝑘𝑖𝑗 (∇ · 𝒱) − 𝑔𝑘𝑖𝑙 − 𝑔𝑙𝑖𝑗
𝜕𝑥𝑙 𝜕𝑥𝑙
Call signature

de_sd_piezo_coupling (material, virtual, state, parameter_mv)

(material, state, virtual, parameter_mv)
(material, parameter_v, parameter_s, parameter_mv)

Arguments 1
• material : 𝑔𝑘𝑖𝑗
• virtual/parameter_v : 𝑣
• state/parameter_s : 𝑝
• parameter_mv : 𝒱
Arguments 2
• material : 𝑔𝑘𝑖𝑗
• state : 𝑢
• virtual : 𝑞
• parameter_mv : 𝒱

arg_shapes = {'material': 'D, S', 'parameter_mv': 'D', 'parameter_s': 1,

'parameter_v': 'D', 'state/div': 'D', 'state/grad': 1, 'virtual/div': (1, None),
'virtual/grad': ('D', None)}
arg_types = (('material', 'virtual', 'state', 'parameter_mv'), ('material', 'state',
'virtual', 'parameter_mv'), ('material', 'parameter_v', 'parameter_s',
'parameter_mv'))
geometries = ['2_3', '2_4', '3_4', '3_8']
get_function(mat, vvar, svar, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('grad', 'div', 'eval')

name = 'de_sd_piezo_coupling'
class sfepy.terms.terms_sensitivity.ESDStokesTerm(*args, **kwargs)
Stokes problem coupling term. Corresponds to weak forms of gradient and divergence terms.
Definition
∫︁ ∫︁
𝜕𝑣𝑖 𝜕𝑢𝑖
𝑝 𝐼𝑖𝑗 , 𝑞 𝐼𝑖𝑗
Ω 𝜕𝑥𝑗 Ω 𝜕𝑥𝑗
𝜕𝒱𝑗
𝐼ˆ𝑖𝑗 = 𝛿𝑖𝑗 ∇ · 𝒱 −
𝜕𝑥𝑖
Call signature

de_sd_stokes (opt_material, virtual, state, parameter_mv)

(opt_material, state, virtual, parameter_mv)
(opt_material, parameter_v, parameter_s, parameter_mv)

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Arguments 1
• virtual/parameter_v: 𝑣
• state/parameter_s: 𝑝
• parameter_mv: 𝒱
Arguments 2
• state : 𝑢
• virtual : 𝑞
• parameter_mv: 𝒱

arg_shapes = [{'opt_material': '1, 1', 'virtual/grad': ('D', None), 'state/grad':

1, 'virtual/div': (1, None), 'state/div': 'D', 'parameter_v': 'D', 'parameter_s':
1, 'parameter_mv': 'D'}, {'opt_material': None}]
arg_types = (('opt_material', 'virtual', 'state', 'parameter_mv'), ('opt_material',
'state', 'virtual', 'parameter_mv'), ('opt_material', 'parameter_v', 'parameter_s',
'parameter_mv'))
get_function(coef, vvar, svar, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

modes = ('grad', 'div', 'eval')

name = 'de_sd_stokes'
sfepy.terms.terms_sensitivity.get_nonsym_grad_op(sgrad)

sfepy.terms.terms_shells module

Terms implementing shell elements.

class sfepy.terms.terms_shells.Shell10XTerm(name, arg_str, integral, region, **kwargs)
The shell10x element term based on the Reissner-Mindlin theory [1], [2], corresponding to a shell of thickness
𝑡.
The term requires a custom 3D quadrature, where the 𝑧 components of quadrature point coordinates are trans-
formed from [0, 1] to [−𝑡/2, 𝑡/2], and the quadrature weights are multiplied by 𝑡. The variables 𝑣 and 𝑢
have to use Shell10XField and have six components. The reference element mapping is implemented by
Shell10XMapping. The term does not implement the piezo-electric components of the shell10x element yet.
The term has to be used with quadrilateral cells in 3D and should behave as the linear elastic term, but with fewer
degrees of freedom for the same accuracy for shell-like structures. The shell has six degrees of freedom in each
of the four nodes: u𝑖 = [𝑢𝑖 , 𝑣𝑖 , 𝑤𝑖 , 𝛼𝑖 , 𝛽𝑖 , 𝛾𝑖 ]𝑇 , 𝑖 = 1, 2, 3, 4. The strain and stress vectors are calculated in a
local (co-rotational) coordinate system given by basis vectors e′1 , e′2 and e′3 . It holds that

[𝑢′𝑖 , 𝑣𝑖′ , 𝑤𝑖′ , 𝛼𝑖′ , 𝛽𝑖′ , 𝛾𝑖′ ]𝑇 = Ĥ𝑇 u𝑖

where
[︂ ]︂
H
Ĥ = and H = [e′1 e′2 e′3 ]
H

is a nodal DOF transformation matrix.

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The local displacements 𝑢′ , 𝑣 ′ and 𝑤′ at any point in the layer characterized by the isoparametric coordinates 𝜉,
𝜂 and 𝜁 (𝜉, 𝜂, 𝜁 ∈ ⟨−1, 1⟩) are interpolated from the nodal displacement and rotation values (i.e. both membrane
and bending components) using standard isoparametric approximation functions for a quadrilateral, hence
4
𝑢′ (𝜉, 𝜂, 𝜁) 𝑁𝑖 (𝜉, 𝜂) · (𝑢′𝑖 + 𝑢
∑︀
= ¯𝑖 ) ,
𝑖=1
4
𝑣 ′ (𝜉, 𝜂, 𝜁) 𝑁𝑖 (𝜉, 𝜂) · (𝑣𝑖′ + 𝑣¯𝑖 ) ,
∑︀
=
𝑖=1
4
𝑤′ (𝜉, 𝜂, 𝜁) 𝑁𝑖 (𝜉, 𝜂) · (𝑤𝑖′ + 𝑤
∑︀
= ¯𝑖 )
𝑖=1

where 𝑢˜𝑖 , 𝑣˜𝑖 and 𝑤

˜𝑖 are the bending components of displacements calculated from displacements due to rotations
˜ 𝑖 and 𝛽˜𝑖 about local nodal axes ẽ𝑖 as
𝛼
⎡ ⎤ ⎡ ⎤ ⎡ ′ ⎤
𝑢
¯ [︂ 𝑇 ]︂ 𝛼
⎣ 𝑣¯ ⎦ = 𝜁˜ ⎣ ẽ1 −ẽ2 ⎦ ẽ 2 ⎣ 𝛽′ ⎦
𝑇
ẽ1 𝑖
𝑤¯ 𝑖 𝑖
𝛾′ 𝑖

where 𝜁˜ = (𝑡/2)𝜁. The local nodal axes ẽ𝑖 are constructed in order to describe the behavior of warped (non-
planar) elements adequately.
The term employs three shell element enhancements:
• DSG method
• EAS method
• drilling rotations lock (parameter 𝜒 - a good value is about 10−7 )
For detailed theoretical information see the references.
High-Performance 4-Node Shell Element with Piezoelectric Coupling Mechanics of Advanced Materials and
Structures Vol. 13, Iss. 5, doi:10.1080/15376490600777657
High-performance four-node shell element with piezoelectric coupling for the analysis of smart laminated struc-
tures. Int. J. Numer. Meth. Engng., 70: 934–961. doi:10.1002/nme.1909
Definition
∫︁
𝐷𝑖𝑗𝑘𝑙 𝑒𝑖𝑗 (𝑣)𝑒𝑘𝑙 (𝑢)
Ω
Call signature

dw_shell10x (material_d, material_drill, virtual, state)

Arguments
• material_d : 𝐷
• material_drill : 𝜒
• virtual : 𝑣
• state : 𝑢

arg_shapes = {'material_d': '6, 6', 'material_drill': '.: 1', 'state': 6,

'virtual': (6, 'state')}
arg_types = ('material_d', 'material_drill', 'virtual', 'state')
static function(out, mtx_k, el_u, fmode)

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geometries = ['3_2_4']
get_fargs(mtx_d, drill, virtual, state, mode=None, term_mode=None, diff_var=None, **kwargs)

get_physical_qps()
Get physical quadrature points corresponding to the term region and integral.
integration = 'custom'
name = 'dw_shell10x'
poly_space_base = 'shell10x'
set_integral(integral)
Set the term integral.

sfepy.terms.terms_surface module

class sfepy.terms.terms_surface.ContactPlaneTerm(*args, **kwargs)

Small deformation elastic contact plane term with penetration penalty.
The plane is given by an anchor point 𝐴 and a normal 𝑛. The contact occurs in points that orthogonally project
onto the plane into a polygon given by orthogonal projections of boundary points {𝐵 𝑖 }, 𝑖 = 1, . . . , 𝑁𝐵 on the
plane. In such points, a penetration distance 𝑑(𝑢) = (𝑋 + 𝑢 − 𝐴, 𝑛) is computed, and a force 𝑓 (𝑑(𝑢))𝑛 is
applied. The force depends on the non-negative parameters 𝑘 (stiffness) and 𝑓0 (force at zero penetration):
• If 𝑓0 = 0:

𝑓 (𝑑) = 0 for 𝑑 ≤ 0 ,
𝑓 (𝑑) = 𝑘𝑑 for 𝑑 > 0 .

• If 𝑓0 > 0:
2𝑟0
𝑓 (𝑑) = 0 for 𝑑 ≤ − ,
𝑘
𝑘2 2 2𝑟0
𝑓 (𝑑) = 𝑑 + 𝑘𝑑 + 𝑟0 for − <𝑑≤0,
4𝑟0 𝑘
𝑓 (𝑑) = 𝑘𝑑 + 𝑓0 for 𝑑 > 0 .

In this case the dependence 𝑓 (𝑑) is smooth, and a (small) force is applied even for (small) negative pene-
trations: − 2𝑟𝑘0 < 𝑑 ≤ 0.

Definition
∫︁
𝑣 · 𝑓 (𝑑(𝑢))𝑛
Γ
Call signature

dw_contact_plane (material_f, material_n, material_a, material_b, virtual, state)

Arguments
• material_f : [𝑘, 𝑓0 ]
• material_n : 𝑛 (special)
• material_a : 𝐴 (special)

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• material_b : {𝐵 𝑖 }, 𝑖 = 1, . . . , 𝑁𝐵 (special)
• virtual : 𝑣
• state : 𝑢

arg_shapes = {'material_a': '.: D', 'material_b': '.: N, D', 'material_f': '1,

2', 'material_n': '.: D', 'state': 'D', 'virtual': ('D', 'state')}
arg_types = ('material_f', 'material_n', 'material_a', 'material_b', 'virtual',
'state')
static function(out, force, normal, geo, fmode)

geometries = ['3_4', '3_8']

get_fargs(force_pars, normal, anchor, bounds, virtual, state, mode=None, term_mode=None,
diff_var=None, **kwargs)

integration = 'surface'
name = 'dw_contact_plane'
static smooth_f(d, k, f0, a, eps, diff )

class sfepy.terms.terms_surface.ContactSphereTerm(*args, **kwargs)

Small deformation elastic contact sphere term with penetration penalty.
The sphere is given by a centre point 𝐶 and a radius 𝑅. The contact occurs in points that are closer to 𝐶 than
𝑅. In such points, a penetration distance 𝑑(𝑢) = 𝑅 − ||𝑋 + 𝑢 − 𝐶|| is computed, and a force 𝑓 (𝑑(𝑢))𝑛(𝑢)
is applied, where 𝑛(𝑢) = (𝑋 + 𝑢 − 𝐶)/||𝑋 + 𝑢 − 𝐶||. The force depends on the non-negative parameters 𝑘
(stiffness) and 𝑓0 (force at zero penetration):
• If 𝑓0 = 0:

𝑓 (𝑑) = 0 for 𝑑 ≤ 0 ,
𝑓 (𝑑) = 𝑘𝑑 for 𝑑 > 0 .

• If 𝑓0 > 0:
2𝑟0
𝑓 (𝑑) = 0 for 𝑑 ≤ − ,
𝑘
𝑘2 2 2𝑟0
𝑓 (𝑑) = 𝑑 + 𝑘𝑑 + 𝑟0 for − <𝑑≤0,
4𝑟0 𝑘
𝑓 (𝑑) = 𝑘𝑑 + 𝑓0 for 𝑑 > 0 .

In this case the dependence 𝑓 (𝑑) is smooth, and a (small) force is applied even for (small) negative pene-
trations: − 2𝑟𝑘0 < 𝑑 ≤ 0.

Definition
∫︁
𝑣 · 𝑓 (𝑑(𝑢))𝑛(𝑢)
Γ
Call signature

dw_contact_sphere (material_f, material_c, material_r, virtual, state)

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Arguments
• material_f : [𝑘, 𝑓0 ]
• material_c : 𝐶 (special)
• material_r : 𝑅 (special)
• virtual : 𝑣
• state : 𝑢

arg_shapes = {'material_c': '.: D', 'material_f': '1, 2', 'material_r': '.: 1',
'state': 'D', 'virtual': ('D', 'state')}
arg_types = ('material_f', 'material_c', 'material_r', 'virtual', 'state')
static function(out, force, normals, fd, geo, fmode)

geometries = ['3_4', '3_8']

get_fargs(force_pars, centre, radius, virtual, state, mode=None, term_mode=None, diff_var=None,
**kwargs)

integration = 'surface'
name = 'dw_contact_sphere'
class sfepy.terms.terms_surface.LinearTractionTerm(name, arg_str, integral, region, **kwargs)
Linear traction forces, where, depending on dimension of ‘material’ argument, 𝜎 · 𝑛 is 𝑝¯𝐼 · 𝑛 for a given scalar
pressure, 𝑓 for a traction vector, and itself for a stress tensor.
The material parameter can have one of the following shapes: 1 or (1, 1), (D, 1), (S, 1) in all modes, or (D, D)
in the eval mode only. The symmetric tensor storage (S, 1) is as follows: in 3D S = 6 and the indices ordered as
[11, 22, 33, 12, 13, 23], in 2D S = 3 and the indices ordered as [11, 22, 12].
Definition
∫︁ ∫︁
𝑣 · 𝜎 · 𝑛, 𝑣 · 𝑛,
Γ Γ
Call signature

dw_surface_ltr (opt_material, virtual)

(opt_material, parameter)

Arguments
• material : 𝜎
• virtual : 𝑣

arg_shapes = [{'opt_material': 'S, 1', 'virtual': ('D', None), 'parameter': 'D'},

{'opt_material': 'D, 1'}, {'opt_material': '1, 1'}, {'opt_material': 'D, D'},
{'opt_material': None}]
arg_types = (('opt_material', 'virtual'), ('opt_material', 'parameter'))
static d_fun(out, traction, val, sg)

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get_eval_shape(traction, virtual, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(traction, virtual, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'surface'
modes = ('weak', 'eval')
name = 'dw_surface_ltr'
set_arg_types()

class sfepy.terms.terms_surface.SDLinearTractionTerm(name, arg_str, integral, region, **kwargs)

Sensitivity of the linear traction term.
Definition
∫︁ ∫︁
𝑣 · (𝜎 𝑛), 𝑣 · 𝑛,
Γ Γ
Call signature

ev_sd_surface_ltr (opt_material, parameter, parameter_mv)

Arguments
• material : 𝜎
• parameter : 𝑣

arg_shapes = [{'opt_material': 'S, 1', 'parameter': 'D', 'parameter_mv': 'D'},

{'opt_material': '1, 1'}, {'opt_material': 'D, 1'}, {'opt_material': 'D, D'},
{'opt_material': None}]
arg_types = ('opt_material', 'parameter', 'parameter_mv')
static d_fun(out, traction, val, grad_mv, div_mv, sg)

get_eval_shape(traction, par_u, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(traction, par_u, par_mv, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'surface'
name = 'ev_sd_surface_ltr'
set_arg_types()

class sfepy.terms.terms_surface.SDSufaceIntegrateTerm(name, arg_str, integral, region, **kwargs)

Sensitivity of scalar traction.
Definition
∫︁
𝑝∇ · 𝒱
Γ
Call signature

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ev_sd_surface_integrate (parameter, parameter_mv)

Arguments
• parameter : 𝑝
• parameter_mv : 𝒱

arg_shapes = {'parameter': 1, 'parameter_mv': 'D'}

arg_types = ('parameter', 'parameter_mv')
static function(out, val_p, div_v, sg)

get_eval_shape(par, par_v, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(par, par_v, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'surface'
name = 'ev_sd_surface_integrate'
class sfepy.terms.terms_surface.SufaceNormalDotTerm(name, arg_str, integral, region, **kwargs)
“Scalar traction” term, (weak form).
Definition
∫︁
𝑞𝑐 · 𝑛
Γ
Call signature

dw_surface_ndot (material, virtual)

(material, parameter)

Arguments
• material : 𝑐
• virtual : 𝑞

arg_shapes = {'material': 'D, 1', 'parameter': 1, 'virtual': (1, None)}

arg_types = (('material', 'virtual'), ('material', 'parameter'))
static d_fun(out, material, val, sg)

static dw_fun(out, material, bf, sg)

get_eval_shape(mat, virtual, mode=None, term_mode=None, diff_var=None, **kwargs)

get_fargs(mat, virtual, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'surface'
modes = ('weak', 'eval')

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name = 'dw_surface_ndot'
set_arg_types()

class sfepy.terms.terms_surface.SurfaceJumpTerm(name, arg_str, integral, region, **kwargs)

Interface jump condition.
Definition
∫︁
𝑐 𝑞(𝑝1 − 𝑝2 )
Γ
Call signature

dw_jump (opt_material, virtual, state_1, state_2)

Arguments
• material : 𝑐
• virtual : 𝑞
• state_1 : 𝑝1
• state_2 : 𝑝2

arg_shapes = [{'opt_material': '1, 1', 'virtual': (1, None), 'state_1': 1,

'state_2': 1}, {'opt_material': None}]
arg_types = ('opt_material', 'virtual', 'state_1', 'state_2')
static function(out, jump, mul, bf1, bf2, sg, fmode)

get_fargs(coef, virtual, state1, state2, mode=None, term_mode=None, diff_var=None, **kwargs)

integration = 'surface'
name = 'dw_jump'

sfepy.terms.terms_th module

class sfepy.terms.terms_th.ETHTerm(name, arg_str, integral, region, **kwargs)

Base class for terms depending on time history with exponential convolution kernel (fading memory terms).
advance_eth_data(ts, data)

get_eth_data(key, state, decay, values)

class sfepy.terms.terms_th.THTerm(name, arg_str, integral, region, **kwargs)

Base class for terms depending on time history (fading memory terms).
eval_real(shape, fargs, mode='eval', term_mode=None, diff_var=None, **kwargs)

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sfepy.terms.terms_volume module

class sfepy.terms.terms_volume.LinearVolumeForceTerm(name, arg_str, integral, region, **kwargs)

Vector or scalar linear volume forces (weak form) — a right-hand side source term.
Definition
∫︁ ∫︁
𝑓 · 𝑣 or 𝑓𝑞
Ω Ω
Call signature

dw_volume_lvf (material, virtual)

Arguments
• material : 𝑓 or 𝑓
• virtual : 𝑣 or 𝑞

arg_shapes = [{'material': 'D, 1', 'virtual': ('D', None)}, {'material': '1, 1',
'virtual': (1, None)}]
arg_types = ('material', 'virtual')
static function()

get_fargs(mat, virtual, mode=None, term_mode=None, diff_var=None, **kwargs)

name = 'dw_volume_lvf'

sfepy.terms.utils module

sfepy.terms.utils.check_finiteness(data, info)

sfepy.terms.utils.get_range_indices(num)
Return indices and slices in given range.
Returns
indx [list of tuples] The list of (ii, slice(ii, ii + 1)) of the indices. The first item is the index itself,
the second item is a convenience slice to index components of material parameters.

sfepy.terms.extmods.terms module

Low level term evaluation functions.

sfepy.terms.extmods.terms.actBfT()

sfepy.terms.extmods.terms.d_biot_div()

sfepy.terms.extmods.terms.d_diffusion()

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sfepy.terms.extmods.terms.d_laplace()

sfepy.terms.extmods.terms.d_lin_elastic()

sfepy.terms.extmods.terms.d_of_nsMinGrad()

sfepy.terms.extmods.terms.d_of_nsSurfMinDPress()

sfepy.terms.extmods.terms.d_piezo_coupling()

sfepy.terms.extmods.terms.d_sd_convect()

sfepy.terms.extmods.terms.d_sd_diffusion()

sfepy.terms.extmods.terms.d_sd_div()

sfepy.terms.extmods.terms.d_sd_div_grad()

sfepy.terms.extmods.terms.d_sd_lin_elastic()

sfepy.terms.extmods.terms.d_sd_st_grad_div()

sfepy.terms.extmods.terms.d_sd_st_pspg_c()

sfepy.terms.extmods.terms.d_sd_st_pspg_p()

sfepy.terms.extmods.terms.d_sd_st_supg_c()

sfepy.terms.extmods.terms.d_sd_volume_dot()

sfepy.terms.extmods.terms.d_surface_flux()

sfepy.terms.extmods.terms.d_tl_surface_flux()

sfepy.terms.extmods.terms.d_tl_volume_surface()

sfepy.terms.extmods.terms.d_volume_surface()

sfepy.terms.extmods.terms.de_cauchy_strain()

sfepy.terms.extmods.terms.de_cauchy_stress()

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sfepy.terms.extmods.terms.de_he_rtm()

sfepy.terms.extmods.terms.di_surface_moment()

sfepy.terms.extmods.terms.dq_cauchy_strain()

sfepy.terms.extmods.terms.dq_def_grad()

sfepy.terms.extmods.terms.dq_div_vector()

sfepy.terms.extmods.terms.dq_finite_strain_tl()

sfepy.terms.extmods.terms.dq_finite_strain_ul()

sfepy.terms.extmods.terms.dq_grad()

sfepy.terms.extmods.terms.dq_state_in_qp()

sfepy.terms.extmods.terms.dq_tl_finite_strain_surface()

sfepy.terms.extmods.terms.dq_tl_he_stress_bulk()

sfepy.terms.extmods.terms.dq_tl_he_stress_bulk_active()

sfepy.terms.extmods.terms.dq_tl_he_stress_mooney_rivlin()

sfepy.terms.extmods.terms.dq_tl_he_stress_neohook()

sfepy.terms.extmods.terms.dq_tl_he_tan_mod_bulk()

sfepy.terms.extmods.terms.dq_tl_he_tan_mod_bulk_active()

sfepy.terms.extmods.terms.dq_tl_he_tan_mod_mooney_rivlin()

sfepy.terms.extmods.terms.dq_tl_he_tan_mod_neohook()

sfepy.terms.extmods.terms.dq_tl_stress_bulk_pressure()

sfepy.terms.extmods.terms.dq_tl_tan_mod_bulk_pressure_u()

sfepy.terms.extmods.terms.dq_ul_he_stress_bulk()

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sfepy.terms.extmods.terms.dq_ul_he_stress_mooney_rivlin()

sfepy.terms.extmods.terms.dq_ul_he_stress_neohook()

sfepy.terms.extmods.terms.dq_ul_he_tan_mod_bulk()

sfepy.terms.extmods.terms.dq_ul_he_tan_mod_mooney_rivlin()

sfepy.terms.extmods.terms.dq_ul_he_tan_mod_neohook()

sfepy.terms.extmods.terms.dq_ul_stress_bulk_pressure()

sfepy.terms.extmods.terms.dq_ul_tan_mod_bulk_pressure_u()

sfepy.terms.extmods.terms.dw_adj_convect1()

sfepy.terms.extmods.terms.dw_adj_convect2()

sfepy.terms.extmods.terms.dw_biot_div()

sfepy.terms.extmods.terms.dw_biot_grad()

sfepy.terms.extmods.terms.dw_convect_v_grad_s()

sfepy.terms.extmods.terms.dw_diffusion()

sfepy.terms.extmods.terms.dw_diffusion_r()

sfepy.terms.extmods.terms.dw_div()

sfepy.terms.extmods.terms.dw_electric_source()

sfepy.terms.extmods.terms.dw_grad()

sfepy.terms.extmods.terms.dw_he_rtm()

sfepy.terms.extmods.terms.dw_laplace()

sfepy.terms.extmods.terms.dw_lin_convect()

sfepy.terms.extmods.terms.dw_lin_elastic()

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sfepy.terms.extmods.terms.dw_lin_prestress()

sfepy.terms.extmods.terms.dw_lin_strain_fib()

sfepy.terms.extmods.terms.dw_nonsym_elastic()

sfepy.terms.extmods.terms.dw_piezo_coupling()

sfepy.terms.extmods.terms.dw_st_adj1_supg_p()

sfepy.terms.extmods.terms.dw_st_adj2_supg_p()

sfepy.terms.extmods.terms.dw_st_adj_supg_c()

sfepy.terms.extmods.terms.dw_st_grad_div()

sfepy.terms.extmods.terms.dw_st_pspg_c()

sfepy.terms.extmods.terms.dw_st_supg_c()

sfepy.terms.extmods.terms.dw_st_supg_p()

sfepy.terms.extmods.terms.dw_surface_flux()

sfepy.terms.extmods.terms.dw_surface_ltr()

sfepy.terms.extmods.terms.dw_surface_s_v_dot_n()

sfepy.terms.extmods.terms.dw_surface_v_dot_n_s()

sfepy.terms.extmods.terms.dw_tl_diffusion()

sfepy.terms.extmods.terms.dw_tl_surface_traction()

sfepy.terms.extmods.terms.dw_tl_volume()

sfepy.terms.extmods.terms.dw_ul_volume()

sfepy.terms.extmods.terms.dw_v_dot_grad_s_sw()

sfepy.terms.extmods.terms.dw_v_dot_grad_s_vw()

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sfepy.terms.extmods.terms.dw_volume_dot_scalar()

sfepy.terms.extmods.terms.dw_volume_dot_vector()

sfepy.terms.extmods.terms.dw_volume_lvf()

sfepy.terms.extmods.terms.errclear()

sfepy.terms.extmods.terms.he_eval_from_mtx()

sfepy.terms.extmods.terms.he_residuum_from_mtx()

sfepy.terms.extmods.terms.mulAB_integrate()

sfepy.terms.extmods.terms.sym2nonsym()

sfepy.terms.extmods.terms.term_ns_asm_convect()

sfepy.terms.extmods.terms.term_ns_asm_div_grad()

Tests

sfepy.tests.conftest module

sfepy.tests.conftest.output_dir(request, tmpdir_factory)
Output directory for tests.
sfepy.tests.conftest.pytest_addoption(parser)

sfepy.tests.conftest.pytest_configure(config)

sfepy.tests.test_assembling module

sfepy.tests.test_assembling.data()

sfepy.tests.test_assembling.test_assemble_matrix(data)

sfepy.tests.test_assembling.test_assemble_matrix_complex(data)

sfepy.tests.test_assembling.test_assemble_vector(data)

sfepy.tests.test_assembling.test_assemble_vector_complex(data)

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sfepy.tests.test_base module

sfepy.tests.test_base.test_container_add()

sfepy.tests.test_base.test_parse_conf()

sfepy.tests.test_base.test_resolve_deps()

sfepy.tests.test_base.test_struct_add()

sfepy.tests.test_base.test_struct_i_add()

sfepy.tests.test_base.test_verbose_output()

sfepy.tests.test_cmesh module

sfepy.tests.test_cmesh.filename_meshes()

sfepy.tests.test_cmesh.test_cmesh_counts(filename_meshes)

sfepy.tests.test_cmesh.test_entity_volumes()

sfepy.tests.test_conditions module

sfepy.tests.test_conditions.check_vec(vec, ii, ok, conds, variables)

sfepy.tests.test_conditions.data()

sfepy.tests.test_conditions.init_vec(variables)

sfepy.tests.test_conditions.test_ebcs(data)

sfepy.tests.test_conditions.test_epbcs(data)

sfepy.tests.test_conditions.test_ics(data)

sfepy.tests.test_conditions.test_save_ebc(data, output_dir)

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sfepy.tests.test_declarative_examples module

sfepy.tests.test_declarative_examples.inedir(filename)

sfepy.tests.test_declarative_examples.test_examples(ex_filename, output_dir)

sfepy.tests.test_declarative_examples.test_examples_dg(ex_filename, output_dir)

sfepy.tests.test_dg_field module

class sfepy.tests.test_dg_field.TestDGField

test_create_output1D()

test_create_output2D()

test_get_bc_facet_values_1D()

test_get_bc_facet_values_2D()

test_get_bc_facet_values_2D_const()

test_get_facet_idx1D()

test_get_facet_idx2D()

test_get_facet_neighbor_idx_1d()

test_get_facet_neighbor_idx_2d()

test_set_dofs_1D()

test_set_dofs_2D()

sfepy.tests.test_dg_field.prepare_dgfield(approx_order, mesh)

sfepy.tests.test_dg_field.prepare_dgfield_1D(approx_order)

sfepy.tests.test_dg_field.prepare_field_2D(approx_order)

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sfepy.tests.test_dg_terms_calls module

sfepy.tests.test_domain module

sfepy.tests.test_domain.compare_mesh(geo_name, coors, conn)

sfepy.tests.test_domain.domain()

sfepy.tests.test_domain.refine(domain, out_dir, level=3)

sfepy.tests.test_domain.test_facets(domain)

sfepy.tests.test_domain.test_refine_2_3(output_dir)

sfepy.tests.test_domain.test_refine_2_4(output_dir)

sfepy.tests.test_domain.test_refine_3_4(output_dir)

sfepy.tests.test_domain.test_refine_3_8(output_dir)

sfepy.tests.test_domain.test_refine_hexa(output_dir)

sfepy.tests.test_domain.test_refine_tetra(domain, output_dir)

sfepy.tests.test_eigenvalue_solvers module

sfepy.tests.test_eigenvalue_solvers.data()

sfepy.tests.test_eigenvalue_solvers.mesh_hook(mesh, mode)
Generate the block mesh.
sfepy.tests.test_eigenvalue_solvers.test_eigenvalue_solvers(data)

sfepy.tests.test_elasticity_small_strain module

sfepy.tests.test_elasticity_small_strain.get_pars(dim, full=False)

sfepy.tests.test_elasticity_small_strain.solutions(output_dir)

sfepy.tests.test_elasticity_small_strain.test_converged(solutions)

sfepy.tests.test_elasticity_small_strain.test_linear_terms(solutions)

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sfepy.tests.test_fem module

sfepy.tests.test_fem.gels()

sfepy.tests.test_fem.test_base_functions_delta(gels)
Test 𝛿 property of base functions evaluated in the reference element nodes.
sfepy.tests.test_fem.test_base_functions_values(gels)
Compare base function values and their gradients with correct data. Also test that sum of values over all element
nodes gives one.

sfepy.tests.test_functions module

sfepy.tests.test_functions.get_circle(coors, domain=None)

sfepy.tests.test_functions.get_p_edge(ts, coors, bc=None, **kwargs)

sfepy.tests.test_functions.get_pars(ts, coors, mode=None, extra_arg=None, equations=None,

term=None, problem=None, **kwargs)

sfepy.tests.test_functions.get_u_edge(ts, coors, bc=None, **kwargs)

sfepy.tests.test_functions.problem()

sfepy.tests.test_functions.test_ebc_functions(problem, output_dir)

sfepy.tests.test_functions.test_material_functions(problem)

sfepy.tests.test_functions.test_region_functions(problem, output_dir)

sfepy.tests.test_high_level module

sfepy.tests.test_high_level.data()

sfepy.tests.test_high_level.fix_u_fun(ts, coors, bc=None, problem=None, extra_arg=None)

sfepy.tests.test_high_level.test_solving(data, output_dir)

sfepy.tests.test_high_level.test_term_arithmetics(data)

sfepy.tests.test_high_level.test_term_evaluation(data)

sfepy.tests.test_high_level.test_variables(data)

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sfepy.tests.test_homogenization_engine module

sfepy.tests.test_homogenization_engine.test_chunk_micro()

sfepy.tests.test_homogenization_engine.test_dependencies()

sfepy.tests.test_homogenization_perfusion module

sfepy.tests.test_homogenization_perfusion.compare_scalars(s1, s2, l1='s1', l2='s2',

allowed_error=1e-08)

sfepy.tests.test_homogenization_perfusion.test_solution(output_dir)

sfepy.tests.test_hyperelastic_tlul module

sfepy.tests.test_hyperelastic_tlul.test_solution(output_dir)

sfepy.tests.test_io module

sfepy.tests.test_io.test_recursive_dict_hdf5(output_dir)

sfepy.tests.test_io.test_sparse_matrix_hdf5(output_dir)

sfepy.tests.test_laplace_unit_disk module

sfepy.tests.test_laplace_unit_disk.data()

sfepy.tests.test_laplace_unit_disk.test_boundary_fluxes(data)

sfepy.tests.test_laplace_unit_square module

sfepy.tests.test_laplace_unit_square.data()

sfepy.tests.test_laplace_unit_square.linear(bc, ts, coor, which)

sfepy.tests.test_laplace_unit_square.linear_x(bc, ts, coor)

sfepy.tests.test_laplace_unit_square.linear_y(bc, ts, coor)

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sfepy.tests.test_laplace_unit_square.linear_z(bc, ts, coor)

sfepy.tests.test_laplace_unit_square.test_boundary_fluxes(data, output_dir)

sfepy.tests.test_laplace_unit_square.test_solution(data)

sfepy.tests.test_lcbcs module

sfepy.tests.test_lcbcs.test_elasticity_rigid(mesh_filename, output_dir)

sfepy.tests.test_lcbcs.test_laplace_shifted_periodic(output_dir)

sfepy.tests.test_lcbcs.test_stokes_slip_bc(output_dir)

sfepy.tests.test_linalg module

sfepy.tests.test_linalg.test_assemble1d()

sfepy.tests.test_linalg.test_geometry()

sfepy.tests.test_linalg.test_tensors()

sfepy.tests.test_linalg.test_unique_rows()

sfepy.tests.test_linear_solvers module

class sfepy.tests.test_linear_solvers.DiagPC
Diagonal (Jacobi) preconditioner.
Equivalent to setting ‘precond’ : ‘jacobi’.
apply(pc, x, y)

setUp(pc)

sfepy.tests.test_linear_solvers.problem()

sfepy.tests.test_linear_solvers.setup_petsc_precond(mtx, problem)

sfepy.tests.test_linear_solvers.test_ls_reuse(problem)

sfepy.tests.test_linear_solvers.test_solvers(problem, output_dir)

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sfepy.tests.test_linearization module

sfepy.tests.test_linearization.test_linearization(output_dir)

sfepy.tests.test_log module

sfepy.tests.test_log.log(log_filename)

sfepy.tests.test_log.log_filename(output_dir)

sfepy.tests.test_log.test_log_rw(log_filename, log, output_dir)

sfepy.tests.test_matcoefs module

sfepy.tests.test_matcoefs.test_conversion_functions()

sfepy.tests.test_matcoefs.test_elastic_constants()

sfepy.tests.test_matcoefs.test_stiffness_tensors()

sfepy.tests.test_mesh_expand module

sfepy.tests.test_mesh_expand.test_mesh_expand()

sfepy.tests.test_mesh_generators module

sfepy.tests.test_mesh_generators.test_gen_block_mesh(output_dir)

sfepy.tests.test_mesh_generators.test_gen_cylinder_mesh(output_dir)

sfepy.tests.test_mesh_generators.test_gen_extended_block_mesh(output_dir)

sfepy.tests.test_mesh_generators.test_gen_mesh_from_geom(output_dir)

sfepy.tests.test_mesh_generators.test_gen_mesh_from_voxels(output_dir)

sfepy.tests.test_mesh_generators.test_gen_tiled_mesh(output_dir)

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sfepy.tests.test_mesh_interp module

sfepy.tests.test_mesh_interp.do_interpolation(m2, m1, data, field_name, force=False)

Interpolate data from m1 to m2.
sfepy.tests.test_mesh_interp.gen_datas(meshes)

sfepy.tests.test_mesh_interp.in_dir(adir)

sfepy.tests.test_mesh_interp.prepare_variable(filename, n_components)

sfepy.tests.test_mesh_interp.test_evaluate_at()

sfepy.tests.test_mesh_interp.test_field_gradient()

sfepy.tests.test_mesh_interp.test_interpolation(output_dir)

sfepy.tests.test_mesh_interp.test_interpolation_two_meshes(output_dir)

sfepy.tests.test_mesh_interp.test_invariance()

sfepy.tests.test_mesh_interp.test_invariance_qp()

sfepy.tests.test_mesh_smoothing module

sfepy.tests.test_mesh_smoothing.get_volume(el, nd)

sfepy.tests.test_mesh_smoothing.test_mesh_smoothing(output_dir)

sfepy.tests.test_meshio module

sfepy.tests.test_meshio.mesh_hook(mesh, mode)
Define a mesh programmatically.
sfepy.tests.test_meshio.test_compare_same_meshes()
Compare same meshes in various formats.
sfepy.tests.test_meshio.test_hdf5_meshio()

sfepy.tests.test_meshio.test_read_dimension()

sfepy.tests.test_meshio.test_read_meshes()
Try to read all listed meshes.
sfepy.tests.test_meshio.test_write_read_meshes(output_dir)
Try to write and then read all supported formats.

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sfepy.tests.test_msm_laplace module

sfepy.tests.test_msm_laplace.ebc(ts, coor, **kwargs)

sfepy.tests.test_msm_laplace.problem()

sfepy.tests.test_msm_laplace.rhs(ts, coor, mode=None, expression=None, **kwargs)

sfepy.tests.test_msm_laplace.test_msm_laplace(problem, output_dir)

sfepy.tests.test_msm_symbolic module

sfepy.tests.test_msm_symbolic.ebc(ts, coor, solution=None)

sfepy.tests.test_msm_symbolic.problem()

sfepy.tests.test_msm_symbolic.rhs(ts, coor, mode=None, expression=None, **kwargs)

sfepy.tests.test_msm_symbolic.test_msm_symbolic_diffusion(problem, output_dir)

sfepy.tests.test_msm_symbolic.test_msm_symbolic_laplace(problem, output_dir)

sfepy.tests.test_normals module

sfepy.tests.test_normals.test_normals()
Check orientations of surface normals on the reference elements.

sfepy.tests.test_parsing module

sfepy.tests.test_parsing.test_parse_equations()

sfepy.tests.test_parsing.test_parse_regions()

sfepy.tests.test_poly_spaces module

Test continuity of polynomial basis and its gradients along an edge on 𝑦 line (2D) or on a face in 𝑥-𝑦 plane (3D) between
two elements aligned with the coordinate system, stack one on top of the other. The evaluation occurs in several points
shifted by a very small amount from the boundary between the elements into the top and the bottom element.
For H1 space, the basis should be continuous. The components of its gradient parallel to the edge/face should be
continuous as well, while the perpendicular component should have the same absolute value, but different sign in the
top and the bottom element.
All connectivity permutations of the two elements are tested.

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The serendipity basis implementation is a pure python proof-of-concept. Its order in continuity tests is limited to 2 on
3_8 elements to decrease the tests run time.
sfepy.tests.test_poly_spaces.gels()

sfepy.tests.test_poly_spaces.test_continuity(gels)

sfepy.tests.test_poly_spaces.test_gradients(gels)

sfepy.tests.test_poly_spaces.test_hessians(gels)
Test the second partial derivatives of basis functions using finite differences.
sfepy.tests.test_poly_spaces.test_partition_of_unity(gels)

sfepy.tests.test_projections module

sfepy.tests.test_projections.data()

sfepy.tests.test_projections.test_mass_matrix(data)

sfepy.tests.test_projections.test_project_tensors(data)

sfepy.tests.test_projections.test_projection_iga_fem()

sfepy.tests.test_projections.test_projection_tri_quad(data, output_dir)

sfepy.tests.test_quadratures module

sfepy.tests.test_quadratures.get_poly(order, dim, is_simplex=False)

Construct a polynomial of given order in space dimension dim, and integrate it symbolically over a rectangular
or simplex domain for coordinates in [0, 1].
sfepy.tests.test_quadratures.symarray(prefix, shape)
Copied from SymPy so that the tests pass for its different versions.
sfepy.tests.test_quadratures.test_quadratures()
Test if the quadratures have orders they claim to have, using symbolic integration by sympy.
sfepy.tests.test_quadratures.test_weight_consistency()
Test if integral of 1 (= sum of weights) gives the domain volume.

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sfepy.tests.test_ref_coors module

sfepy.tests.test_ref_coors.test_ref_coors_fem()

sfepy.tests.test_ref_coors.test_ref_coors_iga()

sfepy.tests.test_refine_hanging module

Test continuity along a boundary with hanging nodes due to a mesh refinement.
sfepy.tests.test_refine_hanging.eval_fun(ts, coors, mode, **kwargs)

sfepy.tests.test_refine_hanging.gels()

sfepy.tests.test_refine_hanging.test_continuity(gels, output_dir)

sfepy.tests.test_refine_hanging.test_preserve_coarse_entities(output_dir)

sfepy.tests.test_regions module

sfepy.tests.test_regions.data()

sfepy.tests.test_regions.get_cells(coors, domain=None)

sfepy.tests.test_regions.get_vertices(coors, domain=None)

sfepy.tests.test_regions.test_operators(data)
Test operators in region selectors.
sfepy.tests.test_regions.test_selectors(data)
Test basic region selectors.

sfepy.tests.test_semismooth_newton module

sfepy.tests.test_semismooth_newton.convert_to_csr(m_in)

sfepy.tests.test_semismooth_newton.define_matrices()

sfepy.tests.test_semismooth_newton.eval_matrix(mtx, **kwargs)

sfepy.tests.test_semismooth_newton.test_semismooth_newton()

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sfepy.tests.test_sparse module

sfepy.tests.test_sparse.test_compose_sparse()

sfepy.tests.test_splinebox module

sfepy.tests.test_splinebox.test_spbox_2d()
Check position of a given vertex in the deformed mesh.
sfepy.tests.test_splinebox.test_spbox_3d()
Check volume change of the mesh which is deformed using the SplineBox functions.
sfepy.tests.test_splinebox.test_spbox_field()
‘Field’ vs. ‘coors’.
sfepy.tests.test_splinebox.test_spregion2d()
Check position of a given vertex in the deformed mesh.
sfepy.tests.test_splinebox.tetravolume(cells, vertices)

sfepy.tests.test_tensors module

sfepy.tests.test_tensors.get_ortho_d(phi1, phi2)

sfepy.tests.test_tensors.test_stress_transform()

sfepy.tests.test_tensors.test_tensors()

sfepy.tests.test_tensors.test_transform_data()

sfepy.tests.test_tensors.test_transform_data4()

sfepy.tests.test_term_call_modes module

sfepy.tests.test_term_call_modes.data()

sfepy.tests.test_term_call_modes.make_term_args(arg_shapes, arg_kinds, arg_types, ats_mode, domain,

material_value=None, poly_space_base=None)

sfepy.tests.test_term_call_modes.test_term_call_modes(data)

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sfepy.tests.test_term_consistency module

sfepy.tests.test_term_consistency.get_pars(ts, coor, mode=None, term=None, **kwargs)

sfepy.tests.test_term_consistency.problem()

sfepy.tests.test_term_consistency.test_consistency_d_dw(problem)

sfepy.tests.test_term_consistency.test_ev_div(problem)

sfepy.tests.test_term_consistency.test_ev_grad(problem)

sfepy.tests.test_term_consistency.test_eval_matrix(problem)

sfepy.tests.test_term_consistency.test_surface_evaluate(problem)

sfepy.tests.test_term_consistency.test_vector_matrix(problem)

sfepy.tests.test_term_sensitivity module

sfepy.tests.test_term_sensitivity.modify_mesh(val, spbox, dv_mode, cp_pos)

sfepy.tests.test_term_sensitivity.problem()

sfepy.tests.test_term_sensitivity.test_sensitivity(problem)

sfepy.tests.test_units module

sfepy.tests.test_units.test_consistent_sets()

sfepy.tests.test_units.test_units()

sfepy.tests.test_volume module

Test computing volumes by volume or surface integrals.

sfepy.tests.test_volume.problem()

sfepy.tests.test_volume.test_volume(problem)

sfepy.tests.test_volume.test_volume_tl(problem)

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1032 Chapter 2. Development

 BIBLIOGRAPHY

[Logg2012] A. Logg: Efficient Representation of Computational Meshes. 2012

[1] Remacle, J.-F., Chevaugeon, N., Marchandise, E., & Geuzaine, C. (2007). Efficient visualization of high-
order finite elements. International Journal for Numerical Methods in Engineering, 69(4), 750-771. https:
//doi.org/10.1002/nme.1787
[1] Krivodonova (2007): Limiters for high-order discontinuous Galerkin methods
[1] Hesthaven, J. S., & Warburton, T. (2008). Nodal Discontinuous Galerkin Methods. Journal of Physics
A: Mathematical and Theoretical (Vol. 54). New York, NY: Springer New York. http://doi.org/10.1007/
978-0-387-72067-8, p. 63
[1] Gottlieb, S., & Shu, C.-W. (2002). Total variation diminishing Runge-Kutta schemes. Mathemat-
ics of Computation of the American Mathematical Society, 67(221), 73–85. https://doi.org/10.1090/
s0025-5718-98-00913-2
[1] Zemčík, R., Rolfes, R., Rose, M. and Tessmer, J. (2006),
[2] Zemčík, R., Rolfes, R., Rose, M. and Teßmer, J. (2007),

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1034 Bibliography
 PYTHON MODULE INDEX

b s
blockgen, 648 save_basis, 656
build_helpers, 645 sfepy.applications.application, 658
sfepy.applications.evp_solver_app, 658
c sfepy.applications.pde_solver_app, 659
convert_mesh, 648 sfepy.base.base, 659
cylindergen, 648 sfepy.base.compat, 666
sfepy.base.conf, 669
d sfepy.base.getch, 672
dg_plot_1D, 649 sfepy.base.goptions, 672
sfepy.base.ioutils, 672
e sfepy.base.log, 677
edit_identifiers, 649 sfepy.base.log_plotter, 678
eval_ns_forms, 650 sfepy.base.mem_usage, 679
eval_tl_forms, 650 sfepy.base.multiproc, 679
extract_edges, 650 sfepy.base.multiproc_mpi, 680
extract_surface, 651 sfepy.base.multiproc_proc, 682
extractor, 640 sfepy.base.parse_conf, 683
sfepy.base.plotutils, 684
g sfepy.base.reader, 684
gen_gallery, 651 sfepy.base.resolve_deps, 685
gen_iga_patch, 652 sfepy.base.testing, 685
gen_legendre_simplex_base, 652 sfepy.base.timing, 686
gen_lobatto1d_c, 653 sfepy.config, 657
gen_mesh_prev, 653 sfepy.discrete.common.dof_info, 726
gen_release_notes, 653 sfepy.discrete.common.domain, 728
gen_serendipity_basis, 654 sfepy.discrete.common.extmods._fmfield, 729
gen_solver_table, 654 sfepy.discrete.common.extmods._geommech, 729
gen_term_table, 654 sfepy.discrete.common.extmods.assemble, 729
sfepy.discrete.common.extmods.cmesh, 730
p sfepy.discrete.common.extmods.crefcoors, 732
phonon, 641 sfepy.discrete.common.extmods.mappings, 733
plot_condition_numbers, 655 sfepy.discrete.common.fields, 734
plot_logs, 655 sfepy.discrete.common.global_interp, 736
plot_mesh, 655 sfepy.discrete.common.mappings, 738
plot_quadratures, 655 sfepy.discrete.common.poly_spaces, 740
plot_times, 656 sfepy.discrete.common.region, 741
postproc, 641 sfepy.discrete.conditions, 686
probe, 642 sfepy.discrete.dg.dg_1D_vizualizer, 775
sfepy.discrete.dg.fields, 779
r sfepy.discrete.dg.limiters, 789
sfepy.discrete.dg.poly_spaces, 786
resview, 643

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sfepy.discrete.equations, 688 sfepy.homogenization.engine, 815

sfepy.discrete.evaluate, 693 sfepy.homogenization.homogen_app, 817
sfepy.discrete.evaluate_variable, 696 sfepy.homogenization.micmac, 818
sfepy.discrete.fem._serendipity, 774 sfepy.homogenization.recovery, 818
sfepy.discrete.fem.domain, 744 sfepy.homogenization.utils, 821
sfepy.discrete.fem.extmods.bases, 745 sfepy.linalg.check_derivatives, 822
sfepy.discrete.fem.extmods.lobatto_bases, 746 sfepy.linalg.eigen, 822
sfepy.discrete.fem.facets, 746 sfepy.linalg.geometry, 823
sfepy.discrete.fem.fe_surface, 748 sfepy.linalg.sparse, 825
sfepy.discrete.fem.fields_base, 748 sfepy.linalg.sympy_operators, 827
sfepy.discrete.fem.fields_hierarchic, 753 sfepy.linalg.utils, 827
sfepy.discrete.fem.fields_nodal, 754 sfepy.mechanics.contact_bodies, 830
sfepy.discrete.fem.fields_positive, 755 sfepy.mechanics.elastic_constants, 831
sfepy.discrete.fem.geometry_element, 755 sfepy.mechanics.extmods.ccontres, 841
sfepy.discrete.fem.history, 756 sfepy.mechanics.matcoefs, 831
sfepy.discrete.fem.lcbc_operators, 756 sfepy.mechanics.membranes, 833
sfepy.discrete.fem.linearizer, 759 sfepy.mechanics.shell10x, 835
sfepy.discrete.fem.mappings, 759 sfepy.mechanics.tensors, 837
sfepy.discrete.fem.mesh, 760 sfepy.mechanics.units, 839
sfepy.discrete.fem.meshio, 761 sfepy.mesh.bspline, 842
sfepy.discrete.fem.periodic, 768 sfepy.mesh.geom_tools, 846
sfepy.discrete.fem.poly_spaces, 769 sfepy.mesh.mesh_generators, 848
sfepy.discrete.fem.refine, 773 sfepy.mesh.mesh_tools, 851
sfepy.discrete.fem.refine_hanging, 774 sfepy.mesh.splinebox, 852
sfepy.discrete.fem.utils, 774 sfepy.parallel.evaluate, 853
sfepy.discrete.functions, 696 sfepy.parallel.parallel, 854
sfepy.discrete.iga.domain, 791 sfepy.parallel.plot_parallel_dofs, 856
sfepy.discrete.iga.domain_generators, 792 sfepy.postprocess.domain_specific, 856
sfepy.discrete.iga.extmods.igac, 793 sfepy.postprocess.plot_cmesh, 857
sfepy.discrete.iga.fields, 795 sfepy.postprocess.plot_dofs, 858
sfepy.discrete.iga.iga, 796 sfepy.postprocess.plot_facets, 858
sfepy.discrete.iga.io, 801 sfepy.postprocess.plot_quadrature, 859
sfepy.discrete.iga.mappings, 801 sfepy.postprocess.probes_vtk, 859
sfepy.discrete.iga.plot_nurbs, 802 sfepy.postprocess.sources, 860
sfepy.discrete.iga.utils, 802 sfepy.postprocess.time_history, 862
sfepy.discrete.integrals, 697 sfepy.postprocess.utils, 863
sfepy.discrete.materials, 698 sfepy.postprocess.utils_vtk, 863
sfepy.discrete.parse_equations, 700 sfepy.postprocess.viewer, 864
sfepy.discrete.parse_regions, 700 sfepy.solvers.auto_fallback, 868
sfepy.discrete.probes, 701 sfepy.solvers.eigen, 868
sfepy.discrete.problem, 704 sfepy.solvers.ls, 870
sfepy.discrete.projections, 715 sfepy.solvers.ls_mumps, 875
sfepy.discrete.quadratures, 715 sfepy.solvers.ls_mumps_parallel, 889
sfepy.discrete.simplex_cubature, 717 sfepy.solvers.nls, 890
sfepy.discrete.structural.fields, 803 sfepy.solvers.optimize, 893
sfepy.discrete.structural.mappings, 804 sfepy.solvers.oseen, 894
sfepy.discrete.variables, 717 sfepy.solvers.qeigen, 895
sfepy.homogenization.band_gaps_app, 804 sfepy.solvers.semismooth_newton, 896
sfepy.homogenization.coefficients, 805 sfepy.solvers.solvers, 897
sfepy.homogenization.coefs_base, 806 sfepy.solvers.ts, 898
sfepy.homogenization.coefs_elastic, 809 sfepy.solvers.ts_dg_solvers, 790
sfepy.homogenization.coefs_perfusion, 809 sfepy.solvers.ts_solvers, 900
sfepy.homogenization.coefs_phononic, 810 sfepy.terms.extmods.terms, 1013
sfepy.homogenization.convolutions, 814 sfepy.terms.terms, 905

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sfepy.terms.terms_adj_navier_stokes, 910 sfepy.tests.test_mesh_generators, 1025

sfepy.terms.terms_basic, 919 sfepy.tests.test_mesh_interp, 1026
sfepy.terms.terms_biot, 924 sfepy.tests.test_mesh_smoothing, 1026
sfepy.terms.terms_compat, 927 sfepy.tests.test_meshio, 1026
sfepy.terms.terms_constraints, 930 sfepy.tests.test_msm_laplace, 1027
sfepy.terms.terms_contact, 932 sfepy.tests.test_msm_symbolic, 1027
sfepy.terms.terms_dg, 933 sfepy.tests.test_normals, 1027
sfepy.terms.terms_diffusion, 938 sfepy.tests.test_parsing, 1027
sfepy.terms.terms_dot, 944 sfepy.tests.test_poly_spaces, 1027
sfepy.terms.terms_elastic, 950 sfepy.tests.test_projections, 1028
sfepy.terms.terms_electric, 960 sfepy.tests.test_quadratures, 1028
sfepy.terms.terms_fibres, 960 sfepy.tests.test_ref_coors, 1029
sfepy.terms.terms_hyperelastic_base, 961 sfepy.tests.test_refine_hanging, 1029
sfepy.terms.terms_hyperelastic_tl, 963 sfepy.tests.test_regions, 1029
sfepy.terms.terms_hyperelastic_ul, 971 sfepy.tests.test_semismooth_newton, 1029
sfepy.terms.terms_membrane, 975 sfepy.tests.test_sparse, 1030
sfepy.terms.terms_multilinear, 976 sfepy.tests.test_splinebox, 1030
sfepy.terms.terms_navier_stokes, 987 sfepy.tests.test_tensors, 1030
sfepy.terms.terms_piezo, 996 sfepy.tests.test_term_call_modes, 1030
sfepy.terms.terms_point, 999 sfepy.tests.test_term_consistency, 1031
sfepy.terms.terms_sensitivity, 1000 sfepy.tests.test_term_sensitivity, 1031
sfepy.terms.terms_shells, 1005 sfepy.tests.test_units, 1031
sfepy.terms.terms_surface, 1007 sfepy.tests.test_volume, 1031
sfepy.terms.terms_th, 1012 sfepy.version, 658
sfepy.terms.terms_volume, 1013 show_authors, 656
sfepy.terms.utils, 1013 show_mesh_info, 656
sfepy.tests.conftest, 1018 show_terms_use, 656
sfepy.tests.test_assembling, 1018 simple, 645
sfepy.tests.test_base, 1019 simple_homog_mpi, 645
sfepy.tests.test_cmesh, 1019 sync_module_docs, 656
sfepy.tests.test_conditions, 1019
sfepy.tests.test_declarative_examples, 1020 t
sfepy.tests.test_dg_field, 1020 test_install, 647
sfepy.tests.test_domain, 1021 tile_periodic_mesh, 657
sfepy.tests.test_eigenvalue_solvers, 1021
sfepy.tests.test_elasticity_small_strain,
1021
sfepy.tests.test_fem, 1022
sfepy.tests.test_functions, 1022
sfepy.tests.test_high_level, 1022
sfepy.tests.test_homogenization_engine, 1023
sfepy.tests.test_homogenization_perfusion,
1023
sfepy.tests.test_hyperelastic_tlul, 1023
sfepy.tests.test_io, 1023
sfepy.tests.test_laplace_unit_disk, 1023
sfepy.tests.test_laplace_unit_square, 1023
sfepy.tests.test_lcbcs, 1024
sfepy.tests.test_linalg, 1024
sfepy.tests.test_linear_solvers, 1024
sfepy.tests.test_linearization, 1025
sfepy.tests.test_log, 1025
sfepy.tests.test_matcoefs, 1025
sfepy.tests.test_mesh_expand, 1025

Python Module Index 1037

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1038 Python Module Index

 INDEX

Symbols AcousticBandGapsApp (class in

__call__() (sfepy.solvers.nls.Newton method), 890 sfepy.homogenization.band_gaps_app), 804
__call__() (sfepy.solvers.nls.PETScNonlinearSolver AcousticMassLiquidTensor (class in
method), 892 sfepy.homogenization.coefs_phononic), 810
__call__() (sfepy.solvers.nls.ScipyBroyden method), AcousticMassTensor (class in
892 sfepy.homogenization.coefs_phononic), 810
__init__() (sfepy.solvers.nls.Newton method), 891 acquire() (sfepy.base.multiproc_mpi.RemoteLock
__init__() (sfepy.solvers.nls.PETScNonlinearSolver method), 680
method), 892 actBfT() (in module sfepy.terms.extmods.terms), 1013
__init__() (sfepy.solvers.nls.ScipyBroyden method), adapt_time_step() (in module
892 sfepy.solvers.ts_solvers), 904
__module__ (sfepy.solvers.nls.Newton attribute), 891 AdaptiveTimeSteppingSolver (class in
__module__ (sfepy.solvers.nls.PETScNonlinearSolver at- sfepy.solvers.ts_solvers), 900
tribute), 892 add_arg_dofs() (sfepy.terms.terms_multilinear.ExpressionBuilder
__module__ (sfepy.solvers.nls.ScipyBroyden attribute), method), 986
892 add_bf() (sfepy.terms.terms_multilinear.ExpressionBuilder
method), 986
A add_bfg() (sfepy.terms.terms_multilinear.ExpressionBuilder
a (sfepy.solvers.ls_mumps.mumps_struc_c_4 attribute), method), 986
876 add_circle_probe() (sfepy.postprocess.probes_vtk.Probe
a (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at- method), 859
tribute), 879 add_constant() (sfepy.terms.terms_multilinear.ExpressionBuilder
a (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at- method), 986
tribute), 882 add_data_to_dataset()
a (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at- (sfepy.postprocess.sources.GenericFileSource
tribute), 885 method), 861
a_elt (sfepy.solvers.ls_mumps.mumps_struc_c_4 at- add_eas_dofs() (in module sfepy.mechanics.shell10x),
tribute), 876 835
a_elt (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at- add_equation() (sfepy.discrete.equations.Equations
tribute), 879 method), 688
a_elt (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at- add_eye() (sfepy.terms.terms_multilinear.ExpressionBuilder
tribute), 882 method), 986
a_elt (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at- add_from_bc() (sfepy.discrete.fem.lcbc_operators.LCBCOperators
tribute), 885 method), 757
a_loc (sfepy.solvers.ls_mumps.mumps_struc_c_4 at- add_glyphs() (in module sfepy.postprocess.viewer),
tribute), 876 867
a_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at- add_group() (sfepy.base.log.Log method), 677
tribute), 879 add_iso_surface() (in module
a_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at- sfepy.postprocess.viewer), 867
tribute), 882 add_line_probe() (sfepy.postprocess.probes_vtk.Probe
a_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at- method), 859
tribute), 885 add_mat_id_to_grid() (in module resview), 644

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add_material_arg() (sfepy.terms.terms_multilinear.ExpressionBuilder
AdjDivGradTerm (class in
method), 986 sfepy.terms.terms_adj_navier_stokes), 911
add_missing() (sfepy.base.conf.ProblemConf method), advance() (sfepy.discrete.equations.Equations method),
669 689
add_points_probe() (sfepy.postprocess.probes_vtk.Probeadvance() (sfepy.discrete.problem.Problem method),
method), 859 705
add_psg() (sfepy.terms.terms_multilinear.ExpressionBuilder
advance() (sfepy.discrete.variables.Variable method),
method), 986 721
add_pvg() (sfepy.terms.terms_multilinear.ExpressionBuilder
advance() (sfepy.discrete.variables.Variables method),
method), 986 723
add_ray_probe() (sfepy.postprocess.probes_vtk.Probe advance() (sfepy.solvers.ts.TimeStepper method), 898
method), 860 advance() (sfepy.solvers.ts.VariableTimeStepper
add_scalar_cut_plane() (in module method), 899
sfepy.postprocess.viewer), 867 advance() (sfepy.terms.terms.Term method), 905
add_state_arg() (sfepy.terms.terms_multilinear.ExpressionBuilder
advance_eth_data() (sfepy.terms.terms_th.ETHTerm
method), 986 method), 1012
add_strain_rs() (in module AdvectDivFreeTerm (class in
sfepy.homogenization.recovery), 818 sfepy.terms.terms_diffusion), 938
add_stress_p() (in module AdvectionDGFluxTerm (class in sfepy.terms.terms_dg),
sfepy.homogenization.recovery), 818 933
add_subdomains_surface() (in module alf (sfepy.terms.terms_dg.NonlinearHyperbolicDGFluxTerm
sfepy.postprocess.viewer), 867 attribute), 936
add_surf() (in module sfepy.postprocess.viewer), 867 all_bfs (sfepy.discrete.fem.poly_spaces.SerendipityTensorProductPolySpa
add_text() (in module sfepy.postprocess.viewer), 867 attribute), 771
add_vector_cut_plane() (in module alloc_extra_data() (sfepy.discrete.common.extmods.mappings.CMappin
sfepy.postprocess.viewer), 867 method), 733
add_virtual_arg() (sfepy.terms.terms_multilinear.ExpressionBuilder
alpha (sfepy.terms.terms_dg.AdvectionDGFluxTerm at-
method), 986 tribute), 934
addline() (sfepy.mesh.geom_tools.geometry method), animate1D_dgsol() (in module
846 sfepy.discrete.dg.dg_1D_vizualizer), 775
addlines() (sfepy.mesh.geom_tools.geometry method), animate_1D_DG_sol() (in module
846 sfepy.discrete.dg.dg_1D_vizualizer), 776
addphysicalsurface() ANSYSCDBMeshIO (class in sfepy.discrete.fem.meshio),
(sfepy.mesh.geom_tools.geometry method), 761
846 any_from_args() (sfepy.discrete.common.poly_spaces.PolySpace
addphysicalvolume() static method), 740
(sfepy.mesh.geom_tools.geometry method), any_from_conf() (sfepy.homogenization.coefs_base.MiniAppBase
846 static method), 808
addpoint() (sfepy.mesh.geom_tools.geometry method), any_from_conf() (sfepy.solvers.solvers.Solver static
846 method), 897
addpoints() (sfepy.mesh.geom_tools.geometry any_from_filename()
method), 846 (sfepy.discrete.fem.meshio.MeshIO static
addsurface() (sfepy.mesh.geom_tools.geometry method), 766
method), 846 append() (sfepy.base.base.Container method), 660
addsurfaces() (sfepy.mesh.geom_tools.geometry append() (sfepy.discrete.fem.history.History method),
method), 846 756
addvolume() (sfepy.mesh.geom_tools.geometry append() (sfepy.discrete.fem.lcbc_operators.LCBCOperators
method), 846 method), 757
addvolumes() (sfepy.mesh.geom_tools.geometry append() (sfepy.terms.terms.Terms method), 908
method), 846 append_all() (in module
AdjConvect1Term (class in sfepy.terms.terms_multilinear), 987
sfepy.terms.terms_adj_navier_stokes), 910 append_bubbles() (sfepy.discrete.fem.poly_spaces.LagrangeNodes
AdjConvect2Term (class in static method), 769
sfepy.terms.terms_adj_navier_stokes), 910 append_declarations() (in module gen_lobatto1d_c),

1040 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

653 method), 844

append_edges() (sfepy.discrete.fem.poly_spaces.LagrangeNodes
approximate_exponential() (in module
static method), 769 sfepy.homogenization.convolutions), 814
append_faces() (sfepy.discrete.fem.poly_spaces.LagrangeNodes
approximation_example() (in module
static method), 770 sfepy.mesh.bspline), 845
append_lists() (in module gen_lobatto1d_c), 653 are_close() (in module sfepy.solvers.oseen), 895
append_polys() (in module gen_lobatto1d_c), 653 are_disjoint() (in module
append_raw() (sfepy.discrete.common.dof_info.DofInfo sfepy.discrete.common.region), 744
method), 726 arg_shapes (sfepy.terms.terms.Term attribute), 905
append_tp_bubbles() arg_shapes (sfepy.terms.terms_adj_navier_stokes.AdjConvect1Term
(sfepy.discrete.fem.poly_spaces.LagrangeNodes attribute), 910
static method), 770 arg_shapes (sfepy.terms.terms_adj_navier_stokes.AdjConvect2Term
append_tp_edges() (sfepy.discrete.fem.poly_spaces.LagrangeNodesattribute), 910
static method), 770 arg_shapes (sfepy.terms.terms_adj_navier_stokes.AdjDivGradTerm
append_tp_faces() (sfepy.discrete.fem.poly_spaces.LagrangeNodesattribute), 911
static method), 770 arg_shapes (sfepy.terms.terms_adj_navier_stokes.NSOFMinGradTerm
append_variable() (sfepy.discrete.common.dof_info.DofInfo attribute), 911
method), 727 arg_shapes (sfepy.terms.terms_adj_navier_stokes.NSOFSurfMinDPressDi
Application (class in sfepy.applications.application), attribute), 912
658 arg_shapes (sfepy.terms.terms_adj_navier_stokes.NSOFSurfMinDPressTe
AppliedLoadTensor (class in attribute), 912
sfepy.homogenization.coefs_phononic), 810 arg_shapes (sfepy.terms.terms_adj_navier_stokes.SDConvectTerm
apply() (sfepy.tests.test_linear_solvers.DiagPC attribute), 913
method), 1024 arg_shapes (sfepy.terms.terms_adj_navier_stokes.SDDivGradTerm
apply_commands() (sfepy.base.log_plotter.LogPlotter attribute), 913
method), 678 arg_shapes (sfepy.terms.terms_adj_navier_stokes.SDDivTerm
apply_ebc() (sfepy.discrete.equations.Equations attribute), 914
method), 689 arg_shapes (sfepy.terms.terms_adj_navier_stokes.SDDotTerm
apply_ebc() (sfepy.discrete.variables.DGFieldVariable attribute), 915
method), 717 arg_shapes (sfepy.terms.terms_adj_navier_stokes.SDGradDivStabilization
apply_ebc() (sfepy.discrete.variables.FieldVariable attribute), 915
method), 718 arg_shapes (sfepy.terms.terms_adj_navier_stokes.SDPSPGCStabilizationT
apply_ebc() (sfepy.discrete.variables.Variables attribute), 916
method), 723 arg_shapes (sfepy.terms.terms_adj_navier_stokes.SDPSPGPStabilizationT
apply_ebc_to_matrix() (in module attribute), 917
sfepy.discrete.evaluate), 693 arg_shapes (sfepy.terms.terms_adj_navier_stokes.SDSUPGCStabilizationT
apply_ic() (sfepy.discrete.equations.Equations attribute), 917
method), 689 arg_shapes (sfepy.terms.terms_adj_navier_stokes.SUPGCAdjStabilization
apply_ic() (sfepy.discrete.variables.FieldVariable attribute), 918
method), 718 arg_shapes (sfepy.terms.terms_adj_navier_stokes.SUPGPAdj1Stabilizatio
apply_ic() (sfepy.discrete.variables.Variables method), attribute), 918
723 arg_shapes (sfepy.terms.terms_adj_navier_stokes.SUPGPAdj2Stabilizatio
apply_layout() (sfepy.terms.terms_multilinear.ExpressionBuilder attribute), 919
method), 986 arg_shapes (sfepy.terms.terms_basic.IntegrateMatTerm
apply_to_sequence() (in module sfepy.linalg.utils), attribute), 920
827 arg_shapes (sfepy.terms.terms_basic.IntegrateOperatorTerm
apply_unit_multipliers() (in module attribute), 920
sfepy.mechanics.units), 841 arg_shapes (sfepy.terms.terms_basic.IntegrateTerm at-
apply_units_to_pars() (in module tribute), 921
sfepy.mechanics.units), 841 arg_shapes (sfepy.terms.terms_basic.SumNodalValuesTerm
apply_view_options() (in module gen_gallery), 651 attribute), 922
approximate() (sfepy.mesh.bspline.BSpline method), arg_shapes (sfepy.terms.terms_basic.SurfaceMomentTerm
842 attribute), 922
approximate() (sfepy.mesh.bspline.BSplineSurf arg_shapes (sfepy.terms.terms_basic.VolumeSurfaceTerm

Index 1041
SfePy Documentation, Release version: 2022.1+git.f9873484

attribute), 923 attribute), 947

arg_shapes (sfepy.terms.terms_basic.VolumeTerm at- arg_shapes (sfepy.terms.terms_dot.ScalarDotGradIScalarTerm
tribute), 923 attribute), 947
arg_shapes (sfepy.terms.terms_basic.ZeroTerm at- arg_shapes (sfepy.terms.terms_dot.ScalarDotMGradScalarTerm
tribute), 924 attribute), 948
arg_shapes (sfepy.terms.terms_biot.BiotETHTerm at- arg_shapes (sfepy.terms.terms_dot.VectorDotGradScalarTerm
tribute), 925 attribute), 949
arg_shapes (sfepy.terms.terms_biot.BiotStressTerm at- arg_shapes (sfepy.terms.terms_dot.VectorDotScalarTerm
tribute), 925 attribute), 950
arg_shapes (sfepy.terms.terms_biot.BiotTerm attribute), arg_shapes (sfepy.terms.terms_elastic.CauchyStrainTerm
927 attribute), 951
arg_shapes (sfepy.terms.terms_biot.BiotTHTerm at- arg_shapes (sfepy.terms.terms_elastic.CauchyStressETHTerm
tribute), 926 attribute), 951
arg_shapes (sfepy.terms.terms_constraints.NonPenetrationPenaltyTerm
arg_shapes (sfepy.terms.terms_elastic.CauchyStressTerm
attribute), 930 attribute), 953
arg_shapes (sfepy.terms.terms_constraints.NonPenetrationTerm
arg_shapes (sfepy.terms.terms_elastic.CauchyStressTHTerm
attribute), 931 attribute), 952
arg_shapes (sfepy.terms.terms_contact.ContactTerm at- arg_shapes (sfepy.terms.terms_elastic.ElasticWaveCauchyTerm
tribute), 932 attribute), 953
arg_shapes (sfepy.terms.terms_dg.AdvectionDGFluxTerm arg_shapes (sfepy.terms.terms_elastic.ElasticWaveTerm
attribute), 934 attribute), 954
arg_shapes (sfepy.terms.terms_dg.DiffusionDGFluxTerm arg_shapes (sfepy.terms.terms_elastic.LinearElasticETHTerm
attribute), 935 attribute), 955
arg_shapes (sfepy.terms.terms_dg.DiffusionInteriorPenaltyTerm
arg_shapes (sfepy.terms.terms_elastic.LinearElasticIsotropicTerm
attribute), 935 attribute), 955
arg_shapes (sfepy.terms.terms_dg.NonlinearHyperbolicDGFluxTerm
arg_shapes (sfepy.terms.terms_elastic.LinearElasticTerm
attribute), 936 attribute), 957
arg_shapes (sfepy.terms.terms_dg.NonlinearScalarDotGradTerm
arg_shapes (sfepy.terms.terms_elastic.LinearElasticTHTerm
attribute), 937 attribute), 956
arg_shapes (sfepy.terms.terms_diffusion.AdvectDivFreeTermarg_shapes (sfepy.terms.terms_elastic.LinearPrestressTerm
attribute), 938 attribute), 957
arg_shapes (sfepy.terms.terms_diffusion.ConvectVGradSTermarg_shapes (sfepy.terms.terms_elastic.LinearStrainFiberTerm
attribute), 938 attribute), 958
arg_shapes (sfepy.terms.terms_diffusion.DiffusionCouplingarg_shapes (sfepy.terms.terms_elastic.NonsymElasticTerm
attribute), 939 attribute), 959
arg_shapes (sfepy.terms.terms_diffusion.DiffusionRTerm arg_shapes (sfepy.terms.terms_elastic.SDLinearElasticTerm
attribute), 940 attribute), 959
arg_shapes (sfepy.terms.terms_diffusion.DiffusionTerm arg_shapes (sfepy.terms.terms_electric.ElectricSourceTerm
attribute), 940 attribute), 960
arg_shapes (sfepy.terms.terms_diffusion.DiffusionVelocityTerm
arg_shapes (sfepy.terms.terms_fibres.FibresActiveTLTerm
attribute), 941 attribute), 961
arg_shapes (sfepy.terms.terms_diffusion.LaplaceTerm arg_shapes (sfepy.terms.terms_hyperelastic_base.DeformationGradientTe
attribute), 942 attribute), 962
arg_shapes (sfepy.terms.terms_diffusion.SDDiffusionTerm arg_shapes (sfepy.terms.terms_hyperelastic_base.HyperElasticBase
attribute), 942 attribute), 962
arg_shapes (sfepy.terms.terms_diffusion.SurfaceFluxOperatorTerm
arg_shapes (sfepy.terms.terms_hyperelastic_tl.BulkPressureTLTerm
attribute), 943 attribute), 964
arg_shapes (sfepy.terms.terms_diffusion.SurfaceFluxTerm arg_shapes (sfepy.terms.terms_hyperelastic_tl.DiffusionTLTerm
attribute), 944 attribute), 965
arg_shapes (sfepy.terms.terms_dot.BCNewtonTerm at- arg_shapes (sfepy.terms.terms_hyperelastic_tl.GenYeohTLTerm
tribute), 944 attribute), 966
arg_shapes (sfepy.terms.terms_dot.DotSProductVolumeOperatorWETHTerm
arg_shapes (sfepy.terms.terms_hyperelastic_tl.OgdenTLTerm
attribute), 946 attribute), 968
arg_shapes (sfepy.terms.terms_dot.DotSProductVolumeOperatorWTHTerm
arg_shapes (sfepy.terms.terms_hyperelastic_tl.SurfaceFluxTLTerm

1042 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

attribute), 969 attribute), 989

arg_shapes (sfepy.terms.terms_hyperelastic_tl.SurfaceTractionTLTerm
arg_shapes (sfepy.terms.terms_navier_stokes.GradDivStabilizationTerm
attribute), 969 attribute), 990
arg_shapes (sfepy.terms.terms_hyperelastic_tl.VolumeSurfaceTLTerm
arg_shapes (sfepy.terms.terms_navier_stokes.GradTerm
attribute), 970 attribute), 991
arg_shapes (sfepy.terms.terms_hyperelastic_tl.VolumeTLTerm
arg_shapes (sfepy.terms.terms_navier_stokes.LinearConvect2Term
attribute), 970 attribute), 991
arg_shapes (sfepy.terms.terms_hyperelastic_ul.BulkPressureULTerm
arg_shapes (sfepy.terms.terms_navier_stokes.LinearConvectTerm
attribute), 972 attribute), 992
arg_shapes (sfepy.terms.terms_hyperelastic_ul.CompressibilityULTerm
arg_shapes (sfepy.terms.terms_navier_stokes.PSPGCStabilizationTerm
attribute), 972 attribute), 992
arg_shapes (sfepy.terms.terms_hyperelastic_ul.VolumeULTerm
arg_shapes (sfepy.terms.terms_navier_stokes.StokesTerm
attribute), 974 attribute), 995
arg_shapes (sfepy.terms.terms_membrane.TLMembraneTerm arg_shapes (sfepy.terms.terms_navier_stokes.StokesWaveDivTerm
attribute), 975 attribute), 995
arg_shapes (sfepy.terms.terms_multilinear.ECauchyStressTerm
arg_shapes (sfepy.terms.terms_navier_stokes.StokesWaveTerm
attribute), 976 attribute), 996
arg_shapes (sfepy.terms.terms_multilinear.EConvectTerm arg_shapes (sfepy.terms.terms_navier_stokes.SUPGCStabilizationTerm
attribute), 976 attribute), 993
arg_shapes (sfepy.terms.terms_multilinear.EDiffusionTermarg_shapes (sfepy.terms.terms_navier_stokes.SUPGPStabilizationTerm
attribute), 977 attribute), 994
arg_shapes (sfepy.terms.terms_multilinear.EDivGradTermarg_shapes (sfepy.terms.terms_piezo.PiezoCouplingTerm
attribute), 977 attribute), 997
arg_shapes (sfepy.terms.terms_multilinear.EDivTerm arg_shapes (sfepy.terms.terms_piezo.PiezoStrainTerm
attribute), 978 attribute), 997
arg_shapes (sfepy.terms.terms_multilinear.EDotTerm arg_shapes (sfepy.terms.terms_piezo.PiezoStressTerm
attribute), 978 attribute), 998
arg_shapes (sfepy.terms.terms_multilinear.EGradTerm arg_shapes (sfepy.terms.terms_piezo.SDPiezoCouplingTerm
attribute), 979 attribute), 999
arg_shapes (sfepy.terms.terms_multilinear.EIntegrateOperatorTerm
arg_shapes (sfepy.terms.terms_point.ConcentratedPointLoadTerm
attribute), 979 attribute), 999
arg_shapes (sfepy.terms.terms_multilinear.ELaplaceTerm arg_shapes (sfepy.terms.terms_point.LinearPointSpringTerm
attribute), 980 attribute), 1000
arg_shapes (sfepy.terms.terms_multilinear.ELinearConvectTerm
arg_shapes (sfepy.terms.terms_sensitivity.ESDDiffusionTerm
attribute), 980 attribute), 1000
arg_shapes (sfepy.terms.terms_multilinear.ELinearElasticTerm
arg_shapes (sfepy.terms.terms_sensitivity.ESDDivGradTerm
attribute), 981 attribute), 1001
arg_shapes (sfepy.terms.terms_multilinear.ELinearTractionTerm
arg_shapes (sfepy.terms.terms_sensitivity.ESDDotTerm
attribute), 982 attribute), 1002
arg_shapes (sfepy.terms.terms_multilinear.ENonPenetrationPenaltyTerm
arg_shapes (sfepy.terms.terms_sensitivity.ESDLinearElasticTerm
attribute), 982 attribute), 1003
arg_shapes (sfepy.terms.terms_multilinear.ENonSymElasticTerm
arg_shapes (sfepy.terms.terms_sensitivity.ESDLinearTractionTerm
attribute), 983 attribute), 1003
arg_shapes (sfepy.terms.terms_multilinear.EScalarDotMGradScalarTerm
arg_shapes (sfepy.terms.terms_sensitivity.ESDPiezoCouplingTerm
attribute), 983 attribute), 1004
arg_shapes (sfepy.terms.terms_multilinear.EStokesTerm arg_shapes (sfepy.terms.terms_sensitivity.ESDStokesTerm
attribute), 984 attribute), 1005
arg_shapes (sfepy.terms.terms_navier_stokes.ConvectTermarg_shapes (sfepy.terms.terms_shells.Shell10XTerm at-
attribute), 988 tribute), 1006
arg_shapes (sfepy.terms.terms_navier_stokes.DivGradTerm arg_shapes (sfepy.terms.terms_surface.ContactPlaneTerm
attribute), 988 attribute), 1008
arg_shapes (sfepy.terms.terms_navier_stokes.DivOperatorTerm
arg_shapes (sfepy.terms.terms_surface.ContactSphereTerm
attribute), 989 attribute), 1009
arg_shapes (sfepy.terms.terms_navier_stokes.DivTerm arg_shapes (sfepy.terms.terms_surface.LinearTractionTerm

Index 1043
SfePy Documentation, Release version: 2022.1+git.f9873484

attribute), 1009 arg_types (sfepy.terms.terms_basic.IntegrateTerm at-

arg_shapes (sfepy.terms.terms_surface.SDLinearTractionTerm tribute), 921
attribute), 1010 arg_types (sfepy.terms.terms_basic.SumNodalValuesTerm
arg_shapes (sfepy.terms.terms_surface.SDSufaceIntegrateTerm attribute), 922
attribute), 1011 arg_types (sfepy.terms.terms_basic.SurfaceMomentTerm
arg_shapes (sfepy.terms.terms_surface.SufaceNormalDotTerm attribute), 922
attribute), 1011 arg_types (sfepy.terms.terms_basic.VolumeSurfaceTerm
arg_shapes (sfepy.terms.terms_surface.SurfaceJumpTerm attribute), 923
attribute), 1012 arg_types (sfepy.terms.terms_basic.VolumeTerm
arg_shapes (sfepy.terms.terms_volume.LinearVolumeForceTerm attribute), 923
attribute), 1013 arg_types (sfepy.terms.terms_basic.ZeroTerm at-
arg_shapes_dict (sfepy.terms.terms_dot.BCNewtonTerm tribute), 924
attribute), 944 arg_types (sfepy.terms.terms_biot.BiotETHTerm
arg_shapes_dict (sfepy.terms.terms_dot.DotProductTerm attribute), 925
attribute), 945 arg_types (sfepy.terms.terms_biot.BiotStressTerm at-
arg_types (sfepy.terms.terms.Term attribute), 905 tribute), 925
arg_types (sfepy.terms.terms_adj_navier_stokes.AdjConvect1Term
arg_types (sfepy.terms.terms_biot.BiotTerm attribute),
attribute), 910 927
arg_types (sfepy.terms.terms_adj_navier_stokes.AdjConvect2Term
arg_types (sfepy.terms.terms_biot.BiotTHTerm at-
attribute), 910 tribute), 926
arg_types (sfepy.terms.terms_adj_navier_stokes.AdjDivGradTerm
arg_types (sfepy.terms.terms_constraints.NonPenetrationPenaltyTerm
attribute), 911 attribute), 930
arg_types (sfepy.terms.terms_adj_navier_stokes.NSOFMinGradTerm
arg_types (sfepy.terms.terms_constraints.NonPenetrationTerm
attribute), 911 attribute), 931
arg_types (sfepy.terms.terms_adj_navier_stokes.NSOFSurfMinDPressDiffTerm
arg_types (sfepy.terms.terms_contact.ContactTerm at-
attribute), 912 tribute), 932
arg_types (sfepy.terms.terms_adj_navier_stokes.NSOFSurfMinDPressTerm
arg_types (sfepy.terms.terms_dg.AdvectionDGFluxTerm
attribute), 912 attribute), 934
arg_types (sfepy.terms.terms_adj_navier_stokes.SDConvectTerm
arg_types (sfepy.terms.terms_dg.DiffusionDGFluxTerm
attribute), 913 attribute), 935
arg_types (sfepy.terms.terms_adj_navier_stokes.SDDivGradTerm
arg_types (sfepy.terms.terms_dg.DiffusionInteriorPenaltyTerm
attribute), 914 attribute), 935
arg_types (sfepy.terms.terms_adj_navier_stokes.SDDivTermarg_types (sfepy.terms.terms_dg.NonlinearHyperbolicDGFluxTerm
attribute), 914 attribute), 937
arg_types (sfepy.terms.terms_adj_navier_stokes.SDDotTermarg_types (sfepy.terms.terms_dg.NonlinearScalarDotGradTerm
attribute), 915 attribute), 937
arg_types (sfepy.terms.terms_adj_navier_stokes.SDGradDivStabilizationTerm
arg_types (sfepy.terms.terms_diffusion.AdvectDivFreeTerm
attribute), 915 attribute), 938
arg_types (sfepy.terms.terms_adj_navier_stokes.SDPSPGCStabilizationTerm
arg_types (sfepy.terms.terms_diffusion.ConvectVGradSTerm
attribute), 916 attribute), 938
arg_types (sfepy.terms.terms_adj_navier_stokes.SDPSPGPStabilizationTerm
arg_types (sfepy.terms.terms_diffusion.DiffusionCoupling
attribute), 917 attribute), 939
arg_types (sfepy.terms.terms_adj_navier_stokes.SDSUPGCStabilizationTerm
arg_types (sfepy.terms.terms_diffusion.DiffusionRTerm
attribute), 917 attribute), 940
arg_types (sfepy.terms.terms_adj_navier_stokes.SUPGCAdjStabilizationTerm
arg_types (sfepy.terms.terms_diffusion.DiffusionTerm
attribute), 918 attribute), 940
arg_types (sfepy.terms.terms_adj_navier_stokes.SUPGPAdj1StabilizationTerm
arg_types (sfepy.terms.terms_diffusion.DiffusionVelocityTerm
attribute), 919 attribute), 941
arg_types (sfepy.terms.terms_adj_navier_stokes.SUPGPAdj2StabilizationTerm
arg_types (sfepy.terms.terms_diffusion.LaplaceTerm at-
attribute), 919 tribute), 942
arg_types (sfepy.terms.terms_basic.IntegrateMatTerm arg_types (sfepy.terms.terms_diffusion.SDDiffusionTerm
attribute), 920 attribute), 942
arg_types (sfepy.terms.terms_basic.IntegrateOperatorTermarg_types (sfepy.terms.terms_diffusion.SurfaceFluxOperatorTerm
attribute), 920 attribute), 943

1044 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

arg_types (sfepy.terms.terms_diffusion.SurfaceFluxTerm arg_types (sfepy.terms.terms_hyperelastic_tl.BulkPressureTLTerm

attribute), 944 attribute), 964
arg_types (sfepy.terms.terms_dot.BCNewtonTerm at- arg_types (sfepy.terms.terms_hyperelastic_tl.DiffusionTLTerm
tribute), 944 attribute), 965
arg_types (sfepy.terms.terms_dot.DotProductTerm at- arg_types (sfepy.terms.terms_hyperelastic_tl.SurfaceFluxTLTerm
tribute), 945 attribute), 969
arg_types (sfepy.terms.terms_dot.DotSProductVolumeOperatorWETHTerm
arg_types (sfepy.terms.terms_hyperelastic_tl.SurfaceTractionTLTerm
attribute), 946 attribute), 969
arg_types (sfepy.terms.terms_dot.DotSProductVolumeOperatorWTHTerm
arg_types (sfepy.terms.terms_hyperelastic_tl.VolumeSurfaceTLTerm
attribute), 947 attribute), 970
arg_types (sfepy.terms.terms_dot.ScalarDotGradIScalarTerm arg_types (sfepy.terms.terms_hyperelastic_tl.VolumeTLTerm
attribute), 947 attribute), 971
arg_types (sfepy.terms.terms_dot.ScalarDotMGradScalarTerm arg_types (sfepy.terms.terms_hyperelastic_ul.BulkPressureULTerm
attribute), 948 attribute), 972
arg_types (sfepy.terms.terms_dot.VectorDotGradScalarTerm arg_types (sfepy.terms.terms_hyperelastic_ul.CompressibilityULTerm
attribute), 949 attribute), 972
arg_types (sfepy.terms.terms_dot.VectorDotScalarTerm arg_types (sfepy.terms.terms_hyperelastic_ul.VolumeULTerm
attribute), 950 attribute), 974
arg_types (sfepy.terms.terms_elastic.CauchyStrainTerm arg_types (sfepy.terms.terms_membrane.TLMembraneTerm
attribute), 951 attribute), 975
arg_types (sfepy.terms.terms_elastic.CauchyStressETHTerm arg_types (sfepy.terms.terms_multilinear.ECauchyStressTerm
attribute), 951 attribute), 976
arg_types (sfepy.terms.terms_elastic.CauchyStressTerm arg_types (sfepy.terms.terms_multilinear.EConvectTerm
attribute), 953 attribute), 976
arg_types (sfepy.terms.terms_elastic.CauchyStressTHTermarg_types (sfepy.terms.terms_multilinear.EDiffusionTerm
attribute), 952 attribute), 977
arg_types (sfepy.terms.terms_elastic.ElasticWaveCauchyTermarg_types (sfepy.terms.terms_multilinear.EDivGradTerm
attribute), 954 attribute), 977
arg_types (sfepy.terms.terms_elastic.ElasticWaveTerm arg_types (sfepy.terms.terms_multilinear.EDivTerm at-
attribute), 954 tribute), 978
arg_types (sfepy.terms.terms_elastic.LinearElasticETHTerm arg_types (sfepy.terms.terms_multilinear.EDotTerm at-
attribute), 955 tribute), 979
arg_types (sfepy.terms.terms_elastic.LinearElasticIsotropicTerm
arg_types (sfepy.terms.terms_multilinear.EGradTerm
attribute), 955 attribute), 979
arg_types (sfepy.terms.terms_elastic.LinearElasticTerm arg_types (sfepy.terms.terms_multilinear.EIntegrateOperatorTerm
attribute), 957 attribute), 980
arg_types (sfepy.terms.terms_elastic.LinearElasticTHTermarg_types (sfepy.terms.terms_multilinear.ELaplaceTerm
attribute), 956 attribute), 980
arg_types (sfepy.terms.terms_elastic.LinearPrestressTerm arg_types (sfepy.terms.terms_multilinear.ELinearConvectTerm
attribute), 957 attribute), 981
arg_types (sfepy.terms.terms_elastic.LinearStrainFiberTermarg_types (sfepy.terms.terms_multilinear.ELinearElasticTerm
attribute), 958 attribute), 981
arg_types (sfepy.terms.terms_elastic.NonsymElasticTerm arg_types (sfepy.terms.terms_multilinear.ELinearTractionTerm
attribute), 959 attribute), 982
arg_types (sfepy.terms.terms_elastic.SDLinearElasticTermarg_types (sfepy.terms.terms_multilinear.ENonPenetrationPenaltyTerm
attribute), 959 attribute), 982
arg_types (sfepy.terms.terms_electric.ElectricSourceTerm arg_types (sfepy.terms.terms_multilinear.ENonSymElasticTerm
attribute), 960 attribute), 983
arg_types (sfepy.terms.terms_fibres.FibresActiveTLTerm arg_types (sfepy.terms.terms_multilinear.EScalarDotMGradScalarTerm
attribute), 961 attribute), 983
arg_types (sfepy.terms.terms_hyperelastic_base.DeformationGradientTerm
arg_types (sfepy.terms.terms_multilinear.EStokesTerm
attribute), 962 attribute), 984
arg_types (sfepy.terms.terms_hyperelastic_base.HyperElasticBase
arg_types (sfepy.terms.terms_navier_stokes.ConvectTerm
attribute), 962 attribute), 988

Index 1045
SfePy Documentation, Release version: 2022.1+git.f9873484

arg_types (sfepy.terms.terms_navier_stokes.DivGradTermarg_types (sfepy.terms.terms_surface.ContactSphereTerm

attribute), 988 attribute), 1009
arg_types (sfepy.terms.terms_navier_stokes.DivOperatorTerm
arg_types (sfepy.terms.terms_surface.LinearTractionTerm
attribute), 989 attribute), 1009
arg_types (sfepy.terms.terms_navier_stokes.DivTerm arg_types (sfepy.terms.terms_surface.SDLinearTractionTerm
attribute), 989 attribute), 1010
arg_types (sfepy.terms.terms_navier_stokes.GradDivStabilizationTerm
arg_types (sfepy.terms.terms_surface.SDSufaceIntegrateTerm
attribute), 990 attribute), 1011
arg_types (sfepy.terms.terms_navier_stokes.GradTerm arg_types (sfepy.terms.terms_surface.SufaceNormalDotTerm
attribute), 991 attribute), 1011
arg_types (sfepy.terms.terms_navier_stokes.LinearConvect2Term
arg_types (sfepy.terms.terms_surface.SurfaceJumpTerm
attribute), 991 attribute), 1012
arg_types (sfepy.terms.terms_navier_stokes.LinearConvectTerm
arg_types (sfepy.terms.terms_volume.LinearVolumeForceTerm
attribute), 992 attribute), 1013
arg_types (sfepy.terms.terms_navier_stokes.PSPGCStabilizationTerm
argsort_rows() (in module sfepy.linalg.utils), 827
attribute), 992 as_dict() (sfepy.base.base.Container method), 660
arg_types (sfepy.terms.terms_navier_stokes.StokesTerm as_float_or_complex() (in module sfepy.base.base),
attribute), 995 662
arg_types (sfepy.terms.terms_navier_stokes.StokesWaveDivTerm
assemble1d() (in module sfepy.linalg.utils), 827
attribute), 995 assemble_by_blocks() (in module
arg_types (sfepy.terms.terms_navier_stokes.StokesWaveTerm sfepy.discrete.evaluate), 693
attribute), 996 assemble_contact_residual_and_stiffness() (in
arg_types (sfepy.terms.terms_navier_stokes.SUPGCStabilizationTerm module sfepy.mechanics.extmods.ccontres), 841
attribute), 993 assemble_matrix() (in module
arg_types (sfepy.terms.terms_navier_stokes.SUPGPStabilizationTerm sfepy.discrete.common.extmods.assemble),
attribute), 994 729
arg_types (sfepy.terms.terms_piezo.PiezoCouplingTerm assemble_matrix_complex() (in module
attribute), 997 sfepy.discrete.common.extmods.assemble),
arg_types (sfepy.terms.terms_piezo.PiezoStressTerm at- 729
tribute), 998 assemble_mtx_to_petsc() (in module
arg_types (sfepy.terms.terms_piezo.SDPiezoCouplingTerm sfepy.parallel.parallel), 854
attribute), 999 assemble_rhs_to_petsc() (in module
arg_types (sfepy.terms.terms_point.ConcentratedPointLoadTerm sfepy.parallel.parallel), 854
attribute), 999 assemble_to() (sfepy.terms.terms.Term method), 905
arg_types (sfepy.terms.terms_point.LinearPointSpringTermassemble_vector() (in module
attribute), 1000 sfepy.discrete.common.extmods.assemble),
arg_types (sfepy.terms.terms_sensitivity.ESDDiffusionTerm 729
attribute), 1001 assemble_vector_complex() (in module
arg_types (sfepy.terms.terms_sensitivity.ESDDivGradTerm sfepy.discrete.common.extmods.assemble),
attribute), 1001 729
arg_types (sfepy.terms.terms_sensitivity.ESDDotTerm assert_() (in module sfepy.base.base), 662
attribute), 1002 assert_equal() (in module sfepy.base.testing), 685
arg_types (sfepy.terms.terms_sensitivity.ESDLinearElasticTerm
assign_args() (sfepy.terms.terms.Term method), 905
attribute), 1003 assign_args() (sfepy.terms.terms.Terms method), 908
arg_types (sfepy.terms.terms_sensitivity.ESDLinearTractionTerm
assign_standard_hooks() (in module
attribute), 1003 sfepy.applications.pde_solver_app), 659
arg_types (sfepy.terms.terms_sensitivity.ESDPiezoCouplingTerm
AutoDirect (class in sfepy.solvers.auto_fallback), 868
attribute), 1004 AutoFallbackSolver (class in
arg_types (sfepy.terms.terms_sensitivity.ESDStokesTerm sfepy.solvers.auto_fallback), 868
attribute), 1005 AutoIterative (class in sfepy.solvers.auto_fallback),
arg_types (sfepy.terms.terms_shells.Shell10XTerm at- 868
tribute), 1006 aux (sfepy.solvers.ls_mumps.mumps_struc_c_x at-
arg_types (sfepy.terms.terms_surface.ContactPlaneTerm tribute), 889
attribute), 1008 average_qp_to_vertices()

1046 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

(sfepy.discrete.fem.fields_base.SurfaceField build_helpers
method), 752 module, 645
average_qp_to_vertices() build_interpol_scheme()
(sfepy.discrete.fem.fields_base.VolumeField (sfepy.discrete.dg.poly_spaces.LegendreTensorProductPolySpace
method), 752 method), 788
average_to_vertices() build_mlab_pipeline()
(sfepy.discrete.fem.fields_nodal.H1DiscontinuousField (sfepy.postprocess.viewer.Viewer method),
method), 754 865
average_vertex_var_in_cells() (in module build_op_pi() (in module sfepy.homogenization.utils),
sfepy.postprocess.time_history), 862 821
build_orientation_map() (in module
B sfepy.discrete.fem.facets), 746
BandGaps (class in sfepy.homogenization.coefs_phononic), build_solver_kwargs() (sfepy.solvers.solvers.Solver
810 method), 897
barycentric_coors() (in module bulk_from_lame() (in module
sfepy.linalg.geometry), 823 sfepy.mechanics.matcoefs), 832
base1d (sfepy.discrete.fem.extmods.bases.CLagrangeContextbulk_from_youngpoisson() (in module
attribute), 745 sfepy.mechanics.matcoefs), 832
basis_function_dg() (sfepy.mesh.bspline.BSpline BulkActiveTLTerm (class in
static method), 842 sfepy.terms.terms_hyperelastic_tl), 963
basis_function_dg0() (sfepy.mesh.bspline.BSpline BulkPenaltyTLTerm (class in
static method), 842 sfepy.terms.terms_hyperelastic_tl), 963
BatheTS (class in sfepy.solvers.ts_solvers), 900 BulkPenaltyULTerm (class in
BCNewtonTerm (class in sfepy.terms.terms_dot), 944 sfepy.terms.terms_hyperelastic_ul), 971
BernsteinSimplexPolySpace (class in BulkPressureTLTerm (class in
sfepy.discrete.fem.poly_spaces), 769 sfepy.terms.terms_hyperelastic_tl), 964
BernsteinTensorProductPolySpace (class in BulkPressureULTerm (class in
sfepy.discrete.fem.poly_spaces), 769 sfepy.terms.terms_hyperelastic_ul), 971
bf (sfepy.discrete.common.extmods.mappings.CMapping
attribute), 733 C
bf (sfepy.discrete.iga.extmods.igac.CNURBSContext at- cache (sfepy.discrete.probes.Probe attribute), 702
tribute), 793 cache_name (sfepy.terms.terms_hyperelastic_tl.HyperElasticSurfaceTLFam
bfg (sfepy.discrete.common.extmods.mappings.CMapping attribute), 966
attribute), 733 cache_name (sfepy.terms.terms_hyperelastic_tl.HyperElasticTLFamilyData
bfg (sfepy.discrete.iga.extmods.igac.CNURBSContext at- attribute), 966
tribute), 793 cache_name (sfepy.terms.terms_hyperelastic_ul.HyperElasticULFamilyDat
BiotETHTerm (class in sfepy.terms.terms_biot), 924 attribute), 973
BiotStressTerm (class in sfepy.terms.terms_biot), 925 Cached (class in sfepy.base.ioutils), 672
BiotTerm (class in sfepy.terms.terms_biot), 926 calculate() (sfepy.homogenization.engine.HomogenizationWorker
BiotTHTerm (class in sfepy.terms.terms_biot), 925 static method), 815
block_solve() (sfepy.discrete.problem.Problem calculate_req() (sfepy.homogenization.engine.HomogenizationWorker
method), 705 static method), 815
blockgen calculate_req_multi()
module, 648 (sfepy.homogenization.engine.HomogenizationWorkerMulti
boundary() (in module sfepy.linalg.sympy_operators), static method), 816
827 call() (sfepy.applications.evp_solver_app.EVPSolverApp
BSpline (class in sfepy.mesh.bspline), 842 method), 658
BSplineSurf (class in sfepy.mesh.bspline), 844 call() (sfepy.applications.pde_solver_app.PDESolverApp
bufBN (sfepy.discrete.iga.extmods.igac.CNURBSContext method), 659
attribute), 793 call() (sfepy.homogenization.band_gaps_app.AcousticBandGapsApp
build() (sfepy.terms.terms_multilinear.ExpressionBuilder method), 804
method), 986 call() (sfepy.homogenization.engine.HomogenizationEngine
build_expression() (sfepy.terms.terms_multilinear.ETermBase method), 815
method), 984

Index 1047
SfePy Documentation, Release version: 2022.1+git.f9873484

call() (sfepy.homogenization.homogen_app.HomogenizationAppcell_types (sfepy.discrete.common.extmods.cmesh.CMesh

method), 817 attribute), 730
call_basic() (sfepy.applications.application.Application cell_types (sfepy.discrete.fem.meshio.MeshioLibIO at-
method), 658 tribute), 767
call_empty() (sfepy.postprocess.viewer.Viewer cells (sfepy.discrete.common.region.Region property),
method), 865 741
call_function() (sfepy.terms.terms.Term method), cg_eigs() (in module sfepy.linalg.eigen), 822
905 check_args() (sfepy.terms.terms.Term method), 905
call_function() (sfepy.terms.terms_contact.ContactTermcheck_conditions() (in module sfepy.base.testing),
method), 932 685
call_function() (sfepy.terms.terms_dg.DGTerm check_finiteness() (in module sfepy.terms.utils),
method), 934 1013
call_get_fargs() (sfepy.terms.terms.Term method), check_format_suffix() (in module
905 sfepy.discrete.fem.meshio), 768
call_in_rank_order() (in module check_fx() (in module sfepy.linalg.check_derivatives),
sfepy.parallel.parallel), 854 822
call_mlab() (sfepy.postprocess.viewer.Viewer method), check_gradient() (in module sfepy.solvers.optimize),
865 894
call_msg (sfepy.discrete.fem.meshio.MeshIO attribute), check_names() (in module sfepy.base.base), 662
766 check_output() (in module test_install), 647
call_parametrized() check_shapes() (sfepy.terms.terms.Term method), 905
(sfepy.applications.application.Application check_tangent_matrix() (in module
method), 658 sfepy.solvers.nls), 892
can_backend (sfepy.terms.terms_multilinear.ETermBase check_vec() (in module sfepy.tests.test_conditions),
attribute), 985 1019
canonize_dof_names() check_vec_size() (sfepy.discrete.variables.Variables
(sfepy.discrete.conditions.Condition method), method), 723
686 check_vfvx() (in module
canonize_dof_names() sfepy.linalg.check_derivatives), 822
(sfepy.discrete.conditions.Conditions method), ChristoffelAcousticTensor (class in
686 sfepy.homogenization.coefs_phononic), 811
canonize_dof_names() chunk_micro_tasks()
(sfepy.discrete.conditions.LinearCombinationBC (sfepy.homogenization.engine.HomogenizationWorkerMulti
method), 687 static method), 816
canonize_dof_names() CircleProbe (class in sfepy.discrete.probes), 701
(sfepy.discrete.conditions.PeriodicBC method), CLagrangeContext (class in
688 sfepy.discrete.fem.extmods.bases), 745
CauchyStrainSTerm (class in classify_args() (sfepy.terms.terms.Term method),
sfepy.terms.terms_compat), 927 905
CauchyStrainTerm (class in sfepy.terms.terms_elastic), Clean (class in build_helpers), 645
950 clean() (sfepy.base.multiproc_mpi.RemoteQueueMaster
CauchyStressETHTerm (class in method), 681
sfepy.terms.terms_elastic), 951 clear_cache() (sfepy.terms.terms_multilinear.ETermBase
CauchyStressTerm (class in sfepy.terms.terms_elastic), method), 985
952 clear_equations() (sfepy.discrete.problem.Problem
CauchyStressTHTerm (class in method), 705
sfepy.terms.terms_elastic), 952 clear_evaluate_cache()
CBasisContext (class in (sfepy.discrete.variables.FieldVariable
sfepy.discrete.common.extmods.crefcoors), method), 718
732 clear_facet_neighbour_idx_cache()
CConnectivity (class in (sfepy.discrete.dg.fields.DGField method),
sfepy.discrete.common.extmods.cmesh), 730 779
cell_groups (sfepy.discrete.common.extmods.cmesh.CMesh clear_facet_qp_base()
attribute), 730 (sfepy.discrete.dg.fields.DGField method),

1048 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

780 806
clear_facet_vols_cache() CoefNonSymNonSym (class in
(sfepy.discrete.dg.fields.DGField method), sfepy.homogenization.coefs_base), 806
780 CoefOne (class in sfepy.homogenization.coefs_base), 807
clear_mappings() (sfepy.discrete.common.fields.Field CoefRegion (class in sfepy.homogenization.coefs_perfusion),
method), 734 809
clear_normals_cache() CoefSum (class in sfepy.homogenization.coefs_base), 807
(sfepy.discrete.dg.fields.DGField method), CoefSym (class in sfepy.homogenization.coefs_base), 807
780 CoefSymSym (class in sfepy.homogenization.coefs_base),
clear_qp_base() (sfepy.discrete.fem.fields_base.FEField 807
method), 748 CoefVolume (class in sfepy.homogenization.engine), 815
clear_surface_groups() collect_conn_info()
(sfepy.discrete.fem.domain.FEDomain (sfepy.discrete.equations.Equation method),
method), 744 688
close() (sfepy.base.multiproc_mpi.MPIFileHandler collect_conn_info()
method), 680 (sfepy.discrete.equations.Equations method),
ClosingHandler (class in sfepy.postprocess.viewer), 689
864 collect_materials()
CMapping (class in sfepy.discrete.common.extmods.mappings), (sfepy.discrete.equations.Equation method),
733 688
cmem_statistics() (in module collect_materials()
sfepy.discrete.common.extmods.cmesh), 732 (sfepy.discrete.equations.Equations method),
CMesh (class in sfepy.discrete.common.extmods.cmesh), 689
730 collect_modifiers() (in module
cntl (sfepy.solvers.ls_mumps.mumps_struc_c_4 at- sfepy.terms.terms_multilinear), 987
tribute), 876 collect_term() (in module
cntl (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 sfepy.discrete.parse_equations), 700
attribute), 879 collect_variables()
cntl (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 (sfepy.discrete.equations.Equation method),
attribute), 882 688
cntl (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 collect_variables()
attribute), 886 (sfepy.discrete.equations.Equations method),
CNURBSContext (class in 689
sfepy.discrete.iga.extmods.igac), 793 colsca (sfepy.solvers.ls_mumps.mumps_struc_c_4
coef_arrays_to_dicts() (in module attribute), 876
sfepy.homogenization.coefficients), 805 colsca (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at-
CoefDim (class in sfepy.homogenization.coefs_base), 806 tribute), 879
CoefDimDim (class in sfepy.homogenization.coefs_base), colsca (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at-
806 tribute), 882
CoefDimSym (class in sfepy.homogenization.coefs_base), colsca (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at-
806 tribute), 886
CoefDummy (class in sfepy.homogenization.coefs_base), colsca_from_mumps (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
806 attribute), 879
CoefEval (class in sfepy.homogenization.coefs_base), colsca_from_mumps (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
806 attribute), 882
CoefExprPar (class in colsca_from_mumps (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
sfepy.homogenization.coefs_base), 806 attribute), 886
Coefficients (class in combine() (in module sfepy.linalg.utils), 827
sfepy.homogenization.coefficients), 805 combine_bezier_extraction() (in module
CoefMN (class in sfepy.homogenization.coefs_base), 806 sfepy.discrete.iga.iga), 796
CoefN (class in sfepy.homogenization.coefs_base), 806 combine_scalar_grad() (in module
CoefNone (class in sfepy.homogenization.coefs_base), sfepy.homogenization.recovery), 818
806 comm_fortran (sfepy.solvers.ls_mumps.mumps_struc_c_4
CoefNonSym (class in sfepy.homogenization.coefs_base), attribute), 876

Index 1049
SfePy Documentation, Release version: 2022.1+git.f9873484

comm_fortran (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 sfepy.discrete.fem.utils), 774

attribute), 879 compute_p_corr_steady() (in module
comm_fortran (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 sfepy.homogenization.recovery), 818
attribute), 882 compute_p_corr_time() (in module
comm_fortran (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 sfepy.homogenization.recovery), 818
attribute), 886 compute_p_from_macro() (in module
comm_fortran (sfepy.solvers.ls_mumps.mumps_struc_c_x sfepy.homogenization.recovery), 819
attribute), 889 compute_stress() (sfepy.terms.terms_hyperelastic_base.HyperElasticBas
compare_mesh() (in module sfepy.tests.test_domain), method), 962
1021 compute_stress_strain_u() (in module
compare_scalars() (in module sfepy.homogenization.recovery), 819
sfepy.tests.test_homogenization_perfusion), compute_tan_mod() (sfepy.terms.terms_hyperelastic_base.HyperElasticBa
1023 method), 962
compare_vectors() (in module sfepy.base.testing), 685 compute_u_corr_steady() (in module
compile_flags() (sfepy.config.Config method), 657 sfepy.homogenization.recovery), 819
compose_sparse() (in module sfepy.linalg.sparse), 825 compute_u_corr_time() (in module
ComposedLimiter (class in sfepy.discrete.dg.limiters), sfepy.homogenization.recovery), 819
789 compute_u_from_macro() (in module
CompressibilityULTerm (class in sfepy.homogenization.recovery), 819
sfepy.terms.terms_hyperelastic_ul), 972 ComsolMeshIO (class in sfepy.discrete.fem.meshio), 762
compute_bezier_control() (in module ConcentratedPointLoadTerm (class in
sfepy.discrete.iga.iga), 797 sfepy.terms.terms_point), 999
compute_bezier_extraction() (in module Condition (class in sfepy.discrete.conditions), 686
sfepy.discrete.iga.iga), 797 Conditions (class in sfepy.discrete.conditions), 686
compute_bezier_extraction_1d() (in module Config (class in sfepy.config), 657
sfepy.discrete.iga.iga), 797 configure_output() (in module sfepy.base.base), 662
compute_cat_dim_dim() (in module ConnInfo (class in sfepy.terms.terms), 905
sfepy.homogenization.coefs_phononic), 812 conns (sfepy.discrete.common.extmods.cmesh.CMesh at-
compute_cat_dim_sym() (in module tribute), 730
sfepy.homogenization.coefs_phononic), 813 ConstantFunction (class in sfepy.discrete.functions),
compute_cat_sym_sym() (in module 696
sfepy.homogenization.coefs_phononic), 813 ConstantFunctionByRegion (class in
compute_correctors() sfepy.discrete.functions), 696
(sfepy.homogenization.coefs_base.TCorrectorsViaPressureEVP
ContactInfo (class in sfepy.terms.terms_contact), 932
method), 809 ContactPlane (class in
compute_data() (sfepy.terms.terms_hyperelastic_tl.BulkPressureTLTerm
sfepy.mechanics.contact_bodies), 830
method), 964 ContactPlaneTerm (class in
compute_data() (sfepy.terms.terms_hyperelastic_ul.BulkPressureULTerm
sfepy.terms.terms_surface), 1007
method), 972 ContactSphere (class in
compute_eigenmomenta() (in module sfepy.mechanics.contact_bodies), 830
sfepy.homogenization.coefs_phononic), 813 ContactSphereTerm (class in
compute_fibre_strain() (in module sfepy.terms.terms_surface), 1008
sfepy.terms.terms_fibres), 961 ContactTerm (class in sfepy.terms.terms_contact), 932
compute_jacobian() (sfepy.solvers.semismooth_newton.SemismoothNewton
Container (class in sfepy.base.base), 660
method), 896 contains() (sfepy.discrete.common.region.Region
compute_mac_stress_part() (in module method), 741
sfepy.homogenization.recovery), 818 conv_test() (in module sfepy.solvers.nls), 892
compute_mean_decay() (in module conv_test() (in module sfepy.solvers.optimize), 894
sfepy.homogenization.convolutions), 814 ConvectTerm (class in sfepy.terms.terms_navier_stokes),
compute_micro_u() (in module 987
sfepy.homogenization.recovery), 818 ConvectVGradSTerm (class in
compute_nodal_edge_dirs() (in module sfepy.terms.terms_diffusion), 938
sfepy.discrete.fem.utils), 774 convert_complex_output() (in module
compute_nodal_normals() (in module sfepy.discrete.fem.meshio), 768

1050 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

convert_mesh create_adof_conns() (in module

module, 648 sfepy.discrete.variables), 726
convert_to_csr() (in module create_arg_parser() (in module sfepy.terms.terms),
sfepy.tests.test_semismooth_newton), 1029 909
ConvolutionKernel (class in create_basis_context()
sfepy.homogenization.convolutions), 814 (sfepy.discrete.fem.fields_hierarchic.H1HierarchicVolumeField
convolve_field_scalar() (in module method), 753
sfepy.homogenization.recovery), 819 create_basis_context()
convolve_field_sym_tensor() (in module (sfepy.discrete.fem.fields_nodal.H1NodalMixin
sfepy.homogenization.recovery), 819 method), 754
coo_is_symmetric() (in module create_basis_context()
sfepy.solvers.ls_mumps), 876 (sfepy.discrete.fem.fields_nodal.H1SNodalVolumeField
coor_to_sym() (in module sfepy.homogenization.utils), method), 755
821 create_basis_context()
coors (sfepy.discrete.common.extmods.cmesh.CMesh at- (sfepy.discrete.fem.fields_positive.H1BernsteinVolumeField
tribute), 730 method), 755
coors (sfepy.discrete.fem.mesh.Mesh property), 760 create_basis_context()
copy() (sfepy.base.base.Struct method), 661 (sfepy.discrete.iga.fields.IGField method),
copy() (sfepy.discrete.common.region.Region method), 795
741 create_bnf() (in module sfepy.base.parse_conf ), 683
copy() (sfepy.discrete.fem.mesh.Mesh method), 760 create_bnf() (in module
copy() (sfepy.discrete.problem.Problem method), 705 sfepy.discrete.parse_equations), 700
CorrDim (class in sfepy.homogenization.coefs_base), 807 create_bnf() (in module sfepy.discrete.parse_regions),
CorrDimDim (class in sfepy.homogenization.coefs_base), 700
807 create_boundary_qp() (in module
CorrEqPar (class in sfepy.homogenization.coefs_base), sfepy.discrete.iga.iga), 797
807 create_bqp() (sfepy.discrete.fem.fields_base.FEField
CorrEval (class in sfepy.homogenization.coefs_base), method), 748
807 create_conn_graph() (sfepy.discrete.fem.mesh.Mesh
CorrMiniApp (class in method), 760
sfepy.homogenization.coefs_base), 807 create_connectivity() (in module
CorrN (class in sfepy.homogenization.coefs_base), 807 sfepy.discrete.iga.iga), 797
CorrNN (class in sfepy.homogenization.coefs_base), 808 create_connectivity_1d() (in module
CorrOne (class in sfepy.homogenization.coefs_base), 808 sfepy.discrete.iga.iga), 798
CorrRegion (class in sfepy.homogenization.coefs_perfusion),
create_context() (sfepy.discrete.fem.poly_spaces.LagrangePolySpace
809 method), 770
CorrSetBCS (class in sfepy.homogenization.coefs_base), create_context() (sfepy.discrete.fem.poly_spaces.LagrangeSimplexBPoly
808 method), 770
CorrSolution (class in create_context() (sfepy.discrete.fem.poly_spaces.SerendipityTensorProd
sfepy.homogenization.coefs_base), 808 method), 773
count (sfepy.base.log.Log attribute), 677 create_dataset() (sfepy.postprocess.sources.GenericFileSource
cprint() (sfepy.discrete.common.extmods.cmesh.CConnectivity method), 861
method), 730 create_drl_transform() (in module
cprint() (sfepy.discrete.common.extmods.cmesh.CMesh sfepy.mechanics.shell10x), 835
method), 730 create_elastic_tensor() (in module
cprint() (sfepy.discrete.common.extmods.mappings.CMapping sfepy.mechanics.shell10x), 835
method), 733 create_eps() (sfepy.solvers.eigen.SLEPcEigenvalueSolver
cprint() (sfepy.discrete.fem.extmods.bases.CLagrangeContext method), 869
method), 745 create_eval_mesh() (sfepy.discrete.common.fields.Field
cprint() (sfepy.discrete.iga.extmods.igac.CNURBSContext method), 734
method), 793 create_eval_mesh() (sfepy.discrete.iga.fields.IGField
cpu_count() (in module sfepy.base.multiproc_mpi), 681 method), 795
create_adof_conn() (in module create_evaluable() (in module
sfepy.discrete.variables), 726 sfepy.discrete.evaluate), 693

Index 1051
SfePy Documentation, Release version: 2022.1+git.f9873484

create_evaluable() (sfepy.discrete.problem.Problem method), 904

method), 705 create_nlst1() (sfepy.solvers.ts_solvers.BatheTS
create_expression_output() (in module method), 901
sfepy.discrete.fem.fields_base), 752 create_nlst2() (sfepy.solvers.ts_solvers.BatheTS
create_file_source() (in module method), 901
sfepy.postprocess.sources), 862 create_omega() (in module sfepy.terms.terms_fibres),
create_from_igakit() (in module 961
sfepy.discrete.iga.domain_generators), 792 create_output() (in module
create_gather_scatter() (in module sfepy.discrete.fem.linearizer), 759
sfepy.parallel.parallel), 854 create_output() (sfepy.discrete.dg.fields.DGField
create_gather_to_zero() (in module method), 780
sfepy.parallel.parallel), 854 create_output() (sfepy.discrete.fem.fields_base.FEField
create_geometry_elements() (in module method), 749
sfepy.discrete.fem.geometry_element), 756 create_output() (sfepy.discrete.iga.fields.IGField
create_ksp() (sfepy.solvers.ls.PETScKrylovSolver method), 795
method), 872 create_output() (sfepy.discrete.structural.fields.Shell10XField
create_linear_fe_mesh() (in module method), 803
sfepy.discrete.iga.utils), 802 create_output() (sfepy.discrete.variables.FieldVariable
create_local_bases() (in module method), 718
sfepy.mechanics.shell10x), 835 create_output() (sfepy.discrete.variables.Variables
create_local_petsc_vector() (in module method), 723
sfepy.parallel.parallel), 854 create_parser() (in module gen_term_table), 654
create_mapping() (in module create_petsc_matrix() (in module
sfepy.mechanics.membranes), 833 sfepy.parallel.parallel), 854
create_mapping() (sfepy.discrete.dg.fields.DGField create_petsc_matrix()
method), 780 (sfepy.solvers.eigen.SLEPcEigenvalueSolver
create_mapping() (sfepy.discrete.fem.fields_base.FEField method), 869
method), 748 create_petsc_matrix()
create_mapping() (sfepy.discrete.iga.fields.IGField (sfepy.solvers.ls.PETScKrylovSolver method),
method), 795 872
create_mapping() (sfepy.discrete.structural.fields.Shell10XField
create_petsc_system() (in module
method), 803 sfepy.parallel.parallel), 854
create_mass_matrix() (in module create_pis() (in module sfepy.homogenization.utils),
sfepy.discrete.projections), 715 821
create_materials() (sfepy.discrete.problem.Problem create_prealloc_data() (in module
method), 706 sfepy.parallel.parallel), 854
create_matrix_graph() create_problem() (in module extractor), 641
(sfepy.discrete.equations.Equations method), create_reduced_vec()
689 (sfepy.discrete.equations.Equations method),
create_mesh() (sfepy.discrete.fem.fields_base.FEField 689
method), 749 create_reduced_vec()
create_mesh() (sfepy.discrete.iga.fields.IGField (sfepy.discrete.variables.Variables method),
method), 795 723
create_mesh_and_output() (in module create_region() (sfepy.discrete.common.domain.Domain
sfepy.discrete.iga.utils), 803 method), 728
create_mesh_graph() (in module create_regions() (sfepy.discrete.common.domain.Domain
sfepy.discrete.common.extmods.cmesh), 732 method), 728
create_new() (sfepy.discrete.common.extmods.cmesh.CMesh create_rotation_ops() (in module
method), 730 sfepy.mechanics.shell10x), 836
create_nlst() (sfepy.solvers.ts_solvers.GeneralizedAlphaTS create_scalar() (in module eval_ns_forms), 650
method), 902 create_scalar_base() (in module eval_ns_forms),
create_nlst() (sfepy.solvers.ts_solvers.NewmarkTS 650
method), 902 create_scalar_base_grad() (in module
create_nlst() (sfepy.solvers.ts_solvers.VelocityVerletTS eval_ns_forms), 650

1052 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

create_scalar_pis() (in module cut_freq_range() (in module

sfepy.homogenization.utils), 821 sfepy.homogenization.coefs_phononic), 813
create_scalar_var_data() (in module cvt_array_index() (in module
eval_ns_forms), 650 sfepy.base.parse_conf ), 683
create_source() (sfepy.postprocess.sources.GenericFileSource
cvt_cmplx() (in module sfepy.base.parse_conf ), 683
method), 861 cvt_int() (in module sfepy.base.parse_conf ), 683
create_source() (sfepy.postprocess.sources.VTKFileSource cvt_none() (in module sfepy.base.parse_conf ), 683
method), 861 cvt_real() (in module sfepy.base.parse_conf ), 683
create_source() (sfepy.postprocess.sources.VTKSequenceFileSource
cw2us() (in module edit_identifiers), 649
method), 862 cycle() (in module sfepy.linalg.utils), 828
create_spb() (sfepy.mesh.splinebox.SplineBox static cylindergen
method), 852 module, 648
create_spb() (sfepy.mesh.splinebox.SplineRegion2D
static method), 853 D
create_state() (sfepy.discrete.problem.Problem d_biot_div() (in module sfepy.terms.extmods.terms),
method), 707 1013
create_strain_matrix() (in module d_diffusion() (in module sfepy.terms.extmods.terms),
sfepy.mechanics.shell10x), 836 1013
create_strain_transform() (in module d_div_grad() (sfepy.terms.terms_navier_stokes.DivGradTerm
sfepy.mechanics.shell10x), 836 method), 988
create_subequations() d_dot() (sfepy.terms.terms_dot.DotProductTerm static
(sfepy.discrete.equations.Equations method), method), 945
689 d_dot() (sfepy.terms.terms_dot.VectorDotScalarTerm
create_subproblem() static method), 950
(sfepy.discrete.problem.Problem method), d_eval() (sfepy.terms.terms_navier_stokes.StokesTerm
707 static method), 995
create_surface_facet() d_fun() (sfepy.terms.terms_diffusion.DiffusionCoupling
(sfepy.discrete.fem.geometry_element.GeometryElement static method), 939
method), 755 d_fun() (sfepy.terms.terms_surface.LinearTractionTerm
create_surface_group() static method), 1009
(sfepy.discrete.fem.domain.FEDomain d_fun() (sfepy.terms.terms_surface.SDLinearTractionTerm
method), 744 static method), 1010
create_task_dof_maps() (in module d_fun() (sfepy.terms.terms_surface.SufaceNormalDotTerm
sfepy.parallel.parallel), 854 static method), 1011
create_transformation_matrix() (in module d_laplace() (in module sfepy.terms.extmods.terms),
sfepy.mechanics.membranes), 833 1013
create_transformation_matrix() (in module d_lin_elastic() (in module
sfepy.mechanics.shell10x), 836 sfepy.terms.extmods.terms), 1014
create_ts_coef() (in module d_lin_prestress() (sfepy.terms.terms_elastic.LinearPrestressTerm
sfepy.homogenization.coefs_base), 809 method), 957
create_u_operator() (in module eval_ns_forms), 650 d_of_nsMinGrad() (in module
create_variables() (sfepy.discrete.problem.Problem sfepy.terms.extmods.terms), 1014
method), 707 d_of_nsSurfMinDPress() (in module
create_vec() (sfepy.discrete.equations.Equations sfepy.terms.extmods.terms), 1014
method), 690 d_piezo_coupling() (in module
create_vec() (sfepy.discrete.variables.Variables sfepy.terms.extmods.terms), 1014
method), 723 d_sd_convect() (in module sfepy.terms.extmods.terms),
create_vector() (in module eval_ns_forms), 650 1014
create_vector_base() (in module eval_ns_forms), d_sd_diffusion() (in module
650 sfepy.terms.extmods.terms), 1014
create_vector_base_grad() (in module d_sd_div() (in module sfepy.terms.extmods.terms),
eval_ns_forms), 650 1014
create_vector_var_data() (in module d_sd_div_grad() (in module
eval_ns_forms), 650 sfepy.terms.extmods.terms), 1014

Index 1053
SfePy Documentation, Release version: 2022.1+git.f9873484

d_sd_lin_elastic() (in module dechunk_reqs_coefs()

sfepy.terms.extmods.terms), 1014 (sfepy.homogenization.engine.HomogenizationWorkerMulti
d_sd_st_grad_div() (in module static method), 817
sfepy.terms.extmods.terms), 1014 default_space_variables() (in module
d_sd_st_pspg_c() (in module sfepy.linalg.sympy_operators), 827
sfepy.terms.extmods.terms), 1014 deficiency (sfepy.solvers.ls_mumps.mumps_struc_c_4
d_sd_st_pspg_p() (in module attribute), 876
sfepy.terms.extmods.terms), 1014 deficiency (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
d_sd_st_supg_c() (in module attribute), 879
sfepy.terms.extmods.terms), 1014 deficiency (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
d_sd_volume_dot() (in module attribute), 882
sfepy.terms.extmods.terms), 1014 deficiency (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
d_surface_flux() (in module attribute), 886
sfepy.terms.extmods.terms), 1014 define_box_regions() (in module
d_tl_surface_flux() (in module sfepy.homogenization.utils), 821
sfepy.terms.extmods.terms), 1014 define_control_points()
d_tl_volume_surface() (in module (sfepy.mesh.splinebox.SplineRegion2D static
sfepy.terms.extmods.terms), 1014 method), 853
d_volume_surface() (in module define_matrices() (in module
sfepy.terms.extmods.terms), 1014 sfepy.tests.test_semismooth_newton), 1029
data() (in module sfepy.tests.test_assembling), 1018 define_volume_coef()
data() (in module sfepy.tests.test_conditions), 1019 (sfepy.homogenization.engine.HomogenizationEngine
data() (in module sfepy.tests.test_eigenvalue_solvers), static method), 815
1021 DeformationGradientTerm (class in
data() (in module sfepy.tests.test_high_level), 1022 sfepy.terms.terms_hyperelastic_base), 961
data() (in module sfepy.tests.test_laplace_unit_disk), delete_zero_faces()
1023 (sfepy.discrete.common.region.Region method),
data() (in module sfepy.tests.test_laplace_unit_square), 741
1023 DensityVolumeInfo (class in
data() (in module sfepy.tests.test_projections), 1028 sfepy.homogenization.coefs_phononic), 811
data() (in module sfepy.tests.test_regions), 1029 describe() (sfepy.discrete.common.extmods.mappings.CMapping
data() (in module sfepy.tests.test_term_call_modes), method), 733
1030 describe_deformation() (in module
data_names (sfepy.terms.terms_hyperelastic_tl.HyperElasticSurfaceTLFamilyData
sfepy.mechanics.membranes), 834
attribute), 966 describe_gaps() (in module
data_names (sfepy.terms.terms_hyperelastic_tl.HyperElasticTLFamilyData
sfepy.homogenization.coefs_phononic), 813
attribute), 966 describe_geometry() (in module
data_names (sfepy.terms.terms_hyperelastic_ul.HyperElasticULFamilyData
sfepy.mechanics.membranes), 834
attribute), 973 describe_nodes() (sfepy.discrete.fem.poly_spaces.FEPolySpace
data_shapes (sfepy.terms.terms_hyperelastic_base.HyperElasticFamilyData
method), 769
attribute), 963 description (build_helpers.DoxygenDocs attribute),
DataMarker (class in sfepy.base.ioutils), 672 646
DataSoftLink (class in sfepy.base.ioutils), 672 description (build_helpers.SphinxHTMLDocs at-
de_cauchy_strain() (in module tribute), 646
sfepy.terms.extmods.terms), 1014 description (build_helpers.SphinxPDFDocs attribute),
de_cauchy_stress() (in module 646
sfepy.terms.extmods.terms), 1014 destroy_pool() (in module
de_he_rtm() (in module sfepy.terms.extmods.terms), sfepy.homogenization.recovery), 820
1014 det (sfepy.discrete.common.extmods.mappings.CMapping
debug() (in module sfepy.base.base), 659, 662 attribute), 733
debug_flags() (sfepy.config.Config method), 657 detect_band_gaps() (in module
debug_on_error() (in module sfepy.base.base), 662 sfepy.homogenization.coefs_phononic), 813
dec() (in module sfepy.base.ioutils), 674 dets_fast() (in module sfepy.linalg.utils), 828
dec() (in module sfepy.solvers.ls_mumps), 876 dg_plot_1D

1054 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

module, 649 dkeep (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at-

DGEssentialBC (class in sfepy.discrete.conditions), 686 tribute), 882
DGField (class in sfepy.discrete.dg.fields), 779 dkeep (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at-
DGFieldVariable (class in sfepy.discrete.variables), tribute), 886
717 do_interpolation() (in module
DGLimiter (class in sfepy.discrete.dg.limiters), 789 sfepy.tests.test_mesh_interp), 1026
DGMultiStageTSS (class in sfepy.solvers.ts_dg_solvers), DofInfo (class in sfepy.discrete.common.dof_info), 726
790 Domain (class in sfepy.discrete.common.domain), 728
DGPeriodicBC (class in sfepy.discrete.conditions), 687 domain() (in module sfepy.tests.test_domain), 1021
DGTerm (class in sfepy.terms.terms_dg), 934 DomainSpecificPlot (class in
di_surface_moment() (in module sfepy.postprocess.domain_specific), 856
sfepy.terms.extmods.terms), 1015 dot_sequences() (in module sfepy.linalg.utils), 828
DiagPC (class in sfepy.tests.test_linear_solvers), 1024 DotProductTerm (class in sfepy.terms.terms_dot), 945
dict_extend() (in module sfepy.base.base), 662 DotSProductVolumeOperatorWETHTerm (class in
dict_from_keys_init() (in module sfepy.base.base), sfepy.terms.terms_dot), 946
662 DotSProductVolumeOperatorWTHTerm (class in
dict_from_options() (in module sfepy.base.conf ), sfepy.terms.terms_dot), 946
670 DotSurfaceProductTerm (class in
dict_from_string() (in module sfepy.base.conf ), 670 sfepy.terms.terms_compat), 928
dict_to_array() (in module sfepy.base.base), 662 DotVolumeProductTerm (class in
dict_to_struct() (in module sfepy.base.base), 662 sfepy.terms.terms_compat), 928
diff_dt() (sfepy.homogenization.convolutions.ConvolutionKernel
DoxygenDocs (class in build_helpers), 645
method), 814 dq_cauchy_strain() (in module
DiffusionCoupling (class in sfepy.terms.extmods.terms), 1015
sfepy.terms.terms_diffusion), 939 dq_def_grad() (in module sfepy.terms.extmods.terms),
DiffusionDGFluxTerm (class in sfepy.terms.terms_dg), 1015
934 dq_div_vector() (in module
DiffusionInteriorPenaltyTerm (class in sfepy.terms.extmods.terms), 1015
sfepy.terms.terms_dg), 935 dq_finite_strain_tl() (in module
DiffusionRTerm (class in sfepy.terms.terms_diffusion), sfepy.terms.extmods.terms), 1015
939 dq_finite_strain_ul() (in module
DiffusionTerm (class in sfepy.terms.terms_diffusion), sfepy.terms.extmods.terms), 1015
940 dq_grad() (in module sfepy.terms.extmods.terms), 1015
DiffusionTLTerm (class in dq_state_in_qp() (in module
sfepy.terms.terms_hyperelastic_tl), 964 sfepy.terms.extmods.terms), 1015
DiffusionVelocityTerm (class in dq_tl_finite_strain_surface() (in module
sfepy.terms.terms_diffusion), 941 sfepy.terms.extmods.terms), 1015
dim (sfepy.discrete.common.extmods.cmesh.CMesh dq_tl_he_stress_bulk() (in module
attribute), 730 sfepy.terms.extmods.terms), 1015
dim (sfepy.discrete.common.extmods.mappings.CMapping dq_tl_he_stress_bulk_active() (in module
attribute), 733 sfepy.terms.extmods.terms), 1015
dim2sym() (in module sfepy.mechanics.tensors), 837 dq_tl_he_stress_mooney_rivlin() (in module
distribute_field_dofs() (in module sfepy.terms.extmods.terms), 1015
sfepy.parallel.parallel), 854 dq_tl_he_stress_neohook() (in module
distribute_fields_dofs() (in module sfepy.terms.extmods.terms), 1015
sfepy.parallel.parallel), 855 dq_tl_he_tan_mod_bulk() (in module
div() (in module sfepy.linalg.sympy_operators), 827 sfepy.terms.extmods.terms), 1015
DivGradTerm (class in sfepy.terms.terms_navier_stokes), dq_tl_he_tan_mod_bulk_active() (in module
988 sfepy.terms.extmods.terms), 1015
DivOperatorTerm (class in dq_tl_he_tan_mod_mooney_rivlin() (in module
sfepy.terms.terms_navier_stokes), 989 sfepy.terms.extmods.terms), 1015
DivTerm (class in sfepy.terms.terms_navier_stokes), 989 dq_tl_he_tan_mod_neohook() (in module
dkeep (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at- sfepy.terms.extmods.terms), 1015
tribute), 879 dq_tl_stress_bulk_pressure() (in module

Index 1055
SfePy Documentation, Release version: 2022.1+git.f9873484

sfepy.terms.extmods.terms), 1015 dw_div() (in module sfepy.terms.extmods.terms), 1016

dq_tl_tan_mod_bulk_pressure_u() (in module dw_dot() (sfepy.terms.terms_dot.DotProductTerm static
sfepy.terms.extmods.terms), 1015 method), 945
dq_ul_he_stress_bulk() (in module dw_dot() (sfepy.terms.terms_dot.VectorDotScalarTerm
sfepy.terms.extmods.terms), 1015 static method), 950
dq_ul_he_stress_mooney_rivlin() (in module dw_electric_source() (in module
sfepy.terms.extmods.terms), 1015 sfepy.terms.extmods.terms), 1016
dq_ul_he_stress_neohook() (in module dw_fun() (sfepy.terms.terms_diffusion.DiffusionCoupling
sfepy.terms.extmods.terms), 1016 static method), 939
dq_ul_he_tan_mod_bulk() (in module dw_fun() (sfepy.terms.terms_dot.ScalarDotGradIScalarTerm
sfepy.terms.extmods.terms), 1016 static method), 947
dq_ul_he_tan_mod_mooney_rivlin() (in module dw_fun() (sfepy.terms.terms_surface.SufaceNormalDotTerm
sfepy.terms.extmods.terms), 1016 static method), 1011
dq_ul_he_tan_mod_neohook() (in module dw_grad() (in module sfepy.terms.extmods.terms), 1016
sfepy.terms.extmods.terms), 1016 dw_he_rtm() (in module sfepy.terms.extmods.terms),
dq_ul_stress_bulk_pressure() (in module 1016
sfepy.terms.extmods.terms), 1016 dw_laplace() (in module sfepy.terms.extmods.terms),
dq_ul_tan_mod_bulk_pressure_u() (in module 1016
sfepy.terms.extmods.terms), 1016 dw_lin_convect() (in module
dR_dx (sfepy.discrete.iga.extmods.igac.CNURBSContext sfepy.terms.extmods.terms), 1016
attribute), 793 dw_lin_elastic() (in module
dR_dxi (sfepy.discrete.iga.extmods.igac.CNURBSContext sfepy.terms.extmods.terms), 1016
attribute), 793 dw_lin_prestress() (in module
draw() (sfepy.mesh.bspline.BSpline method), 842 sfepy.terms.extmods.terms), 1016
draw() (sfepy.mesh.bspline.BSplineSurf method), 844 dw_lin_strain_fib() (in module
draw_arrow() (in module sfepy.postprocess.plot_facets), sfepy.terms.extmods.terms), 1017
858 dw_nonsym_elastic() (in module
draw_basis() (sfepy.mesh.bspline.BSpline method), sfepy.terms.extmods.terms), 1017
843 dw_piezo_coupling() (in module
draw_data() (in module sfepy.base.log_plotter), 679 sfepy.terms.extmods.terms), 1017
DSumNodalValuesTerm (class in dw_st_adj1_supg_p() (in module
sfepy.terms.terms_compat), 927 sfepy.terms.extmods.terms), 1017
DSurfaceFluxTerm (class in dw_st_adj2_supg_p() (in module
sfepy.terms.terms_compat), 927 sfepy.terms.extmods.terms), 1017
DSurfaceMomentTerm (class in dw_st_adj_supg_c() (in module
sfepy.terms.terms_compat), 928 sfepy.terms.extmods.terms), 1017
dump_to_vtk() (in module dw_st_grad_div() (in module
sfepy.postprocess.time_history), 862 sfepy.terms.extmods.terms), 1017
DVolumeSurfaceTerm (class in dw_st_pspg_c() (in module sfepy.terms.extmods.terms),
sfepy.terms.terms_compat), 928 1017
dw_adj_convect1() (in module dw_st_supg_c() (in module sfepy.terms.extmods.terms),
sfepy.terms.extmods.terms), 1016 1017
dw_adj_convect2() (in module dw_st_supg_p() (in module sfepy.terms.extmods.terms),
sfepy.terms.extmods.terms), 1016 1017
dw_biot_div() (in module sfepy.terms.extmods.terms), dw_surface_flux() (in module
1016 sfepy.terms.extmods.terms), 1017
dw_biot_grad() (in module sfepy.terms.extmods.terms), dw_surface_ltr() (in module
1016 sfepy.terms.extmods.terms), 1017
dw_convect_v_grad_s() (in module dw_surface_s_v_dot_n() (in module
sfepy.terms.extmods.terms), 1016 sfepy.terms.extmods.terms), 1017
dw_diffusion() (in module sfepy.terms.extmods.terms), dw_surface_v_dot_n_s() (in module
1016 sfepy.terms.extmods.terms), 1017
dw_diffusion_r() (in module dw_tl_diffusion() (in module
sfepy.terms.extmods.terms), 1016 sfepy.terms.extmods.terms), 1017

1056 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

dw_tl_surface_traction() (in module EIntegrateOperatorTerm (class in

sfepy.terms.extmods.terms), 1017 sfepy.terms.terms_multilinear), 979
dw_tl_volume() (in module sfepy.terms.extmods.terms), ELaplaceTerm (class in sfepy.terms.terms_multilinear),
1017 980
dw_ul_volume() (in module sfepy.terms.extmods.terms), ElasticConstants (class in sfepy.mechanics.matcoefs),
1017 831
dw_v_dot_grad_s_sw() (in module ElasticWaveCauchyTerm (class in
sfepy.terms.extmods.terms), 1017 sfepy.terms.terms_elastic), 953
dw_v_dot_grad_s_vw() (in module ElasticWaveTerm (class in sfepy.terms.terms_elastic),
sfepy.terms.extmods.terms), 1017 954
dw_volume_dot_scalar() (in module ElastodynamicsBaseTS (class in
sfepy.terms.extmods.terms), 1017 sfepy.solvers.ts_solvers), 901
dw_volume_dot_vector() (in module ElectricSourceTerm (class in
sfepy.terms.extmods.terms), 1018 sfepy.terms.terms_electric), 960
dw_volume_lvf() (in module elems_q2t() (in module sfepy.mesh.mesh_tools), 851
sfepy.terms.extmods.terms), 1018 elevate() (sfepy.discrete.iga.domain.NurbsPatch
method), 792
E ELinearConvectTerm (class in
e_coors_max (sfepy.discrete.fem.extmods.bases.CLagrangeContext sfepy.terms.terms_multilinear), 980
attribute), 745 ELinearElasticTerm (class in
e_coors_max (sfepy.discrete.iga.extmods.igac.CNURBSContext sfepy.terms.terms_multilinear), 981
attribute), 793 ELinearTractionTerm (class in
ebase2fbase() (in module gen_gallery), 651 sfepy.terms.terms_multilinear), 981
ebc() (in module sfepy.tests.test_msm_laplace), 1027 eltptr (sfepy.solvers.ls_mumps.mumps_struc_c_4
ebc() (in module sfepy.tests.test_msm_symbolic), 1027 attribute), 876
ECauchyStressTerm (class in eltptr (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at-
sfepy.terms.terms_multilinear), 976 tribute), 879
EConvectTerm (class in sfepy.terms.terms_multilinear), eltptr (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at-
976 tribute), 882
edge_oris (sfepy.discrete.common.extmods.cmesh.CMesh eltptr (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at-
attribute), 730 tribute), 886
EdgeDirectionOperator (class in eltvar (sfepy.solvers.ls_mumps.mumps_struc_c_4
sfepy.discrete.fem.lcbc_operators), 756 attribute), 876
edges (sfepy.discrete.common.region.Region property), eltvar (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at-
741 tribute), 879
EDiffusionTerm (class in eltvar (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at-
sfepy.terms.terms_multilinear), 976 tribute), 882
edit() (in module edit_identifiers), 649 eltvar (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at-
edit() (sfepy.base.conf.ProblemConf method), 669 tribute), 886
edit_dict_strings() (in module sfepy.base.base), 662 enc() (in module sfepy.base.ioutils), 674
edit_filename() (in module sfepy.base.ioutils), 674 encode_animation() (sfepy.postprocess.viewer.Viewer
edit_identifiers method), 866
module, 649 ENonPenetrationPenaltyTerm (class in
edit_tuple_strings() (in module sfepy.base.base), sfepy.terms.terms_multilinear), 982
663 ENonSymElasticTerm (class in
EDivGradTerm (class in sfepy.terms.terms_multilinear), sfepy.terms.terms_multilinear), 982
977 ensure_path() (in module sfepy.base.ioutils), 674
EDivTerm (class in sfepy.terms.terms_multilinear), 978 entities (sfepy.discrete.common.extmods.cmesh.CMesh
EDotTerm (class in sfepy.terms.terms_multilinear), 978 attribute), 730
EGradTerm (class in sfepy.terms.terms_multilinear), 979 enum() (in module sfepy.base.multiproc_mpi), 681
eig() (in module sfepy.solvers.eigen), 870 Equation (class in sfepy.discrete.equations), 688
Eigenmomenta (class in equation_mapping() (sfepy.discrete.variables.FieldVariable
sfepy.homogenization.coefs_phononic), 811 method), 718
EigenvalueSolver (class in sfepy.solvers.solvers), 897 equation_mapping() (sfepy.discrete.variables.Variables

Index 1057
SfePy Documentation, Release version: 2022.1+git.f9873484

method), 723 eval_in_els_and_qp() (in module

EquationMap (class in sfepy.discrete.common.dof_info), sfepy.discrete.evaluate), 695
727 eval_in_tp_coors() (in module
Equations (class in sfepy.discrete.equations), 688 sfepy.discrete.iga.extmods.igac), 793
errclear() (in module sfepy.terms.extmods.terms), eval_lobatto1d() (in module
1018 sfepy.discrete.fem.extmods.lobatto_bases),
EScalarDotMGradScalarTerm (class in 746
sfepy.terms.terms_multilinear), 983 eval_lobatto_tensor_product() (in module
ESDDiffusionTerm (class in sfepy.discrete.fem.extmods.lobatto_bases), 746
sfepy.terms.terms_sensitivity), 1000 eval_mapping_data_in_qp() (in module
ESDDivGradTerm (class in sfepy.discrete.iga.extmods.igac), 794
sfepy.terms.terms_sensitivity), 1001 eval_mapping_data_in_qp() (in module
ESDDotTerm (class in sfepy.terms.terms_sensitivity), sfepy.discrete.iga.iga), 798
1001 eval_matrix() (in module
ESDLinearElasticTerm (class in sfepy.tests.test_semismooth_newton), 1029
sfepy.terms.terms_sensitivity), 1002 eval_membrane_mooney_rivlin() (in module
ESDLinearTractionTerm (class in sfepy.terms.terms_membrane), 975
sfepy.terms.terms_sensitivity), 1003 eval_nodal_coors() (in module
ESDPiezoCouplingTerm (class in sfepy.discrete.fem.fields_base), 753
sfepy.terms.terms_sensitivity), 1003 eval_ns_forms
ESDStokesTerm (class in sfepy.terms.terms_sensitivity), module, 650
1004 eval_nurbs_basis_tp() (in module
EssentialBC (class in sfepy.discrete.conditions), 687 sfepy.discrete.iga.iga), 799
EStokesTerm (class in sfepy.terms.terms_multilinear), eval_op_cells() (sfepy.discrete.common.region.Region
984 method), 741
ETermBase (class in sfepy.terms.terms_multilinear), 984 eval_op_edges() (sfepy.discrete.common.region.Region
ETHTerm (class in sfepy.terms.terms_th), 1012 method), 741
EulerStepSolver (class in sfepy.solvers.ts_dg_solvers), eval_op_faces() (sfepy.discrete.common.region.Region
790 method), 741
eval() (sfepy.mesh.bspline.BSpline method), 843 eval_op_facets() (sfepy.discrete.common.region.Region
eval() (sfepy.mesh.bspline.BSplineSurf method), 844 method), 742
eval_base() (sfepy.discrete.common.poly_spaces.PolySpace eval_op_vertices() (sfepy.discrete.common.region.Region
method), 740 method), 742
eval_basis() (sfepy.mesh.bspline.BSpline method), eval_real() (in module
843 sfepy.discrete.evaluate_variable), 696
eval_bernstein_basis() (in module eval_real() (sfepy.terms.terms.Term method), 905
sfepy.discrete.iga.extmods.igac), 793 eval_real() (sfepy.terms.terms_contact.ContactTerm
eval_bernstein_basis() (in module method), 932
sfepy.discrete.iga.iga), 798 eval_real() (sfepy.terms.terms_dg.DGTerm method),
eval_complex() (in module 934
sfepy.discrete.evaluate_variable), 696 eval_real() (sfepy.terms.terms_th.THTerm method),
eval_complex() (sfepy.terms.terms.Term method), 905 1012
eval_coor_expression() (in module eval_residual() (sfepy.discrete.evaluate.Evaluator
sfepy.base.testing), 685 method), 693
eval_equations() (in module sfepy.discrete.evaluate), eval_residual() (sfepy.parallel.evaluate.PETScParallelEvaluator
694 method), 853
eval_equations() (sfepy.discrete.problem.Problem eval_residuals() (sfepy.discrete.equations.Equations
method), 707 method), 690
eval_exponential() (in module eval_tangent_matrices()
sfepy.homogenization.convolutions), 814 (sfepy.discrete.equations.Equations method),
eval_fun() (in module sfepy.tests.test_refine_hanging), 690
1029 eval_tangent_matrix()
eval_function() (sfepy.terms.terms_membrane.TLMembraneTerm (sfepy.discrete.evaluate.Evaluator method),
static method), 975 693

1058 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

eval_tangent_matrix() sfepy.discrete.common.dof_info), 728

(sfepy.parallel.evaluate.PETScParallelEvaluator expand_schur() (sfepy.solvers.ls_mumps.MumpsSolver
method), 853 method), 875
eval_tl_forms ExpressionArg (class in sfepy.terms.terms_multilinear),
module, 650 986
eval_variable_in_qp() (in module ExpressionBuilder (class in
sfepy.discrete.iga.extmods.igac), 794 sfepy.terms.terms_multilinear), 986
eval_variable_in_qp() (in module extend() (sfepy.base.base.Container method), 660
sfepy.discrete.iga.iga), 799 extend_cell_data() (in module
evaluate() (sfepy.discrete.equations.Equation method), sfepy.discrete.fem.utils), 774
688 extend_dofs() (sfepy.discrete.fem.fields_base.FEField
evaluate() (sfepy.discrete.equations.Equations method), 749
method), 690 extend_dofs() (sfepy.discrete.fem.fields_nodal.H1DiscontinuousField
evaluate() (sfepy.discrete.fem.extmods.bases.CLagrangeContext method), 754
method), 745 extract_edges
evaluate() (sfepy.discrete.iga.domain.NurbsPatch module, 650
method), 792 extract_edges() (in module extract_edges), 650
evaluate() (sfepy.discrete.iga.extmods.igac.CNURBSContext extract_surface
method), 793 module, 651
evaluate() (sfepy.discrete.problem.Problem method), extract_time_history() (in module
707 sfepy.postprocess.time_history), 862
evaluate() (sfepy.discrete.variables.FieldVariable extract_times() (in module
method), 718 sfepy.postprocess.time_history), 862
evaluate() (sfepy.homogenization.coefs_phononic.AcousticMassTensor
extractor
method), 810 module, 640
evaluate() (sfepy.homogenization.coefs_phononic.AppliedLoadTensor
method), 810 F
evaluate() (sfepy.mesh.splinebox.SplineBox method), face_oris (sfepy.discrete.common.extmods.cmesh.CMesh
852 attribute), 730
evaluate() (sfepy.terms.terms.Term method), 905 faces (sfepy.discrete.common.region.Region property),
evaluate_at() (sfepy.discrete.common.fields.Field 742
method), 734 facet_oris (sfepy.discrete.common.extmods.cmesh.CMesh
evaluate_at() (sfepy.discrete.variables.FieldVariable attribute), 730
method), 719 facets (sfepy.discrete.common.region.Region property),
evaluate_bfbgm() (sfepy.discrete.common.extmods.mappings.CMapping 742
method), 733 factorial() (in module
evaluate_contact_constraints() (in module sfepy.discrete.simplex_cubature), 717
sfepy.mechanics.extmods.ccontres), 841 family_data_names (sfepy.terms.terms_fibres.FibresActiveTLTerm
evaluate_derivative() attribute), 961
(sfepy.mesh.splinebox.SplineBox method), family_data_names (sfepy.terms.terms_hyperelastic_tl.BulkActiveTLTerm
852 attribute), 963
evaluate_in_rc() (in module family_data_names (sfepy.terms.terms_hyperelastic_tl.BulkPenaltyTLTer
sfepy.discrete.common.extmods.crefcoors), attribute), 964
732 family_data_names (sfepy.terms.terms_hyperelastic_tl.BulkPressureTLTe
Evaluator (class in sfepy.discrete.evaluate), 693 attribute), 964
EVPSolverApp (class in family_data_names (sfepy.terms.terms_hyperelastic_tl.DiffusionTLTerm
sfepy.applications.evp_solver_app), 658 attribute), 965
expand2d() (in module sfepy.mesh.mesh_tools), 851 family_data_names (sfepy.terms.terms_hyperelastic_tl.GenYeohTLTerm
expand_basis() (in module sfepy.discrete.variables), attribute), 966
726 family_data_names (sfepy.terms.terms_hyperelastic_tl.MooneyRivlinTLTe
expand_dofs() (in module sfepy.parallel.parallel), 855 attribute), 967
expand_nodes_to_dofs() (in module family_data_names (sfepy.terms.terms_hyperelastic_tl.NeoHookeanTLTer
sfepy.discrete.common.dof_info), 728 attribute), 967
expand_nodes_to_equations() (in module

Index 1059
SfePy Documentation, Release version: 2022.1+git.f9873484

family_data_names (sfepy.terms.terms_hyperelastic_tl.OgdenTLTerm
FEMapping (class in sfepy.discrete.fem.mappings), 759
attribute), 968 FEPolySpace (class in sfepy.discrete.fem.poly_spaces),
family_data_names (sfepy.terms.terms_hyperelastic_tl.SurfaceFluxTLTerm
769
attribute), 969 FESurface (class in sfepy.discrete.fem.fe_surface), 748
family_data_names (sfepy.terms.terms_hyperelastic_tl.SurfaceTractionTLTerm
FibresActiveTLTerm (class in
attribute), 969 sfepy.terms.terms_fibres), 960
family_data_names (sfepy.terms.terms_hyperelastic_tl.VolumeSurfaceTLTerm
Field (class in sfepy.discrete.common.fields), 734
attribute), 970 FieldOptsToListAction (class in resview), 644
family_data_names (sfepy.terms.terms_hyperelastic_tl.VolumeTLTerm
fields_from_conf() (in module
attribute), 971 sfepy.discrete.common.fields), 736
family_data_names (sfepy.terms.terms_hyperelastic_ul.BulkPenaltyULTerm
FieldVariable (class in sfepy.discrete.variables), 718
attribute), 971 file_changed() (sfepy.postprocess.sources.FileSource
family_data_names (sfepy.terms.terms_hyperelastic_ul.BulkPressureULTerm
method), 860
attribute), 972 file_changed() (sfepy.postprocess.sources.GenericFileSource
family_data_names (sfepy.terms.terms_hyperelastic_ul.CompressibilityULTerm
method), 861
attribute), 972 file_changed() (sfepy.postprocess.sources.GenericSequenceFileSource
family_data_names (sfepy.terms.terms_hyperelastic_ul.MooneyRivlinULTerm
method), 861
attribute), 973 filename_meshes() (in module sfepy.tests.test_cmesh),
family_data_names (sfepy.terms.terms_hyperelastic_ul.NeoHookeanULTerm
1019
attribute), 974 FileSource (class in sfepy.postprocess.sources), 860
family_data_names (sfepy.terms.terms_hyperelastic_ul.VolumeULTerm
fill_state() (sfepy.discrete.variables.Variables
attribute), 974 method), 723
family_function() (sfepy.terms.terms_hyperelastic_tl.HyperElasticSurfaceTLFamilyData
finalize() (sfepy.discrete.common.region.Region
static method), 966 method), 742
family_function() (sfepy.terms.terms_hyperelastic_tl.HyperElasticTLFamilyData
finalize() (sfepy.discrete.fem.lcbc_operators.LCBCOperators
static method), 966 method), 757
family_function() (sfepy.terms.terms_hyperelastic_ul.BulkPressureULTerm
finalize_options() (build_helpers.NoOptionsDocs
static method), 972 method), 646
family_function() (sfepy.terms.terms_hyperelastic_ul.HyperElasticULFamilyData
find() (sfepy.base.base.OneTypeList method), 660
static method), 973 find_facet_substitutions() (in module
family_name (sfepy.discrete.dg.fields.DGField at- sfepy.discrete.fem.refine_hanging), 774
tribute), 781 find_free_indices() (in module
family_name (sfepy.discrete.fem.fields_hierarchic.H1HierarchicVolumeField
sfepy.terms.terms_multilinear), 987
attribute), 753 find_level_interface() (in module
family_name (sfepy.discrete.fem.fields_nodal.H1DiscontinuousField sfepy.discrete.fem.refine_hanging), 774
attribute), 754 find_map() (in module sfepy.discrete.fem.mesh), 761
family_name (sfepy.discrete.fem.fields_nodal.H1NodalSurfaceField
find_ref_coors() (in module
attribute), 754 sfepy.discrete.common.extmods.crefcoors),
family_name (sfepy.discrete.fem.fields_nodal.H1NodalVolumeField 732
attribute), 754 find_ref_coors_convex() (in module
family_name (sfepy.discrete.fem.fields_nodal.H1SNodalSurfaceField sfepy.discrete.common.extmods.crefcoors),
attribute), 755 733
family_name (sfepy.discrete.fem.fields_nodal.H1SNodalVolumeField
find_subclasses() (in module sfepy.base.base), 663
attribute), 755 find_ts() (sfepy.mesh.splinebox.SplineRegion2D
family_name (sfepy.discrete.fem.fields_positive.H1BernsteinSurfaceField
method), 853
attribute), 755 find_zero() (in module
family_name (sfepy.discrete.fem.fields_positive.H1BernsteinVolumeField
sfepy.homogenization.coefs_phononic), 813
attribute), 755 fit_exponential() (in module
family_name (sfepy.discrete.iga.fields.IGField at- sfepy.homogenization.convolutions), 815
tribute), 795 fix_double_nodes() (in module
family_name (sfepy.discrete.structural.fields.Shell10XField sfepy.discrete.fem.mesh), 761
attribute), 804 fix_eig_range() (sfepy.homogenization.coefs_phononic.BandGaps
FEDomain (class in sfepy.discrete.fem.domain), 744 method), 811
FEField (class in sfepy.discrete.fem.fields_base), 748 fix_element_orientation()

1060 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

(sfepy.discrete.fem.domain.FEDomain method), 696

method), 744 from_conf() (sfepy.discrete.integrals.Integrals static
fix_u_fun() (in module sfepy.tests.test_high_level), method), 697
1022 from_conf() (sfepy.discrete.materials.Material static
flag_points_in_polygon2d() (in module method), 698
sfepy.linalg.geometry), 823 from_conf() (sfepy.discrete.materials.Materials static
FMinSteepestDescent (class in sfepy.solvers.optimize), method), 699
893 from_conf() (sfepy.discrete.problem.Problem static
font_size() (in module sfepy.base.plotutils), 684 method), 708
format (sfepy.discrete.fem.meshio.ANSYSCDBMeshIO from_conf() (sfepy.discrete.variables.Variable static
attribute), 761 method), 721
format (sfepy.discrete.fem.meshio.ComsolMeshIO from_conf() (sfepy.discrete.variables.Variables static
attribute), 762 method), 723
format (sfepy.discrete.fem.meshio.GmshIO attribute), from_conf() (sfepy.solvers.ts.TimeStepper static
762 method), 898
format (sfepy.discrete.fem.meshio.HDF5MeshIO at- from_conf() (sfepy.solvers.ts.VariableTimeStepper
tribute), 764 static method), 899
format (sfepy.discrete.fem.meshio.HDF5XdmfMeshIO from_conf_file() (sfepy.discrete.problem.Problem
attribute), 765 static method), 708
format (sfepy.discrete.fem.meshio.HypermeshAsciiMeshIO from_data() (sfepy.discrete.common.extmods.cmesh.CMesh
attribute), 765 method), 731
format (sfepy.discrete.fem.meshio.Mesh3DMeshIO at- from_data() (sfepy.discrete.fem.mesh.Mesh static
tribute), 765 method), 760
format (sfepy.discrete.fem.meshio.MeshIO attribute), from_data() (sfepy.discrete.iga.domain.IGDomain
766 static method), 791
format (sfepy.discrete.fem.meshio.MeshioLibIO at- from_desc() (sfepy.discrete.equations.Equation static
tribute), 767 method), 688
format (sfepy.discrete.fem.meshio.NEUMeshIO at- from_desc() (sfepy.terms.terms.Term static method),
tribute), 767 906
format (sfepy.discrete.fem.meshio.UserMeshIO at- from_desc() (sfepy.terms.terms.Terms static method),
tribute), 767 908
format (sfepy.discrete.fem.meshio.XYZMeshIO at- from_dict() (sfepy.base.conf.ProblemConf static
tribute), 768 method), 669
format_next() (in module gen_term_table), 654 from_facets() (sfepy.discrete.common.region.Region
format_next() (in module sfepy.solvers.solvers), 898 static method), 742
free_connectivity() from_file() (sfepy.base.conf.ProblemConf static
(sfepy.discrete.common.extmods.cmesh.CMesh method), 669
method), 730 from_file() (sfepy.discrete.fem.mesh.Mesh static
from_args() (sfepy.discrete.common.fields.Field static method), 760
method), 735 from_file() (sfepy.discrete.iga.domain.IGDomain
from_args() (sfepy.discrete.common.mappings.Mapping static method), 791
static method), 738 from_file_and_options()
from_array() (sfepy.linalg.utils.MatrixAction static (sfepy.base.conf.ProblemConf static method),
method), 827 670
from_cells() (sfepy.discrete.common.region.Region from_file_hdf5() (sfepy.discrete.fem.history.Histories
static method), 742 static method), 756
from_conf() (sfepy.base.log.Log static method), 677 from_file_hdf5() (sfepy.homogenization.coefficients.Coefficients
from_conf() (sfepy.discrete.common.fields.Field static static method), 805
method), 735 from_function() (sfepy.linalg.utils.MatrixAction static
from_conf() (sfepy.discrete.conditions.Conditions method), 827
static method), 686 from_gmsh_file() (sfepy.mesh.geom_tools.geometry
from_conf() (sfepy.discrete.equations.Equations static static method), 846
method), 690 from_module() (sfepy.base.conf.ProblemConf static
from_conf() (sfepy.discrete.functions.Functions static method), 670

Index 1061
SfePy Documentation, Release version: 2022.1+git.f9873484

from_region() (sfepy.discrete.fem.mesh.Mesh static static method), 923

method), 760 function() (sfepy.terms.terms_basic.VolumeTerm static
from_sequence() (sfepy.discrete.fem.history.History method), 923
static method), 756 function() (sfepy.terms.terms_basic.ZeroTerm static
from_table() (sfepy.discrete.quadratures.QuadraturePoints method), 924
static method), 716 function() (sfepy.terms.terms_biot.BiotStressTerm
from_term_arg() (sfepy.terms.terms_multilinear.ExpressionArg static method), 925
static method), 986 function() (sfepy.terms.terms_constraints.NonPenetrationPenaltyTerm
from_vertices() (sfepy.discrete.common.region.Region static method), 930
static method), 742 function() (sfepy.terms.terms_constraints.NonPenetrationTerm
Function (class in sfepy.discrete.functions), 696 static method), 931
function() (sfepy.terms.terms_adj_navier_stokes.AdjConvect1Term
function() (sfepy.terms.terms_contact.ContactTerm
static method), 910 static method), 932
function() (sfepy.terms.terms_adj_navier_stokes.AdjConvect2Term
function() (sfepy.terms.terms_dg.AdvectionDGFluxTerm
static method), 910 method), 934
function() (sfepy.terms.terms_adj_navier_stokes.AdjDivGradTerm
function() (sfepy.terms.terms_dg.DiffusionDGFluxTerm
static method), 911 method), 935
function() (sfepy.terms.terms_adj_navier_stokes.NSOFMinGradTerm
function() (sfepy.terms.terms_dg.DiffusionInteriorPenaltyTerm
static method), 911 method), 935
function() (sfepy.terms.terms_adj_navier_stokes.NSOFSurfMinDPressTerm
function() (sfepy.terms.terms_dg.NonlinearHyperbolicDGFluxTerm
static method), 912 method), 937
function() (sfepy.terms.terms_adj_navier_stokes.SDConvectTerm
function() (sfepy.terms.terms_dg.NonlinearScalarDotGradTerm
static method), 913 static method), 937
function() (sfepy.terms.terms_adj_navier_stokes.SDDivGradTerm
function() (sfepy.terms.terms_diffusion.ConvectVGradSTerm
static method), 914 method), 938
function() (sfepy.terms.terms_adj_navier_stokes.SDDivTerm
function() (sfepy.terms.terms_diffusion.DiffusionRTerm
static method), 914 static method), 940
function() (sfepy.terms.terms_adj_navier_stokes.SDDotTerm
function() (sfepy.terms.terms_diffusion.DiffusionVelocityTerm
static method), 915 static method), 941
function() (sfepy.terms.terms_adj_navier_stokes.SDGradDivStabilizationTerm
function() (sfepy.terms.terms_diffusion.SDDiffusionTerm
static method), 915 static method), 942
function() (sfepy.terms.terms_adj_navier_stokes.SDPSPGCStabilizationTerm
function() (sfepy.terms.terms_diffusion.SurfaceFluxOperatorTerm
static method), 916 method), 943
function() (sfepy.terms.terms_adj_navier_stokes.SDPSPGPStabilizationTerm
function() (sfepy.terms.terms_diffusion.SurfaceFluxTerm
static method), 917 static method), 944
function() (sfepy.terms.terms_adj_navier_stokes.SDSUPGCStabilizationTerm
function() (sfepy.terms.terms_dot.DotSProductVolumeOperatorWETHTer
static method), 917 static method), 946
function() (sfepy.terms.terms_adj_navier_stokes.SUPGCAdjStabilizationTerm
function() (sfepy.terms.terms_dot.DotSProductVolumeOperatorWTHTerm
static method), 918 static method), 947
function() (sfepy.terms.terms_adj_navier_stokes.SUPGPAdj1StabilizationTerm
function() (sfepy.terms.terms_dot.ScalarDotMGradScalarTerm
static method), 919 static method), 948
function() (sfepy.terms.terms_adj_navier_stokes.SUPGPAdj2StabilizationTerm
function() (sfepy.terms.terms_elastic.CauchyStrainTerm
static method), 919 static method), 951
function() (sfepy.terms.terms_basic.IntegrateMatTerm function() (sfepy.terms.terms_elastic.CauchyStressTerm
static method), 920 static method), 953
function() (sfepy.terms.terms_basic.IntegrateOperatorTerm
function() (sfepy.terms.terms_elastic.ElasticWaveCauchyTerm
static method), 920 static method), 954
function() (sfepy.terms.terms_basic.IntegrateTerm function() (sfepy.terms.terms_elastic.ElasticWaveTerm
static method), 921 static method), 954
function() (sfepy.terms.terms_basic.SumNodalValuesTermfunction() (sfepy.terms.terms_elastic.LinearElasticETHTerm
static method), 922 static method), 955
function() (sfepy.terms.terms_basic.SurfaceMomentTerm function() (sfepy.terms.terms_elastic.LinearElasticTHTerm
static method), 922 static method), 956
function() (sfepy.terms.terms_basic.VolumeSurfaceTerm function() (sfepy.terms.terms_elastic.LinearStrainFiberTerm

1062 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

static method), 958 static method), 999

function() (sfepy.terms.terms_elastic.SDLinearElasticTermfunction() (sfepy.terms.terms_point.LinearPointSpringTerm
method), 959 static method), 1000
function() (sfepy.terms.terms_electric.ElectricSourceTermfunction() (sfepy.terms.terms_shells.Shell10XTerm
static method), 960 static method), 1006
function() (sfepy.terms.terms_hyperelastic_base.DeformationGradientTerm
function() (sfepy.terms.terms_surface.ContactPlaneTerm
static method), 962 static method), 1008
function() (sfepy.terms.terms_hyperelastic_base.HyperElasticBase
function() (sfepy.terms.terms_surface.ContactSphereTerm
static method), 962 static method), 1009
function() (sfepy.terms.terms_hyperelastic_tl.DiffusionTLTerm
function() (sfepy.terms.terms_surface.SDSufaceIntegrateTerm
static method), 965 static method), 1011
function() (sfepy.terms.terms_hyperelastic_tl.SurfaceFluxTLTerm
function() (sfepy.terms.terms_surface.SurfaceJumpTerm
static method), 969 static method), 1012
function() (sfepy.terms.terms_hyperelastic_tl.SurfaceTractionTLTerm
function() (sfepy.terms.terms_volume.LinearVolumeForceTerm
static method), 969 static method), 1013
function() (sfepy.terms.terms_hyperelastic_tl.VolumeSurfaceTLTerm
function_silent() (sfepy.terms.terms_multilinear.ETermBase
static method), 970 static method), 985
function() (sfepy.terms.terms_hyperelastic_tl.VolumeTLTerm
function_timer() (sfepy.terms.terms_multilinear.ETermBase
static method), 971 static method), 985
function() (sfepy.terms.terms_hyperelastic_ul.CompressibilityULTerm
function_weak() (sfepy.terms.terms_contact.ContactTerm
static method), 973 static method), 932
function() (sfepy.terms.terms_hyperelastic_ul.VolumeULTerm
Functions (class in sfepy.discrete.functions), 696
static method), 974
function() (sfepy.terms.terms_membrane.TLMembraneTerm G
static method), 975 gels() (in module sfepy.tests.test_fem), 1022
function() (sfepy.terms.terms_navier_stokes.ConvectTermgels() (in module sfepy.tests.test_poly_spaces), 1028
static method), 988 gels() (in module sfepy.tests.test_refine_hanging), 1029
function() (sfepy.terms.terms_navier_stokes.DivGradTerm geme_mulAVSB3py() (in module
static method), 988 sfepy.discrete.common.extmods._geommech),
function() (sfepy.terms.terms_navier_stokes.DivOperatorTerm 729
static method), 989 gen_block_mesh() (in module
function() (sfepy.terms.terms_navier_stokes.DivTerm sfepy.mesh.mesh_generators), 848
static method), 989 gen_cp_idxs() (sfepy.mesh.splinebox.SplineBox static
function() (sfepy.terms.terms_navier_stokes.GradDivStabilizationTerm
method), 852
static method), 990 gen_cylinder_mesh() (in module
function() (sfepy.terms.terms_navier_stokes.GradTerm sfepy.mesh.mesh_generators), 848
static method), 991 gen_datas() (in module sfepy.tests.test_mesh_interp),
function() (sfepy.terms.terms_navier_stokes.LinearConvect2Term 1026
static method), 991 gen_extended_block_mesh() (in module
function() (sfepy.terms.terms_navier_stokes.LinearConvectTerm sfepy.mesh.mesh_generators), 849
static method), 992 gen_gallery
function() (sfepy.terms.terms_navier_stokes.PSPGCStabilizationTerm
module, 651
static method), 992 gen_iga_patch
function() (sfepy.terms.terms_navier_stokes.StokesWaveDivTerm module, 652
static method), 995 gen_legendre_simplex_base
function() (sfepy.terms.terms_navier_stokes.StokesWaveTerm module, 652
static method), 996 gen_lobatto() (in module gen_lobatto1d_c), 653
function() (sfepy.terms.terms_navier_stokes.SUPGCStabilizationTerm
gen_lobatto1d_c
static method), 993 module, 653
function() (sfepy.terms.terms_navier_stokes.SUPGPStabilizationTerm
gen_mesh_from_geom() (in module
static method), 994 sfepy.mesh.mesh_generators), 849
function() (sfepy.terms.terms_piezo.PiezoStressTerm gen_mesh_from_string() (in module
static method), 998 sfepy.mesh.mesh_generators), 849
function() (sfepy.terms.terms_point.ConcentratedPointLoadTerm

Index 1063
SfePy Documentation, Release version: 2022.1+git.f9873484

gen_mesh_from_voxels() (in module geometries (sfepy.terms.terms_elastic.ElasticWaveCauchyTerm

sfepy.mesh.mesh_generators), 849 attribute), 954
gen_mesh_prev geometries (sfepy.terms.terms_elastic.ElasticWaveTerm
module, 653 attribute), 954
gen_mesh_probe_png() geometries (sfepy.terms.terms_elastic.LinearElasticIsotropicTerm
(sfepy.postprocess.probes_vtk.Probe method), attribute), 956
860 geometries (sfepy.terms.terms_elastic.NonsymElasticTerm
gen_misc_mesh() (in module attribute), 959
sfepy.mesh.mesh_generators), 850 geometries (sfepy.terms.terms_elastic.SDLinearElasticTerm
gen_multi_vec_packing() (in module attribute), 959
sfepy.solvers.ts_solvers), 904 geometries (sfepy.terms.terms_hyperelastic_tl.GenYeohTLTerm
gen_patch_block_domain() (in module attribute), 966
sfepy.discrete.iga.domain_generators), 792 geometries (sfepy.terms.terms_hyperelastic_tl.OgdenTLTerm
gen_points() (sfepy.discrete.probes.RayProbe attribute), 968
method), 703 geometries (sfepy.terms.terms_membrane.TLMembraneTerm
gen_release_notes attribute), 975
module, 653 geometries (sfepy.terms.terms_navier_stokes.StokesWaveDivTerm
gen_serendipity_basis attribute), 996
module, 654 geometries (sfepy.terms.terms_navier_stokes.StokesWaveTerm
gen_shot() (in module gen_mesh_prev), 653 attribute), 996
gen_solver_table geometries (sfepy.terms.terms_piezo.SDPiezoCouplingTerm
module, 654 attribute), 999
gen_solver_table() (in module gen_solver_table), geometries (sfepy.terms.terms_sensitivity.ESDLinearElasticTerm
654 attribute), 1003
gen_term_table geometries (sfepy.terms.terms_sensitivity.ESDPiezoCouplingTerm
module, 654 attribute), 1004
gen_term_table() (in module gen_term_table), 654 geometries (sfepy.terms.terms_shells.Shell10XTerm at-
gen_tiled_mesh() (in module tribute), 1006
sfepy.mesh.mesh_generators), 850 geometries (sfepy.terms.terms_surface.ContactPlaneTerm
GeneralizedAlphaTS (class in sfepy.solvers.ts_solvers), attribute), 1008
901 geometries (sfepy.terms.terms_surface.ContactSphereTerm
generate_a_pyrex_source() (in module attribute), 1009
build_helpers), 646 geometry (class in sfepy.mesh.geom_tools), 846
generate_decreasing_nonnegative_tuples_summing_to() GeometryElement (class in
(in module sfepy.discrete.simplex_cubature), sfepy.discrete.fem.geometry_element), 755
717 geomobject (class in sfepy.mesh.geom_tools), 847
generate_gallery() (in module gen_gallery), 651 get() (sfepy.base.base.Container method), 660
generate_images() (in module gen_gallery), 652 get() (sfepy.base.base.Struct method), 662
generate_permutations() (in module get() (sfepy.base.multiproc_mpi.RemoteDict method),
sfepy.discrete.simplex_cubature), 717 680
generate_probes() (in module probe), 643 get() (sfepy.base.multiproc_mpi.RemoteQueue method),
generate_rst_files() (in module gen_gallery), 652 681
generate_thumbnails() (in module gen_gallery), 652 get() (sfepy.base.multiproc_mpi.RemoteQueueMaster
generate_unique_permutations() (in module method), 681
sfepy.discrete.simplex_cubature), 717 get() (sfepy.base.multiproc_proc.MyQueue method),
GenericFileSource (class in 682
sfepy.postprocess.sources), 861 get() (sfepy.discrete.integrals.Integrals method), 697
GenericSequenceFileSource (class in get() (sfepy.mechanics.matcoefs.ElasticConstants
sfepy.postprocess.sources), 861 method), 831
GenYeohTLTerm (class in get() (sfepy.terms.terms.Term method), 906
sfepy.terms.terms_hyperelastic_tl), 965 get_2d_points() (in module sfepy.mesh.bspline), 845
geo_ctx (sfepy.discrete.fem.extmods.bases.CLagrangeContextget_a0() (sfepy.solvers.ts_solvers.ElastodynamicsBaseTS
attribute), 745 method), 901
geometries (sfepy.terms.terms.Term attribute), 906 get_AABB() (in module

1064 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

sfepy.mechanics.extmods.ccontres), 841 (sfepy.mechanics.tensors.StressTransform

get_actual_cache() (sfepy.discrete.probes.Probe method), 837
method), 702 get_cell_conn() (sfepy.discrete.common.extmods.cmesh.CMesh
get_actual_order() (in module method), 731
sfepy.discrete.quadratures), 716 get_cell_indices() (sfepy.discrete.common.region.Region
get_animation_info() method), 743
(sfepy.postprocess.viewer.Viewer method), get_cell_normals_per_facet()
866 (sfepy.discrete.dg.fields.DGField method),
get_arg_kinds() (in module sfepy.terms.terms), 909 782
get_arg_name() (sfepy.terms.terms.Term method), 906 get_cells() (in module sfepy.tests.test_regions), 1029
get_args() (sfepy.terms.terms.Term method), 906 get_cells() (sfepy.discrete.common.region.Region
get_args_by_name() (sfepy.terms.terms.Term method), method), 743
906 get_centroids() (sfepy.discrete.common.domain.Domain
get_arguments() (in module sfepy.base.base), 663 method), 728
get_assembling_cells() (sfepy.terms.terms.Term get_centroids() (sfepy.discrete.common.extmods.cmesh.CMesh
method), 906 method), 731
get_base() (sfepy.discrete.fem.fields_base.FEField get_charfun() (sfepy.discrete.common.region.Region
method), 749 method), 743
get_base() (sfepy.discrete.fem.mappings.FEMapping get_circle() (in module sfepy.tests.test_functions),
method), 759 1022
get_base() (sfepy.discrete.fem.mappings.SurfaceMapping get_cmem_usage() (in module
method), 759 sfepy.discrete.common.extmods.cmesh), 732
get_basic_info() (in module sfepy.version), 658 get_coef() (sfepy.homogenization.coefs_base.CoefMN
get_bc_facet_idx() (sfepy.discrete.dg.fields.DGField method), 806
method), 781 get_coef() (sfepy.homogenization.coefs_base.CoefN
get_bc_facet_values() method), 806
(sfepy.discrete.dg.fields.DGField method), get_coefs() (sfepy.homogenization.coefs_phononic.AcousticMassLiquidT
781 method), 810
get_bezier_element_entities() (in module get_coefs() (sfepy.homogenization.coefs_phononic.AcousticMassTensor
sfepy.discrete.iga.iga), 799 method), 810
get_bezier_topology() (in module get_complete() (sfepy.discrete.common.extmods.cmesh.CMesh
sfepy.discrete.iga.iga), 800 method), 731
get_bf() (sfepy.terms.terms_multilinear.ExpressionArg get_composite_sizes() (in module
method), 986 sfepy.parallel.parallel), 855
get_both_facet_base_vals() get_condition_value() (in module
(sfepy.discrete.dg.fields.DGField method), sfepy.discrete.conditions), 688
781 get_conn() (sfepy.discrete.common.extmods.cmesh.CMesh
get_both_facet_state_vals() method), 731
(sfepy.discrete.dg.fields.DGField method), get_conn() (sfepy.discrete.fem.domain.FEDomain
781 method), 744
get_bounding_box() (sfepy.discrete.fem.mesh.Mesh get_conn() (sfepy.discrete.fem.mesh.Mesh method), 760
method), 760 get_conn_as_graph()
get_bounding_box() (sfepy.postprocess.sources.GenericFileSource(sfepy.discrete.common.extmods.cmesh.CMesh
method), 861 method), 731
get_bounding_box() (sfepy.postprocess.sources.VTKFileSourceget_conn_info() (sfepy.terms.terms.Term method),
method), 862 906
get_box_matrix() (sfepy.mesh.splinebox.SplineBox get_conn_key() (sfepy.terms.terms.Term method), 906
method), 852 get_conn_permutations()
get_box_volume() (in module (sfepy.discrete.fem.geometry_element.GeometryElement
sfepy.homogenization.utils), 821 method), 755
get_callback() (in module get_connectivity() (sfepy.discrete.fem.fe_surface.FESurface
sfepy.homogenization.coefs_phononic), 813 method), 748
get_camera_position() (in module resview), 644 get_connectivity() (sfepy.discrete.fem.fields_base.FEField
get_cauchy_from_2pk() method), 749

Index 1065
SfePy Documentation, Release version: 2022.1+git.f9873484

get_consistent_unit_set() (in module sfepy.discrete.common.region), 744

sfepy.mechanics.units), 841 get_deviator() (in module sfepy.mechanics.tensors),
get_constant_data() 837
(sfepy.discrete.materials.Material method), get_diameter() (sfepy.discrete.fem.domain.FEDomain
698 method), 744
get_contact_info() (sfepy.terms.terms_contact.ContactTerm get_dict() (in module sfepy.base.multiproc_mpi), 681
method), 932 get_dict() (in module sfepy.base.multiproc_proc), 682
get_control_points() (sfepy.mesh.bspline.BSpline get_dict_idxval() (in module
method), 843 sfepy.homogenization.engine), 817
get_control_points() get_dim() (sfepy.discrete.problem.Problem method),
(sfepy.mesh.bspline.BSplineSurf method), 708
844 get_distance() (sfepy.mechanics.contact_bodies.ContactPlane
get_control_points() method), 830
(sfepy.mesh.splinebox.SplineBox method), get_distance() (sfepy.mechanics.contact_bodies.ContactSphere
852 method), 830
get_coor() (sfepy.discrete.dg.fields.DGField method), get_dof_conn() (sfepy.discrete.variables.FieldVariable
782 method), 719
get_coor() (sfepy.discrete.fem.fields_base.FEField get_dof_conn_type() (sfepy.terms.terms.Term
method), 749 method), 907
get_coors_in_ball() (in module get_dof_info() (sfepy.discrete.variables.FieldVariable
sfepy.linalg.geometry), 823 method), 720
get_coors_in_tube() (in module get_dofs() (in module save_basis), 656
sfepy.linalg.geometry), 823 get_dofs() (sfepy.terms.terms_multilinear.ExpressionArg
get_coors_shape() (sfepy.mesh.splinebox.SplineBox method), 986
method), 852 get_dofs_in_region()
get_correctors_from_file_hdf5() (in module (sfepy.discrete.dg.fields.DGField method),
sfepy.homogenization.micmac), 818 782
get_data() (sfepy.discrete.materials.Material method), get_dofs_in_region()
698 (sfepy.discrete.fem.fields_base.FEField
get_data_name() (in module sfepy.discrete.probes), method), 750
703 get_dofs_in_region()
get_data_names() (sfepy.postprocess.viewer.Viewer (sfepy.discrete.iga.fields.IGField method),
method), 866 796
get_data_ranges() (in module sfepy.postprocess.utils), get_domain() (sfepy.discrete.equations.Equations
863 method), 690
get_data_shape() (sfepy.discrete.dg.fields.DGField get_dsg_strain() (in module
method), 782 sfepy.mechanics.shell10x), 836
get_data_shape() (sfepy.discrete.fem.fields_base.FEFieldget_dual() (sfepy.discrete.variables.Variable method),
method), 749 721
get_data_shape() (sfepy.discrete.iga.fields.IGField get_dual_names() (sfepy.discrete.variables.Variables
method), 795 method), 723
get_data_shape() (sfepy.discrete.variables.FieldVariableget_ebc_indices() (sfepy.discrete.problem.Problem
method), 719 method), 708
get_data_shape() (sfepy.terms.terms.Term method), get_econn() (sfepy.discrete.dg.fields.DGField method),
906 782
get_debug() (in module sfepy.base.base), 663 get_econn() (sfepy.discrete.fem.fields_base.SurfaceField
get_default() (in module sfepy.base.base), 663 method), 752
get_default_attr() (in module sfepy.base.base), 663 get_econn() (sfepy.discrete.fem.fields_base.VolumeField
get_default_time_step() method), 752
(sfepy.solvers.ts.VariableTimeStepper method), get_econn() (sfepy.discrete.iga.fields.IGField method),
899 796
get_default_ts() (sfepy.discrete.problem.Problem get_edge_graph() (sfepy.discrete.common.region.Region
method), 708 method), 743
get_dependency_graph() (in module get_edge_paths() (in module sfepy.discrete.fem.utils),

1066 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

775 method), 923

get_edges_per_face() get_eval_shape() (sfepy.terms.terms_basic.VolumeTerm
(sfepy.discrete.fem.geometry_element.GeometryElement method), 923
method), 755 get_eval_shape() (sfepy.terms.terms_biot.BiotTerm
get_einsum_ops() (in module method), 927
sfepy.terms.terms_multilinear), 987 get_eval_shape() (sfepy.terms.terms_contact.ContactTerm
get_element_diameters() method), 932
(sfepy.discrete.common.extmods.mappings.CMappingget_eval_shape() (sfepy.terms.terms_diffusion.DiffusionCoupling
method), 733 method), 939
get_element_diameters() get_eval_shape() (sfepy.terms.terms_diffusion.DiffusionTerm
(sfepy.discrete.fem.domain.FEDomain method), 940
method), 745 get_eval_shape() (sfepy.terms.terms_diffusion.DiffusionVelocityTerm
get_element_diameters() method), 941
(sfepy.discrete.variables.FieldVariable get_eval_shape() (sfepy.terms.terms_diffusion.SDDiffusionTerm
method), 720 method), 942
get_entities() (sfepy.discrete.common.region.Region get_eval_shape() (sfepy.terms.terms_diffusion.SurfaceFluxTerm
method), 743 method), 944
get_eth_data() (sfepy.terms.terms_th.ETHTerm get_eval_shape() (sfepy.terms.terms_dot.DotProductTerm
method), 1012 method), 945
get_eval_coors() (in module get_eval_shape() (sfepy.terms.terms_dot.VectorDotGradScalarTerm
sfepy.discrete.fem.linearizer), 759 method), 949
get_eval_dofs() (in module get_eval_shape() (sfepy.terms.terms_dot.VectorDotScalarTerm
sfepy.discrete.fem.linearizer), 759 method), 950
get_eval_expression() (in module get_eval_shape() (sfepy.terms.terms_elastic.CauchyStrainTerm
sfepy.discrete.fem.fields_base), 753 method), 951
get_eval_shape() (sfepy.terms.terms_adj_navier_stokes.NSOFMinGradTerm
get_eval_shape() (sfepy.terms.terms_elastic.CauchyStressETHTerm
method), 911 method), 951
get_eval_shape() (sfepy.terms.terms_adj_navier_stokes.NSOFSurfMinDPressTerm
get_eval_shape() (sfepy.terms.terms_elastic.CauchyStressTerm
method), 912 method), 953
get_eval_shape() (sfepy.terms.terms_adj_navier_stokes.SDConvectTerm
get_eval_shape() (sfepy.terms.terms_elastic.CauchyStressTHTerm
method), 913 method), 952
get_eval_shape() (sfepy.terms.terms_adj_navier_stokes.SDDivGradTerm
get_eval_shape() (sfepy.terms.terms_elastic.LinearElasticIsotropicTerm
method), 914 method), 956
get_eval_shape() (sfepy.terms.terms_adj_navier_stokes.SDDivTerm
get_eval_shape() (sfepy.terms.terms_elastic.LinearElasticTerm
method), 914 method), 957
get_eval_shape() (sfepy.terms.terms_adj_navier_stokes.SDDotTerm
get_eval_shape() (sfepy.terms.terms_elastic.LinearPrestressTerm
method), 915 method), 957
get_eval_shape() (sfepy.terms.terms_adj_navier_stokes.SDGradDivStabilizationTerm
get_eval_shape() (sfepy.terms.terms_elastic.NonsymElasticTerm
method), 915 method), 959
get_eval_shape() (sfepy.terms.terms_adj_navier_stokes.SDPSPGCStabilizationTerm
get_eval_shape() (sfepy.terms.terms_elastic.SDLinearElasticTerm
method), 916 method), 959
get_eval_shape() (sfepy.terms.terms_adj_navier_stokes.SDPSPGPStabilizationTerm
get_eval_shape() (sfepy.terms.terms_fibres.FibresActiveTLTerm
method), 917 method), 961
get_eval_shape() (sfepy.terms.terms_adj_navier_stokes.SDSUPGCStabilizationTerm
get_eval_shape() (sfepy.terms.terms_hyperelastic_base.DeformationGra
method), 917 method), 962
get_eval_shape() (sfepy.terms.terms_basic.IntegrateMatTerm
get_eval_shape() (sfepy.terms.terms_hyperelastic_base.HyperElasticBas
method), 920 method), 962
get_eval_shape() (sfepy.terms.terms_basic.IntegrateTermget_eval_shape() (sfepy.terms.terms_hyperelastic_tl.BulkPressureTLTer
method), 921 method), 964
get_eval_shape() (sfepy.terms.terms_basic.SumNodalValuesTerm
get_eval_shape() (sfepy.terms.terms_hyperelastic_tl.DiffusionTLTerm
method), 922 method), 965
get_eval_shape() (sfepy.terms.terms_basic.SurfaceMomentTerm
get_eval_shape() (sfepy.terms.terms_hyperelastic_tl.SurfaceFluxTLTerm
method), 922 method), 969
get_eval_shape() (sfepy.terms.terms_basic.VolumeSurfaceTerm
get_eval_shape() (sfepy.terms.terms_hyperelastic_tl.VolumeSurfaceTLTe

Index 1067
SfePy Documentation, Release version: 2022.1+git.f9873484

method), 970 sfepy.discrete.fem.facets), 747

get_eval_shape() (sfepy.terms.terms_hyperelastic_tl.VolumeTLTerm
get_facet_indices()
method), 971 (sfepy.discrete.common.region.Region method),
get_eval_shape() (sfepy.terms.terms_hyperelastic_ul.BulkPressureULTerm
743
method), 972 get_facet_neighbor_idx()
get_eval_shape() (sfepy.terms.terms_hyperelastic_ul.VolumeULTerm (sfepy.discrete.dg.fields.DGField method),
method), 974 783
get_eval_shape() (sfepy.terms.terms_membrane.TLMembraneTerm
get_facet_normals()
method), 975 (sfepy.discrete.common.extmods.cmesh.CMesh
get_eval_shape() (sfepy.terms.terms_multilinear.ETermBase method), 731
method), 985 get_facet_qp() (sfepy.discrete.dg.fields.DGField
get_eval_shape() (sfepy.terms.terms_navier_stokes.DivGradTerm method), 783
method), 988 get_facet_vols() (sfepy.discrete.dg.fields.DGField
get_eval_shape() (sfepy.terms.terms_navier_stokes.DivTerm method), 783
method), 990 get_family_data (sfepy.terms.terms_hyperelastic_tl.HyperElasticSurface
get_eval_shape() (sfepy.terms.terms_navier_stokes.GradTerm attribute), 966
method), 991 get_family_data (sfepy.terms.terms_hyperelastic_tl.HyperElasticTLBase
get_eval_shape() (sfepy.terms.terms_navier_stokes.StokesTerm attribute), 966
method), 995 get_family_data (sfepy.terms.terms_hyperelastic_ul.HyperElasticULBas
get_eval_shape() (sfepy.terms.terms_piezo.PiezoCouplingTerm attribute), 973
method), 997 get_fargs() (sfepy.terms.terms_adj_navier_stokes.AdjConvect1Term
get_eval_shape() (sfepy.terms.terms_piezo.PiezoStrainTerm method), 910
method), 998 get_fargs() (sfepy.terms.terms_adj_navier_stokes.AdjConvect2Term
get_eval_shape() (sfepy.terms.terms_piezo.PiezoStressTerm method), 910
method), 998 get_fargs() (sfepy.terms.terms_adj_navier_stokes.AdjDivGradTerm
get_eval_shape() (sfepy.terms.terms_surface.LinearTractionTerm method), 911
method), 1009 get_fargs() (sfepy.terms.terms_adj_navier_stokes.NSOFMinGradTerm
get_eval_shape() (sfepy.terms.terms_surface.SDLinearTractionTerm method), 911
method), 1010 get_fargs() (sfepy.terms.terms_adj_navier_stokes.NSOFSurfMinDPressD
get_eval_shape() (sfepy.terms.terms_surface.SDSufaceIntegrateTerm method), 912
method), 1011 get_fargs() (sfepy.terms.terms_adj_navier_stokes.NSOFSurfMinDPressT
get_eval_shape() (sfepy.terms.terms_surface.SufaceNormalDotTerm method), 912
method), 1011 get_fargs() (sfepy.terms.terms_adj_navier_stokes.SDConvectTerm
get_evaluate_cache() method), 913
(sfepy.discrete.fem.fields_base.FEField get_fargs() (sfepy.terms.terms_adj_navier_stokes.SDDivGradTerm
method), 750 method), 914
get_evaluate_cache() (sfepy.discrete.probes.Probe get_fargs() (sfepy.terms.terms_adj_navier_stokes.SDDivTerm
method), 702 method), 914
get_evaluator() (sfepy.discrete.problem.Problem get_fargs() (sfepy.terms.terms_adj_navier_stokes.SDDotTerm
method), 708 method), 915
get_examples() (in module gen_term_table), 654 get_fargs() (sfepy.terms.terms_adj_navier_stokes.SDGradDivStabilizatio
get_exp() (sfepy.homogenization.convolutions.ConvolutionKernel method), 915
method), 814 get_fargs() (sfepy.terms.terms_adj_navier_stokes.SDPSPGCStabilization
get_expression_arg_names() (in module method), 916
sfepy.discrete.equations), 693 get_fargs() (sfepy.terms.terms_adj_navier_stokes.SDPSPGPStabilization
get_expressions() (sfepy.terms.terms_multilinear.ExpressionBuildermethod), 917
method), 986 get_fargs() (sfepy.terms.terms_adj_navier_stokes.SDSUPGCStabilization
get_face_areas() (in module sfepy.linalg.geometry), method), 917
824 get_fargs() (sfepy.terms.terms_adj_navier_stokes.SUPGCAdjStabilizatio
get_facet_axes() (in module sfepy.discrete.iga.iga), method), 918
800 get_fargs() (sfepy.terms.terms_adj_navier_stokes.SUPGPAdj1Stabilizati
get_facet_base() (sfepy.discrete.dg.fields.DGField method), 919
method), 783 get_fargs() (sfepy.terms.terms_adj_navier_stokes.SUPGPAdj2Stabilizati
get_facet_dof_permutations() (in module method), 919

1068 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

get_fargs() (sfepy.terms.terms_basic.IntegrateMatTerm get_fargs() (sfepy.terms.terms_diffusion.SurfaceFluxTerm

method), 920 method), 944
get_fargs() (sfepy.terms.terms_basic.IntegrateOperatorTerm
get_fargs() (sfepy.terms.terms_dot.BCNewtonTerm
method), 920 method), 944
get_fargs() (sfepy.terms.terms_basic.IntegrateTerm get_fargs() (sfepy.terms.terms_dot.DotProductTerm
method), 921 method), 945
get_fargs() (sfepy.terms.terms_basic.SumNodalValuesTerm get_fargs() (sfepy.terms.terms_dot.DotSProductVolumeOperatorWETHT
method), 922 method), 946
get_fargs() (sfepy.terms.terms_basic.SurfaceMomentTermget_fargs() (sfepy.terms.terms_dot.DotSProductVolumeOperatorWTHTer
method), 922 method), 947
get_fargs() (sfepy.terms.terms_basic.VolumeSurfaceTermget_fargs() (sfepy.terms.terms_dot.ScalarDotGradIScalarTerm
method), 923 method), 947
get_fargs() (sfepy.terms.terms_basic.VolumeTerm get_fargs() (sfepy.terms.terms_dot.ScalarDotMGradScalarTerm
method), 923 method), 948
get_fargs() (sfepy.terms.terms_basic.ZeroTerm get_fargs() (sfepy.terms.terms_dot.VectorDotGradScalarTerm
method), 924 method), 949
get_fargs() (sfepy.terms.terms_biot.BiotETHTerm get_fargs() (sfepy.terms.terms_dot.VectorDotScalarTerm
method), 925 method), 950
get_fargs() (sfepy.terms.terms_biot.BiotStressTerm get_fargs() (sfepy.terms.terms_elastic.CauchyStrainTerm
method), 925 method), 951
get_fargs() (sfepy.terms.terms_biot.BiotTerm method), get_fargs() (sfepy.terms.terms_elastic.CauchyStressETHTerm
927 method), 951
get_fargs() (sfepy.terms.terms_biot.BiotTHTerm get_fargs() (sfepy.terms.terms_elastic.CauchyStressTerm
method), 926 method), 953
get_fargs() (sfepy.terms.terms_constraints.NonPenetrationPenaltyTerm
get_fargs() (sfepy.terms.terms_elastic.CauchyStressTHTerm
method), 930 method), 952
get_fargs() (sfepy.terms.terms_constraints.NonPenetrationTerm
get_fargs() (sfepy.terms.terms_elastic.ElasticWaveCauchyTerm
method), 931 method), 954
get_fargs() (sfepy.terms.terms_contact.ContactTerm get_fargs() (sfepy.terms.terms_elastic.ElasticWaveTerm
method), 932 method), 954
get_fargs() (sfepy.terms.terms_dg.AdvectionDGFluxTermget_fargs() (sfepy.terms.terms_elastic.LinearElasticETHTerm
method), 934 method), 955
get_fargs() (sfepy.terms.terms_dg.DiffusionDGFluxTermget_fargs() (sfepy.terms.terms_elastic.LinearElasticIsotropicTerm
method), 935 method), 956
get_fargs() (sfepy.terms.terms_dg.DiffusionInteriorPenaltyTerm
get_fargs() (sfepy.terms.terms_elastic.LinearElasticTerm
method), 935 method), 957
get_fargs() (sfepy.terms.terms_dg.NonlinearHyperbolicDGFluxTerm
get_fargs() (sfepy.terms.terms_elastic.LinearElasticTHTerm
method), 937 method), 956
get_fargs() (sfepy.terms.terms_dg.NonlinearScalarDotGradTerm
get_fargs() (sfepy.terms.terms_elastic.LinearPrestressTerm
method), 937 method), 958
get_fargs() (sfepy.terms.terms_diffusion.ConvectVGradSTerm
get_fargs() (sfepy.terms.terms_elastic.LinearStrainFiberTerm
method), 939 method), 958
get_fargs() (sfepy.terms.terms_diffusion.DiffusionCoupling
get_fargs() (sfepy.terms.terms_elastic.NonsymElasticTerm
method), 939 method), 959
get_fargs() (sfepy.terms.terms_diffusion.DiffusionRTerm get_fargs() (sfepy.terms.terms_elastic.SDLinearElasticTerm
method), 940 method), 960
get_fargs() (sfepy.terms.terms_diffusion.DiffusionTerm get_fargs() (sfepy.terms.terms_electric.ElectricSourceTerm
method), 940 method), 960
get_fargs() (sfepy.terms.terms_diffusion.DiffusionVelocityTerm
get_fargs() (sfepy.terms.terms_fibres.FibresActiveTLTerm
method), 941 method), 961
get_fargs() (sfepy.terms.terms_diffusion.SDDiffusionTermget_fargs() (sfepy.terms.terms_hyperelastic_base.DeformationGradientT
method), 943 method), 962
get_fargs() (sfepy.terms.terms_diffusion.SurfaceFluxOperatorTerm
get_fargs() (sfepy.terms.terms_hyperelastic_base.HyperElasticBase
method), 943 method), 962

Index 1069
SfePy Documentation, Release version: 2022.1+git.f9873484

get_fargs() (sfepy.terms.terms_hyperelastic_tl.BulkPressureTLTerm
get_fargs() (sfepy.terms.terms_piezo.PiezoStressTerm
method), 964 method), 998
get_fargs() (sfepy.terms.terms_hyperelastic_tl.DiffusionTLTerm
get_fargs() (sfepy.terms.terms_point.ConcentratedPointLoadTerm
method), 965 method), 999
get_fargs() (sfepy.terms.terms_hyperelastic_tl.SurfaceFluxTLTerm
get_fargs() (sfepy.terms.terms_point.LinearPointSpringTerm
method), 969 method), 1000
get_fargs() (sfepy.terms.terms_hyperelastic_tl.SurfaceTractionTLTerm
get_fargs() (sfepy.terms.terms_shells.Shell10XTerm
method), 969 method), 1007
get_fargs() (sfepy.terms.terms_hyperelastic_tl.VolumeSurfaceTLTerm
get_fargs() (sfepy.terms.terms_surface.ContactPlaneTerm
method), 970 method), 1008
get_fargs() (sfepy.terms.terms_hyperelastic_tl.VolumeTLTerm
get_fargs() (sfepy.terms.terms_surface.ContactSphereTerm
method), 971 method), 1009
get_fargs() (sfepy.terms.terms_hyperelastic_ul.BulkPressureULTerm
get_fargs() (sfepy.terms.terms_surface.LinearTractionTerm
method), 972 method), 1010
get_fargs() (sfepy.terms.terms_hyperelastic_ul.CompressibilityULTerm
get_fargs() (sfepy.terms.terms_surface.SDLinearTractionTerm
method), 973 method), 1010
get_fargs() (sfepy.terms.terms_hyperelastic_ul.VolumeULTerm
get_fargs() (sfepy.terms.terms_surface.SDSufaceIntegrateTerm
method), 974 method), 1011
get_fargs() (sfepy.terms.terms_membrane.TLMembraneTerm get_fargs() (sfepy.terms.terms_surface.SufaceNormalDotTerm
method), 975 method), 1011
get_fargs() (sfepy.terms.terms_multilinear.ETermBase get_fargs() (sfepy.terms.terms_surface.SurfaceJumpTerm
method), 985 method), 1012
get_fargs() (sfepy.terms.terms_navier_stokes.ConvectTerm get_fargs() (sfepy.terms.terms_volume.LinearVolumeForceTerm
method), 988 method), 1013
get_fargs() (sfepy.terms.terms_navier_stokes.DivGradTerm get_field() (sfepy.discrete.variables.FieldVariable
method), 988 method), 720
get_fargs() (sfepy.terms.terms_navier_stokes.DivOperatorTerm
get_filename_trunk()
method), 989 (sfepy.discrete.fem.meshio.MeshIO method),
get_fargs() (sfepy.terms.terms_navier_stokes.DivTerm 766
method), 990 get_filename_trunk()
get_fargs() (sfepy.terms.terms_navier_stokes.GradDivStabilizationTerm
(sfepy.discrete.fem.meshio.UserMeshIO
method), 990 method), 767
get_fargs() (sfepy.terms.terms_navier_stokes.GradTerm get_full() (sfepy.discrete.variables.DGFieldVariable
method), 991 method), 717
get_fargs() (sfepy.terms.terms_navier_stokes.LinearConvect2Term
get_full() (sfepy.discrete.variables.FieldVariable
method), 991 method), 720
get_fargs() (sfepy.terms.terms_navier_stokes.LinearConvectTerm
get_full() (sfepy.homogenization.convolutions.ConvolutionKernel
method), 992 method), 814
get_fargs() (sfepy.terms.terms_navier_stokes.PSPGCStabilizationTerm
get_full_indices() (in module
method), 992 sfepy.mechanics.tensors), 837
get_fargs() (sfepy.terms.terms_navier_stokes.StokesTermget_function() (sfepy.base.conf.ProblemConf
method), 995 method), 670
get_fargs() (sfepy.terms.terms_navier_stokes.StokesWaveDivTerm
get_function() (sfepy.terms.terms_multilinear.ECauchyStressTerm
method), 996 method), 976
get_fargs() (sfepy.terms.terms_navier_stokes.StokesWaveTerm
get_function() (sfepy.terms.terms_multilinear.EConvectTerm
method), 996 method), 976
get_fargs() (sfepy.terms.terms_navier_stokes.SUPGCStabilizationTerm
get_function() (sfepy.terms.terms_multilinear.EDiffusionTerm
method), 993 method), 977
get_fargs() (sfepy.terms.terms_navier_stokes.SUPGPStabilizationTerm
get_function() (sfepy.terms.terms_multilinear.EDivGradTerm
method), 994 method), 977
get_fargs() (sfepy.terms.terms_piezo.PiezoCouplingTermget_function() (sfepy.terms.terms_multilinear.EDivTerm
method), 997 method), 978
get_fargs() (sfepy.terms.terms_piezo.PiezoStrainTerm get_function() (sfepy.terms.terms_multilinear.EDotTerm
method), 998 method), 979

1070 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

get_function() (sfepy.terms.terms_multilinear.EGradTerm method), 756

method), 979 get_grid_plane() (in module
get_function() (sfepy.terms.terms_multilinear.EIntegrateOperatorTerm
sfepy.discrete.fem.periodic), 768
method), 980 get_homog_coefs_linear() (in module
get_function() (sfepy.terms.terms_multilinear.ELaplaceTerm sfepy.homogenization.micmac), 818
method), 980 get_homog_coefs_nonlinear() (in module
get_function() (sfepy.terms.terms_multilinear.ELinearConvectTermsfepy.homogenization.micmac), 818
method), 981 get_incident() (sfepy.discrete.common.extmods.cmesh.CMesh
get_function() (sfepy.terms.terms_multilinear.ELinearElasticTermmethod), 731
method), 981 get_indx() (sfepy.discrete.variables.Variables method),
get_function() (sfepy.terms.terms_multilinear.ELinearTractionTerm724
method), 982 get_info() (sfepy.discrete.common.dof_info.DofInfo
get_function() (sfepy.terms.terms_multilinear.ENonPenetrationPenaltyTerm
method), 727
method), 982 get_initial_condition()
get_function() (sfepy.terms.terms_multilinear.ENonSymElasticTerm (sfepy.discrete.variables.Variable method),
method), 983 722
get_function() (sfepy.terms.terms_multilinear.EScalarDotMGradScalarTerm
get_initial_state()
method), 983 (sfepy.discrete.problem.Problem method),
get_function() (sfepy.terms.terms_multilinear.EStokesTerm 708
method), 984 get_initial_vec() (sfepy.solvers.ts_solvers.ElastodynamicsBaseTS
get_function() (sfepy.terms.terms_piezo.SDPiezoCouplingTerm method), 901
method), 999 get_int_value() (in module
get_function() (sfepy.terms.terms_sensitivity.ESDDiffusionTerm sfepy.base.multiproc_mpi), 681
method), 1001 get_int_value() (in module
get_function() (sfepy.terms.terms_sensitivity.ESDDivGradTerm sfepy.base.multiproc_proc), 682
method), 1001 get_integrals() (sfepy.discrete.problem.Problem
get_function() (sfepy.terms.terms_sensitivity.ESDDotTerm method), 708
method), 1002 get_inter_facets() (in module
get_function() (sfepy.terms.terms_sensitivity.ESDLinearElasticTerm
sfepy.parallel.parallel), 855
method), 1003 get_interp_coors() (sfepy.discrete.variables.FieldVariable
get_function() (sfepy.terms.terms_sensitivity.ESDLinearTractionTerm
method), 720
method), 1003 get_interpol_scheme()
get_function() (sfepy.terms.terms_sensitivity.ESDPiezoCouplingTerm
(sfepy.discrete.dg.poly_spaces.LegendrePolySpace
method), 1004 method), 786
get_function() (sfepy.terms.terms_sensitivity.ESDStokesTerm
get_interpolation_name()
method), 1005 (sfepy.discrete.fem.geometry_element.GeometryElement
get_gap_ranges() (in module method), 756
sfepy.homogenization.coefs_phononic), 814 get_invariants() (in module
get_gdict_key() (sfepy.base.multiproc_mpi.RemoteQueueMaster sfepy.mechanics.membranes), 834
static method), 681 get_item_by_name() (sfepy.base.conf.ProblemConf
get_gel() (in module sfepy.discrete.dg.fields), 785 method), 670
get_geometry() (sfepy.discrete.fem.mappings.FEMappingget_jacobian() (in module
method), 759 sfepy.discrete.common.mappings), 739
get_geometry() (sfepy.discrete.iga.mappings.IGMapping get_keys() (sfepy.discrete.materials.Material method),
method), 802 698
get_geometry_types() (sfepy.terms.terms.Term get_knot_vector() (sfepy.mesh.bspline.BSpline
method), 907 method), 843
get_glyphs_scale_factor() (in module get_kwargs() (sfepy.terms.terms.Term method), 907
sfepy.postprocess.viewer), 867 get_lattice_volume() (in module
get_graph_conns() (sfepy.discrete.equations.Equations sfepy.homogenization.utils), 821
method), 691 get_lcbc_operator()
get_green_strain_sym3d() (in module (sfepy.discrete.equations.Equations method),
sfepy.mechanics.membranes), 834 691
get_grid() (sfepy.discrete.fem.geometry_element.GeometryElement
get_lcbc_operator()

Index 1071
SfePy Documentation, Release version: 2022.1+git.f9873484

(sfepy.discrete.variables.Variables method), 907

724 get_matrices() (sfepy.solvers.ts_solvers.ElastodynamicsBaseTS
get_list() (in module sfepy.base.multiproc_proc), 682 method), 901
get_local_entities() get_matrix_shape() (sfepy.discrete.variables.Variables
(sfepy.discrete.common.extmods.cmesh.CMesh method), 724
method), 731 get_mem_usage() (in module sfepy.base.mem_usage),
get_local_ids() (sfepy.discrete.common.extmods.cmesh.CMesh 679
method), 731 get_mesh_bounding_box()
get_local_ordering() (in module (sfepy.discrete.fem.domain.FEDomain
sfepy.parallel.parallel), 855 method), 745
get_lock() (in module sfepy.base.multiproc_proc), 682 get_mesh_coors() (sfepy.discrete.fem.domain.FEDomain
get_log_freqs() (in module method), 745
sfepy.homogenization.coefs_phononic), 814 get_mesh_coors() (sfepy.discrete.problem.Problem
get_log_name() (sfepy.base.log.Log method), 677 method), 708
get_logger() (in module sfepy.base.multiproc_mpi), get_micro_cache_key()
681 (sfepy.homogenization.homogen_app.HomogenizationApp
get_logging_conf() (in module sfepy.base.log), 677 method), 817
get_longest_edge_and_gps() (in module get_min_dt() (in module sfepy.solvers.ts_solvers), 904
sfepy.mechanics.extmods.ccontres), 841 get_min_value() (in module sfepy.discrete.fem.utils),
get_loop_indices() (in module 775
sfepy.terms.terms_multilinear), 987 get_min_vertex_distance() (in module
get_ls() (sfepy.discrete.problem.Problem method), 708 sfepy.discrete.fem.mesh), 761
get_manager() (in module sfepy.base.multiproc_proc), get_min_vertex_distance_naive() (in module
682 sfepy.discrete.fem.mesh), 761
get_mapping() (sfepy.discrete.common.fields.Field get_mirror_region()
method), 735 (sfepy.discrete.common.region.Region method),
get_mapping() (sfepy.discrete.fem.mappings.SurfaceMapping 743
method), 759 get_mpdict_value() (in module
get_mapping() (sfepy.discrete.fem.mappings.VolumeMapping sfepy.base.multiproc_proc), 682
method), 759 get_mtx_i() (sfepy.discrete.fem.poly_spaces.FEPolySpace
get_mapping() (sfepy.discrete.iga.mappings.IGMapping method), 769
method), 802 get_mtx_i() (sfepy.discrete.fem.poly_spaces.LagrangeTensorProductPolyS
get_mapping() (sfepy.discrete.structural.mappings.Shell10XMappingmethod), 770
method), 804 get_multiproc() (in module sfepy.base.multiproc), 679
get_mapping() (sfepy.discrete.variables.FieldVariable get_n_cells() (sfepy.discrete.common.region.Region
method), 720 method), 743
get_mapping() (sfepy.terms.terms.Term method), 907 get_n_dof_total() (sfepy.discrete.common.dof_info.DofInfo
get_mapping_data() (in module method), 727
sfepy.discrete.common.mappings), 739 get_n_el_nod() (in module
get_mapping_data() (in module sfepy.discrete.dg.poly_spaces), 788
sfepy.mechanics.shell10x), 837 get_names() (sfepy.base.base.Container method), 660
get_maps() (sfepy.solvers.oseen.StabilizationFunction get_names() (sfepy.base.base.OneTypeList method),
method), 895 661
get_mat_id() (sfepy.postprocess.sources.FileSource get_nls() (sfepy.discrete.problem.Problem method),
method), 860 708
get_mat_id() (sfepy.postprocess.sources.GenericFileSource get_nls_functions()
method), 861 (sfepy.discrete.problem.Problem method),
get_material_names() (sfepy.terms.terms.Term 708
method), 907 get_nodal_values() (sfepy.discrete.dg.fields.DGField
get_material_names() (sfepy.terms.terms.Terms method), 784
method), 908 get_non_diagonal_indices() (in module
get_materials() (sfepy.discrete.problem.Problem sfepy.mechanics.tensors), 837
method), 708 get_nonsym_grad_op() (in module
get_materials() (sfepy.terms.terms.Term method), sfepy.terms.terms_sensitivity), 1005

1072 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

get_normals() (in module method), 985

sfepy.discrete.common.mappings), 740 get_perpendiculars() (in module
get_normals() (sfepy.terms.terms_multilinear.ETermBase sfepy.linalg.geometry), 824
method), 985 get_physical_qps() (in module
get_nth_fun() (sfepy.discrete.dg.poly_spaces.LegendrePolySpace sfepy.discrete.common.mappings), 740
method), 786 get_physical_qps() (sfepy.discrete.fem.mappings.FEMapping
get_nth_fun_der() (sfepy.discrete.dg.poly_spaces.LegendrePolySpace method), 759
method), 787 get_physical_qps() (sfepy.discrete.iga.mappings.IGMapping
get_num_workers() (in module sfepy.base.multiproc), method), 802
679 get_physical_qps() (sfepy.discrete.structural.mappings.Shell10XMappin
get_nums() (in module sfepy.base.resolve_deps), 685 method), 804
get_opacities() (in module sfepy.postprocess.viewer), get_physical_qps() (sfepy.terms.terms.Term method),
867 907
get_operands() (sfepy.terms.terms_multilinear.ETermBase get_physical_qps() (sfepy.terms.terms_shells.Shell10XTerm
method), 985 method), 1007
get_operator() (sfepy.discrete.common.dof_info.EquationMap get_points() (sfepy.discrete.probes.CircleProbe
method), 727 method), 701
get_or_create_hdf5_group() (in module get_points() (sfepy.discrete.probes.LineProbe
sfepy.base.ioutils), 674 method), 701
get_orientations() (sfepy.discrete.common.extmods.cmesh.CMesh
get_points() (sfepy.discrete.probes.PointsProbe
method), 731 method), 701
get_ortho_d() (in module sfepy.tests.test_tensors), get_points() (sfepy.discrete.probes.RayProbe
1030 method), 703
get_output() (sfepy.homogenization.coefs_base.CorrMiniApp get_poly() (in module sfepy.tests.test_quadratures),
method), 807 1028
get_output_approx_order() get_position_counts() (in module
(sfepy.discrete.fem.fields_base.FEField sfepy.postprocess.viewer), 867
method), 750 get_potential_cells() (in module
get_output_function() (sfepy.base.base.Output sfepy.discrete.common.global_interp), 736
method), 661 get_prefix() (sfepy.mechanics.units.Unit static
get_output_name() (sfepy.discrete.problem.Problem method), 841
method), 709 get_primary() (sfepy.discrete.variables.Variable
get_output_prefix() (sfepy.base.base.Output method), 722
method), 661 get_primary_name() (sfepy.discrete.variables.Variable
get_output_shape() (in module method), 722
sfepy.terms.terms_multilinear), 987 get_print_info() (in module sfepy.base.ioutils), 674
get_output_suffix() (in module get_print_info() (in module sfepy.solvers.ts), 899
sfepy.homogenization.recovery), 820 get_qp() (sfepy.discrete.fem.fields_base.FEField
get_p_edge() (in module sfepy.tests.test_functions), method), 750
1022 get_qp() (sfepy.discrete.integrals.Integral method), 697
get_parameter_names() (sfepy.terms.terms.Term get_qp_key() (sfepy.terms.terms.Term method), 907
method), 907 get_queue() (in module sfepy.base.multiproc_mpi), 681
get_parameter_variables() (sfepy.terms.terms.Term get_queue() (in module sfepy.base.multiproc_proc),
method), 907 682
get_parents() (in module get_range_indices() (in module sfepy.terms.utils),
sfepy.discrete.common.region), 744 1013
get_pars() (in module get_ranges() (in module
sfepy.tests.test_elasticity_small_strain), 1021 sfepy.homogenization.coefs_phononic), 814
get_pars() (in module sfepy.tests.test_functions), 1022 get_raveled_index() (in module
get_pars() (in module sfepy.discrete.iga.iga), 800
sfepy.tests.test_term_consistency), 1031 get_raveler() (in module sfepy.discrete.dg.fields), 785
get_patch_box_regions() (in module get_raw() (sfepy.base.conf.ProblemConf method), 670
sfepy.discrete.iga.iga), 800 get_reduced() (sfepy.discrete.variables.FieldVariable
get_paths() (sfepy.terms.terms_multilinear.ETermBase method), 720

Index 1073
SfePy Documentation, Release version: 2022.1+git.f9873484

get_reduced_state() sfepy.base.conf ), 670

(sfepy.discrete.variables.Variables method), get_standard_type_defs() (in module
724 sfepy.base.parse_conf ), 683
get_ref_coors() (in module get_state() (sfepy.discrete.variables.Variables
sfepy.discrete.common.global_interp), 736 method), 724
get_ref_coors_convex() (in module get_state() (sfepy.solvers.ts.TimeStepper method), 898
sfepy.discrete.common.global_interp), 737 get_state() (sfepy.solvers.ts.VariableTimeStepper
get_ref_coors_general() (in module method), 899
sfepy.discrete.common.global_interp), 738 get_state_in_region()
get_region() (sfepy.terms.terms.ConnInfo method), (sfepy.discrete.variables.FieldVariable
905 method), 720
get_region() (sfepy.terms.terms.Term method), 907 get_state_names() (sfepy.terms.terms.Term method),
get_region_info() (sfepy.discrete.dg.fields.DGField 907
static method), 784 get_state_parts() (sfepy.discrete.variables.Variables
get_region_name() (sfepy.terms.terms.ConnInfo method), 724
method), 905 get_state_variables() (sfepy.terms.terms.Term
get_restart_filename() method), 907
(sfepy.discrete.problem.Problem method), get_step_time() (sfepy.postprocess.sources.FileSource
709 method), 860
get_save_name() (sfepy.homogenization.coefs_base.CorrMiniApp
get_str() (sfepy.terms.terms.Term method), 907
method), 807 get_subdict() (in module sfepy.base.base), 663
get_save_name_base() get_subset_info() (sfepy.discrete.common.dof_info.DofInfo
(sfepy.homogenization.coefs_base.CorrMiniApp method), 727
method), 807 get_surface_basis()
get_schur() (sfepy.solvers.ls_mumps.MumpsSolver (sfepy.discrete.fem.fields_nodal.GlobalNodalLikeBasis
method), 875 method), 754
get_shape() (sfepy.discrete.common.mappings.PhysicalQPs get_surface_basis()
method), 739 (sfepy.discrete.iga.fields.IGField method),
get_shape_kind() (in module sfepy.terms.terms), 909 796
get_simplex_circumcentres() (in module get_surface_degrees() (in module
sfepy.linalg.geometry), 824 sfepy.discrete.iga.iga), 800
get_simplex_cubature() (in module get_surface_entities()
sfepy.discrete.simplex_cubature), 717 (sfepy.discrete.fem.geometry_element.GeometryElement
get_simplex_volumes() (in module method), 756
sfepy.linalg.geometry), 824 get_surface_faces() (in module extract_surface),
get_size_hint() (sfepy.postprocess.viewer.Viewer 651
method), 866 get_surface_facets()
get_sizes() (in module sfepy.parallel.parallel), 855 (sfepy.discrete.common.extmods.cmesh.CMesh
get_sizes() (in module sfepy.terms.terms_multilinear), method), 731
987 get_sym_indices() (in module
get_slaves() (in module sfepy.base.multiproc_mpi), sfepy.mechanics.tensors), 837
681 get_t4_from_t2s() (in module
get_slice_ops() (in module sfepy.mechanics.tensors), 837
sfepy.terms.terms_multilinear), 987 get_tangent_stress_matrix() (in module
get_solver() (sfepy.discrete.problem.Problem sfepy.mechanics.membranes), 835
method), 709 get_tensor_product_conn() (in module
get_solver_conf() (sfepy.discrete.problem.Problem sfepy.mesh.mesh_generators), 850
method), 709 get_timestepper() (sfepy.discrete.problem.Problem
get_sorted_dependencies() method), 709
(sfepy.homogenization.engine.HomogenizationWorkerget_tolerance() (sfepy.solvers.solvers.LinearSolver
static method), 816 method), 897
get_sphinx_make_command() (in module get_trace() (in module sfepy.mechanics.tensors), 838
build_helpers), 647 get_true_order() (sfepy.discrete.fem.fields_base.FEField
get_standard_keywords() (in module method), 750

1074 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

get_true_order() (sfepy.discrete.iga.fields.IGField get_vectors() (sfepy.discrete.fem.lcbc_operators.NormalDirectionOpera

method), 796 method), 758
get_trunk() (in module sfepy.base.ioutils), 674 get_vertices() (in module sfepy.tests.test_regions),
get_ts_info() (sfepy.postprocess.sources.FileSource 1029
method), 860 get_vertices() (sfepy.discrete.fem.fields_base.FEField
get_ts_val() (sfepy.homogenization.coefs_base.CorrSolution method), 750
method), 808 get_virtual_name() (sfepy.terms.terms.Term method),
get_tss() (sfepy.discrete.problem.Problem method), 908
709 get_virtual_variable() (sfepy.terms.terms.Term
get_tss_functions() method), 908
(sfepy.discrete.problem.Problem method), get_volume() (in module sfepy.homogenization.utils),
709 821
get_type() (sfepy.base.ioutils.DataSoftLink method), get_volume() (in module
672 sfepy.tests.test_mesh_smoothing), 1026
get_u_edge() (in module sfepy.tests.test_functions), get_volumes() (sfepy.discrete.common.extmods.cmesh.CMesh
1022 method), 731
get_unraveled_indices() (in module get_volumetric_tensor() (in module
sfepy.discrete.iga.iga), 801 sfepy.mechanics.tensors), 838
get_unraveler() (in module sfepy.discrete.dg.fields), get_von_mises_stress() (in module
786 sfepy.mechanics.tensors), 838
get_user_names() (sfepy.terms.terms.Term method), get_vtk_by_group() (in module
907 sfepy.postprocess.utils_vtk), 863
get_user_names() (sfepy.terms.terms.Terms method), get_vtk_edges() (in module
908 sfepy.postprocess.utils_vtk), 863
get_var_names() (sfepy.discrete.conditions.LinearCombinationBC
get_vtk_from_file() (in module
method), 688 sfepy.postprocess.utils_vtk), 863
get_variable() (sfepy.discrete.equations.Equations get_vtk_from_mesh() (in module
method), 691 sfepy.postprocess.utils_vtk), 864
get_variable_dependencies() get_vtk_surface() (in module
(sfepy.discrete.equations.Equations method), sfepy.postprocess.utils_vtk), 864
691 getBCnum() (sfepy.mesh.geom_tools.geometry method),
get_variable_names() 846
(sfepy.discrete.equations.Equations method), getcenterpoint() (sfepy.mesh.geom_tools.surface
691 method), 847
get_variable_names() (sfepy.terms.terms.Term getholepoints() (sfepy.mesh.geom_tools.surface
method), 907 method), 847
get_variable_names() (sfepy.terms.terms.Terms getinsidepoint() (sfepy.mesh.geom_tools.surface
method), 909 method), 847
get_variables() (sfepy.discrete.problem.Problem getinsidepoint() (sfepy.mesh.geom_tools.volume
method), 709 method), 848
get_variables() (sfepy.homogenization.coefs_perfusion.CoefRegion
getlines() (sfepy.mesh.geom_tools.surface method),
method), 809 847
get_variables() (sfepy.homogenization.coefs_perfusion.CorrRegion
getn() (sfepy.mesh.geom_tools.geomobject method), 847
method), 809 getpoints() (sfepy.mesh.geom_tools.line method), 847
get_variables() (sfepy.terms.terms.Term method), getpoints() (sfepy.mesh.geom_tools.surface method),
908 848
get_vec_part() (sfepy.discrete.variables.Variables getstr() (sfepy.mesh.geom_tools.point method), 847
method), 724 getsurfaces() (sfepy.mesh.geom_tools.physicalsurface
get_vector() (sfepy.terms.terms.Term method), 908 method), 847
get_vector_format() getsurfaces() (sfepy.mesh.geom_tools.volume
(sfepy.discrete.fem.meshio.MeshIO method), method), 848
766 getvolumes() (sfepy.mesh.geom_tools.physicalvolume
get_vectors() (sfepy.discrete.fem.lcbc_operators.EdgeDirectionOperator
method), 847
method), 756 getxyz() (sfepy.mesh.geom_tools.point method), 847

Index 1075
SfePy Documentation, Release version: 2022.1+git.f9873484

GlobalNodalLikeBasis (class in has_extra_nodes() (sfepy.discrete.fem.poly_spaces.NodeDescription

sfepy.discrete.fem.fields_nodal), 754 method), 770
GmshIO (class in sfepy.discrete.fem.meshio), 762 has_faces() (sfepy.discrete.common.domain.Domain
grad() (in module sfepy.linalg.sympy_operators), 827 method), 728
grad_as_vector() (in module has_key() (sfepy.base.base.Container method), 660
sfepy.terms.terms_adj_navier_stokes), 919 has_same_mesh() (sfepy.discrete.variables.FieldVariable
grad_v() (in module sfepy.linalg.sympy_operators), 827 method), 720
grad_vector_to_matrix() (in module has_virtuals() (sfepy.discrete.variables.Variables
eval_ns_forms), 650 method), 724
GradDivStabilizationTerm (class in have_good_cython() (in module build_helpers), 647
sfepy.terms.terms_navier_stokes), 990 HDF5BaseData (class in sfepy.base.ioutils), 673
gradjacobiP() (sfepy.discrete.dg.poly_spaces.LegendrePolySpace
HDF5ContextManager (class in sfepy.base.ioutils), 673
method), 787 HDF5Data (class in sfepy.base.ioutils), 673
gradlegendreP() (sfepy.discrete.dg.poly_spaces.LegendrePolySpace
HDF5MeshIO (class in sfepy.discrete.fem.meshio), 764
method), 787 HDF5XdmfMeshIO (class in sfepy.discrete.fem.meshio),
GradTerm (class in sfepy.terms.terms_navier_stokes), 765
990 he_eval_from_mtx() (in module
graph_components() (in module sfepy.terms.extmods.terms), 1018
sfepy.discrete.common.extmods.cmesh), 732 he_residuum_from_mtx() (in module
group_by_variables() sfepy.terms.extmods.terms), 1018
(sfepy.discrete.conditions.Conditions method), head() (in module sfepy.discrete.dg.dg_1D_vizualizer),
686 776
group_chains() (in module Histories (class in sfepy.discrete.fem.history), 756
sfepy.discrete.common.dof_info), 728 History (class in sfepy.discrete.fem.history), 756
guess() (sfepy.discrete.fem.meshio.ANSYSCDBMeshIO HomogenizationApp (class in
static method), 761 sfepy.homogenization.homogen_app), 817
guess_time_units() (in module HomogenizationEngine (class in
sfepy.postprocess.time_history), 862 sfepy.homogenization.engine), 815
HomogenizationWorker (class in
H sfepy.homogenization.engine), 815
H1BernsteinSurfaceField (class in HomogenizationWorkerMulti (class in
sfepy.discrete.fem.fields_positive), 755 sfepy.homogenization.engine), 816
H1BernsteinVolumeField (class in HomogenizationWorkerMultiMPI (class in
sfepy.discrete.fem.fields_positive), 755 sfepy.homogenization.engine), 817
H1DiscontinuousField (class in hyperelastic_mode (sfepy.terms.terms_hyperelastic_tl.HyperElasticTLBa
sfepy.discrete.fem.fields_nodal), 754 attribute), 966
H1HierarchicVolumeField (class in hyperelastic_mode (sfepy.terms.terms_hyperelastic_ul.HyperElasticULB
sfepy.discrete.fem.fields_hierarchic), 753 attribute), 973
H1Mixin (class in sfepy.discrete.fem.fields_base), 751 HyperElasticBase (class in
H1NodalMixin (class in sfepy.discrete.fem.fields_nodal), sfepy.terms.terms_hyperelastic_base), 962
754 HyperElasticFamilyData (class in
H1NodalSurfaceField (class in sfepy.terms.terms_hyperelastic_base), 962
sfepy.discrete.fem.fields_nodal), 754 HyperElasticSurfaceTLBase (class in
H1NodalVolumeField (class in sfepy.terms.terms_hyperelastic_tl), 966
sfepy.discrete.fem.fields_nodal), 754 HyperElasticSurfaceTLFamilyData (class in
H1SNodalSurfaceField (class in sfepy.terms.terms_hyperelastic_tl), 966
sfepy.discrete.fem.fields_nodal), 755 HyperElasticTLBase (class in
H1SNodalVolumeField (class in sfepy.terms.terms_hyperelastic_tl), 966
sfepy.discrete.fem.fields_nodal), 755 HyperElasticTLFamilyData (class in
has_attr() (in module sfepy.config), 657 sfepy.terms.terms_hyperelastic_tl), 966
has_cells() (sfepy.discrete.common.region.Region HyperElasticULBase (class in
method), 743 sfepy.terms.terms_hyperelastic_ul), 973
has_ebc() (sfepy.discrete.variables.Variables method), HyperElasticULFamilyData (class in
724 sfepy.terms.terms_hyperelastic_ul), 973

1076 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

HypermeshAsciiMeshIO (class in init_data_struct() (sfepy.terms.terms_hyperelastic_base.HyperElasticF

sfepy.discrete.fem.meshio), 765 method), 963
init_global_search() (in module
I sfepy.mechanics.extmods.ccontres), 841
icntl (sfepy.solvers.ls_mumps.mumps_struc_c_4 at- init_history() (sfepy.discrete.variables.Variable
tribute), 876 method), 722
icntl (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at- init_history() (sfepy.discrete.variables.Variables
tribute), 879 method), 724
icntl (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at- init_petsc_args() (in module sfepy.parallel.parallel),
tribute), 883 855
icntl (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at- init_seq_selection()
tribute), 886 (sfepy.postprocess.viewer.SetStep method),
icntl (sfepy.solvers.ls_mumps.mumps_struc_c_x at- 864
tribute), 889 init_slepc_args() (in module sfepy.solvers.eigen),
IdentityLimiter (class in sfepy.discrete.dg.limiters), 870
789 init_solvers() (sfepy.discrete.problem.Problem
iel (sfepy.discrete.fem.extmods.bases.CLagrangeContext method), 709
attribute), 745 init_solvers() (sfepy.homogenization.coefs_base.MiniAppBase
iel (sfepy.discrete.iga.extmods.igac.CNURBSContext at- method), 808
tribute), 793 init_state() (sfepy.discrete.equations.Equations
IGDomain (class in sfepy.discrete.iga.domain), 791 method), 691
IGField (class in sfepy.discrete.iga.fields), 795 init_state() (sfepy.discrete.variables.Variables
IGMapping (class in sfepy.discrete.iga.mappings), 801 method), 724
import_file() (in module sfepy.base.base), 663 init_subproblems() (sfepy.solvers.ls.MultiProblem
in1d() (in module sfepy.base.compat), 666 method), 871
in_dir() (in module sfepy.tests.test_mesh_interp), 1026 init_time() (sfepy.discrete.equations.Equations
IndexedStruct (class in sfepy.base.base), 660 method), 691
indices (sfepy.discrete.common.extmods.cmesh.CConnectivity init_time() (sfepy.discrete.problem.Problem method),
attribute), 730 710
InDir (class in sfepy.base.ioutils), 673 init_vec() (in module sfepy.tests.test_conditions), 1019
inedir() (in module sfepy.tests.test_declarative_examples),InitialCondition (class in sfepy.discrete.conditions),
1020 687
infinity_norm() (in module sfepy.linalg.sparse), 826 initialize_options()
info (sfepy.solvers.ls_mumps.mumps_struc_c_4 at- (build_helpers.NoOptionsDocs method),
tribute), 876 646
info (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 insert() (sfepy.base.base.Container method), 660
attribute), 879 insert() (sfepy.terms.terms.Terms method), 909
info (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 insert_as_static_method() (in module
attribute), 883 sfepy.base.base), 664
info (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 insert_knot() (sfepy.mesh.bspline.BSpline method),
attribute), 886 843
infog (sfepy.solvers.ls_mumps.mumps_struc_c_4 at- insert_method() (in module sfepy.base.base), 664
tribute), 876 insert_sparse_to_csr() (in module
infog (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at- sfepy.linalg.sparse), 826
tribute), 879 insert_static_method() (in module sfepy.base.base),
infog (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at- 664
tribute), 883 insert_strided_axis() (in module sfepy.linalg.utils),
infog (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at- 829
tribute), 886 insert_sub_reqs() (in module
init() (sfepy.mechanics.matcoefs.ElasticConstants sfepy.homogenization.engine), 817
method), 831 instance_number (sfepy.solvers.ls_mumps.mumps_struc_c_4
init_data() (sfepy.discrete.variables.Variable method), attribute), 876
722 instance_number (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
attribute), 879

Index 1077
SfePy Documentation, Release version: 2022.1+git.f9873484

instance_number (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 integration (sfepy.terms.terms_basic.VolumeTerm at-

attribute), 883 tribute), 923
instance_number (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 integration (sfepy.terms.terms_biot.BiotStressTerm at-
attribute), 886 tribute), 925
int_dt() (sfepy.homogenization.convolutions.ConvolutionKernel
integration (sfepy.terms.terms_constraints.NonPenetrationPenaltyTerm
method), 814 attribute), 931
Integral (class in sfepy.discrete.integrals), 697 integration (sfepy.terms.terms_constraints.NonPenetrationTerm
integral (sfepy.discrete.common.extmods.mappings.CMapping attribute), 931
attribute), 733 integration (sfepy.terms.terms_contact.ContactTerm
IntegralMeanValueOperator (class in attribute), 932
sfepy.discrete.fem.lcbc_operators), 757 integration (sfepy.terms.terms_dg.AdvectionDGFluxTerm
IntegralProbe (class in sfepy.discrete.probes), 701 attribute), 934
Integrals (class in sfepy.discrete.integrals), 697 integration (sfepy.terms.terms_dg.DiffusionDGFluxTerm
integrate() (sfepy.discrete.common.extmods.mappings.CMapping attribute), 935
method), 733 integration (sfepy.terms.terms_dg.NonlinearHyperbolicDGFluxTerm
integrate() (sfepy.discrete.integrals.Integral method), attribute), 937
697 integration (sfepy.terms.terms_diffusion.DiffusionVelocityTerm
integrate() (sfepy.terms.terms_contact.ContactTerm attribute), 941
static method), 932 integration (sfepy.terms.terms_diffusion.SurfaceFluxOperatorTerm
integrate() (sfepy.terms.terms_hyperelastic_base.HyperElasticBaseattribute), 943
static method), 962 integration (sfepy.terms.terms_diffusion.SurfaceFluxTerm
integrate_along_line() (in module probe), 643 attribute), 944
integrate_in_time() (in module integration (sfepy.terms.terms_dot.BCNewtonTerm at-
sfepy.homogenization.utils), 821 tribute), 944
IntegrateMatTerm (class in sfepy.terms.terms_basic), integration (sfepy.terms.terms_dot.DotProductTerm
919 attribute), 946
IntegrateOperatorTerm (class in integration (sfepy.terms.terms_elastic.CauchyStrainTerm
sfepy.terms.terms_basic), 920 attribute), 951
IntegrateSurfaceMatTerm (class in integration (sfepy.terms.terms_elastic.CauchyStressTerm
sfepy.terms.terms_compat), 928 attribute), 953
IntegrateSurfaceOperatorTerm (class in integration (sfepy.terms.terms_hyperelastic_tl.SurfaceFluxTLTerm
sfepy.terms.terms_compat), 928 attribute), 969
IntegrateSurfaceTerm (class in integration (sfepy.terms.terms_hyperelastic_tl.SurfaceTractionTLTerm
sfepy.terms.terms_compat), 929 attribute), 970
IntegrateTerm (class in sfepy.terms.terms_basic), 921 integration (sfepy.terms.terms_hyperelastic_tl.VolumeSurfaceTLTerm
IntegrateVolumeMatTerm (class in attribute), 970
sfepy.terms.terms_compat), 929 integration (sfepy.terms.terms_membrane.TLMembraneTerm
IntegrateVolumeOperatorTerm (class in attribute), 975
sfepy.terms.terms_compat), 929 integration (sfepy.terms.terms_multilinear.EDotTerm
IntegrateVolumeTerm (class in attribute), 979
sfepy.terms.terms_compat), 929 integration (sfepy.terms.terms_multilinear.EIntegrateOperatorTerm
integration (sfepy.terms.terms.Term attribute), 908 attribute), 980
integration (sfepy.terms.terms_adj_navier_stokes.NSOFSurfMinDPressTerm
integration (sfepy.terms.terms_multilinear.ELinearTractionTerm
attribute), 912 attribute), 982
integration (sfepy.terms.terms_basic.IntegrateMatTerm integration (sfepy.terms.terms_multilinear.ENonPenetrationPenaltyTerm
attribute), 920 attribute), 982
integration (sfepy.terms.terms_basic.IntegrateOperatorTerm integration (sfepy.terms.terms_navier_stokes.DivTerm
attribute), 921 attribute), 990
integration (sfepy.terms.terms_basic.IntegrateTerm at- integration (sfepy.terms.terms_navier_stokes.GradTerm
tribute), 921 attribute), 991
integration (sfepy.terms.terms_basic.SurfaceMomentTermintegration (sfepy.terms.terms_point.ConcentratedPointLoadTerm
attribute), 922 attribute), 999
integration (sfepy.terms.terms_basic.VolumeSurfaceTermintegration (sfepy.terms.terms_point.LinearPointSpringTerm
attribute), 923 attribute), 1000

1078 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

integration (sfepy.terms.terms_sensitivity.ESDLinearTractionTerm
irhs_sparse (sfepy.solvers.ls_mumps.mumps_struc_c_4
attribute), 1003 attribute), 877
integration (sfepy.terms.terms_shells.Shell10XTerm irhs_sparse (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
attribute), 1007 attribute), 880
integration (sfepy.terms.terms_surface.ContactPlaneTermirhs_sparse (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
attribute), 1008 attribute), 883
integration (sfepy.terms.terms_surface.ContactSphereTerm irhs_sparse (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
attribute), 1009 attribute), 886
integration (sfepy.terms.terms_surface.LinearTractionTermirn (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
attribute), 1010 tribute), 877
integration (sfepy.terms.terms_surface.SDLinearTractionTerm
irn (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at-
attribute), 1010 tribute), 880
integration (sfepy.terms.terms_surface.SDSufaceIntegrateTerm
irn (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at-
attribute), 1011 tribute), 883
integration (sfepy.terms.terms_surface.SufaceNormalDotTerm
irn (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at-
attribute), 1011 tribute), 886
integration (sfepy.terms.terms_surface.SurfaceJumpTermirn_loc (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
attribute), 1012 tribute), 877
interp_conv_mat() (in module irn_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
sfepy.homogenization.utils), 822 attribute), 880
interp_to_qp() (sfepy.discrete.fem.fields_base.FEField irn_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
method), 750 attribute), 883
interp_v_vals_to_n_vals() irn_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
(sfepy.discrete.fem.fields_nodal.H1NodalSurfaceField attribute), 886
method), 754 is_active_bc() (in module
interp_v_vals_to_n_vals() sfepy.discrete.common.dof_info), 728
(sfepy.discrete.fem.fields_nodal.H1NodalVolumeField
is_adjust (sfepy.postprocess.viewer.SetStep attribute),
method), 754 864
invalidate_evaluate_cache() is_bubble (sfepy.discrete.fem.extmods.bases.CLagrangeContext
(sfepy.discrete.variables.FieldVariable attribute), 745
method), 721 is_complex() (sfepy.discrete.variables.Variable
invalidate_evaluate_caches() method), 722
(sfepy.discrete.variables.Variables method), is_cyclic (sfepy.discrete.probes.CircleProbe attribute),
724 701
invalidate_term_caches() is_cyclic (sfepy.discrete.probes.Probe attribute), 702
(sfepy.discrete.equations.Equations method), is_derived_class() (in module sfepy.base.base), 664
691 is_finite() (sfepy.discrete.variables.Variable method),
inverse_element_mapping() (in module 722
sfepy.linalg.geometry), 824 is_higher_order() (sfepy.discrete.fem.fields_base.FEField
invert_dict() (in module sfepy.base.base), 664 method), 751
invert_remap() (in module sfepy.discrete.fem.utils), is_higher_order() (sfepy.discrete.iga.fields.IGField
775 method), 796
iplot() (in module sfepy.base.plotutils), 684 is_integer() (in module sfepy.base.base), 664
ipython_shell() (in module sfepy.base.base), 664 is_kind() (sfepy.discrete.variables.Variable method),
irhs_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 722
attribute), 886 is_linear() (sfepy.discrete.problem.Problem method),
irhs_ptr (sfepy.solvers.ls_mumps.mumps_struc_c_4 at- 710
tribute), 876 is_nurbs() (in module sfepy.discrete.iga.extmods.igac),
irhs_ptr (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 794
attribute), 880 is_parameter() (sfepy.discrete.variables.Variable
irhs_ptr (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 method), 722
attribute), 883 is_real() (sfepy.discrete.variables.Variable method),
irhs_ptr (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 722
attribute), 886 is_release() (sfepy.config.Config method), 657

Index 1079
SfePy Documentation, Release version: 2022.1+git.f9873484

is_remote_dict() (in module sfepy.base.multiproc), iter_from() (sfepy.solvers.ts.VariableTimeStepper

679 method), 899
is_remote_dict() (in module iter_from_current()
sfepy.base.multiproc_mpi), 681 (sfepy.solvers.ts.VariableTimeStepper method),
is_remote_dict() (in module 899
sfepy.base.multiproc_proc), 682 iter_names() (in module sfepy.base.log), 677
is_sequence() (in module sfepy.base.base), 664 iter_nonsym() (in module sfepy.homogenization.utils),
is_state() (sfepy.discrete.variables.Variable method), 822
722 iter_single() (sfepy.discrete.conditions.Condition
is_state_or_parameter() method), 686
(sfepy.discrete.variables.Variable method), iter_solutions() (sfepy.homogenization.coefs_base.CorrSolution
722 method), 808
is_string() (in module sfepy.base.base), 664 iter_state() (sfepy.discrete.variables.Variables
is_surface (sfepy.discrete.dg.fields.DGField attribute), method), 724
784 iter_sym() (in module sfepy.homogenization.utils), 822
is_sym (sfepy.homogenization.coefs_base.CoefNonSym iter_sym() (sfepy.homogenization.coefs_base.CoefNonSym
attribute), 806 static method), 806
is_sym (sfepy.homogenization.coefs_base.CoefNonSymNonSym iter_sym() (sfepy.homogenization.coefs_base.CoefNonSymNonSym
attribute), 806 static method), 806
is_sym (sfepy.homogenization.coefs_base.CoefSym at- iter_sym() (sfepy.homogenization.coefs_base.CoefSym
tribute), 807 static method), 807
is_sym (sfepy.homogenization.coefs_base.CoefSymSym iter_sym() (sfepy.homogenization.coefs_base.CoefSymSym
attribute), 807 static method), 807
is_virtual() (sfepy.discrete.variables.Variable iter_terms() (sfepy.discrete.materials.Material
method), 722 method), 698
isol_loc (sfepy.solvers.ls_mumps.mumps_struc_c_4 at- iter_time_steps() (sfepy.homogenization.coefs_base.CorrSolution
tribute), 877 method), 808
isol_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 iteritems() (sfepy.base.base.Container method), 660
attribute), 880 iterkeys() (sfepy.base.base.Container method), 660
isol_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 itervalues() (sfepy.base.base.Container method), 660
attribute), 883
isol_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 J
attribute), 886 jacobiP() (sfepy.discrete.dg.poly_spaces.LegendrePolySpace
iter0() (in module sfepy.discrete.fem.facets), 747 method), 787
iter01() (in module sfepy.discrete.fem.facets), 747 jcn (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
iter01x01y() (in module sfepy.discrete.fem.facets), 747 tribute), 877
iter01x10y() (in module sfepy.discrete.fem.facets), 747 jcn (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at-
iter01y01x() (in module sfepy.discrete.fem.facets), 747 tribute), 880
iter01y10x() (in module sfepy.discrete.fem.facets), 747 jcn (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at-
iter02() (in module sfepy.discrete.fem.facets), 747 tribute), 883
iter1() (in module sfepy.discrete.fem.facets), 747 jcn (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at-
iter10() (in module sfepy.discrete.fem.facets), 747 tribute), 886
iter10x01y() (in module sfepy.discrete.fem.facets), 747 jcn_loc (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
iter10x10y() (in module sfepy.discrete.fem.facets), 747 tribute), 877
iter10y01x() (in module sfepy.discrete.fem.facets), 747 jcn_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
iter10y10x() (in module sfepy.discrete.fem.facets), 747 attribute), 880
iter12() (in module sfepy.discrete.fem.facets), 747 jcn_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
iter20() (in module sfepy.discrete.fem.facets), 747 attribute), 883
iter21() (in module sfepy.discrete.fem.facets), 747 jcn_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
iter_by_order() (in module attribute), 886
sfepy.discrete.dg.poly_spaces), 788 job (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
iter_dict_of_lists() (in module sfepy.base.base), tribute), 877
664 job (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at-
iter_from() (sfepy.solvers.ts.TimeStepper method), 898 tribute), 880

1080 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

job (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at- label_points() (in module

tribute), 883 sfepy.postprocess.plot_quadrature), 859
job (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at- LagrangeNodes (class in
tribute), 886 sfepy.discrete.fem.poly_spaces), 769
job (sfepy.solvers.ls_mumps.mumps_struc_c_x at- LagrangePolySpace (class in
tribute), 889 sfepy.discrete.fem.poly_spaces), 770
join_subscripts() (sfepy.terms.terms_multilinear.ExpressionBuilder
LagrangeSimplexBPolySpace (class in
static method), 986 sfepy.discrete.fem.poly_spaces), 770
join_tokens() (in module LagrangeSimplexPolySpace (class in
sfepy.discrete.parse_regions), 700 sfepy.discrete.fem.poly_spaces), 770
LagrangeTensorProductPolySpace (class in
K sfepy.discrete.fem.poly_spaces), 770
keep (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 lame_from_stiffness() (in module
attribute), 880 sfepy.mechanics.matcoefs), 832
keep (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 lame_from_youngpoisson() (in module
attribute), 883 sfepy.mechanics.matcoefs), 832
keep (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 laplace() (in module sfepy.linalg.sympy_operators),
attribute), 887 827
keep8 (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at- LaplaceTerm (class in sfepy.terms.terms_diffusion), 941
tribute), 880 layout_letters (sfepy.terms.terms_multilinear.ETermBase
keep8 (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at- attribute), 985
tribute), 883 LCBCOperator (class in
keep8 (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at- sfepy.discrete.fem.lcbc_operators), 757
tribute), 887 LCBCOperators (class in
key_to_index (sfepy.discrete.common.extmods.cmesh.CMesh sfepy.discrete.fem.lcbc_operators), 757
attribute), 731 leaveonlyphysicalsurfaces()
keys (sfepy.discrete.common.poly_spaces.PolySpace at- (sfepy.mesh.geom_tools.geometry method),
tribute), 741 846
keys() (sfepy.base.goptions.ValidatedDict method), 672 leaveonlyphysicalvolumes()
keys() (sfepy.base.multiproc_mpi.RemoteDict method), (sfepy.mesh.geom_tools.geometry method),
680 847
legendre_funs (sfepy.discrete.dg.poly_spaces.LegendrePolySpace
kind (sfepy.discrete.fem.lcbc_operators.EdgeDirectionOperator
attribute), 757 attribute), 788
legendreP() (sfepy.discrete.dg.poly_spaces.LegendrePolySpace
kind (sfepy.discrete.fem.lcbc_operators.IntegralMeanValueOperator
attribute), 757 method), 787
kind (sfepy.discrete.fem.lcbc_operators.NodalLCOperator LegendrePolySpace (class in
attribute), 758 sfepy.discrete.dg.poly_spaces), 786
kind (sfepy.discrete.fem.lcbc_operators.NoPenetrationOperator
LegendreSimplexPolySpace (class in
attribute), 758 sfepy.discrete.dg.poly_spaces), 788
kind (sfepy.discrete.fem.lcbc_operators.NormalDirectionOperator
LegendreTensorProductPolySpace (class in
attribute), 758 sfepy.discrete.dg.poly_spaces), 788
kind (sfepy.discrete.fem.lcbc_operators.RigidOperator letters (sfepy.terms.terms_multilinear.ExpressionBuilder
attribute), 758 attribute), 986
light_copy() (sfepy.discrete.common.region.Region
kind (sfepy.discrete.fem.lcbc_operators.ShiftedPeriodicOperator
attribute), 758 method), 743
line (class in sfepy.mesh.geom_tools), 847
L linear() (in module sfepy.tests.test_laplace_unit_square),
label_dofs() (in module 1023
sfepy.parallel.plot_parallel_dofs), 856 linear_x() (in module
label_global_entities() (in module sfepy.tests.test_laplace_unit_square), 1023
sfepy.postprocess.plot_cmesh), 857 linear_y() (in module
label_local_entities() (in module sfepy.tests.test_laplace_unit_square), 1023
sfepy.postprocess.plot_cmesh), 857 linear_z() (in module
sfepy.tests.test_laplace_unit_square), 1023

Index 1081
SfePy Documentation, Release version: 2022.1+git.f9873484

LinearCombinationBC (class in attribute), 762

sfepy.discrete.conditions), 687 load_state_1D_vtk() (in module
LinearConvect2Term (class in sfepy.discrete.dg.dg_1D_vizualizer), 777
sfepy.terms.terms_navier_stokes), 991 LobattoTensorProductPolySpace (class in
LinearConvectTerm (class in sfepy.discrete.fem.poly_spaces), 770
sfepy.terms.terms_navier_stokes), 991 LOBPCGEigenvalueSolver (class in
LinearElasticETHTerm (class in sfepy.solvers.eigen), 868
sfepy.terms.terms_elastic), 954 locate_files() (in module sfepy.base.ioutils), 675
LinearElasticIsotropicTerm (class in lock_drilling_rotations() (in module
sfepy.terms.terms_elastic), 955 sfepy.mechanics.shell10x), 837
LinearElasticTerm (class in Log (class in sfepy.base.log), 677
sfepy.terms.terms_elastic), 956 log() (in module sfepy.tests.test_log), 1025
LinearElasticTHTerm (class in log_filename() (in module sfepy.tests.test_log), 1025
sfepy.terms.terms_elastic), 956 LogPlotter (class in sfepy.base.log_plotter), 678
linearize() (sfepy.discrete.fem.fields_base.FEField look_ahead_line() (in module sfepy.base.ioutils), 675
method), 751 LQuadraticEVPSolver (class in sfepy.solvers.qeigen),
LinearPointSpringTerm (class in 895
sfepy.terms.terms_point), 999 lredrhs (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
LinearPrestressTerm (class in tribute), 877
sfepy.terms.terms_elastic), 957 lredrhs (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
LinearSolver (class in sfepy.solvers.solvers), 897 attribute), 880
LinearStrainFiberTerm (class in lredrhs (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
sfepy.terms.terms_elastic), 958 attribute), 883
LinearTractionTerm (class in lredrhs (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
sfepy.terms.terms_surface), 1009 attribute), 887
LinearVolumeForceTerm (class in lrhs (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
sfepy.terms.terms_volume), 1013 tribute), 877
LineProbe (class in sfepy.discrete.probes), 701 lrhs (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
link_duals() (sfepy.discrete.variables.Variables attribute), 880
method), 724 lrhs (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
link_flags() (sfepy.config.Config method), 657 attribute), 883
list_dict() (in module sfepy.base.parse_conf ), 683 lrhs (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
list_of() (in module sfepy.base.parse_conf ), 683 attribute), 887
listvar_schur (sfepy.solvers.ls_mumps.mumps_struc_c_4lrhs_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
attribute), 877 attribute), 887
listvar_schur (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 lsol_loc (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
attribute), 880 tribute), 877
listvar_schur (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 lsol_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
attribute), 883 attribute), 880
listvar_schur (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 lsol_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
attribute), 887 attribute), 883
load_1D_vtks() (in module lsol_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
sfepy.discrete.dg.dg_1D_vizualizer), 776 attribute), 887
load_and_plot_fun() (in module dg_plot_1D), 649 lwk_user (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
load_classes() (in module sfepy.base.base), 664 tribute), 877
load_dict() (sfepy.applications.pde_solver_app.PDESolverApp
lwk_user (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
method), 659 attribute), 880
load_library() (in module sfepy.solvers.ls_mumps), lwk_user (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
876 attribute), 883
load_mumps_libraries() (in module lwk_user (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
sfepy.solvers.ls_mumps), 876 attribute), 887
load_restart() (sfepy.discrete.problem.Problem
method), 710 M
load_slices (sfepy.discrete.fem.meshio.GmshIO main() (in module blockgen), 648

1082 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

main() (in module convert_mesh), 648 make_full_vec() (sfepy.discrete.evaluate.Evaluator

main() (in module cylindergen), 648 method), 693
main() (in module dg_plot_1D), 649 make_full_vec() (sfepy.discrete.variables.Variables
main() (in module edit_identifiers), 649 method), 724
main() (in module eval_ns_forms), 650 make_function() (sfepy.terms.terms_multilinear.ETermBase
main() (in module eval_tl_forms), 650 method), 985
main() (in module extract_edges), 651 make_get_conf() (in module sfepy.solvers.solvers), 898
main() (in module extract_surface), 651 make_global_operator()
main() (in module extractor), 641 (sfepy.discrete.fem.lcbc_operators.LCBCOperators
main() (in module gen_gallery), 652 method), 757
main() (in module gen_iga_patch), 652 make_h1_projection_data() (in module
main() (in module gen_legendre_simplex_base), 652 sfepy.discrete.projections), 715
main() (in module gen_lobatto1d_c), 653 make_is_save() (in module sfepy.discrete.problem),
main() (in module gen_mesh_prev), 653 714
main() (in module gen_release_notes), 653 make_knot_vector() (sfepy.mesh.bspline.BSpline
main() (in module gen_serendipity_basis), 654 method), 843
main() (in module gen_solver_table), 654 make_knot_vector() (sfepy.mesh.bspline.BSplineSurf
main() (in module gen_term_table), 654 method), 844
main() (in module phonon), 641 make_l2_projection() (in module
main() (in module plot_condition_numbers), 655 sfepy.discrete.projections), 715
main() (in module plot_logs), 655 make_l2_projection_data() (in module
main() (in module plot_mesh), 655 sfepy.discrete.projections), 715
main() (in module plot_quadratures), 655 make_line_matrix() (in module
main() (in module plot_times), 656 sfepy.discrete.fem.facets), 747
main() (in module postproc), 642 make_mesh() (in module sfepy.discrete.fem.mesh), 761
main() (in module probe), 643 make_option_docstring() (in module
main() (in module resview), 644 sfepy.solvers.solvers), 898
main() (in module save_basis), 656 make_psg() (sfepy.terms.terms_multilinear.ExpressionBuilder
main() (in module sfepy.mesh.bspline), 845 method), 987
main() (in module sfepy.mesh.mesh_generators), 850 make_pvg() (sfepy.terms.terms_multilinear.ExpressionBuilder
main() (in module show_authors), 656 method), 987
main() (in module show_mesh_info), 656 make_sfepy_function() (in module
main() (in module show_terms_use), 656 sfepy.discrete.functions), 696
main() (in module simple), 645 make_square_matrix() (in module
main() (in module simple_homog_mpi), 645 sfepy.discrete.fem.facets), 747
main() (in module sync_module_docs), 657 make_term_args() (in module
main() (in module test_install), 648 sfepy.tests.test_term_call_modes), 1030
main() (in module tile_periodic_mesh), 657 make_triangle_matrix() (in module
make_animation() (in module sfepy.discrete.fem.facets), 747
sfepy.postprocess.viewer), 867 map_equations() (sfepy.discrete.common.dof_info.EquationMap
make_axes() (sfepy.base.log_plotter.LogPlotter method), 727
method), 678 map_permutations() (in module sfepy.linalg.utils), 829
make_axis_rotation_matrix() (in module Mapping (class in sfepy.discrete.common.mappings), 738
sfepy.linalg.geometry), 824 mapping (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
make_cells_from_conn() (in module resview), 644 tribute), 877
make_eye() (sfepy.terms.terms_multilinear.ExpressionBuilder
mapping (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
method), 986 attribute), 880
make_format() (sfepy.discrete.fem.meshio.ANSYSCDBMeshIO mapping (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
static method), 761 attribute), 883
make_full() (sfepy.applications.evp_solver_app.EVPSolverApp
mapping (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
method), 658 attribute), 887
make_full_vec() (sfepy.discrete.equations.Equations mark_subdomains() (in module
method), 691 sfepy.parallel.plot_parallel_dofs), 856
mask_points() (sfepy.mechanics.contact_bodies.ContactPlane

Index 1083
SfePy Documentation, Release version: 2022.1+git.f9873484

method), 830 attribute), 745

mask_points() (sfepy.mechanics.contact_bodies.ContactSphere
mesh_from_groups() (in module
method), 830 sfepy.discrete.fem.meshio), 768
master_loop() (in module sfepy.base.multiproc_mpi), mesh_hook() (in module
681 sfepy.tests.test_eigenvalue_solvers), 1021
master_send_continue() (in module mesh_hook() (in module sfepy.tests.test_meshio), 1026
sfepy.base.multiproc_mpi), 681 MeshIO (class in sfepy.discrete.fem.meshio), 765
master_send_task() (in module MeshioLibIO (class in sfepy.discrete.fem.meshio), 767
sfepy.base.multiproc_mpi), 681 metis_options (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
match_candidate() (in module edit_identifiers), 649 attribute), 887
match_coors() (in module sfepy.discrete.fem.periodic), mini_newton() (in module sfepy.linalg.utils), 829
768 MiniAppBase (class in
match_grid_line() (in module sfepy.homogenization.coefs_base), 808
sfepy.discrete.fem.periodic), 768 minmod() (in module sfepy.discrete.dg.limiters), 789
match_grid_plane() (in module minmod_seq() (in module sfepy.discrete.dg.limiters),
sfepy.discrete.fem.periodic), 768 789
match_plane_by_dir() (in module mode (sfepy.discrete.common.extmods.mappings.CMapping
sfepy.discrete.fem.periodic), 768 attribute), 733
match_x_line() (in module mode (sfepy.terms.terms_diffusion.AdvectDivFreeTerm
sfepy.discrete.fem.periodic), 769 attribute), 938
match_x_plane() (in module mode (sfepy.terms.terms_dot.BCNewtonTerm attribute),
sfepy.discrete.fem.periodic), 769 944
match_y_line() (in module modes (sfepy.terms.terms_biot.BiotETHTerm attribute),
sfepy.discrete.fem.periodic), 769 925
match_y_plane() (in module modes (sfepy.terms.terms_biot.BiotTerm attribute), 927
sfepy.discrete.fem.periodic), 769 modes (sfepy.terms.terms_biot.BiotTHTerm attribute),
match_z_line() (in module 926
sfepy.discrete.fem.periodic), 769 modes (sfepy.terms.terms_constraints.NonPenetrationTerm
match_z_plane() (in module attribute), 931
sfepy.discrete.fem.periodic), 769 modes (sfepy.terms.terms_dg.AdvectionDGFluxTerm at-
Material (class in sfepy.discrete.materials), 698 tribute), 934
Materials (class in sfepy.discrete.materials), 699 modes (sfepy.terms.terms_dg.DiffusionDGFluxTerm at-
MatlabEigenvalueSolver (class in tribute), 935
sfepy.solvers.eigen), 868 modes (sfepy.terms.terms_dg.DiffusionInteriorPenaltyTerm
MatrixAction (class in sfepy.linalg.utils), 827 attribute), 936
max_diff_csr() (in module sfepy.linalg.utils), 829 modes (sfepy.terms.terms_dg.NonlinearHyperbolicDGFluxTerm
mbfg (sfepy.discrete.fem.extmods.bases.CLagrangeContext attribute), 937
attribute), 745 modes (sfepy.terms.terms_dg.NonlinearScalarDotGradTerm
mblock (sfepy.solvers.ls_mumps.mumps_struc_c_4 attribute), 937
attribute), 877 modes (sfepy.terms.terms_diffusion.DiffusionCoupling
mblock (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at- attribute), 939
tribute), 880 modes (sfepy.terms.terms_diffusion.DiffusionTerm at-
mblock (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at- tribute), 940
tribute), 883 modes (sfepy.terms.terms_diffusion.LaplaceTerm at-
mblock (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at- tribute), 942
tribute), 887 modes (sfepy.terms.terms_dot.DotProductTerm attribute),
mc2us() (in module edit_identifiers), 649 946
merge_lines() (in module extract_edges), 651 modes (sfepy.terms.terms_dot.ScalarDotMGradScalarTerm
merge_mesh() (in module sfepy.discrete.fem.mesh), 761 attribute), 948
Mesh (class in sfepy.discrete.fem.mesh), 760 modes (sfepy.terms.terms_dot.VectorDotGradScalarTerm
Mesh3DMeshIO (class in sfepy.discrete.fem.meshio), 765 attribute), 949
mesh_conn (sfepy.discrete.fem.extmods.bases.CLagrangeContext
modes (sfepy.terms.terms_dot.VectorDotScalarTerm at-
attribute), 745 tribute), 950
mesh_coors (sfepy.discrete.fem.extmods.bases.CLagrangeContext
modes (sfepy.terms.terms_elastic.ElasticWaveCauchyTerm

1084 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

attribute), 954 attribute), 1010

modes (sfepy.terms.terms_elastic.LinearElasticTerm at- modes (sfepy.terms.terms_surface.SufaceNormalDotTerm
tribute), 957 attribute), 1011
modes (sfepy.terms.terms_elastic.LinearPrestressTerm modify_mesh() (in module
attribute), 958 sfepy.tests.test_term_sensitivity), 1031
modes (sfepy.terms.terms_elastic.NonsymElasticTerm at- module
tribute), 959 blockgen, 648
modes (sfepy.terms.terms_multilinear.EConvectTerm at- build_helpers, 645
tribute), 976 convert_mesh, 648
modes (sfepy.terms.terms_multilinear.EDiffusionTerm at- cylindergen, 648
tribute), 977 dg_plot_1D, 649
modes (sfepy.terms.terms_multilinear.EDivGradTerm at- edit_identifiers, 649
tribute), 977 eval_ns_forms, 650
modes (sfepy.terms.terms_multilinear.EDivTerm at- eval_tl_forms, 650
tribute), 978 extract_edges, 650
modes (sfepy.terms.terms_multilinear.EDotTerm at- extract_surface, 651
tribute), 979 extractor, 640
modes (sfepy.terms.terms_multilinear.ELaplaceTerm at- gen_gallery, 651
tribute), 980 gen_iga_patch, 652
modes (sfepy.terms.terms_multilinear.ELinearConvectTerm gen_legendre_simplex_base, 652
attribute), 981 gen_lobatto1d_c, 653
modes (sfepy.terms.terms_multilinear.ELinearElasticTerm gen_mesh_prev, 653
attribute), 981 gen_release_notes, 653
modes (sfepy.terms.terms_multilinear.ELinearTractionTerm gen_serendipity_basis, 654
attribute), 982 gen_solver_table, 654
modes (sfepy.terms.terms_multilinear.ENonSymElasticTerm gen_term_table, 654
attribute), 983 phonon, 641
modes (sfepy.terms.terms_multilinear.EScalarDotMGradScalarTerm
plot_condition_numbers, 655
attribute), 984 plot_logs, 655
modes (sfepy.terms.terms_multilinear.EStokesTerm plot_mesh, 655
attribute), 984 plot_quadratures, 655
modes (sfepy.terms.terms_navier_stokes.DivGradTerm plot_times, 656
attribute), 988 postproc, 641
modes (sfepy.terms.terms_navier_stokes.StokesTerm at- probe, 642
tribute), 995 resview, 643
modes (sfepy.terms.terms_navier_stokes.StokesWaveDivTerm save_basis, 656
attribute), 996 sfepy.applications.application, 658
modes (sfepy.terms.terms_piezo.PiezoCouplingTerm at- sfepy.applications.evp_solver_app, 658
tribute), 997 sfepy.applications.pde_solver_app, 659
modes (sfepy.terms.terms_sensitivity.ESDDiffusionTerm sfepy.base.base, 659
attribute), 1001 sfepy.base.compat, 666
modes (sfepy.terms.terms_sensitivity.ESDDivGradTerm sfepy.base.conf, 669
attribute), 1001 sfepy.base.getch, 672
modes (sfepy.terms.terms_sensitivity.ESDDotTerm sfepy.base.goptions, 672
attribute), 1002 sfepy.base.ioutils, 672
modes (sfepy.terms.terms_sensitivity.ESDLinearElasticTerm sfepy.base.log, 677
attribute), 1003 sfepy.base.log_plotter, 678
modes (sfepy.terms.terms_sensitivity.ESDLinearTractionTerm sfepy.base.mem_usage, 679
attribute), 1003 sfepy.base.multiproc, 679
modes (sfepy.terms.terms_sensitivity.ESDPiezoCouplingTerm sfepy.base.multiproc_mpi, 680
attribute), 1004 sfepy.base.multiproc_proc, 682
modes (sfepy.terms.terms_sensitivity.ESDStokesTerm at- sfepy.base.parse_conf, 683
tribute), 1005 sfepy.base.plotutils, 684
modes (sfepy.terms.terms_surface.LinearTractionTerm sfepy.base.reader, 684

Index 1085
SfePy Documentation, Release version: 2022.1+git.f9873484

sfepy.base.resolve_deps, 685 sfepy.discrete.iga.domain, 791

sfepy.base.testing, 685 sfepy.discrete.iga.domain_generators, 792
sfepy.base.timing, 686 sfepy.discrete.iga.extmods.igac, 793
sfepy.config, 657 sfepy.discrete.iga.fields, 795
sfepy.discrete.common.dof_info, 726 sfepy.discrete.iga.iga, 796
sfepy.discrete.common.domain, 728 sfepy.discrete.iga.io, 801
sfepy.discrete.common.extmods._fmfield, sfepy.discrete.iga.mappings, 801
729 sfepy.discrete.iga.plot_nurbs, 802
sfepy.discrete.common.extmods._geommech, sfepy.discrete.iga.utils, 802
729 sfepy.discrete.integrals, 697
sfepy.discrete.common.extmods.assemble, sfepy.discrete.materials, 698
729 sfepy.discrete.parse_equations, 700
sfepy.discrete.common.extmods.cmesh, 730 sfepy.discrete.parse_regions, 700
sfepy.discrete.common.extmods.crefcoors, sfepy.discrete.probes, 701
732 sfepy.discrete.problem, 704
sfepy.discrete.common.extmods.mappings, sfepy.discrete.projections, 715
733 sfepy.discrete.quadratures, 715
sfepy.discrete.common.fields, 734 sfepy.discrete.simplex_cubature, 717
sfepy.discrete.common.global_interp, 736 sfepy.discrete.structural.fields, 803
sfepy.discrete.common.mappings, 738 sfepy.discrete.structural.mappings, 804
sfepy.discrete.common.poly_spaces, 740 sfepy.discrete.variables, 717
sfepy.discrete.common.region, 741 sfepy.homogenization.band_gaps_app, 804
sfepy.discrete.conditions, 686 sfepy.homogenization.coefficients, 805
sfepy.discrete.dg.dg_1D_vizualizer, 775 sfepy.homogenization.coefs_base, 806
sfepy.discrete.dg.fields, 779 sfepy.homogenization.coefs_elastic, 809
sfepy.discrete.dg.limiters, 789 sfepy.homogenization.coefs_perfusion, 809
sfepy.discrete.dg.poly_spaces, 786 sfepy.homogenization.coefs_phononic, 810
sfepy.discrete.equations, 688 sfepy.homogenization.convolutions, 814
sfepy.discrete.evaluate, 693 sfepy.homogenization.engine, 815
sfepy.discrete.evaluate_variable, 696 sfepy.homogenization.homogen_app, 817
sfepy.discrete.fem._serendipity, 774 sfepy.homogenization.micmac, 818
sfepy.discrete.fem.domain, 744 sfepy.homogenization.recovery, 818
sfepy.discrete.fem.extmods.bases, 745 sfepy.homogenization.utils, 821
sfepy.discrete.fem.extmods.lobatto_bases, sfepy.linalg.check_derivatives, 822
746 sfepy.linalg.eigen, 822
sfepy.discrete.fem.facets, 746 sfepy.linalg.geometry, 823
sfepy.discrete.fem.fe_surface, 748 sfepy.linalg.sparse, 825
sfepy.discrete.fem.fields_base, 748 sfepy.linalg.sympy_operators, 827
sfepy.discrete.fem.fields_hierarchic, 753 sfepy.linalg.utils, 827
sfepy.discrete.fem.fields_nodal, 754 sfepy.mechanics.contact_bodies, 830
sfepy.discrete.fem.fields_positive, 755 sfepy.mechanics.elastic_constants, 831
sfepy.discrete.fem.geometry_element, 755 sfepy.mechanics.extmods.ccontres, 841
sfepy.discrete.fem.history, 756 sfepy.mechanics.matcoefs, 831
sfepy.discrete.fem.lcbc_operators, 756 sfepy.mechanics.membranes, 833
sfepy.discrete.fem.linearizer, 759 sfepy.mechanics.shell10x, 835
sfepy.discrete.fem.mappings, 759 sfepy.mechanics.tensors, 837
sfepy.discrete.fem.mesh, 760 sfepy.mechanics.units, 839
sfepy.discrete.fem.meshio, 761 sfepy.mesh.bspline, 842
sfepy.discrete.fem.periodic, 768 sfepy.mesh.geom_tools, 846
sfepy.discrete.fem.poly_spaces, 769 sfepy.mesh.mesh_generators, 848
sfepy.discrete.fem.refine, 773 sfepy.mesh.mesh_tools, 851
sfepy.discrete.fem.refine_hanging, 774 sfepy.mesh.splinebox, 852
sfepy.discrete.fem.utils, 774 sfepy.parallel.evaluate, 853
sfepy.discrete.functions, 696 sfepy.parallel.parallel, 854

1086 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

sfepy.parallel.plot_parallel_dofs, 856 sfepy.tests.conftest, 1018

sfepy.postprocess.domain_specific, 856 sfepy.tests.test_assembling, 1018
sfepy.postprocess.plot_cmesh, 857 sfepy.tests.test_base, 1019
sfepy.postprocess.plot_dofs, 858 sfepy.tests.test_cmesh, 1019
sfepy.postprocess.plot_facets, 858 sfepy.tests.test_conditions, 1019
sfepy.postprocess.plot_quadrature, 859 sfepy.tests.test_declarative_examples,
sfepy.postprocess.probes_vtk, 859 1020
sfepy.postprocess.sources, 860 sfepy.tests.test_dg_field, 1020
sfepy.postprocess.time_history, 862 sfepy.tests.test_domain, 1021
sfepy.postprocess.utils, 863 sfepy.tests.test_eigenvalue_solvers, 1021
sfepy.postprocess.utils_vtk, 863 sfepy.tests.test_elasticity_small_strain,
sfepy.postprocess.viewer, 864 1021
sfepy.solvers.auto_fallback, 868 sfepy.tests.test_fem, 1022
sfepy.solvers.eigen, 868 sfepy.tests.test_functions, 1022
sfepy.solvers.ls, 870 sfepy.tests.test_high_level, 1022
sfepy.solvers.ls_mumps, 875 sfepy.tests.test_homogenization_engine,
sfepy.solvers.ls_mumps_parallel, 889 1023
sfepy.solvers.nls, 890 sfepy.tests.test_homogenization_perfusion,
sfepy.solvers.optimize, 893 1023
sfepy.solvers.oseen, 894 sfepy.tests.test_hyperelastic_tlul, 1023
sfepy.solvers.qeigen, 895 sfepy.tests.test_io, 1023
sfepy.solvers.semismooth_newton, 896 sfepy.tests.test_laplace_unit_disk, 1023
sfepy.solvers.solvers, 897 sfepy.tests.test_laplace_unit_square,
sfepy.solvers.ts, 898 1023
sfepy.solvers.ts_dg_solvers, 790 sfepy.tests.test_lcbcs, 1024
sfepy.solvers.ts_solvers, 900 sfepy.tests.test_linalg, 1024
sfepy.terms.extmods.terms, 1013 sfepy.tests.test_linear_solvers, 1024
sfepy.terms.terms, 905 sfepy.tests.test_linearization, 1025
sfepy.terms.terms_adj_navier_stokes, 910 sfepy.tests.test_log, 1025
sfepy.terms.terms_basic, 919 sfepy.tests.test_matcoefs, 1025
sfepy.terms.terms_biot, 924 sfepy.tests.test_mesh_expand, 1025
sfepy.terms.terms_compat, 927 sfepy.tests.test_mesh_generators, 1025
sfepy.terms.terms_constraints, 930 sfepy.tests.test_mesh_interp, 1026
sfepy.terms.terms_contact, 932 sfepy.tests.test_mesh_smoothing, 1026
sfepy.terms.terms_dg, 933 sfepy.tests.test_meshio, 1026
sfepy.terms.terms_diffusion, 938 sfepy.tests.test_msm_laplace, 1027
sfepy.terms.terms_dot, 944 sfepy.tests.test_msm_symbolic, 1027
sfepy.terms.terms_elastic, 950 sfepy.tests.test_normals, 1027
sfepy.terms.terms_electric, 960 sfepy.tests.test_parsing, 1027
sfepy.terms.terms_fibres, 960 sfepy.tests.test_poly_spaces, 1027
sfepy.terms.terms_hyperelastic_base, 961 sfepy.tests.test_projections, 1028
sfepy.terms.terms_hyperelastic_tl, 963 sfepy.tests.test_quadratures, 1028
sfepy.terms.terms_hyperelastic_ul, 971 sfepy.tests.test_ref_coors, 1029
sfepy.terms.terms_membrane, 975 sfepy.tests.test_refine_hanging, 1029
sfepy.terms.terms_multilinear, 976 sfepy.tests.test_regions, 1029
sfepy.terms.terms_navier_stokes, 987 sfepy.tests.test_semismooth_newton, 1029
sfepy.terms.terms_piezo, 996 sfepy.tests.test_sparse, 1030
sfepy.terms.terms_point, 999 sfepy.tests.test_splinebox, 1030
sfepy.terms.terms_sensitivity, 1000 sfepy.tests.test_tensors, 1030
sfepy.terms.terms_shells, 1005 sfepy.tests.test_term_call_modes, 1030
sfepy.terms.terms_surface, 1007 sfepy.tests.test_term_consistency, 1031
sfepy.terms.terms_th, 1012 sfepy.tests.test_term_sensitivity, 1031
sfepy.terms.terms_volume, 1013 sfepy.tests.test_units, 1031
sfepy.terms.utils, 1013 sfepy.tests.test_volume, 1031

Index 1087
SfePy Documentation, Release version: 2022.1+git.f9873484

sfepy.version, 658 n (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at-

show_authors, 656 tribute), 880
show_mesh_info, 656 n (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at-
show_terms_use, 656 tribute), 884
simple, 645 n (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at-
simple_homog_mpi, 645 tribute), 887
sync_module_docs, 656 n_coor (sfepy.discrete.common.extmods.cmesh.CMesh
test_install, 647 attribute), 731
tile_periodic_mesh, 657 n_el (sfepy.discrete.common.extmods.cmesh.CMesh at-
MomentLimiter1D (class in sfepy.discrete.dg.limiters), tribute), 731
789 n_el (sfepy.discrete.common.extmods.mappings.CMapping
MomentLimiter2D (class in sfepy.discrete.dg.limiters), attribute), 733
789 n_ep (sfepy.discrete.common.extmods.mappings.CMapping
MooneyRivlinTLTerm (class in attribute), 733
sfepy.terms.terms_hyperelastic_tl), 966 n_incident (sfepy.discrete.common.extmods.cmesh.CConnectivity
MooneyRivlinULTerm (class in attribute), 730
sfepy.terms.terms_hyperelastic_ul), 973 n_qp (sfepy.discrete.common.extmods.mappings.CMapping
move_control_point() attribute), 733
(sfepy.mesh.splinebox.SplineBox method), name (sfepy.discrete.dg.limiters.DGLimiter attribute), 789
852 name (sfepy.discrete.dg.limiters.IdentityLimiter attribute),
MPIFileHandler (class in sfepy.base.multiproc_mpi), 789
680 name (sfepy.discrete.dg.limiters.MomentLimiter1D
MPILogFile (class in sfepy.base.multiproc_mpi), 680 attribute), 789
MRLCBCOperator (class in name (sfepy.discrete.dg.limiters.MomentLimiter2D
sfepy.discrete.fem.lcbc_operators), 757 attribute), 789
mtx_t (sfepy.discrete.common.extmods.mappings.CMappingname (sfepy.discrete.dg.poly_spaces.LegendreSimplexPolySpace
attribute), 733 attribute), 788
mulAB_integrate() (in module name (sfepy.discrete.dg.poly_spaces.LegendreTensorProductPolySpace
sfepy.terms.extmods.terms), 1018 attribute), 788
MultiProblem (class in sfepy.solvers.ls), 871 name (sfepy.discrete.fem.poly_spaces.BernsteinSimplexPolySpace
mumps_parallel_solve() (in module attribute), 769
sfepy.solvers.ls_mumps_parallel), 889 name (sfepy.discrete.fem.poly_spaces.BernsteinTensorProductPolySpace
mumps_pcomplex (in module sfepy.solvers.ls_mumps), attribute), 769
876 name (sfepy.discrete.fem.poly_spaces.LagrangeSimplexBPolySpace
mumps_preal (in module sfepy.solvers.ls_mumps), 876 attribute), 770
mumps_struc_c_4 (class in sfepy.solvers.ls_mumps), name (sfepy.discrete.fem.poly_spaces.LagrangeSimplexPolySpace
876 attribute), 770
mumps_struc_c_5_0 (class in sfepy.solvers.ls_mumps), name (sfepy.discrete.fem.poly_spaces.LagrangeTensorProductPolySpace
879 attribute), 770
mumps_struc_c_5_1 (class in sfepy.solvers.ls_mumps), name (sfepy.discrete.fem.poly_spaces.LobattoTensorProductPolySpace
882 attribute), 770
mumps_struc_c_5_2 (class in sfepy.solvers.ls_mumps), name (sfepy.discrete.fem.poly_spaces.SerendipityTensorProductPolySpace
885 attribute), 773
mumps_struc_c_x (class in sfepy.solvers.ls_mumps), name (sfepy.solvers.auto_fallback.AutoDirect attribute),
889 868
MUMPSParallelSolver (class in sfepy.solvers.ls), 870 name (sfepy.solvers.auto_fallback.AutoIterative attribute),
MUMPSSolver (class in sfepy.solvers.ls), 870 868
MumpsSolver (class in sfepy.solvers.ls_mumps), 875 name (sfepy.solvers.eigen.LOBPCGEigenvalueSolver at-
MyQueue (class in sfepy.base.multiproc_proc), 682 tribute), 868
name (sfepy.solvers.eigen.MatlabEigenvalueSolver
N attribute), 869
n (sfepy.solvers.ls_mumps.mumps_struc_c_4 attribute), name (sfepy.solvers.eigen.ScipyEigenvalueSolver at-
877 tribute), 870
name (sfepy.solvers.eigen.ScipySGEigenvalueSolver at-

1088 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

tribute), 870 name (sfepy.terms.terms_adj_navier_stokes.AdjDivGradTerm

name (sfepy.solvers.eigen.SLEPcEigenvalueSolver at- attribute), 911
tribute), 869 name (sfepy.terms.terms_adj_navier_stokes.NSOFMinGradTerm
name (sfepy.solvers.ls.MultiProblem attribute), 871 attribute), 911
name (sfepy.solvers.ls.MUMPSParallelSolver attribute), name (sfepy.terms.terms_adj_navier_stokes.NSOFSurfMinDPressDiffTerm
870 attribute), 912
name (sfepy.solvers.ls.MUMPSSolver attribute), 871 name (sfepy.terms.terms_adj_navier_stokes.NSOFSurfMinDPressTerm
name (sfepy.solvers.ls.PETScKrylovSolver attribute), 872 attribute), 912
name (sfepy.solvers.ls.PyAMGKrylovSolver attribute), name (sfepy.terms.terms_adj_navier_stokes.SDConvectTerm
872 attribute), 913
name (sfepy.solvers.ls.PyAMGSolver attribute), 873 name (sfepy.terms.terms_adj_navier_stokes.SDDivGradTerm
name (sfepy.solvers.ls.SchurMumps attribute), 873 attribute), 914
name (sfepy.solvers.ls.ScipyDirect attribute), 873 name (sfepy.terms.terms_adj_navier_stokes.SDDivTerm
name (sfepy.solvers.ls.ScipyIterative attribute), 874 attribute), 914
name (sfepy.solvers.ls.ScipySuperLU attribute), 874 name (sfepy.terms.terms_adj_navier_stokes.SDDotTerm
name (sfepy.solvers.ls.ScipyUmfpack attribute), 874 attribute), 915
name (sfepy.solvers.nls.Newton attribute), 891 name (sfepy.terms.terms_adj_navier_stokes.SDGradDivStabilizationTerm
name (sfepy.solvers.nls.PETScNonlinearSolver attribute), attribute), 915
892 name (sfepy.terms.terms_adj_navier_stokes.SDPSPGCStabilizationTerm
name (sfepy.solvers.nls.ScipyBroyden attribute), 892 attribute), 916
name (sfepy.solvers.optimize.FMinSteepestDescent name (sfepy.terms.terms_adj_navier_stokes.SDPSPGPStabilizationTerm
attribute), 893 attribute), 917
name (sfepy.solvers.optimize.ScipyFMinSolver attribute), name (sfepy.terms.terms_adj_navier_stokes.SDSUPGCStabilizationTerm
894 attribute), 917
name (sfepy.solvers.oseen.Oseen attribute), 895 name (sfepy.terms.terms_adj_navier_stokes.SUPGCAdjStabilizationTerm
name (sfepy.solvers.qeigen.LQuadraticEVPSolver at- attribute), 918
tribute), 895 name (sfepy.terms.terms_adj_navier_stokes.SUPGPAdj1StabilizationTerm
name (sfepy.solvers.semismooth_newton.SemismoothNewton attribute), 919
attribute), 896 name (sfepy.terms.terms_adj_navier_stokes.SUPGPAdj2StabilizationTerm
name (sfepy.solvers.ts_dg_solvers.DGMultiStageTSS at- attribute), 919
tribute), 790 name (sfepy.terms.terms_basic.IntegrateMatTerm at-
name (sfepy.solvers.ts_dg_solvers.EulerStepSolver at- tribute), 920
tribute), 790 name (sfepy.terms.terms_basic.IntegrateOperatorTerm
name (sfepy.solvers.ts_dg_solvers.RK4StepSolver at- attribute), 921
tribute), 791 name (sfepy.terms.terms_basic.IntegrateTerm attribute),
name (sfepy.solvers.ts_dg_solvers.TVDRK3StepSolver at- 921
tribute), 791 name (sfepy.terms.terms_basic.SumNodalValuesTerm at-
name (sfepy.solvers.ts_solvers.AdaptiveTimeSteppingSolver tribute), 922
attribute), 900 name (sfepy.terms.terms_basic.SurfaceMomentTerm at-
name (sfepy.solvers.ts_solvers.BatheTS attribute), 901 tribute), 922
name (sfepy.solvers.ts_solvers.GeneralizedAlphaTS name (sfepy.terms.terms_basic.VolumeSurfaceTerm at-
attribute), 902 tribute), 923
name (sfepy.solvers.ts_solvers.NewmarkTS attribute), 903 name (sfepy.terms.terms_basic.VolumeTerm attribute),
name (sfepy.solvers.ts_solvers.SimpleTimeSteppingSolver 923
attribute), 903 name (sfepy.terms.terms_basic.ZeroTerm attribute), 924
name (sfepy.solvers.ts_solvers.StationarySolver attribute), name (sfepy.terms.terms_biot.BiotETHTerm attribute),
903 925
name (sfepy.solvers.ts_solvers.VelocityVerletTS attribute), name (sfepy.terms.terms_biot.BiotStressTerm attribute),
904 925
name (sfepy.terms.terms.Term attribute), 908 name (sfepy.terms.terms_biot.BiotTerm attribute), 927
name (sfepy.terms.terms_adj_navier_stokes.AdjConvect1Term name (sfepy.terms.terms_biot.BiotTHTerm attribute), 926
attribute), 910 name (sfepy.terms.terms_compat.CauchyStrainSTerm at-
name (sfepy.terms.terms_adj_navier_stokes.AdjConvect2Term tribute), 927
attribute), 911 name (sfepy.terms.terms_compat.DotSurfaceProductTerm

Index 1089
SfePy Documentation, Release version: 2022.1+git.f9873484

attribute), 928 tribute), 939

name (sfepy.terms.terms_compat.DotVolumeProductTerm name (sfepy.terms.terms_diffusion.DiffusionRTerm
attribute), 928 attribute), 940
name (sfepy.terms.terms_compat.DSumNodalValuesTerm name (sfepy.terms.terms_diffusion.DiffusionTerm at-
attribute), 927 tribute), 940
name (sfepy.terms.terms_compat.DSurfaceFluxTerm at- name (sfepy.terms.terms_diffusion.DiffusionVelocityTerm
tribute), 928 attribute), 941
name (sfepy.terms.terms_compat.DSurfaceMomentTerm name (sfepy.terms.terms_diffusion.LaplaceTerm at-
attribute), 928 tribute), 942
name (sfepy.terms.terms_compat.DVolumeSurfaceTerm name (sfepy.terms.terms_diffusion.SDDiffusionTerm at-
attribute), 928 tribute), 943
name (sfepy.terms.terms_compat.IntegrateSurfaceMatTerm name (sfepy.terms.terms_diffusion.SurfaceFluxOperatorTerm
attribute), 928 attribute), 943
name (sfepy.terms.terms_compat.IntegrateSurfaceOperatorTerm
name (sfepy.terms.terms_diffusion.SurfaceFluxTerm at-
attribute), 929 tribute), 944
name (sfepy.terms.terms_compat.IntegrateSurfaceTerm name (sfepy.terms.terms_dot.BCNewtonTerm attribute),
attribute), 929 945
name (sfepy.terms.terms_compat.IntegrateVolumeMatTerm name (sfepy.terms.terms_dot.DotProductTerm attribute),
attribute), 929 946
name (sfepy.terms.terms_compat.IntegrateVolumeOperatorTerm
name (sfepy.terms.terms_dot.DotSProductVolumeOperatorWETHTerm
attribute), 929 attribute), 946
name (sfepy.terms.terms_compat.IntegrateVolumeTerm name (sfepy.terms.terms_dot.DotSProductVolumeOperatorWTHTerm
attribute), 929 attribute), 947
name (sfepy.terms.terms_compat.SDVolumeDotTerm at- name (sfepy.terms.terms_dot.ScalarDotGradIScalarTerm
tribute), 929 attribute), 947
name (sfepy.terms.terms_compat.SurfaceDivTerm at- name (sfepy.terms.terms_dot.ScalarDotMGradScalarTerm
tribute), 929 attribute), 948
name (sfepy.terms.terms_compat.SurfaceGradTerm name (sfepy.terms.terms_dot.VectorDotGradScalarTerm
attribute), 930 attribute), 949
name (sfepy.terms.terms_compat.SurfaceTerm attribute), name (sfepy.terms.terms_dot.VectorDotScalarTerm
930 attribute), 950
name (sfepy.terms.terms_compat.VolumeXTerm at- name (sfepy.terms.terms_elastic.CauchyStrainTerm
tribute), 930 attribute), 951
name (sfepy.terms.terms_constraints.NonPenetrationPenaltyTerm
name (sfepy.terms.terms_elastic.CauchyStressETHTerm
attribute), 931 attribute), 951
name (sfepy.terms.terms_constraints.NonPenetrationTerm name (sfepy.terms.terms_elastic.CauchyStressTerm
attribute), 931 attribute), 953
name (sfepy.terms.terms_contact.ContactTerm attribute), name (sfepy.terms.terms_elastic.CauchyStressTHTerm at-
932 tribute), 952
name (sfepy.terms.terms_dg.AdvectionDGFluxTerm at- name (sfepy.terms.terms_elastic.ElasticWaveCauchyTerm
tribute), 934 attribute), 954
name (sfepy.terms.terms_dg.DiffusionDGFluxTerm name (sfepy.terms.terms_elastic.ElasticWaveTerm at-
attribute), 935 tribute), 954
name (sfepy.terms.terms_dg.DiffusionInteriorPenaltyTerm name (sfepy.terms.terms_elastic.LinearElasticETHTerm
attribute), 936 attribute), 955
name (sfepy.terms.terms_dg.NonlinearHyperbolicDGFluxTerm name (sfepy.terms.terms_elastic.LinearElasticIsotropicTerm
attribute), 937 attribute), 956
name (sfepy.terms.terms_dg.NonlinearScalarDotGradTerm name (sfepy.terms.terms_elastic.LinearElasticTerm
attribute), 938 attribute), 957
name (sfepy.terms.terms_diffusion.AdvectDivFreeTerm name (sfepy.terms.terms_elastic.LinearElasticTHTerm at-
attribute), 938 tribute), 956
name (sfepy.terms.terms_diffusion.ConvectVGradSTerm name (sfepy.terms.terms_elastic.LinearPrestressTerm at-
attribute), 939 tribute), 958
name (sfepy.terms.terms_diffusion.DiffusionCoupling at- name (sfepy.terms.terms_elastic.LinearStrainFiberTerm

1090 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

attribute), 958 tribute), 977

name (sfepy.terms.terms_elastic.NonsymElasticTerm at- name (sfepy.terms.terms_multilinear.EDivGradTerm at-
tribute), 959 tribute), 978
name (sfepy.terms.terms_elastic.SDLinearElasticTerm at- name (sfepy.terms.terms_multilinear.EDivTerm attribute),
tribute), 960 978
name (sfepy.terms.terms_electric.ElectricSourceTerm at- name (sfepy.terms.terms_multilinear.EDotTerm attribute),
tribute), 960 979
name (sfepy.terms.terms_fibres.FibresActiveTLTerm at- name (sfepy.terms.terms_multilinear.EGradTerm at-
tribute), 961 tribute), 979
name (sfepy.terms.terms_hyperelastic_base.DeformationGradientTerm
name (sfepy.terms.terms_multilinear.EIntegrateOperatorTerm
attribute), 962 attribute), 980
name (sfepy.terms.terms_hyperelastic_tl.BulkActiveTLTerm name (sfepy.terms.terms_multilinear.ELaplaceTerm at-
attribute), 963 tribute), 980
name (sfepy.terms.terms_hyperelastic_tl.BulkPenaltyTLTermname (sfepy.terms.terms_multilinear.ELinearConvectTerm
attribute), 964 attribute), 981
name (sfepy.terms.terms_hyperelastic_tl.BulkPressureTLTermname (sfepy.terms.terms_multilinear.ELinearElasticTerm
attribute), 964 attribute), 981
name (sfepy.terms.terms_hyperelastic_tl.DiffusionTLTerm name (sfepy.terms.terms_multilinear.ELinearTractionTerm
attribute), 965 attribute), 982
name (sfepy.terms.terms_hyperelastic_tl.GenYeohTLTerm name (sfepy.terms.terms_multilinear.ENonPenetrationPenaltyTerm
attribute), 966 attribute), 982
name (sfepy.terms.terms_hyperelastic_tl.MooneyRivlinTLTermname (sfepy.terms.terms_multilinear.ENonSymElasticTerm
attribute), 967 attribute), 983
name (sfepy.terms.terms_hyperelastic_tl.NeoHookeanTLTermname (sfepy.terms.terms_multilinear.EScalarDotMGradScalarTerm
attribute), 967 attribute), 984
name (sfepy.terms.terms_hyperelastic_tl.OgdenTLTerm name (sfepy.terms.terms_multilinear.EStokesTerm at-
attribute), 968 tribute), 984
name (sfepy.terms.terms_hyperelastic_tl.SurfaceFluxTLTermname (sfepy.terms.terms_navier_stokes.ConvectTerm at-
attribute), 969 tribute), 988
name (sfepy.terms.terms_hyperelastic_tl.SurfaceTractionTLTerm
name (sfepy.terms.terms_navier_stokes.DivGradTerm at-
attribute), 970 tribute), 988
name (sfepy.terms.terms_hyperelastic_tl.VolumeSurfaceTLTerm
name (sfepy.terms.terms_navier_stokes.DivOperatorTerm
attribute), 970 attribute), 989
name (sfepy.terms.terms_hyperelastic_tl.VolumeTLTerm name (sfepy.terms.terms_navier_stokes.DivTerm at-
attribute), 971 tribute), 990
name (sfepy.terms.terms_hyperelastic_ul.BulkPenaltyULTerm name (sfepy.terms.terms_navier_stokes.GradDivStabilizationTerm
attribute), 971 attribute), 990
name (sfepy.terms.terms_hyperelastic_ul.BulkPressureULTermname (sfepy.terms.terms_navier_stokes.GradTerm at-
attribute), 972 tribute), 991
name (sfepy.terms.terms_hyperelastic_ul.CompressibilityULTerm
name (sfepy.terms.terms_navier_stokes.LinearConvect2Term
attribute), 973 attribute), 991
name (sfepy.terms.terms_hyperelastic_ul.MooneyRivlinULTermname (sfepy.terms.terms_navier_stokes.LinearConvectTerm
attribute), 973 attribute), 992
name (sfepy.terms.terms_hyperelastic_ul.NeoHookeanULTerm name (sfepy.terms.terms_navier_stokes.PSPGCStabilizationTerm
attribute), 974 attribute), 992
name (sfepy.terms.terms_hyperelastic_ul.VolumeULTerm name (sfepy.terms.terms_navier_stokes.PSPGPStabilizationTerm
attribute), 974 attribute), 993
name (sfepy.terms.terms_membrane.TLMembraneTerm name (sfepy.terms.terms_navier_stokes.StokesTerm
attribute), 975 attribute), 995
name (sfepy.terms.terms_multilinear.ECauchyStressTerm name (sfepy.terms.terms_navier_stokes.StokesWaveDivTerm
attribute), 976 attribute), 996
name (sfepy.terms.terms_multilinear.EConvectTerm at- name (sfepy.terms.terms_navier_stokes.StokesWaveTerm
tribute), 976 attribute), 996
name (sfepy.terms.terms_multilinear.EDiffusionTerm at- name (sfepy.terms.terms_navier_stokes.SUPGCStabilizationTerm

Index 1091
SfePy Documentation, Release version: 2022.1+git.f9873484

attribute), 993 tribute), 887

name (sfepy.terms.terms_navier_stokes.SUPGPStabilizationTerm
nelt (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
attribute), 994 tribute), 877
name (sfepy.terms.terms_piezo.PiezoCouplingTerm nelt (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
attribute), 997 attribute), 880
name (sfepy.terms.terms_piezo.PiezoStrainTerm at- nelt (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
tribute), 998 attribute), 884
name (sfepy.terms.terms_piezo.PiezoStressTerm at- nelt (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
tribute), 998 attribute), 887
name (sfepy.terms.terms_piezo.SDPiezoCouplingTerm at- NeoHookeanTLTerm (class in
tribute), 999 sfepy.terms.terms_hyperelastic_tl), 967
name (sfepy.terms.terms_point.ConcentratedPointLoadTerm NeoHookeanULTerm (class in
attribute), 999 sfepy.terms.terms_hyperelastic_ul), 973
name (sfepy.terms.terms_point.LinearPointSpringTerm NEUMeshIO (class in sfepy.discrete.fem.meshio), 767
attribute), 1000 new() (sfepy.terms.terms.Term static method), 908
name (sfepy.terms.terms_sensitivity.ESDDiffusionTerm new_ulf_iteration()
attribute), 1001 (sfepy.discrete.evaluate.Evaluator static
name (sfepy.terms.terms_sensitivity.ESDDivGradTerm at- method), 693
tribute), 1001 new_vtk_polyline() (sfepy.postprocess.probes_vtk.Probe
name (sfepy.terms.terms_sensitivity.ESDDotTerm at- method), 860
tribute), 1002 NewmarkTS (class in sfepy.solvers.ts_solvers), 902
name (sfepy.terms.terms_sensitivity.ESDLinearElasticTerm Newton (class in sfepy.solvers.nls), 890
attribute), 1003 nloc_rhs (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
name (sfepy.terms.terms_sensitivity.ESDLinearTractionTerm attribute), 887
attribute), 1003 NLSStatus (class in sfepy.base.testing), 685
name (sfepy.terms.terms_sensitivity.ESDPiezoCouplingTermnnz (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at-
attribute), 1004 tribute), 884
name (sfepy.terms.terms_sensitivity.ESDStokesTerm at- nnz (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at-
tribute), 1005 tribute), 887
name (sfepy.terms.terms_shells.Shell10XTerm attribute), nnz_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
1007 attribute), 884
name (sfepy.terms.terms_surface.ContactPlaneTerm at- nnz_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
tribute), 1008 attribute), 887
name (sfepy.terms.terms_surface.ContactSphereTerm at- NodalLCOperator (class in
tribute), 1009 sfepy.discrete.fem.lcbc_operators), 758
name (sfepy.terms.terms_surface.LinearTractionTerm at- NodeDescription (class in
tribute), 1010 sfepy.discrete.fem.poly_spaces), 770
name (sfepy.terms.terms_surface.SDLinearTractionTerm NonlinearHyperbolicDGFluxTerm (class in
attribute), 1010 sfepy.terms.terms_dg), 936
name (sfepy.terms.terms_surface.SDSufaceIntegrateTerm NonlinearScalarDotGradTerm (class in
attribute), 1011 sfepy.terms.terms_dg), 937
name (sfepy.terms.terms_surface.SufaceNormalDotTerm NonlinearSolver (class in sfepy.solvers.solvers), 897
attribute), 1011 NonPenetrationPenaltyTerm (class in
name (sfepy.terms.terms_surface.SurfaceJumpTerm at- sfepy.terms.terms_constraints), 930
tribute), 1012 NonPenetrationTerm (class in
name (sfepy.terms.terms_volume.LinearVolumeForceTerm sfepy.terms.terms_constraints), 931
attribute), 1013 NonsymElasticTerm (class in
nblock (sfepy.solvers.ls_mumps.mumps_struc_c_4 sfepy.terms.terms_elastic), 958
attribute), 877 NoOptionsDocs (class in build_helpers), 646
nblock (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at- NoPenetrationOperator (class in
tribute), 880 sfepy.discrete.fem.lcbc_operators), 758
nblock (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at- norm_l2_along_axis() (in module sfepy.linalg.utils),
tribute), 884 830
nblock (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at- normal (sfepy.discrete.common.extmods.mappings.CMapping

1092 Index
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attribute), 733 attribute), 881

NormalDirectionOperator (class in nz_alloc (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
sfepy.discrete.fem.lcbc_operators), 758 attribute), 884
normalize_time() (sfepy.solvers.ts.TimeStepper nz_alloc (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
method), 898 attribute), 888
normalize_vectors() (in module sfepy.linalg.utils), nz_loc (sfepy.solvers.ls_mumps.mumps_struc_c_4
830 attribute), 878
npcol (sfepy.solvers.ls_mumps.mumps_struc_c_4 at- nz_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at-
tribute), 877 tribute), 881
npcol (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at- nz_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at-
tribute), 880 tribute), 884
npcol (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at- nz_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at-
tribute), 884 tribute), 888
npcol (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at- nz_rhs (sfepy.solvers.ls_mumps.mumps_struc_c_4
tribute), 887 attribute), 878
nprow (sfepy.solvers.ls_mumps.mumps_struc_c_4 at- nz_rhs (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at-
tribute), 877 tribute), 881
nprow (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at- nz_rhs (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at-
tribute), 881 tribute), 884
nprow (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at- nz_rhs (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at-
tribute), 884 tribute), 888
nprow (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at-
tribute), 887 O
nrhs (sfepy.solvers.ls_mumps.mumps_struc_c_4 at- object_button_quit_changed()
tribute), 877 (sfepy.postprocess.viewer.ClosingHandler
nrhs (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 method), 864
attribute), 881 offset (sfepy.discrete.common.extmods.cmesh.CConnectivity
nrhs (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 attribute), 730
attribute), 884 offsets (sfepy.discrete.common.extmods.cmesh.CConnectivity
nrhs (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 attribute), 730
attribute), 887 OgdenTLTerm (class in
NSOFMinGradTerm (class in sfepy.terms.terms_hyperelastic_tl), 967
sfepy.terms.terms_adj_navier_stokes), 911 OnesDim (class in sfepy.homogenization.coefs_base), 808
NSOFSurfMinDPressDiffTerm (class in OneTypeList (class in sfepy.base.base), 660
sfepy.terms.terms_adj_navier_stokes), 911 ooc_prefix (sfepy.solvers.ls_mumps.mumps_struc_c_4
NSOFSurfMinDPressTerm (class in attribute), 878
sfepy.terms.terms_adj_navier_stokes), 912 ooc_prefix (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
num (sfepy.discrete.common.extmods.cmesh.CConnectivity attribute), 881
attribute), 730 ooc_prefix (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
num (sfepy.discrete.common.extmods.cmesh.CMesh attribute), 884
attribute), 731 ooc_prefix (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
numpydoc_path() (sfepy.config.Config method), 657 attribute), 888
NurbsPatch (class in sfepy.discrete.iga.domain), 792 ooc_tmpdir (sfepy.solvers.ls_mumps.mumps_struc_c_4
nz (sfepy.solvers.ls_mumps.mumps_struc_c_4 attribute), attribute), 878
877 ooc_tmpdir (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
nz (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at- attribute), 881
tribute), 881 ooc_tmpdir (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
nz (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at- attribute), 884
tribute), 884 ooc_tmpdir (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
nz (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at- attribute), 888
tribute), 887 OptimizationSolver (class in sfepy.solvers.solvers),
nz_alloc (sfepy.solvers.ls_mumps.mumps_struc_c_4 at- 897
tribute), 878 OptsToListAction (class in resview), 644
nz_alloc (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 ordered_iteritems() (in module sfepy.base.base), 664

Index 1093
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orient_elements() (in module path_of_hdf5_group() (in module sfepy.base.ioutils),

sfepy.discrete.common.extmods.cmesh), 732 675
Oseen (class in sfepy.solvers.oseen), 894 pause() (in module sfepy.base.base), 664
Output (class in sfepy.base.base), 661 PDESolverApp (class in
output (sfepy.base.log_plotter.LogPlotter attribute), 678 sfepy.applications.pde_solver_app), 659
output_array_stats() (in module sfepy.linalg.utils), PeriodicBC (class in sfepy.discrete.conditions), 688
830 perm_in (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
output_dir() (in module sfepy.tests.conftest), 1018 tribute), 878
output_mesh_formats() (in module perm_in (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
sfepy.discrete.fem.meshio), 768 attribute), 881
output_step_info() (sfepy.solvers.ts_dg_solvers.DGMultiStageTSS
perm_in (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
method), 790 attribute), 884
output_step_info() (sfepy.solvers.ts_solvers.AdaptiveTimeSteppingSolver
perm_in (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
method), 900 attribute), 888
output_step_info() (sfepy.solvers.ts_solvers.SimpleTimeSteppingSolver
permutations() (in module sfepy.linalg.utils), 830
method), 903 petsc_call() (in module sfepy.solvers.ls), 874
PETScKrylovSolver (class in sfepy.solvers.ls), 871
P PETScNonlinearSolver (class in sfepy.solvers.nls), 891
package_check() (in module build_helpers), 647 PETScParallelEvaluator (class in
par (sfepy.solvers.ls_mumps.mumps_struc_c_4 at- sfepy.parallel.evaluate), 853
tribute), 878 PhaseVelocity (class in
par (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at- sfepy.homogenization.coefs_phononic), 812
tribute), 881 phonon
par (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at- module, 641
tribute), 884 PhysicalQPs (class in
par (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at- sfepy.discrete.common.mappings), 739
tribute), 888 physicalsurface (class in sfepy.mesh.geom_tools), 847
par (sfepy.solvers.ls_mumps.mumps_struc_c_x at- physicalvolume (class in sfepy.mesh.geom_tools), 847
tribute), 889 PiezoCouplingTerm (class in sfepy.terms.terms_piezo),
parametrize() (sfepy.applications.application.Application 996
method), 658 PiezoStrainTerm (class in sfepy.terms.terms_piezo),
parse_approx_order() (in module 997
sfepy.discrete.common.fields), 736 PiezoStressTerm (class in sfepy.terms.terms_piezo),
parse_approx_order() (in module 998
sfepy.discrete.iga.fields), 796 pivnul_list (sfepy.solvers.ls_mumps.mumps_struc_c_4
parse_definition() (in module attribute), 878
sfepy.discrete.equations), 693 pivnul_list (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
parse_linearization() (in module extractor), 641 attribute), 881
parse_options() (in module resview), 644 pivnul_list (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
parse_shape() (in module attribute), 884
sfepy.discrete.common.fields), 736 pivnul_list (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
parse_term_expression() (in module attribute), 888
sfepy.terms.terms_multilinear), 987 plot1D_legendre_dofs() (in module
ParseDomainSpecific (class in postproc), 641 sfepy.discrete.dg.dg_1D_vizualizer), 777
ParseGroupNames (class in postproc), 642 plot_band_gaps() (sfepy.homogenization.band_gaps_app.AcousticBandG
ParseOpacity (class in postproc), 642 method), 804
ParseRanges (class in postproc), 642 plot_bezier_mesh() (in module
ParseRc (class in plot_logs), 655 sfepy.discrete.iga.plot_nurbs), 802
ParseRepeat (class in tile_periodic_mesh), 657 plot_bezier_nurbs_basis_1d() (in module
ParseResolution (class in postproc), 642 sfepy.discrete.iga.plot_nurbs), 802
ParseSubdomains (class in postproc), 642 plot_cmesh() (in module
ParseView (class in postproc), 642 sfepy.postprocess.plot_cmesh), 857
partition_mesh() (in module sfepy.parallel.parallel), plot_condition_numbers
855 module, 655

1094 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

plot_control_mesh() (in module plot_polys() (in module gen_lobatto1d_c), 653

sfepy.discrete.iga.plot_nurbs), 802 plot_quadrature() (in module
plot_data() (sfepy.base.log.Log method), 677 sfepy.postprocess.plot_quadrature), 859
plot_dispersion() (sfepy.homogenization.band_gaps_app.AcousticBandGapsApp
plot_quadratures
method), 804 module, 655
plot_displacements() (in module plot_times
sfepy.postprocess.domain_specific), 856 module, 656
plot_edges() (in module sfepy.postprocess.plot_facets), plot_velocity() (in module
858 sfepy.postprocess.domain_specific), 856
plot_eigs() (in module plot_vlines() (sfepy.base.log.Log method), 677
sfepy.homogenization.band_gaps_app), 804 plot_warp_scalar() (in module
plot_entities() (in module sfepy.postprocess.domain_specific), 857
sfepy.postprocess.plot_cmesh), 858 plot_weighted_points() (in module
plot_faces() (in module sfepy.postprocess.plot_facets), sfepy.postprocess.plot_quadrature), 859
858 plot_wireframe() (in module
plot_gap() (in module sfepy.postprocess.plot_cmesh), 858
sfepy.homogenization.band_gaps_app), 805 plotsXT() (in module
plot_gaps() (in module sfepy.discrete.dg.dg_1D_vizualizer), 777
sfepy.homogenization.band_gaps_app), 805 point (class in sfepy.mesh.geom_tools), 847
plot_geometry() (in module points_in_poly() (sfepy.mesh.splinebox.SplineRegion2D
sfepy.postprocess.plot_facets), 859 static method), 853
plot_global_dofs() (in module points_in_simplex() (in module
sfepy.postprocess.plot_dofs), 858 sfepy.linalg.geometry), 825
plot_iso_lines() (in module PointsProbe (class in sfepy.discrete.probes), 701
sfepy.discrete.iga.plot_nurbs), 802 PolarizationAngles (class in
plot_local_dofs() (in module sfepy.homogenization.coefs_phononic), 812
sfepy.parallel.plot_parallel_dofs), 856 poll_draw() (sfepy.base.log_plotter.LogPlotter
plot_local_dofs() (in module method), 678
sfepy.postprocess.plot_dofs), 858 poll_file() (sfepy.postprocess.sources.FileSource
plot_log() (in module sfepy.base.log), 678 method), 860
plot_logs poly_space_base (sfepy.terms.terms_dg.DGTerm at-
module, 655 tribute), 934
plot_logs() (in module poly_space_base (sfepy.terms.terms_shells.Shell10XTerm
sfepy.homogenization.band_gaps_app), 805 attribute), 1007
plot_matrix_diff() (in module sfepy.base.plotutils), PolySpace (class in sfepy.discrete.common.poly_spaces),
684 740
plot_mesh post_process() (sfepy.homogenization.coefs_phononic.SchurEVP
module, 655 method), 812
plot_mesh() (in module sfepy.postprocess.plot_dofs), post_process() (sfepy.homogenization.coefs_phononic.SimpleEVP
858 method), 812
plot_nodes() (in module sfepy.postprocess.plot_dofs), postproc
858 module, 641
plot_nurbs_basis_1d() (in module postprocess() (in module probe), 643
sfepy.discrete.iga.plot_nurbs), 802 prefix (sfepy.base.base.Output property), 661
plot_parametric_mesh() (in module prepare_cylindrical_transform() (in module
sfepy.discrete.iga.plot_nurbs), 802 sfepy.mechanics.tensors), 838
plot_partitioning() (in module prepare_dgfield() (in module
sfepy.parallel.plot_parallel_dofs), 856 sfepy.tests.test_dg_field), 1020
plot_points() (in module prepare_dgfield_1D() (in module
sfepy.mechanics.contact_bodies), 830 sfepy.tests.test_dg_field), 1020
plot_points() (in module sfepy.postprocess.plot_dofs), prepare_field_2D() (in module
858 sfepy.tests.test_dg_field), 1020
plot_polygon() (in module prepare_matrices() (sfepy.homogenization.coefs_phononic.SchurEVP
sfepy.mechanics.contact_bodies), 830 method), 812

Index 1095
SfePy Documentation, Release version: 2022.1+git.f9873484

prepare_matrices() (sfepy.homogenization.coefs_phononic.SimpleEVP
problem() (in module sfepy.tests.test_linear_solvers),
method), 812 1024
prepare_matrix() (in module sfepy.discrete.problem), problem() (in module sfepy.tests.test_msm_laplace),
714 1027
prepare_remap() (in module sfepy.discrete.fem.utils), problem() (in module sfepy.tests.test_msm_symbolic),
775 1027
prepare_translate() (in module problem() (in module sfepy.tests.test_term_consistency),
sfepy.discrete.fem.utils), 775 1031
prepare_variable() (in module problem() (in module sfepy.tests.test_term_sensitivity),
sfepy.tests.test_mesh_interp), 1026 1031
presolve() (sfepy.homogenization.coefs_base.PressureEigenvalueProblem
problem() (in module sfepy.tests.test_volume), 1031
method), 808 ProblemConf (class in sfepy.base.conf ), 669
presolve() (sfepy.solvers.ls.MUMPSSolver method), process_command() (sfepy.base.log_plotter.LogPlotter
871 method), 678
presolve() (sfepy.solvers.ls.ScipyDirect method), 873 process_conf() (sfepy.solvers.solvers.Solver class
presolve() (sfepy.solvers.solvers.LinearSolver method), method), 897
897 process_options() (sfepy.applications.evp_solver_app.EVPSolverApp
PressureEigenvalueProblem (class in static method), 658
sfepy.homogenization.coefs_base), 808 process_options() (sfepy.applications.pde_solver_app.PDESolverApp
PressureRHSVector (class in static method), 659
sfepy.homogenization.coefs_elastic), 809 process_options() (sfepy.homogenization.band_gaps_app.AcousticBand
print_array_info() (in module sfepy.linalg.utils), 830 static method), 804
print_leaf() (in module sfepy.discrete.parse_regions), process_options() (sfepy.homogenization.coefs_base.MiniAppBase
700 method), 808
print_matrix_diff() (in module sfepy.base.plotutils), process_options() (sfepy.homogenization.coefs_phononic.BandGaps
684 method), 811
print_mem_usage() (in module process_options() (sfepy.homogenization.coefs_phononic.ChristoffelAco
sfepy.base.mem_usage), 679 method), 811
print_names() (sfepy.base.base.Container method), process_options() (sfepy.homogenization.coefs_phononic.Eigenmoment
660 method), 812
print_names() (sfepy.base.base.OneTypeList method), process_options() (sfepy.homogenization.coefs_phononic.PhaseVelocity
661 method), 812
print_op() (in module sfepy.discrete.parse_regions), process_options() (sfepy.homogenization.coefs_phononic.PolarizationA
700 method), 812
print_shapes() (sfepy.terms.terms_multilinear.ExpressionBuilder
process_options() (sfepy.homogenization.coefs_phononic.SimpleEVP
method), 987 method), 812
print_solvers() (in module simple), 645 process_options() (sfepy.homogenization.engine.HomogenizationEngine
print_stack() (in module static method), 815
sfepy.discrete.parse_regions), 700 process_options() (sfepy.homogenization.homogen_app.Homogenization
print_structs() (in module sfepy.base.base), 664 static method), 817
print_terms() (in module simple), 645 process_options_pv()
print_terms() (sfepy.discrete.equations.Equations (sfepy.homogenization.band_gaps_app.AcousticBandGapsApp
method), 691 static method), 804
printinfo() (sfepy.mesh.geom_tools.geometry process_reqs_coefs()
method), 847 (sfepy.homogenization.engine.HomogenizationWorkerMulti
probe static method), 817
module, 642 project_by_component() (in module
Probe (class in sfepy.discrete.probes), 702 sfepy.discrete.projections), 715
Probe (class in sfepy.postprocess.probes_vtk), 859 project_to_facets() (in module
probe() (sfepy.discrete.probes.Probe method), 702 sfepy.discrete.projections), 715
ProbeFromFile (class in sfepy.postprocess.probes_vtk), ps (sfepy.discrete.common.extmods.mappings.CMapping
860 attribute), 733
Problem (class in sfepy.discrete.problem), 704 PSPGCStabilizationTerm (class in
problem() (in module sfepy.tests.test_functions), 1022 sfepy.terms.terms_navier_stokes), 992

1096 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

PSPGPStabilizationTerm (class in read_bounding_box()

sfepy.terms.terms_navier_stokes), 993 (sfepy.discrete.fem.meshio.ANSYSCDBMeshIO
put() (sfepy.base.multiproc_mpi.RemoteQueue method), method), 761
681 read_bounding_box()
put() (sfepy.base.multiproc_mpi.RemoteQueueMaster (sfepy.discrete.fem.meshio.HDF5MeshIO
method), 681 method), 764
put() (sfepy.base.multiproc_proc.MyQueue method), read_bounding_box()
682 (sfepy.discrete.fem.meshio.MeshioLibIO
pv_plot() (in module resview), 644 method), 767
PyAMGKrylovSolver (class in sfepy.solvers.ls), 872 read_bounding_box()
PyAMGSolver (class in sfepy.solvers.ls), 872 (sfepy.discrete.fem.meshio.XYZMeshIO
pytest_addoption() (in module sfepy.tests.conftest), method), 768
1018 read_common() (sfepy.postprocess.sources.GenericFileSource
pytest_configure() (in module sfepy.tests.conftest), method), 861
1018 read_common() (sfepy.postprocess.sources.GenericSequenceFileSource
python_include() (sfepy.config.Config method), 657 method), 861
python_shell() (in module sfepy.base.base), 664 read_data() (sfepy.discrete.fem.meshio.GmshIO
python_version() (sfepy.config.Config method), 657 method), 762
read_data() (sfepy.discrete.fem.meshio.HDF5MeshIO
Q method), 764
qp (sfepy.discrete.common.extmods.mappings.CMapping read_data() (sfepy.discrete.fem.meshio.MeshIO
attribute), 733 method), 766
QuadraticEVPSolver (class in sfepy.solvers.solvers), read_data() (sfepy.discrete.fem.meshio.MeshioLibIO
897 method), 767
QuadraturePoints (class in read_data_header() (sfepy.discrete.fem.meshio.HDF5MeshIO
sfepy.discrete.quadratures), 716 method), 764
Quantity (class in sfepy.mechanics.units), 839 read_dict_hdf5() (in module sfepy.base.ioutils), 675
read_dimension() (sfepy.discrete.fem.meshio.ANSYSCDBMeshIO
R method), 762
R (sfepy.discrete.iga.extmods.igac.CNURBSContext read_dimension() (sfepy.discrete.fem.meshio.HDF5MeshIO
attribute), 793 method), 764
raise_if_too_large() (in module read_dimension() (sfepy.discrete.fem.meshio.HypermeshAsciiMeshIO
sfepy.base.mem_usage), 679 method), 765
RayProbe (class in sfepy.discrete.probes), 703 read_dimension() (sfepy.discrete.fem.meshio.Mesh3DMeshIO
read() (sfepy.discrete.fem.meshio.ANSYSCDBMeshIO method), 765
method), 761 read_dimension() (sfepy.discrete.fem.meshio.MeshioLibIO
read() (sfepy.discrete.fem.meshio.ComsolMeshIO method), 767
method), 762 read_dimension() (sfepy.discrete.fem.meshio.NEUMeshIO
read() (sfepy.discrete.fem.meshio.HDF5MeshIO method), 767
method), 764 read_dimension() (sfepy.discrete.fem.meshio.XYZMeshIO
read() (sfepy.discrete.fem.meshio.HypermeshAsciiMeshIO method), 768
method), 765 read_domain_from_hdf5()
read() (sfepy.discrete.fem.meshio.Mesh3DMeshIO (sfepy.discrete.iga.domain.IGDomain static
method), 765 method), 791
read() (sfepy.discrete.fem.meshio.MeshIO method), 766 read_from_hdf5() (in module sfepy.base.ioutils), 675
read() (sfepy.discrete.fem.meshio.MeshioLibIO read_header() (in module sfepy.discrete.probes), 703
method), 767 read_iga_data() (in module sfepy.discrete.iga.io), 801
read() (sfepy.discrete.fem.meshio.NEUMeshIO method), read_last_step() (sfepy.discrete.fem.meshio.HDF5MeshIO
767 method), 764
read() (sfepy.discrete.fem.meshio.UserMeshIO method), read_last_step() (sfepy.discrete.fem.meshio.MeshIO
768 method), 766
read() (sfepy.discrete.fem.meshio.XYZMeshIO method), read_list() (in module sfepy.base.ioutils), 675
768 read_log() (in module sfepy.base.log), 678
read_array() (in module sfepy.base.ioutils), 675 read_mesh() (in module resview), 644

Index 1097
SfePy Documentation, Release version: 2022.1+git.f9873484

read_mesh_from_hdf5() method), 745

(sfepy.discrete.fem.meshio.HDF5MeshIO refine_1_2() (in module sfepy.discrete.fem.refine), 773
static method), 764 refine_2_3() (in module sfepy.discrete.fem.refine), 773
read_results() (in module sfepy.discrete.probes), 703 refine_2_4() (in module sfepy.discrete.fem.refine), 773
read_sparse_matrix_from_hdf5() (in module refine_3_4() (in module sfepy.discrete.fem.refine), 773
sfepy.base.ioutils), 675 refine_3_8() (in module sfepy.discrete.fem.refine), 773
read_sparse_matrix_hdf5() (in module refine_mesh() (in module sfepy.discrete.fem.utils), 775
sfepy.base.ioutils), 676 refine_pars() (sfepy.discrete.probes.Probe static
read_time_history() method), 702
(sfepy.discrete.fem.meshio.HDF5MeshIO refine_points() (sfepy.discrete.probes.PointsProbe
method), 764 method), 701
read_time_stepper() refine_points() (sfepy.discrete.probes.Probe
(sfepy.discrete.fem.meshio.HDF5MeshIO method), 702
method), 764 refine_points() (sfepy.discrete.probes.RayProbe
read_times() (sfepy.discrete.fem.meshio.HDF5MeshIO method), 703
method), 764 refine_reference() (in module
read_times() (sfepy.discrete.fem.meshio.MeshIO sfepy.discrete.fem.refine), 773
method), 766 refine_region() (in module
read_token() (in module sfepy.base.ioutils), 676 sfepy.discrete.fem.refine_hanging), 774
read_variables_time_history() refine_uniformly() (sfepy.discrete.problem.Problem
(sfepy.discrete.fem.meshio.HDF5MeshIO method), 710
method), 764 refmap_memory_factor() (sfepy.config.Config
Reader (class in sfepy.base.reader), 684 method), 657
reconstruct_legendre_dofs() (in module Region (class in sfepy.discrete.common.region), 741
sfepy.discrete.dg.dg_1D_vizualizer), 777 region_leaf() (in module
recover_bones() (in module sfepy.discrete.common.domain), 729
sfepy.homogenization.recovery), 820 region_op() (in module
recover_micro_hook() (in module sfepy.discrete.common.domain), 729
sfepy.homogenization.recovery), 820 release() (sfepy.base.multiproc_mpi.RemoteLock
recover_micro_hook_eps() (in module method), 680
sfepy.homogenization.recovery), 820 ReloadSource (class in sfepy.postprocess.viewer), 864
recover_micro_hook_init() (in module remap_dict() (in module sfepy.base.base), 665
sfepy.homogenization.recovery), 820 remote_get() (sfepy.base.multiproc_mpi.RemoteDictMaster
recover_paraflow() (in module method), 680
sfepy.homogenization.recovery), 820 remote_get() (sfepy.base.multiproc_mpi.RemoteQueueMaster
recursive_glob() (in module build_helpers), 647 method), 681
redrhs (sfepy.solvers.ls_mumps.mumps_struc_c_4 remote_get_in() (sfepy.base.multiproc_mpi.RemoteDictMaster
attribute), 878 method), 680
redrhs (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at- remote_get_keys() (sfepy.base.multiproc_mpi.RemoteDictMaster
tribute), 881 method), 680
redrhs (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at- remote_get_len() (sfepy.base.multiproc_mpi.RemoteDictMaster
tribute), 884 method), 680
redrhs (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at- remote_put() (sfepy.base.multiproc_mpi.RemoteQueueMaster
tribute), 888 method), 681
reduce_on_datas() (sfepy.discrete.materials.Material remote_set() (sfepy.base.multiproc_mpi.RemoteDictMaster
method), 698 method), 680
reduce_vec() (sfepy.discrete.equations.Equations RemoteDict (class in sfepy.base.multiproc_mpi), 680
method), 691 RemoteDictMaster (class in sfepy.base.multiproc_mpi),
reduce_vec() (sfepy.discrete.variables.Variables 680
method), 725 RemoteInt (class in sfepy.base.multiproc_mpi), 680
refine() (in module sfepy.discrete.fem.refine_hanging), RemoteInt.IntDesc (class in
774 sfepy.base.multiproc_mpi), 680
refine() (in module sfepy.tests.test_domain), 1021 RemoteLock (class in sfepy.base.multiproc_mpi), 680
refine() (sfepy.discrete.fem.domain.FEDomain RemoteQueue (class in sfepy.base.multiproc_mpi), 680

1098 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

RemoteQueueMaster (class in method), 658

sfepy.base.multiproc_mpi), 681 restore_dofs() (sfepy.discrete.fem.fields_base.FEField
remove_bcs() (sfepy.discrete.problem.Problem method), 751
method), 710 restore_step_time() (sfepy.solvers.ts.TimeStepper
remove_extra_dofs() method), 898
(sfepy.discrete.fem.fields_base.FEField restore_substituted()
method), 751 (sfepy.discrete.fem.fields_base.FEField
remove_extra_dofs() method), 751
(sfepy.discrete.fem.fields_nodal.H1DiscontinuousField
resview
method), 754 module, 643
remove_files() (in module sfepy.base.ioutils), 676 resview_plot() (in module gen_gallery), 652
remove_files_patterns() (in module rhs (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
sfepy.base.ioutils), 676 tribute), 878
remove_known() (in module sfepy.base.resolve_deps), rhs (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at-
685 tribute), 881
remove_name() (sfepy.base.base.Container method), rhs (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at-
660 tribute), 884
render_scene() (sfepy.postprocess.viewer.Viewer rhs (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at-
method), 866 tribute), 888
replace() (in module sfepy.discrete.parse_regions), 700 rhs() (in module sfepy.discrete.parse_equations), 700
replace_with_region() (in module rhs() (in module sfepy.tests.test_msm_laplace), 1027
sfepy.discrete.parse_regions), 700 rhs() (in module sfepy.tests.test_msm_symbolic), 1027
report() (in module sfepy.base.testing), 685 rhs_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
report() (in module test_install), 648 attribute), 888
report() (sfepy.discrete.probes.CircleProbe method), rhs_sparse (sfepy.solvers.ls_mumps.mumps_struc_c_4
701 attribute), 878
report() (sfepy.discrete.probes.LineProbe method), 701 rhs_sparse (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
report() (sfepy.discrete.probes.PointsProbe method), attribute), 881
701 rhs_sparse (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
report() (sfepy.discrete.probes.Probe method), 702 attribute), 884
report() (sfepy.discrete.probes.RayProbe method), 703 rhs_sparse (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
report2() (in module test_install), 648 attribute), 888
report_tests() (in module test_install), 648 RigidOperator (class in
reset() (sfepy.base.timing.Timer method), 686 sfepy.discrete.fem.lcbc_operators), 758
reset() (sfepy.discrete.materials.Material method), 698 rinfo (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
reset() (sfepy.discrete.materials.Materials method), tribute), 878
699 rinfo (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at-
reset() (sfepy.discrete.problem.Problem method), 710 tribute), 881
reset() (sfepy.discrete.variables.Variable static rinfo (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at-
method), 722 tribute), 884
reset() (sfepy.postprocess.sources.FileSource method), rinfo (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at-
861 tribute), 888
reset_materials() (sfepy.discrete.equations.Equations rinfog (sfepy.solvers.ls_mumps.mumps_struc_c_4
method), 692 attribute), 878
reset_refinement() (sfepy.discrete.probes.Probe rinfog (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at-
method), 702 tribute), 881
reset_regions() (sfepy.discrete.common.domain.Domainrinfog (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at-
method), 728 tribute), 885
reset_view() (sfepy.postprocess.viewer.Viewer rinfog (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at-
method), 866 tribute), 888
resolve() (in module sfepy.base.resolve_deps), 685 RK4StepSolver (class in sfepy.solvers.ts_dg_solvers),
resolve_chains() (in module 790
sfepy.discrete.common.dof_info), 728 rm_multi() (in module sfepy.homogenization.utils), 822
restore() (sfepy.applications.application.Application rotate_elastic_tensor() (in module

Index 1099
SfePy Documentation, Release version: 2022.1+git.f9873484

sfepy.mechanics.shell10x), 837 save_log() (sfepy.homogenization.coefs_phononic.BandGaps

rotation_matrix2d() (in module static method), 811
sfepy.linalg.geometry), 825 save_mappings() (sfepy.discrete.common.fields.Field
rowsca (sfepy.solvers.ls_mumps.mumps_struc_c_4 method), 735
attribute), 878 save_only() (in module
rowsca (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at- sfepy.applications.pde_solver_app), 659
tribute), 881 save_options() (in module sfepy.base.ioutils), 676
rowsca (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at- save_prefix (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
tribute), 885 attribute), 885
rowsca (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at- save_prefix (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
tribute), 888 attribute), 888
rowsca_from_mumps (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
save_raw_bg_logs() (in module
attribute), 881 sfepy.homogenization.band_gaps_app), 805
rowsca_from_mumps (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
save_recovery_region() (in module
attribute), 885 sfepy.homogenization.recovery), 820
rowsca_from_mumps (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
save_regions() (sfepy.discrete.common.domain.Domain
attribute), 888 method), 728
run() (build_helpers.Clean method), 645 save_regions() (sfepy.discrete.problem.Problem
run() (build_helpers.DoxygenDocs method), 646 method), 711
run() (build_helpers.SphinxHTMLDocs method), 646 save_regions_as_groups()
run() (build_helpers.SphinxPDFDocs method), 646 (sfepy.discrete.common.domain.Domain
run_declaratice_example() (in module method), 729
sfepy.base.testing), 685 save_regions_as_groups()
(sfepy.discrete.problem.Problem method),
S 711
save() (sfepy.homogenization.coefs_base.CorrMiniApp save_restart() (sfepy.discrete.problem.Problem
method), 807 method), 711
save_results() (sfepy.applications.evp_solver_app.EVPSolverApp
save() (sfepy.homogenization.coefs_base.TCorrectorsViaPressureEVP
method), 809 method), 658
save() (sfepy.homogenization.coefs_phononic.SimpleEVP save_sol_snap() (in module
method), 812 sfepy.discrete.dg.dg_1D_vizualizer), 778
save_animation() (in module save_sparse_txt() (in module sfepy.linalg.sparse),
sfepy.discrete.dg.dg_1D_vizualizer), 778 826
save_animation() (sfepy.postprocess.viewer.Viewer save_state() (sfepy.discrete.problem.Problem
method), 866 method), 711
save_as_mesh() (sfepy.discrete.variables.FieldVariable save_time_history() (in module
method), 721 sfepy.postprocess.time_history), 863
save_basis ScalarDotGradIScalarTerm (class in
module, 656 sfepy.terms.terms_dot), 947
save_basis() (in module sfepy.discrete.iga.utils), 803 ScalarDotMGradScalarTerm (class in
save_basis_on_mesh() (in module save_basis), 656 sfepy.terms.terms_dot), 947
scale_matrix() (in module sfepy.solvers.oseen), 895
save_dict() (sfepy.applications.pde_solver_app.PDESolverApp
method), 659 schur (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
save_dir (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 tribute), 878
attribute), 885 schur (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at-
save_dir (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 tribute), 881
attribute), 888 schur (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at-
save_ebc() (sfepy.discrete.problem.Problem method), tribute), 885
710 schur (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at-
save_field_meshes() tribute), 888
(sfepy.discrete.problem.Problem method), schur_lld (sfepy.solvers.ls_mumps.mumps_struc_c_4
711 attribute), 878
save_image() (sfepy.postprocess.viewer.Viewer schur_lld (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
method), 867 attribute), 881

1100 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

schur_lld (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 sfepy.terms.terms_adj_navier_stokes), 916

attribute), 885 SDSufaceIntegrateTerm (class in
schur_lld (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 sfepy.terms.terms_surface), 1010
attribute), 888 SDSUPGCStabilizationTerm (class in
schur_mloc (sfepy.solvers.ls_mumps.mumps_struc_c_4 sfepy.terms.terms_adj_navier_stokes), 917
attribute), 878 SDVolumeDotTerm (class in sfepy.terms.terms_compat),
schur_mloc (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 929
attribute), 881 select_bcs() (sfepy.discrete.problem.Problem
schur_mloc (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 method), 711
attribute), 885 select_by_names() (in module sfepy.base.base), 665
schur_mloc (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 select_materials() (sfepy.discrete.problem.Problem
attribute), 888 method), 711
schur_nloc (sfepy.solvers.ls_mumps.mumps_struc_c_4 select_variables() (sfepy.discrete.problem.Problem
attribute), 878 method), 711
schur_nloc (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 SemismoothNewton (class in
attribute), 882 sfepy.solvers.semismooth_newton), 896
schur_nloc (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 separate() (sfepy.mesh.geom_tools.surface method),
attribute), 885 848
schur_nloc (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 separator (resview.FieldOptsToListAction attribute),
attribute), 889 644
SchurEVP (class in sfepy.homogenization.coefs_phononic), separator (resview.OptsToListAction attribute), 644
812 SerendipityTensorProductPolySpace (class in
SchurMumps (class in sfepy.solvers.ls), 873 sfepy.discrete.fem.poly_spaces), 770
ScipyBroyden (class in sfepy.solvers.nls), 892 set_accuracy() (in module sfepy.discrete.fem.mesh),
ScipyDirect (class in sfepy.solvers.ls), 873 761
ScipyEigenvalueSolver (class in sfepy.solvers.eigen), set_accuracy() (in module
869 sfepy.discrete.fem.periodic), 769
ScipyFMinSolver (class in sfepy.solvers.optimize), 893 set_adof_conns() (sfepy.discrete.variables.Variables
ScipyIterative (class in sfepy.solvers.ls), 873 method), 725
ScipySGEigenvalueSolver (class in set_all_data() (sfepy.discrete.materials.Material
sfepy.solvers.eigen), 870 method), 698
ScipySuperLU (class in sfepy.solvers.ls), 874 set_approx_points() (sfepy.mesh.bspline.BSpline
ScipyUmfpack (class in sfepy.solvers.ls), 874 method), 843
SDConvectTerm (class in set_approx_points() (sfepy.mesh.bspline.BSplineSurf
sfepy.terms.terms_adj_navier_stokes), 913 method), 845
SDDiffusionTerm (class in set_arg_types() (sfepy.terms.terms.Term method),
sfepy.terms.terms_diffusion), 942 908
SDDivGradTerm (class in set_arg_types() (sfepy.terms.terms_biot.BiotTerm
sfepy.terms.terms_adj_navier_stokes), 913 method), 927
SDDivTerm (class in sfepy.terms.terms_adj_navier_stokes), set_arg_types() (sfepy.terms.terms_diffusion.DiffusionCoupling
914 method), 939
SDDotTerm (class in sfepy.terms.terms_adj_navier_stokes), set_arg_types() (sfepy.terms.terms_diffusion.DiffusionTerm
914 method), 941
SDGradDivStabilizationTerm (class in set_arg_types() (sfepy.terms.terms_diffusion.LaplaceTerm
sfepy.terms.terms_adj_navier_stokes), 915 method), 942
SDLinearElasticTerm (class in set_arg_types() (sfepy.terms.terms_dot.DotProductTerm
sfepy.terms.terms_elastic), 959 method), 946
SDLinearTractionTerm (class in set_arg_types() (sfepy.terms.terms_dot.ScalarDotGradIScalarTerm
sfepy.terms.terms_surface), 1010 method), 947
SDPiezoCouplingTerm (class in set_arg_types() (sfepy.terms.terms_dot.VectorDotGradScalarTerm
sfepy.terms.terms_piezo), 998 method), 949
SDPSPGCStabilizationTerm (class in set_arg_types() (sfepy.terms.terms_dot.VectorDotScalarTerm
sfepy.terms.terms_adj_navier_stokes), 915 method), 950
SDPSPGPStabilizationTerm (class in set_arg_types() (sfepy.terms.terms_elastic.LinearElasticTerm

Index 1101
SfePy Documentation, Release version: 2022.1+git.f9873484

method), 957 725

set_arg_types() (sfepy.terms.terms_elastic.LinearPrestressTerm
set_default() (sfepy.base.base.Struct method), 662
method), 958 set_default_state()
set_arg_types() (sfepy.terms.terms_elastic.NonsymElasticTerm (sfepy.discrete.problem.Problem method),
method), 959 712
set_arg_types() (sfepy.terms.terms_navier_stokes.DivGradTerm
set_defaults() (in module sfepy.base.base), 665
method), 989 set_dim() (in module sfepy.linalg.sympy_operators),
set_arg_types() (sfepy.terms.terms_navier_stokes.StokesTerm 827
method), 995 set_dofs() (sfepy.discrete.common.fields.Field
set_arg_types() (sfepy.terms.terms_piezo.PiezoCouplingTerm method), 735
method), 997 set_dofs() (sfepy.discrete.dg.fields.DGField method),
set_arg_types() (sfepy.terms.terms_surface.LinearTractionTerm 784
method), 1010 set_dofs() (sfepy.discrete.fem.fields_hierarchic.H1HierarchicVolumeField
set_arg_types() (sfepy.terms.terms_surface.SDLinearTractionTermmethod), 753
method), 1010 set_dofs() (sfepy.discrete.fem.fields_nodal.H1NodalMixin
set_arg_types() (sfepy.terms.terms_surface.SufaceNormalDotTermmethod), 754
method), 1012 set_equations() (sfepy.discrete.problem.Problem
set_axes_font_size() (in module method), 712
sfepy.base.plotutils), 684 set_equations_instance()
set_backend() (sfepy.terms.terms_multilinear.ETermBase (sfepy.discrete.problem.Problem method),
method), 985 712
set_basis_indices() set_extra_args() (sfepy.discrete.functions.Function
(sfepy.discrete.fem.mappings.SurfaceMapping method), 696
method), 759 set_extra_args() (sfepy.discrete.materials.Material
set_basis_transform() method), 698
(sfepy.discrete.fem.fields_base.FEField set_facet_dofs() (sfepy.discrete.dg.fields.DGField
method), 751 method), 785
set_bcs() (sfepy.discrete.problem.Problem method), set_field_split() (sfepy.solvers.ls.PETScKrylovSolver
711 method), 872
set_cell_dofs() (sfepy.discrete.dg.fields.DGField set_field_split() (sfepy.solvers.solvers.Solver
method), 784 method), 897
set_colormap() (in module sfepy.postprocess.viewer), set_fields() (sfepy.discrete.problem.Problem
867 method), 712
set_conf_solvers() (sfepy.discrete.problem.Problem set_filename() (sfepy.postprocess.sources.GenericFileSource
method), 711 method), 861
set_constant() (sfepy.discrete.variables.Variable set_filename() (sfepy.postprocess.sources.GenericSequenceFileSource
method), 722 method), 861
set_control_points() (sfepy.mesh.bspline.BSpline set_filename() (sfepy.postprocess.sources.VTKFileSource
method), 843 method), 862
set_control_points() set_filename() (sfepy.postprocess.sources.VTKSequenceFileSource
(sfepy.mesh.bspline.BSplineSurf method), method), 862
845 set_float_format() (sfepy.discrete.fem.meshio.MeshIO
set_control_points() method), 767
(sfepy.mesh.splinebox.SplineBox method), set_from_data() (sfepy.solvers.ts.TimeStepper
852 method), 898
set_coors() (sfepy.discrete.fem.fields_base.FEField set_from_data() (sfepy.solvers.ts.VariableTimeStepper
method), 751 method), 899
set_data() (sfepy.discrete.equations.Equations set_from_function()
method), 692 (sfepy.discrete.variables.FieldVariable
set_data() (sfepy.discrete.materials.Material method), method), 721
698 set_from_mesh_vertices()
set_data() (sfepy.discrete.variables.Variable method), (sfepy.discrete.variables.FieldVariable
722 method), 721
set_data() (sfepy.discrete.variables.Variables method), set_from_other() (sfepy.discrete.variables.FieldVariable

1102 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

method), 721 703

set_from_qp() (sfepy.discrete.variables.FieldVariable set_output() (sfepy.base.base.Output method), 661
method), 721 set_output_dir() (sfepy.discrete.problem.Problem
set_from_ts() (sfepy.solvers.ts.TimeStepper method), method), 712
898 set_output_prefix() (sfepy.base.base.Output
set_from_ts() (sfepy.solvers.ts.VariableTimeStepper method), 661
method), 899 set_param() (sfepy.mesh.bspline.BSpline method), 844
set_full_state() (sfepy.discrete.variables.Variables set_param_n() (sfepy.mesh.bspline.BSpline method),
method), 725 844
set_function() (sfepy.discrete.functions.Function set_param_n() (sfepy.mesh.bspline.BSplineSurf
method), 696 method), 845
set_function() (sfepy.discrete.materials.Material set_rcd_centralized()
method), 698 (sfepy.solvers.ls_mumps.MumpsSolver
set_ics() (sfepy.discrete.problem.Problem method), method), 875
712 set_reduced_state()
set_integral() (sfepy.terms.terms.Term method), 908 (sfepy.discrete.variables.Variables method),
set_integral() (sfepy.terms.terms_shells.Shell10XTerm 725
method), 1007 set_regions() (sfepy.discrete.problem.Problem
set_kind() (sfepy.discrete.common.region.Region method), 712
method), 743 set_rhs() (sfepy.solvers.ls_mumps.MumpsSolver
set_kind_tdim() (sfepy.discrete.common.region.Region method), 875
method), 743 set_section() (in module gen_term_table), 654
set_knot_vector() (sfepy.mesh.bspline.BSpline set_silent() (sfepy.solvers.ls_mumps.MumpsSolver
method), 844 method), 875
set_linear() (sfepy.discrete.problem.Problem set_solver() (sfepy.discrete.problem.Problem
method), 712 method), 712
set_local_entities() set_source_filename()
(sfepy.discrete.common.extmods.cmesh.CMesh (sfepy.postprocess.viewer.Viewer method),
method), 731 867
set_logging_level() (in module set_state() (sfepy.discrete.equations.Equations
sfepy.base.multiproc_mpi), 681 method), 692
set_materials() (sfepy.discrete.problem.Problem set_state() (sfepy.discrete.variables.Variables
method), 712 method), 725
set_mesh_coors() (in module set_state() (sfepy.solvers.ts.TimeStepper method), 898
sfepy.discrete.fem.fields_base), 753 set_state() (sfepy.solvers.ts.VariableTimeStepper
set_mesh_coors() (sfepy.discrete.problem.Problem method), 899
method), 712 set_state_parts() (sfepy.discrete.variables.Variables
set_method() (sfepy.solvers.nls.ScipyBroyden method), method), 725
892 set_step() (sfepy.solvers.ts.TimeStepper method), 899
set_method() (sfepy.solvers.optimize.ScipyFMinSolver set_step() (sfepy.solvers.ts.VariableTimeStepper
method), 894 method), 899
set_micro_states() (sfepy.homogenization.engine.HomogenizationEngine
set_substep_time() (sfepy.solvers.ts.TimeStepper
method), 815 method), 899
set_mtx_centralized() set_time_step() (sfepy.solvers.ts.VariableTimeStepper
(sfepy.solvers.ls_mumps.MumpsSolver method), 899
method), 875 set_variables() (sfepy.discrete.problem.Problem
set_n_digit_from_min_dt() method), 713
(sfepy.solvers.ts.VariableTimeStepper method), set_variables_default()
899 (sfepy.homogenization.coefs_base.CoefExprPar
set_n_point() (sfepy.discrete.probes.Probe method), static method), 806
702 set_variables_default()
set_nonlin_states() (in module (sfepy.homogenization.coefs_base.CoefMN
sfepy.homogenization.utils), 822 static method), 806
set_options() (sfepy.discrete.probes.Probe method), set_variables_default()

Index 1103
SfePy Documentation, Release version: 2022.1+git.f9873484

(sfepy.homogenization.coefs_base.CoefN method), 809

static method), 806 setup_extra_data() (in module
set_variables_default() sfepy.discrete.common.fields), 736
(sfepy.homogenization.coefs_base.CoefOne setup_extra_data() (sfepy.discrete.dg.fields.DGField
static method), 807 method), 785
set_variables_default() setup_extra_data() (sfepy.discrete.fem.fields_base.SurfaceField
(sfepy.homogenization.coefs_base.CorrN method), 752
static method), 808 setup_extra_data() (sfepy.discrete.fem.fields_base.VolumeField
set_variables_default() method), 752
(sfepy.homogenization.coefs_base.CorrNN setup_extra_data() (sfepy.discrete.iga.fields.IGField
static method), 808 method), 796
set_variables_default() setup_formal_args() (sfepy.terms.terms.Term
(sfepy.homogenization.coefs_base.CorrOne method), 908
static method), 808 setup_from_highest()
set_vec_part() (sfepy.discrete.variables.Variables (sfepy.discrete.common.region.Region method),
method), 725 744
set_verbose() (sfepy.solvers.ls_mumps.MumpsSolver setup_from_vertices()
method), 875 (sfepy.discrete.common.region.Region method),
set_verbosity() (sfepy.terms.terms_multilinear.ETermBase 744
method), 985 setup_hooks() (sfepy.discrete.problem.Problem
SetStep (class in sfepy.postprocess.viewer), 864 method), 713
setup() (in module gen_solver_table), 654 setup_initial_conditions()
setup() (in module gen_term_table), 654 (sfepy.discrete.equations.Equations method),
setup() (sfepy.base.conf.ProblemConf method), 670 692
setup() (sfepy.discrete.fem.lcbc_operators.LCBCOperator setup_initial_conditions()
method), 757 (sfepy.discrete.variables.FieldVariable
setup() (sfepy.discrete.fem.lcbc_operators.MRLCBCOperator method), 721
method), 757 setup_initial_conditions()
setup() (sfepy.solvers.oseen.StabilizationFunction (sfepy.discrete.variables.Variables method),
method), 895 726
setup() (sfepy.terms.terms.Term method), 908 setup_integration() (sfepy.terms.terms.Term
setup() (sfepy.terms.terms.Terms method), 909 method), 908
setUp() (sfepy.tests.test_linear_solvers.DiagPC setup_lcbc_operators()
method), 1024 (sfepy.discrete.variables.Variables method),
setup_args() (sfepy.terms.terms.Term method), 908 726
setup_axis() (in module setup_lines() (in module
sfepy.discrete.dg.dg_1D_vizualizer), 778 sfepy.discrete.dg.dg_1D_vizualizer), 779
setup_composite_dofs() (in module setup_macro_data() (sfepy.homogenization.homogen_app.Homogenizati
sfepy.parallel.parallel), 855 method), 817
setup_connectivity() setup_mat_id() (sfepy.postprocess.sources.FileSource
(sfepy.discrete.common.extmods.cmesh.CMesh method), 861
method), 731 setup_mirror_connectivity()
setup_coors() (sfepy.discrete.fem.fields_base.FEField (sfepy.discrete.fem.fe_surface.FESurface
method), 751 method), 748
setup_default_output() setup_mirror_region()
(sfepy.discrete.problem.Problem method), (sfepy.discrete.common.region.Region method),
713 744
setup_dof_info() (sfepy.discrete.variables.Variables setup_notification()
method), 725 (sfepy.postprocess.sources.FileSource method),
setup_dtype() (sfepy.discrete.variables.Variables 861
method), 725 setup_options() (sfepy.applications.application.Application
setup_entities() (sfepy.discrete.common.extmods.cmesh.CMesh method), 658
method), 732 setup_options() (sfepy.applications.evp_solver_app.EVPSolverApp
setup_equations() (sfepy.homogenization.coefs_base.TCorrectorsViaPressureEVP
method), 658

1104 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

setup_options() (sfepy.applications.pde_solver_app.PDESolverApp
sfepy.base.multiproc_mpi
method), 659 module, 680
setup_options() (sfepy.homogenization.band_gaps_app.AcousticBandGapsApp
sfepy.base.multiproc_proc
method), 804 module, 682
setup_options() (sfepy.homogenization.engine.HomogenizationEngine
sfepy.base.parse_conf
method), 815 module, 683
setup_options() (sfepy.homogenization.homogen_app.HomogenizationApp
sfepy.base.plotutils
method), 817 module, 684
setup_ordering() (sfepy.discrete.variables.Variables sfepy.base.reader
method), 726 module, 684
setup_orientation() (in module sfepy.base.resolve_deps
sfepy.discrete.fem.geometry_element), 756 module, 685
setup_output() (sfepy.applications.evp_solver_app.EVPSolverApp
sfepy.base.testing
method), 658 module, 685
setup_output() (sfepy.discrete.problem.Problem sfepy.base.timing
method), 713 module, 686
setup_output() (sfepy.homogenization.coefs_base.CorrMiniApp
sfepy.config
method), 807 module, 657
setup_output_info() sfepy.discrete.common.dof_info
(sfepy.applications.pde_solver_app.PDESolverApp module, 726
method), 659 sfepy.discrete.common.domain
setup_petsc_precond() (in module module, 728
sfepy.tests.test_linear_solvers), 1024 sfepy.discrete.common.extmods._fmfield
setup_point_data() (sfepy.discrete.fem.fields_base.VolumeField
module, 729
method), 752 sfepy.discrete.common.extmods._geommech
setup_surface_data() module, 729
(sfepy.discrete.fem.fields_base.VolumeField sfepy.discrete.common.extmods.assemble
method), 752 module, 729
sfepy.applications.application sfepy.discrete.common.extmods.cmesh
module, 658 module, 730
sfepy.applications.evp_solver_app sfepy.discrete.common.extmods.crefcoors
module, 658 module, 732
sfepy.applications.pde_solver_app sfepy.discrete.common.extmods.mappings
module, 659 module, 733
sfepy.base.base sfepy.discrete.common.fields
module, 659 module, 734
sfepy.base.compat sfepy.discrete.common.global_interp
module, 666 module, 736
sfepy.base.conf sfepy.discrete.common.mappings
module, 669 module, 738
sfepy.base.getch sfepy.discrete.common.poly_spaces
module, 672 module, 740
sfepy.base.goptions sfepy.discrete.common.region
module, 672 module, 741
sfepy.base.ioutils sfepy.discrete.conditions
module, 672 module, 686
sfepy.base.log sfepy.discrete.dg.dg_1D_vizualizer
module, 677 module, 775
sfepy.base.log_plotter sfepy.discrete.dg.fields
module, 678 module, 779
sfepy.base.mem_usage sfepy.discrete.dg.limiters
module, 679 module, 789
sfepy.base.multiproc sfepy.discrete.dg.poly_spaces
module, 679 module, 786

Index 1105
SfePy Documentation, Release version: 2022.1+git.f9873484

sfepy.discrete.equations sfepy.discrete.iga.domain_generators
module, 688 module, 792
sfepy.discrete.evaluate sfepy.discrete.iga.extmods.igac
module, 693 module, 793
sfepy.discrete.evaluate_variable sfepy.discrete.iga.fields
module, 696 module, 795
sfepy.discrete.fem._serendipity sfepy.discrete.iga.iga
module, 774 module, 796
sfepy.discrete.fem.domain sfepy.discrete.iga.io
module, 744 module, 801
sfepy.discrete.fem.extmods.bases sfepy.discrete.iga.mappings
module, 745 module, 801
sfepy.discrete.fem.extmods.lobatto_bases sfepy.discrete.iga.plot_nurbs
module, 746 module, 802
sfepy.discrete.fem.facets sfepy.discrete.iga.utils
module, 746 module, 802
sfepy.discrete.fem.fe_surface sfepy.discrete.integrals
module, 748 module, 697
sfepy.discrete.fem.fields_base sfepy.discrete.materials
module, 748 module, 698
sfepy.discrete.fem.fields_hierarchic sfepy.discrete.parse_equations
module, 753 module, 700
sfepy.discrete.fem.fields_nodal sfepy.discrete.parse_regions
module, 754 module, 700
sfepy.discrete.fem.fields_positive sfepy.discrete.probes
module, 755 module, 701
sfepy.discrete.fem.geometry_element sfepy.discrete.problem
module, 755 module, 704
sfepy.discrete.fem.history sfepy.discrete.projections
module, 756 module, 715
sfepy.discrete.fem.lcbc_operators sfepy.discrete.quadratures
module, 756 module, 715
sfepy.discrete.fem.linearizer sfepy.discrete.simplex_cubature
module, 759 module, 717
sfepy.discrete.fem.mappings sfepy.discrete.structural.fields
module, 759 module, 803
sfepy.discrete.fem.mesh sfepy.discrete.structural.mappings
module, 760 module, 804
sfepy.discrete.fem.meshio sfepy.discrete.variables
module, 761 module, 717
sfepy.discrete.fem.periodic sfepy.homogenization.band_gaps_app
module, 768 module, 804
sfepy.discrete.fem.poly_spaces sfepy.homogenization.coefficients
module, 769 module, 805
sfepy.discrete.fem.refine sfepy.homogenization.coefs_base
module, 773 module, 806
sfepy.discrete.fem.refine_hanging sfepy.homogenization.coefs_elastic
module, 774 module, 809
sfepy.discrete.fem.utils sfepy.homogenization.coefs_perfusion
module, 774 module, 809
sfepy.discrete.functions sfepy.homogenization.coefs_phononic
module, 696 module, 810
sfepy.discrete.iga.domain sfepy.homogenization.convolutions
module, 791 module, 814

1106 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

sfepy.homogenization.engine sfepy.postprocess.domain_specific
module, 815 module, 856
sfepy.homogenization.homogen_app sfepy.postprocess.plot_cmesh
module, 817 module, 857
sfepy.homogenization.micmac sfepy.postprocess.plot_dofs
module, 818 module, 858
sfepy.homogenization.recovery sfepy.postprocess.plot_facets
module, 818 module, 858
sfepy.homogenization.utils sfepy.postprocess.plot_quadrature
module, 821 module, 859
sfepy.linalg.check_derivatives sfepy.postprocess.probes_vtk
module, 822 module, 859
sfepy.linalg.eigen sfepy.postprocess.sources
module, 822 module, 860
sfepy.linalg.geometry sfepy.postprocess.time_history
module, 823 module, 862
sfepy.linalg.sparse sfepy.postprocess.utils
module, 825 module, 863
sfepy.linalg.sympy_operators sfepy.postprocess.utils_vtk
module, 827 module, 863
sfepy.linalg.utils sfepy.postprocess.viewer
module, 827 module, 864
sfepy.mechanics.contact_bodies sfepy.solvers.auto_fallback
module, 830 module, 868
sfepy.mechanics.elastic_constants sfepy.solvers.eigen
module, 831 module, 868
sfepy.mechanics.extmods.ccontres sfepy.solvers.ls
module, 841 module, 870
sfepy.mechanics.matcoefs sfepy.solvers.ls_mumps
module, 831 module, 875
sfepy.mechanics.membranes sfepy.solvers.ls_mumps_parallel
module, 833 module, 889
sfepy.mechanics.shell10x sfepy.solvers.nls
module, 835 module, 890
sfepy.mechanics.tensors sfepy.solvers.optimize
module, 837 module, 893
sfepy.mechanics.units sfepy.solvers.oseen
module, 839 module, 894
sfepy.mesh.bspline sfepy.solvers.qeigen
module, 842 module, 895
sfepy.mesh.geom_tools sfepy.solvers.semismooth_newton
module, 846 module, 896
sfepy.mesh.mesh_generators sfepy.solvers.solvers
module, 848 module, 897
sfepy.mesh.mesh_tools sfepy.solvers.ts
module, 851 module, 898
sfepy.mesh.splinebox sfepy.solvers.ts_dg_solvers
module, 852 module, 790
sfepy.parallel.evaluate sfepy.solvers.ts_solvers
module, 853 module, 900
sfepy.parallel.parallel sfepy.terms.extmods.terms
module, 854 module, 1013
sfepy.parallel.plot_parallel_dofs sfepy.terms.terms
module, 856 module, 905

Index 1107
SfePy Documentation, Release version: 2022.1+git.f9873484

sfepy.terms.terms_adj_navier_stokes sfepy.tests.test_assembling
module, 910 module, 1018
sfepy.terms.terms_basic sfepy.tests.test_base
module, 919 module, 1019
sfepy.terms.terms_biot sfepy.tests.test_cmesh
module, 924 module, 1019
sfepy.terms.terms_compat sfepy.tests.test_conditions
module, 927 module, 1019
sfepy.terms.terms_constraints sfepy.tests.test_declarative_examples
module, 930 module, 1020
sfepy.terms.terms_contact sfepy.tests.test_dg_field
module, 932 module, 1020
sfepy.terms.terms_dg sfepy.tests.test_domain
module, 933 module, 1021
sfepy.terms.terms_diffusion sfepy.tests.test_eigenvalue_solvers
module, 938 module, 1021
sfepy.terms.terms_dot sfepy.tests.test_elasticity_small_strain
module, 944 module, 1021
sfepy.terms.terms_elastic sfepy.tests.test_fem
module, 950 module, 1022
sfepy.terms.terms_electric sfepy.tests.test_functions
module, 960 module, 1022
sfepy.terms.terms_fibres sfepy.tests.test_high_level
module, 960 module, 1022
sfepy.terms.terms_hyperelastic_base sfepy.tests.test_homogenization_engine
module, 961 module, 1023
sfepy.terms.terms_hyperelastic_tl sfepy.tests.test_homogenization_perfusion
module, 963 module, 1023
sfepy.terms.terms_hyperelastic_ul sfepy.tests.test_hyperelastic_tlul
module, 971 module, 1023
sfepy.terms.terms_membrane sfepy.tests.test_io
module, 975 module, 1023
sfepy.terms.terms_multilinear sfepy.tests.test_laplace_unit_disk
module, 976 module, 1023
sfepy.terms.terms_navier_stokes sfepy.tests.test_laplace_unit_square
module, 987 module, 1023
sfepy.terms.terms_piezo sfepy.tests.test_lcbcs
module, 996 module, 1024
sfepy.terms.terms_point sfepy.tests.test_linalg
module, 999 module, 1024
sfepy.terms.terms_sensitivity sfepy.tests.test_linear_solvers
module, 1000 module, 1024
sfepy.terms.terms_shells sfepy.tests.test_linearization
module, 1005 module, 1025
sfepy.terms.terms_surface sfepy.tests.test_log
module, 1007 module, 1025
sfepy.terms.terms_th sfepy.tests.test_matcoefs
module, 1012 module, 1025
sfepy.terms.terms_volume sfepy.tests.test_mesh_expand
module, 1013 module, 1025
sfepy.terms.utils sfepy.tests.test_mesh_generators
module, 1013 module, 1025
sfepy.tests.conftest sfepy.tests.test_mesh_interp
module, 1018 module, 1026

1108 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

sfepy.tests.test_mesh_smoothing Shell10XMapping (class in

module, 1026 sfepy.discrete.structural.mappings), 804
sfepy.tests.test_meshio Shell10XTerm (class in sfepy.terms.terms_shells), 1005
module, 1026 ShiftedPeriodicOperator (class in
sfepy.tests.test_msm_laplace sfepy.discrete.fem.lcbc_operators), 758
module, 1027 show_authors
sfepy.tests.test_msm_symbolic module, 656
module, 1027 show_mesh_info
sfepy.tests.test_normals module, 656
module, 1027 show_scalar_bars() (sfepy.postprocess.viewer.Viewer
sfepy.tests.test_parsing method), 867
module, 1027 show_terms_use
sfepy.tests.test_poly_spaces module, 656
module, 1027 simple
sfepy.tests.test_projections module, 645
module, 1028 simple_example() (in module sfepy.mesh.bspline), 845
sfepy.tests.test_quadratures simple_homog_mpi
module, 1028 module, 645
sfepy.tests.test_ref_coors SimpleEVP (class in sfepy.homogenization.coefs_phononic),
module, 1029 812
sfepy.tests.test_refine_hanging SimpleTimeSteppingSolver (class in
module, 1029 sfepy.solvers.ts_solvers), 903
sfepy.tests.test_regions size_schur (sfepy.solvers.ls_mumps.mumps_struc_c_4
module, 1029 attribute), 878
sfepy.tests.test_semismooth_newton size_schur (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
module, 1029 attribute), 882
sfepy.tests.test_sparse size_schur (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
module, 1030 attribute), 885
sfepy.tests.test_splinebox size_schur (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
module, 1030 attribute), 889
sfepy.tests.test_tensors skip_read_line() (in module sfepy.base.ioutils), 676
module, 1030 slave_get_task() (in module
sfepy.tests.test_term_call_modes sfepy.base.multiproc_mpi), 682
module, 1030 slave_task_done() (in module
sfepy.tests.test_term_consistency sfepy.base.multiproc_mpi), 682
module, 1031 SLEPcEigenvalueSolver (class in sfepy.solvers.eigen),
sfepy.tests.test_term_sensitivity 869
module, 1031 smooth_f() (sfepy.terms.terms_surface.ContactPlaneTerm
sfepy.tests.test_units static method), 1008
module, 1031 smooth_mesh() (in module sfepy.mesh.mesh_tools), 851
sfepy.tests.test_volume SoftLink (class in sfepy.base.ioutils), 674
module, 1031 sol_frame() (in module
sfepy.version sfepy.discrete.dg.dg_1D_vizualizer), 779
module, 658 sol_loc (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
shape (sfepy.discrete.common.extmods.mappings.CMapping tribute), 878
attribute), 733 sol_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
ShapeDim (class in sfepy.homogenization.coefs_base), attribute), 882
809 sol_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
ShapeDimDim (class in attribute), 885
sfepy.homogenization.coefs_base), 809 sol_loc (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
shell() (in module sfepy.base.base), 665 attribute), 889
Shell10XField (class in sfepy.discrete.structural.fields), solutions() (in module
803 sfepy.tests.test_elasticity_small_strain), 1021
solvable() (in module sfepy.base.resolve_deps), 685

Index 1109
SfePy Documentation, Release version: 2022.1+git.f9873484

solve() (in module sfepy.solvers.ls), 874 attribute), 791

solve() (sfepy.discrete.problem.Problem method), 713 standalone_setup() (sfepy.terms.terms.Term method),
solve_eigen_problem() 908
(sfepy.applications.evp_solver_app.EVPSolverAppstandard_call() (in module sfepy.solvers.eigen), 870
method), 658 standard_call() (in module sfepy.solvers.ls), 875
solve_pde() (in module standard_call() (in module sfepy.solvers.qeigen), 896
sfepy.applications.pde_solver_app), 659 standard_ts_call() (in module
solve_pressure_eigenproblem() sfepy.solvers.ts_solvers), 904
(sfepy.homogenization.coefs_base.PressureEigenvalueProblem
start() (sfepy.base.timing.Timer method), 686
method), 808 StationarySolver (class in sfepy.solvers.ts_solvers),
solve_step() (sfepy.solvers.ts_dg_solvers.DGMultiStageTSS 903
method), 790 step (sfepy.postprocess.viewer.SetStep attribute), 864
solve_step() (sfepy.solvers.ts_dg_solvers.EulerStepSolverstiffness_from_lame() (in module
method), 790 sfepy.mechanics.matcoefs), 832
solve_step() (sfepy.solvers.ts_dg_solvers.RK4StepSolver stiffness_from_lame_mixed() (in module
method), 791 sfepy.mechanics.matcoefs), 833
solve_step() (sfepy.solvers.ts_dg_solvers.TVDRK3StepSolver stiffness_from_youngpoisson() (in module
method), 791 sfepy.mechanics.matcoefs), 833
solve_step() (sfepy.solvers.ts_solvers.AdaptiveTimeSteppingSolver
stiffness_from_youngpoisson_mixed() (in module
method), 900 sfepy.mechanics.matcoefs), 833
solve_step() (sfepy.solvers.ts_solvers.SimpleTimeSteppingSolver
StokesTerm (class in sfepy.terms.terms_navier_stokes),
method), 903 994
solve_step0() (sfepy.solvers.ts_dg_solvers.DGMultiStageTSS StokesWaveDivTerm (class in
method), 790 sfepy.terms.terms_navier_stokes), 995
solve_step0() (sfepy.solvers.ts_solvers.SimpleTimeSteppingSolver
StokesWaveTerm (class in
method), 903 sfepy.terms.terms_navier_stokes), 996
Solver (class in sfepy.solvers.solvers), 897 stop() (sfepy.base.timing.Timer method), 686
SolverMeta (class in sfepy.solvers.solvers), 897 StoreNumberAction (class in resview), 644
sort() (sfepy.discrete.conditions.Conditions method), str_all() (sfepy.base.base.Struct method), 662
686 str_class() (sfepy.base.base.Struct method), 662
sort_by_dependency() (in module stress_function() (sfepy.terms.terms_fibres.FibresActiveTLTerm
sfepy.discrete.common.region), 744 static method), 961
sparse_submat() (sfepy.solvers.ls.MultiProblem stress_function() (sfepy.terms.terms_hyperelastic_tl.BulkActiveTLTerm
method), 871 static method), 963
spause() (in module sfepy.base.base), 665 stress_function() (sfepy.terms.terms_hyperelastic_tl.BulkPenaltyTLTer
SphinxHTMLDocs (class in build_helpers), 646 static method), 964
SphinxPDFDocs (class in build_helpers), 646 stress_function() (sfepy.terms.terms_hyperelastic_tl.BulkPressureTLTe
SplineBox (class in sfepy.mesh.splinebox), 852 static method), 964
SplineRegion2D (class in sfepy.mesh.splinebox), 853 stress_function() (sfepy.terms.terms_hyperelastic_tl.GenYeohTLTerm
split_chunks() (in module method), 966
sfepy.homogenization.coefs_phononic), 814 stress_function() (sfepy.terms.terms_hyperelastic_tl.MooneyRivlinTLTe
split_complex_args() (in module sfepy.terms.terms), static method), 967
909 stress_function() (sfepy.terms.terms_hyperelastic_tl.NeoHookeanTLTer
split_conns_mat_ids() (in module static method), 967
sfepy.discrete.fem.meshio), 768 stress_function() (sfepy.terms.terms_hyperelastic_tl.OgdenTLTerm
split_on() (in module edit_identifiers), 649 method), 968
split_range() (in module sfepy.linalg.utils), 830 stress_function() (sfepy.terms.terms_hyperelastic_ul.BulkPenaltyULTe
splitlines() (sfepy.mesh.geom_tools.geometry static method), 971
method), 847 stress_function() (sfepy.terms.terms_hyperelastic_ul.BulkPressureULT
spy() (in module sfepy.base.plotutils), 684 static method), 972
spy_and_show() (in module sfepy.base.plotutils), 684 stress_function() (sfepy.terms.terms_hyperelastic_ul.MooneyRivlinULT
StabilizationFunction (class in sfepy.solvers.oseen), static method), 973
895 stress_function() (sfepy.terms.terms_hyperelastic_ul.NeoHookeanULTe
stage_updates (sfepy.solvers.ts_dg_solvers.RK4StepSolver static method), 974

1110 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

StressTransform (class in sfepy.mechanics.tensors), sfepy.terms.terms_diffusion), 943

837 SurfaceFluxTLTerm (class in
string (sfepy.discrete.fem.meshio.HDF5MeshIO at- sfepy.terms.terms_hyperelastic_tl), 968
tribute), 765 SurfaceGradTerm (class in sfepy.terms.terms_compat),
Struct (class in sfepy.base.base), 661 930
structify() (in module sfepy.base.base), 665 SurfaceJumpTerm (class in sfepy.terms.terms_surface),
substitute_continuous() (in module 1012
eval_ns_forms), 650 SurfaceMapping (class in sfepy.discrete.fem.mappings),
substitute_dofs() (sfepy.discrete.fem.fields_base.FEField 759
method), 751 SurfaceMomentTerm (class in sfepy.terms.terms_basic),
SufaceNormalDotTerm (class in 922
sfepy.terms.terms_surface), 1011 SurfaceTerm (class in sfepy.terms.terms_compat), 930
suggest_name() (sfepy.discrete.common.poly_spaces.PolySpaceSurfaceTractionTLTerm (class in
static method), 741 sfepy.terms.terms_hyperelastic_tl), 969
SumNodalValuesTerm (class in sym (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
sfepy.terms.terms_basic), 921 tribute), 878
SUPGCAdjStabilizationTerm (class in sym (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 at-
sfepy.terms.terms_adj_navier_stokes), 918 tribute), 882
SUPGCStabilizationTerm (class in sym (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 at-
sfepy.terms.terms_navier_stokes), 993 tribute), 885
SUPGPAdj1StabilizationTerm (class in sym (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 at-
sfepy.terms.terms_adj_navier_stokes), 918 tribute), 889
SUPGPAdj2StabilizationTerm (class in sym (sfepy.solvers.ls_mumps.mumps_struc_c_x at-
sfepy.terms.terms_adj_navier_stokes), 919 tribute), 889
SUPGPStabilizationTerm (class in sym2dim() (in module sfepy.mechanics.tensors), 838
sfepy.terms.terms_navier_stokes), 993 sym2nonsym() (in module sfepy.terms.extmods.terms),
supported_orders (sfepy.discrete.fem.poly_spaces.SerendipityTensorProductPolySpace
1018
attribute), 773 sym2nonsym() (in module
surface (class in sfepy.mesh.geom_tools), 847 sfepy.terms.terms_multilinear), 987
surface_components() (in module extract_surface), sym_perm (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
651 tribute), 879
surface_graph() (in module extract_surface), 651 sym_perm (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
surface_integration attribute), 882
(sfepy.terms.terms_diffusion.DiffusionVelocityTermsym_perm (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
attribute), 941 attribute), 885
surface_integration sym_perm (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
(sfepy.terms.terms_elastic.CauchyStrainTerm attribute), 889
attribute), 951 sym_tri_eigen() (in module sfepy.linalg.eigen), 823
surface_integration symarray() (in module sfepy.tests.test_quadratures),
(sfepy.terms.terms_elastic.CauchyStressTerm 1028
attribute), 953 symbolic (sfepy.terms.terms_dg.AdvectionDGFluxTerm
surface_integration attribute), 934
(sfepy.terms.terms_navier_stokes.DivTerm symbolic (sfepy.terms.terms_dg.NonlinearHyperbolicDGFluxTerm
attribute), 990 attribute), 937
surface_integration symbolic (sfepy.terms.terms_diffusion.DiffusionTerm at-
(sfepy.terms.terms_navier_stokes.GradTerm tribute), 941
attribute), 991 symbolic (sfepy.terms.terms_diffusion.LaplaceTerm at-
SurfaceDivTerm (class in sfepy.terms.terms_compat), tribute), 942
929 sync_module_docs
SurfaceField (class in sfepy.discrete.fem.fields_base), module, 656
751 system() (sfepy.config.Config method), 657
SurfaceFluxOperatorTerm (class in
sfepy.terms.terms_diffusion), 943 T
SurfaceFluxTerm (class in tags (in module sfepy.base.multiproc_mpi), 682

Index 1111
SfePy Documentation, Release version: 2022.1+git.f9873484

tan_mod_function() (sfepy.terms.terms_fibres.FibresActiveTLTermsfepy.tests.test_assembling), 1018

static method), 961 test_assemble_vector() (in module
tan_mod_function() (sfepy.terms.terms_hyperelastic_tl.BulkActiveTLTerm
sfepy.tests.test_assembling), 1018
static method), 963 test_assemble_vector_complex() (in module
tan_mod_function() (sfepy.terms.terms_hyperelastic_tl.BulkPenaltyTLTerm
sfepy.tests.test_assembling), 1018
static method), 964 test_base_functions_delta() (in module
tan_mod_function() (sfepy.terms.terms_hyperelastic_tl.GenYeohTLTermsfepy.tests.test_fem), 1022
method), 966 test_base_functions_values() (in module
tan_mod_function() (sfepy.terms.terms_hyperelastic_tl.MooneyRivlinTLTerm
sfepy.tests.test_fem), 1022
static method), 967 test_boundary_fluxes() (in module
tan_mod_function() (sfepy.terms.terms_hyperelastic_tl.NeoHookeanTLTerm
sfepy.tests.test_laplace_unit_disk), 1023
static method), 967 test_boundary_fluxes() (in module
tan_mod_function() (sfepy.terms.terms_hyperelastic_tl.OgdenTLTerm sfepy.tests.test_laplace_unit_square), 1024
method), 968 test_chunk_micro() (in module
tan_mod_function() (sfepy.terms.terms_hyperelastic_ul.BulkPenaltyULTerm
sfepy.tests.test_homogenization_engine),
static method), 971 1023
tan_mod_function() (sfepy.terms.terms_hyperelastic_ul.MooneyRivlinULTerm
test_cmesh_counts() (in module
static method), 973 sfepy.tests.test_cmesh), 1019
tan_mod_function() (sfepy.terms.terms_hyperelastic_ul.NeoHookeanULTerm
test_compare_same_meshes() (in module
static method), 974 sfepy.tests.test_meshio), 1026
tan_mod_u_function() test_compose_sparse() (in module
(sfepy.terms.terms_hyperelastic_tl.BulkPressureTLTerm sfepy.tests.test_sparse), 1030
static method), 964 test_consistency_d_dw() (in module
tan_mod_u_function() sfepy.tests.test_term_consistency), 1031
(sfepy.terms.terms_hyperelastic_ul.BulkPressureULTerm
test_consistent_sets() (in module
static method), 972 sfepy.tests.test_units), 1031
TCorrectorsPressureViaPressureEVP (class in test_container_add() (in module
sfepy.homogenization.coefs_elastic), 809 sfepy.tests.test_base), 1019
TCorrectorsRSViaPressureEVP (class in test_continuity() (in module
sfepy.homogenization.coefs_elastic), 809 sfepy.tests.test_poly_spaces), 1028
TCorrectorsViaPressureEVP (class in test_continuity() (in module
sfepy.homogenization.coefs_base), 809 sfepy.tests.test_refine_hanging), 1029
tdim (sfepy.discrete.common.extmods.cmesh.CMesh at- test_converged() (in module
tribute), 732 sfepy.tests.test_elasticity_small_strain), 1021
tensor_plane_stress() test_conversion_functions() (in module
(sfepy.mechanics.matcoefs.TransformToPlane sfepy.tests.test_matcoefs), 1025
method), 832 test_create_output1D()
tensor_product() (in module sfepy.discrete.iga.iga), (sfepy.tests.test_dg_field.TestDGField method),
801 1020
Term (class in sfepy.terms.terms), 905 test_create_output2D()
term_ns_asm_convect() (in module (sfepy.tests.test_dg_field.TestDGField method),
sfepy.terms.extmods.terms), 1018 1020
term_ns_asm_div_grad() (in module test_dependencies() (in module
sfepy.terms.extmods.terms), 1018 sfepy.tests.test_homogenization_engine),
terminate() (sfepy.base.log.Log method), 677 1023
terminate() (sfepy.base.log_plotter.LogPlotter test_ebc_functions() (in module
method), 678 sfepy.tests.test_functions), 1022
TermParse (class in sfepy.discrete.parse_equations), 700 test_ebcs() (in module sfepy.tests.test_conditions),
Terms (class in sfepy.terms.terms), 908 1019
test_assemble1d() (in module sfepy.tests.test_linalg), test_eigenvalue_solvers() (in module
1024 sfepy.tests.test_eigenvalue_solvers), 1021
test_assemble_matrix() (in module test_elastic_constants() (in module
sfepy.tests.test_assembling), 1018 sfepy.tests.test_matcoefs), 1025
test_assemble_matrix_complex() (in module test_elasticity_rigid() (in module

1112 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

sfepy.tests.test_lcbcs), 1024 (sfepy.tests.test_dg_field.TestDGField method),

test_entity_volumes() (in module 1020
sfepy.tests.test_cmesh), 1019 test_gradients() (in module
test_epbcs() (in module sfepy.tests.test_conditions), sfepy.tests.test_poly_spaces), 1028
1019 test_hdf5_meshio() (in module
test_ev_div() (in module sfepy.tests.test_meshio), 1026
sfepy.tests.test_term_consistency), 1031 test_hessians() (in module
test_ev_grad() (in module sfepy.tests.test_poly_spaces), 1028
sfepy.tests.test_term_consistency), 1031 test_ics() (in module sfepy.tests.test_conditions), 1019
test_eval_matrix() (in module test_install
sfepy.tests.test_term_consistency), 1031 module, 647
test_evaluate_at() (in module test_interpolation() (in module
sfepy.tests.test_mesh_interp), 1026 sfepy.tests.test_mesh_interp), 1026
test_examples() (in module test_interpolation_two_meshes() (in module
sfepy.tests.test_declarative_examples), 1020 sfepy.tests.test_mesh_interp), 1026
test_examples_dg() (in module test_invariance() (in module
sfepy.tests.test_declarative_examples), 1020 sfepy.tests.test_mesh_interp), 1026
test_facets() (in module sfepy.tests.test_domain), test_invariance_qp() (in module
1021 sfepy.tests.test_mesh_interp), 1026
test_field_gradient() (in module test_laplace_shifted_periodic() (in module
sfepy.tests.test_mesh_interp), 1026 sfepy.tests.test_lcbcs), 1024
test_gen_block_mesh() (in module test_linear_terms() (in module
sfepy.tests.test_mesh_generators), 1025 sfepy.tests.test_elasticity_small_strain), 1021
test_gen_cylinder_mesh() (in module test_linearization() (in module
sfepy.tests.test_mesh_generators), 1025 sfepy.tests.test_linearization), 1025
test_gen_extended_block_mesh() (in module test_log_rw() (in module sfepy.tests.test_log), 1025
sfepy.tests.test_mesh_generators), 1025 test_ls_reuse() (in module
test_gen_mesh_from_geom() (in module sfepy.tests.test_linear_solvers), 1024
sfepy.tests.test_mesh_generators), 1025 test_mass_matrix() (in module
test_gen_mesh_from_voxels() (in module sfepy.tests.test_projections), 1028
sfepy.tests.test_mesh_generators), 1025 test_material_functions() (in module
test_gen_tiled_mesh() (in module sfepy.tests.test_functions), 1022
sfepy.tests.test_mesh_generators), 1025 test_mesh_expand() (in module
test_geometry() (in module sfepy.tests.test_linalg), sfepy.tests.test_mesh_expand), 1025
1024 test_mesh_smoothing() (in module
test_get_bc_facet_values_1D() sfepy.tests.test_mesh_smoothing), 1026
(sfepy.tests.test_dg_field.TestDGField method), test_msm_laplace() (in module
1020 sfepy.tests.test_msm_laplace), 1027
test_get_bc_facet_values_2D() test_msm_symbolic_diffusion() (in module
(sfepy.tests.test_dg_field.TestDGField method), sfepy.tests.test_msm_symbolic), 1027
1020 test_msm_symbolic_laplace() (in module
test_get_bc_facet_values_2D_const() sfepy.tests.test_msm_symbolic), 1027
(sfepy.tests.test_dg_field.TestDGField method), test_normals() (in module sfepy.tests.test_normals),
1020 1027
test_get_facet_idx1D() test_operators() (in module sfepy.tests.test_regions),
(sfepy.tests.test_dg_field.TestDGField method), 1029
1020 test_parse_conf() (in module sfepy.tests.test_base),
test_get_facet_idx2D() 1019
(sfepy.tests.test_dg_field.TestDGField method), test_parse_equations() (in module
1020 sfepy.tests.test_parsing), 1027
test_get_facet_neighbor_idx_1d() test_parse_regions() (in module
(sfepy.tests.test_dg_field.TestDGField method), sfepy.tests.test_parsing), 1027
1020 test_partition_of_unity() (in module
test_get_facet_neighbor_idx_2d() sfepy.tests.test_poly_spaces), 1028

Index 1113
SfePy Documentation, Release version: 2022.1+git.f9873484

test_preserve_coarse_entities() (in module sfepy.tests.test_laplace_unit_square), 1024

sfepy.tests.test_refine_hanging), 1029 test_solvers() (in module
test_project_tensors() (in module sfepy.tests.test_linear_solvers), 1024
sfepy.tests.test_projections), 1028 test_solving() (in module sfepy.tests.test_high_level),
test_projection_iga_fem() (in module 1022
sfepy.tests.test_projections), 1028 test_sparse_matrix_hdf5() (in module
test_projection_tri_quad() (in module sfepy.tests.test_io), 1023
sfepy.tests.test_projections), 1028 test_spbox_2d() (in module sfepy.tests.test_splinebox),
test_quadratures() (in module 1030
sfepy.tests.test_quadratures), 1028 test_spbox_3d() (in module sfepy.tests.test_splinebox),
test_read_dimension() (in module 1030
sfepy.tests.test_meshio), 1026 test_spbox_field() (in module
test_read_meshes() (in module sfepy.tests.test_splinebox), 1030
sfepy.tests.test_meshio), 1026 test_spregion2d() (in module
test_recursive_dict_hdf5() (in module sfepy.tests.test_splinebox), 1030
sfepy.tests.test_io), 1023 test_stiffness_tensors() (in module
test_ref_coors_fem() (in module sfepy.tests.test_matcoefs), 1025
sfepy.tests.test_ref_coors), 1029 test_stokes_slip_bc() (in module
test_ref_coors_iga() (in module sfepy.tests.test_lcbcs), 1024
sfepy.tests.test_ref_coors), 1029 test_stress_transform() (in module
test_refine_2_3() (in module sfepy.tests.test_tensors), 1030
sfepy.tests.test_domain), 1021 test_struct_add() (in module sfepy.tests.test_base),
test_refine_2_4() (in module 1019
sfepy.tests.test_domain), 1021 test_struct_i_add() (in module
test_refine_3_4() (in module sfepy.tests.test_base), 1019
sfepy.tests.test_domain), 1021 test_surface_evaluate() (in module
test_refine_3_8() (in module sfepy.tests.test_term_consistency), 1031
sfepy.tests.test_domain), 1021 test_tensors() (in module sfepy.tests.test_linalg),
test_refine_hexa() (in module 1024
sfepy.tests.test_domain), 1021 test_tensors() (in module sfepy.tests.test_tensors),
test_refine_tetra() (in module 1030
sfepy.tests.test_domain), 1021 test_term_arithmetics() (in module
test_region_functions() (in module sfepy.tests.test_high_level), 1022
sfepy.tests.test_functions), 1022 test_term_call_modes() (in module
test_resolve_deps() (in module sfepy.tests.test_term_call_modes), 1030
sfepy.tests.test_base), 1019 test_term_evaluation() (in module
test_save_ebc() (in module sfepy.tests.test_high_level), 1022
sfepy.tests.test_conditions), 1019 test_transform_data() (in module
test_selectors() (in module sfepy.tests.test_regions), sfepy.tests.test_tensors), 1030
1029 test_transform_data4() (in module
test_semismooth_newton() (in module sfepy.tests.test_tensors), 1030
sfepy.tests.test_semismooth_newton), 1029 test_unique_rows() (in module
test_sensitivity() (in module sfepy.tests.test_linalg), 1024
sfepy.tests.test_term_sensitivity), 1031 test_units() (in module sfepy.tests.test_units), 1031
test_set_dofs_1D() (sfepy.tests.test_dg_field.TestDGFieldtest_variables() (in module
method), 1020 sfepy.tests.test_high_level), 1022
test_set_dofs_2D() (sfepy.tests.test_dg_field.TestDGFieldtest_vector_matrix() (in module
method), 1020 sfepy.tests.test_term_consistency), 1031
test_solution() (in module test_verbose_output() (in module
sfepy.tests.test_homogenization_perfusion), sfepy.tests.test_base), 1019
1023 test_volume() (in module sfepy.tests.test_volume),
test_solution() (in module 1031
sfepy.tests.test_hyperelastic_tlul), 1023 test_volume_tl() (in module sfepy.tests.test_volume),
test_solution() (in module 1031

1114 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

test_weight_consistency() (in module to_file_txt() (sfepy.homogenization.coefficients.Coefficients

sfepy.tests.test_quadratures), 1028 method), 805
test_write_read_meshes() (in module to_file_txt() (sfepy.homogenization.coefs_phononic.BandGaps
sfepy.tests.test_meshio), 1026 static method), 811
TestDGField (class in sfepy.tests.test_dg_field), 1020 to_file_txt() (sfepy.homogenization.coefs_phononic.DensityVolumeInfo
tetgen_path() (sfepy.config.Config method), 657 static method), 811
tetrahedralize_vtk_mesh() (in module to_latex() (sfepy.homogenization.coefficients.Coefficients
sfepy.postprocess.utils_vtk), 864 method), 805
tetravolume() (in module sfepy.tests.test_splinebox), to_list() (in module gen_term_table), 654
1030 to_ndarray() (in module sfepy.mesh.bspline), 845
THTerm (class in sfepy.terms.terms_th), 1012 to_poly_file() (sfepy.mesh.geom_tools.geometry
tile_mat() (sfepy.terms.terms.Term static method), 908 method), 847
tile_periodic_mesh to_stack() (in module sfepy.discrete.parse_regions),
module, 657 700
tiled_mesh1d() (in module transform() (sfepy.terms.terms_multilinear.ExpressionBuilder
sfepy.mesh.mesh_generators), 850 method), 987
time (sfepy.postprocess.viewer.SetStep attribute), 864 transform_asm_matrices() (in module
time_update() (sfepy.discrete.equations.Equations sfepy.mechanics.membranes), 835
method), 692 transform_asm_matrices() (in module
time_update() (sfepy.discrete.materials.Material sfepy.mechanics.shell10x), 837
method), 698 transform_asm_vectors() (in module
time_update() (sfepy.discrete.materials.Materials sfepy.mechanics.membranes), 835
method), 699 transform_bar_to_space_coors() (in module
time_update() (sfepy.discrete.problem.Problem sfepy.linalg.geometry), 825
method), 714 transform_basis() (in module
time_update() (sfepy.discrete.variables.FieldVariable sfepy.discrete.common.poly_spaces), 741
method), 721 transform_conditions() (in module sfepy.base.conf ),
time_update() (sfepy.discrete.variables.Variable 670
method), 722 transform_coors() (sfepy.discrete.fem.mesh.Mesh
time_update() (sfepy.discrete.variables.Variables method), 760
method), 726 transform_data() (in module
time_update() (sfepy.terms.terms.Term method), 908 sfepy.mechanics.tensors), 838
time_update_materials() transform_dgebcs() (in module sfepy.base.conf ), 671
(sfepy.discrete.equations.Equations method), transform_dgepbcs() (in module sfepy.base.conf ),
692 671
Timer (class in sfepy.base.timing), 686 transform_ebcs() (in module sfepy.base.conf ), 671
TimeStepper (class in sfepy.solvers.ts), 898 transform_epbcs() (in module sfepy.base.conf ), 671
TimeSteppingSolver (class in sfepy.solvers.solvers), transform_fields() (in module sfepy.base.conf ), 671
898 transform_functions() (in module sfepy.base.conf ),
TLMembraneTerm (class in 671
sfepy.terms.terms_membrane), 975 transform_ics() (in module sfepy.base.conf ), 671
tmpfile() (in module sfepy.solvers.ls_mumps_parallel), transform_input() (sfepy.base.conf.ProblemConf
889 method), 670
to_array() (sfepy.linalg.utils.MatrixAction method), transform_input_trivial()
827 (sfepy.base.conf.ProblemConf method), 670
to_dict() (sfepy.base.base.Struct method), 662 transform_integrals() (in module sfepy.base.conf ),
to_file_hdf5() (sfepy.homogenization.coefficients.Coefficients 671
method), 805 transform_lcbcs() (in module sfepy.base.conf ), 671
to_file_latex() (sfepy.homogenization.coefficients.Coefficients
transform_materials() (in module sfepy.base.conf ),
method), 805 671
to_file_txt (sfepy.homogenization.coefs_phononic.AcousticMassTensor
transform_plot_data() (in module
attribute), 810 sfepy.homogenization.band_gaps_app), 805
to_file_txt (sfepy.homogenization.coefs_phononic.AppliedLoadTensor
transform_regions() (in module sfepy.base.conf ),
attribute), 810 671

Index 1115
SfePy Documentation, Release version: 2022.1+git.f9873484

transform_solvers() (in module sfepy.base.conf ), unpack_data() (sfepy.base.ioutils.HDF5BaseData

671 method), 673
transform_to_i_struct_1() (in module uns_perm (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
sfepy.base.conf ), 671 tribute), 879
transform_to_struct_01() (in module uns_perm (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
sfepy.base.conf ), 671 attribute), 882
transform_to_struct_1() (in module uns_perm (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
sfepy.base.conf ), 671 attribute), 885
transform_to_struct_10() (in module uns_perm (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
sfepy.base.conf ), 671 attribute), 889
transform_variables() (in module sfepy.base.conf ), update() (sfepy.base.base.Container method), 660
671 update() (sfepy.base.base.Struct method), 662
TransformToPlane (class in sfepy.mechanics.matcoefs), update() (sfepy.base.multiproc_mpi.RemoteDict
832 method), 680
treat_pbcs() (sfepy.discrete.fem.lcbc_operators.MRLCBCOperator
update() (sfepy.discrete.common.dof_info.DofInfo
method), 758 method), 727
triangulate() (in module sfepy.mesh.mesh_tools), 851 update() (sfepy.terms.terms_contact.ContactInfo
trim() (in module gen_solver_table), 654 method), 932
try_block() (in module sfepy.base.resolve_deps), 685 update_conf() (sfepy.base.conf.ProblemConf method),
try_imports() (in module sfepy.base.base), 665 670
try_presolve() (sfepy.discrete.problem.Problem update_data() (sfepy.discrete.materials.Material
method), 714 method), 699
try_set_defaults() (in module update_dict_recursively() (in module
sfepy.homogenization.band_gaps_app), 805 sfepy.base.base), 665
TSTimes (class in sfepy.homogenization.coefs_base), 809 update_equations() (sfepy.discrete.problem.Problem
tuple_to_conf() (in module sfepy.base.conf ), 671 method), 714
TVDRK3StepSolver (class in update_expression() (sfepy.terms.terms.Terms
sfepy.solvers.ts_dg_solvers), 791 method), 909
typeset() (in module gen_solver_table), 654 update_materials() (sfepy.discrete.problem.Problem
typeset() (in module gen_term_table), 654 method), 714
typeset_examples() (in module gen_term_table), 654 update_micro_states()
typeset_solvers_table() (in module (sfepy.homogenization.homogen_app.HomogenizationApp
gen_solver_table), 654 method), 817
typeset_term_syntax() (in module gen_term_table), update_shape() (sfepy.discrete.common.region.Region
655 method), 744
typeset_term_table() (in module gen_term_table), update_special_constant_data()
655 (sfepy.discrete.materials.Material method),
typeset_term_tables() (in module gen_term_table), 699
655 update_special_data()
typeset_to_indent() (in module gen_term_table), (sfepy.discrete.materials.Material method),
655 699
typeset_to_indent() (in module update_supported_formats() (in module
sfepy.solvers.solvers), 898 sfepy.discrete.fem.meshio), 768
update_time_stepper()
U (sfepy.discrete.problem.Problem method),
Uncached (class in sfepy.base.ioutils), 674 714
unique() (in module sfepy.base.compat), 667 us2cw() (in module edit_identifiers), 649
unique_rows() (in module sfepy.linalg.utils), 830 us2mc() (in module edit_identifiers), 649
Unit (class in sfepy.mechanics.units), 840 use_first_available() (in module
unpack_data() (sfepy.base.ioutils.DataMarker sfepy.solvers.solvers), 898
method), 672 use_method_with_name() (in module sfepy.base.base),
unpack_data() (sfepy.base.ioutils.DataSoftLink 665
method), 672 user_options (build_helpers.NoOptionsDocs at-
tribute), 646

1116 Index
 SfePy Documentation, Release version: 2022.1+git.f9873484

UserMeshIO (class in sfepy.discrete.fem.meshio), 767 VolumeSurfaceTerm (class in sfepy.terms.terms_basic),

922
V VolumeSurfaceTLTerm (class in
validate (sfepy.base.goptions.ValidatedDict attribute), sfepy.terms.terms_hyperelastic_tl), 970
672 VolumeTerm (class in sfepy.terms.terms_basic), 923
validate() (sfepy.base.conf.ProblemConf method), 670 VolumeTLTerm (class in
validate_bool() (in module sfepy.base.goptions), 672 sfepy.terms.terms_hyperelastic_tl), 970
ValidatedDict (class in sfepy.base.goptions), 672 VolumeULTerm (class in
value (sfepy.base.multiproc_mpi.RemoteInt attribute), sfepy.terms.terms_hyperelastic_ul), 974
680 VolumeXTerm (class in sfepy.terms.terms_compat), 930
values() (sfepy.base.goptions.ValidatedDict method), VTKFileSource (class in sfepy.postprocess.sources), 861
672 VTKSequenceFileSource (class in
var (in module sfepy.discrete.fem.meshio), 768 sfepy.postprocess.sources), 862
Variable (class in sfepy.discrete.variables), 721
Variables (class in sfepy.discrete.variables), 723 W
VariableTimeStepper (class in sfepy.solvers.ts), 899 wait_for_tag() (in module sfepy.base.multiproc_mpi),
VectorDotGradScalarTerm (class in 682
sfepy.terms.terms_dot), 948 wandering_element() (in module
VectorDotScalarTerm (class in sfepy.terms.terms_dot), sfepy.discrete.simplex_cubature), 717
949 weak_dp_function() (sfepy.terms.terms_hyperelastic_tl.BulkPressureTLT
VelocityVerletTS (class in sfepy.solvers.ts_solvers), static method), 964
903 weak_dp_function() (sfepy.terms.terms_hyperelastic_ul.BulkPressureUL
verbosity (sfepy.terms.terms_multilinear.ETermBase static method), 972
attribute), 986 weak_function() (sfepy.terms.terms_hyperelastic_tl.BulkPressureTLTerm
verify_task_dof_maps() (in module static method), 964
sfepy.parallel.parallel), 855 weak_function() (sfepy.terms.terms_hyperelastic_tl.HyperElasticTLBase
version_number (sfepy.solvers.ls_mumps.mumps_struc_c_4 static method), 966
attribute), 879 weak_function() (sfepy.terms.terms_hyperelastic_ul.BulkPressureULTerm
version_number (sfepy.solvers.ls_mumps.mumps_struc_c_5_0 static method), 972
attribute), 882 weak_function() (sfepy.terms.terms_hyperelastic_ul.HyperElasticULBas
version_number (sfepy.solvers.ls_mumps.mumps_struc_c_5_1 static method), 973
attribute), 885 weak_function() (sfepy.terms.terms_membrane.TLMembraneTerm
version_number (sfepy.solvers.ls_mumps.mumps_struc_c_5_2 static method), 975
attribute), 889 wk_user (sfepy.solvers.ls_mumps.mumps_struc_c_4 at-
vertex_groups (sfepy.discrete.common.extmods.cmesh.CMesh tribute), 879
attribute), 732 wk_user (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
vertices (sfepy.discrete.common.region.Region prop- attribute), 882
erty), 744 wk_user (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
view_file() (in module postproc), 642 attribute), 885
view_petsc_local() (in module wk_user (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
sfepy.parallel.parallel), 855 attribute), 889
Viewer (class in sfepy.postprocess.viewer), 864 wrap_function() (in module sfepy.solvers.optimize),
ViewerGUI (class in sfepy.postprocess.viewer), 867 894
visit_stack() (in module write() (sfepy.base.ioutils.HDF5Data method), 673
sfepy.discrete.parse_regions), 700 write() (sfepy.base.ioutils.SoftLink method), 674
volume (class in sfepy.mesh.geom_tools), 848 write() (sfepy.base.multiproc_mpi.MPILogFile
volume (sfepy.discrete.common.extmods.mappings.CMapping method), 680
attribute), 733 write() (sfepy.discrete.fem.mesh.Mesh method), 761
VolumeField (class in sfepy.discrete.fem.fields_base), write() (sfepy.discrete.fem.meshio.ANSYSCDBMeshIO
752 method), 762
VolumeFractions (class in write() (sfepy.discrete.fem.meshio.ComsolMeshIO
sfepy.homogenization.coefs_base), 809 method), 762
VolumeMapping (class in sfepy.discrete.fem.mappings), write() (sfepy.discrete.fem.meshio.GmshIO method),
759 763

Index 1117
SfePy Documentation, Release version: 2022.1+git.f9873484

write() (sfepy.discrete.fem.meshio.HDF5MeshIO sfepy.postprocess.utils_vtk), 864

method), 765 write_xdmf_file() (sfepy.discrete.fem.meshio.HDF5MeshIO
write() (sfepy.discrete.fem.meshio.HDF5XdmfMeshIO static method), 765
method), 765
write() (sfepy.discrete.fem.meshio.HypermeshAsciiMeshIOX
method), 765 XYZMeshIO (class in sfepy.discrete.fem.meshio), 768
write() (sfepy.discrete.fem.meshio.MeshIO method),
767 Y
write() (sfepy.discrete.fem.meshio.MeshioLibIO youngpoisson_from_stiffness() (in module
method), 767 sfepy.mechanics.matcoefs), 833
write() (sfepy.discrete.fem.meshio.NEUMeshIO
method), 767 Z
write() (sfepy.discrete.fem.meshio.UserMeshIO
method), 768 zero_dofs() (sfepy.discrete.conditions.Conditions
write() (sfepy.discrete.fem.meshio.XYZMeshIO method), 686
method), 768 zero_dofs() (sfepy.discrete.conditions.EssentialBC
write_control_net() method), 687
(sfepy.mesh.splinebox.SplineBox method), ZeroTerm (class in sfepy.terms.terms_basic), 923
853
write_control_polygon_vtk()
(sfepy.mesh.bspline.BSplineSurf method),
845
write_data() (sfepy.base.ioutils.DataSoftLink method),
673
write_data() (sfepy.base.ioutils.HDF5Data method),
673
write_dict_hdf5() (in module sfepy.base.ioutils), 676
write_domain_to_hdf5()
(sfepy.discrete.iga.domain.IGDomain method),
791
write_iga_data() (in module sfepy.discrete.iga.io),
801
write_log() (in module sfepy.base.log), 678
write_mesh_to_hdf5()
(sfepy.discrete.fem.meshio.HDF5MeshIO
static method), 765
write_problem (sfepy.solvers.ls_mumps.mumps_struc_c_4
attribute), 879
write_problem (sfepy.solvers.ls_mumps.mumps_struc_c_5_0
attribute), 882
write_problem (sfepy.solvers.ls_mumps.mumps_struc_c_5_1
attribute), 885
write_problem (sfepy.solvers.ls_mumps.mumps_struc_c_5_2
attribute), 889
write_results() (in module sfepy.discrete.probes),
703
write_sparse_matrix_hdf5() (in module
sfepy.base.ioutils), 676
write_sparse_matrix_to_hdf5() (in module
sfepy.base.ioutils), 676
write_surface_vtk() (sfepy.mesh.bspline.BSplineSurf
method), 845
write_to_hdf5() (in module sfepy.base.ioutils), 676
write_vtk_to_file() (in module

1118 Index