<h1>9. Additional tools<aclass="headerlink"href="#additional-tools"title="Permalink to this headline">¶</a></h1>
<p>LAMMPS is designed to be a computational kernel for performing
molecular dynamics computations. Additional pre- and post-processing
steps are often necessary to setup and analyze a simulation. A few
additional tools are provided with the LAMMPS distribution and are
described in this section.</p>
<p>Our group has also written and released a separate toolkit called
<aclass="reference external"href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a> which provides tools for doing setup, analysis,
plotting, and visualization for LAMMPS simulations. Pizza.py is
written in <aclass="reference external"href="http://www.python.org">Python</a> and is available for download from <aclass="reference external"href="http://www.sandia.gov/~sjplimp/pizza.html">the Pizza.py WWW site</a>.</p>
<p>Note that many users write their own setup or analysis tools or use
other existing codes and convert their output to a LAMMPS input format
or vice versa. The tools listed here are included in the LAMMPS
distribution as examples of auxiliary tools. Some of them are not
actively supported by Sandia, as they were contributed by LAMMPS
users. If you have problems using them, we can direct you to the
authors.</p>
<p>The source code for each of these codes is in the tools sub-directory
of the LAMMPS distribution. There is a Makefile (which you may need
to edit for your platform) which will build several of the tools which
reside in that directory. Some of them are larger packages in their
Zr. The files can then be used with the <aclass="reference internal"href="pair_eam.html"><em>pair_style eam/alloy</em></a> command.</p>
<p>The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov,
and is based on his paper:</p>
<p>X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
144113 (2004).</p>
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<divclass="section"id="eam-generate-tool">
<spanid="eamgn"></span><h2>9.9. eam generate tool<aclass="headerlink"href="#eam-generate-tool"title="Permalink to this headline">¶</a></h2>
<p>The tools/eam_generate directory contains several one-file C programs
that convert an analytic formula into a tabulated <aclass="reference internal"href="pair_eam.html"><em>embedded atom method (EAM)</em></a> setfl potential file. The potentials they
produce are in the potentials directory, and can be used with the
<p>The source files and potentials were provided by Gerolf Ziegenhain
(gerolf at ziegenhain.com).</p>
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<divclass="section"id="eff-tool">
<spanid="eff"></span><h2>9.10. eff tool<aclass="headerlink"href="#eff-tool"title="Permalink to this headline">¶</a></h2>
<p>The tools/eff directory contains various scripts for generating
structures and post-processing output for simulations using the
electron force field (eFF).</p>
<p>These tools were provided by Andres Jaramillo-Botero at CalTech
(ajaramil at wag.caltech.edu).</p>
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<divclass="section"id="emacs-tool">
<spanid="emacs"></span><h2>9.11. emacs tool<aclass="headerlink"href="#emacs-tool"title="Permalink to this headline">¶</a></h2>
<p>The tools/emacs directory contains a Lips add-on file for Emacs that
enables a lammps-mode for editing of input scripts when using Emacs,
with various highlighting options setup.</p>
<p>These tools were provided by Aidan Thompson at Sandia
(athomps at sandia.gov).</p>
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<divclass="section"id="fep-tool">
<spanid="fep"></span><h2>9.12. fep tool<aclass="headerlink"href="#fep-tool"title="Permalink to this headline">¶</a></h2>
<p>The tools/fep directory contains Python scripts useful for
post-processing results from performing free-energy perturbation
simulations using the USER-FEP package.</p>
<p>The scripts were contributed by Agilio Padua (Universite Blaise
Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.</p>
<p>See README file in the tools/fep directory.</p>
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<divclass="section"id="i-pi-tool">
<spanid="ipi"></span><h2>9.13. i-pi tool<aclass="headerlink"href="#i-pi-tool"title="Permalink to this headline">¶</a></h2>
<p>The tools/i-pi directory contains a version of the i-PI package, with
all the LAMMPS-unrelated files removed. It is provided so that it can
be used with the <aclass="reference internal"href="fix_ipi.html"><em>fix ipi</em></a> command to perform
path-integral molecular dynamics (PIMD).</p>
<p>The i-PI package was created and is maintained by Michele Ceriotti,
michele.ceriotti at gmail.com, to interface to a variety of molecular
dynamics codes.</p>
<p>See the tools/i-pi/manual.pdf file for an overview of i-PI, and the
<aclass="reference internal"href="fix_ipi.html"><em>fix ipi</em></a> doc page for further details on running PIMD
calculations with LAMMPS.</p>
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<divclass="section"id="ipp-tool">
<spanid="ipp"></span><h2>9.14. ipp tool<aclass="headerlink"href="#ipp-tool"title="Permalink to this headline">¶</a></h2>
<p>The tools/ipp directory contains a Perl script ipp which can be used
to facilitate the creation of a complicated file (say, a lammps input
script or tools/createatoms input file) using a template file.</p>
<p>ipp was created and is maintained by Reese Jones (Sandia), rjones at
sandia.gov.</p>
<p>See two examples in the tools/ipp directory. One of them is for the
tools/createatoms tool’s input file.</p>
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<divclass="section"id="kate-tool">
<spanid="kate"></span><h2>9.15. kate tool<aclass="headerlink"href="#kate-tool"title="Permalink to this headline">¶</a></h2>
<p>The file in the tools/kate directory is an add-on to the Kate editor
in the KDE suite that allow syntax highlighting of LAMMPS input
scripts. See the README.txt file for details.</p>
<p>The file was provided by Alessandro Luigi Sellerio
(alessandro.sellerio at ieni.cnr.it).</p>
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<divclass="section"id="lmp2arc-tool">
<spanid="arc"></span><h2>9.16. lmp2arc tool<aclass="headerlink"href="#lmp2arc-tool"title="Permalink to this headline">¶</a></h2>
<p>The lmp2arc sub-directory contains a tool for converting LAMMPS output
files to the format for Accelrys’ Insight MD code (formerly
MSI/Biosym and its Discover MD code). See the README file for more
information.</p>
<p>This tool was written by John Carpenter (Cray), Michael Peachey
(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic
(jec at mayo.edu), but still fields questions about the tool.</p>
<p>This tool was updated for the current LAMMPS C++ version by Jeff
Greathouse at Sandia (jagreat at sandia.gov).</p>
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<divclass="section"id="lmp2cfg-tool">
<spanid="cfg"></span><h2>9.17. lmp2cfg tool<aclass="headerlink"href="#lmp2cfg-tool"title="Permalink to this headline">¶</a></h2>
<p>The lmp2cfg sub-directory contains a tool for converting LAMMPS output
files into a series of <ahref="#id1"><spanclass="problematic"id="id2">*</span></a>.cfg files which can be read into the
<aclass="reference external"href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a> visualizer. See
the README file for more information.</p>
<p>This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).</p>
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<divclass="section"id="lmp2vmd-tool">
<spanid="vmd"></span><h2>9.18. lmp2vmd tool<aclass="headerlink"href="#lmp2vmd-tool"title="Permalink to this headline">¶</a></h2>
<p>The lmp2vmd sub-directory contains a README.txt file that describes
details of scripts and plugin support within the <aclass="reference external"href="http://www.ks.uiuc.edu/Research/vmd">VMD package</a> for visualizing LAMMPS
dump files.</p>
<p>The VMD plugins and other supporting scripts were written by Axel
Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.</p>
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<divclass="section"id="matlab-tool">
<spanid="matlab"></span><h2>9.19. matlab tool<aclass="headerlink"href="#matlab-tool"title="Permalink to this headline">¶</a></h2>
<p>The matlab sub-directory contains several <spanclass="xref std std-ref">MATLAB</span> scripts for
post-processing LAMMPS output. The scripts include readers for log
and dump files, a reader for EAM potential files, and a converter that
reads LAMMPS dump files and produces CFG files that can be visualized
with the <aclass="reference external"href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a>
visualizer.</p>
<p>See the README.pdf file for more information.</p>
<p>These scripts were written by Arun Subramaniyan at Purdue Univ
(asubrama at purdue.edu).</p>
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<divclass="section"id="micelle2d-tool">
<spanid="micelle"></span><h2>9.20. micelle2d tool<aclass="headerlink"href="#micelle2d-tool"title="Permalink to this headline">¶</a></h2>
<p>The file micelle2d.f creates a LAMMPS data file containing short lipid
chains in a monomer solution. It uses a text file containing lipid
definition parameters as an input. The created molecules and solvent
atoms can strongly overlap, so LAMMPS needs to run the system
initially with a “soft” pair potential to un-overlap it. The syntax
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