git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1691 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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tools/python/README
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This directory contains Python scripts for common LAMMPS
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post-processing tasks.
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If you have suggestions or contributions for additional scripts or
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functionality that could be added, built on the Pizza.py modules (as
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explained below), send email to Steve Plimpton (sjplimp at
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sandia.gov).
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log2txt.py convert thermo info in a LAMMPS log file to columns of numbers
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logplot.py plot 2 columns of thermo info from a LAMMPS log file
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dumpsort.py sort the snapshots of atoms in a LAMMPS dump file by atom ID
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dump2cfg.py convert a native LAMMPS dump file to CFG format
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dump2xyz.py convert a native LAMMPS dump file to XYZ format
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dump2pdb.py convert a native LAMMPS dump file to PDB format
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See the top of each script file for syntax, or just run it with no
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arguments to get a syntax message.
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------------------------------
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General info:
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These scripts are very simple. They load Python modules in the pizza
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sub-directory that are part of the Pizza.py toolkit, which do the
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heavy lifting.
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The modules themselves have a lot more functionality than these
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scripts expose, so if you want to do something beyond what these
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scripts perform, you should learn about Pizza.py. See this WWW page
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for details and download info:
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www.sandia.gov/~sjplimp/pizza.html
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The tools in the Pizza.py src directory are identical to those in the
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pizza sub-directory of lammps/tools/python. The header section of the
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tool files lists all the functionality that tool supports.
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To use all the features of Pizza.py modules, you need to be familiar
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with Python syntax. You can then modify the scripts to invoke
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additional Pizza.py functionality or use the Python interpreter itself
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to drive the Pizza.py modules.
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------------------------------
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Before you run the scripts:
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To use these scripts you must set the environment variable
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LAMMPS_TOOLS_PYTHON in your shell to point to the Pizza.py modules
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that the scripts use. This can either be a) the pizza sub-directory
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under lammps/tools/python, or b) the src directory in the Pizza.py
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package if you have installed Pizza.py on your box.
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For example, on my box, either of these lines in my .cshrc works:
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setenv LAMMPS_TOOLS_PYTHON /home/sjplimp/lammps/tools/python/pizza
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setenv LAMMPS_TOOLS_PYTHON /home/sjplimp/pizza/src
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------------------------------
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Running the scripts:
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As with any Python script, you can run these scripts in one of two
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ways. You may want to setup aliases so that you can run them from the
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directory where your data files are.
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% python log2txt.py args ...
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% log2txt.py args ...
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The latter requires 2 things:
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1) that the script be made "executable", e.g. type "chmod +x log2txt.py"
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2) that the 1st line of the script is the path of the Python installed
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on your box, e.g. /usr/local/bin/python
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IMPORTANT NOTE: If you run the logplot.py script using the 1st method
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above, you should type
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% python -i logplot.py args ...
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so that the plot produced by GnuPlot stays visible before Python
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exits.
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------------------------------
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Dependencies:
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To use the logplot.py script you need to have GnuPlot installed on
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your system and its executable "gnuplot" in your path.
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To use any of the scripts which load the dump module to read LAMMPS
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dump files, you must have the Python package Numeric installed in your
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Python. See http://numeric.scipy.org.
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Note that the Pizza.py modules use the older (but still popular)
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Numeric package, not the newer numarray package.
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If Numeric is already installed in your Python, you should be able to
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type the following without getting an error:
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>>> import Numeric
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Numeric can be downloaded from SourceForge at this WWW site:
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http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=1351
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As of July 2007, Version 24.2 was fine. Once unpacked, you can type
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the following from the Numeric directory to install it in your Python.
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sudo python setup.py install
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On my Linux box, when Numeric installed itself under the Python lib in
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/usr/local, it did not set all file permsissions correctly to allow a
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user to import it. So I also needed to do this:
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sudo chmod -R 755 /usr/local/lib/python2.5/site-packages/Numeric
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