LAMMPS pre- and post-processing tools

This directory contains several stand-alone tools for creating LAMMPS
input files and massaging LAMMPS output data.  Instructions on how to
use the tools are discussed in the "Additional Tools" section of the
LAMMPS documentation.

Tools that are single source files in this directory have additional
comments that may be useful at the top of the source file.  Tools that
reside in their own sub-directories have README files you should look
at.

These are the included tools:

amber2lmp	       python scripts for using AMBER to setup LAMMPS input
binary2txt	       convert a LAMMPS dump file from binary to ASCII text
ch2lmp		       convert CHARMM files to LAMMPS input
chain		       create a data file of bead-spring chains
colvars		       post-process output of the fix colvars command        
createatoms	       generate lattices of atoms within a geometry
drude                  create Drude core/electron atom pairs in a data file
eam_database	       one tool to generate EAM alloy potential files
eam_generate	       2nd tool to generate EAM alloy potential files
eff		       scripts for working with the eFF (electron force field)
emacs		       add-ons to EMACS editor for editing LAMMPS input scripts
fep		       scripts for free-energy perturbation with USER-FEP pkg
i-pi                   Python wrapper for performing path-integral MD (PIMD)
ipp		       input pre-processor Perl tool for creating input scripts
kate                   add-ons to Kate editor for editing LAMMPS input scripts
lmp2arc		       convert LAMMPS output to Accelrys Insight format
lmp2cfg		       convert LAMMPS output to CFG files for AtomEye viz
matlab		       MatLab scripts for post-processing LAMMPS output
micelle2d	       create a data file of small lipid chains in solvent
moltemplate            Instructions for installing the Moltemplate builder program
msi2lmp		       use Accelrys Insight code to setup LAMMPS input
phonon                 post-process output of the fix phonon command
polybond               Python tool for programmable polymer bonding
pymol_asphere	       convert LAMMPS output of ellipsoids to PyMol format
python		       Python scripts for post-processing LAMMPS output
reax	       	       Tools for analyzing output of ReaxFF simulations
replica        tool to reorder LAMMPS replica trajectories according to temperature
smd                    convert Smooth Mach Dynamics triangles to VTK
spin                   perform a cubic polynomial interpolation of a GNEB MEP
vim		       add-ons to VIM editor for editing LAMMPS input scripts
xmgrace                a collection of scripts to generate xmgrace plots

For tools that are single C, C++, or Fortran files, a Makefile for
building them is included in this directory.  You may need to edit it
for the compilers and paths on your system.

For tools in their own sub-directories, see their README file for info
on how to build and use it.
