forked from lijiext/lammps
738 lines
20 KiB
Plaintext
738 lines
20 KiB
Plaintext
Additional tools
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================
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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 Pizza.py WWW site <pizza_>`_.
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.. _pizza: http://www.sandia.gov/~sjplimp/pizza.html
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.. _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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* :ref:`amber2lmp <amber>`
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* :ref:`binary2txt <binary>`
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* :ref:`ch2lmp <charmm>`
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* :ref:`chain <chain>`
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* :ref:`colvars <colvars>`
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* :ref:`createatoms <create>`
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* :ref:`data2xmovie <data>`
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* :ref:`eam database <eamdb>`
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* :ref:`eam generate <eamgn>`
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* :ref:`eff <eff>`
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* :ref:`emacs <emacs>`
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* :ref:`fep <fep>`
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* :ref:`i-pi <ipi>`
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* :ref:`ipp <ipp>`
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* :ref:`kate <kate>`
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* :ref:`lmp2arc <arc>`
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* :ref:`lmp2cfg <cfg>`
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* :ref:`lmp2vmd <vmd>`
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* :ref:`matlab <matlab>`
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* :ref:`micelle2d <micelle>`
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* :ref:`moltemplate <moltemplate>`
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* :ref:`msi2lmp <msi>`
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* :ref:`phonon <phonon>`
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* :ref:`polymer bonding <polybond>`
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* :ref:`pymol_asphere <pymol>`
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* :ref:`python <pythontools>`
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* :ref:`reax <reax>`
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* :ref:`restart2data <restart>`
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* :ref:`vim <vim>`
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* :ref:`xmgrace <xmgrace>`
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* :ref:`xmovie <xmovie>`
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----------
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.. _amber:
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amber2lmp tool
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--------------------------
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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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----------
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.. _binary:
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binary2txt tool
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----------------------------
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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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.. parsed-literal::
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binary2txt file1 file2 ...
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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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----------
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.. _charmm:
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ch2lmp tool
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------------------------
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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 at sandia.gov)
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and Paul Crozier (pscrozi at sandia.gov) at Sandia.
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.. _chain:
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chain tool
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----------------------
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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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.. parsed-literal::
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chain < def.chain > data.file
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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 :doc:`chain benchmark <Section_perf>`.
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.. _colvars:
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colvars tools
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---------------------------
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The colvars directory contains a collection of tools for postprocessing
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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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.. parsed-literal::
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Syntax: ./abf_integrate < filename > [-n < nsteps >] [-t < temp >] [-m [0|1] (metadynamics)] [-h < hill_height >] [-f < variable_hill_factor >]
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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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----------
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.. _create:
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createatoms tool
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-----------------------------
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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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----------
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.. _data:
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data2xmovie tool
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---------------------------
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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 :ref:`xmovie <xmovie>` tool, as if it had
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been output with a dump command from LAMMPS itself. The syntax for
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running the tool is
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.. parsed-literal::
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data2xmovie [options] < infile > outfile
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See the top of the data2xmovie.c file for a discussion of the options.
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----------
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.. _eamdb:
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eam database tool
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-----------------------------
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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 :doc:`pair_style eam/alloy <pair_eam>` 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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----------
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.. _eamgn:
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eam generate tool
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-----------------------------
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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 :doc:`embedded atom method (EAM) <pair_eam>` 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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:doc:`pair_style eam/alloy <pair_eam>` 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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.. _eff:
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eff tool
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------------------
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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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----------
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.. _emacs:
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emacs tool
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----------------------
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The tools/emacs directory contains a Lips add-on file for Emacs that
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enables a lammps-mode for editing of input scripts when using Emacs,
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with various highlighting options setup.
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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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----------
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.. _fep:
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fep tool
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------------------
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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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----------
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.. _ipi:
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i-pi tool
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-------------------
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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 :doc:`fix ipi <fix_ipi>` 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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:doc:`fix ipi <fix_ipi>` doc page for further details on running PIMD
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calculations with LAMMPS.
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----------
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.. _ipp:
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ipp tool
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------------------
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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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----------
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.. _kate:
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kate tool
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--------------------
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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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----------
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.. _arc:
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lmp2arc tool
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----------------------
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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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----------
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.. _cfg:
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lmp2cfg tool
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----------------------
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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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----------
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.. _vmd:
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lmp2vmd tool
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----------------------
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The lmp2vmd sub-directory contains a README.txt file that describes
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details of scripts and plugin support within the `VMD package <http://www.ks.uiuc.edu/Research/vmd>`_ for visualizing LAMMPS
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dump files.
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The VMD plugins and other supporting scripts were written by Axel
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Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.
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----------
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.. _matlab:
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matlab tool
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------------------------
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The matlab sub-directory contains several :ref:`MATLAB <matlab>` 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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.. _matlab: http://www.mathworks.com
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----------
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.. _micelle:
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micelle2d tool
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----------------------------
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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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.. parsed-literal::
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micelle2d < def.micelle2d > data.file
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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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:doc:`micelle example <Section_example>`.
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----------
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.. _moltemplate:
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moltemplate tool
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----------------------------------
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The moltemplate sub-directory contains a Python-based tool for
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building molecular systems based on a text-file description, and
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creating LAMMPS data files that encode their molecular topology as
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lists of bonds, angles, dihedrals, etc. See the README.TXT file for
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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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----------
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.. _msi:
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msi2lmp tool
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----------------------
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The msi2lmp sub-directory contains a tool for creating LAMMPS input
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data files from Accelrys' Insight MD code (formerly MSI/Biosym and
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its Discover MD code). See the README file for more information.
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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 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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----------
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.. _phonon:
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phonon tool
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------------------------
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The phonon sub-directory contains a post-processing tool useful for
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analyzing the output of the :doc:`fix phonon <fix_phonon>` 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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----------
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.. _polybond:
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polymer bonding tool
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-----------------------------------
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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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----------
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.. _pymol:
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pymol_asphere tool
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------------------------------
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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 :ref:`PyMol visualization package <pymol>`.
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.. _pymol: http://pymol.sourceforge.net
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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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----------
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.. _pythontools:
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python tool
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-----------------------------
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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 :doc:`NEB <neb>` 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
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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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----------
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.. _reax:
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reax tool
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--------------------
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The reax sub-directory contains stand-alond codes that can
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post-process the output of the :doc:`fix reax/bonds <fix_reax_bonds>`
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command from a LAMMPS simulation using :doc:`ReaxFF <pair_reax>`. 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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----------
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.. _restart:
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restart2data tool
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-------------------------------
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.. note::
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This tool is now obsolete and is not included in the current
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LAMMPS distribution. This is becaues there is now a
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:doc:`write_data <write_data>` command, which can create a data file
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from within an input script. Running LAMMPS with the "-r"
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:ref:`command-line switch <start_7>` as follows:
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lmp_g++ -r restartfile datafile
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is the same as running a 2-line input script:
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read_restart restartfile
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write_data datafile
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which will produce the same data file that the restart2data tool used
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to create. The following information is included in case you have an
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older version of LAMMPS which still includes the restart2data tool.
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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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.. parsed-literal::
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restart2data restart-file data-file (input-file)
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Input-file is optional and if specified will contain LAMMPS input
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commands for the masses and force field parameters, instead of putting
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those in the data-file. Only a few force field styles currently
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support this option.
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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 :doc:`restart <restart>` and
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:doc:`write_restart <write_restart>` 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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----------
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.. _vim:
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vim tool
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------------------
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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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----------
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.. _xmgrace:
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xmgrace tool
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--------------------------
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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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----------
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.. _xmovie:
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xmovie tool
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------------------------
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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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.. parsed-literal::
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xmovie [options] dump.file1 dump.file2 ...
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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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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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