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	<HR>

	<H3>7. Additional tools
	</H3>
	<P>LAMMPS is designed to be a computational kernel for performing
	molecular dynamics computations. Additional pre- and post-processing
	steps are often necessary to setup and analyze a simulation. A few
	additional tools are provided with the LAMMPS distribution and are
	described in this section.
	</P>
	<P>Our group has also written and released a separate toolkit called
	<A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which provides tools for doing setup, analysis,
	plotting, and visualization for LAMMPS simulations. Pizza.py is
	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
	Pizza.py WWW site</A>.
	</P>




	<P>Note that many users write their own setup or analysis tools or use
	other existing codes and convert their output to a LAMMPS input format
	or vice versa. The tools listed here are included in the LAMMPS
	distribution as examples of auxiliary tools. Some of them are not
	actively supported by Sandia, as they were contributed by LAMMPS
	users. If you have problems using them, we can direct you to the
	authors.
	</P>
	<P>The source code for each of these codes is in the tools sub-directory
	of the LAMMPS distribution. There is a Makefile (which you may need
	to edit for your platform) which will build several of the tools which
	reside in that directory. Some of them are larger packages in their
	own sub-directories with their own Makefiles.
	</P>
	<UL><LI><A HREF = "#amber">amber2lammps</A>
	<LI><A HREF = "#binary">binary2txt</A>
	<LI><A HREF = "#charmm">ch2lmp</A>
	<LI><A HREF = "#chain">chain</A>
	<LI><A HREF = "#data">data2xmovie</A>
	<LI><A HREF = "#arc">lmp2arc</A>
	<LI><A HREF = "#cfg">lmp2cfg</A>
	<LI><A HREF = "#traj">lmp2traj</A>
	<LI><A HREF = "#matlab">matlab</A>
	<LI><A HREF = "#micelle">micelle2d</A>
	<LI><A HREF = "#msi">msi2lmp</A>
	<LI><A HREF = "#pymol">pymol_asphere</A>
	<LI><A HREF = "#restart">restart2data</A>
	<LI><A HREF = "#thermo_extract">thermo_extract</A>
	<LI><A HREF = "#xmovie">xmovie</A>
	</UL>
	<HR>

	<H4><A NAME = "amber"></A>amber2lmp tool
	</H4>
	<P>The amber2lmp sub-directory contain two Python scripts for converting
	files back-and-forth between the AMBER MD code and LAMMPS. See the
	README file in amber2lmp for more information.
	</P>
	<P>These tools were written by Keir Novik while he was at Queen Mary
	University of London. Keir is no longer there and cannot support
	these tools which are out-of-date with respect to the current LAMMPS
	version (and maybe with respect to AMBER as well). Since we don't use
	these tools at Sandia, you'll need to experiment with them and make
	necessary modifications yourself.
	</P>
	<HR>

	<H4><A NAME = "binary"></A>binary2txt tool
	</H4>
	<P>The file binary2txt.cpp converts one or more binary LAMMPS dump file
	into ASCII text files. The syntax for running the tool is
	</P>
	<PRE>binary2txt file1 file2 ...
	</PRE>
	<P>which creates file1.txt, file2.txt, etc. 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.
	</P>
	<HR>

	<H4><A NAME = "charmm"></A>ch2lmp tool
	</H4>
	<P>The ch2lmp sub-directory contains tools for converting files
	back-and-forth between the CHARMM MD code and LAMMPS.
	</P>
	<P>They are intended to make it easy to use CHARMM as a builder and as a
	post-processor for LAMMPS. Using charmm2lammps.pl, you can convert an
	ensemble built in CHARMM into its LAMMPS equivalent. Using
	lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files.
	</P>
	<P>See the README file in the ch2lmp sub-directory for more information.
	</P>
	<P>These tools were created by Pieter in't Veld (pjintve at sandia.gov)
	and Paul Crozier (pscrozi at sandia.gov) at Sandia.
	</P>
	<HR>

	<H4><A NAME = "chain"></A>chain tool
	</H4>
	<P>The file chain.f creates a LAMMPS data file containing bead-spring
	polymer chains and/or monomer solvent atoms. It uses a text file
	containing chain definition parameters as an input. The created
	chains and solvent atoms can strongly overlap, so LAMMPS needs to run
	the system initially with a "soft" pair potential to un-overlap it.
	The syntax for running the tool is
	</P>
	<PRE>chain < def.chain > data.file
	</PRE>
	<P>See the def.chain or def.chain.ab files in the tools directory for
	examples of definition files. This tool was used to create the
	system for the <A HREF = "Section_perf.html">chain benchmark</A>.
	</P>
	<HR>

	<H4><A NAME = "data"></A>data2xmovie tool
	</H4>
	<P>The file data2xmovie.c converts a LAMMPS data file into a snapshot
	suitable for visualizing with the <A HREF = "#xmovie">xmovie</A> tool, as if it had
	been output with a dump command from LAMMPS itself. The syntax for
	running the tool is
	</P>
	<PRE>data2xmovie <B>options</B> < infile > outfile
	</PRE>
	<P>See the top of the data2xmovie.c file for a discussion of the options.
	</P>
	<HR>

	<H4><A NAME = "arc"></A>lmp2arc tool
	</H4>
	<P>The lmp2arc sub-directory contains a tool for converting LAMMPS output
	files to the format for Accelrys's Insight MD code (formerly
	MSI/Biosysm and its Discover MD code). See the README file for more
	information.
	</P>
	<P>This tool was written by John Carpenter (Cray), Michael Peachey
	(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic
	(jec at mayo.edu), but still fields questions about the tool.
	</P>
	<P>This tool was updated for the current LAMMPS C++ version by Jeff
	Greathouse at Sandia (jagreat at sandia.gov).
	</P>
	<HR>

	<H4><A NAME = "cfg"></A>lmp2cfg tool
	</H4>
	<P>The lmp2cfg sub-directory contains a tool for converting LAMMPS output
	files into a series of *.cfg files which can be read into the
	<A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A> visualizer. See
	the README file for more information.
	</P>
	<P>This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
	</P>
	<HR>

	<H4><A NAME = "traj"></A>lmp2traj tool
	</H4>
	<P>The lmp2traj sub-directory contains a tool for converting LAMMPS output
	files into 3 analysis files. One file can be used to create contour
	maps of the atom positions over the course of the simulation. The
	other two files provide density profiles and dipole moments. See the
	README file for more information.
	</P>
	<P>This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
	</P>
	<HR>

	<H4><A NAME = "matlab"></A>matlab tool
	</H4>
	<P>The matlab sub-directory contains several <A HREF = "http://www.mathworks.com">MATLAB</A> scripts for
	post-processing LAMMPS output. The scripts include readers for log
	and dump files, a reader for radial distribution output from the <A HREF = "fix_rdf.html">fix
	rdf</A> command, a reader for EAM potential files, and a
	converter that reads LAMMPS dump files and produces CFG files that can
	be visualized with the
	<A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A> visualizer.
	</P>
	<P>See the README.pdf file for more information.
	</P>
	<P>These scripts were written by Arun Subramaniyan at Purdue Univ
	(asubrama at purdue.edu).
	</P>


	<HR>

	<H4><A NAME = "micelle"></A>micelle2d tool
	</H4>
	<P>The file micelle2d.f creates a LAMMPS data file containing short lipid
	chains in a monomer solution. It uses a text file containing lipid
	definition parameters as an input. The created molecules and solvent
	atoms can strongly overlap, so LAMMPS needs to run the system
	initially with a "soft" pair potential to un-overlap it. The syntax
	for running the tool is
	</P>
	<PRE>micelle2d < def.micelle2d > data.file
	</PRE>
	<P>See the def.micelle2d file in the tools directory for an example of a
	definition file. This tool was used to create the system for the
	<A HREF = "Section_example.html">micelle example</A>.
	</P>
	<HR>

	<H4><A NAME = "msi"></A>msi2lmp tool
	</H4>
	<P>The msi2lmp sub-directory contains a tool for creating LAMMPS input
	data files from Accelrys's Insight MD code (formerly MSI/Biosysm and
	its Discover MD code). See the README file for more information.
	</P>
	<P>This tool was written by John Carpenter (Cray), Michael Peachey
	(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic
	(jec at mayo.edu), but still fields questions about the tool.
	</P>
	<P>This tool may be out-of-date with respect to the current LAMMPS and
	Insight versions. Since we don't use it at Sandia, you'll need to
	experiment with it yourself.
	</P>
	<HR>

	<H4><A NAME = "pymol"></A>pymol_asphere tool
	</H4>
	<P>The pymol_asphere sub-directory contains a tool for converting a
	LAMMPS dump file that contains orientation info for ellipsoidal
	particles into an input file for the <A HREF = "http://pymol.sourceforge.net">PyMol visualization
	package</A>.
	</P>


	<P>Specifically, the tool triangulates the ellipsoids so they can be
	viewed as true ellipsoidal particles within PyMol. See the README and
	examples directory within pymol_asphere for more information.
	</P>
	<P>This tool was written by Mike Brown at Sandia.
	</P>
	<HR>

	<H4><A NAME = "restart"></A>restart2data tool
	</H4>
	<P>The file restart2data.cpp converts a binary LAMMPS restart file into
	an ASCII data file. The syntax for running the tool is
	</P>
	<PRE>restart2data restart-file data-file
	</PRE>
	<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.
	</P>
	<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.
	</P>
	<P>If a "%" appears in the specified restart-file, the tool expects a set
	of multiple files to exist. See the <A HREF = "restart.html">restart</A> and
	<A HREF = "write_restart.html">write_restart</A> commands for info on how such sets
	of files are written by LAMMPS, and how the files are named.
	</P>
	<HR>

	<H4><A NAME = "thermo_extract"></A>thermo_extract tool
	</H4>
	<P>The thermo_extract tool reads one of more LAMMPS log files and
	extracts a thermodynamic value (e.g. Temp, Press). It spits out the
	time,value as 2 columns of numbers so the tool can be used as a quick
	way to plot some quantity of interest. See the header of the
	thermo_extract.c file for the syntax of how to run it and other
	details.
	</P>
	<P>This tool was written by Vikas Varshney at Wright Patterson AFB
	(vikas.varshney 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>
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