579 lines
19 KiB
Plaintext
579 lines
19 KiB
Plaintext
"Previous Section"_Examples.html - "LAMMPS WWW Site"_lws - "LAMMPS
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Documentation"_ld - "LAMMPS Commands"_lc - "Next
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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,Commands_all.html)
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:line
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Auxiliary tools :h2
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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 list
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of such tools can be found on the "LAMMPS webpage"_lws at these links:
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"Pre/Post processing"_http://lammps.sandia.gov/prepost.html
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"Offsite LAMMPS packages & tools"_http://lammps.sandia.gov/offsite.html
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"Pizza.py toolkit"_pizza :ul
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The last link for "Pizza.py"_pizza is a Python-based tool developed at
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Sandia which provides tools for doing setup, analysis, plotting, and
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visualization for LAMMPS simulations.
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:link(pizza,http://pizza.sandia.gov)
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:link(python,http://www.python.org)
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Additional tools included in the LAMMPS distribution are described on
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this page.
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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 the LAMMPS developers, as they were contributed
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by LAMMPS users. If you have problems using them, we can direct you
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to the 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. Most of them are larger packages in their
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own sub-directories with their own Makefiles and/or README files.
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:line
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Pre-processing tools :h3
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"amber2lmp"_#amber,
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"ch2lmp"_#charmm,
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"chain"_#chain,
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"createatoms"_#createatoms,
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"drude"_#drude,
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"eam database"_#eamdb,
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"eam generate"_#eamgn,
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"eff"_#eff,
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"ipp"_#ipp,
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"micelle2d"_#micelle,
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"moltemplate"_#moltemplate,
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"msi2lmp"_#msi,
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"polybond"_#polybond :tb(c=6,ea=c,a=l)
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Post-processing tools :h3
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"amber2lmp"_#amber,
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"binary2txt"_#binary,
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"ch2lmp"_#charmm,
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"colvars"_#colvars,
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"eff"_#eff,
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"fep"_#fep,
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"lmp2arc"_#arc,
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"lmp2cfg"_#cfg,
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"matlab"_#matlab,
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"phonon"_#phonon,
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"pymol_asphere"_#pymol,
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"python"_#pythontools,
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"reax"_#reax_tool,
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"replica"_#replica,
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"smd"_#smd,
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"spin"_#spin,
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"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l)
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Miscellaneous tools :h3
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"doxygen"_#doxygen,
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"emacs"_#emacs,
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"i-pi"_#ipi,
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"kate"_#kate,
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"singularity"_#singularity_tool,
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"vim"_#vim :tb(c=5,ea=c,a=l)
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:line
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Tool descriptions :h3
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amber2lmp tool :h4,link(amber)
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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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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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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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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 a
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PDB file with associated CHARMM info, including CHARMM force field
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data, into its LAMMPS equivalent. Support for the CMAP correction of
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CHARMM22 and later is available as an option. This tool can also add
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solvent water molecules and Na+ or Cl- ions to the system.
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Using 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 at sandia.gov)
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and Paul Crozier (pscrozi at sandia.gov) at Sandia.
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CMAP support added and tested by Xiaohu Hu (hux2 at ornl.gov) and
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Robert A. Latour (latourr at clemson.edu), David Hyde-Volpe, and
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Tigran Abramyan, (Clemson University) and
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Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London.
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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 system
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for the "chain benchmark"_Speed_bench.html.
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:line
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colvars tools :h4,link(colvars)
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The colvars directory contains a collection of tools for post-processing
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data produced by the colvars collective variable library.
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To compile the tools, edit the makefile for your system and run "make".
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Please report problems and issues the colvars library and its tools
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at: https://github.com/colvars/colvars/issues
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abf_integrate:
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MC-based integration of multidimensional free energy gradient
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Version 20110511
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Syntax: ./abf_integrate < filename > \[-n < nsteps >\] \[-t < temp >\] \[-m \[0|1\] (metadynamics)\] \[-h < hill_height >\] \[-f < variable_hill_factor >\] :pre
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The LAMMPS interface to the colvars collective variable library, as
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well as these tools, were created by Axel Kohlmeyer (akohlmey at
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gmail.com) at ICTP, Italy.
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:line
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createatoms tool :h4,link(createatoms)
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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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See the included Manual.pdf for details.
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The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
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:line
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doxygen tool :h4,link(doxygen)
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The tools/doxygen directory contains a shell script called
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doxygen.sh which can generate a call graph and API lists using
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the "Doxygen software"_http://doxygen.org.
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See the included README file for details.
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The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com.
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:line
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drude tool :h4,link(drude)
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The tools/drude directory contains a Python script called
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polarizer.py which can add Drude oscillators to a LAMMPS
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data file in the required format.
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See the header of the polarizer.py file for details.
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The tool is authored by Agilio Padua and Alain Dequidt: agilio.padua
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at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
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:line
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eam database tool :h4,link(eamdb)
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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 "pair_style
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eam/alloy"_pair_eam.html command.
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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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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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:line
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eam generate tool :h4,link(eamgn)
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The tools/eam_generate directory contains several one-file C programs
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that convert an analytic formula into a tabulated "embedded atom
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method (EAM)"_pair_eam.html 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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"pair_style eam/alloy"_pair_eam.html command.
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The source files and potentials were provided by Gerolf Ziegenhain
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(gerolf at ziegenhain.com).
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:line
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eff tool :h4,link(eff)
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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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These tools were provided by Andres Jaramillo-Botero at CalTech
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(ajaramil at wag.caltech.edu).
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:line
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emacs tool :h4,link(emacs)
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The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs
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that enables a lammps-mode for editing input scripts when using GNU Emacs,
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with various highlighting options set up.
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These tools were provided by Aidan Thompson at Sandia
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(athomps at sandia.gov).
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:line
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fep tool :h4,link(fep)
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The tools/fep directory contains Python scripts useful for
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post-processing results from performing free-energy perturbation
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simulations using the USER-FEP package.
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The scripts were contributed by Agilio Padua (Universite Blaise
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Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.
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See README file in the tools/fep directory.
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:line
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i-pi tool :h4,link(ipi)
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The tools/i-pi directory contains a version of the i-PI package, with
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all the LAMMPS-unrelated files removed. It is provided so that it can
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be used with the "fix ipi"_fix_ipi.html command to perform
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path-integral molecular dynamics (PIMD).
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The i-PI package was created and is maintained by Michele Ceriotti,
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michele.ceriotti at gmail.com, to interface to a variety of molecular
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dynamics codes.
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See the tools/i-pi/manual.pdf file for an overview of i-PI, and the
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"fix ipi"_fix_ipi.html doc page for further details on running PIMD
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calculations with LAMMPS.
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:line
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ipp tool :h4,link(ipp)
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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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ipp was created and is maintained by Reese Jones (Sandia), rjones at
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sandia.gov.
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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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:line
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kate tool :h4,link(kate)
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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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The file was provided by Alessandro Luigi Sellerio
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(alessandro.sellerio at ieni.cnr.it).
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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' 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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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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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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: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://mt.seas.upenn.edu/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 at sandia.gov).
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:line
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matlab tool :h4,link(matlab)
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The matlab sub-directory contains several "MATLAB"_matlabhome 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 "AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A
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visualizer.
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See the README.pdf file for more information.
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These scripts were written by Arun Subramaniyan at Purdue Univ
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(asubrama at purdue.edu).
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:link(matlabhome,http://www.mathworks.com)
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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"_Examples.html.
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:line
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moltemplate tool :h4,link(moltemplate)
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The moltemplate sub-directory contains instructions for installing
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moltemplate, a Python-based tool for building molecular systems based
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on a text-file description, and creating LAMMPS data files that encode
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their molecular topology as lists of bonds, angles, dihedrals, etc.
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See the README.txt file for more information.
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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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"http://moltemplate.org"_http://moltemplate.org.
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The latest sources can be found "on its GitHub page"_https://github.com/jewettaij/moltemplate/releases
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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 template
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input and data files from BIOVIA's Materias Studio files (formerly
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Accelrys' Insight MD code, formerly MSI/Biosym and its Discover MD code).
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This tool was written by John Carpenter (Cray), Michael Peachey
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(Cray), and Steve Lustig (Dupont). Several people contributed changes
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to remove bugs and adapt its output to changes in LAMMPS.
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This tool has several known limitations and is no longer under active
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development, so there are no changes except for the occasional bug fix.
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See the README file in the tools/msi2lmp folder for more information.
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:line
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phonon tool :h4,link(phonon)
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The phonon sub-directory contains a post-processing tool useful for
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analyzing the output of the "fix phonon"_fix_phonon.html command in
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the USER-PHONON package.
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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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This tool was written by Ling-Ti Kong at Shanghai Jiao Tong
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University.
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:line
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polybond tool :h4,link(polybond)
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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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See the Manual.pdf for details and example scripts.
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This tool was written by Zachary Kraus at Georgia Tech.
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:line
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pymol_asphere tool :h4,link(pymol)
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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 "PyMol visualization
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package"_pymolhome or its "open source variant"_pymolopen.
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:link(pymolhome,http://www.pymol.org)
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:link(pymolopen,http://sourceforge.net/scm/?type=svn&group_id=4546)
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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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This tool was written by Mike Brown at Sandia.
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:line
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python tool :h4,link(pythontools)
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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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extract thermodynamic info from a log file as columns of numbers
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plot two columns of thermodynamic info from a log file using GnuPlot
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sort the snapshots in a dump file by atom ID
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convert multiple "NEB"_neb.html dump files into one dump file for viz
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convert dump files into XYZ, CFG, or PDB format for viz by other packages :ul
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These are simple scripts built on "Pizza.py"_pizza modules. See the
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README for more info on Pizza.py and how to use these scripts.
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:line
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replica tool :h4,link(replica)
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The tools/replica directory contains the reorder_remd_traj python script which
|
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can be used to reorder the replica trajectories (resulting from the use of the
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temper command) according to temperature. This will produce discontinuous
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trajectories with all frames at the same temperature in each trajectory.
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Additional options can be used to calculate the canonical configurational
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log-weight for each frame at each temperature using the pymbar package. See
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the README.md file for further details. Try out the peptide example provided.
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This tool was written by (and is maintained by) Tanmoy Sanyal,
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while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com)
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:line
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reax tool :h4,link(reax_tool)
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The reax sub-directory contains stand-alone codes that can
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post-process the output of the "fix reax/c/bonds"_fix_reaxc_bonds.html
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command from a LAMMPS simulation using "ReaxFF"_pair_reaxc.html. See
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the README.txt file for more info.
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These tools were written by Aidan Thompson at Sandia.
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:line
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smd tool :h4,link(smd)
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The smd sub-directory contains a C++ file dump2vtk_tris.cpp and
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Makefile which can be compiled and used to convert triangle output
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files created by the Smooth-Mach Dynamics (USER-SMD) package into a
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VTK-compatible unstructured grid file. It could then be read in and
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visualized by VTK.
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See the header of dump2vtk.cpp for more details.
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This tool was written by the USER-SMD package author, Georg
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Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics,
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Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
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:line
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spin tool :h4,link(spin)
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The spin sub-directory contains a C file interpolate.c which can
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be compiled and used to perform a cubic polynomial interpolation of
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the MEP following a GNEB calculation.
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See the README file in tools/spin/interpolate_gneb for more details.
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This tool was written by the SPIN package author, Julien
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Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei
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Ivanov, at University of Iceland (ali5 at hi.is).
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:line
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singularity tool :h4,link(singularity_tool)
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The singularity sub-directory contains container definitions files
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that can be used to build container images for building and testing
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LAMMPS on specific OS variants using the "Singularity"_https://sylabs.io
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container software. Contributions for additional variants are welcome.
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:line
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vim tool :h4,link(vim)
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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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These files were provided by Gerolf Ziegenhain (gerolf at
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ziegenhain.com)
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:line
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xmgrace tool :h4,link(xmgrace)
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The files in the tools/xmgrace directory can be used to plot the
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thermodynamic data in LAMMPS log files via the xmgrace plotting
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package. There are several tools in the directory that can be used in
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post-processing mode. The lammpsplot.cpp file can be compiled and
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used to create plots from the current state of a running LAMMPS
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|
simulation.
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See the README file for details.
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These files were provided by Vikas Varshney (vv0210 at gmail.com)
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