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# Resolved Conflicts:
#	doc/Manual.txt
#	doc/pair_reax.html
#	src/USER-PHONON/fix_phonon.cpp
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Axel Kohlmeyer
2015-12-16 07:31:09 -05:00
parent 5568b56ef2 8dff51d5c9
commit 1aeecfb0cf
558 changed files with 56688 additions and 5066 deletions
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8
doc/Manual.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>LAMMPS Documentation &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>LAMMPS Documentation &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<link rel="next" title="1. Introduction" href="Section_intro.html"/>
@ -135,7 +135,7 @@
<H1></H1><div class="section" id="lammps-documentation">
<h1>LAMMPS-ICMS Documentation<a class="headerlink" href="#lammps-documentation" title="Permalink to this headline"></a></h1>
<div class="section" id="dec-2015-version">
<h2>9 Dec 2015 version<a class="headerlink" href="#dec-2015-version" title="Permalink to this headline"></a></h2>
<h2>15 Dec 2015 version<a class="headerlink" href="#dec-2015-version" title="Permalink to this headline"></a></h2>
</div>
<div class="section" id="version-info">
<h2>Version info:<a class="headerlink" href="#version-info" title="Permalink to this headline"></a></h2>
@ -437,7 +437,7 @@ it gives quick access to documentation for all LAMMPS commands.</p>
<script type="text/javascript">
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URL_ROOT:'./',
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VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
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HAS_SOURCE: true

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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="9 Dec 2015 version">
<META NAME="docnumber" CONTENT="15 Dec 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
<H1></H1>
LAMMPS-ICMS Documentation :c,h3
9 Dec 2015 version :c,h4
15 Dec 2015 version :c,h4
Version info: :h4

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<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>5. Accelerating LAMMPS performance &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>5. Accelerating LAMMPS performance &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<link rel="next" title="6. How-to discussions" href="Section_howto.html"/>
<link rel="prev" title="4. Packages" href="Section_packages.html"/>
@ -608,7 +608,7 @@ to benchmark the performance of both packages on your system.</p>
<script type="text/javascript">
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>3. Commands &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>3. Commands &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<link rel="next" title="4. Packages" href="Section_packages.html"/>
<link rel="prev" title="2. Getting Started" href="Section_start.html"/>
@ -1502,7 +1502,7 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>12. Errors &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>12. Errors &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<link rel="next" title="13. Future and history" href="Section_history.html"/>
<link rel="prev" title="11. Python interface to LAMMPS" href="Section_python.html"/>
@ -6344,7 +6344,7 @@ infinity.</dd>
<script type="text/javascript">
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>7. Example problems &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>7. Example problems &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<link rel="next" title="8. Performance &amp; scalability" href="Section_perf.html"/>
<link rel="prev" title="6. How-to discussions" href="Section_howto.html"/>
@ -367,7 +367,7 @@ packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>13. Future and history &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>13. Future and history &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<link rel="prev" title="12. Errors" href="Section_errors.html"/>
@ -279,7 +279,7 @@ internally. A brief listing of their features is given here.</p>
<script type="text/javascript">
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>6. How-to discussions &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>6. How-to discussions &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<link rel="next" title="7. Example problems" href="Section_example.html"/>
<link rel="prev" title="5. Accelerating LAMMPS performance" href="Section_accelerate.html"/>
@ -363,8 +363,8 @@ commands like <a class="reference internal" href="pair_coeff.html"><em>pair_coef
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>. See <a class="reference internal" href="Section_tools.html"><em>Section_tools</em></a>
for additional tools that can use CHARMM or AMBER to assign force
field coefficients and convert their output into LAMMPS input.</p>
<p>See <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
field. See <a class="reference internal" href="special_bonds.html#cornell"><span>(Cornell)</span></a> for a description of the AMBER force
<p>See <a class="reference internal" href="pair_charmm.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
field. See <a class="reference internal" href="dihedral_charmm.html#cornell"><span>(Cornell)</span></a> for a description of the AMBER force
field.</p>
<p>These style choices compute force field formulas that are consistent
with common options in CHARMM or AMBER. See each command&#8217;s
@ -389,7 +389,7 @@ atoms involved in the bond, angle, or torsion terms. DREIDING has an
<a class="reference internal" href="pair_hbond_dreiding.html"><em>explicit hydrogen bond term</em></a> to describe
interactions involving a hydrogen atom on very electronegative atoms
(N, O, F).</p>
<p>See <a class="reference internal" href="special_bonds.html#mayo"><span>(Mayo)</span></a> for a description of the DREIDING force field</p>
<p>See <a class="reference internal" href="pair_hbond_dreiding.html#mayo"><span>(Mayo)</span></a> for a description of the DREIDING force field</p>
<p>These style choices compute force field formulas that are consistent
with the DREIDING force field. See each command&#8217;s
documentation for the formula it computes.</p>
@ -587,7 +587,7 @@ computations between frozen atoms by using this command:</p>
<div class="section" id="tip3p-water-model">
<span id="howto-7"></span><h2>6.7. TIP3P water model<a class="headerlink" href="#tip3p-water-model" title="Permalink to this headline"></a></h2>
<p>The TIP3P water model as implemented in CHARMM
<a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> specifies a 3-site rigid water molecule with
<a class="reference internal" href="pair_charmm.html#mackerell"><span>(MacKerell)</span></a> specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
@ -766,7 +766,7 @@ the partial charge assignemnts change:</p>
<div class="line">H charge = 0.4238</div>
<div class="line"><br /></div>
</div>
<p>See the <a class="reference internal" href="fix_temp_berendsen.html#berendsen"><span>(Berendsen)</span></a> reference for more details on both
<p>See the <a class="reference internal" href="#berendsen"><span>(Berendsen)</span></a> reference for more details on both
the SPC and SPC/E models.</p>
<p>Wikipedia also has a nice article on <a class="reference external" href="http://en.wikipedia.org/wiki/Water_model">water models</a>.</p>
<hr class="docutils" />
@ -2749,7 +2749,7 @@ fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector
model, representes induced dipoles by a pair of charges (the core atom
and the Drude particle) connected by a harmonic spring. The Drude
model has a number of features aimed at its use in molecular systems
(<a class="reference internal" href="tutorial_drude.html#lamoureux"><span>Lamoureux and Roux</span></a>):</p>
(<a class="reference internal" href="#lamoureux"><span>Lamoureux and Roux</span></a>):</p>
<ul class="simple">
<li>Thermostating of the additional degrees of freedom associated with the
induced dipoles at very low temperature, in terms of the reduced
@ -2856,7 +2856,7 @@ Phys, 79, 926 (1983).</p>
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>1. Introduction &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>1. Introduction &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<link rel="next" title="2. Getting Started" href="Section_start.html"/>
<link rel="prev" title="LAMMPS Documentation" href="Manual.html"/>
@ -661,7 +661,7 @@ version of LAMMPS were the following:</p>
<script type="text/javascript">
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>10. Modifying &amp; extending LAMMPS &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>10. Modifying &amp; extending LAMMPS &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<link rel="next" title="11. Python interface to LAMMPS" href="Section_python.html"/>
<link rel="prev" title="9. Additional tools" href="Section_tools.html"/>
@ -1220,7 +1220,7 @@ feature.</p>
<script type="text/javascript">
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6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>4. Packages &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>4. Packages &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<link rel="next" title="5. Accelerating LAMMPS performance" href="Section_accelerate.html"/>
<link rel="prev" title="3. Commands" href="Section_commands.html"/>
@ -1557,7 +1557,7 @@ you have questions.</p>
<script type="text/javascript">
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6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>8. Performance &amp; scalability &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>8. Performance &amp; scalability &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<link rel="next" title="9. Additional tools" href="Section_tools.html"/>
<link rel="prev" title="7. Example problems" href="Section_example.html"/>
@ -270,7 +270,7 @@ on 1500 processors that ran at 85% parallel efficiency.</p>
<script type="text/javascript">
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>11. Python interface to LAMMPS &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>11. Python interface to LAMMPS &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<link rel="next" title="12. Errors" href="Section_errors.html"/>
<link rel="prev" title="10. Modifying &amp; extending LAMMPS" href="Section_modify.html"/>
@ -1016,7 +1016,7 @@ different visualization package options. Click to see larger images:</p>
<script type="text/javascript">
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>2. Getting Started &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>2. Getting Started &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<link rel="next" title="3. Commands" href="Section_commands.html"/>
<link rel="prev" title="1. Introduction" href="Section_intro.html"/>
@ -1955,7 +1955,7 @@ close if you have setup the problem for both codes the same.</p>
<script type="text/javascript">
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6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>9. Additional tools &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>9. Additional tools &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 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"/>
@ -673,7 +673,7 @@ distributing his great tool!</p>
<script type="text/javascript">
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6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>5.USER-CUDA package &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>5.USER-CUDA package &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -338,7 +338,7 @@ occurs, the faster your simulation will run.</li>
<script type="text/javascript">
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>5.GPU package &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>5.GPU package &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -367,7 +367,7 @@ storage by a single MPI process.</li>
<script type="text/javascript">
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6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>5.USER-INTEL package &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>5.USER-INTEL package &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -428,7 +428,7 @@ supported.</p>
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>5.KOKKOS package &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>5.KOKKOS package &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -586,7 +586,7 @@ change in the future.</p>
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>5.USER-OMP package &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>5.USER-OMP package &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -303,7 +303,7 @@ MPI tasks to a (multi-core) socket, should solve this issue.</li>
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>5.OPT package &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>5.OPT package &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -205,7 +205,7 @@ of a run. On most machines for reasonable problem sizes, it will be a
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style charmm command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>angle_style charmm command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -152,7 +152,7 @@ angle_coeff 1 300.0 107.0 50.0 3.0
<p>with an additional Urey_Bradley term based on the distance <em>r</em> between
the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are
coefficients defined for each angle type.</p>
<p>See <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
<p>See <a class="reference internal" href="pair_charmm.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
field.</p>
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in
@ -230,7 +230,7 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style class2 command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>angle_style class2 command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -151,7 +151,7 @@ angle_coeff * ba 3.6551 24.895 1.0119 1.5228
<p>where Ea is the angle term, Ebb is a bond-bond term, and Eba is a
bond-angle term. Theta0 is the equilibrium angle and r1 and r2 are
the equilibrium bond lengths.</p>
<p>See <a class="reference internal" href="pair_modify.html#sun"><span>(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
<p>See <a class="reference internal" href="pair_class2.html#sun"><span>(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
<p>Coefficients for the Ea, Ebb, and Eba formulas must be defined for
each angle type via the <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in
the example above, or in the data file or restart files read by the
@ -257,7 +257,7 @@ for more info on packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_coeff command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>angle_coeff command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -245,7 +245,7 @@ set, either in the input script or in a data file.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style cosine command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>angle_style cosine command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -215,7 +215,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style cosine/delta command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>angle_style cosine/delta command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -219,7 +219,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style cosine/periodic command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>angle_style cosine/periodic command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -151,7 +151,7 @@ used for an octahedral complex and <em>n</em> = 3 might be used for a
trigonal center:</p>
<img alt="_images/angle_cosine_periodic.jpg" class="align-center" src="_images/angle_cosine_periodic.jpg" />
<p>where C, B and n are coefficients defined for each angle type.</p>
<p>See <a class="reference internal" href="special_bonds.html#mayo"><span>(Mayo)</span></a> for a description of the DREIDING force field</p>
<p>See <a class="reference internal" href="pair_hbond_dreiding.html#mayo"><span>(Mayo)</span></a> for a description of the DREIDING force field</p>
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
@ -229,7 +229,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style cosine/shift command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>angle_style cosine/shift command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -220,7 +220,7 @@ section for more info on packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/angle_cosine_shift_exp.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style cosine/shift/exp command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>angle_style cosine/shift/exp command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -231,7 +231,7 @@ section for more info on packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style cosine/squared command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>angle_style cosine/squared command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -219,7 +219,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/angle_dipole.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style dipole command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>angle_style dipole command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -258,7 +258,7 @@ Clarendon Press, Oxford, 1987.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style fourier command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>angle_style fourier command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -216,7 +216,7 @@ section for more info on packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/angle_fourier_simple.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style fourier/simple command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>angle_style fourier/simple command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -215,7 +215,7 @@ section for more info on packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/angle_harmonic.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style harmonic command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>angle_style harmonic command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -224,7 +224,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/angle_hybrid.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style hybrid command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>angle_style hybrid command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -240,7 +240,7 @@ file, you need to re-specify angle_coeff commands.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/angle_none.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style none command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>angle_style none command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -184,7 +184,7 @@ if triplets of angle atoms were listed in the data file read by the
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/angle_quartic.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style quartic command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>angle_style quartic command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -222,7 +222,7 @@ section for more info on packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/angle_sdk.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style sdk command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>angle_style sdk command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -208,7 +208,7 @@ USER-CG-CMM package. See the <a class="reference internal" href="Section_start.
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/angle_style.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>angle_style command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -243,7 +243,7 @@ package.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/angle_table.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style table command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>angle_style table command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -293,7 +293,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/atom_modify.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>atom_modify command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>atom_modify command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -309,7 +309,7 @@ cutoff will be used to set the bin size.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/atom_style.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>atom_style command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>atom_style command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -448,7 +448,7 @@ only enabled if LAMMPS was built with that package. See the <a class="reference
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/balance.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>balance command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>balance command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -508,7 +508,7 @@ appear in <em>dimstr</em> for the <em>shift</em> style.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

110
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Body particles &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>Body particles &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -140,17 +140,10 @@ particle types.</p>
command. It takes a body style as an argument. The current body
styles supported by LAMMPS are as follows. The name in the first
column is used as the <em>bstyle</em> argument for the <a class="reference internal" href="atom_style.html"><em>atom_style body</em></a> command.</p>
<table border="1" class="docutils">
<colgroup>
<col width="28%" />
<col width="72%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><em>nparticle</em></td>
<td>rigid body with N sub-particles</td>
</tr>
</tbody>
</table>
<p><em>rounded/polygon</em> |
+&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8211;+&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;+
| 2d convex polygon with N vertices | |
+&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8211;+&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;+</p>
<p>The body style determines what attributes are stored for each body and
thus how they can be used to compute pairwise body/body or
bond/non-body (point particle) interactions. More details of each
@ -203,11 +196,23 @@ particles of different styles</p>
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="fix_nve_body.html"><em>fix nve/body</em></a></td>
<td>integrate motion of a body particle</td>
<td>integrate motion of a body particle in NVE ensemble</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_body_local.html"><em>compute body/local</em></a></td>
<tr class="row-even"><td><a class="reference internal" href="fix_nvt_body.html"><em>fix nvt/body</em></a></td>
<td>ditto for NVT ensemble</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_npt_body.html"><em>fix npt/body</em></a></td>
<td>ditto for NPT ensemble</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_nph_body.html"><em>fix nph/body</em></a></td>
<td>ditto for NPH ensemble</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="compute_body_local.html"><em>compute body/local</em></a></td>
<td>store sub-particle attributes of a body particle</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="compute_temp_body.html"><em>compute temp/body</em></a></td>
<td>compute temperature of body particles</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="dump.html"><em>dump local</em></a></td>
<td>output sub-particle attributes of a body particle</td>
</tr>
@ -269,7 +274,78 @@ sub-particles in a body particle. The datum has 3 values:</p>
<p>These values are the current position of the sub-particle within the
simulation domain, not a displacement from the center-of-mass (COM) of
the body particle itself. These values are calculated using the
current COM and orientiation of the body particle.</p>
current COM and orientation of the body particle.</p>
<hr class="docutils" />
<p><strong>Specifics of body style rounded/polygon:</strong></p>
<p>The <em>rounded/polygon</em> body style represents body particles as a convex
polygon with a variable number N &gt; 2 of vertices, which can only be
used for 2d models. One example use of this body style is for 2d
discrete element models, as described in <a class="reference internal" href="pair_body_rounded_polygon.html#fraige"><span>Fraige</span></a>. Similar to
body style <em>nparticle</em>, the atom_style body command for this body
style takes two additional arguments:</p>
<div class="highlight-python"><div class="highlight"><pre>atom_style body rounded/polygon Nmin Nmax
Nmin = minimum # of vertices in any body in the system
Nmax = maximum # of vertices in any body in the system
</pre></div>
</div>
<p>The Nmin and Nmax arguments are used to bound the size of data
structures used internally by each particle.</p>
<p>When the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command reads a data file for this
body style, the following information must be provided for each entry
in the <em>Bodies</em> section of the data file:</p>
<div class="highlight-python"><div class="highlight"><pre>atom-ID 1 M
N
ixx iyy izz ixy ixz iyz x1 y1 z1 ...
...
... xN yN zN i j j k ...
</pre></div>
</div>
<p>N is the number of vertices in the body particle. M = 6 + 3*N + 2*N +
1. The integer line has a single value N. The floating point line(s)
list 6 moments of inertia followed by the coordinates of the N
vertices (x1 to zN) as 3N values on as many lines as required. Note
that this in not N lines, but 10 values per line; see the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command for details. The next 2N elements
are the vertex indices corresponding to the ends of the N edges. The
vertex indices (i, j, k, ...) range from 0 to (N-1), consistent with
the order of the vertices listed. The last element is the radius of
the smallest circle encompassing the polygon, which is used to
facilitate the body/body contact detection.</p>
<p>The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
values consistent with the current orientation of the rigid body
around its center of mass. The values are with respect to the
simulation box XYZ axes, not with respect to the prinicpal axes of the
rigid body itself. LAMMPS performs the latter calculation internally.
The coordinates of each vertex are specified as its x,y,z displacement
from the center-of-mass of the body particle. The center-of-mass
position of the particle is specified by the x,y,z values in the
<em>Atoms</em> section of the data file.</p>
<p>For example, the following information would specify a square
particles whose edge length is sqrt(2):</p>
<div class="highlight-python"><div class="highlight"><pre>3 1 27
4
1 1 4 0 0 0 -0.7071 -0.7071 0 -0.7071
0.7071 0 0.7071 0.7071 0 0.7071 -0.7071 0 0 1
1 2 2 3 3 0 1.0
</pre></div>
</div>
<p>The <a class="reference internal" href="pair_body_rounded_polygon.html"><em>pair_style body/rounded/polygon</em></a> command
can be used with this body style to compute body/body interactions.</p>
<p>For output purposes via the <a class="reference internal" href="compute_body_local.html"><em>compute body/local</em></a> and <a class="reference internal" href="dump.html"><em>dump local</em></a>
commands, this body style produces one datum for each of the N
sub-particles in a body particle. The datum has 3 values:</p>
<div class="highlight-python"><div class="highlight"><pre>1 = x position of vertex
2 = y position of vertex
3 = z position of vertex
</pre></div>
</div>
<p>These values are the current position of the vertex within the
simulation domain, not a displacement from the center-of-mass (COM) of
the body particle itself. These values are calculated using the
current COM and orientation of the body particle.</p>
<hr class="docutils" />
<p id="fraige"><strong>(Fraige)</strong> F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds,
Particuology, 6, 455 (2008).</p>
</div>
@ -303,7 +379,7 @@ current COM and orientiation of the body particle.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

93
doc/body.txt
View File

@ -27,7 +27,8 @@ styles supported by LAMMPS are as follows. The name in the first
column is used as the {bstyle} argument for the "atom_style
body"_atom_style.html command.
{nparticle} | rigid body with N sub-particles :tb(c=2,s=|)
{nparticle} | rigid body with N sub-particles
{rounded/polygon} | 2d convex polygon with N vertices :tb(c=2,s=|)
The body style determines what attributes are stored for each body and
thus how they can be used to compute pairwise body/body or
@ -83,8 +84,12 @@ sufaces that inter-penetrate.
These are additional LAMMPS commands that can be used with body
particles of different styles
"fix nve/body"_fix_nve_body.html : integrate motion of a body particle
"fix nve/body"_fix_nve_body.html : integrate motion of a body particle in NVE ensemble
"fix nvt/body"_fix_nvt_body.html : ditto for NVT ensemble
"fix npt/body"_fix_npt_body.html : ditto for NPT ensemble
"fix nph/body"_fix_nph_body.html : ditto for NPH ensemble
"compute body/local"_compute_body_local.html : store sub-particle attributes of a body particle
"compute temp/body"_compute_temp_body.html : compute temperature of body particles
"dump local"_dump.html : output sub-particle attributes of a body particle :tb(s=:)
The pair styles defined for use with specific body styles are listed
@ -151,4 +156,86 @@ sub-particles in a body particle. The datum has 3 values:
These values are the current position of the sub-particle within the
simulation domain, not a displacement from the center-of-mass (COM) of
the body particle itself. These values are calculated using the
current COM and orientiation of the body particle.
current COM and orientation of the body particle.
:line
[Specifics of body style rounded/polygon:]
The {rounded/polygon} body style represents body particles as a convex
polygon with a variable number N > 2 of vertices, which can only be
used for 2d models. One example use of this body style is for 2d
discrete element models, as described in "Fraige"_#Fraige. Similar to
body style {nparticle}, the atom_style body command for this body
style takes two additional arguments:
atom_style body rounded/polygon Nmin Nmax
Nmin = minimum # of vertices in any body in the system
Nmax = maximum # of vertices in any body in the system :pre
The Nmin and Nmax arguments are used to bound the size of data
structures used internally by each particle.
When the "read_data"_read_data.html command reads a data file for this
body style, the following information must be provided for each entry
in the {Bodies} section of the data file:
atom-ID 1 M
N
ixx iyy izz ixy ixz iyz x1 y1 z1 ...
...
... xN yN zN i j j k ... :pre
N is the number of vertices in the body particle. M = 6 + 3*N + 2*N +
1. The integer line has a single value N. The floating point line(s)
list 6 moments of inertia followed by the coordinates of the N
vertices (x1 to zN) as 3N values on as many lines as required. Note
that this in not N lines, but 10 values per line; see the
"read_data"_read_data.html command for details. The next 2N elements
are the vertex indices corresponding to the ends of the N edges. The
vertex indices (i, j, k, ...) range from 0 to (N-1), consistent with
the order of the vertices listed. The last element is the radius of
the smallest circle encompassing the polygon, which is used to
facilitate the body/body contact detection.
The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
values consistent with the current orientation of the rigid body
around its center of mass. The values are with respect to the
simulation box XYZ axes, not with respect to the prinicpal axes of the
rigid body itself. LAMMPS performs the latter calculation internally.
The coordinates of each vertex are specified as its x,y,z displacement
from the center-of-mass of the body particle. The center-of-mass
position of the particle is specified by the x,y,z values in the
{Atoms} section of the data file.
For example, the following information would specify a square
particles whose edge length is sqrt(2):
3 1 27
4
1 1 4 0 0 0 -0.7071 -0.7071 0 -0.7071
0.7071 0 0.7071 0.7071 0 0.7071 -0.7071 0 0 1
1 2 2 3 3 0 1.0 :pre
The "pair_style body/rounded/polygon"_pair_body_rounded_polygon.html command
can be used with this body style to compute body/body interactions.
For output purposes via the "compute
body/local"_compute_body_local.html and "dump local"_dump.html
commands, this body style produces one datum for each of the N
sub-particles in a body particle. The datum has 3 values:
1 = x position of vertex
2 = y position of vertex
3 = z position of vertex :pre
These values are the current position of the vertex within the
simulation domain, not a displacement from the center-of-mass (COM) of
the body particle itself. These values are calculated using the
current COM and orientation of the body particle.
:line
:link(Fraige)
[(Fraige)] F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds,
Particuology, 6, 455 (2008).

8
doc/bond_class2.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style class2 command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>bond_style class2 command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -147,7 +147,7 @@ bond_coeff 1 1.0 100.0 80.0 80.0
<p>The <em>class2</em> bond style uses the potential</p>
<img alt="_images/bond_class2.jpg" class="align-center" src="_images/bond_class2.jpg" />
<p>where r0 is the equilibrium bond distance.</p>
<p>See <a class="reference internal" href="pair_modify.html#sun"><span>(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
<p>See <a class="reference internal" href="pair_class2.html#sun"><span>(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
<p>The following coefficients must be defined for each bond type via the
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
@ -222,7 +222,7 @@ for more info on packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/bond_coeff.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_coeff command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>bond_coeff command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -242,7 +242,7 @@ either in the input script or in a data file.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/bond_fene.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style fene command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>bond_style fene command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -150,7 +150,7 @@ bond_coeff 1 30.0 1.5 1.0 1.0
<p>The <em>fene</em> bond style uses the potential</p>
<img alt="_images/bond_fene.jpg" class="align-center" src="_images/bond_fene.jpg" />
<p>to define a finite extensible nonlinear elastic (FENE) potential
<a class="reference internal" href="special_bonds.html#kremer"><span>(Kremer)</span></a>, used for bead-spring polymer models. The first
<a class="reference internal" href="bond_fene_expand.html#kremer"><span>(Kremer)</span></a>, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive. The
first term extends to R0, the maximum extent of the bond. The 2nd
term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential.</p>
@ -230,7 +230,7 @@ style. LAMMPS will issue a warning it that&#8217;s not the case.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/bond_fene_expand.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style fene/expand command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>bond_style fene/expand command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -147,7 +147,7 @@ bond_coeff 1 30.0 1.5 1.0 1.0 0.5
<p>The <em>fene/expand</em> bond style uses the potential</p>
<img alt="_images/bond_fene_expand.jpg" class="align-center" src="_images/bond_fene_expand.jpg" />
<p>to define a finite extensible nonlinear elastic (FENE) potential
<a class="reference internal" href="special_bonds.html#kremer"><span>(Kremer)</span></a>, used for bead-spring polymer models. The first
<a class="reference internal" href="#kremer"><span>(Kremer)</span></a>, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive.</p>
<p>The <em>fene/expand</em> bond style is similar to <em>fene</em> except that an extra
shift factor of delta (positive or negative) is added to <em>r</em> to
@ -231,7 +231,7 @@ style. LAMMPS will issue a warning it that&#8217;s not the case.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/bond_harmonic.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style harmonic command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>bond_style harmonic command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -220,7 +220,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/bond_harmonic_shift.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style harmonic/shift command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>bond_style harmonic/shift command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -222,7 +222,7 @@ section for more info on packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/bond_harmonic_shift_cut.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style harmonic/shift/cut command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>bond_style harmonic/shift/cut command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -223,7 +223,7 @@ section for more info on packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/bond_hybrid.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style hybrid command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>bond_style hybrid command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -223,7 +223,7 @@ file, you need to re-specify bond_coeff commands.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/bond_morse.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style morse command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>bond_style morse command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -218,7 +218,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/bond_none.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style none command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>bond_style none command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -184,7 +184,7 @@ pairs of bonded atoms were listed in the data file read by the
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/bond_nonlinear.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style nonlinear command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>bond_style nonlinear command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -220,7 +220,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/bond_quartic.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style quartic command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>bond_style quartic command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -252,7 +252,7 @@ dihedral, etc) cannot be used with <em>quartic</em> bonds.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/bond_style.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>bond_style command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -251,7 +251,7 @@ package.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/bond_table.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style table command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>bond_style table command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -290,7 +290,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>boundary command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>boundary command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -248,7 +248,7 @@ of lost atoms.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>box command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>box command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -212,7 +212,7 @@ error.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>change_box command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>change_box command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -466,7 +466,7 @@ change_box command is issued, so long as an <a class="reference internal" href="
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>clear command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>clear command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -192,7 +192,7 @@ input script variables (<a class="reference internal" href="variable.html"><em>v
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>comm_modify command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>comm_modify command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -307,7 +307,7 @@ cutoff = pairwise force cutoff + neighbor skin.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/comm_style.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>comm_style command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>comm_style command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -217,7 +217,7 @@ commands. The decomposition can be changed via the
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -395,7 +395,7 @@ section of <a class="reference internal" href="Section_commands.html#cmd-5"><spa
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute ackland/atom command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute ackland/atom command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -218,7 +218,7 @@ integers defined above.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute angle/local command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute angle/local command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -226,7 +226,7 @@ be in energy <a class="reference internal" href="units.html"><em>units</em></a>.
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute angmom/chunk command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute angmom/chunk command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -236,7 +236,7 @@ mass-velocity-distance <a class="reference internal" href="units.html"><em>units
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute basal/atom command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute basal/atom command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -216,7 +216,7 @@ well-defined basal plane.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute body/local command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute body/local command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -238,7 +238,7 @@ options.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute bond/local command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute bond/local command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -234,7 +234,7 @@ output for <em>eng</em> will be in energy <a class="reference internal" href="un
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute centro/atom command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute centro/atom command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -263,7 +263,7 @@ of 12.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

55
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute chunk/atom command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute chunk/atom command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -149,17 +149,17 @@ style = <em>bin/1d</em> or <em>bin/2d</em> or <em>bin/3d</em> or <em>bin/sphere<
dim = <em>x</em> or <em>y</em> or <em>z</em>
origin = <em>lower</em> or <em>center</em> or <em>upper</em> or coordinate value (distance units)
delta = thickness of spatial bins in dim (distance units)
<em>bin/sphere</em> args = xorig yorig zorig rmin rmax nrbin
<em>bin/sphere</em> args = xorig yorig zorig rmin rmax nsbin
xorig,yorig,zorig = center point of sphere
srmin,srmax = bin from sphere radius rmin to rmax
nsbin = # of bins between rmin and rmax
<em>bin/cylinder</em> args = dim origin delta c1 c2 rmin rmax nrbin
nsbin = # of spherical shell bins between rmin and rmax
<em>bin/cylinder</em> args = dim origin delta c1 c2 rmin rmax ncbin
dim = <em>x</em> or <em>y</em> or <em>z</em> = axis of cylinder axis
origin = <em>lower</em> or <em>center</em> or <em>upper</em> or coordinate value (distance units)
delta = thickness of spatial bins in dim (distance units)
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
crmin,crmax = bin from cylinder radius rmin to rmax (distance units)
ncbin = # of bins between rmin and rmax
ncbin = # of concentric circle bins between rmin and rmax
<em>type</em> args = none
<em>molecule</em> args = none
<em>compute/fix/variable</em> = c_ID, c_ID[I], f_ID, f_ID[I], v_name with no args
@ -288,9 +288,9 @@ box and an <em>origin</em> of 1.0 means to start layers at the upper &#8220;b&#8
cross &#8220;c&#8221; face of the box. A <em>delta</em> value of 0.1 in <em>reduced</em> units
means there will be 10 layers from 0.0 to 1.0, regardless of the
current size or shape of the simulation box.</p>
<p>The <em>bin/sphere</em> style defines a set of spherical shells around the
origin (<em>xorig</em>,*yorig*,*zorig*), using <em>nsbin</em> shells with radii
equally spaced between <em>srmin</em> and <em>srmax</em>, for effectively a 1d
<p>The <em>bin/sphere</em> style defines a set of spherical shell bins around
the origin (<em>xorig</em>,*yorig*,*zorig*), using <em>nsbin</em> bins with radii
equally spaced between <em>srmin</em> and <em>srmax</em>. This is effectively a 1d
vector of bins. For example, if <em>srmin</em> = 1.0 and <em>srmax</em> = 10.0 and
<em>nsbin</em> = 9, then the first bin spans 1.0 &lt; r &lt; 2.0, and the last bin
spans 9.0 &lt; r 10.0. The geometry of the bins is the same whether the
@ -298,29 +298,30 @@ simulation box is orthogonal or triclinic; i.e. the spherical shells
are not tilted or scaled differently in different dimensions to
transform them into ellipsoidal shells.</p>
<p>The <em>bin/cylinder</em> style defines bins for a cylinder oriented along
the axis <em>dim</em> with the axis position in the other two radial
the axis <em>dim</em> with the axis coordinates in the other two radial
dimensions at (<em>c1</em>,*c2*). For dim = x, c1/c2 = y/z; for dim = y,
c1/c2 = x/z; for dim = z, c1/c2 = x/y. These can be thought of as a
2d array of bins, each of which is a pie-shaped wedge (radial
dimensions) of finite height (along the cylinder axis). The bin size
c1/c2 = x/z; for dim = z, c1/c2 = x/y. This is effectively a 2d array
of bins. The first dimension is along the cylinder axis, the second
dimension is radially outward from the cylinder axis. The bin size
and positions along the cylinder axis are specified by the <em>origin</em>
and <em>delta</em> values, the same as for the <em>bin/1d</em>, <em>bin/2d</em>, and
<em>bin/3d</em> styles. There are <em>ncbin</em> concentric circles in the radial
direction from the cylinder axis with radii equally spaced between
<em>crmin</em> and <em>crmax</em>. For example, if <em>crmin</em> = 1.0 and <em>crmax</em> = 10.0
and <em>ncbin</em> = 9, then the first bin spans 1.0 &lt; r &lt; 2.0, and the last
bin spans 9.0 &lt; r 10.0. The geometry of the bins in the radial
dimensions is the same whether the simulation box is orthogonal or
triclinic; i.e. the circles are not tilted or scaled differently in
the two different dimensions to transform them into ellipses.</p>
<em>bin/3d</em> styles. There are <em>ncbin</em> concentric circle bins in the
radial direction from the cylinder axis with radii equally spaced
between <em>crmin</em> and <em>crmax</em>. For example, if <em>crmin</em> = 1.0 and
<em>crmax</em> = 10.0 and <em>ncbin</em> = 9, then the first bin spans 1.0 &lt; r &lt;
2.0, and the last bin spans 9.0 &lt; r 10.0. The geometry of the bins in
the radial dimensions is the same whether the simulation box is
orthogonal or triclinic; i.e. the concetric circles are not tilted or
scaled differently in the two different dimensions to transform them
into ellipses.</p>
<p>The created bins (and hence the chunk IDs) are numbered consecutively
from 1 to the number of bins = <em>Nchunk</em>. For 2d and 3d bins, the
from 1 to the number of bins = <em>Nchunk</em>. For <em>bin2d</em> and <em>bin3d</em>, the
numbering varies most rapidly in the first dimension (which could be
x, y, or z), next rapidly in the 2nd dimension, and most slowly in the
3rd dimension. For spherical 1d bins, the innermost shell is chunk 1
and the outermost shell is chunk Nchunk = <em>nsbin</em>. For cylindrical
2d bins, the numbering varies most rapidly in the dimension along the
cylinder axis and most slowly in the radial direction.</p>
3rd dimension. For <em>bin/sphere</em>, the bin with smallest radii is chunk
1 and the bni with largest radii is chunk Nchunk = <em>ncbin</em>. For
<em>bin/cylinder</em>, the numbering varies most rapidly in the dimension
along the cylinder axis and most slowly in the radial direction.</p>
<p>Each time this compute is invoked, each atom is mapped to a bin based
on its current position. Note that between reneighboring timesteps,
atoms can move outside the current simulation box. If the box is
@ -718,7 +719,7 @@ the restarted simulation begins.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

49
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@ -27,17 +27,17 @@ style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule}
dim = {x} or {y} or {z}
origin = {lower} or {center} or {upper} or coordinate value (distance units)
delta = thickness of spatial bins in dim (distance units)
{bin/sphere} args = xorig yorig zorig rmin rmax nrbin
{bin/sphere} args = xorig yorig zorig rmin rmax nsbin
xorig,yorig,zorig = center point of sphere
srmin,srmax = bin from sphere radius rmin to rmax
nsbin = # of bins between rmin and rmax
{bin/cylinder} args = dim origin delta c1 c2 rmin rmax nrbin
nsbin = # of spherical shell bins between rmin and rmax
{bin/cylinder} args = dim origin delta c1 c2 rmin rmax ncbin
dim = {x} or {y} or {z} = axis of cylinder axis
origin = {lower} or {center} or {upper} or coordinate value (distance units)
delta = thickness of spatial bins in dim (distance units)
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
crmin,crmax = bin from cylinder radius rmin to rmax (distance units)
ncbin = # of bins between rmin and rmax
ncbin = # of concentric circle bins between rmin and rmax
{type} args = none
{molecule} args = none
{compute/fix/variable} = c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name with no args
@ -183,9 +183,9 @@ cross "c" face of the box. A {delta} value of 0.1 in {reduced} units
means there will be 10 layers from 0.0 to 1.0, regardless of the
current size or shape of the simulation box.
The {bin/sphere} style defines a set of spherical shells around the
origin ({xorig},{yorig},{zorig}), using {nsbin} shells with radii
equally spaced between {srmin} and {srmax}, for effectively a 1d
The {bin/sphere} style defines a set of spherical shell bins around
the origin ({xorig},{yorig},{zorig}), using {nsbin} bins with radii
equally spaced between {srmin} and {srmax}. This is effectively a 1d
vector of bins. For example, if {srmin} = 1.0 and {srmax} = 10.0 and
{nsbin} = 9, then the first bin spans 1.0 < r < 2.0, and the last bin
spans 9.0 < r 10.0. The geometry of the bins is the same whether the
@ -194,30 +194,31 @@ are not tilted or scaled differently in different dimensions to
transform them into ellipsoidal shells.
The {bin/cylinder} style defines bins for a cylinder oriented along
the axis {dim} with the axis position in the other two radial
the axis {dim} with the axis coordinates in the other two radial
dimensions at ({c1},{c2}). For dim = x, c1/c2 = y/z; for dim = y,
c1/c2 = x/z; for dim = z, c1/c2 = x/y. These can be thought of as a
2d array of bins, each of which is a pie-shaped wedge (radial
dimensions) of finite height (along the cylinder axis). The bin size
c1/c2 = x/z; for dim = z, c1/c2 = x/y. This is effectively a 2d array
of bins. The first dimension is along the cylinder axis, the second
dimension is radially outward from the cylinder axis. The bin size
and positions along the cylinder axis are specified by the {origin}
and {delta} values, the same as for the {bin/1d}, {bin/2d}, and
{bin/3d} styles. There are {ncbin} concentric circles in the radial
direction from the cylinder axis with radii equally spaced between
{crmin} and {crmax}. For example, if {crmin} = 1.0 and {crmax} = 10.0
and {ncbin} = 9, then the first bin spans 1.0 < r < 2.0, and the last
bin spans 9.0 < r 10.0. The geometry of the bins in the radial
dimensions is the same whether the simulation box is orthogonal or
triclinic; i.e. the circles are not tilted or scaled differently in
the two different dimensions to transform them into ellipses.
{bin/3d} styles. There are {ncbin} concentric circle bins in the
radial direction from the cylinder axis with radii equally spaced
between {crmin} and {crmax}. For example, if {crmin} = 1.0 and
{crmax} = 10.0 and {ncbin} = 9, then the first bin spans 1.0 < r <
2.0, and the last bin spans 9.0 < r 10.0. The geometry of the bins in
the radial dimensions is the same whether the simulation box is
orthogonal or triclinic; i.e. the concetric circles are not tilted or
scaled differently in the two different dimensions to transform them
into ellipses.
The created bins (and hence the chunk IDs) are numbered consecutively
from 1 to the number of bins = {Nchunk}. For 2d and 3d bins, the
from 1 to the number of bins = {Nchunk}. For {bin2d} and {bin3d}, the
numbering varies most rapidly in the first dimension (which could be
x, y, or z), next rapidly in the 2nd dimension, and most slowly in the
3rd dimension. For spherical 1d bins, the innermost shell is chunk 1
and the outermost shell is chunk Nchunk = {nsbin}. For cylindrical
2d bins, the numbering varies most rapidly in the dimension along the
cylinder axis and most slowly in the radial direction.
3rd dimension. For {bin/sphere}, the bin with smallest radii is chunk
1 and the bni with largest radii is chunk Nchunk = {ncbin}. For
{bin/cylinder}, the numbering varies most rapidly in the dimension
along the cylinder axis and most slowly in the radial direction.
Each time this compute is invoked, each atom is mapped to a bin based
on its current position. Note that between reneighboring timesteps,

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute cluster/atom command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute cluster/atom command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -226,7 +226,7 @@ LAMMPS output options.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute cna/atom command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute cna/atom command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -238,7 +238,7 @@ above.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_com.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute com command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute com command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -210,7 +210,7 @@ distance <a class="reference internal" href="units.html"><em>units</em></a>.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_com_chunk.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute com/chunk command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute com/chunk command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -234,7 +234,7 @@ distance <a class="reference internal" href="units.html"><em>units</em></a>.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_contact_atom.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute contact/atom command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute contact/atom command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -203,7 +203,7 @@ above.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_coord_atom.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute coord/atom command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute coord/atom command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -242,7 +242,7 @@ explained above.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_damage_atom.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute damage/atom command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute damage/atom command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -206,7 +206,7 @@ LAMMPS was built with that package. See the <a class="reference internal" href=
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_dihedral_local.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute dihedral/local command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute dihedral/local command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -219,7 +219,7 @@ options.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_dilatation_atom.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute dilatation/atom command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute dilatation/atom command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -208,7 +208,7 @@ LAMMPS was built with that package. See the <a class="reference internal" href=
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_displace_atom.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute displace/atom command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute displace/atom command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -222,7 +222,7 @@ options.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_erotate_asphere.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute erotate/asphere command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute erotate/asphere command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -216,7 +216,7 @@ particles.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_erotate_rigid.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute erotate/rigid command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute erotate/rigid command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -208,7 +208,7 @@ LAMMPS was built with that package. See the <a class="reference internal" href=
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_erotate_sphere.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute erotate/sphere command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute erotate/sphere command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -208,7 +208,7 @@ contribute to the rotational energy.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_erotate_sphere_atom.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute erotate/sphere/atom command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute erotate/sphere/atom command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -207,7 +207,7 @@ LAMMPS output options.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_event_displace.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute event/displace command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute event/displace command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -214,7 +214,7 @@ for more info on packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_fep.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute fep command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute fep command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -413,7 +413,7 @@ Liquids, Oxford University Press (1987)</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_group_group.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute group/group command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute group/group command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -261,7 +261,7 @@ The <em>ewald</em> and <em>pppm</em> styles do.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_gyration.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute gyration command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute gyration command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -222,7 +222,7 @@ distance^2 <a class="reference internal" href="units.html"><em>units</em></a> re
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_gyration_chunk.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute gyration/chunk command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute gyration/chunk command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -253,7 +253,7 @@ represented by the formula above.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_heat_flux.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute heat/flux command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute heat/flux command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -336,7 +336,7 @@ print &quot;average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3&quot;
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
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COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_hexorder_atom.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute hexorder/atom command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute hexorder/atom command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -262,7 +262,7 @@ options.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_improper_local.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute improper/local command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute improper/local command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -219,7 +219,7 @@ options.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_inertia_chunk.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute inertia/chunk command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute inertia/chunk command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -235,7 +235,7 @@ mass*distance^2 <a class="reference internal" href="units.html"><em>units</em></
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_ke.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute ke command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute ke command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -211,7 +211,7 @@ scalar value will be in energy <a class="reference internal" href="units.html"><
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/compute_ke_atom.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute ke/atom command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute ke/atom command &mdash; LAMMPS 15 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -200,7 +200,7 @@ LAMMPS output options.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'9 Dec 2015',
VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

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