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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>7. 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.cs.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.cs.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 = "#data">data2xmovie</A>
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<LI><A HREF = "#eam">eam generate</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 = "#traj">lmp2traj</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 = "#msi">msi2lmp</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 = "#restart">restart2data</A>
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<LI><A HREF = "#thermo_extract">thermo_extract</A>
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<LI><A HREF = "#vim">vim</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 = "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 = "eam"></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.
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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 = "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://164.107.79.177/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 = "traj"></A>lmp2traj tool
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</H4>
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<P>The lmp2traj sub-directory contains a tool for converting LAMMPS output
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files into 3 analysis files. One file can be used to create contour
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maps of the atom positions over the course of the simulation. The
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other two files provide density profiles and dipole moments. See the
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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 some scripts for converting LAMMPS
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files into formats suitable for visualizing with the <A HREF = "http://www.ks.uiuc.edu/Research/vmd/">VMD
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package</A>.
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</P>
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<P>One script extracts bond topology info from a LAMMPS data file. A
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second script attached amino acid (residue) information to what is
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extracted from a data file. See the README file for more information.
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</P>
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<P>These scripts were written by Axel Kohlmeyer (akohlmey at
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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 radial distribution output from the <A HREF = "fix_rdf.html">fix
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rdf</A> command, a reader for EAM potential files, and a
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converter that reads LAMMPS dump files and produces CFG files that can
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be visualized with the
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<A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A> 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 = "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 = "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, like
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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 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.cs.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 = "restart"></A>restart2data tool
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</H4>
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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
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created by a LAMMPS run, since binary files are not compatible across
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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
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file. Hence, continuing a run from a converted data file will
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typically not conform as closely to a previous run as will restarting
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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.
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</P>
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<HR>
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<H4><A NAME = "thermo_extract"></A>thermo_extract tool
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</H4>
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<P>The thermo_extract tool reads one of more LAMMPS log files and
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extracts a thermodynamic value (e.g. Temp, Press). It spits out the
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time,value as 2 columns of numbers so the tool can be used as a quick
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way to plot some quantity of interest. See the header of the
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thermo_extract.c file for the syntax of how to run it and other
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details.
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</P>
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<P>This tool was written by Vikas Varshney at Wright Patterson AFB
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(vikas.varshney at gmail.com).
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</P>
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<HR>
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<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
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that allow easier editing of LAMMPS input scripts. See the README.txt
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file for details.
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</P>
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<P>These files were provided by Gerolf Ziegenhain (gerolf at
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ziegenhain.com)
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</P>
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<HR>
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<H4><A NAME = "xmovie"></A>xmovie tool
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</H4>
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<P>The xmovie tool is an X-based visualization package that can read
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LAMMPS dump files and animate them. It is in its own sub-directory
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with the tools directory. You may need to modify its Makefile so that
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it can find the appropriate X libraries to link against.
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</P>
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<P>The syntax for running xmovie is
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</P>
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<PRE>xmovie <B>options</B> dump.file1 dump.file2 ...
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</PRE>
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<P>If you just type "xmovie" you will see a list of options. Note that
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by default, LAMMPS dump files are in scaled coordinates, so you
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typically need to use the -scale option with xmovie. When xmovie runs
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it opens a visualization window and a control window. The control
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options are straightforward to use.
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</P>
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<P>Xmovie was mostly written by Mike Uttormark (U Wisconsin) while he
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spent a summer at Sandia. It displays 2d projections of a 3d domain.
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While simple in design, it is an amazingly fast program that can
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render large numbers of atoms very quickly. It's a useful tool for
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debugging LAMMPS input and output and making sure your simulation is
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doing what you think it should. The animations on the Examples page
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of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW site</A> were created with xmovie.
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</P>
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<P>I've lost contact with Mike, so I hope he's comfortable with us
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distributing his great tool!
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</P>
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</HTML>
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