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