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<CENTER><A HREF = "Section_perf.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS
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Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_modify.html">Next
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Section</A>
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</CENTER>
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<HR>
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<H3>9. Additional tools
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</H3>
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<P>LAMMPS is designed to be a computational kernel for performing
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molecular dynamics computations. Additional pre- and post-processing
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steps are often necessary to setup and analyze a simulation. A few
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additional tools are provided with the LAMMPS distribution and are
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described in this section.
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</P>
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<P>Our group has also written and released a separate toolkit called
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<A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which provides tools for doing setup, analysis,
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plotting, and visualization for LAMMPS simulations. Pizza.py is
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written in <A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">the
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Pizza.py WWW site</A>.
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</P>
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<P>Note that many users write their own setup or analysis tools or use
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other existing codes and convert their output to a LAMMPS input format
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or vice versa. The tools listed here are included in the LAMMPS
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distribution as examples of auxiliary tools. Some of them are not
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actively supported by Sandia, as they were contributed by LAMMPS
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users. If you have problems using them, we can direct you to the
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authors.
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</P>
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<P>The source code for each of these codes is in the tools sub-directory
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of the LAMMPS distribution. There is a Makefile (which you may need
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to edit for your platform) which will build several of the tools which
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reside in that directory. Some of them are larger packages in their
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own sub-directories with their own Makefiles.
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</P>
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<UL><LI><A HREF = "#amber">amber2lmp</A>
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<LI><A HREF = "#binary">binary2txt</A>
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<LI><A HREF = "#charmm">ch2lmp</A>
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<LI><A HREF = "#chain">chain</A>
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<LI><A HREF = "#create">createatoms</A>
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<LI><A HREF = "#data">data2xmovie</A>
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<LI><A HREF = "#eamdb">eam database</A>
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<LI><A HREF = "#eamgn">eam generate</A>
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<LI><A HREF = "#eff">eff</A>
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<LI><A HREF = "#emacs">emacs</A>
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<LI><A HREF = "#ipp">ipp</A>
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<LI><A HREF = "#kate">kate</A>
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<LI><A HREF = "#arc">lmp2arc</A>
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<LI><A HREF = "#cfg">lmp2cfg</A>
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<LI><A HREF = "#vmd">lmp2vmd</A>
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<LI><A HREF = "#matlab">matlab</A>
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<LI><A HREF = "#micelle">micelle2d</A>
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<LI><A HREF = "#moltemplate">moltemplate</A>
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<LI><A HREF = "#msi">msi2lmp</A>
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<LI><A HREF = "#phonon">phonon</A>
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<LI><A HREF = "#polybond">polymer bonding</A>
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<LI><A HREF = "#pymol">pymol_asphere</A>
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<LI><A HREF = "#pythontools">python</A>
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<LI><A HREF = "#reax">reax</A>
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<LI><A HREF = "#restart">restart2data</A>
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<LI><A HREF = "#vim">vim</A>
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<LI><A HREF = "#xmgrace">xmgrace</A>
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<LI><A HREF = "#xmovie">xmovie</A>
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</UL>
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<HR>
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<H4><A NAME = "amber"></A>amber2lmp tool
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</H4>
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<P>The amber2lmp sub-directory contains two Python scripts for converting
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files back-and-forth between the AMBER MD code and LAMMPS. See the
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README file in amber2lmp for more information.
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</P>
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<P>These tools were written by Keir Novik while he was at Queen Mary
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University of London. Keir is no longer there and cannot support
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these tools which are out-of-date with respect to the current LAMMPS
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version (and maybe with respect to AMBER as well). Since we don't use
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these tools at Sandia, you'll need to experiment with them and make
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necessary modifications yourself.
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</P>
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<HR>
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<H4><A NAME = "binary"></A>binary2txt tool
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</H4>
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<P>The file binary2txt.cpp converts one or more binary LAMMPS dump file
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into ASCII text files. The syntax for running the tool is
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</P>
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<PRE>binary2txt file1 file2 ...
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</PRE>
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<P>which creates file1.txt, file2.txt, etc. This tool must be compiled
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on a platform that can read the binary file created by a LAMMPS run,
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since binary files are not compatible across all platforms.
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</P>
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<HR>
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<H4><A NAME = "charmm"></A>ch2lmp tool
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</H4>
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<P>The ch2lmp sub-directory contains tools for converting files
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back-and-forth between the CHARMM MD code and LAMMPS.
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</P>
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<P>They are intended to make it easy to use CHARMM as a builder and as a
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post-processor for LAMMPS. Using charmm2lammps.pl, you can convert an
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ensemble built in CHARMM into its LAMMPS equivalent. Using
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lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files.
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</P>
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<P>See the README file in the ch2lmp sub-directory for more information.
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</P>
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<P>These tools were created by Pieter in't Veld (pjintve at sandia.gov)
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and Paul Crozier (pscrozi at sandia.gov) at Sandia.
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</P>
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<HR>
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<H4><A NAME = "chain"></A>chain tool
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</H4>
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<P>The file chain.f creates a LAMMPS data file containing bead-spring
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polymer chains and/or monomer solvent atoms. It uses a text file
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containing chain definition parameters as an input. The created
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chains and solvent atoms can strongly overlap, so LAMMPS needs to run
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the system initially with a "soft" pair potential to un-overlap it.
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The syntax for running the tool is
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</P>
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<PRE>chain < def.chain > data.file
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</PRE>
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<P>See the def.chain or def.chain.ab files in the tools directory for
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examples of definition files. This tool was used to create the
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system for the <A HREF = "Section_perf.html">chain benchmark</A>.
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</P>
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<HR>
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<H4><A NAME = "create"></A>createatoms tool
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</H4>
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<P>The tools/createatoms directory contains a Fortran program called
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createAtoms.f which can generate a variety of interesting crystal
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structures and geometries and output the resulting list of atom
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coordinates in LAMMPS or other formats.
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</P>
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<P>See the included Manual.pdf for details.
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</P>
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<P>The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
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</P>
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<HR>
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<H4><A NAME = "data"></A>data2xmovie tool
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</H4>
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<P>The file data2xmovie.c converts a LAMMPS data file into a snapshot
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suitable for visualizing with the <A HREF = "#xmovie">xmovie</A> tool, as if it had
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been output with a dump command from LAMMPS itself. The syntax for
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running the tool is
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</P>
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<PRE>data2xmovie <B>options</B> < infile > outfile
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</PRE>
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<P>See the top of the data2xmovie.c file for a discussion of the options.
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</P>
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<HR>
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<H4><A NAME = "eamdb"></A>eam database tool
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</H4>
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<P>The tools/eam_database directory contains a Fortran program that will
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generate EAM alloy setfl potential files for any combination of 16
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elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti,
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Zr. The files can then be used with the <A HREF = "pair_eam.html">pair_style
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eam/alloy</A> command.
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</P>
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<P>The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov,
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and is based on his paper:
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</P>
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<P>X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
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144113 (2004).
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</P>
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<HR>
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<H4><A NAME = "eamgn"></A>eam generate tool
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</H4>
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<P>The tools/eam_generate directory contains several one-file C programs
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that convert an analytic formula into a tabulated <A HREF = "pair_eam.html">embedded atom
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method (EAM)</A> setfl potential file. The potentials they
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produce are in the potentials directory, and can be used with the
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<A HREF = "pair_eam.html">pair_style eam/alloy</A> command.
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</P>
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<P>The source files and potentials were provided by Gerolf Ziegenhain
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(gerolf at ziegenhain.com).
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</P>
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<HR>
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<H4><A NAME = "eff"></A>eff tool
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</H4>
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<P>The tools/eff directory contains various scripts for generating
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structures and post-processing output for simulations using the
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electron force field (eFF).
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</P>
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<P>These tools were provided by Andres Jaramillo-Botero at CalTech
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(ajaramil at wag.caltech.edu).
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</P>
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<HR>
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<H4><A NAME = "emacs"></A>emacs tool
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</H4>
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<P>The tools/emacs directory contains a Lips add-on file for Emacs that
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enables a lammps-mode for editing of input scripts when using Emacs,
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with various highlighting options setup.
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</P>
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<P>These tools were provided by Aidan Thompson at Sandia
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(athomps at sandia.gov).
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</P>
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<HR>
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<H4><A NAME = "ipp"></A>ipp tool
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</H4>
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<P>The tools/ipp directory contains a Perl script ipp which can be used
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to facilitate the creation of a complicated file (say, a lammps input
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script or tools/createatoms input file) using a template file.
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</P>
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<P>ipp was created and is maintained by Reese Jones (Sandia), rjones at
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sandia.gov.
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</P>
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<P>See two examples in the tools/ipp directory. One of them is for the
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tools/createatoms tool's input file.
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</P>
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<HR>
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<H4><A NAME = "kate"></A>kate tool
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</H4>
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<P>The file in the tools/kate directory is an add-on to the Kate editor
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in the KDE suite that allow syntax highlighting of LAMMPS input
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scripts. See the README.txt file for details.
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</P>
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<P>The file was provided by Alessandro Luigi Sellerio
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(alessandro.sellerio at ieni.cnr.it).
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</P>
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<HR>
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<H4><A NAME = "arc"></A>lmp2arc tool
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</H4>
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<P>The lmp2arc sub-directory contains a tool for converting LAMMPS output
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files to the format for Accelrys' Insight MD code (formerly
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MSI/Biosym and its Discover MD code). See the README file for more
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information.
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</P>
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<P>This tool was written by John Carpenter (Cray), Michael Peachey
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(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic
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(jec at mayo.edu), but still fields questions about the tool.
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</P>
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<P>This tool was updated for the current LAMMPS C++ version by Jeff
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Greathouse at Sandia (jagreat at sandia.gov).
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</P>
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<HR>
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<H4><A NAME = "cfg"></A>lmp2cfg tool
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</H4>
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<P>The lmp2cfg sub-directory contains a tool for converting LAMMPS output
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files into a series of *.cfg files which can be read into the
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<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualizer. See
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the README file for more information.
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</P>
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<P>This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
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</P>
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<HR>
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<H4><A NAME = "vmd"></A>lmp2vmd tool
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</H4>
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<P>The lmp2vmd sub-directory contains a README.txt file that describes
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details of scripts and plugin support within the <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD
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package</A> for visualizing LAMMPS
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dump files.
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</P>
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<P>The VMD plugins and other supporting scripts were written by Axel
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Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.
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</P>
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<HR>
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<H4><A NAME = "matlab"></A>matlab tool
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</H4>
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<P>The matlab sub-directory contains several <A HREF = "http://www.mathworks.com">MATLAB</A> scripts for
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post-processing LAMMPS output. The scripts include readers for log
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and dump files, a reader for EAM potential files, and a converter that
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reads LAMMPS dump files and produces CFG files that can be visualized
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with the <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A>
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visualizer.
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</P>
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<P>See the README.pdf file for more information.
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</P>
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<P>These scripts were written by Arun Subramaniyan at Purdue Univ
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(asubrama at purdue.edu).
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</P>
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<HR>
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<H4><A NAME = "micelle"></A>micelle2d tool
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</H4>
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<P>The file micelle2d.f creates a LAMMPS data file containing short lipid
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chains in a monomer solution. It uses a text file containing lipid
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definition parameters as an input. The created molecules and solvent
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atoms can strongly overlap, so LAMMPS needs to run the system
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initially with a "soft" pair potential to un-overlap it. The syntax
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for running the tool is
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</P>
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<PRE>micelle2d < def.micelle2d > data.file
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</PRE>
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<P>See the def.micelle2d file in the tools directory for an example of a
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definition file. This tool was used to create the system for the
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<A HREF = "Section_example.html">micelle example</A>.
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</P>
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<HR>
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<H4><A NAME = "moltemplate"></A>moltemplate tool
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</H4>
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<P>The moltemplate sub-directory contains a Python-based tool for
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building molecular systems based on a text-file description, and
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creating LAMMPS data files that encode their molecular topology as
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lists of bonds, angles, dihedrals, etc. See the README.TXT file for
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more information.
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</P>
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<P>This tool was written by Andrew Jewett (jewett.aij at gmail.com), who
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supports it. It has its own WWW page at
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<A HREF = "http://moltemplate.org">http://moltemplate.org</A>.
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</P>
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<HR>
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<H4><A NAME = "msi"></A>msi2lmp tool
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</H4>
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<P>The msi2lmp sub-directory contains a tool for creating LAMMPS input
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data files from Accelrys' Insight MD code (formerly MSI/Biosym and
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its Discover MD code). See the README file for more information.
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</P>
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<P>This tool was written by John Carpenter (Cray), Michael Peachey
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(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic
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(jec at mayo.edu), but still fields questions about the tool.
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</P>
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<P>This tool may be out-of-date with respect to the current LAMMPS and
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Insight versions. Since we don't use it at Sandia, you'll need to
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experiment with it yourself.
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</P>
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<HR>
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<H4><A NAME = "phonon"></A>phonon tool
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</H4>
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<P>The phonon sub-directory contains a post-processing tool useful for
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analyzing the output of the <A HREF = "fix_phonon.html">fix phonon</A> command in
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the USER-PHONON package.
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</P>
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<P>See the README file for instruction on building the tool and what
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library it needs. And see the examples/USER/phonon directory
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for example problems that can be post-processed with this tool.
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</P>
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<P>This tool was written by Ling-Ti Kong at Shanghai Jiao Tong
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University.
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</P>
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<HR>
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<H4><A NAME = "polybond"></A>polymer bonding tool
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</H4>
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<P>The polybond sub-directory contains a Python-based tool useful for
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performing "programmable polymer bonding". The Python file
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lmpsdata.py provides a "Lmpsdata" class with various methods which can
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be invoked by a user-written Python script to create data files with
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complex bonding topologies.
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</P>
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<P>See the Manual.pdf for details and example scripts.
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</P>
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<P>This tool was written by Zachary Kraus at Georgia Tech.
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</P>
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<HR>
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<H4><A NAME = "pymol"></A>pymol_asphere tool
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</H4>
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<P>The pymol_asphere sub-directory contains a tool for converting a
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LAMMPS dump file that contains orientation info for ellipsoidal
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particles into an input file for the <A HREF = "http://pymol.sourceforge.net">PyMol visualization
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package</A>.
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</P>
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<P>Specifically, the tool triangulates the ellipsoids so they can be
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viewed as true ellipsoidal particles within PyMol. See the README and
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examples directory within pymol_asphere for more information.
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</P>
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<P>This tool was written by Mike Brown at Sandia.
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</P>
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<HR>
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<H4><A NAME = "pythontools"></A>python tool
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</H4>
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<P>The python sub-directory contains several Python scripts
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that perform common LAMMPS post-processing tasks, such as:
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</P>
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<UL><LI>extract thermodynamic info from a log file as columns of numbers
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<LI>plot two columns of thermodynamic info from a log file using GnuPlot
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<LI>sort the snapshots in a dump file by atom ID
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<LI>convert multiple <A HREF = "neb.html">NEB</A> dump files into one dump file for viz
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<LI>convert dump files into XYZ, CFG, or PDB format for viz by other packages
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</UL>
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<P>These are simple scripts built on <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> modules. See the
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README for more info on Pizza.py and how to use these scripts.
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</P>
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<HR>
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<H4><A NAME = "reax"></A>reax tool
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</H4>
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<P>The reax sub-directory contains stand-alond codes that can
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post-process the output of the <A HREF = "fix_reax_bonds.html">fix reax/bonds</A>
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command from a LAMMPS simulation using <A HREF = "pair_reax.html">ReaxFF</A>. See
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the README.txt file for more info.
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</P>
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<P>These tools were written by Aidan Thompson at Sandia.
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</P>
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<HR>
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<H4><A NAME = "restart"></A>restart2data tool
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</H4>
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<P>IMPORTANT NOTE: LAMMPS now has a <A HREF = "write_data.html">write_data</A> command,
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which can create a data file from within an input script. This means
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a two line input script can read a restart file, and write it as a
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data file. When the write_data command is fully functional, the
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restart2data tool will be obsolete, and will be retired from the
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distribution.
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</P>
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<P>The file restart2data.cpp converts a binary LAMMPS restart file into
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an ASCII data file. The syntax for running the tool is
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</P>
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<PRE>restart2data restart-file data-file (input-file)
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</PRE>
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<P>Input-file is optional and if specified will contain LAMMPS input
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|
commands for the masses and force field parameters, instead of putting
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|
those in the data-file. Only a few force field styles currently
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|
support this option.
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|
</P>
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|
<P>This tool must be compiled on a platform that can read the binary file
|
|
created by a LAMMPS run, since binary files are not compatible across
|
|
all platforms.
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|
</P>
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|
<P>Note that a text data file has less precision than a binary restart
|
|
file. Hence, continuing a run from a converted data file will
|
|
typically not conform as closely to a previous run as will restarting
|
|
from a binary restart file.
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|
</P>
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|
<P>If a "%" appears in the specified restart-file, the tool expects a set
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|
of multiple files to exist. See the <A HREF = "restart.html">restart</A> and
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|
<A HREF = "write_restart.html">write_restart</A> commands for info on how such sets
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|
of files are written by LAMMPS, and how the files are named.
|
|
</P>
|
|
<HR>
|
|
|
|
<H4><A NAME = "vim"></A>vim tool
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|
</H4>
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|
<P>The files in the tools/vim directory are add-ons to the VIM editor
|
|
that allow easier editing of LAMMPS input scripts. See the README.txt
|
|
file for details.
|
|
</P>
|
|
<P>These files were provided by Gerolf Ziegenhain (gerolf at
|
|
ziegenhain.com)
|
|
</P>
|
|
<HR>
|
|
|
|
<H4><A NAME = "xmgrace"></A>xmgrace tool
|
|
</H4>
|
|
<P>The files in the tools/xmgrace directory can be used to plot the
|
|
thermodynamic data in LAMMPS log files via the xmgrace plotting
|
|
package. There are several tools in the directory that can be used in
|
|
post-processing mode. The lammpsplot.cpp file can be compiled and
|
|
used to create plots from the current state of a running LAMMPS
|
|
simulation.
|
|
</P>
|
|
<P>See the README file for details.
|
|
</P>
|
|
<P>These files were provided by Vikas Varshney (vv0210 at gmail.com)
|
|
</P>
|
|
<HR>
|
|
|
|
<H4><A NAME = "xmovie"></A>xmovie tool
|
|
</H4>
|
|
<P>The xmovie tool is an X-based visualization package that can read
|
|
LAMMPS dump files and animate them. It is in its own sub-directory
|
|
with the tools directory. You may need to modify its Makefile so that
|
|
it can find the appropriate X libraries to link against.
|
|
</P>
|
|
<P>The syntax for running xmovie is
|
|
</P>
|
|
<PRE>xmovie <B>options</B> dump.file1 dump.file2 ...
|
|
</PRE>
|
|
<P>If you just type "xmovie" you will see a list of options. Note that
|
|
by default, LAMMPS dump files are in scaled coordinates, so you
|
|
typically need to use the -scale option with xmovie. When xmovie runs
|
|
it opens a visualization window and a control window. The control
|
|
options are straightforward to use.
|
|
</P>
|
|
<P>Xmovie was mostly written by Mike Uttormark (U Wisconsin) while he
|
|
spent a summer at Sandia. It displays 2d projections of a 3d domain.
|
|
While simple in design, it is an amazingly fast program that can
|
|
render large numbers of atoms very quickly. It's a useful tool for
|
|
debugging LAMMPS input and output and making sure your simulation is
|
|
doing what you think it should. The animations on the Examples page
|
|
of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW site</A> were created with xmovie.
|
|
</P>
|
|
<P>I've lost contact with Mike, so I hope he's comfortable with us
|
|
distributing his great tool!
|
|
</P>
|
|
</HTML>
|