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Diffuse Scattering and Defect Structure Simulations A
Cook Book Using the Program DISCUS International
Union of Crystallography Monographs on
Crystallography Reinhard B. Neder Digital Instant
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11 Diffuse scattering and defect structure simulations: a cook book using the program DISCUS
R. B. Neder, T. Proffen
Diffuse Scattering and Defect
Structure Simulations
A cook book using
the program DISCUS

Reinhard B. Neder
Department of Physics, University of Erlangen-Nürnberg

Thomas Proffen
Los Alamos National Laboratory

INTERNATIONAL UNION OF CRYSTALLOGRAPHY

1
 3
Great Clarendon Street, Oxford OX2 6DP
Oxford University Press is a department of the University of Oxford.
It furthers the University’s objective of excellence in research, scholarship,
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Oxford is a registered trade mark of Oxford University Press
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Published in the United States
by Oxford University Press Inc., New York
© R.B.Neder and Th.Proffen 2008
The moral rights of the authors have been asserted
Database right Oxford University Press (maker)
First published 2008
Los Alamos National Laboratory LA-UR-07-7673
All rights reserved. No part of this publication may be reproduced,
stored in a retrieval system, or transmitted, in any form or by any means,
without the prior permission in writing of Oxford University Press,
or as expressly permitted by law, or under terms agreed with the appropriate
reprographics rights organization. Enquiries concerning reproduction
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British Library Cataloguing in Publication Data
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Printed in Great Britain
on acid-free paper by Antony Rowe Ltd, Chippenham

ISBN 978–0–19–923369–4 (Hbk)

1 3 5 7 9 10 8 6 4 2
Preface

The idea of D ISCUS was born during a late afternoon coffee break I
shared with Uli Wildgruber, fellow PhD student in the diffuse scatter-
ing research group of our esteemed teacher Prof. Dr. F. Frey. The talk
we had centered around the difficulty that students had to simultane-
ously see direct space and reciprocal space. Following this informal
talk the basic concepts of the program came to life, initially very much
inspired by the beautiful images in the Atlas of Optical Transforms by
Harburn, Taylor and Welberry. From here, the program quickly took
off into three dimensions, with the intention shifting to the simulation
of disordered structures and their diffuse scattering. Only later on did
the teaching aspects come back into use. Presently the program is well
suited for both aspects, simulation of essentially any structure, crys-
talline or non-crystalline, as well as teaching students the concepts of
diffraction physics.
Life in reciprocal space is exciting, especially if there is lots of diffuse
scattering to spice up the regular, strict world of Bragg reflections. It is
also easy to get lost in this world, and I am grateful to my wife Carolina
and my children Celina and Clarissa, who remind me that maybe there
is a world outside of reciprocal space worth visiting as well. Without
their support and patience this book would not have been possible.
Reinhard B. Neder
Erlangen, November 2007
All of my scientific life, I have been fascinated by disordered materials
and ways to extract as much information as possible from diffraction
experiments. This fascination is a result of my work with a series of
outstanding mentors: Prof. Friedrich Frey at the University of Munich,
Prof. Richard Welberry at the Australian National University, and Prof.
Simon Billinge at Michigan State University. Every new project resulted
in some new addition to D ISCUS, and the quest for the ultimate diffuse
scattering and defect structure simulation program goes on.
Most of all, I would like to thank my parents, my wife Yvonne and
my children Lukas and Klara for their inspiration and never ending
support. I am dedicating this book to my family and especially to my
father Karl-Heinz, who sadly died last year.
Thomas Proffen
Los Alamos, November 2007
v
This page intentionally left blank
Contents

1 Introduction 1

2 How to run DISCUS 3

3 Making computer crystals 7

3.1 Storing the structure . . . . . . . . . . . . . . . . . . . . . 7
3.2 Small assemblies of atoms . . . . . . . . . . . . . . . . . . 8
3.3 Generating the unit cell . . . . . . . . . . . . . . . . . . . . 14
3.4 Generating extended crystal structures . . . . . . . . . . 19
3.5 Unit cell transformations . . . . . . . . . . . . . . . . . . 21
3.6 General symmetry operations . . . . . . . . . . . . . . . . 24
3.7 Creating molecules . . . . . . . . . . . . . . . . . . . . . . 27
3.8 Example: Distorted perovskite . . . . . . . . . . . . . . . 28
3.9 Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . 32

4 Simulating experimental data 35

4.1 Single-crystal scattering . . . . . . . . . . . . . . . . . . . 35
4.1.1 Finite size effects . . . . . . . . . . . . . . . . . . . 36
4.1.2 Coherence . . . . . . . . . . . . . . . . . . . . . . . 38
4.2 Powder diffraction . . . . . . . . . . . . . . . . . . . . . . 39
4.2.1 Complete integration . . . . . . . . . . . . . . . . 40
4.2.2 Debye formula . . . . . . . . . . . . . . . . . . . . 41
4.3 Atomic pair distribution function . . . . . . . . . . . . . 43
4.3.1 Calculating the PDF from a model . . . . . . . . . 43
4.3.2 Modeling of thermal motion . . . . . . . . . . . . 45
4.4 Properties of the Fourier transform . . . . . . . . . . . . . 48
4.5 Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . 49

5 Correlations and creating short-range order 53

5.1 What are correlations? . . . . . . . . . . . . . . . . . . . . 53
5.2 Monte Carlo simulations . . . . . . . . . . . . . . . . . . 54
5.3 Creating chemical short-range order . . . . . . . . . . . . 55
5.4 Creating displacement disorder . . . . . . . . . . . . . . 56
5.4.1 Simple spring . . . . . . . . . . . . . . . . . . . . . 56
5.4.2 Lennard-Jones potential . . . . . . . . . . . . . . . 56
5.4.3 Bond angles . . . . . . . . . . . . . . . . . . . . . . 57
5.5 Example: Chemical short-range order . . . . . . . . . . . 57
vii
viii CONTENTS

5.6 Example: Distortions . . . . . . . . . . . . . . . . . . . . . 62

5.7 Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . 65

6 Creating modulations 69
6.1 Density waves . . . . . . . . . . . . . . . . . . . . . . . . . 70
6.2 Displacement waves . . . . . . . . . . . . . . . . . . . . . 75
6.3 Finite waves . . . . . . . . . . . . . . . . . . . . . . . . . . 79
6.4 Pitfalls when simulating modulations . . . . . . . . . . . 84
6.5 Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . 85

7 Creating structures with stacking faults 87

7.1 Types of stacking faults . . . . . . . . . . . . . . . . . . . . 87
7.1.1 Growth faults . . . . . . . . . . . . . . . . . . . . . 88
7.1.2 Deformation faults . . . . . . . . . . . . . . . . . . 89
7.1.3 Stacking fault parameters . . . . . . . . . . . . . . 89
7.2 Notations for stacking sequences . . . . . . . . . . . . . . 90
7.3 Reciprocal space of layered structures . . . . . . . . . . . 91
7.4 Algorithms to simulate stacking faults . . . . . . . . . . . 93
7.4.1 Growth faults . . . . . . . . . . . . . . . . . . . . . 94
7.4.2 Deformation faults . . . . . . . . . . . . . . . . . . 95
7.4.3 Ordering of faults . . . . . . . . . . . . . . . . . . . 96
7.5 Example: Growth faults . . . . . . . . . . . . . . . . . . . 97
7.6 Example: Deformation faults . . . . . . . . . . . . . . . . 101
7.7 Example: Wurtzite and zincblende structures . . . . . . . 103
7.8 Example: Short-range ordered faults . . . . . . . . . . . . 104
7.9 Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . 108

8 Creating domain structures 113

8.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . 113
8.2 Domain types . . . . . . . . . . . . . . . . . . . . . . . . . 114
8.3 Definitions for a domain . . . . . . . . . . . . . . . . . . . 115
8.4 Ordering and distribution of domains . . . . . . . . . . . 121
8.5 Domain formation in Perovskites . . . . . . . . . . . . . . 124
8.6 Example: Urea inclusion compounds . . . . . . . . . . . . 128
8.7 Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . 135

9 Creating nanoparticles 139

9.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
9.2 Creating simple particles . . . . . . . . . . . . . . . . . . . 140
9.3 PDF of nanoparticles . . . . . . . . . . . . . . . . . . . . . 145
9.4 Creating core–shell particles . . . . . . . . . . . . . . . . . 150
9.5 Carbon nanotubes . . . . . . . . . . . . . . . . . . . . . . . 156
9.6 Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . 159

10 Analyzing disordered structures 161

10.1 Visualizing structures . . . . . . . . . . . . . . . . . . . . 161
10.2 Occupancies . . . . . . . . . . . . . . . . . . . . . . . . . . 165
10.3 Finding neighbors . . . . . . . . . . . . . . . . . . . . . . 166
10.4 Distortions . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
 CONTENTS ix

10.5 Calculating correlations . . . . . . . . . . . . . . . . . . . 168

10.5.1 Occupational correlations . . . . . . . . . . . . . . 168
10.5.2 Displacement correlations . . . . . . . . . . . . . 170
10.5.3 Correlation fields . . . . . . . . . . . . . . . . . . . 171
10.6 Bond valence sums . . . . . . . . . . . . . . . . . . . . . . 171
10.7 Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . 172

11 Refining disordered structures 175

11.1 Reverse Monte Carlo method . . . . . . . . . . . . . . . . 175
11.2 Length-scale dependent PDF refinements . . . . . . . . . 178
11.3 Refining parameters of a disorder model . . . . . . . . . 180
11.3.1 The program D IFFEV . . . . . . . . . . . . . . . . . 183
11.3.2 Required size of the simulated structure . . . . . . 186
11.3.3 Example: Simple disordered structure . . . . . . . 188
11.3.4 Example: ZnSe Nanoparticles . . . . . . . . . . . . 195
11.4 Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . 201

A Appendix 205
A.1 Contents of the CD-ROM . . . . . . . . . . . . . . . . . . 205
A.2 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . 205
A.3 Functional list of commands . . . . . . . . . . . . . . . . 207
A.4 Answers to exercises . . . . . . . . . . . . . . . . . . . . . 210
A.5 DISCUS bibliography . . . . . . . . . . . . . . . . . . . . . 222

Index 227
This page intentionally left blank
Introduction
1
In the past 50–100 years our knowledge of materials has been revo-
lutionized by the ability to determine the atomic structure of increas-
ingly more complex materials. However, with increasing complexity
of materials, it becomes apparent that the traditional crystallographic
structure solution approach is no longer sufficient to understand prop-
erties of materials on an atomic scale. The limitation of a traditional
structure refinement is of course the fact that it only yields the long-
range average structure of the material since it is based on the analysis
of Bragg reflections exclusively. Deviations from the average structure
manifest themselves as weak diffuse scattering. The increase in com-
puting power has made much more complex systems open to proper
interpretations. In the early days of diffuse scattering the interpretation
was limited to simple disorder types like short-range order in binary
alloys or stacking faults. Their effect on the diffraction pattern can be
described analytically. More complex systems like domains or corre-
lated displacements do not allow a straightforward analytical solution.
Computer simulations of a defect structure allow a completely general
approach to the interpretation of diffuse scattering. The increasing in-
terest in analyzing diffuse scattering is apparent in the increasing num-
ber of related publications and also in the appearance of textbooks in
the past few years, covering the subject of diffuse scattering. There are
plenty of books on computational crystallography teaching about the
tools to solve and refine crystal structures. However, what is still a
mystery for many students and researchers is how to analyze observed
diffuse scattering and relate it to defects in the general sense. This book
aims to be a cookbook, giving practical examples including generating
defect structures from simple defects to domain structures or arbitrary
core–shell nanoparticles. We discuss how to calculate diffuse scatter-
ing or the atomic pair distribution function and finally give examples
how to refine these structural models based on experimental data. Each
chapter provides examples as well as references to relevant articles and
books. We also excluded liquids and glasses as well as magnetism from Often non-crystalline are called disor-
this book. This is mainly due to the fact the primary function of D ISCUS dered materials, not to be confused with
crystals showing disorder.
is to simulate disordered crystalline materials.
For the authors, the fascination with diffuse scattering began with
the study of cubic stabilized zirconia, a very hot topic 15–20 years ago.
As ZrO2 is doped with, for example, CaO, oxygen vacancies are pro-
duced. A layer in reciprocal space showing beautiful diffuse neutron
scattering is shown in Fig. 1.1. These data were collected over months

1
2 Introduction

[0 0 1]
2

0
0 1 2 3 4
[h h 0]

Fig. 1.1 Diffuse scattering from ZrO2 -CaO (15 mol%) collected on the MAN-II single-
crystal diffractometer at the Forschungsreaktor in Munich.

on the single-crystal diffractometer MAN-II at the old research reactor

in Garching. Understanding this diffuse scattering became the thesis
subject of both authors of this book and the development of the pro-
gram D ISCUS began around that time. The basic idea was to have a
tool that allows one to generate a disordered structure and calculate
its diffuse scattering pattern. Over the years features such as the cal-
culation of powder patterns or the atomic pair distribution function
were added. Even later the capability of fitting diffuse scattering us-
ing Reverse Monte Carlo or an external minimization program were
added. As the authors were extending into new fields, D ISCUS grew
and needed capabilities were added. However, D ISCUS is not only a
valuable research tool, but also very useful in teaching diffraction. The
http://www.totalscattering.org/ authors created a collection of web pages as an aid to teach diffraction
teaching/ and the newest version features interactive examples that are executed
using D ISCUS. These pages even include a module creating short-range
order using Monte Carlo simulations.
All examples discussed in this book include a detailed recipe allow-
ing readers to run the simulations themselves. The program D ISCUS
as well as all input files required for the examples and exercises are
included on the CD-ROM accompanying this book. We cannot give
complete solutions to all disorder models that can be imagined. We
hope, however, that the algorithms and techniques laid out in this book
will provide sufficient insight into many different recipes. They should
enable the reader to model his own defect structures.
How to run DISCUS
2
Now you are ready to start reading this book, let us start with some
basics on how to run D ISCUS. First you will need to install the program
either from the included CD-ROM or after downloading it from the
Internet (see Appendix A.2). Double click on the D ISCUS icon or type
discus on the command line and the program will start greeting you
with the window shown in Fig. 2. The question is what now?
In contrast to programs relying on a graphical interface, all programs
Fig. 2.1 D ISCUS at startup.
of the D ISCUS package are controlled by a command language that
is based on the FORTRAN programming language. This might seem
somewhat old fashioned, but as we discuss the examples in this book,
it will become apparent that this is actually a powerful feature of the
program. Before discussing elements of the command language, let us
consider macro files. Basically one could just type the commands at
the discus prompt of the program. This might be helpful when ex-
perimenting, but it is impractical for larger projects. In those cases, the
commands can be stored in a text file, that we simply call a macro. In
addition, one can pass parameters to a macro as well as nest macro
files, in other words call a macro from within macro. Let us consider
the simple example shown in the margin. All examples in this book File: discus/add.mac
will be given in a similar way. Note, that the line numbers given are for 1
2
# Simple macro at add two numbers
#
easy reference, but not actually part of the macro file. Also all macro 3
4
variable real,result
#
files used in this book are included on the CD-ROM, so there is no typ- 5
6
result=$1+$2
echo "The sum is %f",result
ing required. The filename of each macro is given just above it. Back
to the example. This macro is stored in a file called add.mac and we
can execute it using the command @add or @add.mac. Just typing this
command will cause an error message, since the macro expects the two
parameters $1 and $2 (line 5) to be specified. Note that the parameters
are separated by a comma as are all parameter lists in D ISCUS. The
macro then adds the two numbers (as the name suggests) and prints
the result to the screen (line 6). For example entering @add 1.5,2.1
will display the result 3.6. All macros shown in this book are executed
in a similar fashion.
A very important feature of D ISCUS is its online help. Simply enter
the command help for a list of available commands. More specific in-
formation about a particular command can be displayed by entering
help command. As we have seen in the earlier example, D ISCUS al-
lows one to use variables. In addition to generic variables, there are pre-
defined variables related to structure properties (Table 2.1). This allows
one to very simply modify a structure in D ISCUS, e.g. the command

3
4 How to run DISCUS

Table 2.1 List of D ISCUS variables.

Variable Description

n[1] Number of atoms within the crystal

n[2] Number of different scattering types, i.e. atoms
n[3] Number of atoms within the unit cell
n[4] Number of molecules within the crystal
n[5] Number of different molecule types
n[6] Number of molecules within the unit cell

cdim[i,1] Lowest coordinate of any atom (i = 1, 2, 3 for x, y, z)

cdim[i,2] Highest coordinate of any atom (i = 1, 2, 3 for x, y, z)

env[i] Index of neighbouring atoms after ’find’ command

menv[i] Index of neighbouring molecules after ’find’ command

lat[i] Lattice parameters (i = 1 . . . 6 for a, b, c, α, β, γ)

vol[1] Unit cell volume
rvol[1] Reciprocal unit cell volume

m[i] Number of scattering type (i.e. atom type) for atom i

b[j] Isotropic thermal factor B for atom type j
x[i] Fractional x position of atom i
y[i] Fractional y position of atom i
z[i] Fractional z position of atom i

mol_cont[i,j] Index of atom j in molecule i

mol_len[i] Number of atoms in molecule i

x[2]=0.254 will set the fractional coordinate x of atom 2 to a value of

0.254. We will use this in some of the examples discussed in Chapter
3. As we have mentioned earlier, the syntax of the command language
is derived from FORTRAN and for those knowing that programming
language, the syntax of conditional statements and loops will be famil-
File: discus/sphere.mac iar. Let us consider the following simple example. The goal is to cut
1
2
variable integer,atom
variable real,distance
a sphere of a given radius out of a two-dimensional square structure.
3
4
#
do atom=1,n[1]
The macro for this task is listed here. First we declare two variables
5
6
distance=sqrt(x[atom]**2+y[atom]**2)
if (distance.gt.$1) then
atom and distance. Next a loop over all atoms is carried out (lines
7 remove atom 4–9). Note that the number of atoms is stored in the variable n[1]
8 endif
9 enddo (Table 2.1). Next we calculate the distance from the origin (line 5) for
this simple case of a two-dimensional square lattice. Note that D ISCUS
structures have the origin (0, 0, 0) in the middle of the structure. Next
we compare the distance to the user-specified value $1 and if it is larger,
the atom is removed (line 7). That’s it !
In line 5 of the above
√ example, we have used the intrinsic function
sqrt(x) to calculate x. D ISCUS has the most common functions im-
 5

Table 2.2 Crystallographic functions.

Type Name Description

real bang(u1,u2,u3, Returns the bond angle in degrees between

v1,v2,v3 u and v at site w. If w is omitted, the an-
[,w1,w2,w3]) gle between direct space vectors u and v is
returned.
real blen(u1,u2,u3 Returns the length of the real space vector
[,v1,v2,v3]) v−u. The vector v defaults to zero.
real dstar(h1,h2,h3 Returns the length of reciprocal vector k−h
[,k1,k2,k3]) in Å−1 . Vector k defaults to zero.
real rang(h1,h2,h3, Returns the angle between reciprocal vec-
k1,k2,k3 tors k−h and k−l at site k. If l is omitted,
[,l1,l2,l3]) the angle between reciprocal vectors h and
k is returned.

plemented such as sin(x) and so on. Refer to the online help of D IS -

CUS for a complete list of functions. In addition, D ISCUS provides a
few crystallographic functions summarized in Table 2.2. In our earlier
example we could also have used the function blen to calculate the
distance even in case of a non-square or three-dimensional lattice.
The basics of the command language are common to all the pro-
grams that are part of the D ISCUS package. In this chapter we have just
scratched the surface to allow readers to follow the examples. Many
more details about the command language are given in the D ISCUS
Users Guide. A list of commands and modules can be found in Ap-
pendix A.3.
This page intentionally left blank
Making computer crystals
3
3.1 Storing the structure
The computer simulation of a crystal structure can be carried out with
two different purposes in mind. The first purpose would be the sim-
ulation of the structure itself, in order to analyze the structure or to
create a graphical representation of the structure. The second purpose
would be the calculation of the Fourier transform of the scattering den-
sity. A number of programs exist for structure simulation, which can
be loosely sorted into plotting, teaching, structure refinement, quantum
mechanical, and defect structure simulation programs.
A crucial point for all purposes is presented by the question of how to
simulate the crystal structure. The structure can either be represented
by a three-dimensional map of the electron density or by a list of atom
positions. The computer memory requirements are very different for
these two different representations. As an example let us take an or-
thorhombic crystal structure with a unit cell of 10 x 10 x 10 Å3 , 60 atoms
in the unit cell and a crystal size of 32 x 32 x 32 unit cells. A grid that
is narrow enough to represent the structure requires steps of 0.2 Å, i.e.
50 x 50 x 50 grid points per unit cell. At 2 bytes per grid point this crys-
tal representation requires 7800 Mbyte. In comparison the storage of
the atom positions requires three numbers per atom for the coordinates
and one for an identification of the atom type. In this representation the
crystal requires 7.5 Mbyte or less than one-thousandth of the electron
density map. If one needs to calculate the intensity while including
anomalous scattering, the electron density must be stored as complex
values, doubling the memory requirements. The type of information
known about the crystal structure is encoded in very different forms.
If the electron density is stored, the primary information content is the
density of electrons per cubic angstrom or, in case of neutron scatter-
ing, of the scattering density. This distinction shows already that the
density is a specialized function. The exact positions and types of the
atoms are not directly accessible. To obtain the position of an atom one
has to perform a search for a maximum density. To recognize which
atom is present at a specific location, one has to integrate the electron
density and deduce the atom type from the total number of electrons
and possibly the shape of the distribution. If similar atoms are present,
this could be a very difficult and time consuming task, especially, if
7
8 Making computer crystals

the crystal is of large size. If your intention is a simulation of a crystal

structure, which you want to modify in order to introduce defects, the
storage of the electron density is not the ideal solution. If, on the other
hand, one stores the structure as atom coordinates and a reference to
the atom type it is easy to quickly locate atoms of a certain type and
modify these accordingly. Secondary data like bond lengths, bond an-
gles or coordination spheres are readily calculated. Now, however, the
calculation of the electron density distribution is a more complex task.
One would have to calculate the convolution of the atom distribution
with the individual electron density distributions of each atom or cal-
culate the Fourier transform, using the tabulated atom form factors for
X-ray scattering or scattering lengths for neutron scattering and then
calculate the inverse Fourier transform. It is well known that you have
to use intensities far into reciprocal space to get electron densities with-
out too serious errors due to the finite Fourier series when doing the
inverse Fourier transform. In Chapter 4 we will present examples that
illustrate this relationship. The graphical output used to realize the first
purpose can take a wide range of forms (Fig. 3.1). This is discussed in
more detail in Section 10.1. Let us analyze the information about the
crystal that is necessary to create a graphical representation. In order
to draw the crystal structure the program must know where the atoms
are located or must be able to calculate the positions from the content
of the asymmetric unit and information about the crystal symmetry. It
is sufficient to store the coordinates of all atoms and their individual
type and optionally the atomic displacement parameter .The plot can
be calculated from the information present in this list. Many structural
parameters can be deduced from this list as well like the shape of co-
ordination polyhedra, the bond lengths and bond angles, etc. For this
type of analysis it is not necessary to create the actual electron density
distribution. If, on the other hand, the purpose of the crystal structure
Fig. 3.1 Typical structure plot showing in-
dividual atoms and polyhedra. simulation is the analysis of bond characteristics, then a map of the
electron density obtained from experimental data is required.
Currently D ISCUS only supports
isotropic displacement parameters. Also
In this chapter we will journey from the simulation of a single atom
note that there are no occupancies. to that of a crystal. Unit cell transformations and general affine opera-
D ISCUS is designed to simulate real tions will conclude this tour. We will develop the steps and algorithms
structures. In large model crystals, needed to simulate a crystal, which most programs apply without the
occupancies are created by removing the
appropriate number of atoms from the expressed need of the user to know the details. An important goal of
system to match the overall occupancy this book is the simulation of extended crystal defects, and to enable the
as we will see in later examples. reader to perform these simulations we cover the basics of a simulation
in extensive detail.

3.2 Small assemblies of atoms

Previously it was outlined that the storage of the atom positions is a
very compact and efficient way to store a simulated crystal structure.
A direct consequence of this is that it is equally possible to simulate
a small finite assembly of atoms instead of a periodic crystal. These
 3.2 Small assemblies of atoms 9

small assemblies may assume any shape and no limitations exist on

the presence of symmetry elements. This section will describe ways to
simulate small finite assemblies of atoms. Every structure simulation,
whether this be a single atom, a non-periodic cluster of atoms or a large
crystal, consists of the following basic steps:
• Define the unit cell parameters, or more generally speaking the
base vectors, to which the atom coordinates will be referred.
• Calculate the metric tensor and the reciprocal metric tensor.
• To facilitate vector algebra the epsilon tensor is useful [1].
• In the case of a crystal, the space group has to be defined and the
corresponding symmetry operations have to be generated.
• Store the x, y and z coordinates and an atom type identifier in
arrays.
Beyond these basics, further information is useful or required depend-
ing on the application of the simulation.
• One must provide various atom properties like radius, plotting
color, plotting size scattering curve, anomalous dispersion ab-
sorption coefficient, . . .
• For a plotting program connectivity information on the bonds be-
tween the atoms must be provided to speed up the representa-
tions of bonds. As for a crystal structure one must provide infor-
mation about the basis for the atom position, i.e. the lengths and
angles between the base vectors. One has the freedom to adopt
any base system that is best suited to the distribution of the atoms,
whether this be a triclinic base or a cartesian base.
We will discuss these steps as we expand our simulation from a sin-
gle atom to a complete crystal. To describe the coordinate system and 0.25

the position of atoms, one must set up a system of base vectors and
provide the atom positions. For our first example we want to create a
y (Å)

0
cartesian space and position a single zirconium atom at the origin. The
necessary D ISCUS commands are shown here. The first command en- –0.25
ters the structure reading submenu of D ISCUS, where the space can be
defined. In this example, D ISCUS does not read a structure but gener-
ates an empty space, defined by the three lattice parameters of 1.0 Å and –0.25 0
x (Å)
0.25

the three angles of 90.0◦. The last command inserts a zirconium atom
at the position 0.0 · a, 0.0 · b, 0.0 · c. The last parameter of the insert Fig. 3.2 Generated structure with single
command defines an isotropic displacement parameter B. All coordi- zirconium atom.
nates are understood as fractional coordinates. The resulting one-atom File: sim/simul.1.mac
1
structure is shown in Fig. 3.2. Further atoms could now be added to 2
read
free 1.0,1.0,1.0,90.0,90.0,90.0
create a larger group of atoms and even a full crystal. It is obvious that 3
4
#
insert zr,0,0,0,0.1
this would become a formidable task for all but very small groups of 5
6
save atom.stru

atoms. A variety of tools are needed to expand the group of atoms. The
most efficient tool to create a large crystal is obviously a list of atoms
in the asymmetric unit in combination with the corresponding space
group symmetry operations and information about the number of unit
cells in the crystal. This procedure will be described in more detail in
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