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9. Additional tools

SPARTA is designed to be a computational kernel for performing DSMC computations. Additional pre- and post-processing steps are often necessary to setup and analyze a simulation. A few additional tools are provided with the SPARTA distribution in the tools directory and are described briefly below.

Our group has also written and released a separate toolkit called Pizza.py which provides tools for doing setup, analysis, plotting, and visualization for SPARTA simulations. Pizza.py is written in Python and is available for download from the Pizza.py web site.

Some of the Pizza.py tools relevant to SPARTA are as follows:

The dump, sdata, and olog tools are included in the SPARTA distribution in the tools/pizza directory, and are used by some of the scripts discussed below.

This is the list of tools included in the tools directory of the SPARTA distribution. Each is described in more detail below.



dump2cfg tool

This is a Python script that converts a SPARTA particle dump file into extended CFG format so that it can be visualized by the AtomEye visualization program. AtomEye is a very fast particle visualizer, capable of interactive visualizations of millions of particles on a desktop machine. It is commonly used in the materials modeling community.

See the header of the script for the syntax used to run it.

This script uses one or more of the "Pizza.py" tools provided in the tools/pizza directory. See the tools/README file for info on how to set an environment variable so that the Pizza.py tool files can be found by Python, as well as instructions on various ways to run a Python script.


dump2xyz tool

This is a Python script that converts a SPARTA particle dump file into XYZ format so that it can be visualized by various visualization packages that read XYZ formatted files. An example is VMD package, commonly used in the molecular dynamics modeling community.

See the header of the script for the syntax used to run it.

This script uses one or more of the "Pizza.py" tools provided in the tools/pizza directory. See the tools/README file for info on how to set an environment variable so that the Pizza.py tool files can be found by Python, as well as instructions on various ways to run a Python script.


grid_refine tool

This is a Python script that creates a SPARTA grid file adapted around the lines or triangles in a SPARTA surface file. The resulting grid file can be read by the read_grid command. The surface file can be read by the read_surf command.

See the header of the script for the various adaptivity options that are supported, and the syntax used to run it.


log2txt tool

This is a Python script that reads a SPARTA log file, extracts selected columns of statistical output, and writes them to a text file. It knows how to concatenate log file info across multiple successive runs. The columnar output can then be read by various plotting packages.

See the header of the script for the syntax used to run it.

This script uses one or more of the "Pizza.py" tools provided in the tools/pizza directory. See the tools/README file for info on how to set an environment variable so that the Pizza.py tool files can be found by Python, as well as instructions on various ways to run a Python script.


logplot tool

This is a Python script that reads a SPARTA log file, extracts the selected columns of statistical output, and plots them via the GnuPlot program. It knows how to concatenate log file info across multiple successive runs.

See the header of the script for the syntax used to run it. You must have GnuPlot installed on your system to use this script. If you can type "gnuplot" from the command line to start GnuPlot, it should work. If not (e.g. because you need a path name), then edit these 2 lines as needed in pizza/gnu.py:

except: PIZZA_GNUPLOT = "gnuplot"
except: PIZZA_GNUTERM = "x11" 

For example, the first could become "/home/smith/bin/gnuplot". The second should only need changing if GnuPlot requires a different setting to plot to your screen.

This script uses one or more of the "Pizza.py" tools provided in the tools/pizza directory. See the tools/README file for info on how to set an environment variable so that the Pizza.py tool files can be found by Python, as well as instructions on various ways to run a Python script.


paraview tools

The tools/paraview directory has scripts which convert SPARTA grid and surface data (input and output) to ParaView format.

ParaView is a popular, powerful, freely-available visualization package. You must have ParaView installed to use the Python scripts. See tools/paraview/README for more details.

The scripts were developed by Tom Otahal (Sandia).


stl2surf tool

This is a Python script that reads a stereolithography (STL) text file and converts it to a SPARTA surface file. STL files contain a collection of triangles and can be created by various mesh-generation programs. The format for SPARTA surface files is described on the read_surf command doc page.

See the header of the script for the syntax used to run it, e.g.

% python stl2surf.py stlfile surffile 

The script also checks the triangulated object to see if it is "watertight" and issues a warning if it is not, since SPARTA will perform the same check. The read_surf command doc page explains what watertight means for 3d objects.


surf_create tool

This is a Python script that creates a SPARTA surface file containing one or more simple objects whose surface is represented as triangules (3d) or line segments (2d). Such files can be read by the read_surf command. The 3d objects it supports are a sphere, box, and spikysphere (randomized radius at each point). The 2d objects it supports are a circle, rectangle, triangle, and spikycircly (randomized radius at each point).

See the header of the script for the syntax used to run it.


surf_transform tool

This is a Python script that transforms a SPARTA surface file into a new surface file using various operations supported by the read_surf command. These operations include translation, scaling, rotation, and inversion (changing which side of the surface is inside vs outside).

See the header of the script for the syntax used to run it.