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doc/Section_tools.txt
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"Previous Section"_Section_perf.html - "LAMMPS WWW Site"_lws - "LAMMPS
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Documentation"_ld - "LAMMPS Commands"_lc - "Next
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Section"_Section_modify.html :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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7. Additional tools :h3
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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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Our group has also written and released a separate toolkit called
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"Pizza.py"_pizza 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 "Python"_python and is available for download from "the
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Pizza.py WWW site"_pizza.
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:link(pizza,http://www.cs.sandia.gov/~sjplimp/pizza.html)
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:link(python,http://www.python.org)
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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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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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"replicate"_#replicate
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"restart2data"_#restart
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"binary2txt"_#binary
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"data2xmovie"_#data
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"chain"_#chain
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"micelle2d"_#micelle
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"xmovie"_#xmovie
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"ch2lmp"_#charmm
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"msi2lmp"_#msi
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"amber2lammps"_#amber
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"lmp2arc"_#arc
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"lmp2cfg"_#cfg
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"lmp2traj"_#traj :ul
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:line
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replicate tool :h4,link(replicate)
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The file replicate.c takes a LAMMPS data file and replicates it into a
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larger system. The syntax for running the tool is
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replicate [options] < infile > outfile :pre
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See the top of the replicate.c file for a discussion of the options.
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This tool is used by some of the "LAMMPS benchmarks"_Section_perf.html
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for creating larger systems to run scaled-size problems on multiple
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processors.
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:line
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restart2data tool :h4,link(restart)
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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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restart2data restart-file data-file :pre
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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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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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If a "%" appears in the specified restart-file, the tool expects a set
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of multiple files to exist. See the "restart"_restart.html and
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"write_restart"_write_restart.html 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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:line
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binary2txt tool :h4,link(binary)
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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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binary2txt file1 file2 ... :pre
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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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:line
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data2xmovie tool :h4,link(data)
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The file data2xmovie.c converts a LAMMPS data file into a snapshot
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suitable for visualizing with the "xmovie"_#xmovie tool, as it 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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data2xmovie [options] < infile > outfile :pre
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See the top of the data2xmovie.c file for a discussion of the options.
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:line
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chain tool :h4,link(chain)
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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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chain < def.chain > data.file :pre
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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 "chain benchmark"_Section_perf.html.
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:line
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micelle2d tool :h4,link(micelle)
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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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micelle2d < def.micelle2d > data.file :pre
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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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"micelle example"_Section_example.html.
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:line
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xmovie tool :h4,link(xmovie)
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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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The syntax for running xmovie is
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xmovie [options] dump.file1 dump.file2 ... :pre
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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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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 "LAMMPS WWW site"_lws were created with xmovie.
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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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:line
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ch2lmp tool :h4,link(charmm)
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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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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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See the README file in the ch2lmp sub-directory for more information.
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These tools were created by Pieter in't Veld (pjintve@sandia.gov) and
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Paul Crozier (pscrozi@sandia.gov) at Sandia.
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:line
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msi2lmp tool :h4,link(msi)
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The msi2lmp sub-directory contains a tool for creating LAMMPS input
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data files from Accelrys's Insight MD code (formerly MSI/Biosysm and
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its Discover MD code). See the README file for more information.
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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@mayo.edu"_mailto:jec@mayo.edu), but still fields questions about
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the tool.
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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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:line
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amber2lmp tool :h4,link(amber)
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The amber2lmp sub-directory contain 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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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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:line
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lmp2arc tool :h4,link(arc)
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The lmp2arc sub-directory contains a tool for converting LAMMPS output
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files to the format for Accelrys's Insight MD code (formerly
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MSI/Biosysm and its Discover MD code). See the README file for more
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information.
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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@mayo.edu"_mailto:jec@mayo.edu), but still fields questions about
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the tool.
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This tool was updated for the current LAMMPS C++ version by Jeff
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Greathouse at Sandia (jagreat@sandia.gov).
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:line
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lmp2cfg tool :h4,link(cfg)
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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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"AtomEye"_http://164.107.79.177/Archive/Graphics/A visualizer. See
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the README file for more information.
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This tool was written by Ara Kooser at Sandia (askoose@sandia.gov).
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:line
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lmp2traj tool :h4,link(traj)
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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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This tool was written by Ara Kooser at Sandia (askoose@sandia.gov).
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