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<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Additional tools &mdash; LAMMPS 15 May 2015 version documentation</title>
<title>9. Additional tools &mdash; LAMMPS 15 May 2015 version documentation</title>
@ -32,7 +32,9 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<link rel="next" title="10. Modifying &amp; extending LAMMPS" href="Section_modify.html"/>
<link rel="prev" title="8. Performance &amp; scalability" href="Section_perf.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -71,44 +73,55 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Additional tools</a><ul>
<li><a class="reference internal" href="#amber2lmp-tool">amber2lmp tool</a></li>
<li><a class="reference internal" href="#binary2txt-tool">binary2txt tool</a></li>
<li><a class="reference internal" href="#ch2lmp-tool">ch2lmp tool</a></li>
<li><a class="reference internal" href="#chain-tool">chain tool</a></li>
<li><a class="reference internal" href="#colvars-tools">colvars tools</a></li>
<li><a class="reference internal" href="#createatoms-tool">createatoms tool</a></li>
<li><a class="reference internal" href="#data2xmovie-tool">data2xmovie tool</a></li>
<li><a class="reference internal" href="#eam-database-tool">eam database tool</a></li>
<li><a class="reference internal" href="#eam-generate-tool">eam generate tool</a></li>
<li><a class="reference internal" href="#eff-tool">eff tool</a></li>
<li><a class="reference internal" href="#emacs-tool">emacs tool</a></li>
<li><a class="reference internal" href="#fep-tool">fep tool</a></li>
<li><a class="reference internal" href="#i-pi-tool">i-pi tool</a></li>
<li><a class="reference internal" href="#ipp-tool">ipp tool</a></li>
<li><a class="reference internal" href="#kate-tool">kate tool</a></li>
<li><a class="reference internal" href="#lmp2arc-tool">lmp2arc tool</a></li>
<li><a class="reference internal" href="#lmp2cfg-tool">lmp2cfg tool</a></li>
<li><a class="reference internal" href="#lmp2vmd-tool">lmp2vmd tool</a></li>
<li><a class="reference internal" href="#matlab-tool">matlab tool</a></li>
<li><a class="reference internal" href="#micelle2d-tool">micelle2d tool</a></li>
<li><a class="reference internal" href="#moltemplate-tool">moltemplate tool</a></li>
<li><a class="reference internal" href="#msi2lmp-tool">msi2lmp tool</a></li>
<li><a class="reference internal" href="#phonon-tool">phonon tool</a></li>
<li><a class="reference internal" href="#polymer-bonding-tool">polymer bonding tool</a></li>
<li><a class="reference internal" href="#pymol-asphere-tool">pymol_asphere tool</a></li>
<li><a class="reference internal" href="#python-tool">python tool</a></li>
<li><a class="reference internal" href="#reax-tool">reax tool</a></li>
<li><a class="reference internal" href="#restart2data-tool">restart2data tool</a></li>
<li><a class="reference internal" href="#vim-tool">vim tool</a></li>
<li><a class="reference internal" href="#xmgrace-tool">xmgrace tool</a></li>
<li><a class="reference internal" href="#xmovie-tool">xmovie tool</a></li>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">9. Additional tools</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#amber2lmp-tool">9.1. amber2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#binary2txt-tool">9.2. binary2txt tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#ch2lmp-tool">9.3. ch2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#chain-tool">9.4. chain tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#colvars-tools">9.5. colvars tools</a></li>
<li class="toctree-l2"><a class="reference internal" href="#createatoms-tool">9.6. createatoms tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#data2xmovie-tool">9.7. data2xmovie tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#eam-database-tool">9.8. eam database tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#eam-generate-tool">9.9. eam generate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#eff-tool">9.10. eff tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#emacs-tool">9.11. emacs tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#fep-tool">9.12. fep tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#i-pi-tool">9.13. i-pi tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#ipp-tool">9.14. ipp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#kate-tool">9.15. kate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#lmp2arc-tool">9.16. lmp2arc tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#lmp2cfg-tool">9.17. lmp2cfg tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#lmp2vmd-tool">9.18. lmp2vmd tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#matlab-tool">9.19. matlab tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#micelle2d-tool">9.20. micelle2d tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#moltemplate-tool">9.21. moltemplate tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#msi2lmp-tool">9.22. msi2lmp tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#phonon-tool">9.23. phonon tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#polymer-bonding-tool">9.24. polymer bonding tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#pymol-asphere-tool">9.25. pymol_asphere tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#python-tool">9.26. python tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#reax-tool">9.27. reax tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#restart2data-tool">9.28. restart2data tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#vim-tool">9.29. vim tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#xmgrace-tool">9.30. xmgrace tool</a></li>
<li class="toctree-l2"><a class="reference internal" href="#xmovie-tool">9.31. xmovie tool</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
@ -131,7 +144,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>Additional tools</li>
<li>9. Additional tools</li>
<li class="wy-breadcrumbs-aside">
@ -146,7 +159,7 @@
<div itemprop="articleBody">
<div class="section" id="additional-tools">
<h1>Additional tools<a class="headerlink" href="#additional-tools" title="Permalink to this headline"></a></h1>
<h1>9. Additional tools<a class="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
@ -203,7 +216,7 @@ own sub-directories with their own Makefiles.</p>
</ul>
<hr class="docutils" />
<div class="section" id="amber2lmp-tool">
<span id="amber"></span><h2>amber2lmp tool<a class="headerlink" href="#amber2lmp-tool" title="Permalink to this headline"></a></h2>
<span id="amber"></span><h2>9.1. amber2lmp tool<a class="headerlink" href="#amber2lmp-tool" title="Permalink to this headline"></a></h2>
<p>The amber2lmp sub-directory contains two Python scripts for converting
files back-and-forth between the AMBER MD code and LAMMPS. See the
README file in amber2lmp for more information.</p>
@ -216,7 +229,7 @@ necessary modifications yourself.</p>
<hr class="docutils" />
</div>
<div class="section" id="binary2txt-tool">
<span id="binary"></span><h2>binary2txt tool<a class="headerlink" href="#binary2txt-tool" title="Permalink to this headline"></a></h2>
<span id="binary"></span><h2>9.2. binary2txt tool<a class="headerlink" href="#binary2txt-tool" title="Permalink to this headline"></a></h2>
<p>The file binary2txt.cpp converts one or more binary LAMMPS dump file
into ASCII text files. The syntax for running the tool is</p>
<div class="highlight-python"><div class="highlight"><pre>binary2txt file1 file2 ...
@ -228,7 +241,7 @@ since binary files are not compatible across all platforms.</p>
<hr class="docutils" />
</div>
<div class="section" id="ch2lmp-tool">
<span id="charmm"></span><h2>ch2lmp tool<a class="headerlink" href="#ch2lmp-tool" title="Permalink to this headline"></a></h2>
<span id="charmm"></span><h2>9.3. ch2lmp tool<a class="headerlink" href="#ch2lmp-tool" title="Permalink to this headline"></a></h2>
<p>The ch2lmp sub-directory contains tools for converting files
back-and-forth between the CHARMM MD code and LAMMPS.</p>
<p>They are intended to make it easy to use CHARMM as a builder and as a
@ -241,7 +254,7 @@ and Paul Crozier (pscrozi at sandia.gov) at Sandia.</p>
<hr class="docutils" />
</div>
<div class="section" id="chain-tool">
<span id="chain"></span><h2>chain tool<a class="headerlink" href="#chain-tool" title="Permalink to this headline"></a></h2>
<span id="chain"></span><h2>9.4. chain tool<a class="headerlink" href="#chain-tool" title="Permalink to this headline"></a></h2>
<p>The file chain.f creates a LAMMPS data file containing bead-spring
polymer chains and/or monomer solvent atoms. It uses a text file
containing chain definition parameters as an input. The created
@ -257,7 +270,7 @@ system for the <a class="reference internal" href="Section_perf.html"><em>chain
<hr class="docutils" />
</div>
<div class="section" id="colvars-tools">
<span id="colvars"></span><h2>colvars tools<a class="headerlink" href="#colvars-tools" title="Permalink to this headline"></a></h2>
<span id="colvars"></span><h2>9.5. colvars tools<a class="headerlink" href="#colvars-tools" title="Permalink to this headline"></a></h2>
<p>The colvars directory contains a collection of tools for postprocessing
data produced by the colvars collective variable library.
To compile the tools, edit the makefile for your system and run &#8220;make&#8221;.</p>
@ -275,7 +288,7 @@ gmail.com) at ICTP, Italy.</p>
<hr class="docutils" />
</div>
<div class="section" id="createatoms-tool">
<span id="create"></span><h2>createatoms tool<a class="headerlink" href="#createatoms-tool" title="Permalink to this headline"></a></h2>
<span id="create"></span><h2>9.6. createatoms tool<a class="headerlink" href="#createatoms-tool" title="Permalink to this headline"></a></h2>
<p>The tools/createatoms directory contains a Fortran program called
createAtoms.f which can generate a variety of interesting crystal
structures and geometries and output the resulting list of atom
@ -285,7 +298,7 @@ coordinates in LAMMPS or other formats.</p>
<hr class="docutils" />
</div>
<div class="section" id="data2xmovie-tool">
<span id="data"></span><h2>data2xmovie tool<a class="headerlink" href="#data2xmovie-tool" title="Permalink to this headline"></a></h2>
<span id="data"></span><h2>9.7. data2xmovie tool<a class="headerlink" href="#data2xmovie-tool" title="Permalink to this headline"></a></h2>
<p>The file data2xmovie.c converts a LAMMPS data file into a snapshot
suitable for visualizing with the <a class="reference internal" href="#xmovie"><span>xmovie</span></a> tool, as if it had
been output with a dump command from LAMMPS itself. The syntax for
@ -297,7 +310,7 @@ running the tool is</p>
<hr class="docutils" />
</div>
<div class="section" id="eam-database-tool">
<span id="eamdb"></span><h2>eam database tool<a class="headerlink" href="#eam-database-tool" title="Permalink to this headline"></a></h2>
<span id="eamdb"></span><h2>9.8. eam database tool<a class="headerlink" href="#eam-database-tool" title="Permalink to this headline"></a></h2>
<p>The tools/eam_database directory contains a Fortran program that will
generate EAM alloy setfl potential files for any combination of 16
elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti,
@ -309,7 +322,7 @@ and is based on his paper:</p>
<hr class="docutils" />
</div>
<div class="section" id="eam-generate-tool">
<span id="eamgn"></span><h2>eam generate tool<a class="headerlink" href="#eam-generate-tool" title="Permalink to this headline"></a></h2>
<span id="eamgn"></span><h2>9.9. eam generate tool<a class="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 <a class="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
@ -319,7 +332,7 @@ produce are in the potentials directory, and can be used with the
<hr class="docutils" />
</div>
<div class="section" id="eff-tool">
<span id="eff"></span><h2>eff tool<a class="headerlink" href="#eff-tool" title="Permalink to this headline"></a></h2>
<span id="eff"></span><h2>9.10. eff tool<a class="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>
@ -328,7 +341,7 @@ electron force field (eFF).</p>
<hr class="docutils" />
</div>
<div class="section" id="emacs-tool">
<span id="emacs"></span><h2>emacs tool<a class="headerlink" href="#emacs-tool" title="Permalink to this headline"></a></h2>
<span id="emacs"></span><h2>9.11. emacs tool<a class="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>
@ -337,7 +350,7 @@ with various highlighting options setup.</p>
<hr class="docutils" />
</div>
<div class="section" id="fep-tool">
<span id="fep"></span><h2>fep tool<a class="headerlink" href="#fep-tool" title="Permalink to this headline"></a></h2>
<span id="fep"></span><h2>9.12. fep tool<a class="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>
@ -347,7 +360,7 @@ Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.</p>
<hr class="docutils" />
</div>
<div class="section" id="i-pi-tool">
<span id="ipi"></span><h2>i-pi tool<a class="headerlink" href="#i-pi-tool" title="Permalink to this headline"></a></h2>
<span id="ipi"></span><h2>9.13. i-pi tool<a class="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 <a class="reference internal" href="fix_ipi.html"><em>fix ipi</em></a> command to perform
@ -361,7 +374,7 @@ calculations with LAMMPS.</p>
<hr class="docutils" />
</div>
<div class="section" id="ipp-tool">
<span id="ipp"></span><h2>ipp tool<a class="headerlink" href="#ipp-tool" title="Permalink to this headline"></a></h2>
<span id="ipp"></span><h2>9.14. ipp tool<a class="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>
@ -372,7 +385,7 @@ tools/createatoms tool&#8217;s input file.</p>
<hr class="docutils" />
</div>
<div class="section" id="kate-tool">
<span id="kate"></span><h2>kate tool<a class="headerlink" href="#kate-tool" title="Permalink to this headline"></a></h2>
<span id="kate"></span><h2>9.15. kate tool<a class="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>
@ -381,7 +394,7 @@ scripts. See the README.txt file for details.</p>
<hr class="docutils" />
</div>
<div class="section" id="lmp2arc-tool">
<span id="arc"></span><h2>lmp2arc tool<a class="headerlink" href="#lmp2arc-tool" title="Permalink to this headline"></a></h2>
<span id="arc"></span><h2>9.16. lmp2arc tool<a class="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&#8217; Insight MD code (formerly
MSI/Biosym and its Discover MD code). See the README file for more
@ -394,7 +407,7 @@ Greathouse at Sandia (jagreat at sandia.gov).</p>
<hr class="docutils" />
</div>
<div class="section" id="lmp2cfg-tool">
<span id="cfg"></span><h2>lmp2cfg tool<a class="headerlink" href="#lmp2cfg-tool" title="Permalink to this headline"></a></h2>
<span id="cfg"></span><h2>9.17. lmp2cfg tool<a class="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 <a href="#id1"><span class="problematic" id="id2">*</span></a>.cfg files which can be read into the
<a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a> visualizer. See
@ -403,7 +416,7 @@ the README file for more information.</p>
<hr class="docutils" />
</div>
<div class="section" id="lmp2vmd-tool">
<span id="vmd"></span><h2>lmp2vmd tool<a class="headerlink" href="#lmp2vmd-tool" title="Permalink to this headline"></a></h2>
<span id="vmd"></span><h2>9.18. lmp2vmd tool<a class="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 <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD package</a> for visualizing LAMMPS
dump files.</p>
@ -412,7 +425,7 @@ Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.</p>
<hr class="docutils" />
</div>
<div class="section" id="matlab-tool">
<span id="matlab"></span><h2>matlab tool<a class="headerlink" href="#matlab-tool" title="Permalink to this headline"></a></h2>
<span id="matlab"></span><h2>9.19. matlab tool<a class="headerlink" href="#matlab-tool" title="Permalink to this headline"></a></h2>
<p>The matlab sub-directory contains several <span class="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
@ -425,7 +438,7 @@ visualizer.</p>
<hr class="docutils" />
</div>
<div class="section" id="micelle2d-tool">
<span id="micelle"></span><h2>micelle2d tool<a class="headerlink" href="#micelle2d-tool" title="Permalink to this headline"></a></h2>
<span id="micelle"></span><h2>9.20. micelle2d tool<a class="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
@ -441,7 +454,7 @@ definition file. This tool was used to create the system for the
<hr class="docutils" />
</div>
<div class="section" id="moltemplate-tool">
<span id="moltemplate"></span><h2>moltemplate tool<a class="headerlink" href="#moltemplate-tool" title="Permalink to this headline"></a></h2>
<span id="moltemplate"></span><h2>9.21. moltemplate tool<a class="headerlink" href="#moltemplate-tool" title="Permalink to this headline"></a></h2>
<p>The moltemplate sub-directory contains a Python-based tool for
building molecular systems based on a text-file description, and
creating LAMMPS data files that encode their molecular topology as
@ -453,7 +466,7 @@ supports it. It has its own WWW page at
<hr class="docutils" />
</div>
<div class="section" id="msi2lmp-tool">
<span id="msi"></span><h2>msi2lmp tool<a class="headerlink" href="#msi2lmp-tool" title="Permalink to this headline"></a></h2>
<span id="msi"></span><h2>9.22. msi2lmp tool<a class="headerlink" href="#msi2lmp-tool" title="Permalink to this headline"></a></h2>
<p>The msi2lmp sub-directory contains a tool for creating LAMMPS input
data files from Accelrys&#8217; Insight MD code (formerly MSI/Biosym and
its Discover MD code). See the README file for more information.</p>
@ -466,7 +479,7 @@ experiment with it yourself.</p>
<hr class="docutils" />
</div>
<div class="section" id="phonon-tool">
<span id="phonon"></span><h2>phonon tool<a class="headerlink" href="#phonon-tool" title="Permalink to this headline"></a></h2>
<span id="phonon"></span><h2>9.23. phonon tool<a class="headerlink" href="#phonon-tool" title="Permalink to this headline"></a></h2>
<p>The phonon sub-directory contains a post-processing tool useful for
analyzing the output of the <a class="reference internal" href="fix_phonon.html"><em>fix phonon</em></a> command in
the USER-PHONON package.</p>
@ -478,7 +491,7 @@ University.</p>
<hr class="docutils" />
</div>
<div class="section" id="polymer-bonding-tool">
<span id="polybond"></span><h2>polymer bonding tool<a class="headerlink" href="#polymer-bonding-tool" title="Permalink to this headline"></a></h2>
<span id="polybond"></span><h2>9.24. polymer bonding tool<a class="headerlink" href="#polymer-bonding-tool" title="Permalink to this headline"></a></h2>
<p>The polybond sub-directory contains a Python-based tool useful for
performing &#8220;programmable polymer bonding&#8221;. The Python file
lmpsdata.py provides a &#8220;Lmpsdata&#8221; class with various methods which can
@ -489,7 +502,7 @@ complex bonding topologies.</p>
<hr class="docutils" />
</div>
<div class="section" id="pymol-asphere-tool">
<span id="pymol"></span><h2>pymol_asphere tool<a class="headerlink" href="#pymol-asphere-tool" title="Permalink to this headline"></a></h2>
<span id="pymol"></span><h2>9.25. pymol_asphere tool<a class="headerlink" href="#pymol-asphere-tool" title="Permalink to this headline"></a></h2>
<p>The pymol_asphere sub-directory contains a tool for converting a
LAMMPS dump file that contains orientation info for ellipsoidal
particles into an input file for the <span class="xref std std-ref">PyMol visualization package</span>.</p>
@ -500,7 +513,7 @@ examples directory within pymol_asphere for more information.</p>
<hr class="docutils" />
</div>
<div class="section" id="python-tool">
<span id="pythontools"></span><h2>python tool<a class="headerlink" href="#python-tool" title="Permalink to this headline"></a></h2>
<span id="pythontools"></span><h2>9.26. python tool<a class="headerlink" href="#python-tool" title="Permalink to this headline"></a></h2>
<p>The python sub-directory contains several Python scripts
that perform common LAMMPS post-processing tasks, such as:</p>
<ul class="simple">
@ -515,7 +528,7 @@ README for more info on Pizza.py and how to use these scripts.</p>
<hr class="docutils" />
</div>
<div class="section" id="reax-tool">
<span id="reax"></span><h2>reax tool<a class="headerlink" href="#reax-tool" title="Permalink to this headline"></a></h2>
<span id="reax"></span><h2>9.27. reax tool<a class="headerlink" href="#reax-tool" title="Permalink to this headline"></a></h2>
<p>The reax sub-directory contains stand-alond codes that can
post-process the output of the <a class="reference internal" href="fix_reax_bonds.html"><em>fix reax/bonds</em></a>
command from a LAMMPS simulation using <a class="reference internal" href="pair_reax.html"><em>ReaxFF</em></a>. See
@ -524,7 +537,7 @@ the README.txt file for more info.</p>
<hr class="docutils" />
</div>
<div class="section" id="restart2data-tool">
<span id="restart"></span><h2>restart2data tool<a class="headerlink" href="#restart2data-tool" title="Permalink to this headline"></a></h2>
<span id="restart"></span><h2>9.28. restart2data tool<a class="headerlink" href="#restart2data-tool" title="Permalink to this headline"></a></h2>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">This tool is now obsolete and is not included in the
@ -563,7 +576,7 @@ of files are written by LAMMPS, and how the files are named.</p>
<hr class="docutils" />
</div>
<div class="section" id="vim-tool">
<span id="vim"></span><h2>vim tool<a class="headerlink" href="#vim-tool" title="Permalink to this headline"></a></h2>
<span id="vim"></span><h2>9.29. vim tool<a class="headerlink" href="#vim-tool" title="Permalink to this headline"></a></h2>
<p>The files in the tools/vim directory are add-ons to the VIM editor
that allow easier editing of LAMMPS input scripts. See the README.txt
file for details.</p>
@ -572,7 +585,7 @@ ziegenhain.com)</p>
<hr class="docutils" />
</div>
<div class="section" id="xmgrace-tool">
<span id="xmgrace"></span><h2>xmgrace tool<a class="headerlink" href="#xmgrace-tool" title="Permalink to this headline"></a></h2>
<span id="xmgrace"></span><h2>9.30. xmgrace tool<a class="headerlink" href="#xmgrace-tool" title="Permalink to this headline"></a></h2>
<p>The files in the tools/xmgrace directory can be used to plot the
thermodynamic data in LAMMPS log files via the xmgrace plotting
package. There are several tools in the directory that can be used in
@ -584,7 +597,7 @@ simulation.</p>
<hr class="docutils" />
</div>
<div class="section" id="xmovie-tool">
<span id="xmovie"></span><h2>xmovie tool<a class="headerlink" href="#xmovie-tool" title="Permalink to this headline"></a></h2>
<span id="xmovie"></span><h2>9.31. xmovie tool<a class="headerlink" href="#xmovie-tool" title="Permalink to this headline"></a></h2>
<p>The xmovie tool is an X-based visualization package that can read
LAMMPS dump files and animate them. It is in its own sub-directory
with the tools directory. You may need to modify its Makefile so that
@ -615,6 +628,15 @@ distributing his great tool!</p>
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