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

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 the

tool files 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_TOOLS_PYTHON 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_TOOLS_PYTHON /home/sjplimp/lammps/tools/python/pizza

setenv LAMMPS_TOOLS_PYTHON /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

#!/usr/local/bin/python

# Script:  dump2cfg.py

# Purpose: convert a LAMMPS dump file to CFG format

# Syntax:  dump2cfg.py dumpfile Nid Ntype Nx Ny Nz cfgfile

#          dumpfile = LAMMPS dump file in native LAMMPS format

#          Nid,Ntype,Nx,Ny,Nz = columns #s for ID,type,x,y,z

#                               (usually 1,2,3,4,5)

#          cfgfile = new CFG file

# Author:  Steve Plimpton (Sandia), sjplimp at sandia.gov

import sys,os

path = os.environ["LAMMPS_PYTHON_TOOLS"]

sys.path.append(path)

from dump import dump

from cfg import cfg

if len(sys.argv) != 8:

  raise StandardError, "Syntax: dump2cfg.py dumpfile Nid Ntype Nx Ny Nz cfgfile"

dumpfile = sys.argv[1]

nid = int(sys.argv[2])

ntype = int(sys.argv[3])

nx = int(sys.argv[4])

ny = int(sys.argv[5])

nz = int(sys.argv[6])

cfgfile = sys.argv[7]

d = dump(dumpfile)

d.map(nid,"id",ntype,"type",nx,"x",ny,"y",nz,"z")

c = cfg(d)

c.one(cfgfile)

#!/usr/local/bin/python

# Script:  dump2pdb.py

# Purpose: convert a LAMMPS dump file to PDB format

# Syntax:  dump2pdb.py dumpfile Nid Ntype Nx Ny Nz pdbfile

#          dumpfile = LAMMPS dump file in native LAMMPS format

#          Nid,Ntype,Nx,Ny,Nz = columns #s for ID,type,x,y,z

#                               (usually 1,2,3,4,5)

#          pdbfile = new PDB file

# Author:  Steve Plimpton (Sandia), sjplimp at sandia.gov

import sys,os

path = os.environ["LAMMPS_PYTHON_TOOLS"]

sys.path.append(path)

from dump import dump

from pdbfile import pdbfile

if len(sys.argv) != 8:

  raise StandardError, "Syntax: dump2pdb.py dumpfile Nid Ntype Nx Ny Nz pdbfile"

dumpfile = sys.argv[1]

nid = int(sys.argv[2])

ntype = int(sys.argv[3])

nx = int(sys.argv[4])

ny = int(sys.argv[5])

nz = int(sys.argv[6])

pfile = sys.argv[7]

d = dump(dumpfile)

d.map(nid,"id",ntype,"type",nx,"x",ny,"y",nz,"z")

p = pdbfile(d)

p.one(pfile)

#!/usr/local/bin/python

# Script:  dump2xyz.py

# Purpose: convert a LAMMPS dump file to XYZ format

# Syntax:  dump2xyz.py dumpfile Nid Ntype Nx Ny Nz xyzfile

#          dumpfile = LAMMPS dump file in native LAMMPS format

#          Nid,Ntype,Nx,Ny,Nz = columns #s for ID,type,x,y,z

#                               (usually 1,2,3,4,5)

#          xyzfile = new XYZ file

# Author:  Steve Plimpton (Sandia), sjplimp at sandia.gov

import sys,os

path = os.environ["LAMMPS_PYTHON_TOOLS"]

sys.path.append(path)

from dump import dump

from xyz import xyz

if len(sys.argv) != 8:

  raise StandardError, "Syntax: dump2xyz.py dumpfile Nid Ntype Nx Ny Nz xyzfile"

dumpfile = sys.argv[1]

nid = int(sys.argv[2])

ntype = int(sys.argv[3])

nx = int(sys.argv[4])

ny = int(sys.argv[5])

nz = int(sys.argv[6])

xyzfile = sys.argv[7]

d = dump(dumpfile)

d.map(nid,"id",ntype,"type",nx,"x",ny,"y",nz,"z")

x = xyz(d)

x.one(xyzfile)

#!/usr/local/bin/python

# Script:  dumpsort.py

# Purpose: sort the snapshots in a LAMMPS dump file by atom ID

# Syntax:  dumpsort.py oldfile N newfile

#          oldfile = old LAMMPS dump file in native LAMMPS format

#          N = column # for atom ID (usually 1)

#          newfile = new sorted LAMMPS dump file

# Author:  Steve Plimpton (Sandia), sjplimp at sandia.gov

import sys,os

path = os.environ["LAMMPS_PYTHON_TOOLS"]

sys.path.append(path)

from dump import dump

if len(sys.argv) != 4:

  raise StandardError, "Syntax: dumpsort.py oldfile N newfile"

oldfile = sys.argv[1]

ncolumn = int(sys.argv[2])

newfile = sys.argv[3]

d = dump(oldfile)

d.map(ncolumn,"id")

d.sort()

d.write(newfile)