Diffusion lammps (lammm-master-deprecated) Browse

Section_tools.html
c7d0f4d9f2delammm-master-deprecated

Section_tools.html
View Options

			<HTML>
			<CENTER><A HREF = "Section_perf.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS
			Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_modify.html">Next
			Section</A>
			</CENTER>






			<HR>

			<H3>9. 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.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.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">amber2lmp</A>
			<LI><A HREF = "#binary">binary2txt</A>
			<LI><A HREF = "#charmm">ch2lmp</A>
			<LI><A HREF = "#chain">chain</A>
			<LI><A HREF = "#colvars">colvars</A>
			<LI><A HREF = "#create">createatoms</A>
			<LI><A HREF = "#data">data2xmovie</A>
			<LI><A HREF = "#eamdb">eam database</A>
			<LI><A HREF = "#eamgn">eam generate</A>
			<LI><A HREF = "#eff">eff</A>
			<LI><A HREF = "#emacs">emacs</A>
			<LI><A HREF = "#fep">fep</A>
			<LI><A HREF = "#ipi">i-pi</A>
			<LI><A HREF = "#ipp">ipp</A>
			<LI><A HREF = "#kate">kate</A>
			<LI><A HREF = "#arc">lmp2arc</A>
			<LI><A HREF = "#cfg">lmp2cfg</A>
			<LI><A HREF = "#vmd">lmp2vmd</A>
			<LI><A HREF = "#matlab">matlab</A>
			<LI><A HREF = "#micelle">micelle2d</A>
			<LI><A HREF = "#moltemplate">moltemplate</A>
			<LI><A HREF = "#msi">msi2lmp</A>
			<LI><A HREF = "#phonon">phonon</A>
			<LI><A HREF = "#polybond">polymer bonding</A>
			<LI><A HREF = "#pymol">pymol_asphere</A>
			<LI><A HREF = "#pythontools">python</A>
			<LI><A HREF = "#reax">reax</A>
			<LI><A HREF = "#restart">restart2data</A>
			<LI><A HREF = "#vim">vim</A>
			<LI><A HREF = "#xmgrace">xmgrace</A>
			<LI><A HREF = "#xmovie">xmovie</A>
			</UL>
			<HR>

			<H4><A NAME = "amber"></A>amber2lmp tool
			</H4>
			<P>The amber2lmp sub-directory contains 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 = "colvars"></A>colvars tools
			</H4>
			<P>The colvars directory contains a collection of tools for postprocessing
			data produced by the colvars collective variable library.
			To compile the tools, edit the makefile for your system and run "make".
			</P>
			<P>Please report problems and issues the colvars library and its tools
			at: https://github.com/colvars/colvars/issues
			</P>
			<P>abf_integrate:
			</P>
			<P>MC-based integration of multidimensional free energy gradient
			Version 20110511
			</P>
			<PRE>Syntax: ./abf_integrate < filename > [-n < nsteps >] [-t < temp >] [-m [0\|1] (metadynamics)] [-h < hill_height >] [-f < variable_hill_factor >]
			</PRE>
			<P>The LAMMPS interface to the colvars collective variable library, as
			well as these tools, were created by Axel Kohlmeyer (akohlmey at
			gmail.com) at ICTP, Italy.
			</P>
			<HR>

			<H4><A NAME = "create"></A>createatoms tool
			</H4>
			<P>The tools/createatoms directory contains a Fortran program called
			createAtoms.f which can generate a variety of interesting crystal
			structures and geometries and output the resulting list of atom
			coordinates in LAMMPS or other formats.
			</P>
			<P>See the included Manual.pdf for details.
			</P>
			<P>The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
			</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 [options] < infile > outfile
			</PRE>
			<P>See the top of the data2xmovie.c file for a discussion of the options.
			</P>
			<HR>

			<H4><A NAME = "eamdb"></A>eam database tool
			</H4>
			<P>The tools/eam_database directory contains a Fortran program that will
			generate EAM alloy setfl potential files for any combination of 16
			elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti,
			Zr. The files can then be used with the <A HREF = "pair_eam.html">pair_style
			eam/alloy</A> command.
			</P>
			<P>The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov,
			and is based on his paper:
			</P>
			<P>X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
			144113 (2004).
			</P>
			<HR>

			<H4><A NAME = "eamgn"></A>eam generate tool
			</H4>
			<P>The tools/eam_generate directory contains several one-file C programs
			that convert an analytic formula into a tabulated <A HREF = "pair_eam.html">embedded atom
			method (EAM)</A> setfl potential file. The potentials they
			produce are in the potentials directory, and can be used with the
			<A HREF = "pair_eam.html">pair_style eam/alloy</A> command.
			</P>
			<P>The source files and potentials were provided by Gerolf Ziegenhain
			(gerolf at ziegenhain.com).
			</P>
			<HR>

			<H4><A NAME = "eff"></A>eff tool
			</H4>
			<P>The tools/eff directory contains various scripts for generating
			structures and post-processing output for simulations using the
			electron force field (eFF).
			</P>
			<P>These tools were provided by Andres Jaramillo-Botero at CalTech
			(ajaramil at wag.caltech.edu).
			</P>
			<HR>

			<H4><A NAME = "emacs"></A>emacs tool
			</H4>
			<P>The tools/emacs directory contains a Lips add-on file for Emacs that
			enables a lammps-mode for editing of input scripts when using Emacs,
			with various highlighting options setup.
			</P>
			<P>These tools were provided by Aidan Thompson at Sandia
			(athomps at sandia.gov).
			</P>
			<HR>

			<H4><A NAME = "fep"></A>fep tool
			</H4>
			<P>The tools/fep directory contains Python scripts useful for
			post-processing results from performing free-energy perturbation
			simulations using the USER-FEP package.
			</P>
			<P>The scripts were contributed by Agilio Padua (Universite Blaise
			Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.
			</P>
			<P>See README file in the tools/fep directory.
			</P>
			<HR>

			<H4><A NAME = "ipi"></A>i-pi tool
			</H4>
			<P>The tools/i-pi directory contains a version of the i-PI package, with
			all the LAMMPS-unrelated files removed. It is provided so that it can
			be used with the <A HREF = "fix_ipi.html">fix ipi</A> command to perform
			path-integral molecular dynamics (PIMD).
			</P>
			<P>The i-PI package was created and is maintained by Michele Ceriotti,
			michele.ceriotti at gmail.com, to interface to a variety of molecular
			dynamics codes.
			</P>
			<P>See the tools/i-pi/manual.pdf file for an overview of i-PI, and the
			<A HREF = "fix_ipi.html">fix ipi</A> doc page for further details on running PIMD
			calculations with LAMMPS.
			</P>
			<HR>

			<H4><A NAME = "ipp"></A>ipp tool
			</H4>
			<P>The tools/ipp directory contains a Perl script ipp which can be used
			to facilitate the creation of a complicated file (say, a lammps input
			script or tools/createatoms input file) using a template file.
			</P>
			<P>ipp was created and is maintained by Reese Jones (Sandia), rjones at
			sandia.gov.
			</P>
			<P>See two examples in the tools/ipp directory. One of them is for the
			tools/createatoms tool's input file.
			</P>
			<HR>

			<H4><A NAME = "kate"></A>kate tool
			</H4>
			<P>The file in the tools/kate directory is an add-on to the Kate editor
			in the KDE suite that allow syntax highlighting of LAMMPS input
			scripts. See the README.txt file for details.
			</P>
			<P>The file was provided by Alessandro Luigi Sellerio
			(alessandro.sellerio at ieni.cnr.it).
			</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' Insight MD code (formerly
			MSI/Biosym 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://mt.seas.upenn.edu/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 = "vmd"></A>lmp2vmd tool
			</H4>
			<P>The lmp2vmd sub-directory contains a README.txt file that describes
			details of scripts and plugin support within the <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD
			package</A> for visualizing LAMMPS
			dump files.
			</P>
			<P>The VMD plugins and other supporting scripts were written by Axel
			Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.
			</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 EAM potential files, and a converter that
			reads LAMMPS dump files and produces CFG files that can be visualized
			with the <A HREF = "http://mt.seas.upenn.edu/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 = "moltemplate"></A>moltemplate tool
			</H4>
			<P>The moltemplate sub-directory contains a Python-based tool for
			building molecular systems based on a text-file description, and
			creating LAMMPS data files that encode their molecular topology as
			lists of bonds, angles, dihedrals, etc. See the README.TXT file for
			more information.
			</P>
			<P>This tool was written by Andrew Jewett (jewett.aij at gmail.com), who
			supports it. It has its own WWW page at
			<A HREF = "http://moltemplate.org">http://moltemplate.org</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' Insight MD code (formerly MSI/Biosym 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 = "phonon"></A>phonon tool
			</H4>
			<P>The phonon sub-directory contains a post-processing tool useful for
			analyzing the output of the <A HREF = "fix_phonon.html">fix phonon</A> command in
			the USER-PHONON package.
			</P>
			<P>See the README file for instruction on building the tool and what
			library it needs. And see the examples/USER/phonon directory
			for example problems that can be post-processed with this tool.
			</P>
			<P>This tool was written by Ling-Ti Kong at Shanghai Jiao Tong
			University.
			</P>
			<HR>

			<H4><A NAME = "polybond"></A>polymer bonding tool
			</H4>
			<P>The polybond sub-directory contains a Python-based tool useful for
			performing "programmable polymer bonding". The Python file
			lmpsdata.py provides a "Lmpsdata" class with various methods which can
			be invoked by a user-written Python script to create data files with
			complex bonding topologies.
			</P>
			<P>See the Manual.pdf for details and example scripts.
			</P>
			<P>This tool was written by Zachary Kraus at Georgia Tech.
			</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 = "pythontools"></A>python tool
			</H4>
			<P>The python sub-directory contains several Python scripts
			that perform common LAMMPS post-processing tasks, such as:
			</P>
			<UL><LI>extract thermodynamic info from a log file as columns of numbers
			<LI>plot two columns of thermodynamic info from a log file using GnuPlot
			<LI>sort the snapshots in a dump file by atom ID
			<LI>convert multiple <A HREF = "neb.html">NEB</A> dump files into one dump file for viz
			<LI>convert dump files into XYZ, CFG, or PDB format for viz by other packages
			</UL>
			<P>These are simple scripts built on <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> modules. See the
			README for more info on Pizza.py and how to use these scripts.
			</P>
			<HR>

			<H4><A NAME = "reax"></A>reax tool
			</H4>
			<P>The reax sub-directory contains stand-alond codes that can
			post-process the output of the <A HREF = "fix_reax_bonds.html">fix reax/bonds</A>
			command from a LAMMPS simulation using <A HREF = "pair_reax.html">ReaxFF</A>. See
			the README.txt file for more info.
			</P>
			<P>These tools were written by Aidan Thompson at Sandia.
			</P>
			<HR>

			<H4><A NAME = "restart"></A>restart2data tool
			</H4>
			<P>IMPORTANT NOTE: This tool is now obsolete and is not included in the
			current LAMMPS distribution. This is becaues there is now a
			<A HREF = "write_data.html">write_data</A> command, which can create a data file
			from within an input script. Running LAMMPS with the "-r"
			<A HREF = "Section_start.html#start_7">command-line switch</A> as follows:
			</P>
			<P>lmp_g++ -r restartfile datafile
			</P>
			<P>is the same as running a 2-line input script:
			</P>
			<P>read_restart restartfile
			write_data datafile
			</P>
			<P>which will produce the same data file that the restart2data tool used
			to create. The following information is included in case you have an
			older version of LAMMPS which still includes the restart2data tool.
			</P>
			<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 (input-file)
			</PRE>
			<P>Input-file is optional and if specified will contain LAMMPS input
			commands for the masses and force field parameters, instead of putting
			those in the data-file. Only a few force field styles currently
			support this option.
			</P>
			<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 = "vim"></A>vim tool
			</H4>
			<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 [options] 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>

lammps/doc/doc2/Section_tools.htmlc7d0f4d9f2delammm-master-deprecated

Section_tools.htmlView Options

lammps/doc/doc2/Section_tools.html
c7d0f4d9f2delammm-master-deprecated

Section_tools.html
View Options