HYSPLIT4 User's Guide

HYSPLIT4 User's Guide

Last Revised: February 2016

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HYSPLIT4 USER's GUIDE

Roland Draxler

Barbara Stunder

Glenn Rolph

Ariel Stein

Albion Taylor

Version 4 - Last Revision: February 20161

TABLE OF CONTENTS

Abstract
The HYSPLIT_4 (Hybrid Single-Particle Lagrangian Integrated Trajectory) Model
installation, configuration,
and operating procedures are reviewed.
Examples are given for setting up the model for trajectory and
concentration
simulations, graphical displays, and creating
publication quality illustrations. The model requires specially
preformatted
meteorological data. Programs that can be used to
create the model's meteorological input data are described. The

User's Guide has been restructured so that the section titles match
the GUI help menu tabs. Although this guide is
designed to support
the PC and UNIX versions of the program, the executable of the
on-line web version is identical.
The only differences are the
options available through the interface.
Features
The HYsplit_4 (HYbrid Single-Particle Lagrangian Integrated Trajectory) model is a complete system for computing
trajectories complex dispersion and deposition simulations using either puff or particle approaches.2
It consists of a
modular library structure with main programs for each primary application: trajectories and air concentrations.
Gridded meteorological data, on a latitude-longitude grid or
one of three conformal (Polar, Lambert, Mercator) map
projections,
are required at regular time intervals. The input data are interpolated to an internal sub-grid centered to
reduce memory requirements and increase computational speed. Calculations may be performed sequentially or
concurrently on multiple meteorological
grids, usually specified from fine to coarse resolution.
Air concentration calculations require the definition of the pollutant's emissions and physical characteristics (if
deposition
is required). When multiple pollutant species are defined, an emission would consist of one particle or puff
associated with each
pollutant type. Alternately, the mass associated with a single puff
may contain several species. The
latter approach is used for calculation
of chemical transformations when all the species follow the same transport

pathway. Some simple chemical transformation routines are provided

with the standard model distribution.
The dispersion of a pollutant is
calculated by assuming either a Gaussian or Top-Hat horizontal
distribution within a
puff or from the dispersal of a fixed number
of particles. A single released puff will expand until its size
exceeds the
meteorological grid cell spacing and then it will split
into several puffs. An alternate approach combines both puff and

particle methods by assuming a puff distribution in the horizontal

and particle dispersion in the vertical direction. The
resulting
calculation may be started with a single particle. As its
horizontal distribution expands beyond the
meteorological grid
size, it will split into multiple particle-puffs, each with their
respective fraction of the pollutant
mass. In this way, the
greater accuracy of the vertical dispersion parameterization of the
particle model is combined
with the advantage of having an
expanding number of particles represent the pollutant distribution
as the spatial
coverage of the pollutant increases and therefore a
single particle can represent increasingly lower concentrations.
Air concentrations are calculated
at a specific grid point for puffs and as cell-average
concentrations for particles. A
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concentration grid is defined by

latitude-longitude intersections. Simultaneous multiple grids with
different horizontal
resolutions and temporal averaging periods can
be defined for each simulation. Each pollutant species is summed

independently on each grid.

The routine meteorological data
fields required for the calculations may be obtained from existing
archives or from
forecast model outputs already formatted for input
to HYSPLIT. In addition, several different pre-processor programs

are provided to convert NOAA, NCAR (National Center for Atmospheric

Research) re-analysis, or ECMWF (European
Centre for Medium-range
Weather Forecasts) model output fields to a format compatible for
direct input to the model.
The model's meteorological data structure is compressed and in "direct-access" format. Each time
period within the
data file contains an index record that includes
grid definitions to locate the spatial domain, check-sums for each
record
to ensure data integrity, variable identification, and level
information. These data files require no conversion between

computing platforms.
The modeling system includes a Graphical User Interface (GUI) to set up a trajectory, air
concentration, or deposition
simulation. The post-processing part
of the model package incorporates graphical programs to generate
multi-color or
black and white publication quality Postscript
printer graphics.
A complete description of all the
equations and model calculation methods for trajectories and air
concentrations has
been published3 and it is also available on-line. The on-line and the version included with the PC installation contains
all the most recent corrections and updates.
Pre-Installation Preparation
There are two installation
programs that can be downloaded. The trial version (HYSPLIT_win{32|64}U.exe
~ 70 Mb)
available to anyone and a fully functional version
(HYSPLIT_win{32|64}R.exe ~ 70 Mb) that requires a user registration

through the web site. Both versions identical, except the trial
version will not work with forecast meteorological data
files. In
addition, several supplemental programs (Ghostview and Tcl/Tk) are
packaged with the trial version for
convenience. It is assumed
that these would have already been installed when the registered
version is installed on top
of the trial version.
The self-installing executable contains only HYSPLIT related programs. No additional software is required to run a
simulation if the
command line interface is sufficient. To enable the model's GUI,
the computer should have Tcl/Tk
script language installed. The
most recent version can be obtained over the Internet from or an
older version is
packaged with some of the other programs on the
HYSPLIT
web site. The installation
of Tcl/Tk will result in the
association of the .tcl suffix
with the Wish executable and all Hysplit GUI scripts will
then show the Tk icon. The
HYSPLIT GUI has been tested with Tcl/Tk
version 8.5.4.
The primary HYSPLIT graphical
display programs convert the trajectory and concentration model
output files to
Postscript format. The Postscript files can also
be viewed directly through the GUI if Ghostscript and Ghostview
have
been installed. See for more information on the Postscript
file viewer. The HYSPLIT code and GUI have been tested
with
Ghostscript 8.63 and Ghostview 4.9. Installation to different
default drives, directories, or other versions might
require
editing the main GUI script's directory pointers (edit file: /guicode/hysplit4.tcl or the directory entry in the

Advanced-Configuration-Directories menu tab.

The third optional GUI feature is
the ability to convert the Postscript output file to a different
graphical formats using
ImageMagick. More information on this
software can be found at The HYSPLIT code and GUI have been tested
with
ImageMagick 6.4. Similar to Ghostscript, installation to a
different default drives or directories as suggested by the

installation process may require editing the main GUI script's

directory pointers. Proper functioning of the conversion
software
with Postscript files requires the installation of Ghostscript. Although the setup script tests for the default
language, it is
possible that installation to non-English default windows operating
systems might require additional
editing of the directory
pointers.
Windows Installation (all operating systems)
HYSPLIT installation to a computer
running Windows is provided through a self-installing file. Executables are
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installed in various directories for trajectories,

dispersion, display and manipulation of results, and the creation
of input
meteorological data files. The trajectory and dispersion
model source code is not provided. However all the Fortran
source
code to create meteorological data files in a format that the model
can read are provided in the /data2arl
directory. Each
subdirectory contains a @readme.txt file with more complete
information about the contents of that
directory.
During the installation you will
be prompted as to the directory location. It is suggested you
select a simple default
location (such as C:/hysplit4). The
installation program installs all code and executables to your
selected directory, and
creates a shortcut on the desktop to
/guicode/hysplit4.tcl with the "Start In" directory as your
selected default. You may
have one of two versions of the
installation program: HYSPLIT_win{32|64}{R|U}.exe. The suffixes R and U
refer to
the Registered or Unregistered versions. The two versions
are almost identical, except that the unregistered version
does not permit calculations with current forecast meteorological data.
HYSPLIT and all the related programs are available for either
32 bit or 64 bit operating systems. The 32 bit version can
be installed
on either OS, while the 64 bit programs can only be installed on a
64 bit OS. An Apple MAC version is
also available (HYSPLIT_mac.dmg).
Installing on top of an old version will bring up a "Continue" or "Cancel" prompt. It is not possible to rename the

installation directory at this stage. Rename your old installation prior to installing the new code if you wish to keep the
original
version.
The installation will contain several sub-directories, some of
which are required for model execution, and some of
which provide
additional documentation and other information. For instance ...
bdyfiles - This directory contains an
ASCII version of gridded land use, roughness length, and terrain
data. The
current file resolution is 360 x 180 at 1 degree. The
upper left corner starts at 180W 90N. The files are read by
both
HYSPLIT executables, hyts_std (trajectory model) and
hycs_std (concentration model), from this directory.
If not
found, the model uses default constant values for land use
and roughness length. The data structure of
these files is defined
in the file ASCDATA.CFG, which should be located in either the model's startup or
/bdyfiles directory. This file defines the grid system and gives an optional directory
location for the landuse and
roughness length files. These
files may be replaced by higher resolution customized user-created
files. However,
regardless of their resolution, the model will
only apply the data from these files at the same resolution as the

input meteorological data grid. More information on the structure

of these files can be found in the local
@readme.txt file.
data2arl - Current forecast or archive
meteorological data can be obtained from the ARL ftp server:

ftp://gus.arlhq.noaa.gov /pub/archives (or /forecasts). Older

archive data can be ordered from the NCDC
(National Climatic Data
Center). However if you have access to your own meteorological
data or data formatted
as GRIB (Gridded Binary), this directory
contains various example decoder programs to convert meteorological

data in various formats to the format (ARL packed) that HYSPLIT can
read. Sample programs include GRIB
decoders for ECMWF model
fields, NCAR/NCEP (National Centers for Environmental Prediction)
re-analysis
data, and NOAA Aviation, ETA, and Regional Spectral
Model files. All the required packing and unpacking
subroutines
can be found in the /source subdirectories. Sample
compilation scripts for Compaq Visual Fortran
6.6 are in some of
the decoder directories. More information on how to run these
programs can be found in the
Meteorology section.
examples - The directory contains several example
scripts and batch files that can be used to create automated

simulations.
html - Contains all the HELP files in
HTML format. These files can be displayed with any browser or

interactively through the GUI. The files that are opened in the
GUI depend upon the context from which HELP is
invoked.
document - This directory contains PDF
(Adobe Portable Document Format) versions of the User's Guide (all
the
HTML help files put together in one document) and other
documentation such as ARL-224, the principal ARL
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Technical
Memorandum describing the model and equations. This User's Guide
(this document) provides
detailed instructions in setting up the
model, modifications to the Control file to perform various
simulations and
output interpretation. The @readme.txt file
contains additional information about compilation, typical CPU

times, and a summary of recent model updates.

exec - Is the directory that contains
all the executable programs. The GUI looks for all programs in this
directory.
When running examples from the command prompt in
certain directories, the relative path should be included
prior to
the executable: "../exec/program.exe"
graphics - There are two types of
graphical plotting programs provided in the ../exec directory.
Publication quality
graphics can be created using the postscript
conversion programs, concplot and trajplot, which use
a Fortran
Postscript library created by Kevin Kohler4. All graphical routines use the map background file arlmap in this
directory. The map background file uses a simple ASCII format and contains the world's coastal and political
boundaries at relatively coarse resolution. Other higher resolution map background files are available in the
/graphics/mapfiles directory or from the HYSPLIT download web page. All graphical programs search the
startup directory
first for arlmap before going to /graphics, therefore
customized maps can be created without
changing the HYSPLIT
installation structure.
guicode - This directory contains a
Tcl/Tk GUI interface source code script for HYSPLIT. The interface
is used to
set up the input Control file as well as run the
graphical output display programs. To use the interface you must

first install Tcl/Tk. The upper-level Tcl script is called

hysplit4.tcl, which calls all other Tcl scripts. Executing

this script starts the HYSPLIT GUI. The Desktop shortcut as well
as the Start Menu options should point to this
script. If the
installation program did not properly setup the Desktop, you can
manually create a shortcut to the
script and edit its properties
such that the "Start In" directory is /hysplit4. You should
also select the HYSPLIT
icon from the /icons directory.
working - This is the Hysplit4 root
directory, which contains sample CONTROL files that can be used
for initial
guidance to set up more complex simulations. These
should be loaded into the GUI from the approprate
"Retrieve" menu
tab. Examples include:
sample_conc - concentration simulation example from users guide
sample_traj - trajectory simulation example from users guide
The "plants.txt" file contains a sample
listing of starting locations that can be opened in the GUI to
select
from a list of previously determined starting locations. This file can easily be customized. The "tilelist.txt"
file
contains the approximate coordinates of NCEP's NAM (North America
Mesoscale model) tile
domains.
Problems
If Tcl/Tk does not exist on your
system or there are other problems with the GUI interface, it is
very easy to run the
sample cases directly in the /working
directory by running the batch file "run_{model}.bat" If the sample
simulation
works well, then it is only necessary to manually edit the
CONTROL file to try out different simulation variations. The

CONTROL file options are explained in more detail in the individual

Trajectory and Concentration
Setup sections.
In general, premature termination
during the model initialization phase will result in messages to
standard output.
However after the model has started, fatal,
diagnostic, and progress notification messages are written to a
file called
Message. If the model output is not what you
expected, first check the Control file to determine if the
input setup is
what is desired, then check the Message file
for indication of abnormal performance. These files are always
written to
the model's startup directory - /Hysplit4 if the
model is run from the GUI. At times error messages may be lost in
the
display buffer after premature termination. In this case the
model should be rerun from the command line window for
proper
display of all standard output messages. The "Advanced"
menu contains a the View MESSAGES tab that
displays the last MESSAGE file for viewing. Other features of the advanced menu are used to modify the model's
configuration file and are explained in more detail in that section. Modifications to these parameters require a complete
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understanding of the model's design and operation.

References
[1]Draxler,

R.R., 1999, HYSPLIT_4 User's Guide, NOAA Technical Memorandum ERL ARL-230, June, 35 pp.

[2]Draxler,

R.R., and G.D. Hess,

1998, An overview of the Hysplit_4 modelling system for
trajectories,
dispersion, and deposition, Australian
Meteorological Magazine, 47, 295-308.

[3]Draxler,

R.R.,
and G.D. Hess, 1997, Description of the Hysplit_4 modeling system,
NOAA Technical
Memorandum ERL ARL-224, December, 24p.

[4]Stein,

A.F., R.R. Draxler, G.D. Rolph, B.J.B. Stunder, M.D. Cohen, and F. Ngan , 2015. NOAAs HYSPLIT
atmospheric transport and dispersion modeling system,
Bulletin of the American Meteorological Society. 96,
20592077. doi: http://dx.doi.org/10.1175/BAMS-D-14-00110.1

[5]PSPLOT

libraries
can be found at www.nova.edu/ocean/psplot.html and were created by
Kevin Kohler
([email protected]).

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HYSPLIT4 User's Guide Help File Index

Model Overview
GUI Overview
METEOROLOGY - Data Overview
ARL Data FTP - External sources of data
Forecast and appended ARL archives for the last two days
Archive of long-term ARL formatted data
Reanalysis data archive from the ARL server
Set Server changes the name and directory of the FTP server
Convert to ARL - Convert data on local computer to ARL format
WRF-ARW Advanced Research WRF NetCDF
NARR archive North America Regional Reanalysis GRIB1
Global Lat-Lon European Centre or NOAA global lat-lon grids
ECMWF ERA ECMWF Reanalysis ERA-40 or Interim GRIB1 files
MM5V3 Regional Version 3 binary output files
MCIP IOAPI formatted files
User entered single station and level user data entry
Display Data - Viewing HYSPLIT formatted meteorological data
Check File all the records in a meteorological file
Contour Map of a single meteorological variable
Text Profile of all variables at a single location
Grid Domain shows a map of meteorological grid locations
Utility Programs - Meteorology / Trajectory / Concentration Menus
GIS to Shapefile converts text GIS output to ESRI Shapefile
Postscript to Image converts to another graphic format
Meteorology Help
Data Format description of the packed meteorological data format
Sample Programs to read ARL and GRIB1 data files

TRAJECTORY - Menu Overview

Quick Start for automatic configuration and execution
Setup Run creates the trajectory simulation CONTROL file
Save / Retrieve Options for custom simulations for future use
Run Model menu tab to execute the trajectory model
Display Options

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Trajectory converts the endpoints file to a graphic

Frequency converts multiple trajectory files to a graphic
Utility Programs
Endpoints to IOAPI converts the endpoints file to IOAPI
Special Simulations - Trajectory simulations with special requirements
Run Ensemble by varying location on meteorology grid
Run Matrix defines a grid of multiple source locations
Multi-time starts at trajectories regular intervals
Multi-space starts new trajectories along a trajectory
Run daily invokes script to do multiple simulations in time
Run Cluster Analysis to find which trajectories belong together
GeoLocation back trajectory analysis from sampling locations
Control File Format line-by-line description
Endpoints File Format description

CONCENTRATION - Menu Overview

Quick Start for automatic configuration and execution
Concentration Setup of the simulation CONTROL file
Pollutant, Deposition, and Grid menu to select items below:
Pollutant definition of the emission characteristics
Grid Definition or the air concentration sampling grid
Deposition definition of the pollutant deposition parameters
Run Model to start the concentration model
Display Options
Concentration Contours converts the binary model file to a graphic
Grid Values uses colorfill to show values on the concentration grid
Pointer Select uses mouse to extract concentration values to a file
Global Grid graphic optimized to plot global concentration grids
Particle displays horizontal and vertical particle distributions
Plume Arrival uses colorfill to show first arrival times after start
Source-Receptor View create graphic from a source-receptor matrix file
Source-Receptor Stats creates a statistics map for multi-source simulations
Ensemble View Map creates probability maps from multiple simulations
Ensemble Box Plot shows the probability distribution at one location
Ensemble Statistics computes ensemble statistical performance
Utility Programs
Binary File Merge adds or masks concentration binary files
Binary File Extract creates a temporal or spatial concentration file extract
Binary File Average adds or masks concentration binary files
Binary File Apply Source multiplies time-varying dispersion factors by source term
Convert to ASCII converts the binary concentration file to an ASCII format file
Convert to DATEM convert to DATEM format and compute verification statistics
Convert to Dose convert a binary file to dose using a dose factor data file

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Convert to IOAPI converts the concentration binary file to IOAPI

Convert to Station extracts the concentrations at a station and writes to a file
Convert PARDUMP converts PARDUMP file to binary concentration file
Particle Adjustment adjust particle positions for improved initialization
Transfer Coefficient using measurements to solve for the emissions vector
Special Simulations - Concentration simulations with special requirements
Run daily invokes a script for multiple simulations in time
Run Matrix configures and runs dispersion for an array of locations
GeoLocate from measurements determine the emissions location
Ensemble Meteorology for simulations using meteorology grid offsets
Ensemble Turbulence for multiple turbulence simulations
Ensemble Physics for multiple physical parameterizations
Global runs a simulation with particle mass transfer to Eulerian global grid
Run Dust Storm for PM10 emissions from dust storms
Daughter Products from nuclear decay from nuclide
Related Concentration Help
Multi-Processor special simulations in multi-processor environment
Concentration File Format line-by-line description
Terrain Overlay using shapefiles to overlay terrain on plots

ADVANCED Overview of features for advanced users

Configuration Setup to edit the SETUP.CFG namelist file
Trajectory edit menu for trajectory simulations
Concentration edit menu for for concentration simulations
Global configures the global Eulerian model (grid-in-plume)
Dynamic Sampling configuration of the LAGSET.CFG file
Emissions File configuration of the point source file
Set GUI Directories configures the directory structure
Panel Labels edit menu for supplemental graphic map labels
Border Labels edit menu for map titles and units labels
Foot and Mouth Disease Virus (FMDV) decay configuration
SETUP.CFG NAMELIST SUMMARY
Summary of all NAMELIST variable defaults
Time Steps
Trajectory Vertical Coordinate
Multiple Trajectories in Time
Trajectory Points Output Frequency
Meteorology Along the Trajectory
Meteorological Ensemble
Mixing Depth Computation Method
Concentration Vertical Coordinate
Release Particles or Puffs
Release Number Limits
Emission Cycling and Input
Turbulence and Dispersion Computations

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Concentration Packing and Output Units

Input and Output Particle Files
In-Line Conversion Modules
Puff-Split-Merge Issues
Variables Not Set in GUI
Satellite Data - access to selected satellite data archives
NASA TOMS FTP Aerosol Index (AI)
TOMS Viewer for AI and model concentration and particle positions
Advanced Help
Special Topics for complex simulation scenarios
PARDUMP file format for particle displays or model restarts
MESSAGE file format to evaluate simulation details
ASCDATA.CFG file format for terrain, land-use, and roughness

VERIFICATION - Model statistics with experimental data

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GUI Overview
Although the model can be configured and run manually from the command line, it is usually much quicker to use the
GUI. A summary of the main features in each of the primary GUI menus is reviewed below. More detailed help
information can be found
with the help button associated with each specific menu.
Meteorology / ARL Data FTP
Forecasts - Links to only the most recent forecast data for a
variety of different meteorological models available
on the ARL FTP server. The data have already processed to a HYSPLIT compatible format. Appended data are
defined as a combination of analysis and short forecasts (e.g. 0h and +3h appended with each new 6h cycle) that
are operationally maintained as a rolling archive valid for 48 hours prior to the most recent forecast cycle.
ARL Archive - Provides access to the long-term data archives
at ARL for the GFS/GDAS (formerly FNL) and the
NAM/NDAS (formerly EDAS) archives. Unless
otherwise noted, some of the archives go back to about 1995.
NOAA Reanalysis - The NCAR/NCEP reanalysis data archived has been reformatted for HYSPLIT and placed on
the ARL ftp server. These data are available from 1948 through the end of the last year. The files are updated
once-a-year.
Set Server - A generic menu that can be customized to open
different backup or user defined FTP servers to
download pre-formatted HYSPLIT compatible
meteorological forecasts.
Meteorology / Convert to ARL
Many of the scripts linked in this menu will convert various data file formats
into the data format used by
HYSPLIT. GRIB version 2 is not yet supported. However,
conversion software from GRIB-2 to GRIB-1 can be
obtained from several different
sources (NOAA-NCEP, ECMWF, WMO). All files must be on the local
computer. FTP is
no longer supported through these menus.
WRF-ARW - Processes fields from NCARs Advanced Research
WRF model into the ARL format. The data
conversion routines require NetCDF routines
currently supported only on UNIX or LINUX platforms.
NARR Archive - Archived GRIB-1 fields from the North American
Regional Reanalysis model (32 km
resolution, 3-hr intervals). The GRIB files must be
independently downloaded from the NCDC NOMADS web
site. The downloaded files need to be
renamed to end with the day-hour {DDHH}. The script is designed only to
work with archive
data to create a multi-day file as long as one month.
Global Lat-Lon - Archived GRIB-1 fields from the global model of ECMWF or NOAA may be processed locally
into ARL format. The procedure is designed only to work with archive data from their current operational model,
where the last four digits of
the file name represent the day.
ERA-40 - Archive GRIB-1 fields from the ECMWF ERA-40 reanalysis
may be processed locally into ARL
format. These files must already be present. The procedure
is designed only to work with the ERA-40 data files.
Three different file types must be
downloaded for this conversion: 3-d fields, 2-d surface fields, and one invariant
field.
MM5V3 format - Output files from MM5V3 can be converted to ARL
format. The script automatically processes
all domains (MMOUT_DOMAIN{X}) found in the selected directory.
MCIP IOAPI - Meteorological output files from MM5 converted to
the CMAQ IOAPI format. Available only
under UNIX systems with NetCDF installed.
User Entered - This menu tab is intended to convert user
entered meteorological data to the ARL packed

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HYSPLIT compatible format. The conversion program will create a data file with one or more time periods
containing a uniform field
in space and height but varying in time. The grid is centered over the location
specified
in the main menu and covers a 50 by 50 km domain.
Meteorology / Display Data
Check File - A program to list the information in the meteorology
file index record as well as the ASCII header
portion of each data record.
Contour Map - A simple postscript contouring program that can be used to view the data fields in any ARL
packed meteorological data set. The output is always written to a file called contour.ps. Multiple time periods
may be processed.
Text Profile - This program is used to extract the meteorological data profile interpolated to a user selected
latitude-longitude position. The raw data values at the surface and each level are output on the left while

temperature converted to potential temperature and winds rotated from grid orientation to true are shown on the
right. Output is shown on the screen and is also written to a file called profile.txt.
Grid Domain - Program to generate a map showing the domain of the meteorological data grid with marks at each
selected data grid point. Output is written to the file showgrid.ps.
Utilities
Convert Postscript - Converts any Postscript file to another format using ImageMagick. Enter the name of the
Postscsript file and the desired name of the output file, with the file suffix indicating the desired conversion.
GIS to Shapefile - When the GIS output option is selected in selected display programs an ASCII text file (in
generate format) is created that contains the latitude-longitude values of each contour. This GIS text file can be

converted to an ERSI Arc View shapefile. This menu tab is available from three different points. From the
meteorology tab the conversion is "line", from the trajectory tab the conversion is "points", and from the
concentration tab the conversion is "polygon".
Trajectory
Quick Start - menu tab can be used to run any simulation in one-step. The last configuration will be used for the
simulation. The menu brings up a global map with the current source location shown as a blue dot which can be
moved to
a new location. The Run Example menu tab resets the control and namelist files
and reruns the example
case. This can be used as a starting point for configurations
that have been corrupted.
Setup Run - This menu is used to write the CONTROL
file that defines all the model simulation parameters. Note
that once a simulation
has been defined it can be "Saved As" and later "
Retrieved." Note that the setup must be
"Saved" before proceeding
to the "Run Model" step.
Run Model - The selection opens the window for
standard output and starts the execution of "hyts_std.exe".
Incremental progress is reported on WinNT and later systems, however on LINUX the display remains frozen
until the calculation has completed (a beep will sound).
Display - Display options are available to label the time increment along the trajectory and the amount of white
space surrounding the trajectory on the map. The HIRES option limits the domain to just fit the trajectory. Output
is written to the file trajplot.ps. The plot title can be defined in a file called labels.cfg which should be placed in
the \working directory. The special frequency display can be used to
plot the spatial frequency distribution of
multiple trajectory simulations.
Special Runs - The Ensemble option invokes a special executable that will run multiple trajectories from the same
location, with each trajectory using meteorological data slightly offset from the origin point. The Matrix option

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GUI Overview (S100)

simultaneously runs a regular grid of trajectory starting locations. Also available are multiple trajectory options in
both time and space as well as a menu to run a series of automated daily trajectories for as long as one month per

execution. Multiple trajectories can also be clustered.

Concentration
Quick Start - menu tab can be used to run any simulation in one-step or rerun the example simulation. It's
functionality is similar to the trajectory
quick start menu.
Setup Run - The menu is almost identical to the Trajectory Setup menu except for the added tab for "Pollutant,

Deposition, and Grids", which is used to customize the concentration computation. Unlike trajectories, which are
terminated at the top of the model domain, pollutant particles reflect at the model top.
Run Model - Similar in function to trajectory run menu, executes "hycs_std.exe".
Display - Output is written to concplot.ps. Options on the menu permit concentration contours to be dynamically
scaled to the maximum for each map (default) or fixed for all maps based upon the highest value on any one map.
Other display programs are available for the color fill of uncontoured gridded data or the horizontal or vertical
display of the particle distributions and the computation of plume
arrival times.
Note that the units label as well
as the plot title can be defined in a file called
LABELS.CFG which should be placed in the \working directory.
Special display programs are available for a source-receptor matrix, ensemble, and
statistical simulation outputs.
Utilities
Convert to ASCII - Writes an ASCII file for each time period of concentration output with one record for every
grid point that has a non-zero concentration value. Each record is identified by the ending date and time of the

sample and the latitude and longitude of each grid point. The output file name is constructed from the name of
the [input file]_[julian day]_[output hour]. Some other output options are available.
Grid to Station - This program is used to extract the time-
series of concentration values for a specific location.
That location may be specified by a single latitude-longitude through the GUI or multiple stations may be defined
by entering the name of a file that contains an integer station number, latitude, and longitude on each record. The
output is written to con2stn.txt which can be read by the time series plotting program to produce the file
timeplot.ps. Note that the time series plot is always in integer units and therefore may require the specification of
a units multiplication factor.
Convert to DATEM - Conceptually similar to Grid-to-Station, this menu is used to convert a binary file to the
DATEM format and then compute model performance statistics. A data file with measurement data in DATEM
format must already exist, and the conversion program will match each model calculated concentration with a
measurement, compute performance statistics, and display a scatter diagram of measured
and calculated values.
Merge Binary Files - Multiple binary concentration files may
be added together for a sum, or the maximum value
is retained at each grid, or one of
the input files may be used as a zero mask, resulting in zero concentrations in
the
other file when the mask file shows a non-zero value.
Special Runs
Daily - Runs a script to rerun the last dispersion model
configuration each time with a different starting day and
time for one month. Output files are labeled with the starting time.
Matrix - Runs the matrix pre-processor to create
a CONTROL file with a grid of starting locations. The sourcereceptor conversion
option needs to be selected in the advanced menu to create the coefficient matrix
required for
source attribution applications.
Geolocation - Runs a special pre-processor that reads a file
of measured sampling data to automatically configure

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GUI Overview (S100)

a CONTROL file for each

sample which is then run in a script to create a source attribution function for each

measured sample.
Ensemble / Meteorology - An application similar to the
trajectory ensemble, in that multiple simulations are run
each with a different offset in
the meteorological data to create an ensemble showing the sensitivity of the
simulation
to gradients in the meteorological data fields.
Ensemble / Turbulence - Instead of starting each
simulation with the same random number seed, multiple
simulations are run, each with a
different seed, which then shows the concentration sensitivity to the turbulence.
Ensemble / Physics - The physics ensemble varies different turbulence and dispersion namelist parameters from
the base simulation to develop an ensemble showing the sensitivity of the calculation to various model physics

assumptions.
Global - The global special run invokes an executable that
contains a global Eulerian module to permit particle
mass to be transferred to the global model at a specified age. A concentration output grid for each computation is

created. One representing local/regional scale plumes, the other the contribution to
global background
concentrations.
Dust Storm - Invokes a pre-processor that creates
a CONTROL file with each location within the selected
computational domain that
contains a desert land-use designation. This option should be used in conjunction with
the advanced menu option to turn on the dust emission module.
Daughter Products - Invokes a pre-processor that creates a
DAUGHTER.TXT file containing the daughter
nuclides produced by a parent nuclide along with the half-life and branching fractions. In addition a CONTROL
file is modified to include the daughter product information. This option should be used in conjunction with the
advanced menu option to turn on the daughter product module and set MAXDIM to the number of daughters.
Advanced Topics
Contains several menus for custom model configurations that can be used to change the nature of the simulation
and the way the model interprets various input parameters. These menus would be used to configure matrix,
ensemble, global, pollutant transformations, and model initialization options.
Trajectory Configuration - Creates the SETUP.CFG
namelist file for trajectory calculations.
Concentration Configuration - Creates the SETUP.CFG
namelist file for concentration-dispersion calculations.
Global Configuration - Creates the GEMPARM.CFG
namelist file to configure the global Eulerian model
subroutines.
Dynamic Sampling - Creates a virtual sampler that can fly
through the computational domain, either passively
with the wind or with a pre-defined
velocity vector.
Emissions File - Opens a simple editor to create a special
emission file that can define point sources that vary in
space, time, and intensity.
Satellite Data / TOMS and Particle Viewer - Permits the download
of TOMS aerosol index data and plots those
data with particle positions or model
generated concentration fields.
Center Reset Button
This will cause any changes to the GUI variables to be set back to the sample trajectory
and concentration simulation
case which uses the oct1618.BIN sample meteorological file.
This button loads the sample_conc and sample_traj
control files from the working directory.

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GUI Overview (S100)

Table of Contents

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Advanced / Special Topics / ASCDATA.CFG (S444)

Advanced / Special Topics / ASCDATA.CFG

The bdyfiles subdirectory contains ASCII files for gridded land-use,

terrain, and roughness length data for HYSPLIT.
The terrain file is used by
some of the programs in data2arl if the terrain is not provided with
the other meteorological
fields. The resolution for these files is one-degree
covering the globe: 360 by 180 grid points. The upper left corner
starts at 180W - 90N. If these files are not found, the model uses default constant
values for land-use and roughness
length.

The structure of these files is given in the ASCDATA.CFG file, which defines
the grid system and gives the directory
location of the land-use, terrain, and roughness length files. The ASCDATA.CFG file should be located in the model's

startup or root directory. The last line in the file should be modified to reflect the path to the bdyfiles directory.
File Format

The ASCDATA.CFG file contains the following six records:

-90.0 -180.0 lat/lon of lower left corner (last record in file)
1.0 1.0 lat/lon spacing in degrees between data points
180 360 lat/lon number of data points
2 default land use category
0.2 default roughness length (meters)
'../bdyfiles/' directory location of data files

These files may be replaced by higher resolution user created files. Note that the first data point on the first record is
assumed to be centered at 179.5W and 89.5N, so that from the northwest corner the the data goes eastward and then
southward. User supplied files should define roughness length (cm - F4)
and the following land use-categories (I4). The
record length of the file should be the number of longitude values times four bytes plus one additional byte for CR.
The 11 Land-Use Categories

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1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.

-urban
-agricultural
-dry range
-deciduous
-coniferous
-mixed forest
-water
-desert
-wetlands
-mixed range
-rocky

The One-Degree Terrain

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Advanced / Special Topics / ASCDATA.CFG (S444)

Table of Contents

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Meteorology / Help / Sample Programs (S142)

Meteorology / Help / Sample Programs

The source code for many different meteorological data
applications can be found in the data2arl directory. A summary
of these programs and some others where only the executable is provided are given below. Some of these are available
for execution through the GUI, others must be run
from the command line. All executables can be found in the
exec
directory.
GRIB records
The various programs and library routines that are required to
convert GRIB formatted meteorological data files to ARL
HYSPLIT
compatible format can be found in the data2arl directory.
Some of these are summarized below:
content - decodes individual GRIB sections in a record
for diagnostic purposes. This program does not unpack the data
but
only lists the contents of the GRIB file.
inventory - decodes all the records within a GRIB file
(without unpacking) providing file content information.
unpacker - decodes GRIB records in a data file to a real
data array.
sample - creates a packed meteorological file using dummy
fields hardwired into the program. The input meteorological
data
subroutines should be replaced by routines reading user supplied
meteorological data files.
grib2arl - a generic program to
convert ECMWF or NOAA global data from ECMWF or NOAA in
GRIB1 format on a
global latitude longitude grid
to the ARL format. ECMWF data may be on the
native hybrid sigma or pressure surfaces.
For computational purposes, HYSPLIT requires either surface pressure or terrain height as a surface field in the
meteorological data file. The
default is that surface pressure is assumed to be available in
the input GRIB file,
otherwise the terrain height is required. This option is set using the "-p" flag. ECMWF GRIB files may contain upperlevel variables in one file, surface variables
in another file, and invariant data in a third file. In this
situation, the upperlevel data are considered the primary file "-i" and the surface data are the supplemental file
"-s", and the invariant data
are the constant file "-c".
-i[primary grib data: file name {required}]
-s[supplemental grib data: file name {optional}]
-c[constant grib data: file name {optional}]
-x[subgrid extract center longitude {-80.0}]
-y[subgrid extract center latitude {60.0}]
-g[output projection {3}]

0 :conformal extract

1 :fixed northern hemisphere polar

2 :fixed southern hemisphere polar

3 :lat-lon global grid (as input)

4 :lat-lon extract grid

-n[number of (x:y) extract grid points {100}]
-k[number of output levels including sfc {16}]
-p[surface defined by {1}:pressure or 0:terrain height]
-q[analyze grib file {0} or use saved configuration: 1]
-r[rain fall accumulation time hours: {6}]
-t[the number of time periods to process: {744}]
-z[zero initialization of output file 0:no {1}:yes]
fcsubs - library routines required for direct access to
variable length records
cmapf - library routines to convert from latitude-longitude
to a conformal map projection

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Meteorology / Help / Sample Programs (S142)

w3arl - library routines of the ARL version of the NCEP w3lib

GRIB record decoder.
ARL Packed Format
The various programs and library routines that are required to
manipulate or display meteorological data already in the
ARL packed
format can be found in the exec directory. Note that when these programs are run from the command line
there will be a typical two line prompt, the first for the directory and second for the file name. A directory name should
always have the proper terminator (/ or \). The following programs can be found:
chk_rec - program to dump the first 50 bytes of each
meteorological data record. Those bytes contain ASCII data

describing the packing.

chk_file - program to examine header and data records of
an ARL packed meteorological data file. The program uses
the same
I/O subroutines common to HYSPLIT code. If this program does not
work with a data file, neither will
HYSPLIT.
chk_data - a simple program that shows how to read and
unpack the ARL format packed meteorological data.
contour - creates postscript file of meteorological data contoured and color filled for a single variable
at a specified time.
The output written to contour.ps
display - creates postscript file of meteorological data
contoured and color filled for a single variable at a specified
time.
The output written to display.ps. This program is
prompted interactive version of the command line program
contour.
edit_miss - a simple missing data interpolation program
to fill in data gaps.
profile - creates text file of the profile of meteorological variables at a specified location and time.
The output is written
to the screen and to the file profile.txt.
showgrid - shows the extent of the meteorological
grid domain with a "+" symbol at the intersection of each node. The
output
is written to showgrid.ps
xtrct_grid - extracts a subgrid from the full grid
meteorological data file. It permits selection by lat-lon corners
and
number of levels from the ground. Creates output file called
extract.bin
xtrct_time - extracts data between two selected time
periods from the designated meteorological file. Creates an output

file called extract.bin

Table of Contents

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Trajectory / Setup Run (S210)

Trajectory / Setup Run

When the Setup Run tab is executed, the
default_traj file is read and the current parameter values
are loaded. The menu
for the example simulation
(sample_traj) is shown below. The options shown on the menu
correspond with the various
lines in the CONTROL file. See the
discussion of the control file format for a
more detailed description for each of
these parameters. However
there are some features of the GUI that require additional
explanation.

Clicking the Setup Starting Locations tab brings up the

menu shown below. If the number of starting locations were to
have
been changed from the default value of three on the main menu, then
there would be that number of starting
location lines set on the
menu, all with the same latitude and longitude. These could then be
manually edited for
different locations or starting heights. The starting
height is by default defined to be above-ground-level (AGL) unless
this
is changed in the Advanced/Configuration/Trajectory menu.
Another possibility would be to click on the List tab,
which
brings up a list of pre-selected starting locations from a file
called plants.txt, which can be found in the

../hysplit4/working directory. This file can be edited to reflect

starting locations of interest to the user.

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Trajectory / Setup Run (S210)

Another important feature of the main menu is how to select or

add meteorological data files. The Clear button will
erase
all file selections, then pressing the Add Meteorology Files
tab brings up the file selection dialog shown below.
Select a file
and click Open and the file will be added to the main menu.
For each additional file, it is necessary to click
again on the
Add Meteorology Files tab. With each new file the selected
files number is incremented by one.

Once the simulation is configured as required, click the

Save menu tab. This causes the GUI menu to over-write the

values in default_traj. Note that the format of

default_traj is identical to the CONTROL file.
Clicking on Save closes
the menu and then when the Run Model tab is executed, default_traj
is first copied to CONTROL, and then the
trajectory model is run.
When the GUI menu system is restarted, it loads the last values
stored in default_traj. The default_traj file may
also be
saved to another name to permit future similar simulations
to be set up more quickly. This option is available through
the Save As and Retrieve menu tab of the setup
menu.

Table of Contents

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Concentration / Setup Run (S310)

Concentration / Setup Run

The initial setup menu for the concentration model is identical
to the trajectory setup run menu in terms of
starting time,
location, and meteorology. These items will not be
discussed again except to note the differences when applied to a

dispersion simulation. The meaning of the entries in the CONTROL

file that correspond to this setup menu are
discussed in more detail below and should be reviewed to
appreciate how the change in the simulation type (from
trajectory
to concentration) changes the meaning and context of the same input
parameters. These parameters consist of
the initial entries of the
CONTROL file. The initial concentration setup menu is shown in the illustration below.

The entries in the Control file for air concentration

simulations consist of four groups of input
data. The first data group
is almost identical to the trajectory
simulation and is described in the next
section. The other three groups define the
pollutant emission characteristics, the concentration grid in terms of spacing and
integration interval, and the pollutant
characteristics relevant to
computing deposition and removal processes.
These latter three entries are accessed through
the "Pollutant,
Deposition, and Grids Setup" tab. Each of the these sections
contains a more detailed description of the
input parameters as
well as the corresponding CONTROL file values that need to
be set for command line simulations.
Initial CONTROL File Section
The concentration model input control file can be created using
any text editor. However if the GUI is not being used, it
would be
easier to let the model create the initial file based upon standard
output prompts. These are described in more
detail below. When data
entry is through the keyboard (a file named CONTROL is not
found), a STARTUP file is
created. This contains a copy of
the input, and which later may be renamed to Control to
permit direct editing and
model execution without data entry. If
you are unsure as to a value required in an input field, just enter
the forward

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Concentration / Setup Run (S310)

slash (/) character, and the indicated default value

will be used. This default procedure is valid for all input fields
except
directory and file names. An automatic default selection
procedure is also available for certain input fields of the

CONTROL file when they are set to zero. Those options are
discussed in more detail below. Each input line is
numbered (only
in this text) according to the order it appears in the file. A
number in parenthesis after the line number
indicates that there is
an input loop and multiple entry lines may be required depending
upon the value of the previous
entry.
1- Enter starting time (year, month, day, hour)
Default: 0 0 0 0
Enter the two digit values for the UTC time that the calculation
is to start. Use 0's to start at the beginning (or end)
of the file
according to the direction of the calculation. All zero values in
this field will force the calculation to
use the time of the first
(or last) record of the meteorological data file. In the special
case where year and month
are zero, day and hour are treated as
relative to the start or end of the file. For example, the first
record of the
meteorological data file usually starts at 0000 UTC.
An entry of "00 00 01 12" would start the calculation 36
hours from
the start of the data file.
2- Number of starting locations
Default: 1
Single or multiple pollutant sources may be simultaneously
tracked. The emission rate that is specified in the
pollutant menu is assigned to each source. If
multiple sources are defined at the same location, the emissions
are
distributed vertically in a layer between the current emission
height and the previous source emission height. The
effective
source will be a vertical line source between the two heights. When
multiple sources are in different
locations, the pollutant is
emitted as a point source from each location at the height
specified. Point and vertical
line sources can be mixed in the same
simulation. The GUI menu can accommodate multiple simultaneous

starting locations, the number depending upon the screen resolution. Specification of additional locations requires
manual editing of the CONTROL file. Area source emissions can be specified from an
input file: emission.txt.
When this file is present in the root
directory, the emission parameters in the CONTROL file are superseded by
the emission rates specified in the file. More information on this file structure can be found in the advanced help
section.
3(1)- Enter starting location (lat, lon, meters, Opt-4, Opt-5)
Default: 40.0 -90.0 50.0
Position in degrees and decimal (West and South are negative).
Height is entered as meters above ground level
unless the mean-sea-level flag has been set.
The optional 4th (emission rate - units per hour) and
5th (emission area - square meters) columns on this
input line
can be used to supersede the value of the emission rate
(line 12-2) when multiple sources are defined, otherwise
all
sources have the same rate as specified on line 12-2. The
5th column defines the virtual size of the source:
point
sources default to "0".
4- Enter total run time (hours)
Default: 48
Sets the duration of the calculation in hours. Backward
calculations are configured by setting the run time to a
negative
value. See the discussion in the advanced
help section on backward "dispersion" calculations.
5- Vertical motion option (0:data 1:isob 2:isen 3:dens
4:sigma 5:diverg 6:msl2agl 7:average 8:damped)

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Default: 0
Indicates the vertical motion calculation method. The default
"data" selection will use the meteorological model's
vertical
velocity fields; other options include isobaric, isentropic,
constant density, constant internal sigma
coordinate, computed from
the velocity divergence, a special transformation to correct
the vertical velocities
when mapped from quasi-horizontal surfaces (such as relative to MSL) to HYSPLIT's internal terrain following
sigma
coordinate, and a special option (7) to spatially average the
vertical velocity. The averaging distance is
automatically
computed from the ratio of the temporal frequency of the data
to the horizontal grid resolution.
6- Top of model domain (internal coordinates m-agl)
Default: 10000.0
Sets the vertical limit of the internal meteorological grid. If
calculations are not required above a certain level,
fewer
meteorological data are processed thus speeding up the computation.
Trajectories will terminate when they
reach this level. A secondary
use of this parameter is to set the model's internal scaling height
- the height at
which the internal sigma surfaces go flat relative
to terrain. The default internal scaling height is set to 25 km but

it is set to the top of the model domain if the entry exceeds 25

km. Further, when meteorological data are
provided on terrain sigma
surfaces it is assumed that the input data were scaled to a height
of 20 km (RAMS) or
34.8 km (COAMPS). If a different height is
required to decode the input data, it should be entered on this
line as
the negative of the height. HYSPLIT's internal scaling
height remains at 25 km unless the absolute value of the
domain top
exceeds 25 km.
7- Number of input data grids
Default: 1
Number of simultaneous input meteorological files. The following
two entries (directory and name) will be
repeated this number of
times. A simulation will terminate when the computation is off all
of the grids in either
space or time. Calculations will check the
grid each time step and use the finest resolution input data
available at
that location at that time. When multiple
meteorological grids have different resolution, there is an
additional
restriction that there should be some overlap between
the grids in time, otherwise it is not possible to transfer a

particle position from one grid to another. If multiple grids are

defined and the model has trouble automatically
transferring the
calculation from one grid to another, the sub-grid size may need to
be increased to its maximum
value.
8(1)- Meteorological data grid # 1 directory
Default: ( \main\sub\data\ )
Directory location of the meteorological file on the grid
specified. Always terminate with the appropriate slash (\
or
/).
9(2)- Meteorological data grid # 1 file name
Default: file_name
Name of the file containing meteorological data. Located in the
previous directory.
Next Section of the CONTROL file
Table of Contents

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Advanced / Special Topics / Message File Format (S443)

Advanced / Special Topics / Message File Format

A MESSAGE file is created during each simulation. The file contains information from certain key subroutines that can
be used for diagnostic purposes if a simulation were to fail. An example file is shown below in the left column from the
test concentration simulation. A trajectory MESSAGE file would be similar but without the particle number and mass
information. In the right column, in red, a more detailed description of each item is provided.
Start Namelist configuration

Internal grid parameters (nlvl,aa,bb,cc): 19 30.0 -25.0 5.0

&SETUP INITD = 4, KHMAX = 9999, NUMPAR = 500, MAXPAR = 10000, MAXDIM = 1,

QCYCLE = 0.0000E+00,

FRME = 0.10000000,

FRMR = 0.0000E+00,

KRND = 6,

DELT = 0.0000E+00,

ISOT = 0,

TKER = 0.50000000,

NDUMP = 0,

NCYCL = 0,

TRATIO = 0.75000000,

MGMIN = 10,

KMSL = 0,

NSTR = 0,

CPACK = 1,

ICHEM = 0,

NOUT = 0, TM_PRES = 0, TM_TPOT = 0, TM_TAMB = 0, TM_RAIN = 0, TM_MIXD = 0,

DXF = 1.0000000,

DYF = 1.0000000,

DZF = 9.9998E-03,

NINIT = 1,

PINPF = PARINIT,

POUTF = PARDUMP
-- End Namelist configuration --
NOTICE main: pollutant initialization flags

Gas pollutant - T

Current version and release date

Tabulates value of namelist variables

Number of internal model sigma levels and the polynomial parameters used to describe the vertical grid. These
are configured automatically based upon the meteorological input data files defined for this simulation.
The value of all variables that can be defined by the SETUP.CFG namelist file are listed. If no SETUP.CFG file
was defined for this simulation, then the default values for these variables are listed.
The settings of all internal deposition flags are shown here. In this case the simulation is for a gas.

NOTICE metpos: (mtime,ftime) - 50379840 0

NOTICE metpos: (mtime,ftime) - 50379960 0

NOTICE advpnt: (kg,nx,ny,nz) - 1 10 10 19

NOTICE sfcinp: reading ASCDATA.CFG

NOTICE metgrd: (kg, xyr,xy1) - 1 10 10 17 9

NOTICE metinp: NGM 1 1 10 10 17 9 50379840 95 10 16 0

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Advanced / Special Topics / Message File Format (S443)

#################################

WARNING prfsig: extrapolation from level (k,m): 16 7159.121

Input data levels: 10

Internal Sigma levels: 19

##################################

NOTICE metinp: NGM 1 63 10 10 17 9 50379960 95 10 16 2

NOTICE main: Initial time step (min) 20

NOTICE main: 1 50379860166 0.33333320

NOTICE main: 1 50379880332 0.6666647

NOTICE main: 1 50379900498 0.9999961

NOTICE main: 2 50379930498 0.9999961

NOTICE main: 2 50379960498 0.9999961

NOTICE metpos: (mtime,ftime) - 50380080 50379840

NOTICE metinp: NGM 1 125 10 10 17 9 50380080 95 10 16 4

The subroutine that determines which meteorological data are required is called for the first time. Data for times
840 and 960 are requested. The zeros for the second field indicate no data are in memory. Times are always in
relative minutes.
The first advection entry sets sub-grid #11 to 10x10 with 19 levels.
The surface boundary files are opened.
The lower left corner of sub-grid #1 is set at position 17,9 of the main meteorological data grid.
The NGM data for the first computational hour are read starting at record #1, loaded into a 10x10 sub-grid, corner
17,9, at time [x]840 for the date: 95 10 16 0
When these data are interpolated to the internal grid, it is determined that there are no input data records above
7159 m, therefore data for those levels are extrapolated.
Computations for the first hour require data at two time periods for interpolation (hours 0 and 2).
The initial time step was set to 20 minutes. Subsequent time steps may change.
The time, number of particles, and the total mass is shown for the three time steps of the first hour. After one hour
the emission stops.
During hour two, no further emissions (or particles) are released. The time step is now 30 minutes.
After the hour 2, new NGM data are required. The data in memory at 0 UTC (time 840) are replaced with data at
4 UTC (time 080).
The new data are input into the same sub-grid location.

NOTICE main: 3 50379990498 0.9999961

NOTICE main: 3 50380020498 0.9999961

NOTICE main: 4 50380050498 0.9999961

NOTICE main: 4 50380080498 0.9999961

NOTICE metpos: (mtime,ftime) - 50380200 50379960

NOTICE metinp: NGM 1 187 10 10 17 9 50380200 95 10 16 6

NOTICE main: 5 50380110498 0.9999961

NOTICE main: 5 50380140498 0.9999961

NOTICE main: 6 50380170498 0.9999961

NOTICE main: 6 50380200498 0.9999961

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Advanced / Special Topics / Message File Format (S443)

Index Height %Mass

6 935.0 1.41
5 630.0 10.84
4 385.0 31.33
3 200.0 29.72
2 75.0 20.48
1 10.0 6.22
Computations proceed as before for computational hours 3 and 4. Particle number remains the same because no
particles have moved off the computational domain. The mass remains
the same because deposition is not turned on for
this simulation.
At the end of hour 4, data are required for 6 UTC (time 200) to proceed with the calculation. These data replace the 2
UTC (time 960) in memory.
Every 6 hours, the model prints out the vertical mass distribution of all the particles within the computational domain.
This is the mass distribution relative to the model's internal sigma levels and there is no relation to the levels that may
be specified for the concentration output file. Only non-zero levels are shown. The internal levels are defined by the
polynomial parameters given at the beginning of the MESSAGE file.
At this point the computation will continue for the number of hours specified in the CONTROL file. Vertical profiles
are shown every 6 hours. As the particles move across the computational domain, the sub-grid position may be moved
(from position 17,9) or expanded larger than 10x10) to match the spatial extent of the particle distribution. This may
occur at any time during the computation or even multiple times during the same computational hour.

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Advanced / Help (S440)

Advanced / Help
This section provides some guidance in configuring the model to perform
certain specialized calculations. These include
deciding between particle or puff releases, dealing with continuous emissions, creating an file with
time variations of
the emission rate, unit-source
simulations with time-varying emissions,
area source emissions,
multiple pollutants,
pollutant transformations, atmospheric chemistry,
deposition and decay,
compilation limits, scripting for automation
applications, backward dispersion for source attribution, configuring the time or spatial variation of the emission rate
using an input file, and how to compute
deposited pollutant transport on ocean water surfaces.
The Advanced menu is
composed of four sections.
1. The Configuration Setup menu permits the
creation and modification of the SETUP.CFG namelist file for either

Trajectory or Air Concentration

calculations. The namelist file is a variable length file that is used to set

additional parameters that can be used to modify the nature of the simulation.
The namelist file is not required
because all the namelist variables take on
default values when the SETUP.CFG file is not found. The same
namelist
file can be used for either trajectory or air concentration simulations but
only certain variables are
applicable to each simulation. Supplemental
plot labeling options are available, a menu to configure
a dynamic
sampler that can move in space and time for
use with the concentration simulation, and a menu to configure the
default
directory structure and location of executable programs
used by the GUI. More complex point source
emissions scenarios can be defined
by creating the EMITIMES emissions file.

2. The Satellite Data menu opens two special menus that deal
with downloading and displaying TOMS satellite
data. The FTP NASA TOMS
satellite data menu opens up an anonymous FTP window to access the current
satellite
archives for the TOMS aerosol index (AI). These data can
then be displayed through the TOMS Viewer.
In
addition to AI, the viewing program will also display the pollutant particle
positions. The particle position file,
called PARDUMP by
default, is a snapshot of all the pollutant particles at a given time. Its creation
is controlled
through the configuration menu.

3. The View MESSAGES menu is used to display the diagnostic message file. For all trajectory or concentration

simulations, diagnostic information is written to standard output until the

initialization process has completed. At
that point the MESSAGE file is
opened and subsequent diagnostic and certain error messages are written to this

file. If the model does not complete properly, some additional diagnostic information may be obtained from this
file.

4. The Scan for Updates menu can be used to make small updates to a
limited number of executables and scripts for
the same HYSPLIT release version.
Updates to executables and scripts may be posted to the ARL web server.
This
menu compares the dates of those updates with the installed versions. If newer
programs are available, you
will be prompted to replace each with the update.
Older programs are copied to the updates directory and the
update can be reversed
if desired. The update process only changes programs in the ./exec directory and
scripts in
the ./guicode directory. Once a significant number of updates have
accumulated, the entire release version will be
updated and a new installation
must be manually downloaded from the ARL server. Only updates to the same
version
number are permitted.

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Advanced / Help (S440)

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Meteorology / Help (S140)

Meteorology / Help
Meteorological data fields to run the model are usually already
available or can be created from routine analysis
archives or
forecast model outputs. More complete descriptions of the different
data sets are available on-line. The
meteorological data available through the menu system are
summarized in the following sections.
The meteorology menu is divided into four sections: data FTP, data
conversion, data display, and utility programs.
The FTP section provides access to various data files that may be FTP'd
from the ARL server compatible for
immediate input
to HYSPLIT. These files include current and appended
forecasts as well as various regional and
global analysis archives and longer term archives such as the
NCAR/NCEP reanalysis data. All data files have
already
been converted for HYSPLIT applications.
The convert menu gives data processing options for files that are stored
on the local computer. Processing of
forecast or analysis files are available
for archive, forecast, and regional or global data files in various formats.

Processing for GRIB1 formatted input files is available for NARR,

Global ECMWF/NOAA, and ERA-40.
In
addition native formatted files from MM5V3 can
be converted locally. NetCDF is supported on UNIX systems
permitting
conversion of WRF-ARW and MCIP IOAPI data files. In addition, a simple interface has been created
to
permit the entry of user generated time-varying
data at a single location.
The display data menu tab provides some simple tools that can
be used to examine the data already in ARL
packed format. The most
basic is the check file listing of the individual data records. The contour map
program
will display a contour plot of any variable at any one time in the file. Multiple time periods may be processed.
The profile program returns a text file of the
profile of meteorological parameters at a pre-selected point. The
grid domain menu shows the extent of the meteorological grid with a mark at each point.
The utility menu permits conversion of Postscript files to any other graphical format and the
creation of shapfiles.
More detailed information about the format of the ARL packed data is available. In addition, various
library routines
and utility programs are
provided to manipulate both the GRIB and ARL packed data files.

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Meteorology / ARL Data FTP / Current and Appended Forecasts (S111)

Meteorology / ARL Data FTP

The ARL web server contains several meteorological model data
sets already converted into a HYSPLIT compatible
format in the
public directories. Direct access via FTP to these data files is
"hardwired" into the GUI. The data files are
automatically updated
on the server with each new forecast cycle. Only an email address
is required for the password to
access the server. The "FTP menu"
is locked until the FTP process is completed, at which point a
message box will
appear indicating the file name that was just
transferred. Alternatively, there is an option to download the files directly

from the NOAA nomads website via HTTP (http://http://nomads.ncep.noaa.gov/pub/data/nccf/com/hysplit/prod/).

Note that the NOAA models run by NCEP may be at higher spatial
resolution than what is archived in a HYSPLIT
compatible format on
the ARL server. If calculations using higher resolution data are
required, then the original GRIB
encoded files must be obtained and
converted as described in the data conversion section. GRIB decoding
can be
difficult. Although the required software is provided through
the GUI, the large file size downloads may limit the
practical
application of these real-time data files.

Meteorology / Data FTP / Current Forecast

Forecast data are available for NOAA's North America Model (NAM),
the Global Forecast System (GFS), and the
Rapid Update Cycle (RUC)
at various resolutions, projections, and forecast time durations.
The files are updated at two
to four hours after the cycle time. Forecast files are available for the last several days depending
upon the server and not
all files are on all FTP servers. All forecast files follow the same file naming convention of
hysplit.t{cycle}z.{name},
where cycle represents the initial UTC
time of the forecast (00,06,12,18) and the names are as follows:
gfsf :: 1-deg 3P +192h (0.7 Gb) global forecast at one-degree
resolution at 3 hour intervals at pressure levels out
to +84 hours
gfslrf :: 2.5d 12P +360h (0.03 Gb) long-range global forecast at
two and half degree resolution at 12 hour
intervals at pressure levels
and from forecast hours +192 to +360.
gfs0p5f :: 0.5-deg 3S +84h (2.6 Gb) global forecast at one-half degree
resolution at 3 hour intervals at hybrid
levels out to +84 hours
namf :: 12-km 3P +84h (1.6 Gb) regional forecast for the entire domain at
12 km resolution every three hours on
pressure levels out to a +84 hours.
namsf :: 12-km 1S +48h (2.7 Gb) regional forecast extracted for CONUS
at 12 km resolution at hour intervals on
sigma surfaces out to +48 hours.
namsf.AK :: 12-km 1S +48h (1.5 Gb) regional forecast extracted for Alaska
at 12 km resolution at hour intervals
on sigma surfaces out to +48 hours.
namsf.HI :: 12-km 1S +48h (1.4 Gb) regional forecast Hawaii nest
at 2 km resolution at hour intervals on sigma
surfaces out to +48 hours.
namsf.FW :: 1-km 1S +36h (2.2 Gb) regional forecast Fire-Weather nest
at 2 km resolution at hour intervals on
sigma surfaces out to +48 hours (location varies from cycle to cycle)
namsf.{XX}tile :: 12-km 1s +48h (0.3 Gb) regional forecast extracted for
the XX quadrant of the US at 12 km
resolution at hour intervals only for sigma
surfaces below 0.6777 out to +48 hours. Quadrants are available for
the northeast
(NE), southeast (SE), southwest (SW), and northwest (NW).
namsf{HH}.CONUS :: 4-km 1S +6h (2.0 Gb) regional forecast CONUS nest for forecast hour beginning at
HH+1h at 4 km resolution at hour intervals on sigma
surfaces out to +6, +12, +18, +24 hours for files
f00,f06,f12,f18, respectively.
rap :: 20-km 1P +12h (0.2 Gb) for the CONUS is at 20 km resolution at hourly
intervals on pressure surfaces out
to +18. Updated every three hours.
Additional information about the forecast data on the ARL server
can be found at the ARL web page.

Meteorology / Data FTP / Appended Forecast

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Meteorology / ARL Data FTP / Current and Appended Forecasts (S111)

The appended forecast files consist of a special time extraction of the previous seven (-48 hr) forecast cycle files to
create a series of pseudo-analysis (0-hour
initialization) and short-time (+3 h or +1,+2,+3,+4,+5) forecasts that have
been
appended to each other to create a continuous data time series for the previous
48 hours in a single file. These
special time extracts are only available for the
following files.
gfsa :: 1-deg 3P -48h (160 Mb)
nama :: 12-km 3P -48h (829 Mb)
ruca :: 20-km 1P -48h (60 Mb)

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Meteorology / ARL Data FTP / Archive (S112)

Meteorology / ARL Data FTP / Archive

The ARL web server contains several meteorological model data
sets already converted into a HYSPLIT compatible
format on the
public directories. Direct access via FTP to these data files is
"hardwired" into the GUI. Only an email
address is required for the
password to access the server. The "FTP menu" is locked until the
FTP process is completed,
at which point a message box will appear
indicating the file name that was just transferred.
The ARL analysis data archive consists of output from the
Global Data Analysis System (GDAS) and the NAM Data
Analysis System
(NDAS - previously called EDAS) covering much of North America. Both
data archives are available
from 1997 in semi-monthly files (SM). The
EDAS was saved at 80-km resolution every 3-h through 2003, and then at

40-km resolution (AWIPS 212 grid) starting in 2004. The GDAS (every
6-h) was saved on a hemispheric projection at
191-km resolution through the end of 2006. The new 1-degree and half-degree GDAS archive
is available every three
hours. See notes below for a more detailed
discussion of each file.
EDAS :: 80 km 3P (<=2003 SM 82 Mb) Semi-Monthly data files at three
hour intervals on pressure surfaces
EDAS :: 40 km 3P (>=2004 SM 600 Mb) Semi-Monthly data files at three
hour intervals on pressure surfaces
GDAS :: 1-deg 3P (>=2005 WK 600 Mb) Weekly files (W1=1-7; W2=8-14;
W3=15-21; W4=22-28; W5=29-end)
every three hours on pressure surfaces
GDAS :: 0.5-deg 3S (>=2010 DA 468 Mb) Daily files every three hours on
the native GFS hybrid sigma
coordinate system. Beginning July 28, 2010.
NAM12 :: 12-km 3P (>=2007 DA 395 Mb) Composite archive 0 to +6 hour forecasts
appended into daily files for
the CONUS at three hour intervals on pressure surfaces
NAMs :: 12 km 1S (>=2008 DA 994 Mb) Composite archive 0 to +6 hour forecasts
appended into daily files for
the CONUS at one hour intervals on sigma surfaces
From the GUI it is necessary to enter the year, month, and data
file period. Semi-monthly files are designated by 001
(1st through
the 15th) and 002 (16th through the end of the month).
Weekly files by the week number and the two-digit
day for the daily files.
The file names are created automatically.
For earlier global archive data see Meteorology - ARL Data FTP - Reanalysis.
Additional information about the data archives on the ARL server
can be found at the ARL web page.

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Meteorology / ARL Data FTP / Reanalysis (S113)

Meteorology / ARL Data FTP / Reanalysis

Global NOAA-NCEP/NCAR pressure level reanalysis data archives were
reprocessed into the HYSPLIT compatible
format and are available on
ARL's web site for 1948 through the end of the previous year. Data
for each additional year
are updated annually. The global data are
on a latitude-longitude grid (2.5 degree) and are archived
as one file (122 Mb)
per month. The GUI menu tab accesses the
correct directory with the proper file name using anonymous ftp
after the
desired year and month have been selected.
The NCEP/NCAR Reanalysis Project is a joint project between the
National Centers for Environmental Prediction
(NCEP, formerly
"NMC") and the National Center for Atmospheric Research (NCAR). The goal of this joint effort is

to produce new atmospheric analyses using historical data (1948

onwards) and as well to produce analyses of the
current atmospheric
state (Climate Data Assimilation System, CDAS). Until recently, the
meteorological community
has had to use analyses that supported the
real-time weather forecasting. More information about the
reanalysis project
and data can be found at the CDC web
site.
A subset of this data (global pressure level only) is available
from ARL in a format suitable for transport and dispersion

calculations using HYSPLIT through the GUI. Data files are named
according to the following syntax: RP{YEAR}
{MONTH}.gbl, where R indicates "Reanalysis", P indicates that the data are on pressure
surfaces, YEAR is a four digit
year, and MONTH is a two digit month.
The file suffix identifies the projection as the 2.5 degree global
latitudelongitude projection (gbl). The projection details are encoded in the file's index record and are processed by HYSPLIT

during trajectory or dispersion computations.

A comparable data set is also available from ECMWF's 40 year
reanalysis project. The GRIB files must be downloaded
independently from the GUI through a
web browser. Although cost free, registration with ECMWF is required.
The
downloaded ECMWF GRIB data files may be converted through the GUI to the ARL format.

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Meteorology / ARL Data FTP / Set Server (S101)

Meteorology / ARL Data FTP / Set Server

Meteorological data files formatted for use by HYSPLIT are available from
several different FTP servers. The GUI
currently supports the definition of
three different servers for forecast and analysis data. The default server
locations
and their root data directories are written to the file default_ftp
when the GUI is started for the first time. The FTP
application will only search for data at one location as shown in the text box. One may select
either the default,
alternate, or backup sites. Not all data files are available at all sites. After selecting a new server, it is only necessary
to
exit the GUI and the location in the text box will be used for all subsequent FTP commands.
It is possible to edit both the server location and root data directory
and the exiting the GUI will cause subsequent FTPs
to use the edited location.
However, if the edits are desired to be saved, then there are two save options.
In the first,
Save Changes, just updates the internal array so that the edited
text is saved in either the default, alternate, or backup
locations, so that
pressing the radiobutton will bring up the edited locations rather than the
original values for those
entries. In the Save to File option, the changes are
saved to the internal array as well as the default_ftp file, so that when
the
GUI is closed and reopened, the new values will be available.

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Meteorology / Convert to ARL / WRF-ARW (S120)

Meteorology / Convert to ARL / WRF-ARW

This menu tab is intended to convert WRF-ARW NetCDF output
files to the ARL packed HYSPLIT compatible format.
Input files can have any name. The reformatted output files are named by
default to ARWDATA.BIN. The output file
can be renamed through
the GUI menu. Multiple time periods from a single file can be processed into one output file.
However, if single-time multiple
files are to be processed, then each time period should be given
a unique name and
then the files can be "cat" or "type" together
into a single file if that is desired. Also note that the HYSPLIT
NetCDF
decoder library is not available under Windows and this
program will only work in a UNIX or MAC environment.

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Meteorology / Convert to ARL / NARR Archive (S119)

METEOROLOGY / Convert to ARL / NARR Archive

This menu item is intended to convert existing NARR GRIB-1 files
to the ARL packed format. The data files to process are determined
by
selecting any file in the GRIB data directory. Subsequent file
names will be constructed automatically between the starting and ending day
at the hour interval set by the radio-button. Day (DD)
and hour (HH) must be embedded the within the GRIB file name according
to the
following NOMADS archive convention: narr-a_221_{YYYY}{MM}{DD}_{HH}00_000.grb.
Year (YYYY) and month (MM) are fixed
according to the file name'
selected to set the base file name. Time intervals of 12 hours or more
should be avoided in transport and
dispersion calculations. Only one
month of data or less should be processed into one output file.
The GRIB files for the North American Regional Reanalysis (NARR)
can be downloaded from the NOMADS web page. When selecting
data to download, all variables and cycles should be obtained. The simplest approach is to use an FTP client
and go to the directories of
the desired data and download all the narr-a_221_{YYYY}{MM}{DD}_{HH}00_000.grb files for the desired period.

However, the NARR GRIB files are bit mapped, meaning some of the corners
do not have data defined due to differences in the internal
grid projection
of the model vesus the output grid. HYSPLIT does not support projections
with a bit map and when running the data
converter a message will be
generated:

WARNING w3fi63: BMS detected in GRIB file

Insure final grid does not intersect BMS

Full domain grid: 349 277

Bitmap reduction: 309 237

which indicates the the grid has been slightly reduced to insure that all data points within the domain have valid data. The reduced domain

is shown below with the + indicating every 10th data point.

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Meteorology / Convert to ARL / NARR Archive (S119)

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Meteorology / Convert to ARL / Global Lat-Lon (S125)

Meteorology / Convert to ARL / Global Lat-Lon

This menu tab is intended to convert existing ECMWF or NOAA GRIB-1 files
to the ARL packed HYSPLIT
compatible format.
Subsequent file names will be constructed automatically between the
starting and ending day at the
hour interval set by the
radio-button. Day and hour are assumed to be the last four digits
of the file name: {base}{DD}
{HH}. Input files could consist of
multiple time period forecasts or single-time period archives. Time
intervals of 12
hours or more should be avoided in transport and
dispersion calculations. Only one month of data or less should be

processed into one output file. HYSPLIT cannot properly position to

the correct starting data record if there is a month
transition
included within a data file.
The input data may be on pressure surfaces or the native
hybrid coordinate system. The "number of levels", counted
from the
surface upwards, can be used to restrict the size of the output
file. This may be particularly useful when the
input file consists
of 60 or more hybrid levels.
Four different grid conversions are available through the menu.
The "Extract" option interpolates the data to a conformal
map
projection of 100x100 grid points at 100 km resolution at the
center of the latitude and longitude selection of the
slider bar.
The Northern- or Southern Hemisphere options create a 95-km
resolution polar stereo-graphic grid centered
about the pole. The
"Input" option results in no interpolation and the program just
converts the original latitudelongitude data (global or regional)
to the ARL packed format.
The conversions from this menu are intended for data sets created
by the operational ECMWF or NOAA forecast
models. These may be
forecast or analysis data. Conversion of ECMWF
reanalysis data is done through a different
menu.

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Meteorology / Convert to ARL / ECMWF ERA (S126)

Meteorology / Convert to ARL / ECMWF ERA

This menu tab is intended to convert
ECMWF reanalysis data archives (ERA-40) GRIB1 files to the ARL packed

HYSPLIT compatible format. Data files must

first be downloaded from the ECMWF web page . The user can select
which fields and time periods to
extract. A GRIB file may contain multiple time periods. No more than
one month's
data should be included in a GRIB file if it is to be
converted to ARL format. All the time periods from one input file

will be processed into one output file. The ECMWF download menu permits
copying all the data on the global grid or
extracting regional sub-grids. The ARL conversion program can handle either option.
The conversion menu is designed to select three different GRIB
file types: upper air data, surface data, and time
invariant data.
The upper air and surface data files should contain data for the
same time periods. To be able to run
HYSPLIT, the upper air data
file must contain at a minimum the following variables:
geopotential, temperature, uvelocity, v-velocity, w-velocity, and
relative humidity. The surface variable file should contain the 2m
temperature, the
10m u- and v- velocity components, and the total
precipitation field, if wet removal calculations are required. The

invariant file should contain the surface geopotential field

(terrain height). Terrain height or surface pressure is required

for HYSPLIT to be able to interpolate pressure level data to its

internal terrain following coordinate system.
The ECMWF input data may be on pressure surfaces or its native
hybrid coordinate system. The "number of levels",
counted from the
surface upwards, can be used to restrict the size of the output
file. This may be particularly useful
when the input file consists
of 60 or more hybrid levels. The rainfall summation time is the
interval in hours at which
the rain "bucket" is emptied. For a pure
forecast, the bucket is never emptied, for the interim data, the
bucket is emptied
every 12 hours.
Four different grid conversions are available through the menu.
The "Extract" option interpolates the data to a conformal
map
projection of 100x100 grid points at 100 km resolution at the
center of the latitude and longitude selection of the
slider bar.
The Northern- or Southern Hemisphere options create a 95-km
resolution polar stereo-graphic grid centered
about the pole. The
"Input" option results in no interpolation and the program just
converts the original latitudelongitude data (global or regional)
to the ARL packed format. The "Input" option must be used for
latitude-longitude
sub-grids because interpolation from input data
sub-grids is not supported.

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Meteorology / Convert to ARL / MM5V3 format (S127)

Meteorology / Convert to ARL / MM5V3 format

This menu tab is intended to convert MM5 Version 3 output
files, usually named MMOUT_DOMAIN{X}, to the ARL
packed HYSPLIT compatible format. Input files can have any
name. The reformatted output files are named by default
to
DATA{X}.ARL, where "X" is the domain number. The output file can be
renamed through the menu. Multiple time
periods can be contained in
one file. Note that the conversion program rounds the output times
to the nearest 15
minutes. This is required because when MM5 is run
on a multiprocessor system, output times may differ be a few

minutes for each output cycle.

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Meteorology / Convert to ARL / MCIP IOAPI (S129)

Meteorology / Convert to ARL / MCIP IOAPI

This menu calls a utility program to convert meteorological
data files created by MCIP
for the CMAQ model. The data
files follow a specific naming
convention and may contain multiple variables and time periods. They are in the IOAPI
format. The conversion program is currently only available on UNIX or LINUX systems and will convert all the

required fields in one pass for all available time periods.

The data from multiple input files, say each file contains
one
day, may be appended automatically by setting the append
file name to a non-null string. If there are time period

overlaps between input files, it is best not to append them,

but to select multiple input files when running HYSPLIT.
There are three required MCIP input meteorological data files: METCRO3D_, METDOT3D_, METCRO2D_, and one
file, GRIDDOT2D_ that
gives the grid information. All data values are interpolated
to the dot grid. In the GUI, only
one input file needs to be selected
and the conversion program uses the file suffix and the standard
naming convention
to determine the names of the other files to open.
Due to file name character length restrictions, the directory

information is removed and all the input files should be in the local working directory.

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Meteorology / Convert to ARL / User entered (S128)

Meteorology / Convert to ARL / User entered

This menu tab is intended to convert user entered meteorological
data to the ARL packed HYSPLIT compatible
format.
The conversion program will create a data file with one or
more time periods containing a uniform field in space and
height
but varying in time. The grid is centered over the location
specified in the main menu and covers a 250 by 250
km domain at a horizontal
resolution of 10 km. It is
intended to be used for very short-range simulations. The main
menu
permits the selection of an existing text input file (space
delimited format), or the creation of a file through the
menu shown
below. After the meteorological data have been entered and saved to
a file, the conversion program is run
from the "Run convert" menu
button.

The data entry widget contains five time fields and four data
fields. The output file time interval is computed
automatically
from the input data. No interpolation is performed and the input
data nearest in time to the output time
are used for the
conversion. The maximum output interval is one hour. Note that the
date-time field defaults to the
current system clock time. The
meteorological variables are wind direction, speed (m/s), mixed
layer depth (m), and
Pasquill stability category (1=A to 7=G).
After filling in the data for the first line, use the Repeat
button the fill the
remaining table entries and then edit the time
and data fileds as required.

The conversion program computes the component turbulent velocity

variances based upon the stability category and
wind speed and
assumes those values are constant with height within the mixed
layer. Above the mixed layer top the
variances are set to the
model's minimum value. Using these data for input the model should
be configured in the
Advanced menu to use the variances for the dispersion. Otherwise the diffusion calculation will default to the
"deformation" method and with a spatially constant wind field; the dispersion will always be at its minimum value.

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Table of Contents

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Meteorology / Display Data / Check File (S130)

Meteorology / Display Data / Check File

The program called through this menu is used to show the
details of the meteorological data file contained in the index

record as well as a listing of the header portion (first 50 bytes)

of each data record. The output is written to a text file

called chkfile.txt. More detailed information about the structure

of a meteorological data file is available.
The check file
program uses the same library routines as HYSPLIT.
Therefore if this program does not work with the meteorological

data file, neither will HYSPLIT.

Table of Contents

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Meteorology / Display Data / Contour Map (S131)

Meteorology / Display data / Contour Map

The contour display program, run from this menu, provides a
simple tool to create a contour map for any variable at any
time
period in any ARL packed format meteorological data file. A simple
configuration is available through the menu
shown below. More
options are available if the program is run through the command
line.

In the example shown above, the sample

meteorological data file has been selected to display the
temperature (TEMP)
variable on model level #2. The time period to
be shown is offset 24 hours from the first time period in the file.
No
additional time periods are shown when the increment is set to
zero. The map will be centered about 40N 90W with a
radius of 20
degrees latitude. The maximum contour value and the temperature
difference (Delta) between contours
will be determined
automatically (-1.0). The radiobuttton default is to draw contour
lines on top of the color fill.
For a latitude-longitude grid, the full grid cannot be plotted. Instead a sub-grid not centered at 0 deg latitude, 0 deg
longitude
must be set.
There are two additional derived display options available.
Selecting the variable "VECT" will produce a wind vector
plot and
selecting "DIVG" will produce a plot of the wind field divergence.
Both of these options require the U and V
velocity fields at the
selected level in the order of U followed by V.
The radio buttons show only the most common set of variables
found in the meteorological data files. The menu does
not know which
variables are available in the selected file. The check file program
can be used to examine the variables
contained in each file. The variable
selected for display using the radio-button may be superseded by replacing the text
entry with the desired variable identification.
The output file contour.ps is created in Postscript
format. It is shown below, as displayed by the Ghostscript viewer,
and
may be converted to GIF through the Convert
Postscript menu tab.

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Table of Contents

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Meteorology / Display Data / Text Profile (S132)

Meteorology / Display Data / Text Profile

The profile program is used to create a profile at a specific
location of the meteorological variables in an ARL format
packed
data file. Output is written to the ASCII text file
profile.txt. Note that the program does not interpolate to
the
selected point, but processes the data at the grid point
nearest to the location selected. In the example shown below the

sample meteorological data file has been selected to display the

profile at 40N 90W. The time period to be shown is
offset 24 hours
from the first time period in the file. No additional time periods
are shown when the increment is set to
zero.

The output is written to a file called profile.txt and

the following would be shown in the GUI's display window. The U

& V wind components shown on the left side are relative to the
grid, while those on the right side are with respect to
north-south
and east-west. They would be the same for a latitude-longitude
grid.

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Table of Contents

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Meteorology / Display Data / Grid Domain (S133)

Meteorology / Display Data / Grid Domain

The showgrid program is used to show the domain of the
ARL packed format meteorological grid file. Output is to a

Postscript file and contains a plus symbol at every grid point

intersection as selected by the integer plotting increment.
A
non-zero value for the Lat-Lon interval draws latitude-longitude
lines at that interval over the map background. The
example below
is shown for the sample meteorological data file.

The following graphic is produced:

Table of Contents

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Meteorology / Utilities / GIS to Shapefile (S135)

Meteorology / Utilities / GIS to Shapefile

A utility tab is provided in the meteorology, trajectory, and concentration menus that will convert an ESRI generate
format text file to a Shapefile for import into ArcView or comparable GIS applications. The "ascii2shp" conversion
software is available under the GNU license from the Free Software foundation. The conversion can be run from the
command line or the GUI menu shown below.

Normally the fields will be blank when the menu is first invoked. Prior to creating the shapefiles it is necessary to create
the "Generate" text file which contains the latitude-longitude points of each contour as created by the contouring
programs available through the display menus. Checking the GIS box in the menu (-a1 option on the command line)

creates these files. All generate format files start with GIS and end with .txt. The remainder of the file name depends
upon the application from which it was created. However in all applications, the two-digit string prior to the .txt
identifies the frame number. There is one GIS output file per frame. Use the upper browse button to set the generate

format input file name.

The generate files can be converted to shapefiles consisting of points or lines (for
trajectories), and lines or polygons
(for concentrations). Polygons are closed lines. A polygon
that runs off the map display is becomes a line and may not
be displayed correctly if
treated as a polygon.
Normally the base.dbf file will contain only the minimum amount of information.
However, the trajectory and
concentration plotting programs automatically create an enhanced
attributes file (GIS_???.att). To add this information
to base.dbf, check one of the
enhanced attributes options.
In the lower text entry box enter the base name of the output shapefiles. All output files
will be created in the working
directory. Note that depending upon the upper level menu from
which the conversion was called, the shapefile
conversion will be either for lines (meteorology),
points (trajectory), or polygons (concentration), although the option
can be superseded by the
checkbox selection.
What is a Shapefile?
The Shapefile format is a working and interchange format promulgated by ESRI for
simple vector data with attributes. It
is apparently the only file format that can be
edited in ARCView 2/3, and can also be exported and imported in
Arc/Info. An excellent white
paper on the shapefile format is available from ESRI, but it is .pdf format, so you will
need
Adobe Acrobat to browse it. The file format actually consists of four files.

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Meteorology / Utilities / GIS to Shapefile (S135)

XXX.shp - holds the actual vertices.

XXX.shx - hold index data pointing to the structures in the .shp file.
XXX.dbf - holds the attributes in xBase (dBase) format.
XXX.prj - holds the projection information.
Copyright
The source for the Shapefile C Library is (c) 1998 Frank Warmerdam, and released under the following conditions. The
intent is that anyone can do anything with the code, but that I do not assume any liability, nor express any warranty for
this code.
As of Shapelib 1.2.6 the core portions of the library are made available under two possible licenses. The licensee can
choose to use the code under either the Library GNU Public License (LGPL) described in LICENSE.LGPL or under
the following MIT style license. Any files in the Shapelib distribution without explicit copyright license terms (such as
this documentation, the Makefile and so forth) should be considered to have the following licensing terms. Some

auxiliary portions of Shapelib, notably some of the components in the contrib directory come under slightly different
license restrictions. Check the source files that you are actually using for conditions.
Default License Terms
Copyright (c) 1999, Frank Warmerdam
This software is available under the following "MIT Style" license, or at the option of the licensee under the LGPL (see
LICENSE.LGPL). This option is discussed in more detail in shapelib.html. Permission is hereby granted, free of
charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in
the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute,
sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject
to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the
Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH
THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

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Meteorology / Utilities / Convert Postscript (S134)

Meteorology / Utilities / Convert Postscript

A utility tab is provided in the meteorology, trajectory, and
concentration menu's that will convert the Postscript graphic
to
another format. The menu shows the name of the last Postscript file
that was created. If that is not the file desired, it
should be
replaced with the appropriate file name. All output files are
assumed to reside in the working directory and
therefore a file
from any menu can be converted from any of the conversion menu
tabs. The file suffix represents the
conversion format. The slider
bar determines the size of the output graphic in pixels per inch.
The default value of 70
will produce an output frame of comparable
size to the input graphic. The checkboxes permit the creation of a

multiframe animation in one file or multiple output files if the

"Frames" option has been checked. The "Crop" option
eliminates
the white space around the graphic. However, the crop option may produce
inconsistent results when used in
conjunction with the animation feature.
The conversion process uses Ghostscript
to read the Postscript file and ImageMagick
to convert that file to a variety of
other supported graphical formats.
These programs can be stand-alone, but they have been linked through the Tcl/Tk
GUI menu. Conversion to GIF
is the default. Proper installation of all the previously mentioned 3rd
party software is
critical in the correct operation of the conversion process.
This software is included with the HYSPLIT trial version but
not with the registered
installation executable. Links to these programs are also available through the
HYSPLIT utilities
web page.
If non-default directories were selected during the installation of Ghostscript and ImageMagick, it may be necessary to

manually edit directory locations. The directory pointers can be changed

from the "Advanced-ConfigurationDirectories" menu
tab, which modifies the file default_exec. In the rare situation when this file
cannot be edited or does
not exist because the GUI did not load because of
problems with Tcl/Tk, then the appropriate lines in the upper-level
Tcl/Tk file
..\guicode\hysplit4.tcl need to be changed. For instance, the lines that
might require editing would be similar
to the following:

set magick_dir "c:/Program Files (x86)/ImageMagick-6.4.4-Q8/convert.exe"

set gsc_dir "c:/Program Files (x86)/gs/gs8.63/bin/gswin32.exe"

set gsv_dir "c:/Program Files/Ghostgum/gsview/gsview32.exe"

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Meteorology / Help / ARL Data Format (S141)

Meteorology / Help / ARL Data Format

The following sections describe the ARL packed data format in a
little more detail to permit the development of
customized
applications. Library routines are provided to simplify the task of
creating a model compatible data file. A
meteorological data file
is composed of one or more time periods. Each time period begins
with one or more ASCII
index records that summarize the valid time,
the grid definition, the variables, and level information. Each
subsequent
record contains one horizontal data field, consisting of
50 ASCII bytes of time, variable, and level information for that

record, followed by X times Y bytes of data, where X and Y are the

number of data points in the horizontal and vertical
directions,
respectively. Floating point or integer data are packed as one byte
per variable. Precision is maintained by
packing the differences
between adjacent grid points rather than packing the absolute
values. In any time period,
although not required, the surface data
precede the upper-level data fields. All records are of the same
length to permit
the model to read the file in a "direct access"
mode. Data files can be read on most computing platforms without
any
transformation and appended to each other using routine
operating system commands such as "cat" or "type". Only
binary
transfers or copies are permitted. All the routines discussed in
this section can be found in the source directory.
Valid Meteorological Data Types
Meteorological variables are identified to the model by a
unique four-character identification field that is written to the

first 50-byte header portion of each data record. Some of the

variables that can be decoded by the model and their units
are
identified below.
Sample Surface Level Parameters

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Description

Units

Identification

Pressure at surface

hPa

PRSS

Pressure at mean sea level

hPa

MSLP

Temperature at surface

TMPS

Total precipitation (6-h)

TPP6

U-Momentum flux

N/m2

UMOF

V-Momentum flux

N/m2

VMOF

Sfc sensible heat flux

W/m2 SHTF

Latent heat flux

W/m2 LTHF

Downward short wave flux

W/m2 DSWF

Temperature at 2 m

T02M

Relative humidity at 2 m

RH2M

U-component of wind at 10 m m/s

U10M

V-component of wind at 10 m m/s

V10M

Total cloud cover

TCLD

Meteorology / Help / ARL Data Format (S141)

Sample Upper-Level Parameters

Description

Units

Identification

U wind component (respect to grid) m/s

UWND

V wind component (respect to grid) m/s

VWND

Geopotential height

gpm* HGTS

Temperature

TEMP

Pressure vertical velocity

hPa/s

WWND

Data may be obtained from any source, however there are certain
minimum data requirements to run the model: surface
pressure or
terrain height, u-v wind components, temperature, and moisture. In
addition, precipitation is required for
wet removal calculations.
Not required, but certainly necessary to improve vertical mixing
calculations, would be some
measure of low-level stability. This
may take the form of a near-surface wind and temperature or the
fluxes of heat and
momentum.
It is also important to have sufficient vertical resolution in
the meteorological data. Some of the NOAA higher
resolution data
files have five or more levels in the boundary layer (<850 hPa)
in addition to wind and temperatures
near the surface, usually at 2
and 10 m agl. These surface values are especially important when
the data are only
available on absolute pressure surfaces, rather
than terrain following sigma surfaces, to avoid interpolation to
the
surface between data levels when the local terrain is well
above sea-level.
Starting with HYSPLIT (Revision 596) the optional field DIFF is recognized as the difference between the original data
and the
packed data: DIFF=ORIGINAL-PACKED. The effect of this is to
increase the precision of variables that have
this additional field.
When the DIFF field is read by HYSPLIT, the values are added to the data field resulting in values
closer to the original data.
Currently only DIFW and DIFR (vertical velocity and precipitation)
are recognized as valid
DIFF fields.
Creation of a Meteorological Input Data File
One may prepare meteorological data from any number of
different sources to be in a suitable format for the model
using a
series of routines described in this section. In general it is
assumed one has access to a meteorological data
source, either the
data fields are already on a grid, such as those output from a
meteorological model, or perhaps from
observations that have been
interpolated to a grid. Some example conversion programs are
provided within the GUI to
convert from either NOAA or ECMWF
GRIB format data files to the HYSPLIT
format.
The meteorological data are processed in time-sequence, calling
the subroutines provided, to create a HYSPLIT
compatible output
file. These subroutines will pack the data and write the index
record. The index record, which
precedes the data records for each
time period, can only be written after the data records are
processed. The packing
routines must first be initialized by
setting the appropriate grid parameters and defining all the
meteorological variables
that will be written to the file. Multiple
output grids may be defined and written simultaneously by invoking
the
PAKSET routine with a different unit number for each
grid. The grid parameters are all defined in a configuration file,

which should be in the directory from which the procedure is

invoked:
CALL PAKSET (kunit,fname,krec,nx,ny,nz)
Kunit is the Fortran unit number to which the data
records will be written. Fname is the character string of
the name of
the configuration file. It can be any name, but it will
default to metdata.cfg. The file is opened internally on
kunit to
read the configuration file. This routine needs to
be called once for each grid. Krec is the starting record
number (of the
index record) to which output will be written. It is
normally set to 1 unless you want to start writing in the middle of
a

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file. The remaining parameters (nx, ny, nz) are returned

by the subroutine and define the horizontal and vertical grid

dimensions. These values can be used to set variable dimensions. It

is your responsibility to open kunit for output after
having
completed the pakset calls:
OPEN(file=myfile, unit=kunit, form='unformatted',
access='direct', recl={50+nx*ny})
The individual data records are packed and written by a call to
PAKREC, once for each variable at each level. The
routine
calculates the record offset from the index record according to the
variable and level information provided in
the arguments and writes
the record according to the order specified in metdata.cfg.
The data can be supplied in any
order. Note that although the level
indicator (LL) goes from 1 to the number of levels, one is
subtracted before it is
written to the 50 byte header to be
consistent with the definition of surface data to be at level "0".
All the records in a
time period may be initialized according to
the value of the kini flag. Initialization fills in the time
variable for all
records and assigns the variable identification
field as null.
CALL PAKREC (kunit,rvar,cvar,nx,ny,nxy,kvar,iy,im,id,ih,mn,ic,ll,kini)

kunit - integer unit number of the defined file

rvar - input array of real*4 data values

cvar - character*1 array of packed data values

nx,ny - integer horizontal grid dimensions

nxy - integer product nx*ny and length of cvar

kvar - character*4 descriptor of variable being written

iy,im - integer year and month

id,ih - integer day and hour

mn - integer minutes (usually 0)

ic - integer forecast hour (hours from initialization)

ll - integer level indicator (1 to NZ)

kini - integer initialization flag (0-no; 1-yes)

When all the data records for a time period have been written,
it is necessary to close that time period by writing its
index
record:
CALL PAKNDX(kunit)
At this point your program can return to PAKREC if data
records for additional time periods are to be added to the
file.
The key to the process is creating the proper configuration
file for the data set you want to create. Some of the sample
data
decoders provided dynamically configure the packing configuration
file based upon the command line input
information. A sample metdata.cfg file for NOAA's global model output is
shown below. An extract of the global onedegree latitude-longitude
GRIB model data have been interpolated to a 100 km resolution
Lambert Conformal
projection 100x100 point grid centered about 45N
90W. The configuration file format is such that the first 20

characters are a dummy identification field followed by the

data.
Example Meteorological Packing Configuration File
Col 1 (A20) .... Col 21 (A4,2I4,12F10,3I4)

Data Source........ GFSX

Grid Number........ 99

Z-Coordinate....... 2

Pole Latitude...... 45.0

Pole Longitude..... -90.0

Reference Latitude. 45.0

Reference Longitude -90.0

Reference grid size 100.0

Orientation........ 0.0
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Tangent Latitude... 45.0

Synch point X...... 50.5

Synch point Y...... 50.5

Synch Latitude..... 45.0

Synch Longitude.... -90.0

Reserved........... 0.0

Number X points.... 100

Number Y points.... 100

Number of Levels... 16
Format: F6.,I3,(1X,A4)

Level 01:.0000 6 PRSS MSLP TPP6 U10M V10M T02M

Level 02:1000. 6 HGTS TEMP UWND VWND WWND RELH

Level 03: 975. 6 HGTS TEMP UWND VWND WWND RELH

Level 04: 950. 6 HGTS TEMP UWND VWND WWND RELH

Level 05: 925. 6 HGTS TEMP UWND VWND WWND RELH

Level 06: 900. 6 HGTS TEMP UWND VWND WWND RELH

Level 07: 850. 6 HGTS TEMP UWND VWND WWND RELH

Level 08: 800. 6 HGTS TEMP UWND VWND WWND RELH

Level 09: 750. 6 HGTS TEMP UWND VWND WWND RELH

Level 10: 700. 6 HGTS TEMP UWND VWND WWND RELH

Level 11: 600. 6 HGTS TEMP UWND VWND WWND RELH

Level 12: 500. 6 HGTS TEMP UWND VWND WWND RELH

Level 13: 400. 6 HGTS TEMP UWND VWND WWND RELH

Level 14: 300. 6 HGTS TEMP UWND VWND WWND RELH

Level 15: 200. 6 HGTS TEMP UWND VWND WWND RELH

Level 16: 100. 6 HGTS TEMP UWND VWND WWND RELH

It is important that the information contained in this file is
correct because it not only controls the writing of the packed

meteorological data file, but much of the information is written

into the index record of each time period. The model
decodes this
information to set up the internal processing of the meteorological
data. Starting with HYSPLIT V4.5, the
model is also capable of
using meteorological data on a latitude-longitude grid. Previous
versions were limited to data
on a conformal map projection. Data
on a regular latitude-longitude grid still need to be converted to
the ARL packed
format. Modifications to the packing configuration
file required to support a latitude-longitude grid are noted below.
A
complete description of metdata.cfg format follows:
Description of the Meteorological Packing Configuration File
Record 1 consists of a four-character string that
identifies the source of the meteorological data. This string will
be
passed through to many of the output graphics.
Record 2 is an optional integer identification of the
meteorological data grid. It was used extensively in previous

meteorological data file formats. It is not used in Hysplit4

applications.
Record 3 is an integer number that identifies the
vertical coordinate system. Only four coordinate types are
recognized:
1-pressure sigma; 2-pressure absolute; 3-terrain sigma;
4-hybrid sigma.
Records 4 & 5 identifies the pole position of the
grid projection. Most projections will either be defined at +90 or
-90
depending upon the hemisphere. The longitude would be the point
180 degrees from which the projection is cut. LatLon Grids
only: contains the latitude and longitude of the grid point
with the maximum grid point value. Note that latlon grids grids
should be defined with reference to the dateline.
Records 6 & 7 is the reference position at which the
grid spacing is defined. Lat-Lon Grids only: contains the
grid
spacing in degrees latitude and longitude.
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Record 8 is the grid spacing in km at the reference

position. Lat-Lon Grids only: a value of zero signals that
the grid is a
lat-lon grid.
Record 9 is the grid orientation or the angle at the
reference point made by the y-axis and the local direction of
north.
Lat-Lon Grids only: value always = 0.
Record 10 is the angle between the axis and the surface
of the cone. For regular projections it is equal to the latitude at

which the grid is tangent to the earth's surface. A polar

stereo-graphic grid would be tangent at either 90 or -90, while a

Mercator projection is tangent at 0 latitude. A Lambert Conformal

projection would be in between the two limits. An
oblique
stereo-graphic projection would have a cone angle of 90. Lat-Lon
Grids only: value always = 0
Records 11 & 12 are used to equate a position on the
grid with a position on the earth as given in the following two

records:
Records 13 & 14. In this example, the position
indicated is the center of the grid located over the North Pole.
Any
position is acceptable. It need not even be on the grid.
Lat-Lon Grids only: contains the latitude and longitude of the
1,1
position grid point.
Record 15 is not currently used.
Records 16 & 17 identify the number of grid points in
each direction.
Record 18 is the number of levels in the vertical,
including the surface level.
Record 19, through the number of levels, identifies the
height of each level in appropriate units according the definition

of the vertical coordinate, the number of variables at that level,

and the four character identification string for each
variable. The
height units are as follows for each coordinate:

1-sigma (fraction)

2-pressure (mb)

3-terrain (fraction)

4-hybrid (mb: offset.fraction)

Decoding Meteorological Data Files
One may want to develop other applications for HYSPLIT compatible meteorological data files. For these situations,
some
lower-level routines are provided in the source code library. The
key to reading the meteorological files is
decoding the index
record. The format for this record is given below. Complete
descriptions are similar to the variables
in the discussion
above.
FORMAT DESCRIPTION
(A4) Data Source
(I3) Forecast hour (>99 the header forecast hr = 99)
(I2) Minutes associated with data time
(12F7) 1- Pole Lat, 2- Pole Lon, 3- Tangent Lat, 4- Tangent Lon, 5- Grid Size, 6- Orientation, 7- Cone Angle, 8Xsynch point, 9- Ysynch point, 10- Synch point lat, 11- Synch point long, 12) Reserved
(3I3) 1) Number x points, 2) Number y points, 3) Number levels
(I2) Vertical coordinate system flag
(I4) Length in bytes of the index record, excluding the first 50 bytes
LOOP through the number of data levels
(F6) height of the first level

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(I2) number of variables at that level

LOOP through the number of variables
(A4) variable identification
(I3) rotating checksum of the packed data
(1X) Reserved space for future use
Once the index record has been read and decoded you have
sufficient information to read and decode the data records. A
data
un-packer is provided to convert the packed character*1 array to a
real*4 array. It can also be used to extract a subgrid from the
full domain through specification of the sub-grid lower left
corner:
CALL PAKINP (rvar,cvar,nx,ny,nx0,ny0,lx,ly,prec,nexp,var1,ksum)

rvar - real output array of integer dimensions lx,ly

cvar - character*1 packed input array of length nx*ny

nx,ny- integer dimensions of the full grid

nx0 - integer sub-grid position of left edge in nx units

ny0 - integer sub-grid position of lower edge in ny units

lx - integer first dimension of sub-grid length

ly - integer second dimension of sub-grid length

prec - real precision of packed data array

nexp - integer scaling exponent of packed data array

var1 - real value of array at position (1,1)

ksum - integer rotating checksum of packed data array

If the entire grid is to be unpacked then nx0=ny0=1 and
nx=lx, ny=ly. The checksum (ksum) that is
returned should be
compared with the corresponding value in a table
generated from reading the index record. If you are not going to

compare the checksum, set ksum = -1, this will save a little
computer time. Due to the sub-grid option the checksum
cannot be
computed in the regular unpacking loop, but requires a second pass
through the data. The checksum pass is
enabled when ksum=0.
It will then return a non-zero value. If you don't reset it to
zero, no further checksums will be
computed.
If you want to create your own packed data by converting a
real*4 array to the character*1 packed data array use the

following:
CALL PAKOUT(rvar,cvar,nx,ny,nxy,prec,nexp,var1,ksum)
Although the structure of the packed data may seem complex,
unpacking is a very simple process, the basic elements of
which are
summarized in the Fortran code shown below. The value of each
element is the sum of the initial value and
the difference stored
in that element location.
SUBROUTINE UNPACK(CPACK,RVAR,NX,NY,NXY,NEXP,VAR1)

CHARACTER*1 CPACK(NXY)

REAL*4 RVAR(NX,NY)

SCALE=2.0**(7-NEXP)

VOLD=VAR1

INDX=0

DO J=1,NY

DO I=1,NX

INDX=INDX+1

RVAR(I,J)=(ICHAR(CPACK(INDX))-127.)/SCALE+VOLD

VOLD=RVAR(I,J)

END DO
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VOLD=RVAR(1,J)

END DO

RETURN

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Trajectory / Help (S260)

Trajectory / Help
The trajectory menu tab is composed of five main sections:
setting up the simulation, executing the model, displaying
the
trajectory, converting the graphic to other formats, and
running special simulations. The model is configured and

executed through the menu and results displayed. However for

experienced users, each component could be run
independently from the
command line and the CONTROL
file could be created using any text editor.
In the Trajectory Setup menu the entire purpose of the GUI is to configure the model's input CONTROL
file. This is a
text file that configures the simulation parameters.
Once the input parameters are set to their desired value, the model
is
executed from the Run Model menu
tab. When complete, the output window is closed and the
Trajectory Display menu
is used to draw and
display the trajectory from the endpoints output
file. The Special Runs menu is used to
configure
several different customized simultaneous multiple trajectory
simulations.
For inexperienced users, a review of the Quick Start Help is highly suggested, which goes through the trajectory
computation step-by-step using the example meteorological data file.

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Trajectory / Quick Start Help (S261)

Trajectory / Quick Start Help

After the initial installation, the model will be configured
to run the example case discussed in more detail below. The
"Quick
Start" menu tab can be used to run any simulation in one-step. The
last configuration will be used for the
simulation. The "Quick
Start" menu brings up a global map with the current source location
shown as a blue dot. A
"right-click" of the mouse button will write
that source location to the control file, click Yes to exit
the window, which
will close the map, run the model simulation, create the output file, and display the graphics. A "left-click" of
the
mouse button will set a new source location. A "left-click-hold-drag-release" will define a new "zoomed" domain
and
the map will be redrawn. An "exit" from the window's menu bar
will close the map without updating the control file or
running the
model. For more detailed simulation configurations, follow the
steps below.
The easiest way to run the model is to use the GUI menu to
create the model's input CONTROL file. For the purposes of

this demonstration appropriate meteorological files are provided.

If for some reason the menu system is not available,
perhaps
because Tcl/Tk was not
installed, the Control file can be created
manually
Step 1 - start the GUI menu system using
\working\hysplit4.tcl or the desktop shortcut to
Hysplit4. A widget will appear
with the HYSPLIT
graphic and three button options: Menu, Help and
Exit.Click on Menu tab.
Step 2 - The four main menus of the Hysplit4 GUI will
appear: Meteorology,
Trajectory,
Concentration, and Advanced.

An additional small widget underneath the main menu gives the

current Hysplit4 version information. Do not delete
this widget as
it will terminate the GUI. It provides the reference frame for the
model's standard output and messages.
Click on the
Trajectory tab.
Step 3 - Five options appear under this item: Setup Run,
Run Model,
Display,
Utilities, and
Special Runs. Normally
these are run in sequence, however any item can be selected
and run if the appropriate input files were created during a
previous
simulation. Click on the Setup tab.
Step 4 - Setup Run is used to enter the
basic model simulation parameters: the starting time of the
calculation; starting
location in terms of latitude, longitude, and
height; the run-time or duration of the trajectory calculation; and
the names
and locations of all required files. When modifications
to this menu are complete, click on Save. However for this

example, you will use the Retrieve option

for predefined configurations, so do nothing here and go on to
Step 5.
Step 5 - The example calculation is configured by
clicking on Retrieve and then entering the
text: sample_traj, which
is the name of the example
simulation control file that was created for this demonstration.
Then click on OK. After the
data entry widget is closed, click on Save and the setup menu will
close.
Step 6 - Click on Run Model, which first copies the setup configuration (default_traj) saved in
the previous step, to the
model's input CONTROL file. The
model calculation is then started. A series of messages will appear
on standard
output text window showing the progress of the calculation.
When the simulation is completed, the trajectory endpoints output file
is ready to be converted for graphical display. Under some operating
systems, the standard output
widget will not show any output until the
end of the calculation and the Trajectory menu items will be locked
until the
calculation completes.
After completion click on Exit to close the window.
Step 7 - Selecting Display will run a special program that converts the text file of trajectory
end-point positions into a
high quality Postscript
file (trajplot.ps) suitable for printing. The conversion widget
provides options for the frequency
of the labels on the trajectory,
a variable zoom factor, and color or black and white graphics options. If
the Postscript
viewer (Ghostscript)
has been installed and associated with the .ps file suffix, then it will be
invoked by the GUI. If the
viewer does not automatically open, it may be necessary to manually edit ../guicode/hysplit4.tcl to change the directory

location associated with the program gsview32.exe. After clicking on

Execute Display, the following graphic will
appear in the Ghostview window:

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Trajectory / Saving and Retrieving (S211)

Trajectory / Saving and Retrieving

The trajectory and concentration
setup menus for the CONTROL file permit a Save As or Retrieve
option. Each of these
menus is shown in the panel below. After a simulation has
been configured, run, displayed, and assuming that the
results are satisfactory
and no more changes are required, then go back to the setup menu tab and Save As
the control
file by giving it a unique name, such as newname_traj in the
example below. There are no restrictions on the naming
convention. If the simulation
is to be rerun, perhaps with some minor variation, the Retrieve option is used
to load those
values back into the setup menu.

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Trajectory / Run Model (S220)

Trajectory / Run Model

Once the Trajectory Setup menu has been
closed with the Save button, the changes to the simulation
parameters are
copied to default_traj. Clicking on the
Run Model menu tab first copies default_traj
to CONTROL and then runs the
trajectory model executable,
hyts_std{.exe}. The executable, by default, attempts to open a
file named CONTROL to
read all the required input
parameters. If not found, the model will prompt to standard output
for values from standard
input. This condition should not occur
running the model through the GUI. When the model execution starts,
output
messages are written to a special window, an example of
which is shown in the illustration below:

Successful completion of a simulation will show a similar

message. Additional run-time diagnostic messages and other
error
messages are always written to a file called MESSAGE. This
file may be viewed through one of the Advanced

Menu tabs. Depending upon the nature of the error message,

perhaps a failure in the model initialization process, error

messages may also appear in above window. Once the model has
completed, press Exit to close the window.

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Trajectory / Display / Trajectory (S230)

Trajectory / Display / Trajectory

The trajectory model generates a text output file of end-point
positions. The end-point position file is processed by

trajplot to produce the Postscript display file.

Trajplot can be accessed through the GUI or run directly
from the
command line. The
display program has a variety of command line options, most of
which are available through the
GUI. There is a one-to-one
relationship between GUI options, an example of which is shown
below, and the command
line options. There are several features
particular to the GUI. First the Trajectory Display menu
will not open unless the
Trajectory Setup menu was first
opened and Saved. This procedure sets all the GUI parameters
to their default_traj
values. These are the values shown in
the Display menu. Normally the map projection is computed
automatically based
upon the location and length of the trajectory.
However some trajectory combinations may give no maps or improperly

scaled maps. In these situations one would want to over-ride the

default projection and try forcing a selection.

Trajplot Command Line Options

The Postscript conversion program trajplot reads the
trajectory endpoints output file, calculates the most optimum map

for display, and creates the output file - trajplot.ps. When

executed from the command line, there are several Unix style

command line options. There should be no space between the option

and any arguments: trajplot -[options (default)]
-a[GIS Output: 0-none, 1-ESRI Generate, 3-Google Earth]
Selecting the ESRI Generate format output creates an ASCII text file for each
output time period that consists of

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the value and latitude-longitude points along each trajectory. This file can be converted to an ESRI Shapefile or
converted for other GIS
applications through the utility menu "GIS to Shapefile. The view checkbox would be
disabled to do just the GIS conversion without opening the Postscript viewer. Selecting Google Earth will create
a compressed file (*.kmz) for use in Google Earth; a free software package to display geo-referenced
information in 3-dimensions. You must have the free Info-Zip file compression software installed to compress
the Google Earth file and associated graphics.
-e[End hour to plot: #, (all hours)]
-f[Frames: (0)-all frames in one file 1-one frame per file]

= 0 - all files plotted on one frame

= 1 - one input file per output frame

-g [Circle overlay: ( )-auto, #circ (4), #circ:dist(km)]

= {blank} - draws four distance rings about source point, automatically scaled

= {#} - draws the indicated number of rings about the source point

= {#1}:{#2} - draws the number {#1} of rings about the source point each {#2} kilometers apart. In the special
case where #1 is zero, the rings are not drawn, but the size of the plot is scaled as if one ring of radius {#2} is to
be drawn.
-h [Hold map at center lat-lon: (source point), lat:lon]

= latitude:longitude - forces the map center to be at the selected location instead of the source point. In
conjunction with the -g0:{km} option it is possible to create a constant map projection for each execution.
-i[Input files: name1+name2+name3+... or +listfile or (tdump)]

= tdump - default file name when the -i option is undefined.

= {user defined file name}

= {name1+name2+...} - to overlay multiple tdump files on the same plot based upon file name1 plot limits.
= +filename - filename is a file of filenames to be plotted following the same convention as the previous
argument (limit <=5000 files).
-j[Map background file: (arlmap) or shapefiles.(txt|suffix)]

= arlmap - default ASCII file

= shapefiles.(txt|suffix) - file of shapefile names

-k[Kolor: 0-B&W (1)-Color, N:colortraj#1,...colortraj#N]

= 0 - for black and white output

= 1 - for color differentiation of multiple trajectories

= N - 1=red,2=blue,3=green,4=cyan,5=magenta,6=yellow,7=olive
-l[Label interval: -12, -6, 0, (6), 12, ... hrs]

= 0 - for no labels along the trajectory

= 6 - for labels every 6 hours

= 12 - for labels every 12 hours

= {X} - positive at synoptic times

= {-X} - negative with respect to traj start

-L[LatLonLineLabels]

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= 0 - none

= 1 - auto

= 2:tenths - at interval specified

-m[Map projection: (0)-auto 1-polar 2-lambert 3-mercator 4-CylEqu]
-o[Output file name: (trajplot.ps)]

= trajplot.ps is the default Postscript output file name, otherwise it may be {user defined}.
-p[Process file name suffix: (ps) or process ID}
-s[Symbol at trajectory origin: 0-no (1)-yes]
-v[Vertical: 0-pressure (1)-agl 2-isentropic 3-meteorology 4-none]

= 0 - The vertical trajectory plot coordinate is in hPa (absolute pressure units).

= 1 - The vertical trajectory plot coordinate is meters above ground level.

= 2 - An isentropic coordinate display requires the trajectory to have been

run in those coordinates.

= 3 - Forces the display of one of the selected meteorological

variables along the trajectory rather than a
trajectory vertical
position coordinate. The meteorological variable is selected in the
"Trajectory" tab of the
Advanced Configuration
menu. Only one meteorological variable can be selected for display. If
multiple
variables are selected, then only the last variable will be
plotted.

= 4 - No vertical projection drawn.

-z[Zoom factor: 0-least zoom, (50), 100-most zoom]

= 50 - for standard resolution maps.

= 100 - for high resolution maps (maximum zoom)

Additional Map Label Customization
Many of the Postscript graphics programs have label information
that can be customized to some extent. This is
accomplished by
placing a file called Labels.cfg in the startup directory
which contains the following valid entries (all
in single quotes
terminated by &) replacing the new string with the desired
text. A sample file called Labels.bak may be
found in the
relevant directory. Not all label strings are valid with every
plotting program. For instance with trajplot,
only the title
entry would be used to replace the top label line of the plot.

'TITLE&','NATIONAL WEATHER SERVICE&'

'MAPID&','PROBABILITY&'

'LAYER&','BOUNDARY LAYER AVERAGE&'

'UNITS&','BQ&'

'VOLUM&','/M3&'
Additional supplemental text may be added at the bottom of the
graphic by creating a file called MAPTEXT.CFG, also
to be
located in the startup directory. This is a generic file used by
all plotting programs but each program will used
different lines in
its display. The file can be created and edited through the Advanced menu tab.
Standard ASCII Map Background File
By default, all mapping programs use the same text map background file,
arlmap, which normally would be located in
the ../graphics
directory. However, all graphics programs first search the local start
directory (../working if running the
GUI), then the ../graphics
directory. Customized map background files can be read instead of the default
file for
specialized applications. Some higher resolution map background
files are available from the HYSPLIT download web
page. These different map files may be accessed
implicitly by putting them in the "../working (the startup directory), or

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explicitly through the GUI by entering the name of the customized

map background file. The map background file
format consists of
three or more records per graphic line with the following format:

2I5 - line number, number of latitude-longitude points in the line

10F6.2 - latitude points in line

10F7.2 - longitude points in line

ESRI Shapefile Map Background Files
Another mapping option would be to specify a special pointer file (origianlly
called shapefiles.txt, but now a suffix other
than "txt" is permitted) to replace the map background file arlmap in
the -j command line option (see above). Note jshapefiles... rather than
-j./shapefiles... is required. This file would contain the name
of one or more shapefiles that can
be used to create the map background.
The line characteristics (spacing, thickness, color) can be specified for
each
shapefile following the format specified below:

Record format: 'file.shp' dash thick red green blue

file.shp = /dir/name of input shapefile in quotes

dash = {0} for solid; {dashes}/in; <0 color fill

thick = line thickness in inches (default = 0.0)

Red Green Blue = RGB values (0.0 0.0 0.0 is black)

Record example for default: 'arlmap.shp' 0 0.005 0.4 0.6 0.8

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Trajectory / Display / Frequency (S231)

Trajectory / Display / Frequency

Multiple trajectory files can be displayed by creating an arbitrary grid over the computational domain and then counting
the number of trajectory intersections over each grid cell and normalizing by the total number of trajectories (or
endpoints, as discussed in the following). A trajectory may intersect a grid cell once or multiple times (with residence
time options 1, 2, or 3). With the default residence time (RT) option (0), the number of trajectories that intersect each
grid cell are divided by the total number of trajectories. With RT=1, the number of endpoints in each grid cell are
divided by the total number of trajectories (in this case, there can be values over 100%). With RT=2, the number of
endpoints in each grid cell are divided by the total number of endpoints. With RT=3, the number of endpoints in each
grid cell are divided by the maximum number of endpoints in any cell. Each trajectory is defined by one output file
which is only permitted to contain one trajectory. Trajectory output file names begin with the base name defined in the
setup menu tdump and are then followed by some arbitrary identification text (such as the date) that is created by the
Run Daily menu option. The trajectory endpoint files should reside in the working directory. The first step in the
processes is to create a file of trajectory file names which will always be called INFILE. The text entry box defines the
trajectory base name which is treated as a wildcard string when the filenames are searched and added to the contents of
INFILE. This file may be manually edited to remove any trajectory files that are not required for the frequency analysis.
Then select the grid resolution according to the scale of the desired result. Too fine a grid with too few trajectories can
result in poorly contoured display. The gridded binary output file is in the HYSPLIT concentration format. The
concentration plotting routine is used to display the trajectory frequency results and hence some of the label options are
inconsistent with this particular application. The trajectory frequency results could be exported to an ASCII file using
one of the concentration convert utility options or displayed using one of the GIS formats.

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Trajectory / Utilities / Endpoints to IOAPI (S243)

Trajectory / Utilities / Endpoints to IOAPI

This menu calls a utility program to convert the HYSPLIT ASCII trajectory endpoint file to the IOAPI ID_referenced
data format. Multiple trajectories and meteorological data values along the trajectory are supported.
The conversion
program is currently only available on UNIX or LINUX systems and will convert all the endpoints for one or
more
trajectories in a file in one pass. The maximum number
of trajectories and variables per trajectory are subject to

compilation limits. The data files follow no specific naming

convention and any input or output file name may be
selected in the menu.

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Trajectory / Special Runs (S253)

Trajectory / Special Runs

The Special simulations menu tab is required because
certain options may require a different executable file,

modifications to the Control file that are not supported by the

GUI, or interactions with other items under the Advanced
Menu tab. More information is provided
below for each special simulation. Some Special Simulations
may not be
available for all operating systems.
Ensemble
The ensemble form of the model automatically starts multiple
trajectories from the selected starting point. Each member
of the
trajectory ensemble is calculated by offsetting the meteorological
data by a fixed grid factor as defined in the
Advanced Trajectory Configuration tab. The
default offset is one meteorological grid point in the horizontal
and 0.01
sigma units in the vertical. This results in 27 members for
all-possible offsets in X, Y, and Z. After the model
calculation
has completed, use the normal Trajectory
Display tab to view the results. Because the offset is computed
in
both directions in the vertical from the starting location, a
starting location at the ground would not provide an optimal

configuration for this type of simulation. The default vertical

offset is about 250 m. Therefore this should be the
minimum
starting height for ensemble trajectories, unless the default
offset is changed in the namelist file. An example
of the ensemble
trajectory using the example meteorological data is shown in the
illustration below.

Matrix
The matrix calculation is a way to set up the CONTROL
file for multiple starting locations that may exceed the GUI
limit
of 6 under the Trajectory Setup tab.
Hundreds or thousands of starting points may be specified. The
Run Matrix
tab just executes the model using a
CONTROL file that is dynamically created from the
default_traj file using a special
program called
latlon that is called from within the GUI. The program reads
a CONTROL file that is required to have

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Trajectory / Special Runs (S253)

three starting
locations and then re-writes the same file with multiple locations.
The multiple starting locations are
computed by the latlon
program based upon the number of starting points that fall in the
domain between starting point
1 and starting point 2. Each new
location is offset by an amount equal to the difference between
starting locations 1 and
3. An example would be more illustrative.
If the original control file has three starting locations: #1 at
40N, 90W, #2 at
50N, 80W, and #3 at 41N, 89W; then the matrix
processing results in a CONTROL file with 121 starting locations,
all
one degree apart, all between 40N 90W and 50N 80W.

The reason for this approach is that only the CONTROL

file is modified and not default_traj. The GUI never reads

CONTROL, therefore the file does not need to conform to the

GUI limits. The final matrix trajectory using the example

meteorological data for this configuration is shown in the

illustration below.

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Trajectory / Special Runs (S253)

Multiple Trajectories in Time

In the normal simulation configuration, all trajectories start
at time that was defined in the first line of the Trajectory
Setup menu. Trajectories starting at a
different time would require an independent simulation. However,
there is
shortcut to permit the calculation of multiple
trajectories in time from the same starting location. Setup the
simulation
for a single trajectory then go to the Advanced Trajectory configuration menu.
Under the Temporal Trajectory Restart
line, edit the
temporal interval in hours from the default of zero (no restarts)
to the desired value. For example, if this
value is set to 6 hours
(corresponding to NSTR=6 in the namelist file
SETUP.CFG), then in addition to the normal
trajectory that
starts at the initial time, new trajectories would be started every
six hours for the duration of the
simulation. The result of this
simulation, using the example meteorological data, is shown in the
illustration below.

Multiple Trajectories in Space and Time

The standard setup options of the GUI permit the calculation of
multiple trajectories in space or height by simply
specifying new
locations in the CONTROL file. A variation of that procedure
was shown above with respect to setting
up a
matrix of starting locations. The model also permits the start
of new trajectories at different locations along an
existing
trajectory. This can be considered a special case of multiple trajectories-in-time because when starting a
new
trajectory along an existing trajectory, the new starting
location differs in time and space from the original trajectory. In

this variation, new trajectories are started at multiple levels at

the temporal restart interval. The multiple restart levels
are
assumed to be the same multiple starting heights specified in the
original setup and therefore the number of restart
heights must
equal the number of starting locations. Go the Advanced Configuration menu and setup the
example as in
the previous case to restart trajectories every 6
hours. Then change the Number of Levels parameter from its
default
value of zero (no new trajectories) to the number of new
trajectories will be started. For example, set the number of
levels
to 2 (sets the NVER=2 parameter in the SETUP.CFG
namelist file). The number of starting locations should also
be set
to two, at the same location, but with release heights of 10 and
1500 m. Two trajectories, at 10 and 1500 m, will
start every 6
hours. The result is shown in the illustration below.
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Daily
Another way to generate multiple trajectories
in time is to use the automated daily trajectory menu option to create an

endpoints file for each starting time. This differs from the previous approach where all trajectory endpoints were
written to one output file. Using this menu the model is executed in a script with a unique output
file name for each
simulation. This method is required for trajectory
clustering.
Clustering
Multiple trajectories may be aggregated into groups to minimize the
difference between trajectories in that group using

clustering methods. The use of the clustering program requires one

endpoints file for each trajectory. Normally a
minimum of 30 trajectories
is recommended for clustering.
Geo-Location
Multiple trajectories can be run from sampling data to determine the
highest frequency of upwind directions associated
with the non-zero
measurements. The geo-location menu automatically
configures the trajectory control file and runs
the model based upon a data
file of measured values such that a trajectory is started from each location
every hour that
there is a non-zero measurement.

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Trajectory / Special Runs / Daily (S254)

Trajectory / Special Runs / Daily

This special menu can be used for either trajectory or concentration
simulations to run automated multiple simulations
for one month. The
script will replace the starting day and hour in the CONTROL file with
values generated in the
script from the menu shown below. In this
example the model will be run four times a day (at 0, 6, 12, and 18
UTC) for
each day from 1 through 31. Note that the start-hour field
is just treated as a string and can be replaced with any
sequence of
starting hours. The model output files are named according to the fields
set in the control file and namelist
file menus, but are appended with
the four digit day and hour field. This approach differs from a single
simulation with
multiple starting times in that each simulation is
independent and a new output file is created for each run.

The model should be configured and run for the first simulation time
through the standard run menu to insure that the
simulation is configured
correctly. If part of the simulation requires meteorological data from the
previous month or the
next month, these should be included in the base
simulation test.
At first it will appear that after pressing the Execute Script
button that nothing is happening. However, as each day's
simulation is
completed, the Start Day entry box increases in value until its value
matches the End Day, at which time
the script is completed. Note that
concentration simulations are much slower than trajectories and it may
take a while
before the start day field is updated.
The dispersion daily run menu contains an additional entry shown below
that determines how the file name is calculated
for each run. The default
approach is the same as with the trajectory calculation, where the day and
hour is appended to
the base name. Another option is to name the files sequentially using a three digit number. Using sequential numbering,
the
output files can be processed by the probability display programs used in conjunction with the ensemble calculation.

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Trajectory / Special Runs / Clustering (S255)

Trajectory / Special Runs / Clustering

The Trajectory Cluster Analysis window has the series
of tasks necessary for running a trajectory cluster analysis. This
differs
from most, if not all, other HYSPLIT GUI windows that only run one program or
do one task. Given a set of
trajectories beginning at one location, the
cluster analysis will objectively result in sub-sets of trajectories, called

clusters, that are each different from the other sub-sets. The program will
usually produce at least one possible
outcome set of clusters. If more than one outcome is given, the user must then subjectively choose one for the final

result.
Description of clustering process:
Initially, total spatial variance is zero. Each trajectory is defined to be a cluster, in other words, there are N trajectories
and N clusters. For the first iteration, which two clusters (trajectories) are paired? For every combination of trajectory
pairs, the cluster spatial variance (SPVAR) is calculated. SPVAR is the sum of the squared distances between the

endpoints of the cluster's component trajectories and the mean of the trajectories
in that cluster. Then the total spatial
variance (TSV), the sum of all the cluster spatial variances, is calculated. The pair of clusters combined are the ones

with the lowest increase in total spatial variance. After the first iteration, the
number of clusters is N-1. Clusters paired
always stay together.

D = distance between a trajectory endpoint and the corresponding cluster-mean endpoint

SPVAR = SUM(all trajectories in cluster) [SUM(all trajectory endpoints) {D*D} ]

TSV = SUM(all SPVAR)

For the second iteration, which two clusters are paired? The clusters are either individual trajectories or the cluster of
two trajectories that were initially paired.
Again every combination is tried, and the SPVAR, and TSV for each is
calculated. The two clusters combined are the ones that result in the lowest increase in TSV. The percent change in
TSV and number of clusters (N-2) are written to a file.
The iterations continue until the last two clusters are combined, resulting in
N trajectories in one cluster.
In the first several clustering iterations the TSV increases greatly, then for much of the clustering it typically increases at
a small, generally constant rate, but at some point it again increases rapidly, indicating that the clusters being
combined
are not very similar. This latter increase suggests where to stop
the clustering and is clearly seen in a plot of percent
change in TSV vs. number of clusters, where the number of clusters are decreasing to the right on
the plot. The iterative
step just before (to the left of on the plot) the large increase in the change of TSV gives the final number of clusters.

Typically there are a few "large" increases.

How to run the cluster analysis:
The window shown is from the Run Example case. For Run Standard, the Run_ID is "Standard", Hours to cluster is
"36", the Endpoints folder (directory) is "c:/hysplit4/cluster/endpts", and the Number of clusters is set to "1". Run
Example performs cluster analysis on the example set of 12-h duration forward trajectories. Note one of the trajectories
has a duration less than 12 hours and so it is not clustered. The number of trajectories in the example set is small to
keep the cluster section of the HYSPLIT PC package a reasonable size.

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Step 1. Inputs.
Run ID - A label to identify each run. The label ends at the first blank space. The other numeric inputs may be
part of the label. For instance if trajectories during 2004 from Ohio were clustered,
the Run_ID could be
Ohio_2004. If you used 48-h trajectories, hourly endpoints, and every other trajectory, a label of
Ohio_2004_48_1_2 could be used. If you later decided to only use the first 36-h of the trajectory
Ohio_2004_36_1_2
might be used.
Hours to cluster - Trajectory durations up to the given hour are used. Must be a positive number. Time is from
trajectory origin whether backward or forward. Trajectories terminating before the given hour will NOT be
included in the clustering.
Premature terminations commonly result from missing meteorology data or the

trajectory reaching the meteorological grid horizontal or top edge. 36 hours is typical.

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Trajectory / Special Runs / Clustering (S255)

Time interval - Identifies which endpoints along a trajectory to use. Typically

every hourly endpoint is used (1).
For long trajectories, skipping endpoints will save
computational time.
Trajectory skip - Identifies which trajectories in a folder to use. A value of 1 means every trajectory will be used;
2 means every other trajectory; 5 every 5th trajectory, etc. Useful with very large sets of trajectories.
Endpoints folder - All trajectory endpoints files containing 'tdump' in their name in this folder will be used for
clustering.
Working folder - Cluster files are written to this folder.
Archive folder - All cluster files may be moved to this folder for archiving or to remove the files from the working
directory. For permanent
archiving, the files need to be moved or renamed since they will be overwritten by files
from subsequent runs.
Projection - Trajectory endpoint latitudes and longitudes are converted to grid points using the specified map
projection in the main cluster program "Run cluster". The projection for the plots is specified separately in Step
3.
Step 2. Run Cluster Program. Possible solutions to the
cluster analysis will be available at the end of this step.
Make INFILE. Trajectories must
have been run previously, such as via TRAJECTORY-Special Simulations Run

Daily. All the trajectory endpoints files need to be in one folder and each must have the name tdump within its
filename. In this
step, a file, INFILE, listing all the tdump files will be created in the working folder.
Note on endpoints files - There can be only one trajectory per file. At least 16 trajectories are needed after
trajectories are skipped, if specified.
Run Cluster The cluster analysis program is run here given the INFILE file, the trajectory endpoints files, and the
above inputs. On a typical PC, a cluster run with 365 trajectories, 36-h
duration, and using every hourly endpoint,
will take a couple minutes. Going
beyond several years of trajectories will result in a run that will take a long

time and/or use much memory. A warning message is given for larger runs,
but there can be hard to tell if a
"large" job fails due to lack of memory and/or is feasible.

For example with 1100 trajectories it may appear not to be running. Try some
intermediate runs - 600
trajectories, 900 trajectories - and note the run time. Add to the number of trajectories as reasonable. Let it run
overnight. If it
takes "too long", increase the "time interval" to say 2 to use every other trajectory
endpoint and/or
set the "trajectory skip" to say 3 to use every third trajectory.
Another option to bypass possible GUI errors is to
run cluster.exe from the command line. To do this, open the "Command Prompt" (for Windows, Start, All
Programs, Accessories), cd to your cluster working directory (e.g.
cd \hysplit4\cluster\working), and run
\hysplit4\exec\cluster.exe. If the file
with the input values CCLUSTER exists in the cluster working directory,

cluster.exe will start running, otherwise you will be prompted for the input values. When done, "exit" the
Command Prompt,
and return to the GUI for the subsequent processing.

The cluster program produces these output files:

CLUSTER trajectory start date/time and endpoints
(tdump) filename for all the trajectories in INFILE; then for
each pass, a
listing of the trajectories in each cluster.
DELPCT the change in total spatial variance of all
the clusters from one pass to the next.
CLUSTERno the filename and trajectory start
date/time of trajectories, if any, not clustered; used to create
cluster
results (CLUSLIST)

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Trajectory / Special Runs / Clustering (S255)

CMESSAGE diagnostics output file

Display plot (optional) shows the percent change in total spatial variance (TSV) for the final
30 iterations. This
data is from the file DELPCT.
Generally there can be seen at least one time when there is a large increase in
the
change of TSV, indicating that different, rather than similar,
clusters are being paired and that the cluster
process should stop before that
occurs.
View possible final number of clusters. Typically a pairing of "different" clusters is indicated by a 30% change in
the
percent change in total spatial variance (see Step 2, Display plot). Runlists the possible final cluster numbers.
If the 30% criterion does not identify any, the 20% criterion may be chosen. The maximum is arbitrarily set to
20 clusters.
Step 3 Get Results. This step may be repeated using
different numbers of clusters. If you exit the GUI, but have not
archived your
results, enter the Run_ID and the Working folder again from Step 1, then continue with Step 3. If you
have already archived the results, but want to try a different number of clusters, manually copy everything from the
archive folder to the cluster working folder, enter the
Run_ID and the Archive and working folders, then enter the
number of clusters, etc.
Number of clusters Enter the final number of
clusters, one of the values listed in Step 2, Run. In general, this will
be a value where the plot from Step 2,Display plot shows a sharp upward turn.
Assign trajectories to clusters "Run" creates a text file listing the trajectory start date/times and filenames in each
cluster
(CLUSLIST_NF, where NF is the final number of clusters). Note
Cluster #0 is for trajectories not
clustered. Depending on the application, this
text file may be the outcome and the plots below may not be
needed.
Display Means produces one map
with the mean trajectory for each cluster (1-NF), given the final number of

clusters, NF. The arbitrary cluster number and percent of trajectories in each
cluster are given.
Display Clusters produces one map for each cluster, showing the
trajectories in each cluster.
Trajectories not usedare those input to the cluster
program, i.e. in the endpoints directory, and at the given skip
interval, that
terminate before the trajectory duration equal to the Step 1, Hours to cluster.
This occurs when the
trajectory reaches the meteorology grid edge or when there
is missing meteorology. Trajectories not used
immediately displays a plot showing the trajectories not used and opens the Trajectory Cluster Display window,
from which the cluster-mean trajectories for the trajectories not used (cluster #0) and all the other clusters may be
displayed. Note the plot showing the trajectories not used must have been previously created in Step 3, Display
Clusters, though it is not displayed there.
Archive All files are moved, not copied, to the given directory. Files created in Step 3 contain the final number of
clusters (NF) in their filename; hence output using various values of NF may be readily archived.

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Trajectory / Special Runs / Geo-Location (S257)

Trajectory / Special Runs / Geo-Location

Summary: This menu is used to configure the model to execute a script to run multiple
iterations of the backward
trajectory calculation for periods that correspond with individual
measured sampling data. The trajectory results can
then be overlaid using the frequency plot
menu option to indicate the most probable source regions. The CONTROL
file should have been
previously defined for a forward calculation that corresponds to the sampling period of the

measured data. The measured data file must be in the DATEM format. The configuration process
is very similar to that
described for dispersion simulations.
Step 1: defines the measured data input used in this series of calculations. The trajectory model is run backward, from
each of the sampling locations, with a trajectory
started (at the beginning, middle, end) for each sampling period with a
non-zero measurement.
Measured values less than or equal to the value in the text entry box are considered to be zero.

Sampling data files are in the ASCII text DATEM

format. The first record provides some general information, the
second record identifies all
the variables that then follow on all subsequent records. There is one data record for each

sample collected. All times are given in UTC.

An example measured data file can be used
with the sample meteorological data to configure multiple trajectory
simulations starting
on 95 10 16 00. Note that the sampling data run from 0600 on the 16th through 1200 on
the 17th,
suggesting at least a 30 h if not 36 h trajectory is required to span the
measurement data domain. First create a
CONTROL file by running a forward simulation for
one trajectory that spans the computational period.
Step 2: creates three CONTROL.{xxx} files for each sampling location with a non-zero measurement at the beginning,
middle, and end of the sampling period using the
dat2cntl program. The CONTROL files are numbered sequentially
from 001 to a maximum of 999. The trajectory output files are labeled using the base name from
the CONTROL file
followed by the sampler ID number and the starting date and time of
the trajectory. A sampler collecting two
contiguous in-time samples will have the
same trajectory computed at the end of one sampling period and the beginning
of the
next sampling period because there will be two different CONTROL files for each.
However, the output file
name will be the same and hence the results will not be
double counted in any statistical analysis. Using the sample
data, running step two
creates 45 CONTROL files from 15 non-zero measurements.
Step 3: sequentially runs the trajectory simulations starting with
CONTROL.001 through the last available control file.
Each simulation uses the
same namelist configuration. Once the calculation has completed, the individual
trajectories
can be gridded and displayed using the trajectory
frequency menu, the results of which are shown below.

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Trajectory / Special Runs / Geo-Location (S257)

In this case the measurement data were created using a forward dispersion simulation from 40N 80W which is near the
maximum point of the trajectory frequency plot, the position of the maximum is also indicated along the left edge plot
label.

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Trajectory / Setup Run / Control File Format (S262)

Trajectory / Setup Run / Control File Format

The trajectory model input control file can be created using
any text editor. However if the GUI is not being used, it
would be
easier to let the model create the initial file based upon standard
output prompts. These are described in more
detail below. When data
entry is through the keyboard (a file named CONTROL is not
found), a STARTUP file is
created. This contains a copy of
the input, and which later may be renamed to CONTROL to
permit direct editing and
model execution without data entry. If
you are unsure as to a value required in an input field, just enter
the forward
slash (/) character, and the indicated default value
will be used. This default procedure is valid for all input fields
except
directory and file names. An automatic default selection
procedure is also available for certain input fields of the

CONTROL file when they are set to zero. Those options are
discussed in more detail below. Each input line is
numbered (only
in this text) according to the order it appears in the file. A
number in parenthesis after the line number
indicates that there is
an input loop and multiple entry lines may be required depending
upon the value of the previous
entry.
1- Enter starting time (year, month, day, hour, {minutes optional})
Default: 00 00 00 00 {00}
Enter the two digit values for the UTC time that the calculation
is to start. Use 0's to start at the beginning (or end)
of the file
according to the direction of the calculation. All zero values in
this field will force the calculation to
use the time of the first
(or last) record of the meteorological data file. In the special
case where year and month
are zero, day and hour are treated as
relative to the start or end of the file. For example, the first
record of the
meteorological data file usually starts at 0000 UTC.
An entry of "00 00 01 12" would start the calculation 36
hours from
the start of the data file. The minutes field is optional but should
only be used when the start time is
explicitly set to a value.
2- Enter number of starting locations
Default: 1
Simultaneous trajectories can be calculated at multiple levels
or starting locations. Specification of additional
locations for certain types of simulations can also be accomplished through the Special Simulations menu tab, or
through manual
editing of the CONTROL file and running the model outside of
the GUI. When multiple starting
locations are specified, all
trajectories start at the same time. A multiple trajectory in time
option is available
through the Advanced
menu through a namelist file parameter setting.
3(1)- Enter starting location (lat, lon, meters)
Default: 40.0 -90.0 50.0
Trajectory starting position in degrees and decimal (West and
South are negative). Height is entered as meters
above ground-level.
An option to treat starting heights as relative to mean-sea-level is
available through the
Advanced menu through a
namelist file parameter setting.
4- Enter total run time (hours)
Default: 48
Specifies the duration of the calculation in hours. Backward
calculations are entered as negative hours. A
backward trajectory
starts from the trajectory termination point and proceeds upwind.
Meteorological data are
processed in reverse-time order.
5- Vertical motion option (0:data 1:isob 2:isen 3:dens 4:sigma 5:diverg 6:msl2agl 7:average)

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Default: 0
Indicates the vertical motion calculation method. The default "data"
selection will use the meteorological model's
vertical velocity fields;
other options include {isob}aric, {isen}tropic, constant {dens}ity, constant internal
{sigma} coordinate, computed from the velocity
{diverg}ence, vertical coordinate remapping from MSL to
AGL, and a special option (7) to spatially average the vertical velocity. The averaging distance is automatically
computed from the ratio of the temporal frequency of the data to the horizontal grid resolution.
6- Top of model domain (internal coordinates m-agl)
Default: 10000.0
Sets the vertical limit of the internal meteorological grid. If
calculations are not required above a certain level,
fewer
meteorological data are processed thus speeding up the computation.
Trajectories will terminate when they
reach this level. A secondary
use of this parameter is to set the model's internal scaling height
- the height at
which the internal sigma surfaces go flat relative
to terrain. The default internal scaling height is set to 25 km but

it is set to the top of the model domain if the entry exceeds 25

km. Further, when meteorological data are
provided on terrain sigma
surfaces it is assumed that the input data were scaled to a height
of 20 km (RAMS) or
34.8 km (COAMPS). If a different height is
required to decode the input data, it should be entered on this
line as
the negative of the height. HYSPLIT's internal scaling
height remains at 25 km unless the absolute value of the
domain top
exceeds 25 km.
7- Number of input data grids
Default: 1
Number of simultaneous input meteorological files. The following
two entries (directory and name) will be
repeated this number of
times. A simulation will terminate when the computation is off all
of the grids in either
space or time. Trajectory calculations will
check the grid each time step and use the finest resolution input
data
available at that location at that time. When multiple
meteorological grids have different resolution, there is an

additional restriction that there should be some overlap between

the grids in time, otherwise it is not possible to
transfer a
trajectory position from one grid to another. If multiple grids are
defined and the model has trouble
automatically transferring the
calculation from one grid to another, the sub-grid size may need to
be increased to
its maximum value.
8(1)- Meteorological data grid # 1 directory
Default: ( \main\sub\data\ )
Directory location of the meteorological file on the grid
specified. Always terminate with the appropriate slash (\
or /).
9(2)- Meteorological data grid # 1 file name
Default: file_name
Name of the file containing meteorological data. Located in the
previous directory.
10- Directory of trajectory output file
Default: ( \main\trajectory\output\ )
Directory location to which the text trajectory end-points file
will be written. Always terminate with the
appropriate slash (\ or /).
11- Name of the trajectory endpoints file
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Trajectory / Setup Run / Control File Format (S262)

Default: file_name
The trajectory end-points output file is named in this entry line.

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Trajectory / Display / Endpoint File Format (S263)

Trajectory / Display / Endpoint File Format

The trajectory model generates its own text output file of
ASCII end-point positions. The trajectory display program
processes
the end-point file. The format of the file is given below:
Record #1

I6 - Number of meteorological grids used in calculation

Records Loop #2 through the number of grids

A8 - Meteorological Model identification

5I6 - Data file starting Year, Month, Day, Hour, Forecast Hour
Record #3

I6 - number of different trajectories in file

1X,A8 - direction of trajectory calculation (FORWARD, BACKWARD)

1X,A8 - vertical motion calculation method (OMEGA, THETA, ...)

Record Loop #4 through the number of different trajectories in file

4I6 - starting year, month, day, hour

2F9.3 - starting latitude, longitude

F8.1 - starting level above ground (meters)

Record #5

I6 - number (n) of diagnostic output variables

n(1X,A8) - label identification of each variable (PRESSURE, THETA, ...)

Record Loop #6 through the number of hours in the simulation

I6 - trajectory number

I6 - meteorological grid number or antecedent trajectory number

5I6 - year month day hour minute of the point

I6 - forecast hour at point

F8.1 - age of the trajectory in hours

2F9.3 - position latitude and longitude

1X,F8.1 - position height in meters above ground

n(1X,F8.1) - n diagnostic output variables (1st to be output is always pressure)

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Concentration / Help (S360)

Concentration / Help
The concentration menu tab is composed of six main sections:
setting up the simulation, executing the model, displaying
the
concentrations, various utility programs for converting the output
to other formats, configuring special simulations,
and simulations
in a multi-processor environment. The model can be entirely
configured and executed through the
menu. However for experienced
users, each component may be run independently from the command
line.
In the Concentration Setup
menu, the entire purpose of the GUI is to
configure the model's input CONTROL file. This is
a text
file that configures the simulation parameters. Once the input
parameters are set to their desired value, the model
is executed
from the Run Standard Model menu tab. When
complete, the output window is closed and Display
Options
menu is used to draw and display the concentration contours from the model's binary concentration output file. The

Special Simulations menu is used to configure

several different customized simultaneous for ensemble applications,

source-receptor matrices, and some simple chemistry simulations.

The Multi-processor tab invokes some of the
same
special simulations but will only run under a multi-processor-
computing environment. Normally this is not an option
available
under MS Windows.
For inexperienced users, a review of the Quick Start Help menu is highly suggested, which goes through
a concentration
computation step-by-step using the example
meteorological data file.

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Concentration / Quick Start Help (S361)

Concentration / Quick Start Help

Upon installation the first time the model will be configured
to run the example case discussed in more detail below.
The "Quick
Start" menu tab can be used to run any simulation in one-step. The
last configuration will be used for the
simulation. The "Quick
Start" menu brings up a global map with the current source location
shown as a blue dot. A
"right-click" of the mouse button will write
that source location to the control file, close the map, run the
model
simulation, create the output file, and display the graphics.
A "left-click" of the mouse button will set a new source
location.
A "left-click-hold-drag-release" will define a new "zoomed" domain
and the map will be redrawn. An "exit"
from the window's menu bar
will close the map without updating the control file or running the
model. For more
detailed simulation configurations, follow the
steps below.
The easiest way to run the model is to use the GUI menu to edit
the model's input CONTROL file. For the purposes of
this
demonstration appropriate meteorological files are provided. If for
some reason the menu system is not available,
the CONTROL
file can be created manually.
Step 1 - start the GUI menu system using the desktop shortcut
Hysplit4 to \working\hysplit4.tcl. A widget will appear

with the HYSPLIT graphic and three button options: Menu, Help Exit. Click on Menu.
Step 2 - The four main menus of Hysplit4 will appear: Meteorology, Trajectory,
Concentration, and the optional

Advanced menu. An additional small widget

underneath the main menu gives the current Hysplit4 version
information.
Do not delete this widget as it will terminate the
GUI. It provides the reference frame for the model's standard
output
and messages and the version number required for updates. Click on Concentration.
Step 3 - Under the concentration menu there are also five
options: concentration setup,
run standard model,

concentration display, utility programs, and special simulations. In general, they should
be executed in sequential order.
Click on Setup Run.
Step 4 - The Setup Run menu brings up similar starting
information requirements as with the trajectory menu.
There are
three additional sub-menus: Pollutant - that can be used set the emission rate, duration, and start time of the
emission;
Grids - to set the location, resolution,
levels, and averaging times of the concentration output grid; and Deposition - to
set the characteristics of each
pollutant. Click on Retrieve, enter name of sample pre-configured control file:
sample_conc, then click on OK. After the data entry widget is closed, click on Save and the setup menu will close.
Step 5 - From the main
concentration menu tab select Run
Model, which copies the setup configuration to the model's
input CONTROL file and starts the model simulation. Messages will appear on standard output showing the progress of
the calculation or after
the calculation has completed. Be patient as concentration calculations
may take considerably
longer than trajectory calculations. Click on Exit to close the message window. At that point the binary
concentration
output file is ready to be converted to a graphical display.
Step 6 - Click on Display / Concentration and then select Contours to run a special program that converts the binary

concentration file to the Postscript file concplot.ps, suitable for

printing. The display widget contains multiple options
for different pollutants (if defined), data grids, levels, and contour options. These are discussed in more detail in the
graphics section. For
this example, accept the defaults and just click on Execute Display.
If the Ghostview Postscript
viewer
has been installed and properly associated with .ps files, then it will be automatically invoked by the GUI. If the
viewer does not open, it may be necessary to manually edit the file hysplit4.tcl for the directory
entry associated with
the program gsview32.exe. The output file can
be printed directly on any Postscript device or printed through

Ghostscript/Ghostview. The 12 hour average air concentration for a one hour release is shown in the illustration below.

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Concentration / Quick Start Help (S361)

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Concentration / Setup Run / Pollutant, Deposition, Grids (S311)

Concentration / Setup Run / Pollutant, Deposition, Grids

There are three menu choices under this tab: Pollutant, Grid, and Deposition. The first permits editing of the
emission
rate parameters, the second defines the concentration
output grid, and the third the deposition characteristics of the

pollutant, if that feature is enabled. This menu is illustrated

below. To edit the parameters for a specific species entry
just
select the appropriate checkbox.

Note that up to 7 pollutant species may be defined by changing

the Num parameter. However, in the current version, the

pollutant and deposition menus must both reference the same number
of species. Multiple species simulations are
calculated
independently, hence there is no computational benefit by doing two
different simulations or combining both
species in one simulation.
The multiple species option is primarily used for chemical
transformation simulations. A
simple example is available from the
configuration menu checkbox of "10% per
hour", which transforms species #1 to
species #2 at a rate of 10%
per hour. The transformation occurs on the same particle and is
discussed in more detail in
the Advanced
Applications section. More complex transformations require a
linkage with compatible external modules.
None are available at
this time for public distribution.

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Concentration / Setup Run / Pollutant Definition (S312)

Concentration / Setup Run / Pollutant Definition

There are four CONTROL file entries, lines 11(1) through
14(4), that correspond with each line of the pollutant menu
shown
in the illustration below.

10- Number of different pollutants

Default: 1
Multiple pollutant species may be defined for emissions. Each
pollutant is assigned to its own particle or puff and
therefore may
behave differently due to deposition or other pollutant specific
characteristics. Each will be tracked
on its own concentration
grid. The following four entries are repeated for each pollutant
defined.
11(1)- Pollutant four Character Identification
Default: TEST
Provides a four-character label that can be used to identify the
pollutant. The label is written with the
concentration output grid
to identify output records associated with that pollutant and will
appear in display
labels. Additional user supplied deposition and
chemistry calculations may be keyed to this identification
string.
12(2)- Emission rate (per hour)
Default: 1.0
Mass units released each hour. Units are arbitrary except when
specific chemical transformation subroutines are
associated with
the calculation. Output air concentration units will be in the same
units as specified on this line.
For instance an input of kg/hr
results in an output of kg/m3. When multiple sources are
defined this rate is
assigned to all sources unless the optional
parameters are present on line 3(1).
13(3)- Hours of emission
Default: 1.0
The duration of emission may be defined in fractional hours. An
emission duration of less than one time-step will
be emitted over
one time-step with a total emission that would yield the requested
rate over the emission
duration.
14(4)- Release start time: year month day hour minute

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Concentration / Setup Run / Pollutant Definition (S312)

Default: [simulation start]

The previously specified hours of emission start at this time.
An entry of zero's in the field, when input is read
from a file,
will also result in the selection of the default values that will
correspond with the starting time of the
meteorological data file.
Day and hour are treated as relative to the file start when month
is set to zero.
Temporal or Area Emission Variations
This menu is only designed to input point source emission
rates. Unless additional input values are provided in the
control
file after each emission location, the same rate will apply to all
defined point sources for the duration of the
emission. When more
complex emission scenarios are required, emission data can be read in from
a file that defines a
diurnal emission cycle for any number of pollutants at any number of locations. If the emission rate is to
vary in time
beyond one diurnal cycle, there is another
input file that can be
defined to set a new rate with each emission
cycle. In
this latter scenario the rate as well as the location may
be changed.
Previous Section of the CONTROL file
Next Section of the CONTROL file
Table of Contents

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Concentration / Setup Run / Grid Definition (S313)

Concentration / Setup Run / Grid Definition

This section is used to define the grid system to which the
concentrations are summed during the integration and
subsequently
for post-processing and display of the model's output. There are 10
entries in the CONTROL file for each
concentration grid that has
been defined. The lines 16(1) through 25(10) correspond with each
of the menu items shown
in the illustration below.

Dispersion calculations are performed on the computational

(meteorological) grid without regard to the definition or
location
of any concentration grid. Therefore it is possible to complete a
simulation and have no results to view if the
concentration grid
was in the wrong location. In addition, very small concentration
grid spacing will reduce the model's
integration time step and may
result is substantially longer simulation clock times.
15- Number of simultaneous concentration grids
Default: 1
Multiple or nested grids may be defined. The concentration
output grids are treated independently. The following
10 entries
will be repeated for each grid defined.
16(1)- Center Latitude, Longitude (degrees)
Default: [source location]
Sets the center position of the concentration sampling grid in
degrees and decimal. Input of zero's will result in
selection of
the default value, the location of the emission source. Sometimes
it may be desirable to move the

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grid center location downwind near

the center of the projected plume position.
17(2)- Grid spacing (degrees) Latitude, Longitude
Default: 1.0 1.0
Sets the interval in degrees between nodes of the sampling grid.
Puffs must pass over a node to contribute
concentration to that
point and therefore if the spacing is too wide, they may pass
between intersection points.
Particle model calculations represent
grid-cell averages, where each cell is centered on a node position,
with its
dimensions equal to the grid spacing. Finer resolution
concentration grids require correspondingly finer
integration
time-steps. This may be mitigated to some extent by limiting fine
resolution grids to only the first few
hours of the simulation.
In the special case of a polar (arc,distance) concentration grid,
defined when the namelist variable cpack=3, the

definition changes such that the latitude grid spacing equals the sector angle in degrees and the longitude grid
spacing equals the sector distance spacing in kilometers.
18(3)- Grid span (deg) Latitude, Longitude
Default: [180.0] [360.0]
Sets the total span of the grid in each direction. For instance,
a span of 10 degrees would cover 5 degrees on each
side of the
center grid location. A plume that goes off the grid would have
cutoff appearance, which can
sometimes be mitigated by moving the
grid center further downwind.
In the special case of a polar (arc,distance) concentration grid,
defined when the namelist variable cpack=3, the
definition changes such that the latitude span always equals 360.0 degrees and the longitude span equals the total
downwind distance in kilometers. Note that the number of grid points equals 360/arc-angle or the total-distance
divided by the sector-distance.
19(4)- Enter grid # 1 directory
Default: ( \main\sub\output\ )
Directory to which the binary concentration output file for this
grid is written. As in other directory entries a
terminating (\)
slash is required.
20(5)- Enter grid # 1 file name
Default: file_name
Name of the concentration output file for each grid. See Section
6 for a description of the format of the
concentration output
file.
21(6)- Number of vertical concentration levels
Default: 1
The number of vertical levels in the concentration grid
including the ground surface level if deposition output is

required.
22(7)- Height of each level (m)
Default: 50
Output grid levels may be defined in any order for the puff
model as long as the deposition level (0) comes first (a
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Concentration / Setup Run / Grid Definition (S313)

height of
zero indicates deposition output). Air concentrations must have a
non-zero height defined. A height for
the puff model indicates the
concentration at that level. A height for the particle model
indicates the average
concentration between that level and the
previous level (or the ground for the first level). Therefore
heights for
the particle model need to be defined in ascending
order. Note that the default is to treat the levels as
aboveground-level (AGL) unless the MSL (above Mean-Sea-Level) flag
has been set (see advanced configuration).
23(8)- Sampling start time: year month day hour minute
Default: [simulation start]
Each concentration grid may have a different starting, stopping,
and output averaging time. Zero entry will result
in setting the
default values. "Backward" calculations require that the stop time
should come before the start time.
24(9)- Sampling stop time: year month day hour minute
Default: 12 31 24 60
After this time no more concentration records are written. Early termination on a high resolution grid (after the
plume has moved
away from the source) is an effective way of speeding up the
computation for high resolution
output near the source because once
turned-off that particular grid resolution is no longer used for
time-step
computations.
25(10)- Sampling interval: type hour minute
Default: 0 24 0
Each grid may have its own sampling or averaging interval. The
interval can be of three different types: averaging
(type=0),
snapshot (type=1), or maximum (type=2). Averaging will produce output
averaged over the specified
interval. For instance, you may want to
define a concentration grid that produces 24-hour average air

concentrations for the duration of the simulation, which in the case

of a 2-day simulation will result in 2 output
maps, one for each day.
Each defined grid can have a different output type and interval. Snapshot (or now) will
give the instantaneous output at the output
interval, and maximum will save the maximum concentration at each
grid
point over the duration of the output interval. Therefore, when a maximum
concentration grid is defined, it is
also required to define an identical
snapshot or average grid over which the maximum will be computed. There
is
also the special case when the type value is less than zero. In that
case the value represents the averaging time in
hours and the output
interval time represents the interval at which the average concentration
is output. For
instance, a setting of {-1 6 0} would output a one-hour
average concentration every six hours.
Previous Section of the CONTROL file
Next Section of the CONTROL file
Table of Contents

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Concentration / Setup Run / Deposition Definitions (S314)

Concentration / Setup Run / Deposition Definitions

This section is used to define the deposition parameters for
emitted pollutants. The number of deposition definitions
must
correspond with the number of pollutants released. There is a
one-to-one correspondence. There are 5 entries in
the
CONTROL file for each defined pollutant. The lines 27(1)
through 31(5) correspond with each of the menu items
shown in the
illustration below. The radio-buttons along the top can be used to
set default deposition parameters, which
can then be edited as
required in the text entry section. The second line of radio-buttons
define the deposition values for
some preconfigured species: Cesium,
Iodine (gaseous and particiulate), and Tritium. The reset button sets
all deposition
parameters back to zero.
Note that turning on deposition will result in the removal of mass and the corresponding reduction in air concentration,

the deposition will not be available in any output unless height "0" is
defined as one of the concentration grid levels.

26 - Number of pollutants depositing

Default: number of pollutants on line # 10
Deposition parameters must be defined for each pollutant species
emitted. Each species may behave differently
for deposition
calculations. Each will be tracked on its own concentration grid.
The following five lines are
repeated for each pollutant defined.
The number here must be identical to the number on line 10.
Deposition is
turned off for pollutants by an entry of zero in all
fields.
27(1)- Particle: Diameter (m), Density (g/cc), and Shape
Default: 0.0 0.0 0.0
These three entries are used to define the pollutant as a
particle for gravitational settling and wet removal
calculations. A
value of zero in any field will cause the pollutant to be treated
as a gas. All three fields must be
defined (>0) for particle
deposition calculations. However, these values only need to be
correct only if
gravitational settling or resistance deposition is
to be computed by the model. Otherwise a nominal value of 1.0
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Concentration / Setup Run / Deposition Definitions (S314)

may
be assigned as the default for each entry to define the pollutant
as a particle. If a dry deposition velocity is
specified as the
first entry in the next line (28), then that value is used as the
particle settling velocity rather than
the value computed from the
particle diameter and density.
If gravitational settling is on and the Shape is set to a
negative value then the Ganser (1993) calculation is used to
replace Stokes equation for estimating particle fallspeeds.
The absolute value of the Shape factor is used for the
calculation.
The Stokes equation overestimates particle fallspeeds for particles larger than about 20 micron
diameter. As this diameter often lies within size distributions of volcanic ash particles, it is desirable to use the
Ganser formulation so that particle fallspeeds can be computed accurately.
Ganser, G.H., 1993: A rational
approach to drag prediction of spherical and nonspherical particles. Powder Technology, 77, 143-152.
.
The particle definitions can be used in conjunction with a special
namelist parameter NBPTYP that determines if
the
model will just release the above defined particles or create a
continuous particle distribution using the
particle definitions as
fixed points within the distribution. This option is only valid if
the model computes the
gravitational settling velocity rather than
pre-defining a velocity for each particle size.
28(2)- Deposition velocity (m/s), Pollutant molecular weight
(Gram/Mole), Surface Reactivity Ratio, Diffusivity Ratio,

Effective Henry's Constant

Default: 0.0 0.0 0.0 0.0 0.0
Dry deposition calculations are performed in the lowest model
layer based upon the relation that the deposition
flux equals the
velocity times the ground-level air concentration. This calculation
is available for gases and
particles. The dry deposition velocity
can be set directly for each pollutant by entering a non-zero value
in the
first field. In the special case where the dry deposition
velocity is set to a value less than zero, the absolute value
will be
used to compute gravitational settling but with no mass removal.
The dry deposition velocity can also be
calculated by the
model using the resistance method which requires setting the
remaining four parameters
(molecular weight, surface reactivity,
diffusivity, and the effective Henry's constant). See the table
below for
more information.

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29(3)- Wet Removal: Actual Henry's constant, In-cloud (GT 1 =L/L; LT 1 =1/s),
Below-cloud (1/s)
Default: 0.0 0.0 0.0
Suggested: 0.0 8.0E-05 8.0E-05
Henry's constant defines the wet removal process for soluble
gases. It is defined only as a first-order process by a
non-zero
value in the field. Wet removal of particles is defined by non-zero
values for the in-cloud and belowcloud parameters. In-cloud removal
can be defined as a ratio of the pollutant in rain (g/liter) measured
at the
ground to that in air (g/liter of air in the cloud layer) when the value in the field is greater than one. For withincloud
values less than one, the removal is defined as a time constant.
Below-cloud removal is always defined
through a removal time
constant. The default cloud bottom and top RH values can be changed
through the
SETUP.CFG namelist file. Wet
removal only occurs in grid cells with both a non-zero precipitation
value and a
defined cloud layer.
30(4)- Radioactive decay half-life (days)
Default: 0.0
A non-zero value in this field initiates the decay process of
both airborne and deposited pollutants. The particle
mass decays
as well as the deposition that has been accumulated on the internal
sampling grid. The deposition
array (but not air concentration) is decayed until the values are written to the output file. Therefore,
the decay is
applied only the the end of each output interval. Once
the values are written to the output file, the values are
fixed.
The default is to decay deposited material. This can be turned off
so that decay only occurs to the particle
mass while airborne by
setting the decay namelist variable
to zero.
31(5)- Pollutant Resuspension (1/m)

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Default: 0.0
Suggested: 1.0E-06
A non-zero value for the re-suspension factor causes deposited
pollutants to be re-emitted based upon soil
conditions, wind
velocity, and particle type. Pollutant re-suspension requires the
definition of a deposition grid,
as the pollutant is re-emitted
from previously deposited material. Under most circumstances, the
deposition
should be accumulated on the grid for the entire
duration of the simulation. Note that the air concentration and

deposition grids may be defined at different temporal and spatial

scales.
Previous Section of the CONTROL file
Table of Contents

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Concentration / Run Model (S320)

Concentration / Run Model

Once the Concentration Setup menu has been closed with the
Save button, the changes to the simulation parameters are

copied to default_conc. Clicking on the Run Standard

Model menu tab first copies default_conc to
CONTROL and then
runs the trajectory model executable,
hycs_std. The executable, by default, attempts to open a
file named CONTROL to
read all the required input
parameters. If not found, the model will prompt to standard output
for values from standard
input. This condition should not occur
running the model through the GUI.
In the situation where the namelist file SETUP.CFG has
been created through the Advanced/Configuration menu tab,

the message shown below will appear. If the intent was to run using
this file, then continue, otherwise one can delete
the file and run,
or terminate the simulation. The situation may arise that the
namelist file was created for a previous
simulation and is not needed
this time.

When the model execution starts, output messages are written

to a special window. Successful completion of a
simulation will
show a message similar to the example shown in the illustration
below:

Additional run-time diagnostic messages and other

error messages are always written to a file called MESSAGE.
This
file may be viewed through one of the Advanced Menu tabs.
Depending upon the nature of the error message, perhaps a
failure
in the model initialization process, error messages may also appear
in above window. Once the model has
completed, press Exit to
close the window.
Sometimes a configuration (long duration, very fine grid, too many particles)
will lead to extremely long run times,
perhaps requiring the model to be
terminated prematurely. Closing the GUI will not terminate the simulation because it

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Concentration / Run Model (S320)

always runs in background. In this situation it is necessary to use the

cntl-alt-del key combination (Windows) to find
and kill the hycs_std
executable.

Table of Contents

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Concentration / Display / Contours (S330)

Concentration / Display / Contours

The concentration model generates a binary (big-endian) output file
on a regular latitude-longitude grid, which is read
by the other programs to produce various displays and other output. The plotting program, concplot, can be accessed
through the GUI, which is shown in the
illustration below, or it can be run directly from the command line. Most, but
not all, of the
command line options are available through the GUI.

Normally only one input file is shown, unless multiple files have
been defined in the Concentration Setup Run
menu.
The default output file name is shown and unless the box is
checked all frames (time periods and/or levels) will be
output to
that one file. The program uses the map background file, arlmap, which by default is located in the \graphics
directory. Other
customized map background files could be defined. Some of these higher
resolution map background
files are available from the HYSPLIT download
web page. This plotting program also supports the use of ESRI
formatted
shapefiles.

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Concentration / Display / Contours (S330)

The GIS output option will create an output file of the contour
polygons (latitude-longitude vectors) in two different
format: the
ESRI generate format for import into ArcMap or ArcExplorer, or XML formatted files packaged by InfoZip for import into Google Earth.
For multiple pollutant files, only one pollutant may be selected for display by individual levels, or averaged between

selected levels. These levels must have been predefined in the Concentration Setup menu. Multipliers can
be defined
for deposition or air concentrations. Normally these
values would default to 1.0, unless it is desired to change the
output
units (for instance, g/m3 to ug/m3
would require a multiplier of 106).
Contours and color fill can be specified as black and white or
color. The none option eliminates the black line defining
contours
and only leaves the color fill. This option is incompatible with
GIS output options, which require computation
of the contour vector.
Contours can be determined DYNamically by the program, changing with each map, or FIXed to
be the same for all maps.
A user can set the contour scaling (difference between contours) to
be computed on an
EXPonential scale or a LINear scale.
Concplot Command Line Options
The Postscript conversion program (concplot), found in the
/exec directory with all other executables, reads the binary

concentration output file, calculates the most optimum map for display,
and creates the output file concplot.ps. Multiple
pollutant species
or levels can be accommodated. Most routine variations can be invoked
from the GUI. More
complicated conversions should be run from the
command line using the following optional parameters:
concplot -[options (default)]
-a[Arcview GIS: (0)-no dump, 1-ESRI (log10), 2-ESRI (decimal), 3-Google Earth]
Selecting the ESRI Generate Format output creates an ASCII text file for each
output time period that consists of
the value and latitude-longitude points along each contour. This file can be converted to an ESRI Shapefile or
converted for other GIS applications through the utility menu "GIS to Shapefile" ". The view checkbox would be
disabled to do just the GIS conversion without opening the Postscript viewer. Selecting Google Earth will create
a compressed file (*.kmz) for use in Google Earth; a free software package to display geo-referenced
information in 3-dimensions. You must have the free Info-Zip file compression software installed to compress
the Google Earth file and associated graphics.
+a[KML altitude mode: 0-clampedToGround, 1-relativeToGround]:
Selecting clampedToGround (0) positions the contoured concentrations
flat on the Google Earth terrain, whereas
selecting relativeToGround will generate 3D contours be extending the edges of the contours to the ground
from
the valid height of the concentration data.
-b[Bottom display level: (0) m]
= 0 - Represents the height (meters) below which no data will be
processed for display. The level information is
interpreted
according to the display (-d) definition.
-c[Contours: (0)]

= 0 - Dynamic contour values (10x intervals) are optimized for each map.

= 1 - Fixed contour values (10x intervals) are the same for all maps.
= 2 - Dynamic contour values (constant interval) are optimized for each map.

= 3 - Fixed contour values (constant interval) are the same for all maps.

= 4 - The contours are set by the user in conjunction with -v option.

=50 - Force contour interval x10 and set dynamically for each frame.

=51 - Force contour interval x10 and set as fixed for all frames.

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Concentration / Display / Contours (S330)

-d[Display: (1)-by level, 2-levels averaged]

= 1 - All output levels that fall between the bottom and top
display heights are shown as individual frames. A
single level will
be displayed if both bottom and top heights equal the calculation
level or they bracket that level.
Deposition plots are produced if
level zero data are available in the concentration file and the
display height is set
to 0.
= 2 - The concentrations at all levels between the specified
range are averaged to produce one output frame per
time period. If
deposition data is available and a plot is required in addition to
the air concentrations, then the
bottom height should be set to 0.
Deposition is not averaged with air concentrations.
-e[Exposure units flag: (0)-concentrations, 1-exposure, 2-threshold,
3-special, 4-mass loading]
= 1 - A custom output format in which all the air
concentrations have been converted to time-integrated units and

vertically averaged for all levels between the bottom and top
heights.
= 4 - A custom output format in which all the air
concentrations have been converted to mass loading.
-f[Frames: (0)-all frames one file, 1-one frame per file]

= 0 - All output frames (one per time period) in one file.

= 1 - Each time period is written to a file: concplot{frame number}.ps

-g[Graphic circle overlay: ( )-auto, 0-numb, numb:dist(50) km]
= ( ) - Auto selection procedure draws four circles with the
distance between them determined by the program
algorithm.
= # - Specifies the number of circles with the default (50 km)
distance interval.
= number:distance - specifies the number of circles and the
distance interval between circles. For the special case
of zero
circles with a distance specified (e.g. -0:1500) the program will
fix the map with the top and bottom edge
at that distance from the
center.
-h[Hold map at center lat-lon: (source point), lat:lon]
= lat:lon - Forces the center of the map to be at the specific
latitude-longitude point rather than the default source
location.
This is normally used in conjunction with the -g option to get the
same map each time or when there are
multiple source locations.
-i[Input file name: (cdump)]
= Name of the binary concentration file for which the graphics will
be produced. Default name {cdump} or user
defined}.
-j[Graphics map background file name: (arlmap)]
The program first searches the local directory, then the
..\graphics directory for the name of the default map
background
file (arlmap). Set this parameter to select the directory/name of
any map background file of
compatible format or specify a special
file of shape file file names.
-k[Kolor: 0-B&W, (1)-Color, 2-No lines Color, 3-No lines B&W]

= 0 - Uses gray shade patterns for the contour color fill.

= 1 - Uses the default four color fill pattern.

= 2 - Default color fill pattern but without black contour lines.

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Concentration / Display / Contours (S330)

= 3 - Black and white color fill but without black contour lines.
-l[Label options: ascii code, (73)-open star]
The default plot symbol over the source location is an open star.
This may be changed to any value defined in the

psplot
ZapfDingbats library. For instance a blank, or no source symbol
would be defined as -l32
-L[LatLonLabels: 0=none, (1)=auto, 2=set:{value tenths}]
= 0 - No latitude or longitude lines are drawn on the map

= 1 - Latitude and longitude lines spacing is determined automatically

= 2:tenths - line spacing is determined by the given value in tenths

-m[Map projection: (0)-Auto, 1-Polar, 2-Lambert, 3-Mercator, 4-CylEqu]
Normally the map projection is automatically determined based upon
the size and latitude of the concentration
pattern. Sometimes this
procedure fails to produce an acceptable map and in these
situations it may be necessary
to force a map projection.
+m[Max-Min value plotting: 0=none, (1)=both, 2=values, 3=max-square]
The default (1) prints the maximum and minimum values below the contours
and plots a red square, the size of
the concentration grid, at the location of
the maximum concentration value. These can be turned off individually
using this
command line option. Note the +m rather than -m prefix.
-n[Number of time periods: (0)-all, number, min:max,-increment]

= 0 - All time periods in the input file are processed.

= # - Sets the number of time periods to be processed starting with the first.

= #1:#2 - Processes time periods, including and between #1 and #2.

= [-#] - Sets the increment between time periods to be processed. For instance,
-n-6 would only process every 6th
time period.
-o[Output file name: (concplot.ps)]
The name of the Postscript output file defaults to concplot.ps unless it is set to a {user defined} value.
-p[Process file name suffix: (ps) or process ID]
The suffix defines the character string that replaces the default
"ps" in the output file name. A different suffix does
not change
the nature of the file. It remains Postscript. The suffix is used
in multi-user environments to maintain
multiple independent output
streams.
-q[Quick DATEM plot file: ( )-none, filename]
By defining the name of a text file in this field where the data
values are defined in the DATEM format, the
values
given in the file will be plotted on each graphic if the starting time of the
sample value falls within the
averaging period of the graphic.
-r[Removal: 0-none, (1)-each time, 2-sum, 3-total]

= 0 - No deposition plots are produced even if the model produced deposition output.

= 1 - One deposition plot is produced for each time period.

= 2 - The deposition is summed such that each new time period represents the total accumulation.

= 3 - Similar to =2, deposition is accumulated to the end of the simulation

and but only one plot is produced at

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Concentration / Display / Contours (S330)

the end.
-s[Species: 0-Sum (1)-Single Pollutant {N}-Species Number]
= {Species Number} - Only one pollutant species may be displayed
per plot sequence if multiple species were
created during a
simulation. However, an entry of "0" will cause all species
concentrations to be summed for
display.
-t[Top display level: (99999) m]
= 99999 - Represents the height (m) above which no data will be
processed for display. The level is interpreted
according to the
display definition.
-u[Units label for mass: (mass), also see "labels.cfg" file]
Defines the character string for the units label. Can also be
modified using the labels.cfg file.
-v[Values (:labels:colors are optional) for up to 10 fixed contours: val1+val2+...val10]
If the contour values are user set (-c4), then it is also possible
to define up to ten individual contours explicitly
through this
option. For instance -v4+3+2+1, would define the contours 4, 3, 2,
and 1. Optionally, a label and/or
color (RGB) can be defined for each contour (e.g. v4:LBL4:000000255+3:LBL3:000255255+2:LBL2:051051255+1:LBL1:255051255). To specify a color but not a
label, two colons must be present (e.g. -v4::000000255).
-w[Grid point scan for contour smoothing (0)-none 1,2,3, ... grid points]
Defines if the gridded concentration data are to be smoothed prior to contouring.
For instance, a value of 1 means
that each grid point value is replaced by the
average value of 9 grid points (center point plus 8 surrounding).
-x[Concentration multiplier: (1.0)]

= 1.0 - No units conversion.

= X - where {X} is the multiplier applied to the air concentration input data before graphics processing.
-y[Deposition multiplier: (1.0)]

= 1.0 - No units conversion.

= X - where {X} is the multiplier applied to the deposition input data before processing.
-z[Zoom factor: 0-least zoom, (50), 100-most zoom]

= 50 - Standard resolution.

= 100 - High resolution map (less white space around the concentration pattern)
Additional supplemental text may be added at the bottom of the
graphic by creating a file called MAPTEXT.CFG, which
should be located in the working directory. This is a generic file used by
all plotting programs but each program will
used different lines in
its display. The file can be created and edited through the Advanced / Panel Labels menu tab.
Units and title information can be edited by creating a LABELS.CFG file which can
also be edited manually or through
the Advanced / Border Labels menu tab.
ESRI Shapefile Map Background Files
Another mapping option would be to specify a special pointer file, (origianlly
called shapefiles.txt, but now a suffix
other than "txt" is permitted) to replace the map background file arlmap in
the -j command line option (see above). Note
-jshapefiles... rather than
-j./shapefiles... is required. This file would contain the name
of one or more shapefiles that can
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Concentration / Display / Contours (S330)

be used to create the map background.

The line characteristics (spacing, thickness, color) can be specified for
each
shapefile following the format specified below:
Record format: 'file.shp' dash thick red green blue

file.shp = /dir/name of input shapefile in quotes

dash = {0} for solid; {dashes}/in; <0 color fill

thick = line thickness in inches (default = 0.0)

Red Green Blue = RGB values (0.0 0.0 0.0 is black)

Record example for default: 'arlmap.shp' 0 0.005 0.4 0.6 0.8

Table of Contents

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Concentration / Display / Grid Values (S338)

Concentration / Display / Grid Values

A generic Postscript equivalent of the Windows-only concentration grid point data display program is available through
this menu. This particular program (gridplot) was designed to plot global
sized concentration grids, although any sized
grid may be displayed.
Concentration values over the entire grid (or a zoomed area) will be shown using a color-fill in
each grid cell according to its
concentration value. The options available through the GUI are setting
the input file,
output file, lowest contour value, contour interval, species number, linear or logarithmic scaling, and the longitude
offset,
the center latitude, the zoom factor, the concentration multiplier,
and the choice of GIS output. By default, each
time period is output to a different file name, gridplot_{???}.ps, where the sequence number {???} is incremented by
one for each time period. When called from the Global Grid menu tab, the default output file name is gemplot rather
than gridplot.
Several other options are available through the command line, which
may be needed if multiple levels have been written
to the concentration
output file. USAGE: gridplot -[options(default)]

-i[input file name (cdump.bin)]

-p[Process output file name suffix]

-o[output name (plot.ps)]

-l[lowest interval value (1.0E-36), -1 = use data minimum]

-m[multi frames one file (0=no) 1=yes]

-c[concentration multiplier (1.0)]

-d[delta interval value (1000.0)]

-s[species number to display: (1); 0-sum]

-h[height of level to display (m) (integer): (0 = dep)]

-j[Graphics map background file name: (arlmap)]

-a[scale: 0-linear, (1)-logarithmic]

-x[longitude offset (0), e.g., o--90: U.S. center; o-90: China center]

-y[latitude center (0), e.g., 40.0: U.S. center]

-f[(0), 1-ascii text output files for mapped values]

-g[GIS: 0-none 1-GENERATE(log10) 2-GENERATE(value) 3-KML 4-partial KML]

-k[KML options: 0-none 1-KML with no extra overlays]

-u[mass units(ie, kg, mg, etc); note these are labels only]

-z[zoom: (0)-no zoom, 99-most zoom]

When called from the Global Grid menu tab, an additional feature is
available through the Add Plume checkbox. In this
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Concentration / Display / Grid Values (S338)

case, the first

plume model concentration grid (if more than one is defined) is added to the
global model concentration
grid as defined in this menu. The merged
concentration file is called concadd.bin which is then displayed
by gridplot.
The two concentration files that are added must be
identical in terms of the number levels and pollutants. However, the
spatial grid
characteristics may be different. The height of the levels at each index do not
have to be identical. If this
issue is important, then the heights heights
corresponding to the global model heights needs to be set in the CONTROL
file
setup menu. Note that the global model vertical heights cannot be changed by the
user and correspond with the
heights of the meteorological data levels. The
horizontal characteristics of the output grid always takes the grid

dimensions of the second grid (-b).

USAGE: concadd -[options(default)]

-i[input file name (cdump)]

-b[base file name to which input is added (gdump)]

-o[output file name with base format (concadd.bin)]

-g[radius (grid points around center) to exclude; default=0]

-c[concentration conversion factor (1.0)]

-p[sum process (0)=add | 1=max value | 2=zero mask | 3=intersect]

| 4=replace]

-z[zero mask value (base set to zero when input>mask; default=0.0)]

if zero mask value < 0 :

base set to zero when input> zero mask value * base

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Concentration / Display / Pointer Select (S336)

Concentration / Display / Pointer Select

The Windows-only concentration data point registration program
is designed to read the binary concentration data file,
display the
data on the screen, and then use the mouse as a pointer device to
pick locations at which the position and
concentration data are
read and written to the text file: wincpick.txt. The
concentration data are displayed over the entire
grid domain. There
are no zoom options. If you want to zoom in on a specific area,
then it is necessary to rerun the
model with a smaller concentration
grid domain. The program is available from the GUI or the command
line with the
following syntax: wincpick [input file name].
The GUI menu, which is shown in the illustration below, only permits

selection of the concentration input file name, which must have been
previously defined in the Concentration Setup
menu.

Upon startup, wincpick will display the domain background

map with a summary of the mouse-based instructions: leftclick
registers the latitude-longitude position of that point to the output
file wincpick.txt. A right-click of the mouse
redraws
the map for the next time period and at the end of the input file
saves and closes all files; and a CNTL-rightclick closes all
files and exits the program before the end of the input file.
Right-click the mouse to go to the first
concentration map.
Maps are drawn in sequence of height, pollutant species, and time.
Left-clicks register the position
of the mouse to the output
file. If you are interested in only one time period, skip past those
times by a right-click,
register the points of interest, then
CNTL-right-click to exit. An illustration of the first output
period from the sample
calculation is shown below.

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Concentration / Display / Particle (S332)

Concentration / Display / Particle

In addition to the normal display programs for air concentrations, which are designed to display and contour the actual
values, the particle display programs only show the instantaneous positions of the
pollutant particles or puffs that are
integrated in time by the model
to produce the air concentration fields. To generate the particle position graphics from
this menu it is necessary to generate a particle
dump file (default name: PARDUMP), which may contain one or more
time
periods of output. The creation of this file is controlled by the
parameters set in the menu tab: "Advanced /
Configuration Setup /
Concentration."
The particle display menu requires the name of the particle position
input file, the base name of the Postscript output
file, the type of particle display requested, and some additional options. Setting the mass
checkbutton changes the size
of the particle display dot according to its
mass, the color option sets the dot color rather than just black. The color
is
set according to the height of the particle or if the age value is non-
zero, then the color is set according to the particle
age. The GIS option
is (valid only for the horizontal plot) and it will output either the ESRI generate format file or a
Google Earth KML file. If there are too many particles, the density of the display can be reduced by plotting only every
Nth particle, the default is 1 to display
every particle. The Set Cross button permits the specification of the actual crosssection vector, rather than letting the program determine
it automatically. Note that similar to the trajectory and
concentration
plotting programs, shapefiles can also be defined for the map background.

The "Plane" option results in the conventional graphic shown below of the
horizonal plane view. There is one black dot
for each particle. The size of the dot varies according to the pollutant mass assigned to the particle. All
examples are 12
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Concentration / Display / Particle (S332)

or 24 hours after the start of the test simulation.

The "vertical" option shows an integrated particle distribution view from

the south looking north (top panel) and from
the east looking west (bottom panel). All particles in the computational domain are shown.

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Concentration / Display / Particle (S332)

The "cross-section" view is a combination of the horizontal plane and vertical

views. The top panel shows the horizontal
particle distribution, while the bottom
panel shows the vertical distribution along the red regression line through the

plume. Again all particles are shown regardless of their distance from the
regression line. The bottom panel view is
from left to right in increasing
longitude, regardless of the orientation of the regression line.

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Concentration / Display / Particle (S332)

The global display is a special program that will always map the particles
on a global equidistant projection. The other
programs try to automatically
scale the plots according the to particle distribution, sometimes resulting
in distorted
plots when the particle coverage becomes global. There are additional command line features in this program (parsplot)
for particle size and color mapping according to the particle mass that are not
available through the GUI.

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Concentration / Display / Particle (S332)

Table of Contents

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Concentration / Display / Time-of-Arrival (S339)

Concentration / Display / Time-of-Arrival

Time of arrival graphic (isochron) shows the time after the start of the
simulation that the concentration exceeds the
given threshold concentration
at each concentration grid cell. The default contour interval (-1) uses the
concentration
averaging period. Otherwise, the time difference field should
be set to hours. A text label with release information may
be printed below the threshold through the LABELS.CFG file.
The GUI and the command line options are similar with the command line
syntax as follows: USAGE: isochron [options(default)]

-c[color fill no:0 yes:(1)] : the =0 option results in contours

-d[difference in hours between contours (-1)]

-f[frames: (0)-all frames one file, 1-one frame per file] : multiple
frames can only be due to multiple levels or
species in the input file

-i[input file name (cdump)] : the input file needs to contain multiple time period

-j[graphics map background file (arlmap)] : the shape file option is not available

-n[number of contours (12)] : only 12 contours fit across the display

-o[output name (toa)] : the output file represents all time periods

-p[Process file name suffix: (ps) or process ID]

-t[threshold value (1.0E-36)]
In the 144 hour duration example simulation shown below, the concentration field
was output every six hours, the
contour interval was set to 12 hours, and the threshold to 0.1E-15 . The one hour duration release took about 72 h to
reach Hudson's Bay and about 144 h to reach into the Atlantic off the east coast of the U.S.

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Concentration / Display / Source-Receptor View (S335)

Concentration / Display / Source-Receptor View

This menu option permits the extraction of information for a
specific source or receptor if the original
model simulation
was configured to produce a source-receptor matrix
formatted output file. The model should have been run with the

matrix option set in the configuration menu. This results in a

special concentration output file that may be called a
source-
receptor matrix, such that each column may be considered a
receptor location and each row a pollutant source
location. The
display program under this menu tab permits the contouring of any
row or column.
If the matrix option was not set in the Advanced Concentration configuration tab, then the output
file produced is a
simple concentration output file, where
the concentrations from all the sources of the defined matrix are
summed on a
single concentration output grid. Source-receptor
information cannot be extracted from such a file.
When a location is selected in the menu, a special program is
called to extract that location from the concentration
matrix output
file and then write a standard concentration file for that location.
The standard concentration display
program is then used to display
the information in the extracted file. The source-receptor matrix
binary extraction file
name will default to SRM_{original file name},
but can be changed in the menu. The Display Matrix menu, shown in

the illustration below, automatically creates the extraction file,

calls the standard display program concplot, and
provides for
additional custom label information to identify the plot as a source-receptor
concentration matrix.

The menu consists of the standard display options such as the

map background file, output file name, zoom factor, and
the
selection of the extraction method: source or receptor. A latitude
and longitude point needs to be entered for all
extractions.
Selection of the "source" extraction method means that the
location entered is considered to be the source
location and the resulting output is a contour map is just a conventional air concentration simulation showing
concentrations from that source.
The "receptor" extraction method means that the location entered is considered to be

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Concentration / Display / Source-Receptor View (S335)

the receptor location and the output

is a map of how much air concentration each source contributes to the selected
receptor. Note that turning on the "normalization" flag divides all concentrations by the sum of all concentrations at
each grid point, resulting in a map that represents a fractional contribution. In addition, a concentration conversion
factor
can be defined, which will be applied to the binary file before
it is contoured.

Table of Contents

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Concentration / Display / Source-Receptor / Stats (S355)

Concentration / Display / Source-Receptor / Stats

Summary: This procedure is intended to find the source location that
provides the best fit with measurement data. After
running HYSPLIT with the
matrix option and ICHEM=1, the script
extracts each source location from the CONTROL
file, converts the output to
the DATEM format, and then calls the statistical anlaysis program which is
converted to a
gridded binary file which can be plotted by any of the
standard concentration plotting programs.

Step 1: defines the DATEM formatted measured data file and unit conversion factor required to convert the HYSPLIT
concentration predictions
to the same units as given in the measured data file.
Step 2: defines name of the statistical output file that will contain
the statistical results from each source location
compared with the measured
data values. Normally the statmain program outputs one results file per
execution. In this
configuration, the results form each source location are appended to a single file, one record per source.
Step 3: defines the root name of the final output graphics file which will
show a plot of the statistical results by source
location. The .ps suffix is
created by default.
Step 4: runs sequentially through all steps of the process, reading each source
location from the CONTROL file, running
matrix to extract that location from the HYSPLIT simulation output file, using c2datem to convert that binary extract to
the
DATEM format, and then running statmain to append the results to the statistical
output file. This step needs only to
be run once.
Step 5: defines which statistic will be shown: Corr - correlation coefficient, NMSE - normalized mean square error, FB
- fractional bias, FMS - figure of merit in space, KSP - Kolomogorov Smirnoff parameter, and finally the rank, which is
a combination of the previous parameters. Once all source locations have been processed, the statistical file is read and

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Concentration / Display / Source-Receptor / Stats (S355)

converted to binary gridded format using stat2grid. This output file can then be plotted with any of the display
programs such as gridplot.
Default file names: The following describes the assigned default input and output
files names for each processing
section, so that they can be identified in the working directory.
File names in italics are the ones that can be changed
through the menu.
matrix
cdump - binary outfile from a single multi-source simulation using the ICHEM=1 option
SRM_cdump - binary concentration output file extracted for one source location
c2datem
SRM_cdump - binary concentration input file from the previous step
measured.txt - measured data file in DATEM format
hysplit_datem.txt - model prediction output for a single source converted to DATEM format
statmain
measured.txt - measured data input file in DATEM format
hysplit_datem.txt - model prediction input file for a single source from previous step
sumstats.txt - statistical summary output appended one record per source location
stat2grid
sumstats.txt - statistical summary input file from previous step
statmap.bin - binary statistical output file gridded in the HYSPLIT
concentration format

Table of Contents

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Concentration / Display / Ensemble Map (S334)

Concentration / Display / Ensemble Map

Multiple concentration output files from the ensemble or variance
dispersion simulation can be processed to produce
probability displays.
The Ensemble View Map menu calls a special program conprob
that reads the concentration files
with the ensemble member three-digit
suffix (001 to 027) and generates various probability files when the
Graphics
Only box is NOT checked. When this box is checked, then
the existing probability files are used to generate all
graphics. The appropriate files are then plotted using concplot according to
the menu selection options. Note that the
ensemble display menu can be
used to convert multiple concentration output files to probability form,
regardless of
how they were generated. It is not necessary to use the
pre-configured ensemble version of
the model to create air
concentration probability maps. Any number of
multiple simulations can be used as long as the file suffixes end with a

numeric three-digit sequence. Menu settings for the output file name should
reflect the base name without the numeric
suffix. An illustration of the Ensemble Display menu is shown below.

The menu includes some of the standard display program (concplot)

mapping choices, such as background file, output
file name, and zoom factor.
One critical difference is that there is an option called Aggregation #.
By default this value
is set to one, which means that only the ensemble
members for one time period are aggregated together to produce the
probability
display. Hence there would be an independent probability map for each time period. However, multiple
time periods may be combined to produce a single
probability plot. The entry represents the number of time periods,

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Concentration / Display / Ensemble Map (S334)

not the
actual time span. For instance, if the model output is set to produce a one-hour average and the model is run for
24 hours, then each ensemble member
will have 24 time periods of output. By default the probability output will

represent the ensemble member variation for each hour, that is 24 frames of
output will be produced. However if the
aggregation period is set to 24, then
all output times will be combined into one output frame and the ensemble result
will represent the hourly variations as well as the member variations.
The menu permits a choice of six different ensemble output display
options:
1. The number of ensemble members at each grid point with concentrations
greater than zero shows the spatial
distribution of the Number of Ensemble
members.
2. The mean concentration of all ensemble members.
3. The variance of all ensemble members (the mean square difference
between individual members and the mean).
4. The coefficient of varition of all ensemble members (sqrt(variance)*100/mean).
5. The probability of concentration produces contours that give the
probability of exceeding a fixed concentration
value at one of three levels:
1% of the maximum concentration, 10% of the maximum, and the maximum
concentration.
The maximum is determined to be the first concentration to a power of 10 that is
less than the
actual maximum value or the value of the maximum set in the data
entry box (exponent of 10). The concentration
level for the probability display
is shown on the graphic with the pollutant identification field set to something

like C14, where 14 represents the concentration to the power of 10-14.

6. The concentration at percentile levels shows the concentration contours of areas where concentrations will be
exceeded only at the given probability level.
Although several output levels are computed, the probability level
choices through
the menu are limited to 50, 90, and 95th percentiles.
The conprob extraction program will always produce all the probability
variations, one to each output file, for a given
aggregation period. If the graphics
only checkbox is marked, then the menu skips computing the probability files and

uses the existing files in the working directory. The output files may also be plotted
individually from the command
line using concplot. The conprob output
files contain the following information:
Cnumb - Number of members
Cmean - Concentration mean of all members
Cvarn - Concentration variance of all members
Ccoev - Concentration coefficient of variation of all members
Cmax05 - Probability of 5% of the concentration maximum
Cmax10 - Probability at 10% of the concentration maximum
Cmax00 - Probability at the maximum concentration level
Prob10 - Concentrations at the 10th percentile
Prob25 - Concentrations at the 25th percentile
Prob50 - Concentrations at the 50th percentile
Prob75 - Concentrations at the 75th percentile
Prob90 - Concentrations at the 90th percentile
Prob95 - Concentrations at the 95th percentile
The command line options for the probability program conprob [-options] are as follows:

-b[base] input file name

-c[concentration maximum] value set

-d[diagnostics = true]

-p[pollutant] index number for multi-pollutant files

-t[temporal] aggregation period

-v[value] of concentration below which is assumed to equal zero

-z[level] index number for multi-level files

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Concentration / Display / Ensemble Map (S334)

Table of Contents

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Concentration / Display / Ensemble Box Plot (S333)

Concentration / Display / Ensemble Box Plot

Multiple concentration output files from the ensemble or variance
dispersion simulation can be processed to produce
probability displays.
The Ensemble / View Map menu calls a special program conprob
that reads the concentration files
with the ensemble member three-digit
suffix (001 to 027) and generates various probability files. Once these

probability files have been created, the concentration distribution at a single location can also be viewed using
this
menu by entering a latitude-longitude location. The nearest grid point
will be selected and the concentration values are
retrieved from the prob{xx} files, which represent the various points on the box plot. In the
illustration shown below,
the limits of the box represent the quartiles (25th and 75th percentiles), the whisker extensions show the 10th and 90th

percentiles, and the circles show the 5th and 95th percentiles. The median
value is shown by the line through the box,
while the mean is shown by the
plus symbol. Up to 12 time periods can be shown in one plot. The graphic is
always
named boxplots.ps.

A second graphic called ensplots.ps is always produced using the

individual ensemble concentration files. The abcissa
and ordinate is
identical to the boxplot, but the contents show the actual concentration
values identified by member
number, where the number is the same as the
concentration file suffix.

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Table of Contents

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Concentration / Display / Ensemble / Statistics (S354)

Concentration / Display / Ensemble / Statistics

Summary: This procedure is intended to analyze the binary output
files from any of the ensemble simulations. The
output file naming convention
is such that they are defined by a base name set in the CONTROL file followed
by a
three digit sequential number suffix (.000). The ensemble simulation needs
to be for a case in which experimental data
are available for verification. The
script converts the output to the DATEM format, and then calls the statistical
anlaysis
program which appends a statistical summary for each member to a single output file.

Step 1: defines the DATEM formatted measured data file and unit conversion factor required to convert the HYSPLIT
concentration predictions
to the same units as given in the measured data file.
Step 2: defines name of the statistical output file that will contain
the statistical results for each ensemble member
compared with the measured
data values. Normally the statmain program outputs one results file per
execution. In this
configuration, a subset of the the complete results for each
member are appended to a single file. The complete
statistics are available in file
named stat_000.txt.
Step 3: runs sequentially through all steps, processing each ensemble member
using c2datem to convert that binary
concentration data to the DATEM format, and then running statmain to append the results to the statistical output file.
Default file names: The following describes the assigned default input and output
files names for each processing
section, so that they can be identified in the working directory.
File names in italics are the ones that can be changed
through the menu.
c2datem
{base name}.{xxx} - binary concentration input file, where xxx = 000 to 999
measured.txt - measured data file in DATEM format
hysplit_datem.txt - model prediction output for a member converted to DATEM format
statmain
measured.txt - measured data input file in DATEM format
hysplit_datem.txt - model prediction input file for a single source from previous step
sumstats.txt - statistical summary output appended one record per source location
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Concentration / Display / Ensemble / Statistics (S354)

stat_{xxx}.txt - complete statistics for each member

Table of Contents

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Concentration / Utilities / Binary File Merge (S344)

Concentration / Utilities / Binary File Merge

The purpose of the Binary File Merge utility menu is to add together two or more gridded HYSPLIT binary
concentration files, where
the contents of the input file are added to the contents of the base file,
the results of which are
written to the output file. The input files need
not be identical in time, but they must have the same number of
pollutants and
levels. Levels and pollutants will be matched by index number and not actual height
or species. The
horizontal grids need to be identical or even multiples of each
other. This means that the concentration grid center
should be explicitly defined
rather than using the default values (0.0). For instance, a half-deg and one-deg

concentration grid needs to at least intersect at the corner points. Summations

will occur regardless of any grid
mismatches. The files are merged at each grid
point according to the processing rules: a simple summation, selecting
the
maximum value, or the sum only at the intersection points. An additional option,
called masking, is defined to be
such that a concentration value greater than
the mask value (normally 0.0) in the input file, will cause the base file to be

set to 0.0 at that grid point. The GUI is shown below.

If the Create Filenames button is selected, an special file called INFILE is created that contains all the file names in the
working directory
that have the wildcard sequence as defined in the Input Name box. These
files are then merged
sequentially according to the process rules. Note that the
concentration multiplier is applied during the writing of the
output file and
during sequential file processing this conversion is disabled.

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Concentration / Utilities / Binary File Merge (S344)

The above example shows how two plume simulations have been merged. Each was run
for a different day and starting
location, however the graphic and its corresponding
binary output file, use only the information provided in the base
file and the
labeling information from the input file has been lost.

In the above example, the input and base files are identical to the previous
illustration, but in this example the mask
checkbox option was selected
and the result clearly illustrates the region of the base plume that was intersected by
the
input plume.

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Concentration / Utilities / Binary File Merge (S344)

The result from the intersection option is shown in the above figure. In this result
only the region where the two plumes
intersect and both exceed the zero mask value
is shown. The region is identical to the missing plume area in the mask
option.

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Concentration / Utilities / Binary File Extract (S349)

Concentration / Utilities / Binary File Extract

Calls the utility program concrop to extract a sub-grid from a HYSPLIT binary
concentration data file. The new
subgrid is written to the file conxtrct.bin.
The utility program can be used to remove the whitespace by resizing the grid
about
the non-zero concentration domain or by specifying a sub-grid. Using the -x option
will force the extract of the
users domain regardless of white space.
USAGE: concrop -[options (default)]

-b[latmin:lonmin:latmax:lonmax (all zeroes will produce full grid extract]

-d[process id (txt)]

-f[FCSTHR.TXT: (0)=none 1=output]

-i[Input file name: (cdump)]

-g[Output plume grid limits rather than cropped file: (0)=no; 1=center-radius -1=from{-b}]

-o[Output file name: (ccrop)]

-p[time extract MMDDHH:MMDDHH]

-x[override white space: (0)=no (default) 1=yes]

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Concentration / Utilities / Binary File Average (S348)

Concentration / Utilities / Binary File Average

This menu calls the utility program conhavrg to spatially average the HYSPLIT binary concentration file and write a
new binary file. Each grid cell is replaced by
the average value of the center cell and the surrounding cells specified by
the scan
radius. The default scan radius of 1 means that 9 grid cells will be averaged together.
USAGE: conhavrg [options]

-i[input file name (cdump)]

-o[output file name (cavrg)]

-s[surrounding grid points to average (1)]

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Concentration / Utilities / Binary File / Apply Source (S340)

Concentration / Utilities / Binary File / Apply Source

When multiple simulations are conducted, each one representing a different emission,
the model results can be analyzed to
determine which simulation provides the best fit
with any available measurements, or more specifically, what emission rate is
required
with each simultion to provide the best fit with the measurements. These simulations
can each represent a different
emission time or location or a combination of both.
Currently the code is configured to automatically generate multiple timevarying
emissions using the namelist parameters QCYCLE and ICHEM.
As an example, if hourly (the minuimum) resolution is desired over a 24 hour
simulation period, then the emission rate needs to
be set to emit one one unit for
a duration of one hour. The namelist variable QCYCLE should also be set to 1.0 hour so that the
emissions effectively become continuous at a rate of one unit per hour. This in combination with ICHEM=10 will result in the
creation of
24 concentration arrays with each particle being tagged according to its release
hour and those particles will only
contribute to concentrations on the grid with
the same release-time tag. The pollutant identification field is used and its value

corresponds to hours after the start of the simulation. The output concentration
grid will appear to be like any other but with 24
pollutants, one for each release
period as defined by the QCYCLE parameter. Make sure that a sufficient
number of particles
have been released to provide consistent results for all time
periods.
Once the simulation has completed, the unit source simulation can be converted
to concentrations by applying an emission rate
factor for each release time. This
is accomplished by clicking on the Concentration / Utilities / Binary File / Apply
Source
menu tab. This menu is only intended to work with a single multi-pollutant
concentration file created in the manner described
previously.

The input required is simply the name of the Transfer Coefficient Matrix (TCM)
input file (the previously created multipollutant=multi-time-period) input file,
the base name of the single pollutant output file which will contain the
concentration
sum of all the release periods after they are multiplied by the
source term, the 4-character pollutant identification field, and the
name of the
time-varying source term file it it exists, otherwise a new file can be created.
An emission rate needs to be defined
for each release time, otherwise it is assumed to be zero.

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The emissions file format is simply the starting time of the emission given
by year, month, day, and hour, and the emission rate
in terms of units per hour.
The first record of all emissions file should contain the column labels then
followed by the data
records, one for each release time period. For example, a constant emission rate corresponding to the 12 hour example test
simulation
(16 October 1995) would appear as follows:

YYYY MM DD HH TEST

1996 10 16 00 1.00E+12

1996 10 16 01 1.00E+12

1996 10 16 02 1.00E+12

1996 10 16 03 1.00E+12

1996 10 16 04 1.00E+12

1996 10 16 05 1.00E+12

1996 10 16 06 1.00E+12

1996 10 16 07 1.00E+12

1996 10 16 08 1.00E+12

1996 10 16 09 1.00E+12

1996 10 16 10 1.00E+12

1996 10 16 11 1.00E+12
Command Line Options - tcmsum
The underlying binary file conversion program can be run from the command line. As with all
other applications, the command
line argument syntax is that there should be no space
between the switch and options. The command line arguments can appear

in any order:
tcmsum -[option {value}]

-c[column number in emissions file (1)]

-i[input file name (cdump)]

-o[output file base name (tcmsum)]

-d[output file name suffix (bin)]

-h[half-life-days (0.0 = none)]

-p[pollutant sum label (SUM)]

-s[source term input file name (cfactors.txt)]

-t[time decay start: MMDDHH (run_start)]

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The procedure described in this section is very similiar to the transfer coefficient solution approach with the exeception that

here the dispersion coefficients for the individual release times are contained in a single file while in the other approach an
input file is required for each release time simulation. The single file created here can be processed through the utility
program
conlight to extract one time period to its own file with each pass
through the program. Currently no GUI script application
exists to perform this task
automatically.

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Concentration / Utilities / Convert to ASCII (S341)

Concentration / Utilities / Convert to ASCII

The Convert to ASCII menu option uses the con2asc program to
convert the binary concentration file to a simple ASCII
file
composed of one record per grid point for all grid points where
concentrations at any level are non-zero.
Concentrations for
multiple levels and pollutant species are all listed on the same
record for each grid point. The
primary purpose of the conversion
is to create a file that can be imported into other applications.
An illustration of the
GUI menu is shown below for the sample
concentration simulation.

The Concentration Setup menu determines the file name selection

option on the GUI. There are some additional
checkboxes that
correspond to various command line conversion options: con2asc -[options (default)]
-c[Convert entire file flag]
This option converts the entire binary input file, including all
index records, to an ASCII output file with the name
{input file}.txt.
This option is not available through the GUI (use -s below).
Another program, called conread,
also not available through the
GUI, can also be used to dump out the contents of the concentration
file. This
program can only be run from the command line. For the -c
option, the output file format follows the binary file
format record-by-record using the following
conventions.

Meteorological model and starting time - A4, 6I4

Starting time and locations - 4I4, 2F8.3, F10.1

Concentration grid and spacing - 2I4, 2F8.4, 2F8.2

Vertical grid index record - I4, 20I8

Pollutant identification record - I4, 20A4

Sample start time - 6I4

Sample end time - 6I4

Concentration record - A4, I6, 255(255E10.2)

-d[Delimit output by comma flag (rather than space delimited)]
Set the Comma Delimited checkbox.

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-i[Input file name (cdump)]

-m[Minimum text output format flag]

Setting this flag turns off the writing of the first output record,
which is the column label field: DAY HOUR LAT
LON SPECIES-LEVEL.
This option corresponds to the Minimum Text checkbox of
the GUI menu.
-o[Output file name base (Input File Name)]

The default base name for the output file is the input file name. A new output file is created for each sampling
period, where the name
of the file is composed of the {base name}_{Julian day}_{hour}
of the sample ending
time. If the Include Minutes box is checked,
then the minutes field of the sample ending time is added to the
end
of file name. This field is not available through the GUI. The name
of each output file is always written to the file
named CON2ASC.OUT
regardless of any other options selected.
-s[Single output file flag]
This option corresponds to the Single File checkbox of the GUI
menu. The multi-time period ASCII output file is
named {input file}.txt.
-t[Time expanded (minutes) file name flag]

-u[Units conversion multiplier for concentration (1.0)]

-U[Units conversion multiplier for deposition (1.0)]

Values other than one in either of these fields will result in the
concentration or deposition results to be multiplied
by these factors
prior to output. Deposition fields are identified by a zero in the
level height field.
-x[Extended precision flag]

The format of each record in the output file is given by:

2I3 - End of Sample: Julian Day and Hour

F7.2, F8.2 - Latitude and Longitude of grid cell

45E9.2 - Concentration data (by level and pollutant)

If the Extended Digits checkbox of the precision options is
set, then the latitude and longitudes will be given by
four digits
after the decimal place.
-z[Zero points output flag]
Setting the zero flag causes the program to output the concentration
values all all grid points, including the ones
that are zero. This corresponds to the Include Zero checkbox of the GUI menu.
Each output record is identified by the day (Julian: 1 to 365)
and hour (UTC) of the ending time of each sample. The
ASCII
conversion of the first file generated by the sample calculation is
shown below in the illustration.

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Table of Contents

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Concentration / Utilities / Convert to DATEM (S345)

Concentration / Utilities / Convert to DATEM

This menu calls a utility program to convert the HYSPLIT binary concentration
file to the DATEM data format
and
compares the model predicted results with the actual measured data.
The Data Archive of Tracer Experiments and
Meteorology (DATEM) web page contains
additional details about each of the experiments, the data formats, and more

complete descriptions of each of the programs used to convert the data and generate the statistical results. The on-line
repository has links to several
different tracer experiments and their associated meterological data. All
experimental
data have been converted to a common format. The meteorological
data are compatible for direct use by HYSPLIT.
To facilitate application of the analysis software, all the experimental data
from the second CAPTEX release are provide
in the ./hysplit/datem directory. Included are the control, namelist, measured data, and meteorological data files.
The
meteorological data is taken from the North American Regional Reanalysis.
The computational sequence is as follows:

1) Configure and Run HYSPLIT

Go to the concentration setup run menu and retrieve ./datem/captex.cnt
Go to the advanced configuaration concentration menu and retrieve ./datem/captex2.cfg
Save and then Run Model

2) Convert HYSPLIT run results to DATEM format

Browse to load the measured data file ./datem/captex2.txt
Create the DATEM file hysplit.txt from the binary file hysplit2.bin
Compute the Statistics and view the Scatter Plot
In the first section of the menu, a measured data file already in DATEM format
should be selected. The input data file
represents the HYSPLIT binary concentration
output file which is then converted to a DATEM formatted text file using
the units
conversion factor. The conversion program will match each measurement with a
model calculated
concentration corresponding to the location and time duration of
the measurement. Note that the model temporal output
frequency needs to be the same
or of finer resolution than the measurement periods, otherwise calculations cannot
be
matched with the measurements.
The rotation angle entry field (default = 0.0) can be used to test the
sensitivity of the model prediction to small changes
in wind direction. Setting
a non-zero angle will result in the rotation of the calculated plume with
respect to the
sampling network in the direction specified. The rotation is
computed using the first source location specified in the
setup menu. The effect of this test is comparable to rotating the transport wind direction by
the same amount. However,
this sensitivity test only makes sense in the context
of plumes that have a relatively homogeneous and stationary
structure.
Once the model output file in DATEM format has been created, the statistical
evaluation program should be run to
compare the model calculations with
the measurements in terms of various performance statistics. Two data processing

options are available. For verification statistics, all values can be compared, only plume values (both measured and
calculated values are greater than zero), or all values but excluding pairs where both measured and calculated values are
zero.
In terms of averaging, the measured and calculated values can be used directly,
temporally averaged resulting in
one value for each location, or spatially averaged
resulting in one value for each time period. The contingency level is
the
concentration value required to be exceeded to compute the false alarm rate, probability of detection, and threatscore. The contingency level is also used as
the plotting threshold for the measured-calculated scatter diagram which is
created
by the Scatter Plot menu button.
Note that simulations with multiple species and levels are not supported. The concentration data files follow no specific
naming convention and any input or output file name may be selected in the menu. Arbitrary input file names can only
be set
through the Setup / Grids menu. The statistical output files are always written
to stat{A|T|S}.txt where the
character A|T|S represents All data, Temporal
averaging, or Spatial averaging. An additional output file, data{A|T|S}.txt
is
created for the scatter diagram plot, which is always named scatter.ps.
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DATEM format description

Record 1 (ASCII) - file identification information
Record 2 (ASCII) - column identification information
Record 3 ... end - individual data records

Field 1 (I4) - start year of sample

Field 2 (I3) - start month of sample

Field 3 (I3) - start day of sample

Field 4 (I5) - start hour minute of sample (HHMM)

Field 5 (I7) - sample duration hours minutes (HHHMM)

Field 6 (F10) - sample location latitude (fractional degrees)

Field 7 (F10) - sample location longitude (fractional degrees)

Field 8 (F10) - sample value

Field 9 (I10) - sample station identification (integer)

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Concentration / Utilities / Convert to Dose (S347)

Concentration / Utilities / Convert to Dose

Converts a HYSPLIT binary concentration and deposition file to dose in rem/hr. The HYSPLIT calculation should be
done using a unit emission so that the concentration
units are m-3 and the deposition units are m-2. This postprocessing step reads the
file activity.txt which contains the activity (Bq) at time=0 for all the isotope
products. Sample
activity.txt files can be created by the program for a high-energy
nuclear detonation or a thermal fission reaction from a
power plant reactor.
The file also contains the half-life and cloud- and ground-shine does conversion
factors for each
radionuclide specified in the file.

For nuclear detonations, the activity.txt file contains columns for either a high-energy or thermal fission reaction
assuming a yield of 1 kT. The emission factor can be specified as a multiple of 1 kT. Activation products resulting from
the fission are not considered. Two fuel sources (U235 and Pu239) are available for each reaction type. The fission
yield data were obtained from T.R. England
and B.F. Rider, Los Alamos National Laboratory, LA-UR-94-3106;
ENDF-349 (1993). The
external dose rate for cloud- and ground-shine is computed from the factors given by
Eckerman
K.F. and Leggett R.W. (1996) DCFPAK: Dose coefficient data file package for
Sandia National Laboratory, Oak Ridge
National Laboratory Report ORNL/TM-13347.

During the processing step, the cumulative product of the activity and dose factor
is computed for each decay weighted
concentration averaging period, independently for noble gases and particles. Command line options exist to turn off the
dose
calculation but still multiplying the dispersion factors by the activity, resulting
in air concentration output. If the
dispersion factors input file contains only
one pollutant type and level, then an option can be set to output each of the
species
defined in the activity.txt file. Concentration units may also be converted from
Bq to pCi.

For nuclear power plant accidents, the same fission product table can be used by
entering the duration of the reactor
operation in terms of mega-watt-hours based upon the relation that 3000 MW-hours releases an energy equivalent to
2.58 kT. An
alternative approach is to generate an activity.txt file that corresponds with the
radionuclide release profile
of the reactor accident. The command line option
-afdnpp will create a sample activity.txt file that corresponds to the
maximum
emissions over a 3-hour period during the Fukushima Daiichi Nuclear Power Plant
accident for the 10 most
critical radionuclides for short-term dose calculations.

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Post Processing Program CON2REM command line options (default):

-a[activity data file name (activity.txt) or {create|fdnpp}]
Names the input file describing activity associated with each species and the dose
conversion factors. The -acreate
option will create a sample activity.txt file
for a 1kT detonation with just a few species to illustrate the format.
The -afdnpp
option will create a file with the top ten radionuclides contributing to dose
during the Fukushima
Daiichi Nuclear Power Plant accident. The activity for those
radionuclides represents the
-b[breathing rate for inhalation dose in m3/h (0.925)

The breathing rate is used as a multiplier for the calculation of the inhalation dose factor. This is only used for the
cloudshine dose calculations.
-c[Output type: (0)-dose, 1-air conc/dep]

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If the flag is set to one, the dose conversion factors are set to one and the output
will be concentration,the product
of the input air concentration (from a unit emission)
times the activity for each radionuclide defined in
activity.txt. The values are summed for all species in each pollutant class (NGAS or RNUC).
-d[Type of dose: (0)=rate (R/hr) 1=summed over the averging period (R)]

When computing dose, the option is to output a rate or the total dose accumulated over
each concentration
averaging period. Note that dose from deposition is always summed
over the duration of the simulation.
-e[include the inhalation dose in the calculation (0)=No 1=Yes]'
This is used in conjunction with the -b option. The default is not to include the
inhalation dose as part of the
cloudshine calculation. If this is turned on, insure that
the inhalation dose factors are correctly defined in the last
column of activity.txt.
-f[fuel (1)=U235 2=P239]

This flag selects which column of the activity.txt file will be used to determine the
emission amount. The first two
columns are for U-235 fission and the last two columns are
for Pu-239 fission. There are columns for highenergy or thermal fission (see -p flag).
Also see the -y and -w flags to scale the emissions to the event.
-g[decay type: 0=normal {c=1}, (1)=time averaged decay]
Prior to computing the dose, the activity is time-decayed to either the end of the
sampling time (0=normal) or as
the time averaged activity between the start and end time
of each sampling period (1=time-averaged, the default).
Normal decay can only be applied
to air concentration calculations. Dose output always requires time-averaged
decay.
-h[help with extended comments]
Provides a short narrative of the functionality of this program with a list of all the
command line options.
-i[input file name (cdump)]
The name of the HYSPLIT air concentration/deposition binary output file. The simulation
can contain both air
concentrations and deposition field. Proper conversion of the model output
fields to dose requires a unit release
rate in the HYSPLIT calculation.
-n[noble gas 4-char ID (NGAS)]
The program searches for this pollutant 4-character identification to use as the dispersion
factor for noble gases.
All other ID values (RNUC, etc) are assumed to be for particles. All
species will be summed to either the NGAS
or the other dispersion factor unless species matiching
is defined (-s1).
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-o[output file name (rdump)]

The output file will contain the same number of levels and time periods as the input file
but with the dispersion
factors (unit concentrations) converted to dose or species concentration
according to the settings of the other
command line options.
-p[process (1)=high-energy 2=thermal]
Defines which column of the activity.txt file to use for a specific fuel type. Option 1 is for high-energy fission
(columns 1 or 3) and option 2 is for thermal fission (columns 2 or 4).
In the case of the FDNPP activity.txt file,
the activity values are the same in all columns.
This feature may be used with customized activity.txt files to
select different source options.
Also see the -f flag for selection the fuel type.
-q[convert dose from rem=0 to sieverts=(1)]

The default dose output is in REM because the conversion factors are defined in the activity.txt
file in REM/Bq.
Setting this value to one converts the dose output from REM to Sieverts
(100 REM = 1 Sievert).
-s[(0)=sum species, 1=match to input, 2=output species]

The default value (0) sums each species in the the activity.txt file to its corresponding
pollutant class (NGAS noble gas, or RNUC - radionuclide particle). The match to input option (1)
just does a one-to-one match of the
pollutant ID in the activity.txt file with the pollutant IDs
used in the simulation. Pollutant IDs can be 4-digit
integer number or character for option (1). In
option (2), the output file can be expanded to include a
concentration for each species defined in
the activity.txt file using the dispersion factors from its pollutant class
from the simulation.
In this configuration, HYSPLIT can only be run with one level and species.
-t[0=no decay input decayed, or decay by species half-life (1)]
The default (1) is for all species to be decayed to the valid time of the concentration output
from the start time of
the simulation which is assumed to be the time fission ceased. The time of
release to the atmosphere can occur
much later. The no decay option is only required when decay
has already been applied in the dispersion
calculation. In general, decay should only be set in
the dispersion calculation for short-duration releases which
coincide with the termination of
fission, otherwise decay may be computed incorrectly. Computing decay within
this post-processing
step is the most accurate way to approach dose simulations.
-u[units conversion Bq->pCi, missing: assume input Bq]
When air concentration output is selected, then the output units can be converted from Bq to pCi.
-w[Fission activity in thermal mega-watt-hours, replaces the -y option value]
If the activity.txt file represents the number of fissions per kT, and the -w field is non-zero, then the activity is
computed with respect to the number of MWh generating the fission products. The assumption is that a 3000
MW reactor creates about 2.58 kT per hour of fission products.
-x[extended decay time in hours beyond calculation (0)]

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Additional decay time can be added using this field to estimate long-term doses. This calculation
applies to either
-t option but only for deposition doses. This option permits longer-term doses to be
computed by adding
additional decay to the existing output files.
-y[yield (1.0)=kT]

The default assumes that the activity levels defined in activity.txt represent the emissions
from a 1 kT device.
Other values are computed as a multiplier to the values defined in the table.
The multiplier can be used in the
context of a detonation in terms of kT or a multiple of the
3-hour emission maximum from the Fukushima
Daiichi Nuclear Power Plant accident.
-z[fixed decay time in hours (0)]'
The fixed decay is computed to the end of the sample time in the output file regardless of the
actual simulation or
release start time. All output periods, regardless of sampling time, will be decayed for these number of hours.

An example of the activity.txt file for a 1 kT detonation:

Mass Nucl T1/2 U235H U235T Pu239H Pu239T Cloudshine Groundshine Inhalation
Hr= 0.00 sec Bq Bq Bq Bq rem/h|Bq/m3 rem/h|Bq/m2 rem/Bq
85 Kr 3.38613E+08 9.44699E+11 7.53098E+11 5.74803E+11 3.27318E+11 9.18000E-11 0.00000E+00
0.00000E+00
90 Sr 9.18326E+08 4.50386E+12 5.67152E+12 2.06059E+12 2.06059E+12 3.53880E-11 5.90400E-13
2.38000E-06
131 I 6.94656E+05 5.31842E+15 3.74884E+15 5.64272E+15 5.00710E+15 6.08400E-09 1.31040E-10 7.38000E07
133 Xe 4.52995E+05 1.10002E+16 1.33275E+16 9.66744E+15 1.39641E+16 5.00400E-10 0.00000E+00
0.00000E+00
137 Cs 9.52093E+08 4.66591E+12 5.85842E+12 4.21162E+12 6.25592E+12 3.34080E-11 1.07640E-12
4.63000E-07
140 Ba 1.10160E+06 3.68093E+15 5.07968E+15 3.02654E+15 4.37621E+15 2.90520E-09 6.84000E-11
1.03000E-07
140 La 1.44979E+05 2.81554E+16 3.86593E+16 2.38668E+16 3.33141E+16 3.99600E-08 7.77600E-10
1.07000E-07

An example of the activity.txt file for the Fukushima-Daichii Nuclear Power Plant Accident for the top ten
radionuclides important for short-term dose calculations. The activity represents the maximum number of Bq released
over a 3 hour period.
Mass Nucl T1/2 U235H U235T Pu239H Pu239T Cloudshine Groundshine Inhalation
Hr= 0.00 sec Bq Bq Bq Bq rem/h Bq/m3 rem/h Bq/m2 rem/Bq
95 Nb 3.02000E+06 1.62000E+13 1.62000E+13 1.62000E+13 1.62000E+13 1.26000E-08 2.62000E-10
2.38000E-06
110 Ag 2.18000E+07 6.48000E+12 6.48000E+12 6.48000E+12 6.48000E+12 4.57000E-08 9.29000E-10
2.38000E-06
132 Te 2.82000E+05 1.62000E+16 1.62000E+16 1.62000E+16 1.62000E+16 3.36000E-09 7.63000E-11
7.38000E-07

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131 I 6.94656E+05 8.10000E+15 8.10000E+15 8.10000E+15 8.10000E+15 6.08400E-09 1.31040E-10 7.38000E07

133 I 7.49000E+04 8.10000E+15 8.10000E+15 8.10000E+15 8.10000E+15 9.94000E-09 2.22000E-10 7.38000E07
133 Xe 4.52995E+05 3.66000E+17 3.66000E+17 3.66000E+17 3.66000E+17 5.00400E-10 0.00000E+00
0.00000E+00
134 Cs 6.50000E+07 8.10000E+14 8.10000E+14 8.10000E+14 8.10000E+14 2.54000E-08 5.33000E-10
4.63000E-07
137 Cs 9.52093E+08 8.10000E+14 8.10000E+14 8.10000E+14 8.10000E+14 3.34080E-11 1.07640E-12
4.63000E-07
140 Ba 1.10160E+06 4.05000E+13 4.05000E+13 4.05000E+13 4.05000E+13 2.90520E-09 6.84000E-11
1.03000E-07
140 La 1.44979E+05 4.05000E+13 4.05000E+13 4.05000E+13 4.05000E+13 3.99600E-08 7.77600E-10
1.07000E-07

As an example, a HYSPLIT simulation could be configured with two species, NGAS for the noble gases and
RNUC for
the radio-nuclide particles. After the emissions stop, the total emissions of both NGAS and
RNUC should equal one.
Then in the post-processing step, con2rem is called and the concentration
and deposition fields are multiplied by the
total emission and dose conversion factor for each species and
added together to get a ground-shine and cloud-shine
dose file, which can then be plotted using any of the standard HYSPLIT display programs. Dose results, by species, are
decayed to the valid time of the
output graphic. An additional time factor can be added for long-term dose estimates.
One aspect of applying the decay in the the post-processing step is that the decay times are referenced to the start of the
simulation rather than the start of the release. This means that the
radionuclide release rate is valid at the start of the
simulation time. This might be the best configuration for a nuclear power plant accident, where the fission is assumed
to have stopped
at the start of the release (and simulation). However in other situations, where emissions might
be
occurring in concert with some other process, then starting the decay at the time when the
radionuclides are released
might be a more appropriate configuration. If the decay is computed
during the model calculation for each species
released then use the con2rem options -s1 -t0 to apply just the emission factors and not decay in the post-processing
step.

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Concentration / Utilities / Convert to IOAPI (S343)

Concentration / Utilities / Convert to IOAPI

This menu calls a utility program to convert the HYSPLIT binary concentration file to the IOAPI gridded data format.
Multiple species, levels, and time periods are supported. The conversion program is currently only available on UNIX
or LINUX systems. The data files follow no specific naming convention and any input or output file name may be
selected in the menu. Arbitrary input file
names can only be set through the Setup / Grids menu.

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Concentration / Utilities / Convert to Station (S342)

Concentration / Utilities / Convert to Station

The purpose of the Convert to Station utility menu (also called time
series data extraction) is to list concentrations at
specific latitude-longitude
locations by extracting that information to a text file. The menu also has an
option to
produce a time series plot at one or more of the stations or a KML
formatted file suitable for display by Google Earth.
An illustration of the menu is shown below. The concentration grid names are determined from the Concentration /
Setup Run menu tabs and therefore the setup menu needs
to be called prior to opening this menu. The species and
height values are index
numbers starting at one. A height index of 1 is the data at the first output
level, regardless of its
actual height value. The date field can be written
as a fractional Julian day (for plotting) or using a MM/DD/YYYY
field
(for spreadsheets) with or without an index record. The no index record option
is used to concatenate multiple
files.
The TCM checkbox is used to flag the input file as having been created
using the ICHEM=10 namelist option. There is
no specific
marker in the concentration to indicate that the file is in this format. The file
contains multiple pollutants,
each associated with a different time of release.
The TCM flag also causes the first output time group with each record
to be associated with the time of release rather than the time of the sample collection. The second time group of the
record becomes the start time of the
sample collection.

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Concentration / Utilities / Convert to Station (S342)

Similar to the other menus in the utility section, the input concentration
file must be defined in the Concentration Setup
menu.
The menu options correspond to the command line
options of the con2stn extraction program. There are two
options that
can be used to define an extraction location. A station location can be defined directly as an entry in the
menu, or a list of stations can be defined using an input file. If the input file does not exist, it can be
created by using
the New File button. In this example illustration,
a file has been defined with three locations that are within the plume
of the
example simulation. The file consists of three records, one for each station:

The extraction program is called con2stn and for these three stations,
produces the output file shown below, called by
default con2stn.txt. The
base name of the output file (con2stn) can be changed in the menu. In contrast to the simulation
shown in all the previous examples, in this
case the output averaging time was decreased from 12 hours to one hour,
to
generate a smoother looking graphic.

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Concentration / Utilities / Convert to Station (S342)

The output file shows the Julian day, month, day, and hour of the sample
start; day and hour of sample ending time, and
the concentrations for each
station (location selected by latitude-longitude). The format of each output
record is as
follows:

F8.3, 6I4 - Starting: Julian day, year, month, day, hour; Ending: day, hour

XF10 - Concentration value at X stations

The lower section of the GUI is used to create a simple time series concentration
plot of the concentration time series or
an output file (con2stn.kml)
suitable for display by Google Earth. The con2stn.txt file is created first
which is then read
by the Google Earth conversion program (stn2ge).
For time series data, one or more stations may be plotted. The plotting feature
is also available through the command
line. The option is
selected from the Display Time Series checkbox. The program, timeplot,
reads the data file
produced by the con2stn conversion program and plots the
concentration values to the timeplot.ps output file. The
illustration for
the previous text file is shown below.

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Concentration / Utilities / Convert to Station (S342)

There are only two plot options supported through the GUI: linear or logarithmic ordinate scaling. If integer ordinate
units are desired then it may
be necessary to specify a units conversion factor, in this case 1015,
to create data in the text
file that can be plotted. With the log scaling option,
the conversion factor can be set to 1.0, and the ordinate scale will
cover the
appropriate order-of-magnitude range to plot all the data.
Command Line Options - con2stn
The program can be run from the command line or through interactive prompts
from the keyboard. The command line
argument syntax is that there should be no
space between the switch and options. The command line arguments can
appear
in any order: con2stn -[option {value}]

-a[rotation angle:latitude:longitude]

-c[input to output concentration multiplier]

-d[mm/dd/yyyy format: (0)=no 1=w-Label 2=wo-Label]

The default date format is to write a fractional Julian date in the first
output field. This format is required
for plotting purposes. However, a more
conventional month/day/year format can be selected, which is
more compatible with
spreadsheet applications. In the first option (=1) an informational header record
is
written. In the other option (=2) the header record is excluded, which is more convenient when appending
multiple files.

-h[half-life-days (one -h entry for each pollutant)]

-i[input concentration file name]

Unspecified file names will result in a standard input prompt.

-m[maximum number of stations (200)]

-o[output concentration file name]

-p[pollutant index (1) or 0 for all pollutants]

Level and pollutant index values can be selected for files with multiple levels
and species. Setting zero (0)
for either index forces the output to be the record
format rather than the column format. Record format
contains the index numbers for
the pollutant and level.

-r[record format 0=record (1)=column 2=datem]

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The default output format is to create multiple columns, one for each station,
for a selected pollutant and
level. Setting the value to one formats the output as one
record for each station, level, and pollutant. A
value of two sets the output to the
DATEM format.

-s[station list file name (contains: id lat lon)]

The station positions can be read from a file (space or comma delimited) with
the first field being an integer
that represents the location identification, followed by the decimal location in latitude and longitude.

-t[transfer coefficient processing]

-x[(n)=neighbor or i for interpolation]

The default interpolation method (-xn) is to use the value at nearest grid point to each latitude-longitude
position, otherwise bilinear interpolation (-xi) is
used.

-z[level index (1) or 0 for all levels]

Command Line Options - stn2ge [option {value}]

-i[input text file name] contains data in the format output from con2stn

-s[station list file name] same file used as input to con2stn

-o[google earth output filename (less .kml)]

Command Line Options - timeplot [option {value}]

-i[input concentration file name] contains data in the same format as output from con2stn

-m[minimum ordinate value (0.0)]

-n[sequential station number]

For files with multiple stations select the station to plot; default for multiple stations
is to plot all stations;
several stations can be selected to plot by appending station numbers
with the plus symbol: hence -n3+5+6
will plot stations 3, 5, and 6.

-p[draw only points, no connecting line]

-y[The default is linear ordinate scaling. The flag sets y-axis log scaling.]

-z[three character time label]

Note that multiple pollutants and levels are not supported. Timeplot labels can also be customized by creating a
LABELS.CFG file. See the Border Labels discussion for more information on this file format.

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par2conc

Convert particle position file to concentration file (S350)

This program reads the HYSPLIT binary particle output file (PARDUMP) and recalculates the concentrations using the
CONTROL file to determine grid dimensions, times, and output file names. Par2conc is used in conjunction with the

namelist variable NDUMP < 0 ( input and output of particle files).

The name of the particle positions output file is specified on the command line as follows:
USAGE: PAR2CONC -[options(default)]
INPUT PARAMETERS: -i[input file name (PARDUMP)]

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Concentration / Utilities / Particle Adjustment (S346)

Concentration / Utilities / Particle Adjustment

This menu calls a utility program that can be used to adjust the particle positions
prior to restarting the simulation from a
saved particle position file. The particle
position file needs to be written by setting the appropriate namelist parameter
as
described in the Advanced/Configuration Setup/Concentration menu tab.
Normally observational data should be
consulted prior to making any adjustments to the
particle positions. Positions are only shifted horizonatally and not
vertically. The same
horizontal adjustment is applied at all heights. If a height adjustment is required, the
model should
be re-run with a different initial particle height distribution.
One or more particle files may be processed by a single execution. A standard simulation
only generates one particle
output file containing positions at one or more time periods.
Multiple particle position files, with a three-digit suffix
(.001, .002, etc), are automatically generated by the ensemble version of the model. The
adjusted output is always
written to a new file name, defaulting to PARINIT, also
the default name for initializing a new simulation.
Regardless of how many time periods are contained in the particle position file,
the adjustment is only applied to one
time period, normally the initialization time period
for the next simulation. If the time field (-t) is not specified, then the
adjustment occurs
to the first time period in the file, otherwise the adjustment is applied to the MMDDHH
designated
in the time argument. Only this one time period is written to the output file,
regardless of how many time periods are
contained within the input file.
A particle position shift can be specified as an angular adjustment in degrees and distance
from a fixed location (such as
the particle source point). A shift may also be specified as
a window translation, where all particles within a given
latitude-longitude window are shifted
by a specified number of degrees in latitude and longitude. No particles outside
of the window
or beyond the radius are shifted unless the blending (-b) flag is set. In this case, the shift
is applied to
each particle in a linearly decreasing fashion to zero adjustment at a distance
of two windows.
The spatial adjustment of the particle positions in the HYSPLIT binary particle output file
are specified on the command
line (or through the GUI) as follows:
USAGE: parshift -[options (default)]
-b[blend shifting outside of the window or distance range]
-i[input base file name particle positions (PARDUMP)]
-o[output base file name of adjusted partciles (PARINIT)]
-r[rotation shift (degrees:kilometers:latitude:longitude)]
-s[search for multiple input files with .000 suffix attached to base name]
-t[time MMDDHH (missing field then process first time only)]
-w[window translation corners lat1:lon1:lat2:lon2 (-90.0:-180.0:90.0:180.0)]
-x[delta longitude for window translation (0.0)]
-y[delta latitude for window translation (0.0)]
The particle position file may be converted to a binary concentration file through the
command line utility program
par2conc.

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Concentration / Utilities / Transfer Coefficient (S337)

Concentration / Utilities / Transfer Coefficient

Overview: This menu can be used to solve the transfer coefficient matrix for the source term vector given a measured
data vector and where the matrix
values are the dilution factors for each source-receptor pair. The measured data vector
at multiple receptor locations and/or times is required and it must be defined in
the DATEM format. The format of this
file is
discussed more detail in the GeoLocation menu. Due to model errors
and insufficient sampling not all
simulations will yield a solution. Results are written
to the file source.txt.
Theory:Assume that the concentration at receptor R is the linear sum of all the
contributing sources S times the dilution
factor D between S and R:
S1D11 + S2D12 = R1
S1D21 + S2D22 = R2

The dilution factors are defined as the transfer coefficient matrix. The sum of each column
product SiDij shows the total
concentrations contributed by source i
to all the receptors. The the sum of the row product SiDij for receptor j would
show the total concentration contributed by all the sources to that
receptor. In this situation it is assumed that S is
known for all sources. The dilution
factors of the coefficient matrix are normally computed explicitly from each source
to all
receptors, the traditional forward downwind dispersion calculation.
In the case where measurements are available at receptor R and source S is the unknown
quantity, the linear relationship
between sources and receptors can be expressed by the
relationship:
Dij Si = Rj,
which has a solution if we can compute the inverse of the coefficient matrix:
Si = (Dij)-1 Rj.
For example, in the case of an unrealistic 2x2 square matrix (the number of sources
equals the number of receptors), the
inverse of D is given by:

| +D22 -D12 | 1/(D11D22-D12D21)

| -D21 +D11 |
The solution for S1 (first row) can be written:
D22R1/(D11D22-D12D21) - D12R2/(D11D22-D12D21)
As a further simplification, assume that there is no transport between S1 and R2(D12 = 0), and then the result is the
trivial solution that the
emission value is just the measured concentration divided by the dilution factor:
S1 = R1/D11
The matrix solution has three possibilities. The most common one is that there are too
many sources and too few
receptors which results in multiple solutions requiring singular
value decomposition methods to obtain a solution. The
opposite problem is that there are too
many receptors and too few unknowns hence an over determined system
requiring regression
methods to reduce the number of equations. Unfortunately, possibilities for a matrix solution
may
be limited at times due to various singularities, such as columns with no contribution to
any receptor or measured
values that have no contribution from any source. The solution to these problems is not always entirely numerical as the
underlying modeling or even the measurements can contain errors. Note that large dilution factors (very small predicted

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concentrations) at locations with large measured values will lead to large emissions to enable
the model prediction to
match those measurements. The opposite problem also exists in that
negative emission values may be required to
balance high predictions with small measurements.
The solution to the coefficient matrix is driven by errors, either in
the measurements, the
dispersion model, or the meteorological data.

Step 1: defines the binary input files which are the output file from the disersion
simulations configured to produce
output at an interval that can be matched to the measured
sampling data. Ideally the model simulation emission rate
should be set to a unit value. Each
simulation should represent a different discrete emission period. For example, a four
day
event might be divided into 16 distinct 6-hour duration emission periods. Therefore the matrix
would consist of 16
sources (columns) and as many rows as there are sampling data. The
entry field in step 1 represents the wild card string
*entry* that will be matched to the files
in the working directory. The file names will be written into a file called
INFILE.
This file should be edited to remove any unwanted entries.
Step 2: defines the measured data input file which is an ASCII text file in the DATEM format. The first record
provides some general information, the second record identifies all the variables that then follow on all subsequent
records. There
is one data record for each sample collected. All times are given in UTC. This file defines the
receptor
data vector for the matrix solution. It may be necessary to edit this file to remove sampling data that are not required or
edit the simulation that produces the coefficient matrix
to insure that each receptor is within the modeling domain.
Step 3: defines the file conversion details from sampling units to the
emission units. For instance, the default value of
10+12 converts the emission
rate units pg/hr to g/hr if the sampling data are measured in pg/m3 (pico = 10-12). The
exponent is +12 rather than -12 because it is applied in the
denominator. The height and species fields are the index
numbers to extract from the concentration file if multiple species and levels were defined in the simulation. The half

life (in days) is only required when dealing with radioactive pollutants and the measured data need to be decay
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corrected back to the simulation start time.

Step 4: creates the comma delimited input file called c2array.csv with the
dilution factors in a column for each source
and where each row represents a specific
receptor location. The last column is the measured value for that receptor. The
column title represents the start time of the emission in days from the year 1900. This step calls
the program c2array
which reads each of the measured data values and matches them to
the input files to extact the dilution factors from
each source to that measured value.
Step 5: solves for the source vector using the SVD (Singular Value Decomposition)
methods from Numerical Recipes,
The Art of Scientific Computing, Press, W.H., Flannery, B.P.,
Teukolsky, S.A., Vetterling, W.T., 1986, Cambridge
University Press, 818 p. The solution may be controlled to some extent by defining a threshold zero dilution factor,
below which
the dilution factors are set to zero. An alternative approach is the define a cumulative
percentage dilution
factor, below which an entire sampling row may be eliminated. For instance,
if the % delete field contains 10, then the
rows representing the lowest 10% of the dilution
factors are removed. In the event the computation fails to produce an
adequate solution, it may be necessary to edit c2array.csv. The solution results are written
to an output file source.txt
and also displayed throught the GUI. A solution
may contain negative values as well as extreme positive emission
results. Such values are not
realistic and are a result of model errors or other uncertainties. This step calls the
program
tcsolve.

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Concentration / Special Runs (S356)

Concentration / Special Runs

Special simulations may require a different executable file,
modifications to the Control file that are not supported by
the
GUI, or interactions with other items under the Advanced Menu tab. More information is provided
below for each
special simulation. Special model configurations may
not be available for all operating systems. Note that most of the

special simulations may be run using a single processor system or

multiprocessor system (supporting MPI).
Daily
This menu will execute a special script to run the last configured
dispersion calculation for multiple starting times,
creating an output file for each simulation. More information is available from
the daily help menu.
Matrix
Although the setup of the concentration matrix calculation is
similar to that of the trajectory
matrix calculation, there is
an additional option that can be
set in the Advanced Menu configuration tab
that changes the nature of the
concentration output file to produce
a source-receptor matrix. This will be discussed further below.
The matrix
calculation is a way to set up the CONTROL file
for multiple starting locations that may exceed the GUI limit under
the
Concentration Setup menu tab. Hundreds or
thousands of starting points may be specified. The Run Matrix
menu tab
first runs a program that reads the CONTROL file with
three starting locations and then rewrites the same CONTROL

file with multiple locations. The multiple locations are computed

from the number of starting points that fall in the
domain between
starting point 1 and starting point 2, where each new location is
offset is the same as that between
starting locations 1 and 3. For
instance, if the original control file has three starting locations:
#1 at 40N, 90W; #2 at
50N, 80W, and #3 at 41N, 89W; then the matrix
processing results in a Control file with 121 starting locations,
all one
degree apart, all between 40N 90W and 50N 80W.

In the normal model execution mode, the concentration contributions

from multiple sources are summed on the
concentration grid, hence it is
not possible to determine the fraction of the material comes from each
source location.
This can be seen in the illustration below using the
above configuration for the first 12 hours of the sample case.

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However, if the "Matrix" conversion module is checked in the Advanced Concentration Configuration menu tab,
then
the multiple source simulation maintains the identity of each
source in the concentration output file. The Display Matrix
menu tab permits extraction of information for
individual sources or receptors from this special concentration
output
file. The results of the same simulation are shown in the
illustration below. In this case the receptor check-box was set
and
the receptor location was identified as 45.0,-75.0 with normalization.
Therefore the graphic illustrates the fractional
contribution of each
region to the first 12 hour average concentration at the designated
receptor.

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The following table illustrates the HYSPLIT matrix configuration.

Emissions occur from each of N source locations and
the receptors represent the concentration grid of M nodes. A single concentration
output file is produced where each
source contributes to its own
concentration grid of M receptors. When selecting a "source" display,
the M columns
from the source location (row) represent the downwind
concentration pattern for that source. When the receptor
location
(column) is selected, the contours represent the concentrations
(each row of that column) contributing to that
receptor from each
of the source locations. Source and receptor grids should be of
comparable resolution.

There are two other more quantitative approaches to source-attribution

available through the menu and both require the
measured sampling data. In
the first approach, menu system is used to configure
the model to execute a script to run
multiple iterations of the upwind dispersion
calculation for periods that correspond with individual measured sampling
data.
The results are then overlaid to determine the most likely source region. In
the second approach, the menu system
is used to solve the
source-receptor coefficient matrix for the source term vector given a measured
data vector and
where the matrix values are the dilution factors for each source-receptor pair as described above.
Geolocation
In a manner similar to the daily menu, the dispersion model can be run for
multiple simulations in time but where each
simulation is configured as an
adjoint calculation (backward in time) from measured concentration data points.
More
information on this procedure can be found in the geolocation help menu.

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Ensemble-Meteorology
The ensemble form of the model, an independent executable, is
similar to the trajectory version of the ensemble. The

meteorological grid is offset in either X, Y, and Z for each member

of the ensemble. The model automatically starts
each member on a
single processor in a multi-processor environment or cycles through
the simulations on one
processor. The calculation offset for each
member of the ensemble is determined by the grid factor as defined
in the
Advanced Concentration
Configuration Tab. The default offset is one meteorological
grid point in the horizontal and
0.01 sigma units in the vertical.
The result is 27 ensemble members for all offsets. The normal Setup Menu tab is used
to configure the
CONTROL file. Note that if fewer than 27 processors are
available, the ensemble configuration menu
permits starting the
calculation at any ensemble member number within the valid range.
Because the ensemble
calculation offsets the starting point, it is
suggested that for ground-level sources, the starting point height
should be at
least 0.01 sigma (about 250 m) above ground. The model
simulation will result in 27 concentration output files named

according the file name setting in the control file "{cdump}.{001

to 027}" with a suffix equivalent to the ensemble
member number. On
a single processor system, the calculation may take some time to
cycle through all the memberes.
The menu will be locked until the
simulation has completed. A message file window will open after
termination.
Computational progress may be monitored by noting the
generation of new concentration output and message files with
the
ensemble number suffix in the /working directory. The concentration
output from each member can be displayed
through the concentration display menu tab. However, to
display the probabilities associated with the multiple
simulations,
it is necessary to pre-process the data through the Display Ensemble menu tab. Using the default
configurations for
the sample simulation, the illustration below represents the 90th
percentile concentrations
aggregating all four output time periods.
For instance the blue contour in this 90th percentile
plot represents the region
in which only 10% of the ensemble
members have air concentrations greater than 10-15. If the meteorological ensemble
is run through a script or batch file instead of the GUI, the executable, with a command line parameter of the member
number, must be run once for each of the 27 members.

Ensemble-Turbulence
Another ensemble variation is the turbulence option, which
also creates 27 ensemble members, but due to variations in
turbulence
rather than variations due to gradients in the gridded meteorological
input data. The variance ensemble
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should only be run in the 3D particle

mode and with fewer particles, in proportion to the number of ensemble
members
to the number of particles required for a single simulation.
For instance, if 27,000 particles are required to obtain a
smooth plume
representation, then each member should be run for 1000 particles. Normally
the same random number
seed is used when computing the turbulent component
of the particle motion. However, in the variance ensemble, the
seed is different for each member, resulting in each member representing one realization of the ensemble.
The variance ensemble can also be used to determine the number of particles required for a simulation, by progressively
increasing the particle
number until the variance decrease with increasing particle number is no
longer significant.
Because the number of particles required for a
simulation increases with increasing distance from the source, a typical

downwind receptor location needs to be selected and then by using the box plot display option, the concentration
variability (max-min range)
can be estimated and then determining when the decrease in range is no
longer cost
effective (in terms of computational time) with increasing
particle number.
Ensemble-Physics
The physics ensemble is created by running a script that varies in
turn the value of one namelist parameters from its
default value. These
are the parameters defined in the file SETUP.CFG and normally set
in the Advanced
Concentration Configuration menu tab.
If the namelist parameters have not been defined through the menu, then the

default values are assigned. In this first iteration, the GUI menu permits
no deviation from the values assigned by the
script. The entry box is for
information purposes only to show the progress of the computation.

A summary of the current 20 ensemble variations is also written to the

file ensemble.txt showing the name of the
concentration output file
and member variation. Check the advanced menu help files for more information
on each
variable.

cdump.001 : initd = 0

cdump.002 : initd = 3

cdump.003 : initd = 4

cdump.004 : kpuff = 1

cdump.005 : kmixd = 1

cdump.006 : kmixd = 2

cdump.007 : kmixd = 1500

cdump.008 : kmix0 = 50

cdump.009 : kzmix = 1

cdump.010 : kzmix = 2 ; tvmix =0.5

cdump.011 : kzmix = 2 ; tvmix =2.0

cdump.012 : kdef = 1

cdump.013 : kbls = 2

cdump.014 : kblt = 1

cdump.015 : kblt = 3

cdump.016 : tker = 0.10

cdump.017 : vscales = 5.0

cdump.018 : vscaleu = 1000.0

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cdump.019 : hscale = 5400.0

cdump.020 : hscale = 21600.0

Ensemble reduction based on minimization of square error
Over the last few years, the use of dispersion model ensembles has been an increasingly attractive approach to study
atmospheric transport in the lower troposphere. Ensembles are constructed either by combining multiple numerical
weather prediction simulations, different dispersion models, introducing variations in a particular models physics
parameterizations or different combinations of these variations. The determination of the optimum number of multimodel members and/or individual model physical features to vary is the primary difficulty to overcome when
constructing these dispersion simulation ensembles. In many studies the ensemble members just consisted of the
available model outputs from different research groups regardless of the model characteristics or the result of
performing an arbitrary number of runs with different configurations by individual researchers. Both approaches
increase the possibility of redundancy which means that many of the ensemble members may not be much different
from each other. In general, any ensemble might contain redundant information that overemphasizes certain transport
and dispersion features that can be inaccurate. For example, perhaps a sub-group of members all use the same
meteorological data, which might not be as accurate as another meteorological data set that is used by fewer members.
Therefore, simply due to a dependency among many of the members to the same data, the ensemble including these
members would be less accurate than one constructed from an ensemble based upon only the independent members.

Conversely, independence among ensemble members does not necessarily imply that the reduced group of runs will be
more accurate than the full ensemble because, by chance, the later
could be also over emphasizing redundant members
that happen to be more accurate. Consequently, we can apply reduction techniques with the intent to produce more
accurate results than those obtained with the full ensemble and therefore requiring fewer computing resources. Solazzo
and Galmarini (2014) demonstrated that an ensemble can be reduced by optimizing the skills of the mean taken among
all the possible subsets of ensemble members. Following this methodology we calculate the average of all the possible
model combinations composed by an increasing number of sub ensemble members up to the total number of members
of the full ensemble and estimate their MSE. Furthermore, if M is the total number of ensemble members and n is the
number of sub ensemble members, then the number of possible combinations is given by M!/(n!*(M-n)!). In other
words, if our ensemble has, say, 24 members we will combine
them in 276 pairs, 2024 trios, 10626 quartets, etc. and
determine which combination provides the minimum MSE.
The reduction technique is applied by running a
postprocessing program that reads the different ensemble member outputs along with the measured data (all in DATEM
format) and calculates the minimum
square errors for each possible model output combination.

E. Solazzo, S. Galmarini, 2014. The Fukushima-137Cs deposition case study: properties of the multi-model ensemble,
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Concentration / Special Runs (S356)

Journal of Environmental Radioactivity, Available online 22 March 2014, ISSN 0265-931X,

http://dx.doi.org/10.1016/j.jenvrad.2014.02.017
Global
The global simulation is a HYSPLIT "grid-in-plume" option, in which the
Lagrangian particle mass can be transferred
to a global Eulerian model after
a designated number of hours. Lagrangian and Eulerian dispersion and transport
can
occur simultaneously. Each model has its own output grid. The advantange
of this approach is that at times very longrange calculations may require too
many particles to properly represent the pollutant distribution. In this way it is

possible to take advantage of the the more precise Lagrangian approach near the
source and the more computationally
efficient Eulerian computation at the
hemispheric and global scales. More information on how to configure this
simulation
can be found in the global model help menu.
Dust Storms
A model for the emission of PM10 dust has been constructed (Draxler, R.R, Gillette, D.A., Kirkpatrick, J.S., Heller, J.,
2001,
Estimating PM10 Air Concentrations from Dust Storms in Iraq,
Kuwait, and Saudi Arabia, Atmospheric
Environment, Vol. 35,
4315-4330) using the concept of a threshold friction velocity which
is dependent on surface
roughness. Surface roughness was correlated
with geomorphology or soil properties and a dust emission rate is

computed where the local wind velocity exceeds the threshold

velocity for the soil characteristics of that emission cell.
A
pre-processing program was developed that accesses the HYSPLIT
land-use file over any selected domain and
modify the input CONTROL
file such that each emission point entry corresponds with a
"desert" (active sand sheet)
land-use grid cell. The original PM10
flux equation was replaced by a more generic relationship
(Westphal, D.L., Toon,
O.B., Carlson, T.N., 1987. A two-dimensional
numerical investigation of the dynamics and microphysics of Saharan

dust storms. J. Geophys. Res., 92, 3027-3029).

The dust storm simulation is configured in the same way as the
matrix calculation in that it is
necessary to define three
source locations, the first two
representing the limits of the domain, and the third defining the
emission grid resolution.
The pre-processor then finds all emission
points within that domain that have a desert category and modify
the
CONTROL file accordingly. The dust box must be checked
in the advanced configuration menu
to compute the PM10
emission rate. As an example, we can configure
the model to run the large Mongolian dust storm of April 2001. An

animation of the calculation results can be downloaded. To run

the same simulation it will be necessary to obtain the
first two
weeks of northern-hemisphere meteorological analysis data (FNL.NH.APR01.001). A
pre-configured
CONTROL file (dust_conc) should be
retrieved from the working directory. The CONTROL file
defines the emission
domain by the three starting locations:
35N-90W to 50N-120W with the grid increment to 36N-91W. There is no
point
in defining an emission grid of less than one-degree
resolution because the resolution of the land-use data file is
onedegree and the meteorological data is closer to two-degrees.
Once the model is setup for the simulation, including the
dust
check-box in the configuration menu, execute the model from the
Special Simulations / Run Dust Storm menu tab.
Not available
through the GUI, but another option in the SETUP.CFG
namelist file, is the emission threshold sensitivity
factor, which
normally defaults to one. For instance, adding the line P10F=0.5
to the namelist file, would cause dust
emissions to occur at half the
normal threshold velocities. Starting the model will cause the window
shown below will
open to indicate the revision of the CONTROL file.

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The message indicates that the initial 3-location CONTROL

file was reconfigured by the dustbdy program for 105
source
locations. That means in the domain specified, 105 one-degree
latititude-longitude grid cells were found to have
a desert
land-use category. If none are found, then the CONTROL file
is deleted to prevent model execution. Click on
Yes or No to
continue - yes just deletes the window. The model execution will
then start. PM10 pollutant dust particles
are only emitted from
those 105 cells where the wind speed exceeds the emission
threshold. Therefore it is possible to
have simulations with no
emissions. An example of the output after 24 hours simulation time
is shown in the
illustration below.

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Concentration / Special Runs (S356)

The concentrations represent a 3-hour average from 21 to 24 hours after the start of the simulations. It is not possible to
say
exactly from when or where particles are emitted except to note
that the 105 potential source locations are shown.
The emission
algorithm emits in units of grams, but the in configuring the
concentration display, the units were
changed to ug by defining a
conversion factor of 106. Maximum concentrations are on
the-order-of 100, but the layer
was defined with a depth of 3 km to
facilitate comparison with satellite observations. The simulation
could be rerun
with a smaller layer to obtain concentrations more
representative of near-ground-level exposures.
Daughter Products
A nuclide daughter product module has been incorporated into HYSPLIT.
Given a chain of decay from a parent nuclide,
the model can calculate the
additional radiological activity due to in-growth of daughter products using the Bateman
equations.
Information about the available daughter products available in the model
can be found in ../auxiliary/ICRP07.NDX.
More information on how to configure this simulation
can be found in the daughter product help menu.

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Concentration / Special Runs / GeoLocation (S357)

Concentration / Special Runs / GeoLocation

Summary: This menu is used to configure the model to execute a script to run multiple
iterations of the upwind
dispersion calculation for periods that correspond with individual
measured sampling data. The model results are then
overlaid to indicate the most probable source regions. The CONTROL file should have been previously defined for a
forward calculation
that corresponds to the sampling period of the measured data. The measured data file must be in
the
DATEM format. The output is written to the source.ps Postscript file in the working directory.

Step 1: defines the measured data input used in this series of calculations. The dispersion model is run in its backward
mode, from each of the sampling locations, with a
particle mass proportional to the measured concentration and with
the particles released
over a period corresponding to the sample collection period. Sampling data files are in the ASCII
text DATEM format. The first record provides some general information, the second record identifies all the variables
that
then follow on all subsequent records. There is one data record for each sample collected.
All times are given in
UTC. The DATEM sampling data records have the following format:
INTEGER - Four digit year for sample start
INTEGER - Two digit month for sample start
INTEGER - Two digit day for sample start
INTEGER - Four digit hour-minutes for sample start
INTEGER - Four digit hour-minutes for duration of the sample
REAL - Latitude of the sampling point (Positive is north)
REAL - Longitude of the sampling point (Positive is east)
REAL - Air concentration in mass units per cubic meter
INTEGER - Site identification
An sampling data file which is used in the following calculations can be found in examples\matrix\measured.txt.
These

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synthetic measurements (units = picograms per cubic meter) were

created from a model simulation using the sample
meteorological data in the working directory for a hypothetical 6-minute (0.1 hr) duration release of 10 kg of material
from 40N 80W starting at 1200 UTC 16 Oct 1995.
Step 2: creates one CONTROL.{xxx} file for each sample (data record)
in the previously defined measured data file.
The CONTROL files are numbered
sequentially from 001 to a maximum of 999, the current limitation of the program
used to overlay the simulation results. The individual simulation
control files are created from the current configuration
shown in the
concentration setup menu. The examples\matrix\control_geo file and the examples\matrix\setup_geo
file
templates should be retrieved into the setup and configuration menus. The template is a configuration for a forward
simulation that encompasses the entire
sampling period, with output intervals that correspond with the sampling

intervals of the measured data. Essentially a configuration that could be used

to predict the concentrations at the
measurement locations if you knew the actual
location and amount of the release. This step calls the pre-processor
program (dat2cntl) which uses the configuration as a template to design each individual simulation CONTROL file.
Each of these CONTROL files is configured as a backward simulation for the entire computational period, with the
particle release occurring over the time of the sample collection. This insures that each simulation output file will
contain an identical number of output periods, regardless of the time of the particle release. The template control file
should have all key parameters specified such as the starting time and the center of the concentration grid. Do not use
the zero default options in the CONTROL file, explicity set all variables. All simulations must be
identical.
There are three solution options. The default option Numerator, discussed
above, uses the measured concentration in the
numerator as the emission rate,
resulting in a source sensitivity map weighted by the measured data. Checking
the
Inverse box sets the source term as the inverse of the measured
concentration. This modeling scenario is comparable to
the S = R/D situation described in the matrix solution help file>. In this case
the model is computing D/R, where D is
the dilution factor computed by the model
and R is the measured concentration. The source term for the calculation is
set to 1/R and only measurements where R is greater than or equal to zero are considered.
Therefore, the resulting
output (D/R) is an estimate of the inverse of the source
term (1/Q) required to match the measured value for that
simulation. A unit conversion factor needs to be set to output the appropriate mass units. The
last option is to set the
Constant radiobutton which results in the emission rate equal to the value set in the constant conversion factor entry
box.
In this type of simulation, each sample gets equal weight and the model results
may be used to determine the
optimal emission rate required to match the
measured data.
Step 3: sequentially runs the dispersion simulations starting with CONTROL.001 through the last available control file.
Each simulation uses the same namelist configuration shown in the menu. Note that a simulation is run for each
measurement, high values as well as zero measurements. Non-zero measurements result in an hourly emission rate
equal to the measurement value, while zero measurements are set to a very small, but non-zero value. In the context of
this particular calculation, the intent of the source-attribution is primarily to determine the source location and perhaps
its timing rather than estimating the emission rate from the measurements. Determination of emission rates should be
done through the matrix menu
option. The measurement data are only used to weight the source-sensitivity
results for
each simulation. Depending upon the model setup and configuration,
simulation wall-clock times may vary
considerably. Each simulation output results in a binary concentration file and message file with the same run number
suffix as the control file.
Step 4: shows the multiple simulation results by averaging the source sensitivity function at each grid point over all the
simulations. The
dispersion model result of the upwind (backward) calculation looks similar to
the air concentration
field of the downwind (forward) calculation, but represents not concentration, but the source regions that may
contribute to
the air concentration at the measurement location from which the upwind
calculation was started. There
are two optional parameters that influence the
output graphic. The time aggregate default is one, meaning that each
sampling
period is represented by one graphic. In the example calculation shown below,
the source sensitivity function
is shown for the last time period of the
simulation and represents the average of all the simulations (zero and non-zero)

from different time periods valid for that 6-hour sampling period. A time aggregation value of 5 would average the
results from all 5 time periods into
one graphic. The zero threshold value can be used eliminate the very low level

contours that result from the zero-emission simulations. For instance, selecting
a value of 1.0E-15 (1/1000 of a pg/m3)
would set to zero any grid points less
than that value.

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The comparable graphic for the inverse calculation is shown below for the mean emission values for 15 simulations that
had non-zero measurements. Before creating control files for the inverse simulation, previous control files should be
deleted to avoid mixing together the two types of simulations. For this example, the measured data file has 15 non-zero
measurements and 30 zero measurements and the
units conversion factor should be set to 1.0E-15 to go from pg to kg.
The resulting
interpretation of the graphic is that the central contour (value = 1) indicates
an average emission of 1 kg
in that region. The outermost contour (0.01) would require 100 kg to be released to match the measured data. Greater
dilution (D is
smaller) require greater corresponding emissions to match the measured data.

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Concentration / Special Runs / Global (S359)

Concentration / Special Runs / Global

The Global Eulerian Model (GEM) is invoked as a series of subroutines within
the main HYSPLIT transport and
dispersion code. Particles or puffs are always first
released in the Lagrangian framework and carried within HYSPLIT
until they exceed a
certain age at which point their mass is transferred to the GEM routines. Particles
can be released
and transferred for the entire duration of the simulation. The only
requirement is that at one pressure-level global
meteorological grid (2.5 degree
reanalysis or 1 degree GFS) needs to be defined for the HYSPLIT calculation.

Additional finer resolution regional meteorological grids can be defined for the
Lagrangian portion of the transport
calculation. Details of the global model have
been previously published: Draxler, R.R., 2007, Demonstration of a global
modeling
methodology to determine the relative importance of local and long-distance sources,
Atmospheric
Environment, 41:776-789, doi:10.1016/j.atmosenv.2006.08.052.

General Instructions
Although the HYSPLIT-GEM version has its own executable, without the required
namelist file GEMPARM.CFG the
calculation will proceed as a standard Lagrangian HYSPLIT simulation. In this situation, the model will write the
default
file gemparm.bak as a reminder that a GEM configuration file is required to
invoke the global subroutines. This
file can then be edited and renamed if not using the GUI interface. GEM and HYSPLIT each create their own
concentration output
files and if the total concentration is required, the results from the two calculations must be added
together. The program concadd is included in the
distribution and can be accessed from the global display menu
by
selecting the plume add checkbox. Furthermore, the GEM concentration grid is
always a snapshot concentration. There
is no averaging option. In general, the model
simulation is configured like any other HYSPLIT simulation, through the
CONTROL
and SETUP.CFG files. Additional GEM specific options are set in the GEMPARM.CFG file. Not all GEM
options are available through the GUI and can
only be modified by editing the file directly.
SETUP.CFG Namelist Configuration

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There are several parameters in the HYSPLIT namelist that are important for the
GEM subroutines. In particular, pay
attention to the following:
1. Set INITD to one of the conversion variables, any value >100, for instance 109
2. Set CONAGE (default=48 hours) for particle conversion into the global model. Note that when CONAGE<0 the
particles switch to the GEM grid when the particle meteorology
grid switches to global meteorological grid or
when the particle age=|conage|
3. When using an EMITIMES file, QCYCLE is not used for emission cycling. Also if
the EMITIMES file has fewer
sources than defined in the CONTROL file, the
emissions specified in the CONTROL file need to be set correctly
and match the
first value in EMITIMES.
GEMPARM.CFG GUI Namelist Options
Only a subset of the namelist options are available to be set through the GUI. Note
that concentration (mass/m3) output
will always be written to gemconc.bin as individual
or averaged layers, but the integrated output (mass/m2) will only be
written to gemzint.bin.
The bottom and top values are given as index numbers where 1 is the bottom layer. Layer
thickness corresponds with the input meteorological data and cannot be modified. The GUI interface is shown
below:

GEMPARM.CFG Namelist Description

HMIX=200000.0 - horizontal mixing (m2/s) at the equator

VMIX=50.0 - maximum vertical mixing (m2/s)
KMASS=2 - flag set to conserve mass (0:skip 1:show 2:yes)
KINIT=0 - concentration initialization (<0:no_run 0:zero 1:lat_bands 2:dew-point 3:last_dump 4:global_v37)
CKON=0.0 - value of initial concentration field if kinit>4
CMIN=0.0 - minimum value when using regression initialization (kinit=1|2)
CMAX=1.0E+25 - regression fit maximum value
WFACT=1.0 - sensitivity of advection to vertical velocity
KDIVG=0 - flag to compute vertical velocity from the divergence field (kdivg=1)
GEMDUMP='gemdump.bin' - daily 3-dimensional dump of concentration field (for initialization kinit=3)
GEMCONC='gemconc.bin' - HYSPLIT formatted concentration output file
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GEMZINT='gemzint.bin' - HYSPLIT formatted vertically integrated concentration

CFACT=1.0 - internal (model) concentration to external (output) concentration units conversion factor
KZBOT=1 - grid cell index for the bottom output (or integration/averaging) level
KZTOP=1 - grid cell index for the top output (or integration/averaging) level
KZAVG=0 - flag for vertical averaging (0:none 1:average{bot-top} 2:integral{bot-top} 3:{2+0} 4:{2+1})
WFREQ=3 - output frequency in hours
IHOUR=0 - initial UTC output hour

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Concentration / Special Runs / Daughter products (S365)

Concentration / Special Runs / Daughter products

Setting up this run consists in the following steps.

Step 1: Define the nuclide parent name (e.g. Cs-137) and run a preprocessor
(nuctree) that creates a summary text file
(DAUGHTER.TXT) that contains
the daughter nuclides produced by a parent nuclide along with the half-life and
branching fractions. This file is required to be in the working directory when running HYSPLIT for this application.
In
addition, the preprocessor will read the CONTROL file and create a new
(CONTROL.DAUGHTER) file containing the
daughter information. The names
of the species will be given in numbers that correspond to the daughter
products
names written in the DAUGHTER.TXT file.
Finaly, the GUI will copy the CONTROL.DAUGHTER back to
CONTROL.
Step 2: configure setup (SETUP.CFG) indicating that the daughter products module will be used (ICHEM=11) and set
Maxdim=#daughters obtained from DAUGHTER.TXT

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Concentration / Multi-processor (S358)

Concentration / Multi-processor
Special simulations may require a different executable file,
modifications to the Control file that are not supported by
the
GUI, or interactions with other items under the Advanced Menu tab. More information is provided
below for each
special simulation that can be run under a
multi-processor environment that supports MPI. These special
simulations
are available only for UNIX operating systems. All the
MPI simulations execute the special script run_mpi.sh which

can be found in the /exec directory. This

script executes the appropriate MPI executable variation of the
concentration
model and almost certainly will require some
customization to match the local operating system environment.
Run MPI Model
The standard concentration model can be run on multi-processor
systems. As pollutant particles are released during the
simulation,
they are parsed out in sequence to the available processors. The
calculation proceeds independently until the
end of a concentration
averaging period. At this point, the concentrations from each
processor are summed, and only
one concentration output file is
updated. The MPI version can be quite effective in speeding up
simulations requiring
the release of many particles. No special
configuration or control file is required and output can be viewed
using the
standard concentration display
menu.
Run Matrix Model
The multiprocessor version of the matrix calculation is
configured the same way as for a single processor system. The
MPI calculation proceeds as described above for the standard MPI model simulation.
Run Ensemble Model
The ensemble model automatically starts each member on a single
processor in a multi-processor environment. The
multiprocessor
version of the ensemble calculation is configured the same way as
for a single processor system.
Note
that if fewer than 27 processors are available, the ensemble
configuration menu permits starting
the calculation at any
ensemble member number within the valid
range of 001 to 027.
The Model Launch Menu
The model launch menu contains four entries: the number of processors
requested for the simualation, the name of the
executable, the Prep-Code, and the working directory. Each of these is assigned a default value depending upon the
calling menu. Normally there should be no reason to
change any of these values except the number of processors. If the
working
directory is changed and does not already exist, a new directory is
created, and the script changes to that
directory before starting the simulation.
The Prep-Code is just an internal flag to set any preprocessor options:
M = matrix
E = ensemble
S = standard
If the Prep-Code field is left blank, the MPI script is not called, and
the named executable will be run in background. In
this way multiple jobs
can be submitted on a multi-processor system in a non-MPI environment.
However, in both MPI
and non-MPI applications, when simultaneous calculations
are desired, it is important that each simulation have its own
working
directory.

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Concentration / Display / File Format (S363)

Concentration / Display / File Format

Concentration packing has been implemented with HYSPLIT version
4.5. The updated format is downward compatible
in that all display
programs can read files produced from versions prior to 4.5, but
older versions of the display
programs cannot read the new packed
output format. Note that HYSPLIT V4.5 can be configured to produced
the older
style unpacked concentration files. Concentration file
packing does not write the same information in fewer bytes, but

rather writes the same information using twice as many bytes. The
packed files are generally smaller because only
concentration
values at the non-zero grid points are written to the output file
by the model. However this requires the
grid point location to be
written with the concentration, hence the additional bytes. If most
of the grid is expected to
have non-zero concentrations, then the
old style format will save space. The output format of the
unformatted binary
(big-endian) concentration file written by
dispersion model (hycs_std) and read by all concentration
display programs is
as follows:
Record #1
CHAR*4 Meteorological MODEL Identification
INT*4 Meteorological file starting time (YEAR, MONTH, DAY, HOUR, FORECAST-HOUR)
INT*4 NUMBER of starting locations
INT*4 Concentration packing flag (0=no 1=yes)
Record #2 Loop to record: Number of starting locations
INT*4 Release starting time (YEAR, MONTH, DAY, HOUR)
REAL*4 Starting location and height (LATITUDE, LONGITUDE, METERS)
INT*4 Release starting time (MINUTES)
Record #3
INT*4 Number of (LATITUDE-POINTS, LONGITUDE-POINTS)
REAL*4 Grid spacing (DELTA-LATITUDE,DELTA-LONGITUDE)
REAL*4 Grid lower left corner (LATITUDE, LONGITUDE)
Record #4
INT*4 NUMBER of vertical levels in concentration grid
INT*4 HEIGHT of each level (meters above ground)
Record #5
INT*4 NUMBER of different pollutants in grid
CHAR*4 Identification STRING for each pollutant
Record #6 Loop to record: Number of output times
INT*4 Sample start (YEAR MONTH DAY HOUR MINUTE FORECAST)
Record #7 Loop to record: Number of output times
INT*4 Sample stop (YEAR MONTH DAY HOUR MINUTE FORECAST)
Record #8 Loop to record: Number levels, Number of pollutant types
CHAR*4 Pollutant type identification STRING
INT*4 Output LEVEL (meters) of this record

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No Packing (all elements)

REAL*4 Concentration output ARRAY
Packing (only non-zero elements)
INT*4 Loop non-zero elements
INT*2 First (I) index value
INT*2 - Second (J) index value
REAL*4 - Concentration at (I,J)

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Concentration / Display Data / Terrain Overlay (S364)

Concentration / Display Data / Terrain Overlay

The use of several menu features is demonstrated here that will permit
the creation of a map of the concentration plume with political
boundaries
and contours of the terrain as defined by the meteorological data. The
basic process is to create a shapefile of the terrain and add that
file
to a shapefile of the political boundaries. Although this demonstration is
for terrain and concentration any line or contour based shapefile
can be
displayed through the concentration or trajectory plotting programs.
Open the Meteorology / Display Data / Contour Map
menu and select the meteorological data file, the station height field (SHGT=terrain), and
set the GIS checkbox, which will output the terrain field in generate format. It might be necessary to force the contours and the center of the
map to get a nice looking display over the region of interest. In this case for the west coast of the U.S. the maximum terrain height was set to

2500 m with an interval of 250 meters between contours.

Run the contour program and the display shown below will be created.
In the working there will be an additional file called GIS_METEO_01.txt
which is the generate format text file of the terrain contours.

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Now open the GIS to Shapefile utility menu and browse for the generate format file name. Select the "Polygons" radiobutton to insure that the
terrain polygons are treated as closed connected lines. After processing the input file, four output files will be created with the base name of
contour. The subsequent plotting programs only need the contour.shp file, but the other files may be needed for import into other GIS
applications.

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If you do not have a plume simulation already completed, open the concentration setup menu and run the default test case, but move the starting
location to 40N 125W and run the model for 24 rather than 12 hours.
To simplify the output, set the concentration grid averaging time to 24 h

and reduce the grid resolution from 0.05 to 0.10. Then run the model.

After the run completes, go to the hysplit/graphics

directory and copy arlmap.shp and shapefiles_arl.txt to the working directory. Rename
shapefiles_arl.txt to shapefiles.txt. Then open notepad in working to edit shapefiles.txt to add the additional file (line) defining the shapefile
with the terrain. For this display, the line is twice as thick as the map background and the color is defined as black (0.0 0.0 0.0).

Now open the concentration / display / contours menu and define the
shapefiles.txt in the field for the map background. This will cause the
display program to use the files defined in this file rather
than the default map background. Multiple shapefiles can be displayed
at the same
time.

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Executing the display will result in the following image showing the
intersection of the plume with the elevated terrain as it moves to the
east.

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Table of Contents

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Advanced / Configuration Setup (S413)

Advanced / Configuration Setup

This section provides some guidance in configuring the model input to perform certain specialized calculations. The
default configuration
supplied with the test meteorological data is confined to a simple
trajectory and inert transport and
dispersion calculation. More complex
scenarios can be configured through the Advanced / Configuration Setup
menu
tabs. There are seven sub menus available.
1. The Trajectory tab opens a menu creation or modification of
the SETUP.CFG namelist file. This can be
accomplished through the GUI
or by directly editing the namelist file. The file is required to be in the
model
startup directory, usually ./working when running the model
through the GUI. More information about the
trajectory namelist variables
can be found in the trajectories help file.
2. The Concentration tab opens a similar menu to the trajectory
tab, but with many more options. The trajectory
and concentration
menus are confined to the variables relevant to the respective model calculation.
More
information about the concentration namelist variables can be found in the
concentration help file.
3. The Global tab opens a menu to create or edit a special namelist
file that configures the Global Eulerian Model
(GEM), a series
of subroutines within the main HYSPLIT transport and dispersion code. Particles or
puffs are
always first released in the Lagrangian framework and carried within HYSPLIT
until they exceed a certain age at
which point their mass is transferred to the GEM
routines. Particles can be released and transferred for the entire
duration of the
simulation.
4. The Dynamic Sampling menu is used to configure a special virtual
sampler that can move in space and time
through the computational
domain during the concentration simulation. Dynamic samplers can move passively
with
the wind or have a define pathway, similar to an airplane.
5. The Emissions File opens a menu to edit or create a point-source emission file that can define more complex
release scenarios than
could be created using just the CONTROL file. Simple scenarios like time-varying
emissions
to more complex moving line or point sources cab be configured.
6. The Set Directories menu is used to configure the GUI's directory structure as well as the location and name of
certain executable programs
used by the GUI. The structure is written to the default_exec file. If that file is
not
found in the startup directory, the GUI attempts to set all the values. Significant
differences are found between
Windows, Apple, and UNIX installations.
7. The Extra Labeling menu opens a simple editor menu to create a file of extra label information that is added to
the bottom of all trajectory or concentration plots. Only
these two display programs support the extra label
function.

Table of Contents

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Advanced / Configuration Setup / Trajectory (S411)

Advanced / Configuration Setup / Trajectory

This section provides some guidance in configuring the model input
to perform certain specialized calculations. The
default configuration
supplied with the test meteorological data is confined to a simple
trajectory calculation. More
complex scenarios can be configured through the Advanced, Configuration Setup, Trajectory menu tab. The menu is
used to modify the SETUP.CFG
namelist file. This file is not required, and if not present in the root
startup directory,
default values are used. These parameters can all be
changed without recompilation by modification of the contents of

SETUP.CFG and in some cases their modification will substantially

change the nature of the simulation. The
configuration file should be
present in the root directory. An illustration of the menu is shown below.

When using the GUI, the namelist file will be deleted and all variables
are returned to their default value by selecting
the "Reset" button.
The following summarizes the namelist variables and their corresponding section
in the GUI menu.
1.
2.
3.
4.
5.
6.
7.
8.

Set fixed or automatic TIME STEPS

Define subgrid and MSL/AGL UNITS
MULTIPLE trajectories in time
Trajectory points OUTPUT FREQUENCY
MIXING DEPTH computation method
Add METEOROLOGY output along trajectory
Meteorological grid offset ENSEMBLE
Summary of all NAMELIST variable defaults

Table of Contents

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Advanced / Configuration Setup / Concentration (S412)

Advanced / Configuration Setup / Concentration

This section provides some guidance in configuring the model input to
perform certain specialized calculations. The
default configuration supplied
with the test meteorological data is confined to a simple dispersion
calculation. More
complex scenarios can be configured through the Advanced / Configuration / Concentration Setup menu tab. The menu

is used to modify the SETUP.CFG namelist file. This file is not

required, and if not present in the root startup directory,
default values
are used. These parameters can all be changed without recompilation by
modification of the contents of
SETUP.CFG and in some cases their
modification will substantially change the nature of the simulation. The

configuration file should be present in the root directory. An illustration

of the upper-level menu is shown below.

When using the GUI, the namelist file will be deleted and all variables are
returned to their default value by selecting
the "Reset" button. The
following summarizes the namelist variables and their corresponding section
in the GUI menu.
Not all variables can be set through the menu system but may
be modified by directly editing the namelist file.
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.

Set fixed or automatic TIME STEPS

Define subgrid and MSL/AGL UNITS
Configure release of PARTICLES or PUFFS
Set the particle/puff RELEASE NUMBER limits
Set the puff SPLIT-MERGE parameters
Define EMISSION CYCLING or input file
Configure the TURBULENCE method
Concentration GRID PACKING method
Input and output PARTICLE FILES
In-line chemical CONVERSION MODULES
Meteorological grid offset ENSEMBLE
Summary of all NAMELIST variable defaults

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Advanced / Configuration Setup / Concentration (S412)

Table of Contents

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Advanced / File Edit / Dynamic Sampling (S415)

Advanced / File Edit / Dynamic Sampling

This menu creates the optional LAGSET.CFG file which is used to configure a dynamic sampler. A dynamic sampler is
defined as a moving sampler that can pass through the model simulation domain, either passively with the wind

(Lagrangian mode) or by using a pre-defined velocity vector (Forced mode). In the current version the dynamic sampler
transport is always vertically isobaric regardless of the vertical motion method selected for the pollutant transport. The
dynamic sampler samples model produced values that are generated internally on a snapshot concentration grid.
The first menu tab defaults to the configuration for one sampler. If multiple samplers are required, then enter the number
in this menu. After
pressing the Configure Samplers button, another menu comes up to
select the sampler number to
configure. Pressing the sampler number button
brings up the menu shown below. Each defined sampler must be
configured
according to the following instructions.

The dynamic sampler configuration file must be located in the model's

startup directory to be found and the name
should always be in uppercase.
The following is an example of the contents of LAGSET.CFG for one dynamic

sampler. Multiple samplers would repeat the last seven line sequence.
1 : number of dynamic samplers
40.0 -90.0 500.0 : release location and height (agl)
0.0 0.0 : force vector - direction, speed (m/s)
95 10 16 00 00 : release start - year month day hour minute
95 10 16 00 00 : sampling start - year month day hour minute
00 : sample averaging (min)
60 : disk file output interval (min)
'LAGOUT.TXT' : sampler output file

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Advanced / File Edit / Dynamic Sampling (S415)

Number of dynamic samplers: Due to file unit number restrictions, the current version only supports 9 simultaneous
sampler definitions. The following seven lines need to be repeated for every defined sampler.
Release location and height: The location is the latitude-longitude point at which the trajectory of the sampler path is
started. Although the subsequent vertical motion is isobaric, the initial starting height must be defined in meters above
ground-level. Note that the isobaric sampler trajectory will not be identical to the HYSPLIT trajectory model isobaric
trajectory because of differences in how the vertical motion is computed between the two models.
Force vector: If the direction (downwind) and speed (m/s) set to zero, then the model computes the sampler trajectory
according to the meteorological input data wind velocity. If any of these values are not zero, then the sampler
trajectory
is computed using these values for its entire length. To simulate a more complex aircraft sampling path, each leg of the
flight pattern requires its own sampler definition. For instance, an aircraft flying east with have a
direction vector of
090.
Release start: The release time of the sampler gives the date and time that sampler starts from the previously defined
release location. Note that in the current version, zero's for this field (relative start time) are not supported.
Sampling start: The sampler may proceed on its trajectory for quite some time before sampling is started. The sampler
start time must be greater than or equal to the release start time.
Sample averaging (minutes): At every computational time step the model determines the sampler position in the
concentration grid and accumulates the concentration value in memory. When the sampler accumulation time reaches
the sample averaging time, all sums are reset to zero. A sample averaging time of zero means that the sample is only
accumulated for one model integration time step.
Disk file output interval (minutes): At the disk output interval, the sampler concentration values are written to the output
file defined on the next input line. The value written is the accumulated concentration divided by the accumulated
minutes. The disk output interval is independent from the sample averaging time.
Sampler output file: The directory and file name should be enclosed in single quotes. If the file is defined without a
directory it is written to the model startup directory.
Concentration Grid Configuration
Note that dynamic sampling will only work if the sampler trajectory passes through a concentration grid covering the
region of interest. That means that a
concentration grid of sufficient resolution, in both the horizontal and vertical is
required for a sampler to capture the pollutant. However too much resolution (too fine a grid) may mean that there
could be an insufficient number of pollutant particles to provide a uniform distribution and therefore the sampling could
provide unrepresentative results. The concentration grid is required to be defined as a snapshot grid. In the current
version, only one pollutant species per simulation is supported.

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Advanced / File Edit / Emissions File (S417)

Advanced / File Edit / Emissions File

This menu creates the optional EMITIMES file which is used to configure more complex point source emissions
scenarios. In the standard model simulation,
the CONTROL file can only be used to define one pollutant release cycle
which
applies equally to all source locations. Although multiple release cycles can
be defined, they must all be at the
same interval. Using the EMITIMES file to
define the point source emissions, multiple release locations can each have

their own emission characteristics, each with different pollutants, if desired.

Furthermore, multiple emission cycles, at
non-regular intervals can also be
defined. By appropriately locating multiple sources in space and time, line-
source as
well as other non-regular emissions configurations can be created.
In version 4.8 the format of this file has changed
from previous HYSPLIT
versions to such an extent that they are incompatible with each other. In all
versions the file
name is defined by the EFILE variable in the namelist configuration file created thorough
the Advanced / Configuration
menu tab.

The first menu tab defaults to the configuration for one source. If multiple sources are required, then enter the number in
this menu. After
pressing the Configure Locations button, another menu comes up to
select the location number to
configure. Pressing the location number button
brings up the menu shown below. The GUI menu only supports the
creation of
a file for one pollutant for one emission cycle. If multiple pollutants are
defined, or multiple cycles are
required, then the file must be edited manually
by duplicating the emission record at each location for all pollutants in
the
order they are defined in the CONTROL file. Each defined release location must
be configured according to the
following instructions. The point source
emissions file must be located in the startup directory the name should always

be in uppercase. The following is an example of the contents of EMITIMES file

for one location. Multiple locations
would have one line per location. The
number of data records should equal the number of sources defined in the

CONTROL file times the number of pollutants released.

The EMITIMES file may also be configured to construct a vertical line source by
having two consecutive emission
points defined at the same spatial location but each
with different heights. Unlike the vertical line source definition
through the
CONTROL file, where the same emission rate is defined for all sources, here the
emission rate may be
varied through the column. For instance, if the source
record N is at the same location as record N-1, the the emission
rate defined for
record N-1 will be used for all particles released in the column from N-1 to N.
This means that the
emission value given for the last record, in a series of records
at the same location will not be used.
Record 1 - Identification record describing the emission cycle header record
Record 2 - Identification record describing a location emission data record
Record 3 - First emission cycle header record
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Advanced / File Edit / Emissions File (S417)

Record 4 - First emission data record in the first emission cycle

Emission Cycle Header Record: {YYYY} {MM} {DD} {HH} {hhhh} {#rec}
{YYYY} {MM} {DD} {HH} - Starting time of the emission cycle, with each new
emission cycle, all previous
emission records are replaced with
those in the new cycle.
{hhhh} - Duration in hours that this emission cycle is valid.
{#rec} - Number of emission records in this cycle (= # sources times # pollutants).
Emission Cycle Data Record: {YYYY} {MM} {DD} {HH} {mm} {HHmm} {Lat} {Lon} {Hgt} {Rate} {Area}
{Heat}
{YYYY} {MM} {DD} {HH} {mm} - Emission start time at this location
{HHmm} - Release duration in hours and minutes (no space).
{Lat} {Lon} {Hgt} - Position and height of the release.
{Rate} - Emission rate in mass units per hour.
{Area} - Emission area in square meters. Zero is treated as a point
source and non-zero values only apply to one
of the horizontal
distribution models (top-hat or Gaussian).
{Heat} - Heat released during the emission. Non-zero values result in a
bouyancy plume rise calculation,
replacing the previous height
value.
The emisson cycle header record defines the valid time period for the subsequent data records.
At the end of the header
record time period {hhhh}, the model will attempt to read the next emission
cycle header record. If no header record is
found, then the EMITIMES emission processing is terminated
and the model reverts to using the emission values
defined in the CONTROL file. For instance, this
means that if a short emission duration is defined in the data records,
but the model simulation
covers a longer period, the header record duration {hhhh} should be long enough to cover the
entire
simulation period. Unless it is indended to use both methods, the emission rate and duration in the
CONTROL
file should both be set to zero when using an EMITIMES file.
Special Case: Backward simulations
In the case of backward simulations, the cycle header record should point to the first (oldest)
emission cycle and all
subsequent emission cycles should be earlier in time. The emission start time
within a cycle corresponds to a time such
that the duration of emissions proceeds backward from that
starting time. The internal backward flag has already been
set from the negative run duration in the CONTROL file and therefore all time durations in the EMITIMES file should
be expressed as positive numbers.

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Advanced / Configuration Setup / Set Directories (S416)

Advanced / Configuration Setup / Set Directories

The installation program installs all code and executables to your
selected directory, and creates a shortcut on the
Window's desktop to
/guicode/hysplit4.tcl with the Start In directory as your selected default. On Unix systems the link
would appear in the /working directory.
When the GUI is first started, it looks for the supplemental programs such
as
Ghostscript, Ghostview, ImageMagick, and Tcl/tk in certain standard
directories, and writes those paths to a file called
default_exec.
If this file already exists, those locations are used instead of the default
search paths. The directories
specified in this file may be edited through
the Set Directories menu tab. Copying the default_exec file
to another
computer with a different directory structure may cause the GUI
to fail to open. In these situations, either delete the file,
or manually
edit the file to reflect the correct directory strucuture.

The default_exec values either reflect a directory location, a file

name, or a directory/executable name. The content is
mostly self-explanatory.
Under UNIX systems, the X-windows directory should point to the location of the
xterm
program. This is optional. If the directory is defined, then many
of the programs called by the GUI will run in their own
xterm window.

Table of Contents
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Advanced / Configuration Setup / Set Directories (S416)

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Advanced / File Edit / Panel Labels (S414)

Advanced / File Edit / Panel Labels

If a file called MAPTEXT.CFG is found in the root or
working directory during the execution of either the trajectory or

concentration plotting program, additional label information is

written at the bottom of each graphic. The Extra Label
menu
tab can be used to edit this information. An illustration of the
menu is shown below, followed by the resulting
trajectory graphic
for the example simulation. Note that the menu entries are entirely
text based and there are no
restrictions regarding content.
However, not all plotting programs display all lines. The example
header text indicates
the appropriate application.

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Advanced / File Edit / Panel Labels (S414)

Table of Contents

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Advanced / File Edit / Border Labels (S418)

Advanced / File Edit / Border Labels

Many of the Postscript graphics programs have label information that can be
customized to some extent. This is
accomplished by placing a file called LABELS.CFG in the working directory which should contain one or more of
the
following valid entries (all in single quotes terminated by &). Replace
the second text string with the new desired text.
Not all label strings are valid
with every plotting program. This file can be created and edited through the
menu system.
Quotes and string terminators are not required in the edit menu.
'TITLE&','NOAA AIR RESOURCES LABORATORY&'
'MAPID&','Air Concentration&'
'LAYER&','Layer Averaged&'
'UNITS&','Bq&'
'VOLUM&','/m3&'
'TZONE&','UTC+00&'
'RELEASE&','Release info&'
'ALLTD&','m&'
The time zone variable can be used to force a specific time zone for the air
concentration contour plot. All calculations
are performed in UTC, but prior to
plotting, all times are converted by the time zone adjustment. The field should

always be six characters in length. The first three represent the time zone label,
such as UTC, the next character is the
sign field (+ to the east or - to the west),
and last two digits are the hours difference of the time zone from UTC.
Altitude units (ALTTD) may be set to feet for concentration output plots.
Table of Contents

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Advanced / File Edit / FMDV Decay (S419)

Advanced / File Edit / FMDV Decay

Foot and Mouth Disease
[email protected], [email protected], April 2015
Foot and Mouth Disease is a contagious viral disease of cattle and sheep, causing ulceration of the hoofs and around the
mouth. Evidence has shown[1] that the Foot and Mouth Disease Virus (FMDV) can be transported via airborne means
making even a single outbreak highly infectious.
HYSPLIT is capable of modelling the dispersion of airborne FMDV. The survival of the FMDV particle is dependent on (a)
the age of the particle, the virus has a natural lifespan which is simulated within the model with a half-life factor, (b) the air
temperature, retrieved from the meteorological file and (c) the air humidity also retrieved from the meteorological file. In
reality, wet and dry deposition also influence the distance travelled by the airborne FMDV.
To activate the Foot and Mouth Disease algorithm in HYSPLIT the species identification label must be set to either FM_0 or
FM_1 or .... FM_7 where the integer behaves as a binary switch for including or excluding particle aging, temperature or
humidity dependence as desired.

The Table below shows the dependences of Foot and Mouth virus survival to the species identification string. FM_7 is the
most realistic option.
Identification Particle Aging Temperature Humidity
FM_0
False
False
False
FM_1
False
False
True
FM_2
False
True
False
FM_3
False
True
True
FM_4
True
False
False
FM_5
True
False
True
FM_6
True
True
False
FM_7
True
True
True

The species identification string can be set in the pollutant emission rate setup menu or automatically using the FMDV
radiobutton in the deposition setup menu in the following section.

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Advanced / File Edit / FMDV Decay (S419)

Default FMDV settings

- Deposition
The species identification string can also be set to a default value by selecting the FMDV radiobutton in the deposition
menu. This button will also set default values for wet and dry deposition. For the Foot and Mouth virus a dry deposition
velocity of 0.01m/s is assumed[1], but it can be changed by the user if required. FMDV wet deposition defaults are simply
those for small particles using the removal time constant of 8x10-5 for both in-cloud and below-cloud removal which is
similar to the value (5x10-5) used by Garner[1].

- Particle age
Various publications use a virus decay constant to simulate particle ageing. For the Foot and Mouth virus estimates of an
effective half-life range from 30 mins[1] to 2 hours[2]. This constant is also dependent on the strain of the virus. To be
conservative the virus decay constant has been defined to be 2 hours by default but this can be easily redefined by the user
in the advanced settings menu (see below). Particle ageing can be turned off altogether if desired by using the species
identification label outlined above.
- Temperature
The survival of the virus depends on temperature. Taking the default temperature threshold of 24oC, all virus particles of
24oC and under are unaffected. The concentration mass of virus particles linearly decreases between 24oC and 30oC so that
none remain by the time they reach 30oC. This threshold of 24oC can be user defined in advanced settings (preserving the
6oC linear fall off) or the temperature dependence can be turned off altogether if required by selecting the appropriate
species identification string outlined above.
- Humidity
The survival of the virus also depends on humidity. The virus survives better in higher humidity. Virus concentrations with
relative humidity higher than 60% are left unaffected. Concentrations decrease exponentially as the humidity falls from 60%
to 1%. This threshold of 60% can be user defined in the advanced settings or the humidity dependence can be turned off

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Advanced / File Edit / FMDV Decay (S419)

altogether if required by selecting the appropriate species identification string outlined above.
FMDV Survival Dependence
... upon Temperature

... upon Humdity

How to change default FMDV dependency thresholds

There are many different variants of FMDV each with their own characteristics. If a different set of threshold dependencies
are know the default FMDV can be changed. To do this open the Advanced / File Edit / FMDV Decay menu to edit the
decay, and critical temperature and humidity defaults. This information is written into the fm_param.txt file which is read
when the HYSPLIT calculation starts.

References
[1] M.G. Garner, G.D. Hess and X. Yang, An integrated modelling approach to access the risk of wind-borne spread of footand-mouth disease virus from infected premises, Environmental Modelling & Assessment (2006) 11: 195-207.
[2] J.H. Sorensen, C.O. Jensen, T. Mikkelsen, D.K.J. Mackay and A.I. Donaldson, Modelling the Atmospheric Dispersion of
Foot and Mouth Virus for Emergency Preparedness, Phys. Chem. Earth (B), Vol. 26, No. 2, pp. 93-97, 2001.
Table of Contents

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Advanced / Configuration Setup / Namelist Variables (S410)

Advanced / Configuration Setup / Namelist Variables

This section provides a summary of the SETUP.CFG namelist file parameters
required in configuring the model to
perform certain specialized calculations. The default value is shown in bold with each variable and a link to the User's

Guide page with a more detailed discussion of the options. The namelist options that
only affect trajectories are shown
in italics.
CAPEMIN=-1 enhanced vertical mixing when CAPE exceeds this value (J/kg)
CMASS=0 compute grid concentrations (0) or grid mass (1)
CONAGE=48 particle to or from puff conversions at conage (hours)
CPACK=1 binary concentration packing 0:none 1:nonzero 2:points 3:polar
DELT=0.0 integration time step (0=autoset GT-0=constant LT-0=minimum)
DXF=1.0 horizontal X-grid adjustment factor for ensemble
DYF=1.0 horizontal Y-grid adjustment factor for ensemble
DZF=0.01 vertical (0.01 ~ 250m) factor for ensemble
EFILE=' ' temporal emission file name
FRHMAX=3.0 maximum value for the horizontal rounding parameter
FRHS=1.00 standard horizontal puff rounding fraction for merge
FRME=0.10 mass rounding fraction for enhanced merging
FRMR=0.0 mass removal fraction during enhanced merging
FRTS=0.10 temporal puff rounding fraction
FRVS=0.01 vertical puff rounding fraction
HSCALE=10800.0 horizontal Lagrangian time scale (sec)
ICHEM=0 chemistry conversion modules 0:none 1:matrix 2:convert 3:dust ...
INITD=0 initial distribution, particle, puff, or combination
KAGL=1 trajectory output heights are written as AGL (1) or as MSL (0)
KBLS=1 boundary layer stability derived from 1:fluxes 2:wind_temperature
KBLT=2 boundary layer turbulence parameterizations 1:Beljaars 2:Kanthar 3:TKE
KDEF=0 horizontal turbulence 0=vertical 1=deformation
KHINP=0 when non-zero sets the age (h) for particles read from PINPF
KHMAX=9999 maximum duration (h) for a particle or trajectory
KMIXD=0 mixed layer obtained from 0:input 1:temperature 2:TKE
KMIX0=250 minimum mixing depth
KMSL=0 starting heights default to AGL=0 or MSL=1
KPUFF=0 horizontal puff dispersion linear (0) or empirical (1) growth
KRAND=2 method to calculate random number 1=precalculated 2=calculated in pardsp 3=none
KRND=6 enhanced merge interval (hours)
KSPL=1 standard splitting interval (hours)
KWET=0 precipitation from an external file
KZMIX=0 vertical mixing adjustments: 0=none 1=PBL-average 2=scale_TVMIX
MAXDIM=1 maximum number of pollutants to carry on one particle
MAXPAR=10000 maximum number of particles carried in simulation
MESSG='MESSAGE' diagnostic message file base name
MGMIN=10 minimum meteorological subgrid size
MHRS=9999 trajectory restart duration limit (hours)
NBPTYP=1 number of redistributed particle size bins per pollutant type
NINIT=1 particle initialization (0-none; 1-once; 2-add; 3-replace)
NCYCL=0 pardump output cycle time
NDUMP=0 dump particles to/from file 0-none or nhrs-output interval
NSTR=0 trajectory restart time interval in hours
NUMPAR=2500 number of puffs or particles to released per cycle
NVER=0 trajectory vertical split number
P10F=1.0 dust threshold velocity sensitivity factor
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Advanced / Configuration Setup / Namelist Variables (S410)

PINBC=' ' particle input file name for time-varying boundary conditions
PINPF=' ' particle input file name for initialization or boundary conditions
POUTF=' ' particle output file name
QCYCLE=0.0 optional cycling of emissions (hours)
RHB=80 is the RH defining the base of a cloud
RHT=60 is the RH defining the top of a cloud
SPLITF=1.0 automatic size adjustment (<0=disable) factor for horizontal splitting
TKERD=0.18 unstable turbulent kinetic energy ratio = w'2/(u'2+v'2)
TKERN=0.18 stable turbulent kinetic energy ratio
TM_PRES=0 trajectory diagnostic output pressure variable marker flag
TM_TPOT=0 trajectory diagnostic output potential temperature
TM_TAMB=0 trajectory diagnostic output ambient temperature
TM_RAIN=0 trajectory diagnostic output rainfall rate
TM_MIXD=0 trajectory diagnostic output mixed layer depth
TM_TERR=0 trajectory diagnostic output terrain height
TM_DSWF=0 trajectory diagnostic output downward short-wave flux
TM_RELH=0 trajectory diagnostic output relative humidity
TOUT=60 trajectory output interval in minutes
TRATIO=0.75 advection stability ratio
TVMIX=1.0 vertical mixing scale factor
VDIST='VMSDIST' diagnostic file vertical mass distribution
VSCALE=200.0 vertical Lagrangian time scale (sec)
VSCALEU=200.0 vertical Lagrangian time scale (sec) for unstable PBL
VSCALES=200.0 vertical Lagrangian time scale (sec) for stable PBL

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Advanced / Configuration Setup / Time Step Selection Criteria (S610)

Advanced / Configuration Setup / Time Step Selection Criteria

Set Ratio - TRATIO (0.75) - defines the fraction of a grid cell that a particle or trajectory is permitted to transit in one

advection time step. Reducing this value will reduce the time step and
increase computational times. Smaller time steps
result in less
integration error. Integration errors can be estimated by computing
a backward trajectory from the forward
trajectory end position and
computing the ratio of the distance between that endpoint and the
original starting point
divided by the total forward and backward
trajectory distance.
Set Value - DELT (0.0) - is used to set the integration time step
to a fixed value in minutes from 1 to 60. It should be
evenly divisible
into 60. The default value of zero causes the program to compute
the time step each hour according to
the maximum wind speed,
meteorological and concentration grid spacing, and the
TRATIO parameter. The fixed time
step option should only be
used when strong winds in regions not relevant to the dispersion
simulation (perhaps the
upper troposphere) are causing the model to
run with small time steps. Improper specification of the time step
could
cause aliasing errors in advection and underestimation of air
concentrations. An alternate approach is to set the a
negative value
which will result in that value (abs) being used as the minimum time step.

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Advanced / Configuration Setup / Define subgrid and MSL/AGL units (S611)

Advanced / Configuration Setup / Define subgrid and MSL/AGL units

Meteorological Sub-grid Size
MGMIN (10) - is the minimum size in grid units of the
meteorological sub-grid. The sub-grid is set dynamically during
the
calculation and depends upon the horizontal distribution of
end-points and the wind speed. Larger sub-grids than
necessary will
slow down the calculation by forcing the processing of
meteorological data in regions where no transport
or dispersion
calculations are being performed. In some situations, such as when
the computation is between
meteorological data files that have no
temporal overlap or insufficient spatial overlap, the model may try
to reload
meteorological data with a new sub-grid. This will result
in a fatal error. One solution to this error would be to increase
the
minimum grid size larger than the meteorological grid to force a full-grid data load.

Height Unit for Input

KMSL (0) - sets the default for input heights to be relative
to the terrain height of the meteorological model. Hence input

heights are specified as AGL. Setting this parameter to "1" forces

the model to subtract the local terrain height from
source input
heights before further processing. Hence input heights should be
specified as relative to Mean Sea Level
(MSL). In concentration
simulations, the MSL option also forces the vertical concentration
grid heights to be
considered relative to mean sea level. The
special option (xBL) sets KMSL to 2 and treats the input height as
a fraction
of the boundary layer (or mixed layer) depth at the
trajectory starting location and time. This option is not valid
with
any multiple trajectory in time configurations or any of the
concentration-dispersion calculations. Valid starting heights
can
be defined as any non-zero fraction less than 2.0.

Height Unit for Output

The namelist variable KAGL (=1) only applies to trajectories, not concentration simulations. For trajectory simulations,
the default option
is to write the heights as AGL (KAGL=1), setting KAGL=0 converts the trajectory
output heights to
MSL. The KMSL namelist parameter described above only applies
to how heights are interpreted in the CONTROL
file, while KAGL determines how
the model heights are written to the output file. This variable
is not available through
the GUI.
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Advanced / Configuration Setup / Define subgrid and MSL/AGL units (S611)

Table of Contents

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Advanced / Configuration Setup / Multiple Trajectories in Time (S612)

Advanced / Configuration Setup / Multiple Trajectories in Time

Restart Interval - NSTR (0) - Hours between trajectory starts for
multiple trajectory-in-time simulations. When greater
than zero, new
trajectories will be started from the original starting location
every NSTR hours from the initial
trajectory starting time. See the
special trajectory simulation
section for more information.
Number of Multiple Levels - NVER (0) - Number of vertical levels that trajectories are restarted when trajectories for
multiple
trajectory-in-time-and-space simulations. When greater than zero,
new trajectories will be started at this
number of levels from the
endpoint position at the NSTR interval. The level heights are set
in the CONTROL file and
must match the number of starting
locations. See the special
trajectory simulation section for more information.
Trajectory Duration - MHRS (9999) - Sets the maximum temporal trajectory
restart period. For instance if you want to
compute one month's worth of
two-day trajectories, then the run duration would be 720 hours,
MHRS would be set to
672 hours (720-48), and KHMAX
(see below) would be set to 48 hours.

Table of Contents

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Advanced / Configuration Setup / Trajectory Points Output Frequency (S613)

Advanced / Configuration Setup / Trajectory Points Output Frequency

The endpoint write interval TOUT(60) sets the time interval in minutes at which
trajectory end-point positions will be
written to the output file. Output intervals of
less than 60 minutes can be selected. This will also force the internal time
step to be
an even multiple of the output interval.
The maximum trajectory duration KHMAX (9999) is the maximum duration of any
one trajectory in hours.

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Advanced / Configuration Setup / Add Meteorology Output Along Trajectory (S614)

Advanced / Configuration Setup / Add Meteorology Output Along

Trajectory
Sets the option to write the value of certain meteorological
variables along the trajectory to the trajectory output file.
The
marker variables are set to (1) to turn on the option. Multiple
variables may be selected for simultaneous output but
only one
variable may be plotted. If multiple variables are selected in
conjunction with the trajectory display option,
then only the last
variable output will be shown in the graphic. The variable output
order is fixed in the program and
cannot be changed.
Potential Temperature in degrees Kelvin TM_TPOT (0|1)
Ambient Temperature in degrees Kelvin TM_TAMB (0|1)
Precipitation rainfall in mm per hour TM_RAIN (0|1)
Mixing Depth in meters TM_MIXD (0|1)
Relative Humidity in percent TM_RELH (0|1)
Specific Humidity in g/(kg air) TM_SPHU (0|1)
Water Vapor Mixing Ratio in g/(kg dry-air) TM_MIXR (0|1)
Solar Radiation downward solar radiation flux in watts per square meter TM_DSWF (0|1)
Terrain Height in meters required for the trajectory
plot to show underlying terrain TM_TERR (0|1)

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Advanced / Configuration Setup / Meteorological Grid Offset Ensemble (S615)

Advanced / Configuration Setup / Meteorological Grid Offset Ensemble

Sets the dimensions at which the meteorological grid will be offset
for the ensemble calculation. Only
one offset (+ or -)
in either X, Y, or Z is applied per member.

Horizontal Shift
Starting and ending member numbers can be selected where:
the range 1-9 applies for no vertical shift,
the range 10-18 applies for a positive vertical shift,
the range 19-27 applies to a negative vertical shift,
and DZF (0.01) is the vertical grid offset factor (0.01 ~ 250m).

Horizontal Shift
DXF (1.0) is the west to east grid factor for offsetting the meteorological
grid in the ensemble calculation.
DYF (1.0) is the south to north grid factor for offsetting the meteorological
grid in the ensemble calculation

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Advanced / Configuration Setup / Mixing Depth Computation Method (S616)

Advanced / Configuration Setup / Mixing Depth Computation Method

Permits the selection of the method used to compute the mixed layer depth.
The mixed layer depth does not affect the
trajectory computation, only the dispersion and resulting air concentrations by changing the rate of dispersion
as well as
providing a lid to vertical mixing of pollutants. Options include
the following:
Use meteorological model - uses the mixed layer depth value from the meteorological
model. Not all model
outputs provide mixed layer depths. Valid field IDs are MXHT,
HPBL, and PBLH.
From temperature profile - computes the height of the mixed layer as the height at
which the potential temperature
is at least two degrees greater than the minimum
potential temperature. The computation is made from the top
down.
Compute from TKE profile - uses the meteorological model's TKE profile to estimate
the mixing depth at the
height at which the TKE either decreases by a factor of two or
falls to a value of less than 0.21. Not all model
outputs contain the TKE field.
Set a constant value (m) - as a last resort the mixing depth can also be set to
a constant value (meters). The kmixd
namelist variable either contains the mixing
depth value or the integers 0,1,2 indicating one of the other choices.

Table of Contents

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Advanced / Configuration Setup / Sub-grid Size and Vertical Coordinate (S621)

Advanced / Configuration Setup / Sub-grid Size and Vertical Coordinate

Meteorological Sub-grid Size
MGMIN (10) is the minimum size in grid units of the meteorological
sub-grid. The sub-grid is set dynamically during
the calculation and
depends upon the horizontal distribution of end-points and the wind
speed. Larger sub-grids than
necessary will slow down the calculation
by forcing the processing of meteorological data in regions where no
transport
or dispersion calculations are being performed. In some
situations, such as when the computation is between
meteorological
data files that have no temporal overlap or insufficient spatial overlap,
the model may try to reload
meteorological data with a new sub-grid. This
will result in a fatal error. One solution to this error would be to increase
the minimum grid size larger than the meteorological grid to
force a full-grid data load.

Vertical Grid Coordinate System

KMSL (0) sets the default for input heights to be relative to the terrain
height of the meteorological model. Hence input
heights are specified as AGL.
Setting this parameter to "1" forces the model to subtract the local terrain
height from
source input heights before further processing. Hence input heights
should be specified as relative to Mean Sea Level
(MSL). In concentration
simulations, the MSL option also forces the vertical concentration grid heights
to be
considered relative to mean sea level. The option to set the release
height dynamically as a fraction of the mixed layer
depth is not available
for concentration-dispersion simulations.

Table of Contents

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Advanced / Configuration Setup / Release Particles or Puffs (S622)

Advanced / Configuration Setup / Release Particles or Puffs

The menu is divided into two sections. In each case the value of the INITD namelist parameter is being set. In the upper
portion of
the menu, the model is configured as either a full 3D particle or puff
model, or some hybrid combination of
the two. The released particles or
puffs maintain their mode for the entire duration of the simulation.
Valid options are:
0 - 3D particle horizontal and vertical (DEFAULT)
1 - Gaussian-horizontal and Top-Hat vertical puff (Gh-THv)
2 - Top-Hat-horizontal and vertical puff (THh-THv)
3 - Gaussian-horizontal puff and vertical particle distribution (Gh-Pv)
4 - Top-Hat-horizontal puff and vertical particle distribution (THh-Pv)
Introduced with the September 2004 version are mixed mode model
calculations, where the mode can change during
transport depending upon
the age (from release) of the particle. A mixed-mode may be selected to
take advantage of the
more accurate representation of the 3D particle
approach near the source and the smoother horizontal distribution
provided
by one of the hybrid puff approaches at the longer transport distances.
In a long-range or regional puff
simulation, where the concentration grid
may be rather coarse, puffs may pass between concentration sampling nodes

during the initial stages of the transport, a stage when the plume is still
narrow. Using mode #104 would start the
simulation with particles (and
concentration grid cells) and then switch to puff mode (and concentration
sampling
nodes) when the particles are distributed over multiple concentration grid cells. Valid options are:
103 - 3D particle (#0) converts to Gh-Pv (#3)
104 - 3D particle (#0) converts to THh-Pv (#4)
130 - Gh-Pv (#3) converts to 3D particle (#0)
140 - THh-Pv (#4) converts to 3D particle (#0)
109 - 3D particle converts to grid (global model)
A new option (109) introduced with the January 2009 version (4.9), converts
3D particles to the Global Eulerian Model
grid. The
particles are transferred to the global grid after the specified number of hours. This approach should only be
used for very long-range (hemispheric)
transport due to the artificial diffusion introduced when converting pollutant

plumes to a gridded advection-diffusion computational approach. The method is

ideal for estimating contributions to
background concentrations. All mixed-
mode particles/puffs (not just 3D) will convert to the global grid if the
global
option is selected from the special runs menu.

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Advanced / Configuration Setup / Release Particles or Puffs (S622)

Table of Contents

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Advanced / Configuration Setup / Particle-Puff Release Number Limits (S623)

Advanced / Configuration Setup / Particle-Puff Release Number Limits

The number of particles released per cycle NUMPAR (2500) would be
the maximum number of particles or puffs
released over the duration of the
emission. NUMPAR has a different meaning for puff and particle
simulations. In a full
puff simulation (INITD = 1 or 2), only one
puff per time step is released, regardless of the value of NUMPAR.
In a
particle or mixed particle-puff simulation (INITD = 0, 3, 4),
NUMPAR represents the total number of particles that are
released
during one release cycle. Multiple release cycles cannot produce more than
MAXPAR number of particles. For
a mixed simulation (particle-puff),
NUMPAR should be greater than one but does not need to be anything
close to what
is required for a full 3D particle simulation.
To simplify certain simulations when a constant particle number release rate
is required, specifying a negative value for
NUMPAR will over-ride the
particle number release rate calculations (in terms of the number of sources, hours
emission, and pollutants) and force the particle release rate to be |NUMPAR| particles per hour for each source and
pollutant.
The maximum number of particles MAXPAR (10000) is the maximum number
permitted to be carried at any time
during a simulation. In all simulation
types, particle or puffs are only emitted if the particle count is less than
MAXPAR.
Note that there are situations where NUMPAR can (and
should) exceed MAXPAR because the actual particle release
rate is
computed by dividing NUMPAR by the number of sources, pollutants,
and release hours.
The maximum particle duration KHMAX (9999) is the number of hours
after release that a particle is dropped from the
simulation. For simulations using
regional meteorological grids, particles are dropped when the reach the grid

boundary. However, when using global meteorological data, it may be computationally

prudent to drop particles after
they are no longer over the region of interest.

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Advanced / Configuration Setup / Emission Cycling and Point Source File (S624)

Advanced / Configuration Setup / Emission Cycling and Point Source File

Emission Cycling
QCYCLE (0.0) are the number of hours between emission start cycles.
A zero value means that the emissions are not
cycled. When non-zero, the number
of emission hours is repeated again at QCYCLE hours after the starting
emission
time specified in the input CONTROL file. The NUMPAR
parameter set in the release number limits menu is defined as
the number of
particles released over the emission duration per cycle unless its value is
less than zero, in that case it
defines the hourly particle number release
rate directly as |NUMPAR|. The QCYCLE parameter is also used
in
conjunction with namelist option ICHEM=10 to that
the concentrations from each release cycle are saved in their own

concentration array.

Optional Point-Source Emission File

EFILE (undefined) is the file name that contains point-source temporal
emission factors, where each record contains the
{year month day hour duration
latitude longitude emission-rate} for each emission period. Multiple emission
periods
can be defined. The values in this file replace the values set in the
CONTROL file. The emission file can be created
from the Advanced Menu tab. The format of this file is more complex than the one
used to multiply time-varying unitsource dispersion
factors created by the ICHEM=10 option described above.

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Advanced / Configuration Setup / Configure Turbulence-Dispersion Computation (S625)

Advanced / Configuration Setup / Configure Turbulence-Dispersion

Computation
Vertical Turbulence
KBLT is a flag used to set the vertical turbulence computational method,
that is how the turbulent velocity variances are
computed from either the heat
and momentum fluxes or the model profiles of wind and temperature. Two different

computational approaches (Beljaars/Holtslag and Kanthar/Clayson - see the technical

documentation for details) are
defined. Another option is the use the TKE (Turbulent Kinetic Energy) output from the meteorological model provided
in the input meteorological data file. Not all model data contain the TKE field. The last
option is a special case where
the input meteorological data are assumed to contain
the 3-dimensional component velocity variance fields, usually a
measured component.
1 - Beljaars/Holtslag and Betchov/Yaglom
2 - Kanthar/Clayson (DEFAULT)
3 - TKE field from the input meteorology data file
4 - Measured velocity variances from the input meteorology
Horizontal Turbulence
KDEF defines the way the horizontal turbulence is computed. The default approach is to compute the horizontal mixing
in proportion to the vertical mixing
using one of the methods defined above (see the technical documentation for
details).
The original computation was to compute the mixing from the deformation of the
horizontal wind field. The
limitation of this method is that for shorter-range
dispersion simulations (<100 km) the deformation parameterization
used in
conjunction with larger scale meteorological fields will not reflect the diurnal
variations in horizontal
turbulence. Using diurnal sensitive methods will not effect longer-range calculations because the particles are
distributed over many
meteorological grid cells where variations in the transport vector dominate the
horizontal
dispersion process.
0 - In proportion to the vertical turbulence (DEFAULT)
1 - Computed from the velocity deformation
Boundary Layer Stability
KBLS defines how the stability is computed. Normally when turbulent fluxes
(heat and momentum) are available from
the meteorological data file, they are used to
compute stability. Sometimes it may be desirable to force the stability to
be computed
from the wind and temperature profiles, especially if the fluxes represent long-time
period averages rather
than instantaneous values. If fluxes are not present, the
profiles are used for the stability computation.
1 - Heat and momentum fluxes (DEFAULT)
2 - Wind and temperature profiles
Vertical Mixing Profile
KZMIX determines if any additional processing is to be performed on the
vertical mixing profile. The current default is
for no adjustments. In previous versions
the boundary layer mixing profile was replaced with its average value. This
compensated
for some meteorological data sets with poor vertical data resolution that might result
in particles being
trapped near the surface due to insufficient mixing. The last two
options are scale factors that can be applied to the
mixing coefficients and currently
are not available for modification through the GUI.
0 - NONE vertical diffusivity in PBL varies with height (DEFAULT)
1 - Vertical diffusivity in PBL single average value
2 - scale boundary-layer values multiplied by TVMIX

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Advanced / Configuration Setup / Configure Turbulence-Dispersion Computation (S625)

3 - scale free-troposphere values multiplied by TVMIX

Mixed Layer Depth Computation
KMIXD is used to control how the boundary layer depth is computed. In addition
as acting as a vertical lid to particle
dispersion (advection is not affected), the mixed layer depth is also used to scale the boundary layer mixing coefficients
and computing turbulent fluxes from wind and temperature profiles. The default is to use
the value provided by the
meteorological model through the input data set. The profile
can also be used if available. The computation defaults to
use temperature profiles
if the mixed layer field is not available. Another option to use for testing is
to replace the index
value (0,1,2) with a value greater than 10. In this situation, that
value will be used as the mixed layer depth and will be
constant for the duration of the
simulation.
0 = Use meteorological model MIXD if available (DEFAULT)
1 = Compute from the temperature profile
2 = Compute from the TKE profile
> = 10 use this value as a constant
KMIX0 is a related parameter that sets the minimum mixing depth. The default
value is 250 meters and is related to the
typical vertical resolution of the meteorological
data. A resolution near the surface of 25 hPa is typical of pressure-level
data files. This
suggests that it is impossible to infer a mixed layer depth of less than 250 m (10 m per hPa) for most
meteorological input data.
250 = The minimum mixing depth (DEFAULT)
Puff Growth Computation Method
KPUFF is the flag to use either the linear with time or the empirical fit
with time dispersion equations for the horizontal
growth rate of puffs. This parameter
does not affect particle dispersion. The linear with time approach suggests that not

all turbulent scales have been sampled and puffs grow in proportion to increasing time.
The empirical fit equation is
similiar but the rate of puff growth decreases with time.
Slower puff growth rate in the linear approach is represented
by the separation of puffs
after splitting due to variations in the flow. The empirical approach should only be used
in
those situations where puff splitting is constrained because of memory or computing
time limitations.
0 = Linear with time puff growth (DEFAULT)
1 = Empirical fit to the puff growth
Turbulence Anisotropy Factors
TKERD and TKERN are the ratios of the vertical to the horizontal turbulence
for daytime and nighttime, respectively.
TKER{D|N} is defined as W'2/(U'2+V'2).
A zero value forces the model to compute a TKE ratio consistent with its
turbulence
parameterization. A non-zero value forces the vertical and horizontal values derived
from the TKE to match
the specified ratio. This option is only valid with KBLT=3.
The Urban button increases the internal TKE by 40% and
slightly raises the nighttime ratio to account for enhanced turbulence in an urban setting. The landuse
file supplied with
the model is not of sufficient resolution to define urban areas and
hence the urban setting applies to all points in the
computational domain.
0.18 = TKERD day (unstable) turbulent kinetic energy ratio
0.18 = TKERN night (stable) turbulent kinetic energy ratio

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Advanced / Configuration Setup / Configure Turbulence-Dispersion Computation (S625)

Turbulence Parameters Not Defined in GUI

1.0 = TVMIX vertical mixing scale factor (in conjunction with KZMIX
200.0 = VSCALE vertical Lagrangian time scale (sec)
200.0 = VSCALEU vertical Lagrangian time scale (sec) for unstable PBL
200.0 = VSCALES vertical Lagrangian time scale (sec) for stable PBL
10800.0 = HSCALE horizontal Lagrangian time scale (sec)
1 = KRAND method to calculate random number (1=precompute 2=dynamic 3=none)

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Advanced / Configuration Setup / Concentration Packing and Output Units (S626)

Advanced / Configuration Setup / Concentration Packing and Output Units

Concentration Packing Method
CPACK is the flag to turn off (set to 0) concentration output packing.
The default is to write the binary concentration
file at only those grid points
that have a non-zero concentration value (set to 1). Setting the flag to zero
results in the
output of the entire concentration grid. Due to the nature of the
packing method, if the plume covers more than 50% of
the concentration grid, the
default concentration packing will result in larger output file than an unpacked
concentration
file.
The Point option (CPACK=2) is a special feature that forces the
concentration grid to have a size of one grid point over
the location of the center
point. It is a way to define a single sampling location.
In the case where CPACK=3 defines a polar concentration grid defined by
radial sectors centered about the origin
latitude-longitude position. In this case
the grid spacing and span defined in the CONTROL file define
the arc sector
size (latitude values) and the sector distances (longitude values).
Polar concentration grids may be displayed using the
program poleplot.
Concentration or Mass Output Units
The default option (CMASS=0) is to output units of mass/volume. However,
if mass-only output is desired, then setting
CMASS=1 will cause the model
not to divide the grid cell sum by its volume.

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Advanced / Configuration Setup / Input and Output of Particle Files (S627)

Advanced / Configuration Setup / Input and Output of Particle Files

Particle File Initialization Options
NINIT sets the type of initialization performed. There are two types of initializations. One occurs at model startup, prior
to the start of the calculations.
This sets the initial conditions for the calculation, any particles on the computational
grid
at model startup are loaded. In the second situation, during the model simulation,
particles are loaded each time step, if
a matching time is found in the boundary
condition file. These particles may represent emissions from a previous
calculation and
can be added to or replace the existing particles in the simulation. When NINIT
is set to "0" no particle
initialization occurs even if the input file is defined. A value of "1" reads the file only during the initialization process.
No initialization
will occur if the time of the particle dump does not match the time of the model
initialization. A value
of "2" will check the file each hour during the simulation, and
if the times match, the particles will be added to those
already contained in the
simulation. A value of "3" is similar to the previous case, except the particles in the
file replace
all the particles in the simulation.
PINPF sets the default name PARINIT for the particle input file that can
be used for initialization or boundary
conditions. Note that particle files are just a
dump of all the pollutants tracked by the model at a particular time and the
file can
consist of either puffs, particles, or a combination of both.
PINBC with a default name PARINBC is a special file that can be used for
boundary conditions while PINPF can be
used for initial conditions or boundary conditions. Setting the PINBC file name is not available through the GUI. For
instance, PINPF can be used for both initial (NINIT=1)
and boundary conditions (NINIT>1), but when PINBC is also
defined, then it would replace PINPF after the initial input time.
Also not yet available through the GUI, the namelist variable
KHINP<>0 sets the particle age that will be read from the
particle initialization
file that may contain particles of many different ages each output time period. This option
is
intended to be used with continuous initialization (NINIT=2). An example of this
application may be to create a particle
file using high resolution regional meteorology, but
only for the first few hours of transport. In the case of continuous
emissions, this file would be read each time period during the coarser grid simulation, but only initializing with

particles that are of age = KHINP. The final output requires that the concentration
grids from the two simulations be
added together.
Also note that when a particle file is used for initialization of a simulation,
the meteorological grid identification of a
particle is retained from the previous simulation
(except when KHINP<>0). This means that if different meteorological
input files are
defined in the two simulations, a particle on the second simulation may not be defined on
the intended
meteorological grid at the start of the calculation.
Particle File Output Options
NDUMP can be set to dump out all the particle/puff points at
selected time intervals to a file called PARDUMP. This
file can be
read from the root directory at the start of a new simulation to continue the
previous calculation. Valid
NDUMP settings are [0] for no I/O or [hours]
to set the number of hours from the start of the simulation at which all the

endpoint positions will be written to the file. A negative value

for NDUMP will dump out the particle/puff points at
each model time step from the start of the simulation up to NDUMP hours. The file must exist in the root directory and
NDUMP<>0 for the model to initialize pollutant particles from the file. NDUMP is used in conjunction with NCYCL
(see below).
NCYCL sets the repeat interval at which the PARDUMP file is
to be written after the first write at hours NDUMP. For
instance, in a multi-day simulation, one application would be to set NDUMP=24 and NCYCL=24 to output all points at
the end of every simulation day. If
the model were to crash unexpectedly, the simulation could be restarted from
the last
PARDUMP output. If NCYCL is less than zero, then the PARDUMP file is over-written, rather than appended, at that
interval.
This means that the file will always contain one time period, a more compact
file for initialization purposes.
Also note that if NDUMP is negative, the NCYCL field is ignored.

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Advanced / Configuration Setup / Input and Output of Particle Files (S627)

POUTF is default name for the particle dump output file PARDUMP.

Although not yet available through the GUI, there is a command line program par2conc that can be used to convert the
particle position file to a binary concentration file.

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Advanced / Configuration Setup / In-Line Conversion Modules (S628)

Advanced / Configuration Setup / In-Line Conversion Modules

Setting the ICHEM variable to a non-zero value changes the model's internal
configuration in terms of how it treats the
pollutants. Some conversion options require
additional modules and specific requirements in setting up the CONTROL
file. See
the linked discussion under each option for more information.
ICHEM is chemistry module selection index:
0=none (DEFAULT)
1=Restructure the concentration grid to a source-receptor format
2=Convert species #1 to species #2 at 10% per hour
3=Enable the PM10 dust storm emission algorithm
4=Force concentration grid to be identical to meteorology grid
5=Deposit particles rather than reducing their mass
6=Divide output mass by air density (kg/m3) to sum as mixing ratio
7=Transport deposited particles on the ocean surface
8=STILT emulation mode: mixing ratio (#6) and varying layer (#9)
9=Set concentration layer one to a fraction of the boundary layer
10=Restructure concentration grid into time-varying transfer matrix
11=Enable daughter product calculation

Additional Chemistry Options

MAXDIM is the maximum number of pollutants that can be attached to one particle. Otherwise, if multiple pollutants
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Advanced / Configuration Setup / In-Line Conversion Modules (S628)

are defined they are released as individual particles. This feature is usually required with chemical conversion modules,
which are not part of the standard distribution. However, the species 1->2 conversion option will automatically set
MAXDIM=2. Both the standard point source and emissions file
input routines are enabled to release multiple species
on the same particle. In addition,
for the daughter product calculation MAXDIM needs to be set equal to the number of
daughter nuclides.
Setting MAXDIM greater than one forces all the species on the same particle, with the limitation
that the number of defined pollutants must equal MAXDIM. No other combinations are permitted. The advantage of
this approach is that not as many particles are required for the calculation
as in the situation where every pollutant is on
its own particle. The limitation is that each
species on the particle should have comparable dynamic characteristics,
such that they are all
gases or have similar settling velocities; otherwise the transport and dispersion simulation would
not be very realistic. In the case of multiple species defined on a single particle, the gravitational settling routine will
use the characteristics of the last defined pollutant to
compute settling for that particle. Deposition, decay, and other
removal processes are still
handled for independently for each pollutant on that particle.

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Advanced / Special Topics / Puff Split-Merge Issues (S630)

Advanced / Special Topics / Puff Split-Merge Issues

When the model is run in 3D particle mode a fixed number of particles are released and
followed for the duration of the
computational period. A sufficient number of particles need
to be released so that at the end of the simulation, after
particles have spread out, adjacent concentration grid cells, have enough particles to be able to properly represent
the
concentration gradients. For very long duration simulations, a large particle number may
be required and the
computational times may become prohibitive. One compromise is to use one
of the hybrid particle-puff combinations.
Fewer number of puffs need to be released because as they grow to the size of the meteorological grid, they will split

into multiple particles. To avoid the particle-puff number quickly exceed the computational
array limits, puffs
occupying the same location may be merged. There are several different
parameter settings that control the splitting and
merging. These are discussed in more detail
in this section.

Basic Namelist Parameters

The namelist parameters KSPL, FRHS, FRVS, FRTS, KRND, FRMR, FRME control the split-merge
routines. Normally
these should all be left at their default values. Split routines are called
at KSPL intervals and merging is always called
hourly. Merging is most sensitive to the horizontal parameter FRHS. When going from the default value of 1 to 4
almost all the puffs are merged once FRHS=4. Because merging is called after splitting, most puffs that are merged are
already in the same vertical position; hence there is little sensitivity to the vertical parameter FRVS. The time parameter
FRTS only matters when there are continuous emissions. KRND controls the interval at which the enhanced merging
routines are invoked. Enhanced merging is similar to standard merging except the parameters are 50% larger and
selectively applied to those puffs at the lower end of the mass range as defined by FRME. Its default value of 0.10

means that only puffs whose total mass only represents 0.10 of the mass of all puffs will be subjected to enhanced
merging.
KSPL (1) is the interval in hours at which the puff splitting routines are called.
FRHS (1.0) is the horizontal distance between puffs in sigma units that puffs have to be
within each other to be
permitted to merge.
FRVS (0.01) is the vertical distance between puffs in sigma units that puffs have to be
within each other to be
permitted to merge. This parameter only applies to 3d puff simulations.
FRTS (0.10) is the fractional difference in the age that puffs have to be within each other
to be permitted to
merge.
KRND (6) is the interval in hours at which enhanced puff merging takes place. Enhanced merging is less
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Advanced / Special Topics / Puff Split-Merge Issues (S630)

restrictive (FRHS, FRVS, FRTS are 50% larger) and will degrade the accuracy of the
simulation. Puffs can be
further apart and still be merged into the same position. Enhanced
merging only occurs when the puff number
exceeds 25% of MAXPAR.
FRME (0.10) is the fraction of the total mass that represents a puff mass at which all
puffs with a mass less that
puff value will only account for FRME of the total mass. These "Low Mass" puffs will be subject to enhanced
merging.
FRMR (0.0) is the fraction of the mass that is permitted to be removed at KRND intervals.
The normal situation is
to permit no mass loss. However for certain simulations, such as
when a pollutant has a high ambient background
relative to a typical plume signal, a small
removal rate could significantly reduce the number of puffs on the grid
with no loss in the accuracy of the simulation. This removal procedure can also be specified for 3D particle
simulations.

Automated Split-Merge Procedures

When the puff-particle number approaches the array limits, further splitting is restricted
until the merge procedures have
freed up additional array space. Each time splitting shuts down,
FRHS is automatically incremented by 0.5 to increase
the effectiveness of puff merging, to a
maximum value of 3 (FRHMAX in the namelist). Further, when splitting shuts
down, those remaining
puffs that are eligible to split but cannot due to the split restriction are prevented from increasing
in size (both horizontal and vertical) until the split restriction has been removed.
Also at the first occurrence of the split
restriction, the size to which a puff is permitted to
grow before splitting is increased in proportion to the namelist
parameter SPLITF. Puff
splitting occurs when the size of the puff reaches SPLITF x METEOROLOGY_GRID_SIZE, or

concentration grid size, whichever is larger. A termination message to standard output has been added prior to
HYSPLIT completion if puff splitting restrictions are in place at the end of the simulation. Such a message would
suggest that it might be necessary to rerun the simulation with added array space or different merge parameters.
FRHMAX (3.0) is the maximum permissible value for FRHS.
SPLITF (1.0) at the default value of 1.0 is automatically recomputed to be
the ratio of the number of
concentration grid cells to the maximum number of particles permitted.
For values less than one this feature is
disabled and splitting occurs as before. For values
greater than one, that value is used to determine when a puff
splits. The distance adjustment
is based upon how many particles are required to cover the concentration grid
(assuming 20% in
the PBL). If there are insufficient number of particles, then the puffs are allowed to grow

larger before they split, providing for smoother patterns.

Theoretical Considerations
For example, if a global simulation is required using a 1-degree resolution concentration grid, that results in about
65,000 grid points at the surface. Clearly a very long duration simulation that is expected to spread over much of the
domain will require a comparable number of puffs as grid cells to provide smooth concentration patterns. If we assume
the lowest layer only represents about 10 percent of the volume over which the puffs have been transported and mixed,
it is not unrealistic to expect such a simulation to require 10 times as many puffs. An alternate approach, would be to
dump the puffs into a global grid
model rather than splitting them as they grow to the size of the meteorological grid.

Concentrations at any point would then be a sum from the two modeling approaches. This is a
variation of a plume-ingrid model.

Parameter Considerations
Very long duration simulations or simulations using very fine resolution meteorological data, which have an insufficient
initial allocation of the puff array space (MAXPAR in the namelist) can result in split shutdown messages or perhaps
even emission shutdown messages. If any of these occur, the simulation results should be viewed with caution. The
results may be noisy and inaccurate if the emissions (new puffs released) have also been restricted. A simulation with
puff split restrictions may be improved by first increasing the array space to a value that still results in acceptable
simulation times. If not effective, or the CPU times become too long, the second choice could be to increase the
frequency of enhanced merging (perhaps decreasing KRND from 6, to 3, 2, or even 1), and perhaps in combination with
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Advanced / Special Topics / Puff Split-Merge Issues (S630)

decreasing the split interval (increasing KSPLT from 1 to 3, 6, or 12). Although decreasing the split interval will not be
effective once splitting has shutdown, it may extend the time at which splitting first shuts down. Enhanced merging has
little effect if most of the puffs have the same mass, perhaps because they were released at the same time. It is most
effective for continuous emission simulations, where there is a large range in puff mass due to the different number of

splits each puff has been subjected. An effective removal method is setting FRMR to a non-zero value. This has the
effect of purging the simulation of low-mass puffs and would be most appropriate for continuous emissions
simulations, where the puffs at longer distances have less importance. Used incorrectly, setting this parameter to a nonzero value can seriously bias the model results. For long-duration continuous emission simulations, it may also be just

as effective to stagger the emissions because it would not be necessary to emit puffs every time step for realistic (and
accurate) results. This could be accomplished by emitting more mass over a shorter duration and then cycling the
emissions. For instance instead of a continuous emission, one could emit 10 times the normal hourly amount over 0.1
hours (6 min) and the repeat the emission cycle (QCYCLE parameter) each hour. The emission cycle could even be
staggered over longer times.

CPU Time Considerations

Long simulations may result in excessive CPU times because puffs will almost certainly be transported to the upper
regions of the atmosphere where the winds are strongest which results in very small integration time steps. If
computational accuracy in these upper regions is not required, perhaps because the only interest is boundary layer
transport, the time step should be set to a fixed value. Given the same number of puffs, the enhanced merging version
of the model should run substantially faster than the original version because when puff splitting shuts down and puffs
continue to grow, they become quite large and cover many more concentration grid points which must all be sampled.
Unrestricted puff splitting or restricting puff growth avoids this computational problem.

Table of Contents

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Advanced / Configuration Setup / Variables Not Set in the GUI (S640)

Advanced / Configuration Setup / Variables Not Set in the GUI

CAPEMIN (-1) - defines the threshold value of CAPE (convective available
potential energy J/kg) to initiate
enhanced vertical mixing. A value less than zero (default = -1) skips the CAPE computation such that if CAPE is
not available in the
input meteorological data file then it is NOT computed. When the value is greater than zero,
CAPE enhanced mixing is turned on and if CAPE is not available in the input data file, it is computed for each
grid point, which may substantially slow
down the overall calculation. CAPE enhanced mixing results in
particles in the cloud-layer being randomly redistributed within the cloud-layer if they reside in a grid cell where
CAPE exceeds CAPEMIN. A initial value of 500 J/kg is suggested to test this computation.
DECAY (1) - when (1=default) lets deposited material radioactively decay
after accumulation on the deposition
grid until it is written to the output
file. When (0) then deposited material does not decay. In both situations,
when
the radioactive half-life is defined in the CONTROL file, the mass on the particles
while airborne will
decay in both cases. This flag only determines what happens
after the material is deposited on the grid and before
the information is written
to the the output file.
HSCALE (10800.0) - the horizontal Lagrangian time scale in seconds.
The default value is about equal to 1/f, the
Coriolis parameter.
K10M (1) - when (1=default) the 10m/2m values for winds and temperatures
are used as the lowest data level if
available in the meteorological file. When set
to zero, these data values will not be used in any computations.
KAGL (1) - KAGL only applies to trajectories, not concentration simulations.
For trajectory simulations, the
default option is to write the heights as AGL (KAGL=1),
setting KAGL=0 converts the trajectory output heights
to MSL. The KMSL namelist
parameter only applies to how heights are interpreted in the CONTROL file, while
KAGL
determines how the model heights are written to the output file.
KHINP (0) - when non-zero sets the particle age in hours that will be read
from the particle initialization file
(PARINIT) that may contain particles of
many different ages each output time period. This option is intended to
be used with
continuous initialization (NINIT=2) in which the calculation is continued
from a previous
simulation in which particles older than KHINP had been terminated by using the namelist variable
KHMAX=KHINP. These continuous
emission simulations require particles to be added each time step. This
configuration
works best when the integration time step is set to the same fixed value for all
simulations.
KRAND (2) - if not otherwise explicitly set, krand=1 when NUMPAR is greater
than 5000, which precomputes all
the random numbers required for the particle turbulence calculations. When NUMPAR is less than or equal to
5000 then krand=2 and the random numbers are computed at each dispersion time step. The dynamic method is
slightly more acurate than the precomputed random numbers but it requires about twice as much CPU time.
With
large particle release rates both methods will provide comparable results. The special case of krand=3 will result
in no turbulent mixing being added to the particle
position; the particle track will follow the mean trajectory. This
option is primarily
intended for diagnostic testing.
KWET (1) - when (1=default) the code uses the precipitation values in the
defined meteorological input data file.
When KWET=2, the code will try to open a
file called raindata.txt which defines the directory, base, and suffix

name of an external precipitation file that is in the ARL standard format. The text
file also defines the 4-character
name of the precipitation variable as well as
the conversion factor from file units to model units (meters/min).
The file name
is automatically constructed from the prefix and suffix names using current
calculation date
following the convention: {prefix}{YYYYMMDD}{suffix}. If the raindata.txt file is not found in the startup
directory, the model will create a template for manual editing and then stop.
MAXDIM (1) - is the maximum number of pollutants that can
be attached to one particle. Otherwise, if multiple
pollutants are
defined they are released as individual particles. This feature is
only required with chemical
conversion modules, which are not part
of the standard distribution. However, the species 1->2
conversion option
will automatically set
MAXDIM=2, but the standard emissions routine will still put each
species on a different
particle in its appropriate array element.
The only emissions routine that is enabled to release multiple
species on
the same particle is the emissions
file option. Setting MAXDIM greater than one forces all the species
on the
same particle with the limitation that the number of defined
pollutants must equal MAXDIM. No other
combinations are permitted.
The advantage of this approach is that not as many particles are
required for the
calculation as in the situation where every
pollutant is on its own particle. The limitation is that each
species on
the particle should have comparable dynamic characteristics,
such that they are all gases or have similar settling
velocities,
otherwise the transport and dispersion simulation would not be
very realistic.
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Advanced / Configuration Setup / Variables Not Set in the GUI (S640)

MESSG (MESSAGE) - is the default base name of the diagnostic MESSAGE file. In normal simulations, the name
defaults to the base
name. In an ensemble multi-processor calculation, the message file name
would be
automatically set to correspond with the process number by
appending the process number to the base name:
{base}.{000}, where the
process number can be any integer between 001 and 999.
NBPTYP (1) - defines the number of bins assigned to each particle
size as defined in the pollutant section of the
CONTROL file. The default value
of one uses the input parameters. A value larger than one will create that

number of particle size bins centered about each value in the CONTROL file.
The program creates the mass
distribution for a range of particle sizes given just a few points within the distribution. We assume that dV/d(log
R) is linear
between the defined points for an increasing cumulative mass distribution with
respect to particle
diameter. The input points in the CONTROL file should be
sorted by increasing particle size within the array. For
instance, if the
CONTROL file defines 3 particle sizes (5, 20, and 50), and NBPTYP=10, then for
the 5 micron
particle generates sizes from 2.3 to 8.1 microns while the 50 micron
input particle generates sizes from 30.2 to
68.9 microns.
OUTDT (0) - defines the output frequency in minutes of the endpoint
positions in the PARTICLE.DAT file when
the STILT emulation mode is
configured. The default value of 0 results in output each time step while the

positive value gives the output frequency in minutes. A negative value disables
output. The output frequency
should be an even multiple of the time step and be
evenly divisible into 60. In STILT emulation mode, the time
step is forced to
one minute.
PINBC - defines the input particle file name (default=PARINBC) that
can be used for boundary conditions during
the simulation.
RHB (80) - defines the initial relative humidity required to define
the base of a cloud.
RHT (60) - the cloud continues upward until the relative humidity
drops below this value. The values represent a
compromise between the cases when
the cloud (and precipitation) covers an entire grid cell and those situations

where the cloud may only cover a fraction of the meteorological grid cell. For
example, using the cloud fractions
as defined in the EDAS (40 km resolution) data, 70% of the time 100% cloud cover occurs when the RH exceeds
80%.
TVMIX - vertical mixing scale factor is applied to vertical
mixing coefficents when KZMIX = 2 for boundary layer
values and
KZMIX = 3 for free-troposerhere values.
VDIST (VMSDIST) - an output file that contains the hourly vertical
mass distribution, similar to the values shown
in the MESSAGE file every six
hours. The output can be disabled by setting the default file name to blank
or null
length. Programs vmsmerge and vmsread are available in the
exec directory to view and process these files.
VSCALE (200.0) - the vertical Lagrangian time scale in seconds
controls the transition of the dispersion rate from
linear to square root
growth as a function of time.
VSCALEU (200.0) - the vertical Lagrangian time scale in seconds
controls the transition of the dispersion rate
from linear to square root
growth as a function of time for unstable PBL conditions.
VSCALES (200.0) - the vertical Lagrangian time scale in seconds
controls the transition of the dispersion rate
from linear to square root
growth as a function of time for stable PBL conditions.

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Advanced / Satellite Data / FTP NASA TOMS (S431)

Advanced / Satellite / FTP NASA TOMS

The FTP menu gets TOMS (Total Ozone Mapping Spectrometer) data from
the following site and directories:

ftp://jwocky.gsfc.nasa.gov/pub/{eptoms|nimbus7}/data/aerosol/{year}/

file = L3_aersl_{ept|n7t}_{year}{month}{day}.txt
More current information is available from the README files on the NASA server.
TOMS Earthprobe datasets are located in the following directory paths:
data/ozYYYY/gaYYMMDD.ept (YYYY=1996 >>) (EarthProbe still reporting data)
Daily gridded (g), ASCII (a) files from year YY, month MM and day DD. The data in
these ASCII files are in the
format used for the Nimbus-7 and Meteor-3 CD-ROM. Details
of this format are explained in the EarthProbe
Data Products User's Guide,
EARTHPROBE_USERGUIDE.PDF, available in the parent directory. A stub
program, RDGRID.FOR
may be used to read these datasets.
The values are in 3 digit groups 111222333444555

Sample ozone value: 234 = 234 du 0 = fill value

data/reflYYYY/gaYYMMDD.epr
Daily reflectivity data. Format similar to that of ozone
data.

The vales are in 3 digit groups 111222333444555

Sample reflectivity value: _83 = 83% 999=fill value

data/a1YYYY/gaYYMMDD.epa
Daily aerosol data. Format similar to that of ozone data.
The data are an aerosol index formed directly from the measured
radiances in two TOMS channels. Positive
values generally represent
absorbing aerosols (dust and smoke) while negative values represent
nonabsorbing
aerosols. The identification is not perfect because of
geophysical reasons (e.g., aerosol too low to the ground).

There will soon be a corresponding data set of optical depths and

single scattering albedos.

The values are in 3 digit groups 111222333444555

The numbers have been multiplied by 10

--1=0.1 -11=1.1 111=11.1

999 = missing or bad data

-- stands for blanks

References:
Herman, J.R., P.K. Bhartia, O.Torres, C. Hsu, C. Seftor, E.
Celarier, Global Distribution of UV-Absorbing
Aerosols From
Nimbus-7/TOMS Data, J.Geophys. Res., 102, 16,911-16,922, 1997.
Torres, O., P.K. Bhartia, J.R. Herman, Z. Ahmad, and J.
Gleason, Derivation of aerosol properties from satellite

measurements of backscattered ultraviolet radiation: Theoretical

basis, J. Geophys. Res. 103, 17099-17110, 1998.
UV Erythemal Irradiance
data/uvYYYY/gaYYMMDD.epe
Daily uv data. RDGRID.FOR may be used to read these data but
see 1README.UV and erynotes.pdf for

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Advanced / Satellite Data / FTP NASA TOMS (S431)

information about
interpreting/decoding the uv data file format.
The values are in 3 digit groups 111222333444555

123 = 2.3x10^1 J/m2 -23 = 2.3 --3 = 0.3 999 = missing or bad data
data/monthly_averages/gmYYMM.ept .
This directory contains gridded monthly (gm) averages of ozone
data from year YY and month MM. At least 20
days of data must be
available for monthly averages to be considered valid.

Monthly averages of aerosol, UV and reflectivity are also provided

in directories located in a path structure
similar to that for
ozone averages.
The Fortran statements that wrote the data records of these
monthly files are:

560

DO 570 IL=1,180
DO 560 jj=1,288
OZONE(JJ)=ozav(JJ,IL)
write(21,'(1X,25I3)') (OZONE(jj),jj=1,275)
write(21,'(1X,13I3,1A17)') (OZONE(jj),jj=276,288), latlab(IL)
CONTINUE

570

data/overpass/OVPxxx.ept
A subset (seconds UT, latitude, longitude, total ozone, surface
reflectivity, solar zenith angle,aerosol index, SOI
index, etc) of
EarthProbe data specific to a particular latitude-longitude
location. xxx designates a numerical site
location as listed in
file "1Sitelist" in this directory.
Fortran statements that can be used to read the 1st header
record and the data records in the OVPxxx files are the

following:

For the header record:

CHARACTER*28 site_name
INTEGER*4
site_id, site_alt
REAL*4
site_lat, site_lon
Read(lun,2) site_name, site_id, site_lat,site_lon, site_alt
2 Format(A30,4X,I3,7X,F7.2,7X,F7.2,7X,I4)

and for the data records:

Format(F7.1,1X,I4,1X,I3,1X,I5,2X,I2,1X,F6.2,1X,F7.2,1X,
I3,1X,I3,1X,F5.2,1X,F5.1,1X,F5.1,1X,F6.2,1X,I4)

1README, in this directory, provides more information about the

OVPxxx files.
data/zonal_means/zm_month.ept and zmday_ YY.ept
Zonal means files. File "zm_month.ept" contains monthly
averages of zonal mean column ozone over each 5
degrees of latitude
for each year of EarthProbe operation to date. Additional files,
named "zmday_YY.ept"
(YY=96, 97...) provide zonal means on a daily
basis. At least 2/3 of possible data must be present for a zonal

mean to be considered valid.

The Fortran statements that wrote the header and data records of
file zm_month are the following:
CHARACTER*69 MONLAB
Data MONLAB/'Jan
Feb
Mar
& Oct
Nov
Dec'/
do 20 j=1,37
lat(j)=-95 + 5*j
20 continue
write(22,'(8x,A69)') MONLAB

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Apr

May

Jun

Jul

Aug

Sep

Advanced / Satellite Data / FTP NASA TOMS (S431)

300

DO 300 IZ=1,36
write(22,'(I3,I4,12f6.1)')
CONTINUE
write(22,'(I3,I4,12f6.1)')
write(22,'(I3,I4,12f6.1)')
write(22,'(I3,I4,12f6.1)')

lat(IZ),lat(IZ+1),(ozm(IM,IZ),IM=1,12)
-65,0,(ozm(IM,37),IM=1,12)
0,65,(ozm(IM,38),IM=1,12)
-65,65,(ozm(IM,39),IM=1,12)

The Fortran statement that wrote the data records of the zmday_YY
files is:
write(21,'(A12,F9.3,1X,36F6.1,3X,3F6.1)') date,yd,zmd

If these EarthProbe/TOMS data are downloaded and used in

publication, please give proper credit to the NASA/GSFC
TOMS Ozone
Processing Team (OPT).
For more information on the EarthProbe/TOMS data set,
contact
Dr. Richard D. McPeters

Code 916

NASA Goddard Space Flight Center

Greenbelt, MD 20771

[email protected]

Table of Contents

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Advanced / Satellite Data / TOMS Viewer (S430)

Advanced / Satellite / TOMS Viewer

The viewer for the TOMS Aerosol Index provides a quick and qualitative
way to evaluate the model calculation for dust
storms, fires, and other events
that may inject a significant number of particles into the atmosphere. This is

accomplished by overlaying the AI values with the model particle positions from
the particle dump file and/or the
concentration field. The TOMS display provides
a color coded representation of analysis of aerosols from the "Total
Ozone
Mapping Spectrometer". A range of warmer colors represents various positive
values corresponding to
absorbing aerosols.
The particle position dump file should have been created during the simulation
by configuring the output of particle files
(item 9) in the advanced configuration
menu. Note that output is only required once-per-day because each TOMS data
file
represents all the overpasses for one day. For any given longitude, the satellite
overpass occurs approximately near
solar noon. Therefore the output time should be
determined according to the predominant particle longitude. For
instance, for the
eastern United States, solar noon occurs around 1600 UTC.
The viewer has several input options that can all be selected through the
GUI. The map center can be set for the dateline
or prime meridians; the AI display
has a minimum value below which nothing will be shown; and there is an AI color

increment that represents the AI difference between the colors. Colors change from
cold (blue) to warm (red) with
increasing AI.
The times in the output files are not matched and they are just displayed in
time sequence, with the TOMS file opened
according to the date-time indicator
written in the particle file. Therefore multiple particle or concentration files
could
be written for each day, but only one TOMS file will be opened for that day.
There are two steps involved in viewing these files. First the map domain needs
to be initialization by first clicking and
holding the left mouse button from the
lower left corner and releasing the button at the upper right corner. The map
will
then be redrawn. Then each left button mouse click draws next data for the next time period. A right button click will
exit the display loop.

Table of Contents

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Advanced / Special Topics (S441)

Advanced / Special Topics

This section provides some guidance in configuring the model input to for certain specialized calculations. The default

configuration supplied with the test meteorological data is confined to a simple trajectory and inert transport and
dispersion calculation. Some of these more complex scenarios are configured through the Advanced menu
Configuration Setup tab which modifies the "SETUP.CFG" namelist file.
Particle or Puff Releases
The concentration model default simulation assumes 3D particle dispersion (horizontal and vertical). Other options are
set with the INITD parameter of the SETUP.CFG namelist
file defined in the advanced menu section. Normally
changes to the
dispersion distribution are straightforward. However, there are some
considerations with regard to the
initial number of particles released.
The default release is set to be 2500 particles over the duration of the
emission
cycle (see NUMPAR). A 3-dimensional (3D)
particle simulation requires many more particles to simulate the proper

pollutant distribution, the number depending upon the maximum downwind

distance of the simulation and the duration
of the release, longer in each
case require more particles. Too few particles result in noisy
concentration fields. A 3D
puff simulation starts with one puff as the
puff-splitting process in conjunction with the vertical dispersion
quickly
generates a sufficient number of puffs to represent the complex
dispersion process.
Continuous Emissions
As noted above the default release is 2500 particles over the
duration of the emission cycle. If continuous emissions are

specified (e.g. over the duration of the simulation), then those

2500 particles are spread out over that time period. This
may easily
result in the release of too few particles each hour to provide
smooth temporal changes in the concentration
field. Imagine a
single particle passing in and out of the vertical concentration
cell due to turbulent diffusion. One
solution would be to increase
the NUMPAR parameter until smoother results are
obtained. Another possibility would
be to cycle the emissions by emitting
particles only for the first time step of each hour. Those particles would contain
the total mass for a one-hour release (see how to set QCYCLE).
Time Variation of the Emission Rate
One way to incorporate a time varying emission rate into the
existing model structure is to use the particle dump feature
to
restart the model each time with a new emission rate. Another
option is to assign the name of a temporal emission
input file to
the "EFILE" variable in the setup.cfg namelist file. This ASCII
file must consist of at least three records,
the first two of which
are used for identification purposes, and the third, and all
subsequent records, define the temporal
sequence of emissions. Each
emission record contains the start time, duration, location, and
emission rate. If the EFILE
is present, the first emission record's
values replace the emission values set in the control file. Once
the model
computation time has passed the emission period defined
on the first emission record, the emission data from the
second
record are loaded and the calculation continues with the new
emission data. The format of the emission file is
given below:
Record #3 -> end
I4 - Start year
I3 - Start month
I3 - Start day
I3 - Start hour
I2 - Start minute
I3 - Duration hours
I2 - Duration minutes
F6.2 - Latitude
F8.2 - Longitude
F8.0 - Emission rate in units/hour

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Advanced / Special Topics (S441)

Time-Varying Unit Source Simuations

The previous approach defined a time-varying emissions file to use with
a single simulation. An alternate approach is
run the model with a unit
source emission rate and in a post-processing step, apply a time-varying
emissions factor.
This can be accomplished by multiple simulations, one for
each emission time period, and then the concentration output
results can be
added together or through a single simulation where individual release time
periods are tagged as distinct
pollutants. This is accomplished using
the namelist parameters QCYCLE and ICHEM.
As an example, if hourly (the minuimum) resolution is desired over a 24 hour
simulation period, then the emission rate
needs to be set to emit one one unit for
a duration of one hour. The namelist variable QCYCLE should also be set to 1.0
hour so that the emissions effectively become continuous at a rate of one unit per hour. This in combination with
ICHEM=10 will result in the creation of
24 concentration arrays with each particle being tagged according to its release

hour and those particles will only contribute to concentrations on the grid with
the same release-time tag. The pollutant
identification field is used and its value
corresponds to hours after the start of the simulation. The output concentration

grid will appear to be like any other but with 24 pollutants, one for each release
period as defined by the QCYCLE
parameter. Make sure that a sufficient
number of particles have been released to provide consistent results for all time

perioids.
The output can be processed like any other concentration file by selecting the
specific pollutant (= release time) or by
two different post-processing applications
that are configured to decode the output file. The apply source
concentration
utility menu multiplies each concentration field with its associated
emission rate defined in an external file. Another
option is to use the convert to station menu to extract the time series of
concentrations contributed by each release time
to each sampling period for a
specific pre-selected location. The TCM format checkbox should be selected to enable
the proper conversion option.
Area Source Emissions
Normally emissions are assumed to be point or vertical line sources. Virtual point sources (initial source area >0) can be

defined two ways: 1) through the definition of an initial area on

the source location input line of the CONTROL file or
2) by the
definition of a gridded emissions file. If the model's root startup
directory contains the file Emission.txt, then
the
pollutants are emitted from each grid cell according to the
definitions previously set in the Control file. Two source

points should be selected, which define the lower left

(1st point) and upper right (2nd point)
corner of the emissions grid
that will be used in the simulation.
This should be a subset of the grid defined in emission.txt.
The release height
represents the height from the ground through
which pollutants will be initially distributed. Note that the structure of
the "emission.txt " file has changed with the HYSPLIT 4.6 revision of October 2003.
The "emission.txt" file contains all the information that is
required to interpret the data in the gridded emission
inventory
file. The file that contains the inventory is now independent of
the emission.txt file. The file's first record
contains information
about the internal grid cell size that is used by the dispersion
model to accumulate the file's
emissions. The emission file defines
the emissions at latitude-longitude points, which may represent the
emissions from
an area or from a point. The values at these points
are accumulated in an internal grid, the size of which is defined
on
the first record. This value can be arbitrarily changed
according to the desired resolution of the simulation. The

pollutant puffs are released with an initial size comparable to the

accumulation cell size. Because the emission file data
are remapped
to an internal grid, the file can consist of emissions data on a
regular grid or just a collection of individual
cells. The emission
rate in the Control file is used as an additional multiplication
factor for the data in the emission file.
Also note that previously
discussed particle number restrictions still apply. The particles
are spread out over the
duration of the emission and the number of
grid cells that are defined in the emission domain. The format of
the
emission.txt file is given below:
Record #1
I4 - Number (n) of pollutant species in file
I4 - Number of emissions defined for each 24 hour period
F10.4 - Conversion factor: file units to model units/hour

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Advanced / Special Topics (S441)

2F10.4 - Accumulation cell size (latitude & longitude)

Record #2
nA4 - Four character pollutant identification string for each pollutant
Record #3
A - The /directory/filename of the emission data file
The actual emission data file will contain one record
identifying the grid location and then two records for each

pollutant species. The first record defines emissions from GMT

hours 0 to 12 and the second record from hours 12 to
24. This pair
of records is repeated for each pollutant species:
Records Loop #1 to the number of i,j grid point
2I4 - I,J grid point of emission cell (arbitrary units for identification)
2F10.4 - Southwest corner Longitude and Latitude of this emission cell
Record Loop #2 to the number of pollutant species
12E10.3 - emissions for pollutant#1 hours 1-12
12E10.3 - emissions for pollutant#1 hours 13-24
Multiple Pollutants
The model can easily be configured to simulate more complex
pollutant episodes with multiple pollutant types on
different
particles or multiple pollutant species on the same particle. The
former is accomplished by defining additional
pollutants in the
CONTROL file. In this configuration, multiple species are
emitted, have no interaction, and may track
differently. This
situation may represent a volcanic ash plume, where each pollutant,
a different sized particle, settles at
a different rate. An example
configuration control_volcano can be retrieved in the
SETUP menu.
Pollutant Transformations
In the latter situation, when multiple pollutants are defined
on the same particle, an external chemistry routine is
required
that converts mass from one species to another, all tracking
together (advecting and dispersing). In this
situation,
MAXDIM should be raised to the required value. Increasing
the MAXDIM value always requires an external
routine to
adjust the mass between species. A simple species conversion
program is included with the standard model
distribution. In the
default configuration it is only necessary to define two different
pollutants in the concentration setup
menu
and select the 10% /hr checkbox in the advanced configuration menu's conversion
section. This option
combination sets MAXDIM=2 and calls the
transformation routine every time step to convert pollutant #1 to
#2 at a rate
of 10% per hour. Other conversion rates or a greater
number of pollutants can be defined by creating the

CHEMRATE.TXT file in the local directory. This file would

consist of one or more records, each record defining a
pollutant
conversion. The data are free-format and consist of four fields,
the integer "from" and "to" pollutant index
numbers, and the real
hourly conversion "rate", and molecular weight adjustment "factor".
For instance, if the file were
to be defined for the default case,
the one data record would have the following values: (1 2 0.10
1.0). The molecular
weight adjustment factor can be used to account
for other reactions not considered in the simple conversion module.

For instance, if one were to define pollutants #1 and #2 as SO2 and

SO4, respectively, then the molecular weight
adjustment factor
should be 1.5 as SO2 transforms to SO4 (the conversion picks up two
additional oxygen molecules).
Complex Chemistry
Although there are other more complex chemical conversion
modules available for HYSPLIT, they are not incorporated
into the
standard compilation. More information on these special
compilations may be found at

http://www.ready.noaa.gov/HYSPLIT_pcchem.php

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Advanced / Special Topics (S441)

One feature, required for all these modules, is that there is a

more complex interaction between the individual pollutant
plumes,
requiring a close link between the concentration grid and the
meteorological data grid. This option is available
in the standard
model compilation. By setting the namelist file parameter ICHEM=4,
the concentration grid is redefined
to be equal to the
meteorological data grid in terms of spatial resolution and extent.
This simplifies the computation of
the grid based chemical
reactions that are dependent upon the meteorological conditions
within each concentration grid
cell.
Deposition and Decay
A simple particle deposition configuration (control_nuclear)
for radioactive Cs-137 can be retrieved into the SETUP
menu,
which shows the default settings for radioactive decay and wet and
dry deposition. In conjunction, a list of sites
can be loaded into
any SETUP menu, from the "Set Starting Locations" tab by
pressing the LIST button. The site
locations can be found in the
file "\working\plants.txt" and could be replaced by any user
generated location file listing.
The normal deposition mode is for particles to loose mass to
deposition when those particles are within the deposition
layer.
An additional option was added to deposit the entire particle's mass
at the surface (the particle is removed) when
subjected to deposition.
To insure the same mass removal rates between the two methods, a
probability of deposition is
computed, so that only a fraction of the
particles within the deposition layer are deposited in any one time step.
The
probability of deposition is a function of the deposition velocity,
time step, and depth of the layer. One limitation of this
method is that
only one mass species may be assigned to a particle. The probability
deposition method can be invoked
from the namelist file with ICHEM=5.
Compilation Limits
With HYSPLIT V4.5 most compilation array limits have been
eliminated through the use of dynamic array allocation.
However,
one restriction remains with regard to the meteorological input
data: meteorological data files are limited to a
maximum of 12 per
simulation, with no more than 75 levels or 35 variables in each file.
This restriction does not limit
any computation with data files
available through the ARL web site, because all available data
files meet the number of
variable and levels restriction.
The use of dynamic memory allocation can result in unpredictable
results if the computer's hardware memory limits are
exceeded. Although
there are several memory error allocation traps that will result in a
message and execution
termination, memory limits can be exceeded in a
variety of different locations, such as when opening a file. Memory
usage
is a primarily a function of the meteorological sub-grid size, meteorological
data grid size, concentration grid
size, and the number of pollutants.
Script Automation and Configuration
Most of the discussion in various sections of the User's Guide are tailored
to individually configured simulations.
However there are several features to
the model that can be used to automate the computational environment. For
instance,
a sample Auto_traj.tcl script is provided in the /examples/scripts/tcl
directory that can be used as a guide to
automate many applications.

# Auto_traj.tcl

# the next line restarts using wish

# exec wish "$0" "$@"

set Start_hgt "10.0"

set Traj_path "../exec"

set Start_time "00 00 00 00"

set Run_hours "24"

set Vert_coord "0"

set Top_model "10000.0"

set Meteo_path "../metdata/"

set Meteo_file "oct1618.BIN"

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Advanced / Special Topics (S441)

set Output_path "./"

set Output_base "tdump"

set Output_numb 1

foreach {Start_lat Start_lon} {35.0 -90.0 40.0 -90.0 45.0 -90.0} {

set Start_loc "$Start_lat $Start_lon $Start_hgt"

set Output_file "$Output_base$Output_numb"

file delete Control

set f [open Control w]

puts $f "$Start_time"

puts $f "1"

puts $f "$Start_loc"

puts $f "$Run_hours"

puts $f "$Vert_coord"

puts $f "$Top_model"

puts $f "1"

puts $f "$Meteo_path"

puts $f "$Meteo_file"

puts $f "$Output_path"

puts $f "$Output_file"

close $f

exec "$Traj_path/hyts_std.exe"

incr Output_numb}
In this particular example the test trajectory case is run for
three different starting locations, each simulation writing a
new
endpoints file with a unique file name. The CONTROL file is recreated for each simulation. It would be trivial to
rewrite the script to set the latitude-longitude and loop through a different number of starting days and hours. With
Tcl/Tk installed, this script can be run under Windows or Unix. For instance, to compute new forecast trajectories each
day, the process can be automated by including a data FTP at the beginning of the script to get the most recent
meteorological forecast file, setting the starting time as
"00 00 00 00" so that the trajectories will start at the beginning

of the file, and finally calling the script once-a-day though the
Unix crontable or the Window's scheduler commands.
One problem with automated operations is that it is possible to
generate simultaneous multiple jobs which may interfere
with each
other. The executables, hycs_std and hyts_std have a command line
option of adding the process ID (PID):
e.g. hyts_std [PID]. In this
situation all standard named input and output files [those not
defined in the Control file]
have the PID added as a suffix to the
file name: e.g. Control.[PID], Setup.[PID], Message.[PID].
An example of another type of operational configuration is the
extended simulation of a pollutant emission using
archive data to
bring the simulation to the current time and then using forecast
meteorological data to provide a daily
projection. Each day the
archive simulation must be updated with the new archive data and a
new forecast product
generated. This process can also be automated
through a script, but for illustration purposes one can use the
advanced
features of the GUI to configure such a case. Assume a
one-hour duration accidental pollutant release that occurred 48

hours prior to the current time. The following sequence

applies:
1) From the "Meteorology" menu tab download the
appropriate archive meteorological data and the most recent

forecast meteorological data (assume it is available to +48h).

2) Setup the concentration simulation to run 96 hours using two
meteorological files starting with the archive data
and then
switching to the forecast data.
3) Under the Advanced menu tab and Configuration
Setup write the initialization file after 72 hours.
4) Run the model.
At the completion of the simulation you will have the plume projection from release (-48 h) through the current forecast
(+48
h). The PARDUMP file will contain all the endpoint positions
at +24 hours, corresponding to the initialization
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Advanced / Special Topics (S441)

time of when the

next forecast will be available (assume there is one forecast per
day).
The next day, when the new forecast data are available, reconfigure
the model to run only with the forecast
meteorological data for a duration of 48 hours. Then write the initialization file after 24 hours
and run the model to
obtain the new projection. In this second part,
we assume that the first 24 hours of the forecast are not much different

than the analysis. In practice, this procedure can be run at the same
frequency that the new forecast data are available,
typically 4 times per
day. Data at the initial forecast hour are identical to the analysis data.
Source Attribution with Dispersion
A common application of atmospheric trajectory and dispersion
models is to try to determine the source of a pollution

measurement. If a high value has been collected at a particular

receptor, from which pollutant source region did the air
originate?
One approach is to calculate the trajectory "backwards" from the
receptor site. In the trajectory calculation
this is accomplished by
setting the integration time step to a negative value. However, the
trajectory only represents the
upwind path of a single point, while the
pollutant measurement may require of hundreds or thousands of
trajectories to
represent the dispersion of the pollutant in time
and space.
Another approach is the run the entire dispersion-trajectory model upstream (backwards), which is computationally
attractive because in a 3D particle model the dispersion process is represented by a turbulent component added to the
trajectory calculation and the advection process (the trajectory) is fully reversible. The trajectory equation can be
correctly integrated in either direction. The interpretation of the output is a bit more complex because dispersion is an
irreversible
process. The upstream numerical calculation will yield a result because the
integration of the dispersion
equation is still in the downstream mode while
the advection is integrated backward upstream. The meaning of the

upwind dispersion result is not as easily interpreted as the downwind

calculation. In any event, as noted in the earlier
instructions, it is
possible to run the dispersion model "backwards" by setting the run
duration to its equivalent negative
value. The stop time of the sampling
should be set prior to the start time. All start and stop times should be
set to their
exact values - relative start-stop times are not supported
in the backward mode.
Transport of Particles Deposited on Water Surfaces
The main code was modified (October 2003 Version 4.6) to permit
particles deposited on water surfaces to continue to
be transported
on the water surface by the wind generated drift current. The
transport output is treated as a deposition
surface for display
purposes. This new deposition method then creates particles that
can be transported on water
surfaces. Particles can be deposited on
any surface. However, if the surface is defined as water, then the
particle is
assigned a unique identification code to distinguish it
from atmospheric particles or puffs. These new particles may

continue to be transported along the surface of the water

contributing to deposition each time step but not air

concentration. Dispersion is not computed for these particles. When

they approach a land surface they are deleted. The
water surface
transport option is invoked from the namelist file with ICHEM=7.
This option automatically forces the
probability deposition
computation (ICHEM=5) and should only be used only with the 3D
particle mode (IN ITD=0).
Surface water deposition can only be
displayed if the deposition output level (0) is defined. Although
particles may
deposit over land, over-land deposition values are
never shown.
The wind induced surface water drift current is assumed to
equal the vector atmospheric friction velocity. The friction

velocity represents the momentum transport to the surface and it is

an approximation of the surface water movement.
Currently only the
GFS meteorological model output file contains the vector momentum
flux components.
Mixing Ratio Output
Setting this option forces the concentration summation calls within
the main program to integrate the mass divided by
the air density (kg/m3)
rather than just the mass, thereby permitting the output fields to be more
easily converted from
mass/volume to mixing ratio. This option would most
likely be used in conjunction with the CMASS
namelist variable
that can be set to sum mass/volume or just mass.
STILT emulation mode

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Advanced / Special Topics (S441)

The STILT model is a variation of HYSPLIT developed by Lin et al.

(2003 - JGR, VOL. 108, NO. D16, 4493,
doi:10.1029/2002JD003161) that can
be used to estimate upwind surface fluxes from atmospheric measurements.

Although HYSPLIT does not contain the mass conservation adjustments and coupled
vertical-mixing horizontaltransport features of STILT, setting this flag causes
the HYSPLIT concentration output field units to be similar to the
STILT
configuration. Two changes are introduced; the mass summation is divided by air
density resulting in a mixing
ratio output field (ICHEM=6) and the lowest
concentration summation layer (concentration layer top depth) is
permitted to
vary with the mixed layer depth (ICHEM=9), so that only particles below 50% of the
mixed layer depth at
each time step are summed to the lowest layer. The ICHEM=8 switch turns on both density and varying layer depth. A
text file of particle position information (PARTICLE.DAT) at each time step will also be created
unless the namelist
parameter OUTDT defining the output
interval (min) is changed.
Concentration layer varies with mixed layer depth
This option changes the height of the lowest concentration layer from a fixed value to a variable, which changes
according to the mixed layer depth each time step. The depth, as a fraction of the mixed layer, is computed by the
height value of the
lowest level, where the height is interpreted in hundreds, such that the a fraction
representing 0.5 of
the mixed layer depth would be entered as 50. Note that in this
mode it may be desired to change the default minimum
mixing depth KMIX0 from its default value of 250 m, which would
result in a minimum sampling layer of 125 m.
Concentration levels above the first
level are unaffected by this option.

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Advanced / Special Topics / Particle Dump File Format (S442)

Advanced / Special Topics / Particle Dump File Format

The concentration configuration menu provides an option to write a model initialization file, which by default is always
named "PARDUMP" (for particle dump). This file can be written at regular intervals during the simulation, a
convenient way to restart a simulation in case of unexpected failure. To restart the model using the PARDUMP file it is
only necessary for the file to be present in the root working directory. If the internal time stamp of the file matches the
start time of the simulation, the model will initialize the particle count from the file before emitting new particles
according to the emission scenario defined in the control file. The format of the PARDUMP file is given below:
Record #1
INT*4 Number of particles
INT*4 Number of pollutants
INT*4 Time of particle dump (YEAR, MONTH, DAY, HOUR, MINUTES)
Record #2 - Loop to record: Number of particles
REAL*4 Particle pollutant mass (times the number of pollutants)
REAL*4 Particle LATITUDE, LONGITUDE, HEIGHT, SIGMA-U,SIGMA-V, SIGMA-X
INT*4 Particle AGE, DISTRIBUTION, POLLUTANT, METEO-GRID,SORT-INDEX
The "Particle" tab of the "Special File Display" menu brings up a Windows based viewer that
shows the particle
positions over a map background. The display can be zoomed and otherwise adjusted using the left and right mouse
buttons in conjunction with the shift and cntl keys. Help is provided on the screen with the left and right side comments
corresponding to the respective mouse button. The particle viewer can also be used to overlay satellite images on the
particle positions. More information on this is provided "FTP Satellite Data" help menu. The particle position file may
be converted to a binary concentration file through the command line utility program par2conc.

Table of Contents

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Advanced / Special Topics / Verification Statistics (S500)

Advanced / Special Topics / Verification Statistics

See the DATEM (Data Archive of Tracer Experiments
and Meteorology) web page for more detailed information on
each of these tracer experiments. The model verification statistics are presented for the un-averaged data, where each
measured and calculated concentration is paired in space and time. Zero-zero pairs are always excluded. Results are
also presented after temporally averaging the measured and calculated values over the duration of each
experiment.
These latter results are paired in space but not time and hence represent the calculation's
spatial performance. Statistics
presented are the correlation coefficient (R), the fractional bias (FB),
the figure-of-merit in space (FMS), the KS
parameter representing the departure of the measured and
calculated cumulative distributions from each other, and the
normalized rank (0 to 4) which is computed
from the normalized sum of the previous four parameters. The URL
includes links to download the measurement
data, meteorological data, statistical programs, and HYSPLIT
configuration files.
Unless otherwise noted, all HYSPLIT calculations used the NCEP North American Regional
Reanalysis (3 hr; 32 km)
meteorological data for the dispersion calculations. The main characteristics of each experimental data set are
summarized as follows:
ACURATE - consisted of measuring the Kr 85 air concentrations from emissions of the Savannah River Plant,
SC. Twelve and 24 hour average air concentrations were collected for 19 months (March 1982 - September 1983)
at 5 locations along the United States east coast from 300 to 1000 km from the plant (Fayetteville, NC to Murray
Hill, NJ).
INEL74 - consisted of a little over two months of Kr-85 releases (February 27th to May 5th, 1974) from Idaho
and continuous 12 h sampling (February 27th to May 4th, 1974) at 11 locations in a line about 1500 km
downwind (Oklahoma City, OK to Minneapolis, MN).
ANATEX - consisted of 66 PerFluorocarbon Tracer (PFT) releases (33 each from two different locations January 5th to March 26th, 1987) every two and one half days. Air samples were collected for 3 months (January
5th to March 29th, 1987) over 24 h periods at 75 sites covering most of the eastern US and southeastern Canada.
PTCH (perfluro-trimethylcyclohexane) was released from Glasgow, Montana (GGW), and PDCH (perflurodimethylcyclohexane) and PMCH (perfluro-monomethylcyclohexane) from St. Cloud, Minnesota (STC).
CAPTEX - during September and October of 1983, consisted of six 3 h PFT releases (September 18th to October
29th, 1983), four from Dayton, Ohio and two from Sudbury, Ontario, Canada with samples collected at 84 sites,
300 to 800 km from the source, at 3 h and 6 h averages for about a 48 hour duration after each release (September
18th to October 30th, 1983).
OKC80 - consisted of single release of two different PFT tracers (July 8th, 1980) over a 3 hour duration with
samples of 3 hour duration collected at 10 sites 100 km and 35 sites 600 km downwind from the Oklahoma City
release point from July 8th to July 11th, 1980.
ETEX - although there were two releases, the primary evaluation data set is from the first release on October 23,
1994 from western France. Three hour duration sampling was conducted in western europe from October 23
through October 27th.
METREX - consisted of 6 hour emissions of perfluorocarbons simulaneously, from two different locations, every
36 hours. The tracer release locations were in suburban Washington, D.C, while 8 hour air samples were colleced
at three locations within the urban area. The experiment ran for one full year. In addition monthly air
concentration samples were collected at about 60 locations throughout the region.
SRP76 - consisted of continuous emissions of Krypton-85 from the Savannah River Plant near Aiken, SC. About
15 sampling locations were placed around the plant at varying distances (15 - 150 km) and directions. Weekly
samples were collected between September 1975 and August 1977. Twice-daily samples were collected over four
months (November 1976, February, April, July of 1977).
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Advanced / Special Topics / Verification Statistics (S500)

Verification Statistics Summary

The HYSPLIT model performance by rank for the time mean
(spatial correlation) and individual sample paired
concentrations for the most recent version of HYSPLIT is given.
The rank is computed from the sum of the correlation,
fractional bias, figure-of-merit in space, and the Kolmogorov-Smirnov parameter. In addition, all required data are
provided with the HYSPLIT
distribution to run CAPTEX release #2 and compute the resulting performance statistics
through the GUI.

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source 40N 80W; start 95101612; 10 kg over 0.1 hrs

year mn dy shr dur lat lon pg/m3 stn
1995 10 16 0600 0600 39.15 -78.25 0.0 3978
1995 10 16 0600 0600 39.27 -78.07 0.0 4078
1995 10 16 0600 0600 39.38 -77.92 0.0 4077
1995 10 16 0600 0600 38.48 -76.85 0.0 3877
1995 10 16 0600 0600 38.68 -76.64 0.0 3977
1995 10 16 0600 0600 38.92 -76.43 0.0 3976
1995 10 16 0600 0600 37.86 -75.59 0.0 3876
1995 10 16 0600 0600 38.14 -75.40 0.0 3875
1995 10 16 0600 0600 38.40 -75.21 0.0 3975
1995 10 16 1200 0600 39.15 -78.25 308.8 3978
1995 10 16 1200 0600 39.27 -78.07 1605.3 4078
1995 10 16 1200 0600 39.38 -77.92 8.7 4077
1995 10 16 1200 0600 38.48 -76.85 0.0 3877
1995 10 16 1200 0600 38.68 -76.64 0.0 3977
1995 10 16 1200 0600 38.92 -76.43 0.0 3976
1995 10 16 1200 0600 37.86 -75.59 0.0 3876
1995 10 16 1200 0600 38.14 -75.40 0.0 3875
1995 10 16 1200 0600 38.40 -75.21 0.0 3975
1995 10 16 1800 0600 39.15 -78.25 5.8 3978
1995 10 16 1800 0600 39.27 -78.07 121.9 4078
1995 10 16 1800 0600 39.38 -77.92 37.8 4077
1995 10 16 1800 0600 38.48 -76.85 445.0 3877
1995 10 16 1800 0600 38.68 -76.64 614.5 3977
1995 10 16 1800 0600 38.92 -76.43 2.9 3976
1995 10 16 1800 0600 37.86 -75.59 106.8 3876
1995 10 16 1800 0600 38.14 -75.40 411.1 3875
1995 10 16 1800 0600 38.40 -75.21 0.0 3975
1995 10 17 0000 0600 39.15 -78.25 0.0 3978
1995 10 17 0000 0600 39.27 -78.07 0.0 4078
1995 10 17 0000 0600 39.38 -77.92 0.0 4077
1995 10 17 0000 0600 38.48 -76.85 0.0 3877
1995 10 17 0000 0600 38.68 -76.64 2.9 3977
1995 10 17 0000 0600 38.92 -76.43 0.0 3976
1995 10 17 0000 0600 37.86 -75.59 21.9 3876
1995 10 17 0000 0600 38.14 -75.40 224.4 3875
1995 10 17 0000 0600 38.40 -75.21 10.9 3975
1995 10 17 0600 0600 39.15 -78.25 0.0 3978
1995 10 17 0600 0600 39.27 -78.07 0.0 4078
1995 10 17 0600 0600 39.38 -77.92 0.0 4077
1995 10 17 0600 0600 38.48 -76.85 0.0 3877
1995 10 17 0600 0600 38.68 -76.64 0.0 3977
1995 10 17 0600 0600 38.92 -76.43 0.0 3976
1995 10 17 0600 0600 37.86 -75.59 0.0 3876
1995 10 17 0600 0600 38.14 -75.40 0.0 3875
1995 10 17 0600 0600 38.40 -75.21 0.0 3975

measured.txt[2/9/2016 2:50:13 PM]

95 10 16 06
1
40.0 -80.0 10.0
30
0
10000.0
1
./
oct1618.BIN
1
TEST
100.0
0.1
00 00 00 06 00
1
38.0 -76.0
0.10 0.10
15.0 25.0
./
cdump
1
100
00 00 00 00 00
00 00 00 00 00
00 06 00
1
0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0
0.0
0.0

control_geo[2/9/2016 2:50:14 PM]

&SETUP
tratio = 0.75,
initd = 0,
kpuff = 0,
khmax = 9999,
numpar = 5000,
qcycle = 0.0,
efile = '',
tkerd = 0.18,
tkern = 0.18,
ninit = 1,
ndump = 0,
ncycl = 0,
pinpf = 'PARINIT',
poutf = 'PARDUMP',
mgmin = 10,
kmsl = 0,
maxpar = 5000,
cpack = 1,
cmass = 0,
dxf = 1.0,
dyf = 1.0,
dzf = 0.01,
ichem = 0,
/

setup_geo[2/9/2016 2:50:14 PM]

Image116.gif %d%d pixels

Image116.gif[2/9/2016 2:50:15 PM]