From 66b282b36d03b333911e708d56e579b7f53dc238 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Mon, 14 Mar 2016 18:41:39 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14741
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/Section_commands.txt        |   1 +
 doc/Section_modify.html         |   2 +-
 doc/Section_modify.txt          |   2 +-
 doc/Section_packages.html       |   2 +-
 doc/_sources/Manual.txt         |   4 +-
 doc/_sources/Section_modify.txt |   2 +-
 doc/_sources/compute_pair.txt   |   2 +-
 doc/compute_bond.html           | 242 ++++++++++++++++++++++++++++++++
 doc/compute_bond.txt            |  55 ++++++++
 doc/compute_pair.html           |   2 +-
 doc/compute_pair.txt            |   2 +-
 doc/genindex.html               |   8 +-
 doc/searchindex.js              |   2 +-
 13 files changed, 314 insertions(+), 12 deletions(-)
 create mode 100644 doc/compute_bond.html
 create mode 100644 doc/compute_bond.txt

diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
index f5f6992cae..e4612d66a2 100644
--- a/doc/Section_commands.txt
+++ b/doc/Section_commands.txt
@@ -671,6 +671,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 
 "angle/local"_compute_angle_local.html,
 "angmom/chunk"_compute_angmom_chunk.html,
+"bond"_compute_bond.html,
 "body/local"_compute_body_local.html,
 "bond/local"_compute_bond_local.html,
 "centro/atom"_compute_centro_atom.html,
diff --git a/doc/Section_modify.html b/doc/Section_modify.html
index 9e71715ed7..bf1479816d 100644
--- a/doc/Section_modify.html
+++ b/doc/Section_modify.html
@@ -1060,7 +1060,7 @@ then be accessed by variables) was discussed
 <p>We encourage users to submit new features to <a class="reference external" href="http://lammps.sandia.gov/authors.html">the developers</a> that they add to
 LAMMPS, especially if you think they will be of interest to other
 users.  The preferred way to do this is via GitHub.  Once you have
-prepared the content described below, see <code class="xref doc docutils literal"><span class="pre">this</span> <span class="pre">tutorial</span></code> for instructions on how to submit
+prepared the content described below, see <a class="reference internal" href="tutorial_github.html"><em>this tutorial</em></a> for instructions on how to submit
 your changes or new files.</p>
 <p>If the new features/files are broadly useful we may add them as core
 files to LAMMPS or as part of a <a class="reference internal" href="Section_start.html#start-3"><span>standard package</span></a>.  Else we will add them as a
diff --git a/doc/Section_modify.txt b/doc/Section_modify.txt
index 023484d6fb..609bf93bf1 100644
--- a/doc/Section_modify.txt
+++ b/doc/Section_modify.txt
@@ -626,7 +626,7 @@ developers"_http://lammps.sandia.gov/authors.html that they add to
 LAMMPS, especially if you think they will be of interest to other
 users.  The preferred way to do this is via GitHub.  Once you have
 prepared the content described below, see "this
-tutorial"_doc/tutorial_github.html for instructions on how to submit
+tutorial"_tutorial_github.html for instructions on how to submit
 your changes or new files.
 
 If the new features/files are broadly useful we may add them as core
diff --git a/doc/Section_packages.html b/doc/Section_packages.html
index b689191431..b406473435 100644
--- a/doc/Section_packages.html
+++ b/doc/Section_packages.html
@@ -494,7 +494,7 @@ name links to a sub-section below with more details.</p>
 <td>python</td>
 <td>lib/python</td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="#reax"><span>REAX</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="Section_tools.html#reax"><span>REAX</span></a></td>
 <td>ReaxFF potential</td>
 <td>Aidan Thompson (Sandia)</td>
 <td><a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a></td>
diff --git a/doc/_sources/Manual.txt b/doc/_sources/Manual.txt
index 20bf18c041..905e5a5f37 100644
--- a/doc/_sources/Manual.txt
+++ b/doc/_sources/Manual.txt
@@ -5,8 +5,8 @@
 LAMMPS Documentation
 ====================
 
-1 Mar 2016 version
-------------------
+10 Mar 2016 version
+-------------------
 
 Version info:
 -------------
diff --git a/doc/_sources/Section_modify.txt b/doc/_sources/Section_modify.txt
index db2c86ddb2..5f129e19d9 100644
--- a/doc/_sources/Section_modify.txt
+++ b/doc/_sources/Section_modify.txt
@@ -845,7 +845,7 @@ Submitting new features for inclusion in LAMMPS
 We encourage users to submit new features to `the developers <http://lammps.sandia.gov/authors.html>`_ that they add to
 LAMMPS, especially if you think they will be of interest to other
 users.  The preferred way to do this is via GitHub.  Once you have
-prepared the content described below, see :doc:`this tutorial <doc/tutorial_github>` for instructions on how to submit
+prepared the content described below, see :doc:`this tutorial <tutorial_github>` for instructions on how to submit
 your changes or new files.
 
 If the new features/files are broadly useful we may add them as core
diff --git a/doc/_sources/compute_pair.txt b/doc/_sources/compute_pair.txt
index b1ccb0435f..072134cf12 100644
--- a/doc/_sources/compute_pair.txt
+++ b/doc/_sources/compute_pair.txt
@@ -83,7 +83,7 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute pe <compute_pe>`
+:doc:`compute pe <compute_pe>`, :doc:`compute bond <compute_bond>`
 
 Default
 """""""
diff --git a/doc/compute_bond.html b/doc/compute_bond.html
new file mode 100644
index 0000000000..f5186279d7
--- /dev/null
+++ b/doc/compute_bond.html
@@ -0,0 +1,242 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+  <meta charset="utf-8">
+  
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  
+  <title>compute bond command &mdash; LAMMPS documentation</title>
+  
+
+  
+  
+
+  
+
+  
+  
+    
+
+  
+
+  
+  
+    <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+  
+
+  
+    <link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
+  
+
+  
+    <link rel="top" title="LAMMPS documentation" href="index.html"/> 
+
+  
+  <script src="_static/js/modernizr.min.js"></script>
+
+</head>
+
+<body class="wy-body-for-nav" role="document">
+
+  <div class="wy-grid-for-nav">
+
+    
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-nav-search">
+        
+
+        
+          <a href="Manual.html" class="icon icon-home"> LAMMPS
+        
+
+        
+        </a>
+
+        
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+
+        
+      </div>
+
+      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+        
+          
+          
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+</ul>
+
+          
+        
+      </div>
+      &nbsp;
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
+
+      
+      <nav class="wy-nav-top" role="navigation" aria-label="top navigation">
+        <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+        <a href="Manual.html">LAMMPS</a>
+      </nav>
+
+
+      
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="breadcrumbs navigation">
+  <ul class="wy-breadcrumbs">
+    <li><a href="Manual.html">Docs</a> &raquo;</li>
+      
+    <li>compute bond command</li>
+      <li class="wy-breadcrumbs-aside">
+        
+          
+            <a href="http://lammps.sandia.gov">Website</a>
+            <a href="Section_commands.html#comm">Commands</a>
+        
+      </li>
+  </ul>
+  <hr/>
+  
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+            
+  <div class="section" id="compute-bond-command">
+<span id="index-0"></span><h1>compute bond command<a class="headerlink" href="#compute-bond-command" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="syntax">
+<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID bond bstyle
+</pre></div>
+</div>
+<ul class="simple">
+<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
+<li>bond = style name of this compute command</li>
+<li>bstyle = style name of a bond style that calculates additional values</li>
+</ul>
+</div>
+<div class="section" id="examples">
+<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python"><div class="highlight"><pre>compute 1 all bond harmonic
+compute 2 all bond morse
+</pre></div>
+</div>
+</div>
+<div class="section" id="description">
+<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
+<p>Define a computation that extracts additional values calculated by a
+bond style, sums them across processors, and makes them accessible for
+output or further processing by other commands.  The group specified
+for this command is ignored.</p>
+<p>The specified <em>bstyle</em> must be a bond style used in your simulation
+either by itself or as a sub-style in a <a class="reference internal" href="bond_hybrid.html"><em>bond_style hybrid</em></a>
+command.</p>
+<p>This compute is useful when using <a class="reference internal" href="bond_hybrid.html"><em>bond_style hybrid</em></a>
+if you want to know the portion of the total energy contributed by one
+sub-style.</p>
+<p><strong>Output info:</strong></p>
+<p>This compute calculates a global scalar which is the contribution of
+the named bond style to the bond energy <em>ebond</em>.</p>
+<p>The scalar value calculated by this compute is &#8220;extensive&#8221; and will be
+in energy <a class="reference internal" href="units.html"><em>units</em></a>.</p>
+</div>
+<div class="section" id="restrictions">
+<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
+<blockquote>
+<div>none</div></blockquote>
+</div>
+<div class="section" id="related-commands">
+<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
+<p><a class="reference internal" href="compute_pe.html"><em>compute pe</em></a>, <a class="reference internal" href="compute_pair.html"><em>compute pair</em></a></p>
+</div>
+<div class="section" id="default">
+<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
+<p>The default for <em>evalue</em> is <em>ebond</em>.</p>
+</div>
+</div>
+
+
+           </div>
+          </div>
+          <footer>
+  
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &copy; Copyright 2013 Sandia Corporation.
+    </p>
+  </div>
+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+</footer>
+
+        </div>
+      </div>
+
+    </section>
+
+  </div>
+  
+
+
+  
+
+    <script type="text/javascript">
+        var DOCUMENTATION_OPTIONS = {
+            URL_ROOT:'./',
+            VERSION:'',
+            COLLAPSE_INDEX:false,
+            FILE_SUFFIX:'.html',
+            HAS_SOURCE:  true
+        };
+    </script>
+      <script type="text/javascript" src="_static/jquery.js"></script>
+      <script type="text/javascript" src="_static/underscore.js"></script>
+      <script type="text/javascript" src="_static/doctools.js"></script>
+      <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
+
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+
+  
+  
+    <script type="text/javascript" src="_static/js/theme.js"></script>
+  
+
+  
+  
+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.StickyNav.enable();
+      });
+  </script>
+   
+
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/compute_bond.txt b/doc/compute_bond.txt
new file mode 100644
index 0000000000..03ba4632f4
--- /dev/null
+++ b/doc/compute_bond.txt
@@ -0,0 +1,55 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute bond command :h3
+
+[Syntax:]
+
+compute ID group-ID bond bstyle :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+bond = style name of this compute command
+bstyle = style name of a bond style that calculates additional values :ul
+
+[Examples:]
+
+compute 1 all bond harmonic
+compute 2 all bond morse :pre
+
+[Description:]
+
+Define a computation that extracts additional values calculated by a
+bond style, sums them across processors, and makes them accessible for
+output or further processing by other commands.  The group specified
+for this command is ignored.
+
+The specified {bstyle} must be a bond style used in your simulation
+either by itself or as a sub-style in a "bond_style hybrid"_bond_hybrid.html
+command.
+
+This compute is useful when using "bond_style hybrid"_bond_hybrid.html
+if you want to know the portion of the total energy contributed by one
+sub-style.
+
+[Output info:]
+
+This compute calculates a global scalar which is the contribution of
+the named bond style to the bond energy {ebond}.
+
+The scalar value calculated by this compute is "extensive" and will be
+in energy "units"_units.html.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"compute pe"_compute_pe.html, "compute pair"_compute_pair.html
+
+[Default:]
+
+The default for {evalue} is {ebond}.
diff --git a/doc/compute_pair.html b/doc/compute_pair.html
index af88a7b42d..cf4b1b49a5 100644
--- a/doc/compute_pair.html
+++ b/doc/compute_pair.html
@@ -197,7 +197,7 @@ see the doc page for the pair style for details.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
-<p><a class="reference internal" href="compute_pe.html"><em>compute pe</em></a></p>
+<p><a class="reference internal" href="compute_pe.html"><em>compute pe</em></a>, <a class="reference internal" href="compute_bond.html"><em>compute bond</em></a></p>
 </div>
 <div class="section" id="default">
 <h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
diff --git a/doc/compute_pair.txt b/doc/compute_pair.txt
index c41d42ebf5..3124fa6de3 100644
--- a/doc/compute_pair.txt
+++ b/doc/compute_pair.txt
@@ -78,7 +78,7 @@ see the doc page for the pair style for details.
 
 [Related commands:]
 
-"compute pe"_compute_pe.html
+"compute pe"_compute_pe.html, "compute bond"_compute_bond.html
 
 [Default:]
 
diff --git a/doc/genindex.html b/doc/genindex.html
index 1a6d68f591..d5844a0055 100644
--- a/doc/genindex.html
+++ b/doc/genindex.html
@@ -372,6 +372,10 @@
   </dt>
 
       
+  <dt><a href="compute_bond.html#index-0">compute bond</a>
+  </dt>
+
+      
   <dt><a href="compute_bond_local.html#index-0">compute bond/local</a>
   </dt>
 
@@ -555,12 +559,12 @@
   <dt><a href="compute_pe_atom.html#index-0">compute pe/atom</a>
   </dt>
 
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="compute_plasticity_atom.html#index-0">compute plasticity/atom</a>
   </dt>
 
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="compute_pressure.html#index-0">compute pressure</a>
   </dt>
diff --git a/doc/searchindex.js b/doc/searchindex.js
index 02abbabece..db9ed1ff2e 100644
--- a/doc/searchindex.js
+++ b/doc/searchindex.js
@@ -1 +1 @@
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,509],adjust_dt:[],adjust_radiu:315,adjust_radius_factor:315,admiss:268,adof:[152,212],adopt:[306,502],adp:[],adri:[9,303,443,444],adust:166,advanc:[3,244,386,476,487],advantag:[1,6,8,11,14,18,40,41,42,220,380,405,490,495],advect:[3,6,323],advertis:8,advis:[375,442],afer:3,affect:[1,6,10,14,15,16,17,41,62,63,73,92,123,147,156,170,176,199,200,205,212,213,215,216,217,218,221,222,223,224,226,227,237,243,245,247,253,260,264,265,266,267,269,270,271,277,282,283,284,286,307,308,321,335,345,358,365,371,372,373,375,376,377,380,406,427,428,435,478,479,481,483,484,486,489,491],affin:[16,17,18,226,380,395],afil:241,aforement:18,afresh:[295,489,508],afshar:400,after:[2,3,5,6,11,12,15,21,22,33,40,41,42,45,51,59,60,61,63,65,73,150,151,152,153,154,155,156,159,160,161,162,164,165,172,173,175,176,179,180,185,195,196,197,198,199,200,201,203,204,205,209,210,212,213,220,221,222,223,224,226,230,239,250,251,252,253,254,259,260,261,263,269,270,271,277,282,283,284,286,289,293,297,305,307,310,319,324,326,327,328,330,331,332,333,334,338,340,342,346,349,350,356,364,370,371,373,374,376,378,379,380,381,382,386,393,395,404,405,406,407,413,414,415,426,427,428,430,431,432,433,437,441,443,444,451,452,461,462,464,465,466,469,476,478,480,481,482,483,484,486,487,489,491,493,495,498,499,502,507,508,509,510,511,512],afterrun:489,afterward:3,afterword:42,ag1:171,ag2:171,again:[6,11,12,16,17,64,146,152,158,166,196,200,226,243,293,349,364,375,427,428,476,478,479,481,483,488,495,497,508,510],against:[11,12,13,66,227,375,443,444],aggreg:[6,12,67,70,71,81,97,114,121,243,259,305,307,321,476,509],aggress:[243,495],agilio:[9,13],agre:[3,8,192,373,382,415,444],agreement:[5,7],ahd:412,ahead:342,aidan:[0,5,7,9,13,368],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:199,akohlmei:[7,9,13,201,244],aktulga:[7,9,300,444],al2o3:451,al2o3_001:[124,308],al3:171,ala:[250,451],alain:9,alat:[288,430],alb:[441,464,466],albeit:306,albert:9,alchem:[91,166],alcohol:338,alcu:[381,386],alcu_eam:441,alderton:399,alejandr:[263,264],alessandro:13,algebra:433,algorithm:[0,1,6,7,8,9,42,63,200,209,220,223,226,250,252,253,277,290,298,307,310,311,330,331,335,338,343,371,372,373,377,380,402,406,428,433,448,450,476,478,495],alia:[9,12,16],alias:[1,366],aliceblu:200,align:[6,9,12,29,42,73,174,192,216,220,245,368,481,484,502],alkali:406,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,165,166,167,168,169,170,171,172,173,174,175,176,178,180,185,191,192,193,196,197,198,199,200,201,203,204,205,206,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,256,258,259,261,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,319,320,322,323,324,325,326,327,330,331,332,333,334,335,336,337,338,340,341,342,343,344,345,346,347,348,349,350,354,359,361,363,364,365,366,367,368,370,373,374,375,376,377,379,380,381,382,383,385,386,387,389,390,391,392,393,395,396,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,422,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,472,473,475,476,478,479,480,481,482,483,484,485,486,488,489,490,491,492,493,494,495,496,498,499,500,502,503,507,508,509,510,511,512],allen:[29,91,399,409],allentildeslei:91,allign:3,allindex:347,alloc:[3,5,6,8,9,11,12,62,237,337,374,376,380,439,444,481,489],allocat:3,alloi:[],allosw:73,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,56,59,60,61,63,64,65,79,96,112,114,148,150,151,152,165,170,171,172,174,180,191,192,196,197,199,200,201,203,204,206,208,209,210,212,213,214,215,216,217,218,220,222,223,224,225,226,227,231,232,237,239,240,241,242,244,247,250,253,254,258,260,263,264,288,292,293,294,295,296,297,301,307,308,310,312,314,315,319,323,330,331,332,333,335,336,337,338,339,340,346,348,350,359,365,366,368,373,374,375,376,379,380,383,386,387,388,389,390,391,396,404,406,410,411,412,413,418,422,427,428,433,435,441,444,445,448,450,451,460,470,472,476,479,481,483,484,485,486,487,488,491,493,494,495,498,499,503,508,509],almost:[2,3,12,62,245,297,335,366,377,380,460],alo:396,alon:[6,7,223,303,443,444,479],alond:13,along:[6,8,12,29,41,73,91,124,170,171,172,195,196,199,212,223,245,250,251,255,260,262,297,307,310,312,316,320,321,330,334,335,341,344,346,368,371,372,373,375,396,399,410,413,416,418,422,430,443,444,463,481,484,491,492,508],alonso:[431,432],alpha:[6,12,52,204,250,289,297,298,302,373,381,384,387,396,400,402,404,405,407,412,417,418,430,436,440,465,467,499,502],alpha_:[],alpha_c:426,alpha_i:452,alpha_ialpha_j:[],alpha_lj:426,alphabet:[2,3,22,37,45,56,65,180,191,203,350,359,374,393,461,481],alphanumer:[3,65,203,296,304,348,374,508],alreadi:[3,7,8,9,12,16,17,18,43,172,173,175,198,208,212,216,217,220,222,226,254,295,297,323,346,347,374,375,400,411,413,420,428,460,470,473,477,481,482,486,491,508],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,40,41,42,43,45,55,56,57,60,61,63,65,68,73,74,75,77,79,83,91,93,94,96,98,108,109,110,111,112,113,118,120,122,123,125,146,147,148,149,150,151,152,153,154,155,156,158,159,160,161,162,164,165,166,167,168,169,172,173,174,175,176,178,180,191,192,194,195,196,197,198,199,200,201,203,204,205,206,208,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,232,237,238,239,240,241,243,244,247,248,249,250,260,261,263,264,265,266,267,268,269,270,271,276,279,280,282,283,284,285,286,288,289,290,292,293,294,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,316,317,320,321,323,326,327,328,329,330,334,335,336,337,339,341,344,346,347,348,350,356,359,363,365,366,368,369,370,373,374,375,376,377,379,380,386,390,391,393,397,398,399,400,404,405,406,409,410,412,413,414,422,426,427,430,433,435,437,439,440,441,442,445,446,448,455,456,458,459,461,462,463,464,465,466,467,469,476,478,479,480,481,482,483,484,485,486,488,489,490,491,493,494,495,496,499,500,501,502,503,504,506,507,508,509,510,512],alter:[3,6,8,9,11,12,42,61,149,150,151,152,153,155,158,159,160,161,164,165,172,176,196,197,199,201,204,205,212,221,222,223,224,226,262,263,302,305,307,309,317,323,331,338,345,372,375,413,481,486,488,491,508,509,512],altern:[1,6,8,9,11,12,17,18,95,172,196,203,213,226,234,244,248,263,296,307,330,331,338,351,355,365,372,373,381,382,396,401,402,404,405,407,415,418,426,430,431,432,437,441,442,452,462,464,466,469,479,481,482,494,496,499],although:[29,43,192,253,263,294,298,307,330,364,488,502,512],aluminum:473,alwai:[0,6,11,12,17,18,55,59,65,73,170,200,212,213,214,216,217,218,222,225,239,241,245,299,302,307,323,340,344,345,349,365,366,371,373,374,376,377,380,389,392,404,421,433,443,444,451,453,463,464,466,473,476,481,482,484,486,493,495,498,502,508,509],amap:200,amatrix:241,amaz:11,amazingli:13,amber2lmp:[],amber:[],ambient:199,ambigu:[3,65,203,508],amd:[17,380,433],amend:[],amino:9,amit:9,among:[16,147,210,250],amorph:[172,465],amount:[1,3,6,12,61,92,121,170,174,195,199,210,214,224,225,239,243,247,263,288,294,307,315,323,328,331,336,338,346,365,380,400,439,481,484],amplitud:[226,260,316,341,358,484,508],amu:239,amzallag:451,analag:[6,508],analalog:6,analog:[6,112,146,174,192,410],analys:[7,486],analysi:[7,9,13,65,66,75,201,303,304,313,347,433,452,481,491],analyt:[1,3,9,13,124,166,171,310,365,386,414,415,420,433,441,463],analyz:[6,8,9,13,375,433],andersen:310,anderson:[292,400],andr:[7,9,13],andrew:13,andzelm:460,ang:288,angl:[],angle1:306,angle2:306,angle_coeff:[],angle_cosineshift:27,angle_cosineshiftexp:[26,181],angle_cutof:412,angle_cutoff:412,angle_hybrid:29,angle_info:444,angle_styl:[],angle_typ:41,angleangl:[3,349,356,481],angleangletors:[3,179,481],anglecoeff:3,angletors:[3,179,185,481],angletyp:222,angmom:[],angmomi:[119,196,197,325],angmomx:[119,196,197,325],angmomz:[119,196,197,325],angstrom:[6,10,61,73,124,161,171,172,195,196,197,199,200,208,216,217,226,227,239,244,245,260,300,305,340,342,343,345,366,368,371,377,381,382,391,404,426,430,437,442,443,444,466,473,484,490,507,509],angular:[6,29,41,63,65,68,86,87,88,89,111,119,146,150,151,164,165,172,196,197,203,247,253,259,260,265,266,267,269,270,271,273,274,275,278,280,281,282,283,286,305,307,310,316,325,381,386,395,410,427,428,430,433,441,461,464,465,481,491,508,509],angularm:274,anharmon:[27,54,181,302,495],ani:[1,3,6,7,8,9,10,11,12,13,14,15,16,17,22,29,38,40,41,42,43,45,56,57,60,61,63,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,175,176,178,180,192,195,196,197,198,199,200,203,206,207,208,210,212,213,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,232,236,239,242,243,245,247,250,253,259,260,263,268,288,290,292,293,294,296,298,299,300,302,304,305,307,309,310,312,316,317,320,322,323,324,325,334,335,340,341,342,343,344,345,346,347,348,350,364,365,366,368,370,371,373,374,375,377,378,379,380,382,386,390,391,395,396,399,400,404,405,407,409,413,414,415,422,433,435,441,443,444,445,452,460,461,462,463,464,465,466,467,468,469,474,475,476,478,479,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,499,500,502,503,504,506,507,508,509,510,511,512],anihil:426,anim:[2,4,7,11,13,199,375],anion:[407,451],aniso:[3,224,226,263,264,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304,348,374,379,406,417,441,443,444,451,463,478,479,483,488,489,508,510,511,512],character:[6,69,72,112,122,146,452,476,495],characterist:[248,323,332],charg:[1,3,4,5,6,7,9,11,15,41,91,92,119,124,171,172,196,197,201,203,204,205,210,227,232,239,296,298,299,300,304,325,338,365,366,374,387,389,395,396,398,399,404,406,407,413,418,422,426,438,443,444,451,461,466,467,469,470,472,473,481,482,486,491,493,502,507,508],charmm2lammp:13,charmm:[],chartreus:200,cheap:323,cheaper:[231,409,445],check:[3,6,8,9,11,12,15,17,40,42,73,95,192,210,216,220,221,222,227,236,239,245,246,293,306,310,323,331,333,338,346,348,364,373,374,375,376,377,380,403,414,417,435,444,476,478,479,481,489,495,498,499,508],checkf:192,checkout:503,checkqeq:444,checku:192,chem:[6,13,20,21,25,40,41,44,46,47,91,92,112,118,147,178,179,189,214,225,230,240,241,248,250,262,263,264,284,285,290,294,297,299,307,311,312,323,326,327,330,331,332,333,340,349,358,360,365,366,372,375,382,387,391,392,395,396,397,399,400,402,406,408,409,411,412,418,422,423,426,430,434,435,438,451,460,467,490,493,495,502],chemic:[9,124,166,171,196,197,209,210,239,298,303,304,330,366,443,444,456],chemistri:[297,298,300,386,406,443,444],chen:335,cheng:395,chenoweth:[443,444],chenoweth_2008:[443,444],chi:[97,161,195,288,298,300,361,407,409,509],chiefli:442,child:8,chip:[7,9,12,17,18,380,494],chipot:225,chiral:358,chmod:[11,12],cho:430,chocol:[7,200],choic:[3,6,9,12,15,16,18,41,42,55,91,147,150,151,165,176,192,212,216,217,220,223,226,227,241,247,250,261,263,290,298,307,330,359,366,371,372,375,377,380,413,426,435,439,481,490,491,494,495,501,502,507],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,91,123,162,163,199,221,222,223,224,227,236,247,250,261,263,265,266,267,268,269,270,271,293,294,311,323,327,341,365,366,372,470,476,478,490,496],chose:[464,466],chosen:[2,3,6,12,17,146,172,175,184,192,199,205,210,224,227,236,239,240,248,250,261,263,268,290,293,304,323,327,330,331,336,338,339,345,366,367,372,380,401,402,406,410,417,420,446,464,476,490,495,502],chri:170,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[68,77,94,98,109,111,120,152,167,169,212],chute:[4,9,10,242],ciccotti:310,cieplak:[6,178,493],cii:213,cij:213,ciko:2,circl:[43,73,319],circular:[3,6,150,194],circumst:18,circumv:[96,112,302],citat:[],cite:[3,7,8,12,247,451],civ:9,ckio:2,cko:2,cl1:171,clarendon:[29,399],clarifi:[7,464,466],clariti:348,clark:438,class2:[],classic:[0,3,5,6,7,8,9,237,290,297,302,335,360,406],classifi:[461,469],claus:479,clean:[6,12,14,15,17,489],cleanli:[480,511],clear:[],clearli:7,clebsch:146,clermont:[9,13],clever:485,click:[2,11,22,37,45,56,172,180,191,199,244,350,359,375,393,461,503],client:[244,246],climb:[262,375,495],clinic:[7,13],clo:[161,195,509],clock:[12,476,495],clockwis:341,clone:503,close:[3,6,11,12,13,40,42,69,73,147,175,196,222,223,224,241,248,250,263,284,307,310,341,344,364,366,369,371,372,375,380,382,386,396,397,416,430,435,447,449,463,466,485,491,502,503,505],closer:[3,10,42,122,170,195,196,220,224,228,332,375],closest:[222,288,307,338,409,445,460,470],cloud:[451,502],clovertown:18,clsuter:74,clump1:[292,307],clump2:[292,307],clump3:[292,307],clump:307,cluster:[],clutter:3,cmap:481,cmatrix:241,cmax:430,cmd:[11,12,290,492],cmdarg:11,cmin:430,cmm:[],cmoput:139,cn1:213,cn2:213,cna:[],cnn:213,cnr:[9,13],cnt:[413,485],co2:[41,171,310,374],coars:[7,9,10,29,36,41,55,184,292,307,323,411,446,490,493],coarser:[366,508],coarsest:146,code:[],coeff:[3,7,8,12,21,22,33,45,51,178,179,180,185,349,350,356,393,413,417,435,448,450,453,481],coeffcient:481,coeffici:[],coefficienct:400,coefficient0:404,coefficient1:404,coeffieci:[6,384,416],coeffincientn:404,coexist:[239,406],cohes:[6,407,430],coincid:[128,344,391,427,428,476],colberg:198,cold:[6,157,239,243,376,502],coldest:331,coleman8:9,coleman:[9,124,171,308],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,68,77,87,94,98,103,109,111,120,152,160,167,169,172,196,197,200,212,225,253,259,292,302,305,307,346,365,374,376,394,481,488,494,500,512],collid:[231,323,345],colliex:171,collinear:[3,292],collis:[3,250,323,341,345,403,410,473],colllis:323,colloid:[],colombo:40,colon:[201,346,482],color1:200,color2:200,color:[3,9,42,196,199,200,220,240,297,302],column:[3,6,9,12,13,43,65,67,68,69,70,71,73,77,79,81,83,85,94,96,97,98,109,111,112,114,116,119,120,121,122,123,125,146,147,152,160,167,169,170,171,192,196,197,200,203,211,212,213,215,216,217,218,253,260,261,297,307,324,325,335,345,408,412,443,444,482,496,498,508],columnar:170,colvar:[],colvarmodul:12,com:[],comamnd:226,comand:223,comannd:380,comb3:[],comb:[],comb_1:299,comb_2:299,combiant:397,combin:[3,6,7,9,11,13,36,41,65,67,71,81,91,97,108,114,121,150,151,165,196,199,209,215,244,253,263,290,296,311,327,336,344,347,349,365,366,368,372,380,394,396,397,402,406,407,413,425,426,452,462,464,466,469,472,484,489,494,502,508],come:[],comfort:[12,13],comit:503,comm:[0,3,11,12,63,75,198,244,246,247,366,375,380,400,435,440,463,483],comm_modifi:[],comm_modift:63,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,178,192,196,235,248,307,335,374,375,381,404,405,407,417,430,437,444,451,452,462,463,464,465,466,469,478,479,481,502,503,508],commerci:7,commit:[9,503],commmand:[3,6,12,61,113,285,416,475,476,478,495,511],common:[],commonli:[3,6,9,12,17,25,59,61,110,112,174,196,199,201,360,411,420,452,464,466,481,484,493],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,60,63,64,73,170,175,176,199,200,220,221,222,224,225,226,244,246,250,252,253,254,263,289,296,298,299,300,307,311,323,335,346,363,365,376,377,378,380,402,403,439,474,478,479,490,491,508,510,512],communc:365,comp:[7,198,246,247,310,366,375,406,435,440,445,459,463,465],compact:[65,203,393,461],compani:[5,7],compar:[1,3,4,6,8,12,17,40,90,116,124,155,171,180,191,200,230,298,346,348,365,366,373,375,430,451,476,495,496,502,507],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,9,21,22,37,44,45,56,179,180,191,349,350,359,392,461],compat:[3,5,7,8,9,11,12,13,17,18,42,73,123,125,183,196,201,205,211,212,213,215,216,217,218,220,289,301,327,330,337,340,343,365,380,414,433,435,463,478,479,508],compens:[6,221,222,305,376,406],compet:334,competit:366,compil:[3,7,8,9,12,13,14,15,16,17,18,19,170,196,198,199,201,244,334,366,380,433,481,482,486,508],compl:17,complain:[11,12,17],complement:430,complementari:[7,396,418],complet:[3,6,9,11,12,15,42,61,73,200,216,220,225,253,290,293,296,323,334,336,347,348,364,375,380,407,448,450,468,476,481,486,489,493,495,498,502,508],complex:[4,6,8,11,12,13,25,41,43,64,96,112,146,148,160,172,173,250,319,344,363,375,406,433,463,479,481,484,508],compli:[330,334],complic:[6,7,9,12,13,210,239,479],complier:12,compon:[3,6,8,12,63,65,68,69,75,83,92,93,94,95,96,98,99,102,109,110,111,112,113,114,115,116,118,119,123,133,136,137,138,139,142,143,144,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,167,168,169,195,196,197,199,200,206,207,211,212,213,214,215,216,217,218,219,223,224,226,227,232,237,242,246,247,250,253,255,259,260,262,263,264,268,269,270,271,282,283,284,286,287,289,290,291,294,305,307,309,310,312,316,317,320,323,326,327,328,330,337,338,343,344,345,365,368,372,373,374,375,380,400,406,410,427,428,448,450,451,452,481,482,491,499,508,509],componenet:6,composit:[6,210,250,404],compound:[395,406,407,469],compres:[73,120,212],compress:[],compris:[41,344,445,468],compton:[124,171],comptu:3,compuat:366,comput:[],computation:[3,6,221,222,335,386],computational:502,compute_arrai:8,compute_fep:[205,426],compute_group_group:239,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[124,308],compute_scalar:8,compute_temp:8,compute_ti:205,compute_vector:8,compute_xrd:171,concaten:[2,3,511],concav:344,concentr:[73,404],concept:[6,152,162,212,490],conceptu:[3,6,73,160,224,226,375,396,413,430,486],concern:[6,75,91,198,240],concetr:73,concis:[11,334],conclud:12,concret:8,concurr:[16,366,508],conden:[335,464,466],condens:[6,154,335,382,398,404,418,469],condit:[],conducit:6,conduct:[],cone:484,confer:433,confid:[3,495],config:[12,196,478],configfil:225,configur:[1,2,6,12,15,17,38,61,128,174,192,195,196,199,203,224,225,226,227,231,239,246,247,277,290,298,334,363,373,375,382,386,405,430,433,462,464,466,469,476,481,483,484,495,503],confin:[481,495],conflict:[3,12,41,197,435,479,503],conform:[3,6,13,61,223,224,262,306,312,334,358,375,406,493],confus:[3,469],conjuct:[9,400],conjug:[7,8,247,372,406,443,444],conjunct:[6,7,73,90,91,120,155,160,166,172,176,200,204,205,247,250,254,277,293,294,298,299,300,302,307,311,323,331,338,343,365,366,375,387,389,393,396,400,406,412,418,435,438,446,467,481,484,488,502,512],connect:[3,6,9,91,157,175,223,244,292,307,310,320,375,397,410,460,466,478,479,481,485,502],conput:3,consecut:[3,11,12,40,73,172,200,204,205,227,244,245,396,418,422,476,482,484],consequ:[1,6,210,335,417,495],conserv:[],consid:[6,72,73,80,91,121,154,157,158,175,196,197,200,204,205,211,213,216,220,222,223,227,251,264,289,307,330,331,334,335,338,366,393,406,413,444,445,451,460,476,477,479,482,483,484,486,489,491,499,502,508],consider:[6,8,247,248,326,327,328,380,490],consist:[3,6,8,9,11,12,41,43,67,71,81,97,109,114,117,118,121,152,155,157,172,184,195,201,206,207,212,226,227,230,232,237,240,247,248,249,260,263,265,266,267,268,269,270,271,272,273,275,276,277,278,280,281,282,283,284,285,286,294,297,302,304,306,307,326,327,328,329,339,365,366,368,374,375,380,382,386,388,394,396,406,409,413,416,427,428,430,433,435,445,448,450,451,463,470,479,481,482,483,484,485,486,493,502,508],consistent_fe_initi:209,consit:307,constant:[],constitu:[3,6,253,307,340,344,394,445],constitut:[448,450],constrain:[3,6,8,149,150,151,152,153,155,158,159,160,161,162,164,165,203,212,227,239,240,245,253,257,292,293,305,307,310,321,331,338,373,374,406,486,493,502],constraint:[],construct:[6,8,12,14,38,55,57,63,66,69,72,74,75,79,96,112,124,146,171,224,263,289,306,344,376,380,399,433,435,460,462,463,484,485,500,508],constructor:[8,11],consult:444,consum:[1,302,439,508],consumpt:363,contact:[],contact_stiff:[447,449],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,65,91,95,122,124,146,152,160,170,171,172,174,178,180,191,192,196,197,199,200,201,203,204,205,209,211,212,213,215,216,217,218,220,225,227,232,235,241,245,246,247,250,261,277,288,289,292,293,295,297,300,304,307,308,313,323,330,334,335,344,345,348,364,366,374,375,378,379,381,382,383,386,395,396,399,404,405,406,413,414,430,433,437,441,442,443,444,452,462,463,464,465,466,467,469,476,477,478,479,481,482,483,484,486,488,490,493,495,496,498,499,502,503,508,510,512],content:[4,8,9,12,18,444,497,499],context:[3,6,8,12,17,122,123,200,221,222,227,292,304,339,372,472,481,488,497,507,508,509],contibut:72,contigu:478,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,73,83,108,109,168,200,203,204,205,210,212,213,214,215,216,217,218,220,223,224,225,226,227,239,240,241,243,244,245,247,248,249,255,260,261,263,265,266,267,268,269,270,271,282,283,284,285,286,291,293,296,297,307,308,312,322,323,325,332,333,335,341,344,348,364,379,380,386,400,403,420,423,443,444,445,448,450,465,476,479,481,483,484,489,495,496,498,499,508,510],continuum:[6,7,9,209,335,448,450],contour_integr:209,contract:[61,224,226,263,294,307],contradictori:3,contrain:310,contraint:277,contrari:[241,248],contrast:[1,6,43,56,66,154,157,197,226,346,448,450,472,511],contrib:335,contribut:[3,4,5,6,7,8,9,12,13,17,65,68,70,72,73,76,77,79,82,88,91,92,93,94,95,98,107,109,111,113,114,115,116,118,120,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,205,210,211,212,213,215,216,217,218,224,239,247,250,253,254,258,264,284,285,292,293,301,304,307,308,310,337,365,373,375,383,400,403,404,406,413,427,428,433,435,443,444,451,493,499,502,503],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,91,95,128,146,181,196,197,199,203,209,210,220,224,225,226,243,244,247,248,263,265,266,267,268,269,270,271,294,299,307,314,315,326,327,328,335,339,363,365,377,406,409,433,443,444,447,449,462,466,476,478,490,496,497],control_typ:209,controlfil:444,convect:95,conveni:[6,12,29,196,201,218,308,368,452,503,508],convent:[3,8,29,183,190,191,197,200,306,320,347,404,406,508],converg:[3,6,42,92,196,197,199,201,206,220,223,224,232,237,268,297,299,302,306,310,371,372,373,375,395,396,418,451,476,488,495],convers:[3,8,146,199,200,210,213,294,365,396,397,398,406,418,422,426,438,479,495,507],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,61,65,73,95,172,179,196,199,200,213,218,261,293,346,349,351,355,358,368,375,381,404,433,464,466,473,479,481,482,483,488,498,502,507,508,510,512],convex:[43,344],convinc:[7,12],cook:9,cooki:7,cool:[7,162,243,305],cooordin:[196,197],cooper:[5,7],coord123:120,coord1:[3,120,212,216,217],coord2:[3,120,212,216,217],coord3:[3,120,212,216,217],coord:[],coordb:451,coordbb:451,coordiat:373,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,61,63,64,65,68,70,73,76,77,79,83,91,93,94,98,108,109,111,119,120,122,140,146,155,161,167,169,170,172,176,195,196,197,198,199,200,201,203,206,211,212,215,216,217,220,221,222,223,224,225,226,227,230,232,233,237,239,242,243,244,245,246,247,248,260,262,263,265,266,267,269,270,271,284,287,288,289,292,293,294,304,305,307,309,310,312,317,320,321,322,323,325,333,334,335,342,343,345,346,368,373,374,375,380,381,382,385,405,451,476,481,482,483,484,486,489,491,495,502,508,509],coordn:[120,212],coorind:[],copi:[0,3,4,8,9,11,12,15,17,41,125,199,335,375,393,443,479,503],copper:473,coproccesor:16,coprocessor:[1,7,9,16,17,380,494],coproprocessor:17,copy_arrai:8,copyright:[7,8,292],coral:200,core:[],core_shel:154,coreshel:[],cornel:[6,178,493],corner123i:119,corner123x:119,corner123z:119,corner1i:119,corner1x:119,corner1z:119,corner2i:119,corner2x:119,corner2z:119,corner3i:119,corner3x:119,corner3z:119,corner:[3,6,41,119,199,344,345,368,468,481,503],cornflowerblu:200,cornsilk:200,corp:9,corpor:16,corr:395,correct:[3,6,9,11,12,16,17,61,91,92,107,108,113,116,122,154,159,166,197,199,226,239,241,247,263,264,284,292,294,297,334,340,344,365,375,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,471,472,473,474,481,496,499,502,503],correction_max_iter:209,correctli:[3,8,11,17,73,83,107,108,109,149,150,151,153,155,157,158,159,160,161,164,165,168,196,200,206,227,232,237,248,257,263,264,300,307,310,320,322,341,344,375,376,380,398,428,433,478,479,481,491,503,507,509],correl:[],correpond:235,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,72,73,91,101,102,115,118,119,120,121,124,125,133,136,137,138,139,140,142,143,144,146,149,150,159,166,170,171,178,179,180,181,182,183,184,186,187,189,190,192,195,196,197,199,200,204,205,206,212,214,215,216,217,219,222,224,226,233,237,238,242,247,250,251,259,260,261,263,265,266,267,268,269,270,271,272,273,277,280,282,283,284,286,289,290,294,299,307,309,310,326,328,330,339,340,341,343,344,345,347,349,350,351,352,354,355,358,360,366,370,372,374,375,381,382,384,387,388,389,390,391,392,393,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,416,418,419,420,421,422,423,424,425,426,427,430,431,433,435,436,437,438,440,441,443,444,445,446,451,452,453,462,463,464,465,466,469,471,472,473,476,478,479,481,482,484,494,495,496,498,499,502,508],correspondingli:[427,428,490],corrupt:3,cosin:[],cosineshift:27,cosmo:[241,246],cossq:[],cost:[1,6,10,11,12,17,40,42,73,115,124,147,171,199,200,212,216,217,220,221,222,236,263,299,335,365,366,378,396,418,422,433,435,462,478,490],costheta0:[462,464,466,469],costheta:441,costli:[11,92,241,376],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,61,68,73,77,91,94,98,109,111,115,118,120,152,162,167,169,185,196,197,199,200,204,205,212,213,216,220,226,237,246,296,297,298,302,305,307,309,323,324,330,334,335,336,340,344,346,348,356,362,364,371,373,376,380,383,408,412,413,416,443,444,477,478,479,481,483,485,488,489,496,497,502,508,509],coulomb:[3,5,6,7,8,9,10,12,14,15,18,74,92,113,114,122,147,173,177,298,300,336,365,366,373,380,387,389,390,391,392,395,396,397,398,399,406,410,411,413,418,422,426,429,435,438,443,444,446,451,461,466,467,469,472,486,493,499,502,507],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,65,70,79,95,120,122,123,160,170,176,206,207,210,212,215,216,217,219,220,227,232,236,239,245,263,277,293,310,326,327,344,366,373,374,375,377,380,408,412,435,499,508],counter:[3,341,476,487,489,495],counteract:239,counterbal:243,counterbalanc:29,counterpart:[196,307,476],counterproduct:18,coupl:[],courant:313,cours:[3,8,132,134,166,196,204,205,240,306,320,334,340,342,343,345,346,366,427,453,478,481,494,502,508,510],courtesi:368,cov:451,coval:[6,9,29,406,430,451,502],covari:241,cover:[6,73,192,200,209,250,406,468],coverag:[73,216],cpc:246,cpp:[1,3,6,8,9,11,12,13,91,196,204,205,237,310],cpu:[1,3,9,10,12,14,15,16,17,18,65,73,200,214,230,248,336,363,366,380,393,461,476,494,495,498,499,500,508],cpuremain:499,cr2:171,cr3:171,crack:[4,376],crada:[5,7],crai:[5,7,13,18,196],crash:[3,12,376,502],craympi:380,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:209,create_faceset:209,create_group:198,create_nodeset:209,createatom:[],creation:[],crimson:200,critchlei:292,criteria:[3,122,173,199,200,221,222,223,258,373,440,468,483,486,508],criterion:[12,42,127,172,175,210,220,223,239,277,299,313,341,346,373,375,395,406,410,451,486,495,496],criterioni:495,critic:[6,49,50,261,330,335,373],crmax:73,crmin:73,cross:[3,12,22,73,93,150,170,180,196,197,199,211,216,222,226,260,262,284,307,316,320,322,331,338,350,368,375,391,400,403,404,411,412,413,418,420,422,441,446,448,450,464,466,473,481,485,491,510],crossov:1,crossterm:481,crozier:[0,7,13],crucial:297,crystal:[3,4,6,13,75,112,288,289,333,368,376,481,485,499,502],crystallin:[6,108,289,368,465,502],crystallis:330,crystallogr:[124,171],crystallograph:[368,499],crystallographi:[124,171,368],cs1:171,cs_chunk:6,cs_im:[41,481],cs_re:[41,481],csanyi:[146,442,452],cscl:430,csequ:6,csh:[11,12,393],cshrc:[11,12],csic:[405,462,464,466,469],csinfo:6,csisi:[405,462,464,466,469],csld:[],cst:404,cstherm:6,cstyle:478,csvr:[],ctcm:[381,404],ctemp_cor:230,cterm:312,ctr:9,ctype:11,cu1:171,cu2:171,cu3au:430,cube:[6,42,170,175,220,230,344,368,502],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_hom:[9,15],cuda_prec:[9,15],cufft:14,cuh:386,cummul:[3,6,218,221,222,223,225,236,241,247,249,323,326,327,328,329,331,338,412,499],cumul:[6,210,212,215,216,217,231,239,247,261,263,268,277,307,308,375],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,61,63,65,73,75,83,91,107,108,114,122,123,136,147,152,160,162,168,170,173,176,195,196,197,198,199,200,201,204,205,209,212,216,217,218,220,221,222,223,224,225,226,227,231,232,237,239,241,244,245,247,253,260,263,264,269,270,271,277,282,283,284,286,292,293,298,299,301,304,305,306,307,310,311,312,313,314,315,316,317,319,321,322,323,326,327,328,334,335,338,339,340,341,342,343,345,346,348,363,364,365,366,369,370,372,373,374,375,380,386,393,395,399,404,406,407,410,413,414,417,427,428,430,431,432,435,441,443,444,447,448,449,450,453,464,466,467,470,476,477,478,479,481,482,483,484,485,487,488,489,491,493,495,496,498,499,503,508,509,510,511,512],curv:[6,172,239,289],curvatur:[409,445,473],custom:[],cut0:479,cut1:490,cut2:490,cut:[],cuthi:[288,300],cutinn:[388,427,428],cutlo:[288,300],cutmax:441,cutoff1:[392,399,418,422,426,429,438,446],cutoff2:[387,389,390,392,398,399,418,422,426,429,438,446],cutoff:[3,6,8,10,16,18,40,46,47,55,56,63,72,74,75,79,91,96,112,114,121,122,146,170,173,175,176,222,223,228,235,288,297,298,300,302,304,307,311,323,336,340,344,346,363,365,366,373,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,394,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,444,445,446,451,452,453,454,455,456,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,479,483,486,490,502,508],cutoff_glob:[],cutoff_inn:[],cutoffa:405,cutoffc:405,cuu3:404,cval:171,cvd:330,cvel:312,cvff:[],cwiggl:[3,260,340,343,345,508],cyan:[2,199,200],cycl:[3,239,261,263,264,268],cyclic:[3,192],cygwin:12,cylind:[3,4,73,199,212,245,293,341,344,484],cylindr:[6,245,320,341],cypress:380,cyrot:386,cyrstal:289,d3q15:250,d3q19:250,d_double_doubl:15,d_e:335,d_flag2:296,d_flag:296,d_name:[119,196,296,325,491],d_single_doubl:15,d_single_singl:15,d_sx:296,d_sy:296,d_sz:296,daan:333,dai:12,daili:12,daivi:284,damag:[],dammak:302,damp:[3,6,203,208,247,248,249,254,263,264,268,294,297,298,302,307,326,327,339,341,342,372,373,375,387,389,391,396,399,406,410,418,426,438,446,461,467,495,502],damp_com:248,damp_drud:248,dampen:[307,502],dampflag:[341,410],dan:17,danger:[3,12,239,346,400,499],dangl:175,daniel:9,darden:[366,399],darkblu:200,darkcyan:200,darken:199,darkgoldenrod:200,darkgrai:200,darkgreen:200,darkkhaki:200,darkmagenta:200,darkolivegreen:200,darkorang:200,darkorchid:200,darkr:200,darksalmon:200,darkseagreen:200,darkslateblu:200,darkslategrai:200,darkturquois:200,darkviolet:200,dasgupta:298,dash:[410,498],dat:[6,95,192,209,477],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,308],dataset:308,datatyp:3,date:[0,4,6,12,13,195,443,444,508],datom1:121,datom2:121,datom3:121,datom4:121,datum:[3,6,43,67,70,71,81,97,114,121,196,213],davenport:429,davi:340,david:[9,19,365,366,464,466],daw:[404,441],dbg:14,dcd:[3,6,7,196,198,199,200,201,290,482,486],ddim:195,deactiv:426,dealt:246,debug:[6,7,11,12,13,14,17,124,128,171,172,290,295,363,365,380,414,435,470,479,480,488,491,498,508],deby:[],decai:[96,396,473],decid:[3,6,12,16,73,260,296,307,336,496,503],decipher:368,declar:198,declin:323,decod:199,decompos:[91,452],decomposit:[3,5,7,18,64,209,290,311],decoupl:[6,502],decreas:[3,196,197,206,207,214,223,226,232,237,239,247,334,365],decrement:312,deepli:362,deeppink:200,deepskyblu:200,def:[12,13,479],defaul:63,defect:[6,72,170,433],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,178,179,180,181,182,183,184,186,187,189,190,191,192,193,194,195,196,197,198,199,200,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,220,221,222,223,224,226,227,230,231,232,234,237,238,239,242,245,246,247,248,249,250,258,260,262,263,264,265,266,267,268,269,270,271,273,274,275,278,280,281,282,283,284,285,286,288,289,290,292,293,294,296,298,300,305,307,308,309,310,313,317,321,323,325,326,327,328,329,331,332,333,335,337,338,340,341,342,343,344,345,346,348,349,350,351,352,353,354,355,358,359,360,361,363,365,366,368,370,372,373,374,375,376,377,378,379,380,382,383,384,385,387,388,389,390,391,392,393,394,396,397,399,400,401,402,403,405,406,408,409,410,411,412,413,414,416,418,419,420,421,422,423,424,425,426,427,428,429,433,434,435,436,437,438,440,441,443,444,445,446,447,448,449,450,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,481,482,484,485,486,487,490,491,492,493,495,496,498,499,502,504,505,506,507,508,509],definit:[2,3,6,8,12,13,80,82,122,146,200,212,213,214,215,216,217,218,226,234,245,268,308,325,337,340,343,345,347,359,363,374,383,386,394,401,402,406,416,441,448,450,452,468,479,481,483,490,492,507,508],defint:499,deform:[],deg2theta:171,deg:502,degener:[3,292],degrad:[8,18,289,366,490],degre:[3,6,8,20,21,24,28,29,32,35,36,38,67,81,96,97,99,101,102,104,106,107,112,118,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,171,172,178,179,182,183,190,192,195,199,212,223,230,239,241,242,247,248,253,263,264,268,269,270,271,282,283,284,286,290,292,306,307,310,326,327,328,333,349,351,355,358,360,373,399,404,412,491,499,502,509],degress:[152,212],del:495,delai:[3,6,12,376,403,499],deleg:413,delet:[2,3,7,8,12,55,59,62,65,170,175,176,203,212,213,215,216,217,218,221,223,236,239,263,308,326,327,346,348,364,374,376,379,435,460,481,482,483,484,492,493,498,503,504,506,508,509],delete_atom:[],delete_bond:[],delete_el:209,deli:195,delimit:[479,508],deloc:[264,406,451],delr:430,delt_lo:495,delta:[],delta_1:386,delta_3:386,delta_7:386,delta_conf:3,delta_ij:[430,441],delta_mu:[],delta_pi:386,delta_r:441,delta_sigma:386,delta_ua:[],delx:195,delz:195,dem:[],demand:302,demo:11,demon:287,demonstr:[297,430],den:293,dendrim:412,denniston:[9,250,252,253,254,289],denomin:[7,177],denot:[124,230,248,289,300,302,396,411,413,444,448,450],dens:[73,223,406],densiti:[3,6,7,9,18,41,42,61,105,122,132,146,158,170,172,204,205,209,212,216,217,220,226,237,250,253,256,257,289,293,294,298,335,340,368,370,374,381,386,404,430,431,432,441,445,451,455,457,458,459,481,490,491,499,507],density_continu:450,density_summ:450,depart:[0,7],departur:[261,297],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,63,65,67,70,71,72,73,81,96,97,108,114,115,118,119,120,121,125,146,149,155,159,160,166,172,173,178,179,180,181,182,183,184,186,187,189,190,191,192,195,196,197,199,200,203,204,205,206,207,210,212,214,215,216,218,219,220,222,224,226,232,233,238,241,242,243,245,247,248,250,252,253,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,288,299,302,304,307,309,310,311,317,323,326,327,328,330,332,334,335,337,339,340,343,344,345,346,348,349,350,351,352,354,355,358,360,366,368,373,374,376,377,378,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,430,431,433,434,436,437,438,440,441,443,444,445,446,451,452,453,461,462,463,464,465,466,467,469,471,472,473,476,478,481,483,484,487,491,493,495,498,499,501,508,509],dependend:6,depflag:12,dephas:[476,495],depos:227,deposit:[],deprec:[3,298,443],depth:[52,150,199,335,409,445],dequidt:9,der:[91,113,394,395,426,443,444,472,502],deriv:[6,7,8,9,38,57,65,91,146,166,192,213,224,226,239,247,260,263,265,266,267,268,269,270,271,288,294,298,302,332,333,335,340,341,344,372,374,382,386,394,399,406,407,411,420,424,425,430,433,443,444,461,463,472,502],derjagin:472,derlet:288,descend:200,descent:[7,372],descib:[41,199,298],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,64,65,70,72,73,75,92,116,119,122,124,136,146,147,150,151,152,156,157,160,163,165,166,170,171,172,174,175,184,189,192,196,197,198,203,204,205,212,213,214,215,216,217,218,220,223,224,225,226,227,229,230,235,240,241,244,245,246,247,248,249,250,252,253,254,258,262,263,264,268,276,285,288,290,295,296,297,298,299,300,307,312,320,323,324,325,326,327,328,329,330,331,332,333,338,340,341,343,348,365,366,368,371,372,373,374,375,379,382,383,385,387,388,389,391,392,393,394,395,396,399,404,406,407,409,410,411,413,416,418,419,420,421,422,423,424,425,426,427,428,429,430,433,434,440,441,442,443,444,445,446,451,452,453,460,461,462,463,464,465,466,467,469,471,472,473,474,476,478,479,481,482,483,484,485,491,494,495,498,503,508,509,510],descript:[],descriptor:[146,196,414],deserno:366,design:[0,3,6,7,8,11,13,14,15,17,124,154,157,171,209,223,229,230,263,264,288,289,308,330,335,383,384,385,388,391,396,398,406,426,427,428,431,432,441,444,463],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,61,73,92,95,118,123,147,154,172,185,195,212,218,224,226,237,239,240,247,248,249,253,263,284,292,293,294,295,298,302,307,310,323,326,327,328,329,334,341,356,362,365,366,368,371,373,374,375,400,404,412,427,428,462,464,466,477,478,479,481,485,490,495,496,498,499,508,509,510],desk:7,desktop:[4,6,7,10,12,199],despit:502,destabil:386,destre:358,destroi:[9,11,40,221,222],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,65,68,69,70,73,77,80,94,95,98,107,109,111,113,115,117,118,120,123,125,146,147,149,150,151,152,155,165,166,167,169,172,173,176,177,180,191,195,196,197,199,200,203,204,205,209,212,213,214,215,216,218,220,222,223,224,225,226,227,237,239,240,241,242,244,245,247,249,250,254,260,261,262,263,264,265,266,267,268,269,270,271,275,277,282,283,284,285,286,289,292,293,294,296,297,299,300,301,307,310,311,323,326,327,328,329,330,331,333,334,335,336,337,338,339,346,348,350,359,365,366,369,373,374,376,377,380,381,382,383,385,386,388,390,391,392,393,394,395,396,399,400,406,407,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,429,430,434,435,440,443,444,445,451,452,453,461,468,471,472,474,479,481,482,483,484,486,487,490,491,493,496,499,500,503,508,509,512],detect:[2,3,12,43,63,65,90,96,238,293,334,375,395,412,417,476,478,481,492,495,508],determ:380,determin:[1,3,6,8,9,12,15,40,41,43,52,59,60,61,63,64,70,73,91,107,113,115,118,124,125,133,147,160,161,170,171,172,195,196,197,199,200,201,202,206,207,208,211,212,213,214,215,216,217,218,219,220,224,226,227,230,232,239,242,243,245,247,248,253,258,260,261,263,269,270,271,282,283,284,286,288,290,293,294,297,304,305,306,307,308,309,313,315,317,323,326,327,328,330,336,337,340,341,342,343,344,345,346,359,365,366,368,374,376,377,380,382,383,390,395,399,403,404,408,410,413,414,422,430,433,435,444,445,451,460,463,467,472,478,481,482,484,486,488,491,495,497,498,500,507,508,509],determinist:311,detil:114,devan:[9,446],devanathan:466,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,244,268,292,297,298,301,382,386,406,432,433,451,469,483],devemi:9,deviat:[261,268,288,408],deviator:9,devic:[1,3,12,15,17,244,380],device_typ:380,devin:[299,395],devis:432,dfactor:199,dff:502,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_sin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lon:[3,6,36,46,47,51,54,55,91,178,204,205,239,307,323,340,344,371,373,385,391,392,394,396,397,398,399,409,411,412,413,416,417,418,419,420,421,422,423,424,425,426,429,434,438,445,446,456,462,468,471,472,490,502,507],epsilon_0:473,epsilon_14:391,epsilon_:445,epsilon_d:397,epsilon_i:[409,435,445],epsilon_i_:445,epsilon_i_a:[409,445],epsilon_i_b:[409,445],epsilon_i_c:[409,445],epsilon_ij:435,epsilon_j:[409,435,445],epsilon_j_:445,epsilon_j_a:[409,445],epsilon_j_b:[409,445],epsilon_j_c:[409,445],epsilon_lj:445,epton:440,eqch:167,eqeq:[443,444],eqp:399,eqq:399,equal:[2,3,6,8,11,12,17,40,42,55,65,67,70,71,73,78,81,90,91,95,97,114,116,121,123,125,147,150,166,168,170,172,195,199,200,203,204,205,206,207,210,213,214,215,218,219,220,224,226,227,232,239,240,242,243,245,247,248,250,253,254,260,261,268,279,288,290,293,295,297,298,299,302,304,306,307,309,312,317,319,326,327,328,331,332,333,335,337,338,340,343,345,346,348,364,368,373,375,376,377,379,380,395,400,402,408,409,412,416,427,433,434,441,443,444,445,447,448,449,451,452,453,463,468,469,473,477,478,479,481,483,484,488,489,492,495,497,499,508,509],equat:[3,6,7,8,9,95,112,118,124,171,180,191,203,224,230,231,234,235,241,247,248,250,253,261,262,263,264,268,284,288,290,297,298,302,310,311,323,331,335,338,340,341,343,345,358,365,366,394,399,400,402,406,407,410,415,427,428,430,435,445,448,450,455,456,458,459,473,502],equi:264,equidist:262,equil:[3,298,369,488,512],equilater:491,equilibr:[3,4,5,6,7,9,61,95,172,203,210,213,223,224,239,261,263,264,284,285,297,298,299,300,331,332,333,338,395,396,443,444,477,491],equilibria:338,equilibribum:[221,222],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,44,48,49,50,52,54,57,61,155,156,179,181,224,226,239,240,241,248,250,263,268,284,297,298,302,306,310,312,320,323,330,331,333,338,349,351,355,358,395,430,437,451,502],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:209,equival:[6,12,13,29,61,63,130,131,139,144,170,174,200,215,218,224,226,239,247,263,284,294,306,307,343,400,406,451,464,466,481,484,489,490,499,502],equlibrium:6,equliibr:[298,300],er3:171,eradiu:[41,119,197,406,481],eras:[309,332],erat:[226,428],erc:396,erfc:[396,418,435],erforc:[119,197],erg:507,erhart:[210,404,464,466],ermscal:383,ernst:9,eror:3,eros:430,erose_form:430,erot:[],errata:[464,466],erratum:340,erron:3,error:[],erta:410,ervel:[119,197,481],escap:[227,502],especi:[8,16,160,172,203,210,220,239,297,302,305,306,380,478],espresso:[9,301],essenti:[8,11,12,27,92,134,153,154,155,158,159,160,161,162,164,181,213,268,289,339,366,382,396,418,466,486,499],essex:29,establish:[91,243],estim:[1,3,6,10,12,38,42,57,95,147,209,220,231,261,323,330,365,366,371,435,444,463,495,499],esu:507,esub:430,eta:[6,250,263,297,298,300,339,405,407,409,441,465,469,507],eta_dot:263,eta_ij:441,eta_ji:407,etag:[41,481],etail:499,etap:263,etap_dot:263,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,63,70,93,94,95,99,115,116,119,121,147,149,152,153,154,155,156,158,159,160,161,162,164,166,172,174,175,176,185,196,197,199,200,203,204,209,210,211,212,215,216,217,218,221,222,226,227,237,239,240,247,263,293,304,308,335,336,344,348,364,365,373,374,375,376,378,404,405,413,426,428,433,439,443,444,462,464,466,469,476,479,481,482,483,488,490,491,495,496,497,498,499,500,502,507,508,510,512],ethernet:18,etol:[373,375,476,495],etot0:297,etot:[6,99,101,102,116,147,158,200,230,248,261,297,498,499],eu2:171,eu3:171,euler:[373,375],eulerian:209,euqat:454,europhi:250,ev_tal:8,evalu:[2,3,9,11,12,38,57,73,91,92,95,113,123,125,146,148,152,162,170,172,195,196,197,199,200,204,205,206,207,209,211,212,213,214,215,216,217,218,219,226,232,240,242,243,245,246,247,248,289,295,298,309,313,317,326,327,328,337,340,343,345,346,348,365,366,371,373,380,433,435,441,447,449,451,463,476,477,479,483,484,486,488,489,490,491,495,497,499,508,509],evalut:[348,479],evan:[160,284],evanseck:[6,20,178,391,493],evapor:[],evaul:[8,373],evdwl:[113,443,444,499],even:[3,6,8,12,15,17,18,34,40,42,53,59,61,63,65,72,73,92,113,125,170,173,174,188,192,196,197,200,203,204,205,210,211,212,215,216,217,218,220,221,222,224,226,227,230,245,248,261,263,264,289,293,302,304,307,308,319,323,331,335,338,340,344,346,357,365,371,373,375,380,385,406,407,410,413,416,435,445,469,470,474,481,482,484,486,487,488,490,491,493,496,498,499,500,502,512],evenli:[3,42,147,192,220,250,416,470],event:[],eventu:[3,6,12,15,174,298,495],ever:[9,55,57,246,323],evera:[394,409,445,461],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,73,74,95,119,125,134,160,175,196,197,198,199,200,201,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,231,236,237,239,241,243,244,245,250,251,259,263,264,268,287,288,289,293,294,295,296,297,298,299,300,302,304,305,307,308,310,312,323,325,326,327,328,329,330,331,334,335,336,337,338,346,348,364,366,375,376,377,380,400,403,413,426,443,444,451,457,475,476,477,481,483,485,486,488,489,490,495,496,497,499,503,508,512],everyth:[8,113,503],everywher:[122,420],eviri:406,evolut:[241,250,290,476],evolv:[250,290,336],ewald:[2,3,5,6,7,8,9,12,92,116,124,147,336,365,366,373,387,389,390,396,399,406,418,422,438,446,461,463],ewald_disp:399,ewalddisp:3,exact:[22,42,45,73,128,166,175,180,220,223,240,241,247,248,249,293,302,303,323,335,350,365,393,483,488,495,508,510,512],exactli:[3,6,12,14,17,38,42,43,57,61,73,74,95,122,150,156,163,172,192,204,205,215,220,226,231,235,240,247,248,249,264,276,277,285,289,297,323,328,329,342,380,393,400,404,410,413,427,435,463,483,484,491,495,508],exager:502,examin:[6,8,17,223,289],examp:[479,508],exampl:[],exce:[3,6,16,17,18,42,60,73,174,211,212,215,216,217,218,220,224,226,231,236,263,289,304,308,314,315,323,373,380,481,508],exceed:[3,42,61,220,226,263,323,489],excel:406,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,61,62,65,73,93,94,114,115,118,123,147,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,172,176,178,179,180,181,182,183,184,186,187,189,190,191,192,195,196,197,200,203,206,212,213,215,219,220,224,226,233,238,239,242,245,247,249,263,264,265,266,267,268,269,270,271,272,273,276,277,280,282,283,284,285,286,290,299,300,307,309,310,320,323,326,328,329,335,339,343,346,347,348,349,350,351,352,354,355,358,359,360,365,366,368,370,374,375,376,378,379,380,381,382,384,387,388,389,390,391,392,393,394,395,396,398,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,431,436,437,438,440,443,444,445,446,453,461,462,463,464,465,466,469,471,472,473,476,478,479,481,483,484,486,489,490,491,492,493,495,499,502,507,508,509,511],excess:[214,406],exchang:[2,3,6,8,63,64,203,209,210,239,247,299,307,331,335,338,365,380,406,496],exchange:365,excit:406,exclud:[3,6,9,12,16,17,65,73,118,146,152,159,160,176,196,212,216,221,222,251,259,292,305,307,330,341,346,373,374,376,388,410,413,416,427,428,435,460,493],exclus:[1,3,12,16,91,380,395,433,435,490,500],excurs:[263,476],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,62,173,199,244,301,348,364,367,379,477,479,489,492,495,508],exempl:451,exemplari:240,exemplifi:406,exert:[6,245,248,302,342,343,344,366],exhaust:[209,379,508],exhibit:[96,263,372,406,490],exist:[3,6,7,8,11,12,13,16,37,56,61,70,72,128,172,173,191,198,199,200,203,208,219,222,224,227,239,292,293,295,346,347,349,351,352,353,355,359,369,374,380,401,402,413,443,460,470,477,479,481,482,483,492,493,494,503,508,509,510],exit:[2,3,11,12,42,59,196,220,235,364,379,479,480,489,498,508],exlanatori:3,exp:[],expand:[],expans:[12,146,196,492,508],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,73,107,153,164,170,192,220,232,239,241,260,288,294,296,297,302,307,346,366,376,393,430,433,435,476,479,481,483,486,490,495,508],expens:[6,73,200,288,292,307,335,346,365,366,376,380,479],experi:[6,13,15,17,219,227,244,253,262,294,306,307,371,375,400,435,490,495],experienc:[6,12,252,253],experiment:[239,365,380,495],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,61,65,67,70,71,73,74,75,78,79,81,90,97,152,160,192,196,197,199,200,203,212,213,218,220,222,224,226,263,288,296,307,320,346,348,364,365,368,374,375,379,385,404,416,451,453,468,479,482,483,486,488,491,502,503,508,512],explan:[3,6,61,119,146,196,197,212,262,288,413,475,478,479,481,490],explanatori:[3,8,123,196,197,211,212,215,216,217,307,374,478,508],explantori:[3,303],explic:434,explicit:[6,9,11,22,45,79,91,119,122,166,180,204,205,226,314,315,350,370,382,383,386,391,393,404,406,417,427,467,475,478,482,485,503],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,73,115,118,149,159,162,170,172,178,179,181,182,183,184,186,187,189,190,192,196,197,200,206,216,219,226,233,238,240,242,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,296,297,299,307,309,310,326,328,329,335,339,343,349,351,352,354,355,358,360,374,380,381,382,384,387,388,389,390,391,392,393,394,395,396,397,399,400,403,404,405,407,408,409,410,411,412,413,417,418,419,420,421,422,423,424,425,426,427,431,433,435,436,437,438,440,445,446,453,454,455,456,457,458,459,461,462,463,464,465,466,467,469,471,472,473,481,483,484,490,491,493,494,500,502,503],explictli:[16,494],exploit:[15,17,290],explor:[124,171],expon:[3,298,300,404,409,412,426,434,446],exponenti:[91,441,462,469,473,495,508],expos:11,exposit:[209,400,403],express:[6,146,158,172,204,205,224,260,288,298,335,341,348,386,404,406,420,430,451,452,461,508],expressiont:386,extend:[],extens:[3,6,9,17,45,46,47,54,56,65,86,87,88,91,92,95,99,102,103,113,115,123,125,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,197,203,206,207,210,218,219,225,228,232,237,238,239,241,242,243,245,247,249,261,263,268,277,288,289,305,306,307,309,312,317,320,322,326,327,328,329,330,332,333,335,337,340,344,345,409,430,433,444,445,452,498,499],extent:[1,3,42,43,46,59,73,170,174,196,208,216,220,245,342,345,365,368,382,447,449,463,478,481,484],exterior:[3,6,170,344],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,63,73,107,115,116,118,124,147,149,150,151,153,155,158,159,160,161,162,164,165,171,172,173,174,178,200,215,220,222,263,295,296,297,307,323,373,374,377,378,399,410,413,416,430,435,478,479,481,484,493,502,508],extract:[3,6,11,13,36,65,91,113,121,123,125,204,205,300,375,396,407,430,452,479,486,498],extract_atom:11,extract_comput:[11,479],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,60,199,214,224,226,263,333,406,465,502],extrema:426,extrins:209,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[168,337],f_a:[464,465,466],f_ave:123,f_c:465,f_f:466,f_fix_id:297,f_foo:508,f_harm:333,f_i:[29,441],f_id:[6,73,123,125,196,197,203,211,212,213,214,215,216,217,218,258,325,337,499,508],f_ij:441,f_indent:218,f_int:332,f_j:29,f_jj:95,f_k:441,f_langevin:335,f_max:[297,302],f_msst:261,f_r:[248,464,465,466],f_sigma:386,f_solid:333,f_ss:6,f_temp:[],face:[3,6,59,61,73,160,170,174,208,216,217,340,342,343,344,345,368,409,430,445,481,484],face_threshold:170,facet:170,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,241,293,323,333,410,451,493],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,59,60,61,74,91,95,107,114,121,122,124,146,166,171,174,178,189,195,196,199,200,204,205,213,220,224,226,227,239,244,247,249,250,261,263,264,268,290,294,298,306,310,313,315,323,327,331,338,339,340,344,355,366,368,374,380,382,383,386,387,389,391,396,397,398,400,401,402,406,410,413,417,418,430,433,435,437,438,444,446,453,462,467,478,481,484,485,490,493,495,496,499,502,507,508],factori:[3,479],factoriz:365,fail:[3,9,11,12,61,176,224,227,365,373,375,398,444,479],failur:[127,448,480,508],fairli:[11,435,490,495,503],faken:75,falcon:244,fall:[3,6,200,215,293,479,508],fals:[90,346,348,451,508],fame:8,famili:[469,478],familiar:[0,11,503],fan:441,far:[3,6,12,17,59,61,63,90,196,197,200,201,220,221,222,224,227,263,288,306,307,323,340,351,355,371,375,376,468,479,481,486,499],farago:247,farrel:[464,466],farther:196,fashion:[6,8,42,73,172,200,203,204,205,210,216,220,222,227,239,241,245,260,261,263,265,266,267,268,269,270,271,279,282,283,284,285,286,296,297,299,307,312,316,322,325,333,335,339,340,341,343,345,375,413,427,484,493,508,511],fasolino:415,fast:[6,7,9,12,13,17,40,196,197,274,297,336,365,366,388,427,428,433,461,463,483,488,490,499,509,512],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,63,65,110,115,118,149,159,178,179,181,182,183,184,186,187,189,190,192,196,197,200,206,219,220,226,233,238,242,246,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,294,298,299,307,309,310,323,326,328,330,332,335,339,343,349,351,352,354,355,358,360,365,366,377,378,380,381,382,384,386,387,388,389,390,391,392,393,394,395,396,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,436,437,438,440,445,446,453,461,462,463,464,465,466,469,471,472,473,476,484,490,494,502],fastest:[1,6,14,17,160,216,335,336,380,478],fatal:[3,498],fault:[72,444],faulti:12,fava:409,favor:223,favorit:7,fbmc:330,fcc:[],fcm:[279,508],fdirect:230,fdotr:414,fdt:[],fdti:91,fe2:171,fe3:171,fe_md_boundari:209,featu:8,featur:[],fecr:404,feedback:[7,244],feel:[7,244,245,253,288,344,346,375,435],felling:432,felt:344,femtosecond:507,fene:[],fennel:[396,418],fep:[],ferguson:[6,178,493],fermi:[1,9,10,12,15,158,380,466],fermion:406,fernando:429,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,65,201,211,212,213,215,216,217,218,248,263,293,296,298,310,337,365,373,374,375,382,451,478,481,486,490,492,500,510],fewer:[1,3,11,15,16,63,253,490],fewest:3,fextern:237,feynman:290,fff:479,ffield:[395,407,443,444,451],ffmpeg:[3,12,199],ffplai:199,fft:[1,3,7,9,11,12,14,15,92,115,116,147,289,365,366,490],fft_inc:[12,366],fft_lib:12,fft_path:12,fftbench:[365,500],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],ficiti:460,fictiti:[6,206,207,232,237,241,290,306,396,418,422,460],field1:[482,486],field2:482,field:[],fifth:[320,437],figur:[1,3,8,12,297,478,479,503],fij:399,file0:288,file1:[11,13,288,334,348,374,486,488,492],file2:[11,13,334,348,374,486,488,492],file:[],file_from:198,filen:374,filenam:[3,12,13,38,42,57,192,196,197,199,200,201,209,212,213,214,215,216,217,218,220,225,235,288,292,295,298,299,300,303,304,307,308,334,335,362,363,364,374,375,381,382,386,396,404,405,407,415,430,431,432,437,441,442,443,444,451,452,462,463,464,465,466,469,477,478,479,482,483,488,492,499,508,510,511,512],filennam:488,filep:[3,196,197,200,483,488,512],filepo:304,fill:[7,9,172,199,293,335,368,376,386,433,444,484,503],filter:[200,209],final_integr:8,final_integrate_respa:8,finchham:[6,154,398],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,63,73,75,91,123,175,192,201,210,223,224,235,236,239,262,288,293,294,302,306,371,373,375,376,396,413,418,422,430,451,461,463,502,503,508],find_custom:8,fine:[16,17,176,206,232,333,376,380,503,508],finer:[146,172,508],finest:365,finger:[172,195,260,484],finish:[6,11,42,220,348,362,364,365,377,379,380,468,486,508,509],finit:[],finni:[7,404,461],finvers:230,fiorin:[9,225],fire:[],firebrick:200,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,59,61,63,64,73,83,92,95,108,109,110,112,118,122,123,133,136,139,140,144,147,157,160,166,168,170,171,173,174,175,179,192,196,197,198,199,200,201,203,204,212,213,215,216,217,218,220,223,226,235,239,240,245,250,260,261,262,263,288,290,295,296,297,299,304,307,310,312,320,321,323,324,325,332,333,334,335,337,341,346,348,349,356,368,373,374,375,376,379,380,381,382,385,386,387,389,391,393,395,396,404,406,407,410,411,413,414,415,416,417,418,422,427,428,430,432,433,435,437,441,443,444,451,452,460,462,463,464,465,466,469,473,476,477,478,479,481,482,483,486,488,490,493,494,495,498,499,502,503,508,509,510,512],fischer:[6,9,19,20,178,391,493],fit:[3,6,9,12,38,57,192,235,306,323,382,386,415,430,435,456,463,465,489,503,508],five:[75,158,297,374,386,431,481,495],fix:[],fix_adapt:[166,205,426],fix_atom_swap:[],fix_bal:64,fix_deposit:[3,210,293],fix_eo:9,fix_evapor:210,fix_flux:209,fix_gcmc:[210,374],fix_gl:241,fix_gld:241,fix_grav:293,fix_id:[3,224,261,263,265,266,267,268,269,270,271,294,297],fix_manifoldforc:503,fix_modifi:[],fix_mov:[195,341],fix_nh:8,fix_npt:241,fix_nv:503,fix_nvt:[210,239],fix_poem:[3,6,9],fix_pour:[3,227],fix_qbmsst:9,fix_qeq:[3,395],fix_rattl:310,fix_reax_bond:443,fix_rigid:[253,385],fix_saed_vtk:308,fix_setforc:8,fix_shak:310,fix_shardlow:9,fix_srd:3,fix_styl:268,fix_temp_rescal:329,fixedpoint:[224,263],fixextern:237,fixid:209,fji:399,flag1:[229,378],flag2:[229,378],flag:[3,8,9,11,12,14,15,16,17,41,68,76,77,83,90,93,94,98,108,109,111,124,167,171,175,196,197,199,200,201,218,223,225,229,244,247,251,253,259,260,289,296,307,320,322,323,330,334,343,346,363,366,374,378,379,380,382,412,417,430,433,460,476,478,479,481,482,483,485,486,487,491,503,508],flag_buck:390,flag_coul:[390,399,422],flag_lj:[399,422],flagfld:[388,427,428],flaghi:[3,388,427,428],flaglog:[388,427,428],flagn:229,flagvf:[388,427,428],flat:[6,335,340,341,345],flavor:[2,7,12],fld:[],flen:383,flex_press:383,flexibl:[3,6,8,173,199,212,216,225,241,264,331,338,406,465,499],flip:[3,6,226,263,342,343],floor:508,flop:12,floralwhit:200,flow:[],fluctuat:[6,66,91,224,239,240,247,250,263,268,288,289,311,333,335,358,402],fluid:[],fluid_veloc:254,flush:[3,200,498],flux:[],flv:199,fly:[7,9,12,42,199,203,209,214,227,230,307,310,336,386,433,499,502],fmackai:9,fmag:228,fmass:290,fmax:[373,499],fmomentum:230,fmsec:[2,200,247,248,260,263,294,307,326,327,490,501,507,509],fname:364,fno:[9,12,16],fnorm:[373,499],fnpt:230,fnvt:230,foce:413,fock:383,focu:310,fogarti:[9,300,444],foil:[146,288,452],fold:[321,490],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,61,65,66,72,73,75,84,95,96,101,102,112,119,122,123,125,146,147,150,151,152,158,160,165,168,170,172,173,178,181,182,183,184,186,187,189,190,192,196,198,199,200,203,209,210,211,212,213,214,215,216,217,218,220,225,226,227,230,231,234,235,237,239,240,241,244,246,247,248,250,253,261,263,268,269,270,271,282,283,284,286,289,290,292,295,296,297,298,300,302,304,306,307,308,310,325,326,327,328,331,332,333,334,335,337,338,346,347,351,352,353,354,355,358,360,363,368,370,373,374,375,380,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,435,436,437,438,440,441,442,443,444,445,446,448,450,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,468,469,471,472,473,474,476,478,479,481,482,484,486,488,489,490,493,495,496,497,502,503,508,509,511],foo:[4,8,11,12,196,199,237,479,492,508],foot:6,footprint:[12,380],fopenmp:[9,12,16,18],forc:[],force_uvm:17,forceatom:253,forcefield:[306,412],forcegroup:250,forcezero:371,ford:399,forestgreen:200,forev:73,forget:[248,502],forgiv:263,fork:[12,196],form:[2,3,6,8,12,19,22,45,55,65,68,76,77,79,83,91,93,94,96,98,108,109,111,122,146,147,166,167,176,180,200,203,204,205,222,240,241,247,249,253,260,284,289,300,302,306,307,335,340,344,349,350,353,358,370,372,374,375,382,383,386,393,401,402,404,406,408,412,413,417,429,430,432,433,437,438,441,443,444,445,451,452,453,461,463,464,465,466,472,475,478,479,481,486,491,498,502,508],formal:[6,80,82,95,240,241,247,263,290,323,331,451],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,70,79,180,192,196,197,198,199,200,201,212,215,216,217,218,220,222,235,289,292,296,298,300,303,307,308,319,334,335,346,347,350,370,374,375,381,382,386,393,404,407,417,430,432,442,443,444,446,452,463,469,470,478,479,481,482,483,486,497,498,499,508,510],former:[6,12,16,40,42,200,220,335,339,386,388,487,493,508],formerli:[7,13],formul:[1,9,41,66,147,206,232,247,263,284,298,300,306,310,334,365,382,386,404,406,409,430,440],formula:[2,3,6,7,13,21,22,37,45,55,56,72,75,91,93,94,95,99,101,102,111,118,124,125,147,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,171,172,177,179,180,191,195,196,204,205,206,207,212,213,214,215,218,219,226,232,242,243,245,247,248,260,288,289,295,304,309,317,321,323,326,327,328,337,340,343,345,346,348,349,350,352,35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reneighbor:[3,8,12,40,59,73,216,220,239,323,336,346,400,498,499],renssela:292,renumb:73,reorder:[3,12,40,478],rep:496,repeat:[2,6,199,200,216,223,224,239,316,368,386,464,466,468,476,495],repeatedli:2,repel:245,repes:196,replac:[2,3,6,11,12,42,65,93,94,123,149,150,151,152,153,154,155,158,159,160,161,162,164,165,196,197,199,200,201,212,213,215,216,217,218,220,223,227,247,268,295,302,304,396,420,463,482,483,488,489,499,508,509,510,512],replic:[],replica:[],replica_fil:12,report:[],repositori:[7,9,12,414,442,443,444],reprens:335,repres:[1,3,6,8,9,12,15,41,42,43,61,69,73,94,119,122,184,192,196,197,199,212,213,214,215,216,217,218,224,230,240,242,247,250,263,290,292,294,302,307,308,312,320,335,337,344,366,375,381,386,409,416,426,427,428,430,431,432,438,441,443,444,467,468,476,478,481,491,493,496,502,508,510],represent:[3,6,8,9,59,61,140,174,196,240,241,290,335,386,406,409,433,445,481,484,502],reprocess:486,reproduc:[3,263,341,396,404,410],repul:430,repuls:[6,7,36,41,46,47,114,245,298,340,341,344,382,386,394,396,400,406,410,412,426,430,434,451,460,466,469,472,473,491],reqir:[298,300],request:[3,6,8,12,42,108,175,192,196,244,250,305,311,323,325,363,365,435,443,444,476,486,491,495,503,508,509,510],requir:[],rerun:[],rescal:[],research:[5,7,84,85,234,250,254,311,433,476,495],resembl:[302,503],resepct:6,reserv:[12,244,502],reservoir:[95,239,243,247,335],reset:[],reset_atomic_reference_posit:209,reset_dt:8,reset_target:8,reset_tim:209,reset_timestep:[],resid:13,residu:244,residue1:376,resist:[6,244],resolut:[214,451,463],resolv:[224,290,323,428,503],resort:3,resourc:[7,381,404],respa:[3,16,231,244,263,378,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,428,429,430,431,432,433,434,436,438,440,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,468,469,471,472,473,474,489,490,501,508],respecifi:433,respect:[1,6,9,13,14,15,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,46,47,48,49,50,52,54,55,57,61,72,73,91,93,101,102,115,118,124,128,149,154,157,159,166,170,171,178,179,181,182,183,184,186,187,189,190,192,197,199,200,215,216,217,222,223,224,226,242,245,247,248,250,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,298,299,307,308,312,320,322,335,340,343,349,351,352,354,355,358,360,363,365,366,370,373,374,379,380,381,382,384,386,387,388,389,390,391,392,394,395,396,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,430,431,433,435,436,437,438,440,445,446,450,451,452,453,462,463,464,465,466,467,469,471,472,473,478,482,491,494,502,508,510,512],respon:9,respond:[6,7,155,226,406,440],respons:[6,7,261,331,338],resquar:[],rest:[6,8,12,296,300,306,386,428,430,498,499,502],restart1:290,restart2:290,restart2data:[],restart:[],restartfil:[12,13],restor:[3,8,62,63,108,172,204,205,296,312,320,325,347,498,499],restore_bia:8,restore_bias_al:8,restrain:[],restraint:[9,225,261,306,322,417],restratin:306,restrict:[],result:[1,2,3,6,7,9,10,11,12,13,15,16,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,46,47,48,49,50,52,54,55,57,65,66,68,69,73,77,91,94,95,98,108,109,111,115,116,118,120,121,122,123,124,125,147,149,152,155,159,166,167,169,171,172,175,178,179,181,182,183,184,186,187,189,190,192,195,196,197,199,200,203,206,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,230,233,235,238,239,240,242,247,248,250,254,261,263,265,266,267,268,269,270,271,272,273,280,282,283,284,285,286,289,290,298,299,304,305,307,309,310,323,326,328,331,332,333,335,336,337,339,340,341,343,345,348,349,351,352,354,355,358,360,365,366,375,378,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,430,431,433,435,436,437,438,440,444,445,446,453,462,463,464,465,466,467,469,471,472,473,476,478,481,483,484,485,486,490,491,492,493,495,507,508,509],resum:508,retain:[2,221,222,386,433,478],retart:[33,51,185,356],retir:[3,443],retreiv:8,retriev:[6,8,237,431,432,508],reus:[3,493],rev:[6,13,66,72,96,112,116,146,147,160,210,241,247,249,261,263,264,268,284,289,299,302,307,312,323,327,330,332,333,338,372,386,394,395,396,399,404,405,406,409,410,415,420,427,428,429,430,432,441,445,452,462,464,465,466,469,476],revers:[2,6,8,91,183,223,245,263,287,288,298,316,331,332,338,375,426,490,502],review:[146,298,312,330,433,442,452,476,495,502,503],rewind:364,rewrap:196,rewrit:[5,12],rewritten:19,rezwanur:440,rfac0:[146,452],rfactor:323,rfile:307,rg0:321,rgb:200,rh3:171,rh4:171,rhaphson:3,rheolog:6,rhi:463,rho0:[430,448,450,458,459],rho0_meam:430,rho:[],rho_0:[458,459],rho_alpha_beta:404,rho_bkgd:430,rho_colloid:340,rho_e:335,rho_fin:334,rho_i:[431,432],rho_initi:334,rho_ref_meam:430,rho_wal:340,rhodo:[9,10],rhodopsin:[1,10],rhohi:293,rholo:293,rhosum:[],ribier:372,richard:9,richardson:307,richi:[9,19],rick:[298,299,395,451],rick_and_stuart:299,ridg:[9,19],right:[3,6,11,12,42,148,172,190,191,19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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying &amp; extending LAMMPS","4. Packages","8. Performance &amp; scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","&lt;no title&gt;","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","&lt;no title&gt;","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":221,"default":[37,40,41,56,59,60,61,63,64,73,91,92,96,107,108,110,112,113,124,128,129,146,152,160,161,165,171,172,175,177,191,194,195,196,197,199,200,201,202,204,205,206,208,209,210,212,216,217,218,221,222,224,225,226,227,231,236,239,240,245,247,248,249,250,251,253,258,261,263,264,268,284,285,289,290,293,294,295,296,297,299,302,304,305,307,308,323,325,330,331,332,333,336,338,340,342,346,359,363,365,366,368,369,371,372,374,376,377,378,380,383,386,388,406,427,428,433,435,443,444,460,461,476,477,478,481,482,484,486,488,489,490,493,495,497,498,499,500,501,507,509,510,511],"function":508,"long":[214,387,389,390,391,392,396,398,399,418,422,426,438,446],"new":8,"static":12,acceler:1,account:503,ackland:66,acknowledg:7,adapt:[204,205],addforc:206,addit:[12,13,503],addtorqu:207,adiabat:6,adjust_dt:313,adp:381,after:503,airebo:382,alloi:404,amber2lmp:13,amber:6,angl:[8,67],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:68,append:208,arrai:6,aspher:[6,9,86,150,265,269,273,274,282],atc:[9,209],atom:[6,7,8,66,69,72,73,74,75,78,79,80,82,83,85,89,96,100,101,104,105,106,112,116,117,119,146,147,170,208,210,211,296,508],atom_modifi:40,atom_styl:41,attract:5,aug:[],aveforc:219,awpmd:[9,383],balanc:[42,220],barostat:6,basal:69,beck:384,berendsen:[294,326],between:6,binary2txt:13,bodi:[6,8,9,43,70,151,266,270,275,283,385],bond:[8,13,71,221,222,223,303],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,58],bop:386,born:[387,398],boundari:[7,59],box:[6,60,224],branch:503,brownian:388,buck:[389,390,398,429],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:72,ch2lmp:13,chain:13,chang:503,change_box:61,charmm:[6,20,178,391,426],chunk:[6,68,73,77,94,98,109,111,120,152,167,169,212],citat:7,class2:[9,21,44,179,349,392],clear:62,cluster:74,cmm:9,cna:75,code:6,coeffici:6,colloid:[9,340,394,472],colvar:[9,13,225],com:[76,77,153],comb3:395,comb:[299,395],come:5,comm_modifi:63,comm_styl:64,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,504,505,506,507,508,509,510,511,512],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,508],compute_modifi:107,condit:7,conduct:[6,331],conserv:401,constant:[6,508],constraint:7,contact:[78,126],contact_radiu:[],coord:79,core:6,coreshel:9,correl:[213,214],cosin:[23,24,25,26,27,28,181],cossq:351,coul:[387,389,390,391,392,396,397,398,411,418,422,426,438,446],coupl:6,creat:222,create_atom:172,create_bond:173,create_box:174,createatom:13,creation:7,csld:327,csvr:327,cubic:420,cuda:[9,14,115,118,149,159,206,219,233,238,242,263,272,309,310,326,328,339,387,389,391,392,404,410,411,418,419,421,424,436,462,464],custom:[8,196,197],cut:[50,383,389,392,396,399,406,408,418,419,426,434,438],cvff:352,damag:[80,127],data2xmovi:13,data:6,databas:13,deby:[3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4,18,40,41,42,221,381,406,491,496],advect:[3,6,324],advertis:8,advis:[376,443],afer:3,affect:[1,6,10,14,15,16,17,41,62,63,74,93,124,148,157,171,177,200,201,206,213,214,216,217,218,219,222,223,224,225,227,228,238,244,246,248,254,261,265,266,267,268,270,271,272,278,283,284,285,287,308,309,322,336,346,359,366,372,373,374,376,377,378,381,407,428,429,436,479,480,482,484,485,487,490,492],affin:[16,17,18,227,381,396],afil:242,aforement:18,afresh:[296,490,509],afshar:401,after:[],afterrun:490,afterward:3,afterword:42,ag1:172,ag2:172,again:[6,11,12,16,17,64,147,153,159,167,197,201,227,244,294,350,365,376,428,429,477,479,480,482,484,489,496,498,509,511],against:[11,12,13,66,228,376,444,445],aggreg:[6,12,67,70,72,82,98,115,122,244,260,306,308,322,477,510],aggress:[244,496],agilio:[9,13],agre:[3,8,193,374,383,416,445],agreement:[5,7],ahd:413,ahead:343,aidan:[0,5,7,9,13,369],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:200,akohlmei:[7,9,13,202,245],aktulga:[7,9,301,445],al2o3:452,al2o3_001:[125,309],al3:172,ala:[251,452],alain:9,alat:[289,431],alb:[442,465,467],albeit:307,albert:9,alchem:[92,167],alcohol:339,alcu:[382,387],alcu_eam:442,alderton:400,alejandr:[264,265],alessandro:13,algebra:434,algorithm:[0,1,6,7,8,9,42,63,201,210,221,224,227,251,253,254,278,291,299,308,311,312,331,332,336,339,344,372,373,374,378,381,403,407,429,434,449,451,477,479,496],alia:[9,12,16],alias:[1,367],aliceblu:201,align:[6,9,12,29,42,74,175,193,217,221,246,369,482,485,503],alkali:407,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,161,166,167,168,169,170,171,172,173,174,175,176,177,179,181,186,192,193,194,197,198,199,200,201,202,204,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,257,259,260,262,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,281,282,283,284,285,286,287,288,289,290,291,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,320,321,323,324,325,326,327,328,331,332,333,334,335,336,337,338,339,341,342,343,344,345,346,347,348,349,350,351,355,360,362,364,365,366,367,368,369,371,374,375,376,377,378,380,381,382,383,384,386,387,388,390,391,392,393,394,396,397,400,401,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,427,428,429,430,431,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,479,480,481,482,483,484,485,486,487,489,490,491,492,493,494,495,496,497,499,500,501,503,504,508,509,510,511,512,513],allen:[29,92,400,410],allentildeslei:92,allign:3,allindex:348,alloc:[3,5,6,8,9,11,12,62,238,338,375,377,381,440,445,482,490],allocat:3,alloi:[],allosw:74,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,56,59,60,61,63,64,65,80,97,113,115,149,151,152,153,166,171,172,173,175,181,192,193,197,198,200,201,202,204,205,207,209,210,211,213,214,215,216,217,218,219,221,223,224,225,226,227,228,232,233,238,240,241,242,243,245,248,251,254,255,259,261,264,265,289,293,294,295,296,297,298,302,308,309,311,313,315,316,320,324,331,332,333,334,336,337,338,339,340,341,347,349,351,360,366,367,369,374,375,376,377,380,381,384,387,388,389,390,391,392,397,405,407,411,412,413,414,419,423,428,429,434,436,442,445,446,449,451,452,461,471,473,477,480,482,484,485,486,487,488,489,492,494,495,496,499,500,504,509,510],almost:[2,3,12,62,246,298,336,367,378,381,461],alo:397,alon:[6,7,224,304,444,445,480],alond:13,along:[6,8,12,29,41,74,92,125,171,172,173,196,197,200,213,224,246,251,252,256,261,263,298,308,311,313,317,321,322,331,335,336,342,345,347,369,372,373,374,376,397,400,411,414,417,419,423,431,444,445,464,482,485,492,493,509],alonso:[432,433],alpha:[6,12,52,205,251,290,298,299,303,374,382,385,388,397,401,403,405,406,408,413,418,419,431,437,441,466,468,500,503],alpha_:[],alpha_c:427,alpha_i:453,alpha_ialpha_j:[],alpha_lj:427,alphabet:[2,3,22,37,45,56,65,181,192,204,351,360,375,394,462,482],alphanumer:[3,65,204,297,305,349,375,509],alreadi:[3,7,8,9,12,16,17,18,43,173,174,176,199,209,213,217,218,221,223,227,255,296,298,324,347,348,375,376,401,412,414,421,429,461,471,474,478,482,483,487,492,509],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,40,41,42,43,45,55,56,57,60,61,63,65,68,74,75,76,78,80,84,92,94,95,97,99,109,110,111,112,113,114,119,121,123,124,126,147,148,149,150,151,152,153,154,155,156,157,159,160,161,162,163,165,166,167,168,169,170,173,174,175,176,177,179,181,192,193,195,196,197,198,199,200,201,202,204,205,206,207,209,212,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7,193,213,217,218,221,224,227,228,242,248,251,262,264,291,299,308,331,360,367,372,373,376,378,381,414,427,436,440,482,491,492,495,496,502,503,508],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,92,124,163,164,200,222,223,224,225,228,237,248,251,262,264,266,267,268,269,270,271,272,294,295,312,324,328,342,366,367,373,471,477,479,491,497],chose:[465,467],chosen:[2,3,6,12,17,147,173,176,185,193,200,206,211,225,228,237,240,241,249,251,262,264,269,291,294,305,324,328,331,332,337,339,340,346,367,368,373,381,402,403,407,411,418,421,447,465,477,491,496,503],chri:171,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[68,78,95,99,110,112,121,153,168,170,213],chute:[4,9,10,243],ciccotti:311,cieplak:[6,179,494],cii:214,cij:214,ciko:2,circl:[43,74,320],circular:[3,6,151,195],circumst:18,circumv:[97,113,303],citat:[],cite:[3,7,8,12,248,452],civ:9,ckio:2,cko:2,cl1:172,clarendon:[29,400],clarifi:[7,465,467],clariti:349,clark:439,class2:[],classic:[0,3,5,6,7,8,9,238,291,298,303,336,361,407],classifi:[462,470],claus:480,clean:[6,12,14,15,17,490],cleanli:[481,512],clear:[],clearli:7,clebsch:147,clermont:[9,13],clever:486,click:[2,11,22,37,45,56,173,181,192,200,245,351,360,376,394,462,504],client:[245,247],climb:[263,376,496],clinic:[7,13],clo:[162,196,510],clock:[12,477,496],clockwis:342,clone:504,close:[3,6,11,12,13,40,42,69,74,148,176,197,223,224,225,242,249,251,264,285,308,311,342,345,365,367,370,372,373,376,381,383,387,397,398,417,431,436,448,450,464,467,486,492,503,504,506],closer:[3,10,42,123,171,196,197,221,225,229,333,376],closest:[223,289,308,339,410,446,461,471],cloud:[452,503],clovertown:18,clsuter:75,clump1:[293,308],clump2:[293,308],clump3:[293,308],clump:308,cluster:[],clutter:3,cmap:482,cmatrix:242,cmax:431,cmd:[11,12,291,493],cmdarg:11,cmin:431,cmm:[],cmoput:140,cn1:214,cn2:214,cna:[],cnn:214,cnr:[9,13],cnt:[414,486],co2:[41,172,311,375],coars:[7,9,10,29,36,41,55,185,293,308,324,412,447,491,494],coarser:[367,509],coarsest:147,code:[],coeff:[3,7,8,12,21,22,33,45,51,179,180,181,186,350,351,357,394,414,418,436,449,451,454,482],coeffcient:482,coeffici:[],coefficienct:401,coefficient0:405,coefficient1:405,coeffieci:[6,385,417],coeffincientn:405,coexist:[240,407],cohes:[6,408,431],coincid:[129,345,392,428,429,477],colberg:199,cold:[6,158,240,244,377,503],coldest:332,coleman8:9,coleman:[9,125,172,309],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,68,78,88,95,99,104,110,112,121,153,161,168,170,173,197,198,201,213,226,254,260,293,303,306,308,347,366,375,377,395,482,489,495,501,513],collid:[232,324,346],colliex:172,collinear:[3,293],collis:[3,251,324,342,346,404,411,474],colllis:324,colloid:[],colombo:40,colon:[202,347,483],color1:201,color2:201,color:[3,9,42,197,200,201,221,241,298,303],column:[3,6,9,12,13,43,65,67,68,69,70,72,74,78,80,82,84,86,95,97,98,99,110,112,113,115,117,120,121,122,123,124,126,147,148,153,161,168,170,171,172,193,197,198,201,204,212,213,214,216,217,218,219,254,261,262,298,308,325,326,336,346,409,413,444,445,483,497,499,509],columnar:171,colvar:[],colvarmodul:12,com:[],comamnd:227,comand:224,comannd:381,comb3:[],comb:[],comb_1:300,comb_2:300,combiant:398,combin:[3,6,7,9,11,13,36,41,65,67,72,82,92,98,109,115,122,151,152,166,197,200,210,216,245,254,264,291,297,312,328,337,345,348,350,366,367,369,373,381,395,397,398,403,407,408,414,426,427,453,463,465,467,470,473,485,490,495,503,509],come:[],comfort:[12,13],comit:504,comm:[0,3,11,12,63,76,199,245,247,248,367,376,381,401,436,441,464,484],comm_modifi:[],comm_modift:63,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,179,193,197,236,249,308,336,375,376,382,405,406,408,418,431,438,445,452,453,463,464,465,466,467,470,479,480,482,503,504,509],commerci:7,commit:[9,504],commmand:[3,6,12,61,114,286,417,476,477,479,496,512],common:[],commonli:[3,6,9,12,17,25,59,61,111,113,175,197,200,202,361,412,421,453,465,467,482,485,494],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,60,63,64,74,171,176,177,200,201,221,222,223,225,226,227,245,247,251,253,254,255,264,290,297,299,300,301,308,312,324,336,347,364,366,377,378,379,381,403,404,440,475,479,480,491,492,509,511,513],communc:366,comp:[7,199,247,248,311,367,376,407,436,441,446,460,464,466],compact:[65,204,394,462],compani:[5,7],compar:[1,3,4,6,8,12,17,40,91,117,125,156,172,181,192,201,231,299,347,349,366,367,374,376,431,452,477,496,497,503,508],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,9,21,22,37,44,45,56,180,181,192,350,351,360,393,462],compat:[3,5,7,8,9,11,12,13,17,18,42,74,124,126,184,197,202,206,212,213,214,216,217,218,219,221,290,302,328,331,338,341,344,366,381,415,434,436,464,479,480,509],compens:[6,222,223,306,377,407],compet:335,competit:367,compil:[3,7,8,9,12,13,14,15,16,17,18,19,171,197,199,200,202,245,335,367,381,434,482,483,487,509],compl:17,complain:[11,12,17],complement:431,complementari:[7,397,419],complet:[3,6,9,11,12,15,42,61,74,201,217,221,226,254,291,294,297,324,335,337,348,349,365,376,381,408,449,451,469,477,482,487,490,494,496,499,503,509],complex:[4,6,8,11,12,13,25,41,43,64,97,113,147,149,161,173,174,251,320,345,364,376,407,434,464,480,482,485,509],compli:[331,335],complic:[6,7,9,12,13,211,240,480],complier:12,compon:[3,6,8,12,63,65,68,69,76,84,93,94,95,96,97,99,100,103,110,111,112,113,114,115,116,117,119,120,124,134,137,138,139,140,143,144,145,147,148,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,168,169,170,196,197,198,200,201,207,208,212,213,214,215,216,217,218,219,220,224,225,227,228,233,238,243,247,248,251,254,256,260,261,263,264,265,269,270,271,272,283,284,285,287,288,290,291,292,295,306,308,310,311,313,317,318,321,324,327,328,329,331,338,339,344,345,346,366,369,373,374,375,376,381,401,407,411,428,429,449,451,452,453,482,483,492,500,509,510],componenet:6,composit:[6,211,251,405],compound:[396,407,408,470],compres:[74,121,213],compress:[],compris:[41,345,446,469],compton:[125,172],comptu:3,compuat:367,comput:[],computation:[3,6,222,223,336,387],computational:503,compute_arrai:8,compute_fep:[206,427],compute_group_group:240,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[125,309],compute_scalar:8,compute_temp:8,compute_ti:206,compute_vector:8,compute_xrd:172,concaten:[2,3,512],concav:345,concentr:[74,405],concept:[6,153,163,213,491],conceptu:[3,6,74,161,225,227,376,397,414,431,487],concern:[6,76,92,199,241],concetr:74,concis:[11,335],conclud:12,concret:8,concurr:[16,367,509],conden:[336,465,467],condens:[6,155,336,383,399,405,419,470],condit:[],conducit:6,conduct:[],cone:485,confer:434,confid:[3,496],config:[12,197,479],configfil:226,configur:[1,2,6,12,15,17,38,61,129,175,193,196,197,200,204,225,226,227,228,232,240,247,248,278,291,299,335,364,374,376,383,387,406,431,434,463,465,467,470,477,482,484,485,496,504],confin:[482,496],conflict:[3,12,41,198,436,480,504],conform:[3,6,13,61,224,225,263,307,313,335,359,376,407,494],confus:[3,470],conjuct:[9,401],conjug:[7,8,248,373,407,444,445],conjunct:[6,7,74,91,92,121,156,161,167,173,177,201,205,206,248,251,255,278,294,295,299,300,301,303,308,312,324,332,339,344,366,367,376,388,390,394,397,401,407,413,419,436,439,447,468,482,485,489,503,513],connect:[3,6,9,92,158,176,224,245,293,308,311,321,376,398,411,461,467,479,480,482,486,503],conput:3,consecut:[3,11,12,40,74,173,201,205,206,228,245,246,397,419,423,477,483,485],consequ:[1,6,211,336,418,496],conserv:[],consid:[6,73,74,81,92,122,155,158,159,176,197,198,201,205,206,212,214,217,221,223,224,228,252,265,290,308,331,332,335,336,339,367,394,407,414,445,446,452,461,477,478,480,483,484,485,487,490,492,500,503,509],consider:[6,8,248,249,327,328,329,381,491],consist:[3,6,8,9,11,12,41,43,67,72,82,98,110,115,118,119,122,153,156,158,173,185,196,202,207,208,213,227,228,231,233,238,241,248,249,250,261,264,266,267,268,269,270,271,272,273,274,276,277,278,279,281,282,283,284,285,286,287,295,298,303,305,307,308,327,328,329,330,340,366,367,369,375,376,381,383,387,389,395,397,407,410,414,417,428,429,431,434,436,446,449,451,452,464,471,480,482,483,484,485,486,487,494,503,509],consistent_fe_initi:210,consit:308,constant:[],constitu:[3,6,254,308,341,345,395,446],constitut:[449,451],constrain:[3,6,8,150,151,152,153,154,156,159,160,161,162,163,165,166,204,213,228,240,241,246,254,258,293,294,306,308,311,322,332,339,374,375,407,487,494,503],constraint:[],construct:[6,8,12,14,38,55,57,63,66,69,73,75,76,80,97,113,125,147,172,225,264,290,307,345,377,381,400,434,436,461,463,464,485,486,501,509],constructor:[8,11],consult:445,consum:[1,303,440,509],consumpt:364,contact:[],contact_stiff:[448,450],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,65,92,96,123,125,147,153,161,171,172,173,175,179,181,192,193,197,198,200,201,202,204,205,206,210,212,213,214,216,217,218,219,221,226,228,233,236,242,246,247,248,251,262,278,289,290,293,294,296,298,301,305,308,309,314,324,331,335,336,345,346,349,365,367,375,376,379,380,382,383,384,387,396,397,400,405,406,407,414,415,431,434,438,442,443,444,445,453,463,464,465,466,467,468,470,477,478,479,480,482,483,484,485,487,489,491,494,496,497,499,500,503,504,509,511,513],content:[4,8,9,12,18,445,498,500],context:[3,6,8,12,17,123,124,201,222,223,228,293,305,340,373,473,482,489,498,508,509,510],contibut:73,contigu:479,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,74,84,109,110,169,201,204,205,206,211,213,214,215,216,217,218,219,221,224,225,226,227,228,240,241,242,244,245,246,248,249,250,256,261,262,264,266,267,268,269,270,271,272,283,284,285,286,287,292,294,297,298,308,309,313,323,324,326,333,334,336,342,345,349,365,380,381,387,401,404,421,424,444,445,446,449,451,466,477,480,482,484,485,490,496,497,499,500,509,511],continuum:[6,7,9,210,336,449,451],contour_integr:210,contract:[61,225,227,264,295,308],contradictori:3,contrain:311,contraint:278,contrari:[242,249],contrast:[1,6,43,56,66,155,158,198,227,347,449,451,473,512],contrib:336,contribut:[3,4,5,6,7,8,9,12,13,17,65,68,70,71,73,74,77,78,80,83,89,92,93,94,95,96,99,108,110,112,114,115,116,117,119,121,124,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,206,211,212,213,214,216,217,218,219,225,240,248,251,254,255,259,265,285,286,293,294,302,305,308,309,311,338,366,374,376,384,401,404,405,407,414,428,429,434,436,444,445,452,494,500,503,504],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,92,96,129,147,182,197,198,200,204,210,211,221,225,226,227,244,245,248,249,264,266,267,268,269,270,271,272,295,300,308,315,316,327,328,329,336,340,364,366,378,407,410,434,444,445,448,450,463,467,477,479,491,497,498],control_typ:210,controlfil:445,convect:96,conveni:[6,12,29,197,202,219,309,369,453,504,509],convent:[3,8,29,184,191,192,198,201,307,321,348,405,407,509],converg:[3,6,42,93,197,198,200,202,207,221,224,225,233,238,269,298,300,303,307,311,372,373,374,376,396,397,419,452,477,489,496],convers:[3,8,147,200,201,211,214,295,366,397,398,399,407,419,423,427,439,480,496,508],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,61,65,74,96,173,180,197,200,201,214,219,262,294,347,350,352,356,359,369,376,382,405,434,465,467,474,480,482,483,484,489,499,503,508,509,511,513],convex:[43,345],convinc:[7,12],cook:9,cooki:7,cool:[7,163,244,306],cooordin:[197,198],cooper:[5,7],coord123:121,coord1:[3,121,213,217,218],coord2:[3,121,213,217,218],coord3:[3,121,213,217,218],coord:[],coordb:452,coordbb:452,coordiat:374,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,61,63,64,65,68,70,74,77,78,80,84,92,94,95,99,109,110,112,120,121,123,141,147,156,162,168,170,171,173,177,196,197,198,199,200,201,202,204,207,212,213,216,217,218,221,222,223,224,225,226,227,228,231,233,234,238,240,243,244,245,246,247,248,249,261,263,264,266,267,268,270,271,272,285,288,289,290,293,294,295,305,306,308,310,311,313,318,321,322,323,324,326,334,335,336,343,344,346,347,369,374,375,376,381,382,383,386,406,452,477,482,483,484,485,487,490,492,496,503,509,510],coordn:[121,213],coorind:[],copi:[0,3,4,8,9,11,12,15,17,41,126,200,336,376,394,444,480,504],copper:474,coproccesor:16,coprocessor:[1,7,9,16,17,381,495],coproprocessor:17,copy_arrai:8,copyright:[7,8,293],coral:201,core:[],core_shel:155,coreshel:[],cornel:[6,179,494],corner123i:120,corner123x:120,corner123z:120,corner1i:120,corner1x:120,corner1z:120,corner2i:120,corner2x:120,corner2z:120,corner3i:120,corner3x:120,corner3z:120,corner:[3,6,41,120,200,345,346,369,469,482,504],cornflowerblu:201,cornsilk:201,corp:9,corpor:16,corr:396,correct:[3,6,9,11,12,16,17,61,92,93,108,109,114,117,123,155,160,167,198,200,227,240,242,248,264,265,285,293,295,298,335,341,345,366,376,382,383,384,385,386,387,388,389,390,391,392,393,395,396,397,398,399,400,401,404,405,406,407,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,469,470,472,473,474,475,482,497,500,503,504],correction_max_iter:210,correctli:[3,8,11,17,74,84,108,109,110,150,151,152,154,156,158,159,160,161,162,165,166,169,197,201,207,228,233,238,249,258,264,265,301,308,311,321,323,342,345,376,377,381,399,429,434,479,480,482,492,504,508,510],correl:[],correpond:236,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,73,74,92,102,103,116,119,120,121,122,125,126,134,137,138,139,140,141,143,144,145,147,150,151,160,167,171,172,179,180,181,182,183,184,185,187,188,190,191,193,196,197,198,200,201,205,206,207,213,215,216,217,218,220,223,225,227,234,238,239,243,248,251,252,260,261,262,264,266,267,268,269,270,271,272,273,274,278,281,283,284,285,287,290,291,295,300,308,310,311,327,329,331,340,341,342,344,345,346,348,350,351,352,353,355,356,359,361,367,371,373,375,376,382,383,385,388,389,390,391,392,393,394,395,396,397,400,401,405,406,407,408,409,410,411,412,413,414,417,419,420,421,422,423,424,425,426,427,428,431,432,434,436,437,438,439,441,442,444,445,446,447,452,453,454,463,464,465,466,467,470,472,473,474,477,479,480,482,483,485,495,496,497,499,500,503,509],correspondingli:[428,429,491],corrupt:3,cosin:[],cosineshift:27,cosmo:[242,247],cossq:[],cost:[1,6,10,11,12,17,40,42,74,116,125,148,172,200,201,213,217,218,221,222,223,237,264,300,336,366,367,379,397,419,423,434,436,463,479,491],costheta0:[463,465,467,470],costheta:442,costli:[11,93,242,377],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,61,68,74,78,92,95,99,110,112,116,119,121,153,163,168,170,186,197,198,200,201,205,206,213,214,217,221,227,238,247,297,298,299,303,306,308,310,324,325,331,335,336,337,341,345,347,349,357,363,365,372,374,377,381,384,409,413,414,417,444,445,478,479,480,482,484,486,489,490,497,498,503,509,510],coulomb:[3,5,6,7,8,9,10,12,14,15,18,75,93,114,115,123,148,174,178,299,301,337,366,367,374,381,388,390,391,392,393,396,397,398,399,400,407,411,412,414,419,423,427,430,436,439,444,445,447,452,462,467,468,470,473,487,494,500,503,508],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,65,70,80,96,121,123,124,161,171,177,207,208,211,213,216,217,218,220,221,228,233,237,240,246,264,278,294,311,327,328,345,367,374,375,376,378,381,409,413,436,500,509],counter:[3,342,477,488,490,496],counteract:240,counterbal:244,counterbalanc:29,counterpart:[197,308,477],counterproduct:18,coupl:[],courant:314,cours:[3,8,133,135,167,197,205,206,241,307,321,335,341,343,344,346,347,367,428,454,479,482,495,503,509,511],courtesi:369,cov:452,coval:[6,9,29,407,431,452,503],covari:242,cover:[6,74,193,201,210,251,407,469],coverag:[74,217],cpc:247,cpp:[1,3,6,8,9,11,12,13,92,197,205,206,238,311],cpu:[1,3,9,10,12,14,15,16,17,18,65,74,201,215,231,249,337,364,367,381,394,462,477,495,496,499,500,501,509],cpuremain:500,cr2:172,cr3:172,crack:[4,377],crada:[5,7],crai:[5,7,13,18,197],crash:[3,12,377,503],craympi:381,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:210,create_faceset:210,create_group:199,create_nodeset:210,createatom:[],creation:[],crimson:201,critchlei:293,criteria:[3,123,174,200,201,222,223,224,259,374,441,469,484,487,509],criterion:[12,42,128,173,176,211,221,224,240,278,300,314,342,347,374,376,396,407,411,452,487,496,497],criterioni:496,critic:[6,49,50,262,331,336,374],crmax:74,crmin:74,cross:[3,12,22,74,94,151,171,181,197,198,200,212,217,223,227,261,263,285,308,317,321,323,332,339,351,369,376,392,401,404,405,412,413,414,419,421,423,442,447,449,451,465,467,474,482,486,492,511],crossov:1,crossterm:482,crozier:[0,7,13],crucial:298,crystal:[3,4,6,13,76,113,289,290,334,369,377,482,486,500,503],crystallin:[6,109,290,369,466,503],crystallis:331,crystallogr:[125,172],crystallograph:[369,500],crystallographi:[125,172,369],cs1:172,cs_chunk:6,cs_im:[41,482],cs_re:[41,482],csanyi:[147,443,453],cscl:431,csequ:6,csh:[11,12,394],cshrc:[11,12],csic:[406,463,465,467,470],csinfo:6,csisi:[406,463,465,467,470],csld:[],cst:405,cstherm:6,cstyle:479,csvr:[],ctcm:[382,405],ctemp_cor:231,cterm:313,ctr:9,ctype:11,cu1:172,cu2:172,cu3au:431,cube:[6,42,171,176,221,231,345,369,503],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_hom:[9,15],cuda_prec:[9,15],cufft:14,cuh:387,cummul:[3,6,219,222,223,224,226,237,242,248,250,324,327,328,329,330,332,339,413,500],cumul:[6,211,213,216,217,218,232,240,248,262,264,269,278,308,309,376],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,61,63,65,74,76,84,92,108,109,115,123,124,137,148,153,161,163,169,171,174,177,196,197,198,199,200,201,202,205,206,210,213,217,218,219,221,222,223,224,225,226,227,228,232,233,238,240,242,245,246,248,254,261,264,265,270,271,272,278,283,284,285,287,293,294,299,300,302,305,306,307,308,311,312,313,314,315,316,317,318,320,322,323,324,327,328,329,335,336,339,340,341,342,343,344,346,347,349,364,365,366,367,370,371,373,374,375,376,381,387,394,396,400,405,407,408,411,414,415,418,428,429,431,432,433,436,442,444,445,448,449,450,451,454,465,467,468,471,477,478,479,480,482,483,484,485,486,488,489,490,492,494,496,497,499,500,504,509,510,511,512,513],curv:[6,173,240,290],curvatur:[410,446,474],custom:[],cut0:480,cut1:491,cut2:491,cut:[],cuthi:[289,301],cutinn:[389,428,429],cutlo:[289,301],cutmax:442,cutoff1:[393,400,419,423,427,430,439,447],cutoff2:[388,390,391,393,399,400,419,423,427,430,439,447],cutoff:[3,6,8,10,16,18,40,46,47,55,56,63,73,75,76,80,92,97,113,115,122,123,147,171,174,176,177,223,224,229,236,289,298,299,301,303,305,308,312,324,337,341,345,347,364,366,367,374,377,378,379,381,382,383,384,385,386,387,388,389,390,391,392,393,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,414,415,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,452,453,454,455,456,457,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,480,484,487,491,503,509],cutoff_glob:[],cutoff_inn:[],cutoffa:406,cutoffc:406,cuu3:405,cval:172,cvd:331,cvel:313,cvff:[],cwiggl:[3,261,341,344,346,509],cyan:[2,200,201],cycl:[3,240,262,264,265,269],cyclic:[3,193],cygwin:12,cylind:[3,4,74,200,213,246,294,342,345,485],cylindr:[6,246,321,342],cypress:381,cyrot:387,cyrstal:290,d3q15:251,d3q19:251,d_double_doubl:15,d_e:336,d_flag2:297,d_flag:297,d_name:[120,197,297,326,492],d_single_doubl:15,d_single_singl:15,d_sx:297,d_sy:297,d_sz:297,daan:334,dai:12,daili:12,daivi:285,damag:[],dammak:303,damp:[3,6,204,209,248,249,250,255,264,265,269,295,298,299,303,308,327,328,340,342,343,373,374,376,388,390,392,397,400,407,411,419,427,439,447,462,468,496,503],damp_com:249,damp_drud:249,dampen:[308,503],dampflag:[342,411],dan:17,danger:[3,12,240,347,401,500],dangl:176,daniel:9,darden:[367,400],darkblu:201,darkcyan:201,darken:200,darkgoldenrod:201,darkgrai:201,darkgreen:201,darkkhaki:201,darkmagenta:201,darkolivegreen:201,darkorang:201,darkorchid:201,darkr:201,darksalmon:201,darkseagreen:201,darkslateblu:201,darkslategrai:201,darkturquois:201,darkviolet:201,dasgupta:299,dash:[411,499],dat:[6,96,193,210,478],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,309],dataset:309,datatyp:3,date:[0,4,6,12,13,196,444,445,509],datom1:122,datom2:122,datom3:122,datom4:122,datum:[3,6,43,67,70,72,82,98,115,122,197,214],davenport:430,davi:341,david:[9,19,366,367,465,467],daw:[405,442],dbg:14,dcd:[3,6,7,197,199,200,201,202,291,483,487],ddim:196,deactiv:427,dealt:247,debug:[6,7,11,12,13,14,17,125,129,172,173,291,296,364,366,381,415,436,471,480,481,489,492,499,509],deby:[],decai:[97,397,474],decid:[3,6,12,16,74,261,297,308,337,497,504],decipher:369,declar:199,declin:324,decod:200,decompos:[92,453],decomposit:[3,5,7,18,64,210,291,312],decoupl:[6,503],decreas:[3,197,198,207,208,215,224,227,233,238,240,248,335,366],decrement:313,deepli:363,deeppink:201,deepskyblu:201,def:[12,13,480],defaul:63,defect:[6,73,171,434],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,179,180,181,182,183,184,185,187,188,190,191,192,193,194,195,196,197,198,199,200,201,204,205,206,207,208,209,210,211,212,213,214,216,217,218,219,220,221,222,223,224,225,227,228,231,232,233,235,238,239,240,243,246,247,248,249,250,251,259,261,263,264,265,266,267,268,269,270,271,272,274,275,276,279,281,282,283,284,285,286,287,289,290,291,293,294,295,297,299,301,306,308,309,310,311,314,318,322,324,326,327,328,329,330,332,333,334,336,338,339,341,342,343,344,345,346,347,349,350,351,352,353,354,355,356,359,360,361,362,364,366,367,369,371,373,374,375,376,377,378,379,380,381,383,384,385,386,388,389,390,391,392,393,394,395,397,398,400,401,402,403,404,406,407,409,410,411,412,413,414,415,417,419,420,421,422,423,424,425,426,427,428,429,430,434,435,436,437,438,439,441,442,444,445,446,447,448,449,450,451,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,479,480,482,483,485,486,487,488,491,492,493,494,496,497,499,500,503,505,506,507,508,509,510],definit:[2,3,6,8,12,13,81,83,123,147,201,213,214,215,216,217,218,219,227,235,246,269,309,326,338,341,344,346,348,360,364,375,384,387,395,402,403,407,417,442,449,451,453,469,480,482,484,491,493,508,509],defint:500,deform:[],deg2theta:172,deg:503,degener:[3,293],degrad:[8,18,290,367,491],degre:[3,6,8,20,21,24,28,29,32,35,36,38,67,82,97,98,100,102,103,105,107,108,113,119,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,172,173,179,180,183,184,191,193,196,200,213,224,231,240,242,243,248,249,254,264,265,269,270,271,272,283,284,285,287,291,293,307,308,311,327,328,329,334,350,352,356,359,361,374,400,405,413,492,500,503,510],degress:[153,213],del:496,delai:[3,6,12,377,404,500],deleg:414,delet:[2,3,7,8,12,55,59,62,65,171,176,177,204,213,214,216,217,218,219,222,224,237,240,264,309,327,328,347,349,365,375,377,380,436,461,482,483,484,485,493,494,499,504,505,507,509,510],delete_atom:[],delete_bond:[],delete_el:210,deli:196,delimit:[480,509],deloc:[265,407,452],delr:431,delt_lo:496,delta:[],delta_1:387,delta_3:387,delta_7:387,delta_conf:3,delta_ij:[431,442],delta_mu:[],delta_pi:387,delta_r:442,delta_sigma:387,delta_ua:[],delx:196,delz:196,dem:[],demand:303,demo:11,demon:288,demonstr:[298,431],den:294,dendrim:413,denniston:[9,251,253,254,255,290],denomin:[7,178],denot:[125,231,249,290,301,303,397,412,414,445,449,451],dens:[74,224,407],densiti:[3,6,7,9,18,41,42,61,106,123,133,147,159,171,173,205,206,210,213,217,218,221,227,238,251,254,257,258,290,294,295,299,336,341,369,371,375,382,387,405,431,432,433,442,446,452,456,458,459,460,482,491,492,500,508],density_continu:451,density_summ:451,depart:[0,7],departur:[262,298],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,63,65,67,70,72,73,74,82,97,98,109,115,116,119,120,121,122,126,147,150,156,160,161,167,173,174,179,180,181,182,183,184,185,187,188,190,191,192,193,196,197,198,200,201,204,205,206,207,208,211,213,215,216,217,219,220,221,223,225,227,233,234,239,242,243,244,246,248,249,251,253,254,261,264,266,267,268,269,270,271,272,273,274,281,283,284,285,287,289,300,303,305,308,310,311,312,318,324,327,328,329,331,333,335,336,338,340,341,344,345,346,347,349,350,351,352,353,355,356,359,361,367,369,374,375,377,378,379,381,382,383,385,386,387,388,389,390,391,392,393,394,395,396,397,398,400,401,405,406,407,408,409,410,411,412,413,414,419,420,421,422,423,424,425,426,427,428,431,432,434,435,437,438,439,441,442,444,445,446,447,452,453,454,462,463,464,465,466,467,468,470,472,473,474,477,479,482,484,485,488,492,494,496,499,500,502,509,510],dependend:6,depflag:12,dephas:[477,496],depos:228,deposit:[],deprec:[3,299,444],depth:[52,151,200,336,410,446],dequidt:9,der:[92,114,395,396,427,444,445,473,503],deriv:[6,7,8,9,38,57,65,92,147,167,193,214,225,227,240,248,261,264,266,267,268,269,270,271,272,289,295,299,303,333,334,336,341,342,345,373,375,383,387,395,400,407,408,412,421,425,426,431,434,444,445,462,464,473,503],derjagin:473,derlet:289,descend:201,descent:[7,373],descib:[41,200,299],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,64,65,70,73,74,76,93,117,120,123,125,137,147,148,151,152,153,157,158,161,164,166,167,171,172,173,175,176,185,190,193,197,198,199,204,205,206,213,214,215,216,217,218,219,221,224,225,226,227,228,230,231,236,241,242,245,246,247,248,249,250,251,253,254,255,259,263,264,265,269,277,286,289,291,296,297,298,299,300,301,308,313,321,324,325,326,327,328,329,330,331,332,333,334,339,341,342,344,349,366,367,369,372,373,374,375,376,380,383,384,386,388,389,390,392,393,394,395,396,397,400,405,407,408,410,411,412,414,417,419,420,421,422,423,424,425,426,427,428,429,430,431,434,435,441,442,443,444,445,446,447,452,453,454,461,462,463,464,465,466,467,468,470,472,473,474,475,477,479,480,482,483,484,485,486,492,495,496,499,504,509,510,511],descript:[],descriptor:[147,197,415],deserno:367,design:[0,3,6,7,8,11,13,14,15,17,125,155,158,172,210,224,230,231,264,265,289,290,309,331,336,384,385,386,389,392,397,399,407,427,428,429,432,433,442,445,464],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,61,74,93,96,119,124,148,155,173,186,196,213,219,225,227,238,240,241,248,249,250,254,264,285,293,294,295,296,299,303,308,311,324,327,328,329,330,335,342,357,363,366,367,369,372,374,375,376,401,405,413,428,429,463,465,467,478,479,480,482,486,491,496,497,499,500,509,510,511],desk:7,desktop:[4,6,7,10,12,200],despit:503,destabil:387,destre:359,destroi:[9,11,40,222,223],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,65,68,69,70,74,78,81,95,96,99,108,110,112,114,116,118,119,121,124,126,147,148,150,151,152,153,156,166,167,168,170,173,174,177,178,181,192,196,197,198,200,201,204,205,206,210,213,214,215,216,217,219,221,223,224,225,226,227,228,238,240,241,242,243,245,246,248,250,251,255,261,262,263,264,265,266,267,268,269,270,271,272,276,278,283,284,285,286,287,290,293,294,295,297,298,300,301,302,308,311,312,324,327,328,329,330,331,332,334,335,336,337,338,339,340,347,349,351,360,366,367,370,374,375,377,378,381,382,383,384,386,387,389,391,392,393,394,395,396,397,400,401,407,408,410,411,412,413,414,419,420,421,422,423,424,425,426,427,428,429,430,431,435,436,441,444,445,446,452,453,454,462,469,472,473,475,480,482,483,484,485,487,488,491,492,494,497,500,501,504,509,510,513],detect:[2,3,12,43,63,65,91,97,239,294,335,376,396,413,418,477,479,482,493,496,509],determ:381,determin:[1,3,6,8,9,12,15,40,41,43,52,59,60,61,63,64,70,74,92,108,114,116,119,125,126,134,148,161,162,171,172,173,196,197,198,200,201,202,203,207,208,209,212,213,214,215,216,217,218,219,220,221,225,227,228,231,233,240,243,244,246,248,249,254,259,261,262,264,270,271,272,283,284,285,287,289,291,294,295,298,305,306,307,308,309,310,314,316,318,324,327,328,329,331,337,338,341,342,343,344,345,346,347,360,366,367,369,375,377,378,381,383,384,391,396,400,404,405,409,411,414,415,423,431,434,436,445,446,452,461,464,468,473,479,482,483,485,487,489,492,496,498,499,501,508,509,510],determinist:312,detil:115,devan:[9,447],devanathan:467,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,245,269,293,298,299,302,383,387,407,433,434,452,470,484],devemi:9,deviat:[262,269,289,409],deviator:9,devic:[1,3,12,15,17,245,381],device_typ:381,devin:[300,396],devis:433,dfactor:200,dff:503,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,367],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,302,434],dhi:[61,196,227,294],dhug:[262,298],dhugoniot:[262,298],dia:431,diagnost:[],diagon:[3,6,88,147,148,149,225,264,295,308,339,449,451],diagonalstyl:453,diagram:[42,125,172,192,221,291],diallo:413,diam:[200,201,294,375],diamet:[3,6,41,43,120,173,197,198,200,201,205,206,248,294,308,324,326,340,342,375,395,410,411,421,446,469,473,482,483,492],diamond:[369,407,431],diamter:[41,294],dick:6,dicsuss:261,dictat:[211,262],did:[3,12,374,401,404,405,411,436,465,467,490],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,169,338,366],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,63,66,70,73,74,92,97,100,102,103,127,147,150,151,152,153,154,156,159,160,161,162,163,165,166,167,173,174,176,181,192,193,196,197,200,201,204,206,209,211,213,216,221,222,223,224,225,226,227,231,236,239,240,241,242,243,244,245,248,249,251,261,264,265,266,267,268,270,271,272,274,276,279,281,282,283,284,287,289,291,293,295,298,299,300,303,306,308,311,313,321,322,324,327,328,329,332,333,334,336,339,340,341,342,345,349,350,360,363,365,366,367,369,370,372,373,375,376,378,379,380,381,382,383,387,391,392,394,395,396,401,402,403,405,407,410,411,412,414,417,419,420,422,423,430,431,432,433,435,436,438,442,444,445,446,447,448,449,451,452,453,454,462,463,464,465,467,469,470,473,476,477,479,480,482,484,485,486,487,490,491,492,494,496,497,499,500,501,503,508,509,510,511],differenti:[1,3,6,29,193,366,397,442,466],difficult:[225,291,381,413,491],difficulti:[97,113,311,444],diffract:[],diffus:[],digit:[2,3,201,349,434,509],dih_table1:193,dih_table2:193,dihder:[],dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:223,dihydrid:407,dij:311,dilat:[],dim1:3,dim2:3,dim:[3,61,74,150,154,155,156,159,160,161,162,163,165,173,196,217,227,246,342,369,431,485,508,509,510],dimdim:509,dimems:290,dimens:[],dimensinon:74,dimension:[3,40,97,119,125,147,150,153,154,155,156,159,160,161,162,163,165,172,195,213,217,263,290,336,369,372,376,442,482,492],dimensionless:[111,128,129,131,134,136,138,143,147,336,367,453,473],diment:3,dimentionless:142,dimer:[6,308,431],dimgrai:201,dimstr:[42,221],dinola:[295,327],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,41,197,198,326,503],dir1:493,dir2:493,dir:[1,3,4,8,10,11,12,262,289,298,323,442,444,445,480,493,509],dirac:147,direc:442,direct:[],directli:[3,6,8,9,11,12,92,120,147,149,197,198,199,200,207,233,242,246,251,290,309,328,340,342,343,344,345,369,373,381,382,383,388,390,391,397,400,405,407,419,423,436,439,447,461,480,492,493,494,500,509],directoi:14,directori:[],disabl:[3,12,16,336,418,480,495,509],disadvantag:[6,221],disallow:[197,227,264],disappear:484,discard:[2,3,42,74,215,217,221,337,345,479,484,485],discontinu:[193,374,425],discourag:431,discov:[13,337],discret:[6,8,41,43,200,201,248,251],discuss:[],disk:[6,89,90,97,166,195,228,240,294,480],disloc:[73,434],disord:[40,73,434],disp:[],dispar:446,disperion:[400,423],dispers:[3,6,7,9,171,290,366,367,391,400,423,428,436,445,464,470],displac:[],displace_atom:[],displace_box:61,displacemet:485,displai:[11,13,22,37,45,56,181,192,197,200,351,360,394,462],dispters:3,disregard:434,dissip:[6,9,41,85,86,235,241,248,290,312,333,334,389,401,402,403,411,428,429,462],dissolut:222,dist:[6,72,96,115,124,197,291,307,404,461,477,510],distanc:[],distinct:[6,231,305,366,446],distinguish:[6,91,147,254,407,481,509],distort:[171,382],distrbut:382,distribut:[],distro:[118,394,441,442],ditto:[8,12,14,15,16,17,18,43,122,223,474,480],div:8,divd:124,diverg:[3,12,40,308,334,484,503,511],divid:[3,6,16,42,96,119,124,133,135,148,170,171,181,192,201,213,214,216,221,227,289,332,339,344,366,374,376,408,445,452,470,491,499,509],divis:[6,251,387,417,427,479,500,509],dl_poli:[6,7],dlambda:167,dlammps_async_imd:245,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,200],dlammps_gzip:[3,12,197,200,335,482,483,487],dlammps_jpeg:[3,12,200],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,200],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,197],dlen:492,dlmp_intel_offload:[9,12,16],dlo:[61,196,227,294],dlopen:6,dlvo:[7,395,473],dm_lb:251,dmax:[324,372],dmpvtk:198,dmpvtp:198,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,56,59,61,65,68,70,78,92,95,99,108,110,111,112,114,116,118,119,121,124,126,148,151,152,153,166,168,170,173,174,175,181,192,196,197,198,199,200,201,202,204,205,206,211,212,213,214,215,216,217,218,219,228,240,248,249,259,264,265,270,271,272,276,283,284,285,286,287,294,297,308,321,324,327,328,329,338,342,345,347,349,351,360,365,374,375,376,381,382,383,386,394,396,397,405,406,408,413,414,416,417,431,432,433,436,438,441,442,443,453,462,463,465,467,469,470,480,482,483,484,485,487,490,491,492,499,500,504,509,510,511,512],docuement:446,dodd:43,dodgerblu:201,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,40,42,43,51,55,57,61,64,65,69,73,74,75,92,93,96,110,114,117,123,124,125,149,151,153,155,156,161,163,167,172,173,174,175,177,179,181,186,192,193,196,197,198,199,200,201,204,210,211,213,217,220,221,223,224,225,227,231,233,236,237,240,241,244,246,248,249,251,254,260,264,265,266,267,268,270,271,272,283,284,285,286,287,295,296,297,301,303,306,308,324,327,329,331,332,336,339,340,341,344,345,346,347,352,353,354,356,357,359,365,366,367,368,369,375,376,377,382,383,384,385,386,387,389,391,392,393,395,396,397,398,400,401,404,405,406,407,409,410,411,412,414,415,416,417,418,421,422,424,425,426,428,429,431,432,433,434,436,442,443,444,445,446,448,449,450,451,452,453,454,455,456,457,458,459,460,461,463,464,465,466,467,468,469,470,472,473,474,475,477,478,479,480,482,483,484,485,486,489,490,492,493,494,495,496,499,500,503,504,509,513],doegenomestolif:7,doesn:[3,7,8,12,173,197,198,211,217,218,321,375,377,381,383,396,406,416,444,445,463,465,466,467,470,482,484],dof:[3,8,119,151,152,153,166,213,308,510],dof_per_atom:[153,213],dof_per_chunk:[153,213],doff:[375,482],doi:[6,226],domain:[3,6,7,12,13,18,40,42,43,60,63,64,74,125,162,172,175,196,199,200,201,204,211,221,225,227,228,244,247,251,264,265,291,303,308,312,336,341,342,366,367,376,381,404,436,477,479,482,486,499],domin:[1,407,496],don:[0,8,9,12,13,123,176,207,233,249,297,345,431,452,480,482,504],donadio:328,done:[1,3,6,7,8,12,14,15,16,17,18,38,40,42,57,61,64,74,167,170,173,176,193,197,200,201,210,211,213,215,216,217,218,219,221,222,223,224,225,227,228,236,238,240,245,246,248,249,256,264,270,271,272,283,284,285,287,288,290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35,36,38,44,48,49,50,52,54,57,61,156,157,180,182,225,227,240,241,242,249,251,264,269,285,298,299,303,307,311,313,321,324,331,332,334,339,350,352,356,359,396,431,438,452,503],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:210,equival:[6,12,13,29,61,63,131,132,140,145,171,175,201,216,219,225,227,240,248,264,285,295,307,308,344,401,407,452,465,467,482,485,490,491,500,503],equlibrium:6,equliibr:[299,301],er3:172,eradiu:[41,120,198,407,482],eras:[310,333],erat:[227,429],erc:397,erfc:[397,419,436],erforc:[120,198],erg:508,erhart:[211,405,465,467],ermscal:384,ernst:9,eror:3,eros:431,erose_form:431,erot:[],errata:[465,467],erratum:341,erron:3,error:[],erta:411,ervel:[120,198,482],escap:[228,503],especi:[8,16,161,173,204,211,221,240,298,303,306,307,381,479],espresso:[9,302],essenti:[8,11,12,27,93,135,154,155,156,159,160,161,162,163,165,182,214,269,290,340,367,383,397,419,467,487,500],essex:29,establish:[92,244],estim:[1,3,6,10,12,38,42,57,96,148,210,221,232,262,324,331,366,367,372,436,445,464,496,500],esu:508,esub:431,eta:[6,251,264,298,299,301,340,406,408,410,442,466,470,508],eta_dot:264,eta_ij:442,eta_ji:408,etag:[41,482],etail:500,etap:264,etap_dot:264,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,63,70,94,95,96,100,116,117,120,122,148,150,153,154,155,156,157,159,160,161,162,163,165,167,173,175,176,177,186,197,198,200,201,204,205,210,211,212,213,216,217,218,219,222,223,227,228,238,240,241,248,264,294,305,309,336,337,345,349,365,366,374,375,376,377,379,405,406,414,427,429,434,440,444,445,463,465,467,470,477,480,482,483,484,489,491,492,496,497,498,499,500,501,503,508,509,511,513],ethernet:18,etol:[374,376,477,496],etot0:298,etot:[6,100,102,103,117,148,159,201,231,249,262,298,499,500],eu2:172,eu3:172,euler:[374,376],eulerian:210,euqat:455,europhi:251,ev_tal:8,evalu:[2,3,9,11,12,38,57,71,74,92,93,96,114,124,126,147,149,153,163,171,173,196,197,198,200,201,205,206,207,208,210,212,213,214,215,216,217,218,219,220,227,233,241,243,244,246,247,248,249,290,296,299,310,314,318,327,328,329,338,341,344,346,347,349,366,367,372,374,381,434,436,442,448,450,452,464,477,478,480,484,485,487,489,490,491,492,496,498,500,509,510],evalut:[349,480],evan:[161,285],evanseck:[6,20,179,392,494],evapor:[],evaul:[8,374],evdwl:[114,444,445,500],even:[3,6,8,12,15,17,18,34,40,42,53,59,61,63,65,73,74,93,114,126,171,174,175,189,193,197,198,201,204,205,206,211,212,213,216,217,218,219,221,222,223,225,227,228,231,246,249,262,264,265,290,294,303,305,308,309,320,324,332,336,339,341,345,347,358,366,372,374,376,381,386,407,408,411,414,417,436,446,470,471,475,482,483,485,487,488,489,491,492,494,497,499,500,501,503,513],evenli:[3,42,148,193,221,251,417,471],event:[],eventu:[3,6,12,15,175,299,496],ever:[9,55,57,247,324],evera:[395,410,446,462],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,74,75,96,120,126,135,161,176,197,198,199,200,201,202,204,205,206,207,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,227,228,232,237,238,240,242,244,245,246,251,252,260,264,265,269,288,289,290,294,295,296,297,298,299,300,301,303,305,306,308,309,311,313,324,326,327,328,329,330,331,332,335,336,337,338,339,347,349,365,367,376,377,378,381,401,404,414,427,444,445,452,458,476,477,478,482,484,486,487,489,490,491,496,497,498,500,504,509,513],everyth:[8,114,504],everywher:[123,421],eviri:407,evolut:[242,251,291,477],evolv:[251,291,337],ewald:[2,3,5,6,7,8,9,12,93,117,125,148,337,366,367,374,388,390,391,397,400,407,419,423,439,447,462,464],ewald_disp:400,ewalddisp:3,exact:[22,42,45,74,129,167,176,181,221,224,241,242,248,249,250,294,303,304,324,336,351,366,394,484,489,496,509,511,513],exactli:[3,6,12,14,17,38,42,43,57,61,74,75,96,123,151,157,164,173,193,205,206,216,221,227,232,236,241,248,249,250,265,277,278,286,290,298,324,329,330,343,381,394,401,405,411,414,428,436,464,484,485,492,496,509],exager:503,examin:[6,8,17,224,290],examp:[480,509],exampl:[],exce:[3,6,16,17,18,42,60,74,175,212,213,216,217,218,219,221,225,227,232,237,264,290,305,309,315,316,324,374,381,482,509],exceed:[3,42,61,221,227,264,324,490],excel:407,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,61,62,65,74,94,95,115,116,119,124,148,150,151,152,153,154,155,156,157,159,160,161,162,163,164,165,166,173,177,179,180,181,182,183,184,185,187,188,190,191,192,193,196,197,198,201,204,207,213,214,216,220,221,225,227,234,239,240,243,246,248,250,264,265,266,267,268,269,270,271,272,273,274,277,278,281,283,284,285,286,287,291,300,301,308,310,311,321,324,327,329,330,336,340,344,347,348,349,350,351,352,353,355,356,359,360,361,366,367,369,371,375,376,377,379,380,381,382,383,385,388,389,390,391,392,393,394,395,396,397,399,400,401,405,406,407,408,409,410,411,412,413,414,419,420,421,422,423,424,425,426,427,428,429,432,437,438,439,441,444,445,446,447,454,462,463,464,465,466,467,470,472,473,474,477,479,480,482,484,485,487,490,491,492,493,494,496,500,503,508,509,510,512],excess:[215,407],exchang:[2,3,6,8,63,64,204,210,211,240,248,300,308,332,336,339,366,381,407,497],exchange:366,excit:407,exclud:[3,6,9,12,16,17,65,74,119,147,153,160,161,177,197,213,217,222,223,252,260,293,306,308,331,342,347,374,375,377,389,411,414,417,428,429,436,461,494],exclus:[1,3,12,16,92,381,396,434,436,491,501],excurs:[264,477],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,62,174,200,245,302,349,365,368,380,478,480,490,493,496,509],exempl:452,exemplari:241,exemplifi:407,exert:[6,246,249,303,343,344,345,367],exhaust:[210,380,509],exhibit:[97,264,373,407,491],exist:[3,6,7,8,11,12,13,16,37,56,61,70,73,129,173,174,192,199,200,201,204,209,220,223,225,228,240,293,294,296,347,348,350,352,353,354,356,360,370,375,381,402,403,414,444,461,471,478,480,482,483,484,493,494,495,504,509,510,511],exit:[2,3,11,12,42,59,197,221,236,365,380,480,481,490,499,509],exlanatori:3,exp:[],expand:[],expans:[12,147,197,493,509],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,74,108,154,165,171,193,221,233,240,242,261,289,295,297,298,303,308,347,367,377,394,431,434,436,477,480,482,484,487,491,496,509],expens:[6,74,201,289,293,308,336,347,366,367,377,381,480],experi:[6,13,15,17,220,228,245,254,263,295,307,308,372,376,401,436,491,496],experienc:[6,12,253,254],experiment:[240,366,381,496],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,61,65,67,70,72,74,75,76,79,80,82,91,98,153,161,193,197,198,200,201,204,213,214,219,221,223,225,227,264,289,297,308,321,347,349,365,366,369,375,376,380,386,405,417,452,454,469,480,483,484,487,489,492,503,504,509,513],explan:[3,6,61,120,147,197,198,213,263,289,414,476,479,480,482,491],explanatori:[3,8,124,197,198,212,213,216,217,218,308,375,479,509],explantori:[3,304],explic:435,explicit:[6,9,11,22,45,80,92,120,123,167,181,205,206,227,315,316,351,371,383,384,387,392,394,405,407,418,428,468,476,479,483,486,504],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,74,116,119,150,160,163,171,173,179,180,182,183,184,185,187,188,190,191,193,197,198,201,207,217,220,227,234,239,241,243,248,264,266,267,268,269,270,271,272,273,274,281,283,284,285,287,297,298,300,308,310,311,327,329,330,336,340,344,350,352,353,355,356,359,361,375,381,382,383,385,388,389,390,391,392,393,394,395,396,397,398,400,401,404,405,406,408,409,410,411,412,413,414,418,419,420,421,422,423,424,425,426,427,428,432,434,436,437,438,439,441,446,447,454,455,456,457,458,459,460,462,463,464,465,466,467,468,470,472,473,474,482,484,485,491,492,494,495,501,503,504],explictli:[16,495],exploit:[15,17,291],explor:[125,172],expon:[3,299,301,405,410,413,427,435,447],exponenti:[92,442,463,470,474,496,509],expos:11,exposit:[210,401,404],express:[6,147,159,173,205,206,225,261,289,299,336,342,349,387,405,407,421,431,452,453,462,509],expressiont:387,extend:[],extens:[3,6,9,17,45,46,47,54,56,65,71,87,88,89,92,93,96,100,103,104,114,116,124,126,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,198,204,207,208,211,219,220,226,229,233,238,239,240,242,243,244,246,248,250,262,264,269,278,289,290,306,307,308,310,313,318,321,323,327,328,329,330,331,333,334,336,338,341,345,346,410,431,434,445,446,453,499,500],extent:[1,3,42,43,46,59,74,171,175,197,209,217,221,246,343,346,366,369,383,448,450,464,479,482,485],exterior:[3,6,171,345],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,63,74,108,116,117,119,125,148,150,151,152,154,156,159,160,161,162,163,165,166,172,173,174,175,179,201,216,221,223,264,296,297,298,308,324,374,375,378,379,400,411,414,417,431,436,479,480,482,485,494,503,509],extract:[3,6,11,13,36,65,71,92,114,122,124,126,205,206,301,376,397,408,431,453,480,487,499],extract_atom:11,extract_comput:[11,480],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,60,200,215,225,227,264,334,407,466,503],extrema:427,extrins:210,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[169,338],f_a:[465,466,467],f_ave:124,f_c:466,f_f:467,f_fix_id:298,f_foo:509,f_harm:334,f_i:[29,442],f_id:[6,74,124,126,197,198,204,212,213,214,215,216,217,218,219,259,326,338,500,509],f_ij:442,f_indent:219,f_int:333,f_j:29,f_jj:96,f_k:442,f_langevin:336,f_max:[298,303],f_msst:262,f_r:[249,465,466,467],f_sigma:387,f_solid:334,f_ss:6,f_temp:[],face:[3,6,59,61,74,161,171,175,209,217,218,341,343,344,345,346,369,410,431,446,482,485],face_threshold:171,facet:171,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,242,294,324,334,411,452,494],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,59,60,61,75,92,96,108,115,122,123,125,147,167,172,175,179,190,196,197,200,201,205,206,214,221,225,227,228,240,245,248,250,251,262,264,265,269,291,295,299,307,311,314,316,324,328,332,339,340,341,345,356,367,369,375,381,383,384,387,388,390,392,397,398,399,401,402,403,407,411,414,418,419,431,434,436,438,439,445,447,454,463,468,479,482,485,486,491,494,496,497,500,503,508,509],factori:[3,480],factoriz:366,fail:[3,9,11,12,61,177,225,228,366,374,376,399,445,480],failur:[128,449,481,509],fairli:[11,436,491,496,504],faken:76,falcon:245,fall:[3,6,201,216,294,480,509],fals:[91,347,349,452,509],fame:8,famili:[470,479],familiar:[0,11,504],fan:442,far:[3,6,12,17,59,61,63,91,197,198,201,202,221,222,223,225,228,264,289,307,308,324,341,352,356,372,376,377,469,480,482,487,500],farago:248,farrel:[465,467],farther:197,fashion:[6,8,42,74,173,201,204,205,206,211,217,221,223,228,240,242,246,261,262,264,266,267,268,269,270,271,272,280,283,284,285,286,287,297,298,300,308,313,317,323,326,334,336,340,341,342,344,346,376,414,428,485,494,509,512],fasolino:416,fast:[6,7,9,12,13,17,40,197,198,275,298,337,366,367,389,428,429,434,462,464,484,489,491,500,510,513],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,63,65,111,116,119,150,160,179,180,182,183,184,185,187,188,190,191,193,197,198,201,207,220,221,227,234,239,243,247,248,264,266,267,268,269,270,271,272,273,274,281,283,284,285,287,295,299,300,308,310,311,324,327,329,331,333,336,340,344,350,352,353,355,356,359,361,366,367,378,379,381,382,383,385,387,388,389,390,391,392,393,394,395,396,397,400,401,405,406,408,409,410,411,412,413,414,419,420,421,422,423,424,425,426,427,428,432,437,438,439,441,446,447,454,462,463,464,465,466,467,470,472,473,474,477,485,491,495,503],fastest:[1,6,14,17,161,217,336,337,381,479],fatal:[3,499],fault:[73,445],faulti:12,fava:410,favor:224,favorit:7,fbmc:331,fcc:[],fcm:[280,509],fdirect:231,fdotr:415,fdt:[],fdti:92,fe2:172,fe3:172,fe_md_boundari:210,featu:8,featur:[],fecr:405,feedback:[7,245],feel:[7,245,246,254,289,345,347,376,436],felling:433,felt:345,femtosecond:508,fene:[],fennel:[397,419],fep:[],ferguson:[6,179,494],fermi:[1,9,10,12,15,159,381,467],fermion:407,fernando:430,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,65,202,212,213,214,216,217,218,219,249,264,294,297,299,311,338,366,374,375,376,383,452,479,482,487,491,493,501,511],fewer:[1,3,11,15,16,63,254,491],fewest:3,fextern:238,feynman:291,fff:480,ffield:[396,408,444,445,452],ffmpeg:[3,12,200],ffplai:200,fft:[1,3,7,9,11,12,14,15,93,116,117,148,290,366,367,491],fft_inc:[12,367],fft_lib:12,fft_path:12,fftbench:[366,501],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],ficiti:461,fictiti:[6,207,208,233,238,242,291,307,397,419,423,461],field1:[483,487],field2:483,field:[],fifth:[321,438],figur:[1,3,8,12,298,479,480,504],fij:400,file0:289,file1:[11,13,289,335,349,375,487,489,493],file2:[11,13,335,349,375,487,489,493],file:[],file_from:199,filen:375,filenam:[3,12,13,38,42,57,193,197,198,200,201,202,210,213,214,215,216,217,218,219,221,226,236,289,293,296,299,300,301,304,305,308,309,335,336,363,364,365,375,376,382,383,387,397,405,406,408,416,431,432,433,438,442,443,444,445,452,453,463,464,465,466,467,470,478,479,480,483,484,489,493,500,509,511,512,513],filennam:489,filep:[3,197,198,201,484,489,513],filepo:305,fill:[7,9,173,200,294,336,369,377,387,434,445,485,504],filter:[201,210],final_integr:8,final_integrate_respa:8,finchham:[6,155,399],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,63,74,76,92,124,176,193,202,211,224,225,236,237,240,263,289,294,295,303,307,372,374,376,377,397,414,419,423,431,452,462,464,503,504,509],find_custom:8,fine:[16,17,177,207,233,334,377,381,504,509],finer:[147,173,509],finest:366,finger:[173,196,261,485],finish:[6,11,42,221,349,363,365,366,378,380,381,469,487,509,510],finit:[],finni:[7,405,462],finvers:231,fiorin:[9,226],fire:[],firebrick:201,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,59,61,63,64,74,84,93,96,109,110,111,113,119,123,124,134,137,140,141,145,148,158,161,167,169,171,172,174,175,176,180,193,197,198,199,200,201,202,204,205,213,214,216,217,218,219,221,224,227,236,240,241,246,251,261,262,263,264,289,291,296,297,298,300,305,308,311,313,321,322,324,325,326,333,334,335,336,338,342,347,349,350,357,369,374,375,376,377,380,381,382,383,386,387,388,390,392,394,396,397,405,407,408,411,412,414,415,416,417,418,419,423,428,429,431,433,434,436,438,442,444,445,452,453,461,463,464,465,466,467,470,474,477,478,479,480,482,483,484,487,489,491,494,495,496,499,500,503,504,509,510,511,513],fischer:[6,9,19,20,179,392,494],fit:[3,6,9,12,38,57,193,236,307,324,383,387,416,431,436,457,464,466,490,504,509],five:[76,159,298,375,387,432,482,496],fix:[],fix_adapt:[167,206,427],fix_atom_swap:[],fix_bal:64,fix_deposit:[3,211,294],fix_eo:9,fix_evapor:211,fix_flux:210,fix_gcmc:[211,375],fix_gl:242,fix_gld:242,fix_grav:294,fix_id:[3,225,262,264,266,267,268,269,270,271,272,295,298],fix_manifoldforc:504,fix_modifi:[],fix_mov:[196,342],fix_nh:8,fix_npt:242,fix_nv:504,fix_nvt:[211,240],fix_poem:[3,6,9],fix_pour:[3,228],fix_qbmsst:9,fix_qeq:[3,396],fix_rattl:311,fix_reax_bond:444,fix_rigid:[254,386],fix_saed_vtk:309,fix_setforc:8,fix_shak:311,fix_shardlow:9,fix_srd:3,fix_styl:269,fix_temp_rescal:330,fixedpoint:[225,264],fixextern:238,fixid:210,fji:400,flag1:[230,379],flag2:[230,379],flag:[3,8,9,11,12,14,15,16,17,41,68,77,78,84,91,94,95,99,109,110,112,125,168,172,176,197,198,200,201,202,219,224,226,230,245,248,252,254,260,261,290,297,308,321,323,324,331,335,344,347,364,367,375,379,380,381,383,413,418,431,434,461,477,479,480,482,483,484,486,487,488,492,504,509],flag_buck:391,flag_coul:[391,400,423],flag_lj:[400,423],flagfld:[389,428,429],flaghi:[3,389,428,429],flaglog:[389,428,429],flagn:230,flagvf:[389,428,429],flat:[6,336,341,342,346],flavor:[2,7,12],fld:[],flen:384,flex_press:384,flexibl:[3,6,8,174,200,213,217,226,242,265,332,339,407,466,500],flip:[3,6,227,264,343,344],floor:509,flop:12,floralwhit:201,flow:[],fluctuat:[6,66,92,225,240,241,248,251,264,269,289,290,312,334,336,359,403],fluid:[],fluid_veloc:255,flush:[3,201,499],flux:[],flv:200,fly:[7,9,12,42,200,204,210,215,228,231,308,311,337,387,434,500,503],fmackai:9,fmag:229,fmass:291,fmax:[374,500],fmomentum:231,fmsec:[2,201,248,249,261,264,295,308,327,328,491,502,508,510],fname:365,fno:[9,12,16],fnorm:[374,500],fnpt:231,fnvt:231,foce:414,fock:384,focu:311,fogarti:[9,301,445],foil:[147,289,453],fold:[322,491],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,61,65,66,73,74,76,85,96,97,102,103,113,120,123,124,126,147,148,151,152,153,159,161,166,169,171,173,174,179,182,183,184,185,187,188,190,191,193,197,199,200,201,204,210,211,212,213,214,215,216,217,218,219,221,226,227,228,231,232,235,236,238,240,241,242,245,247,248,249,251,254,262,264,269,270,271,272,283,284,285,287,290,291,293,296,297,298,299,301,303,305,307,308,309,311,326,327,328,329,332,333,334,335,336,338,339,347,348,352,353,354,355,356,359,361,364,369,371,374,375,376,381,382,383,384,385,386,387,388,389,390,391,392,393,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,436,437,438,439,441,442,443,444,445,446,447,449,451,452,453,454,455,456,457,458,459,460,461,463,464,465,466,467,468,469,470,472,473,474,475,477,479,480,482,483,485,487,489,490,491,494,496,497,498,503,504,509,510,512],foo:[4,8,11,12,197,200,238,480,493,509],foot:6,footprint:[12,381],fopenmp:[9,12,16,18],forc:[],force_uvm:17,forceatom:254,forcefield:[307,413],forcegroup:251,forcezero:372,ford:400,forestgreen:201,forev:74,forget:[249,503],forgiv:264,fork:[],form:[2,3,6,8,12,19,22,45,55,65,68,77,78,80,84,92,94,95,97,99,109,110,112,123,147,148,167,168,177,181,201,204,205,206,223,241,242,248,250,254,261,285,290,301,303,307,308,336,341,345,350,351,354,359,371,373,375,376,383,384,387,394,402,403,405,407,409,413,414,418,430,431,433,434,438,439,442,444,445,446,452,453,454,462,464,465,466,467,473,476,479,480,482,487,492,499,503,509],formal:[6,81,83,96,241,242,248,264,291,324,332,452],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,70,80,181,193,197,198,199,200,201,202,213,216,217,218,219,221,223,236,290,293,297,299,301,304,308,309,320,335,336,347,348,351,371,375,376,382,383,387,394,405,408,418,431,433,443,444,445,447,453,464,470,471,479,480,482,483,484,487,498,499,500,509,511],former:[6,12,16,40,42,201,221,336,340,387,389,488,494,509],formerli:[7,13],formul:[1,9,41,66,148,207,233,248,264,285,299,301,307,311,335,366,383,387,405,407,410,431,441],formula:[2,3,6,7,13,21,22,37,45,55,56,73,76,92,94,95,96,100,102,103,112,119,125,126,148,150,151,152,153,154,155,156,157,159,160,161,162,163,164,165,166,172,173,178,180,181,192,196,197,205,206,207,208,213,214,215,216,219,220,227,233,243,244,246,248,249,261,289,290,296,305,310,318,322,324,327,328,329,338,341,344,346,347,349,350,351,353,360,369,375,383,384,386,387,392,393,394,395,400,401,405,406,410,411,412,413,415,418,419,421,422,423,425,426,428,429,431,435,436,437,446,447,454,462,463,464,465,466,467,470,472,473,478,482,485,492,499,500,508,509,510],forth:[1,6,11,12,13,14,15,380,480,485,489],fortran:[3,6,9,11,12,13,238,405,414,431,444,445],fortun:8,forward:[3,8,92,365,376,381],foster:[387,441,442],foul:176,found:[3,6,9,12,76,167,197,224,226,240,245,251,290,331,337,349,365,377,394,397,400,477,483,484,499],four:[6,11,55,84,109,110,147,169,262,336,359,375,376,434,477],fourier:[],fourth:[6,111,307,321,331,392,438,452],fox:[6,125,179,460,494],fphi:[38,57,464],fpic:12,fplo:[38,57,464],fprime:464,fqdn:247,fqq:400,frac:[],fraction:[1,3,6,8,12,16,40,42,83,116,148,176,196,200,201,211,222,223,224,225,262,294,298,305,306,324,329,330,369,376,381,387,389,411,428,429,487,492],fragment:[43,245,305],fraig:43,frame:[88,147,201,210,262,298,343,410],framer:[200,201],framework:[5,242,382,453],franc:9,fraunhof:9,free:[5,6,7,9,13,29,62,65,73,92,167,205,206,289,324,333,334,335,336,373,376,384,407,427,434,442,473,479],freedom:[3,6,8,100,102,103,105,107,108,119,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,213,224,231,240,242,248,249,254,264,265,269,270,271,272,283,284,285,287,291,293,308,311,327,328,329,334,374,400,500,503,510],freeli:[0,6,7,12,151,152,166,171,200],freez:[],frenkel:[240,334],freq:209,frequenc:[3,6,16,40,109,201,215,278,290,291,298,303,364,401,407,445,452,477,491,496,509,512],frequent:[3,66,69,73,75,76,80,93,97,113,147,201,222,223,237,332,339,436,489],fri:[262,298],friction:[4,5,6,9,10,43,204,242,248,298,303,308,336,340,342,411,492],friedric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:[226,349,453,470],input1:[67,70,72,82,98,115,120,121,122,124,126,326],input2:[67,70,72,82,98,115,120,121,122,124,126,326],input:[],input_doubl:3,inquir:314,insensit:12,insert:[3,5,7,8,9,12,61,173,204,228,240,246,294,366,453,461,480,486,503],insid:[2,3,6,8,11,74,136,142,173,197,198,201,212,217,218,228,229,237,240,246,251,254,294,308,324,341,343,344,345,346,347,364,369,421,480,481,482,484,485,492,496,509],insight:[6,13],instabl:[251,400,451],instal:[],instanc:[6,9,11,205,226,242,343,409,414,436,442,480,503],instantan:[6,65,224,225,241,242,264,269,290,295,298,303,305,308,331,488,500],instanti:[6,11,12,210,414,479],instead:[1,3,6,8,11,12,13,17,18,41,42,61,63,65,73,74,95,109,124,151,155,177,193,197,198,206,213,216,217,218,219,221,225,226,240,248,251,254,255,290,296,306,308,326,344,364,366,367,370,377,381,390,391,405,418,420,427,431,434,477,485,489,496,498,503,509],institut:[9,245,293],instruct:[],insuffici:[3,6,12],insult:264,insur:[3,6,11,12,17,40,41,63,76,108,110,173,174,193,197,198,200,201,207,222,223,228,233,234,237,238,240,243,248,260,296,297,306,308,324,336,341,345,346,347,349,365,375,377,381,395,410,414,440,446,464,475,479,480,482,483,487,490,491,499,500,509,510],int_max:3,inteatom:10,integ:[3,6,8,11,12,40,41,43,66,70,73,74,113,120,122,124,126,147,171,173,176,177,179,183,184,188,193,196,197,200,201,211,213,217,218,222,223,224,228,230,238,240,241,242,245,248,249,250,251,290,293,294,297,298,303,308,324,326,328,331,335,336,355,366,369,389,401,403,404,417,431,444,445,449,451,453,477,479,480,481,482,490,491,492,496,499,509,510],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,215,241,443,482],intens:[1,3,6,9,65,68,77,78,91,94,95,96,99,109,110,111,112,119,121,123,124,125,126,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,168,169,170,172,204,213,214,216,217,218,219,221,222,223,224,232,237,244,254,262,264,269,305,308,309,324,332,336,338,339,499,500],intepol:509,inter:[14,18,43,63,64,153,176,177,197,224,248,250,263,300,308,366,376,387,492,503,509,511,513],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,34,37,40,41,43,45,51,53,55,56,59,63,65,67,72,75,80,82,92,93,97,98,113,114,115,117,119,122,123,129,130,131,132,134,135,136,137,138,139,140,142,143,144,145,147,148,149,151,152,166,167,171,174,175,176,177,178,179,181,185,186,189,192,197,198,204,205,206,222,223,224,239,240,245,246,248,250,254,278,289,291,293,294,299,301,307,308,315,316,324,325,331,336,340,341,342,345,346,351,352,353,354,356,358,360,366,367,374,375,376,377,378,379,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,445,446,447,449,451,452,453,454,461,462,463,464,465,466,467,468,469,470,471,472,473,474,477,480,482,484,486,487,491,492,494,499,500,503,511],interatom:[3,4,7,9,10,173,197,263,333,334,382,387,405,407,415,431,434,452,466,509],intercept:125,interchang:6,interconnect:18,interconvert:407,intereract:40,interesect:345,interest:[1,5,7,8,9,11,13,74,172,291,331,334,367,406,429,444,445,480,509],interf:[381,504],interfac:[],interfer:[12,264,383],interg:[6,503],intergr:[491,495],interi:429,interior:[3,6,42,345,485],interlac:431,interleav:[6,173,490],intermedi:[6,12,61,200,263,289,359,376,480,481,490,494],intermix:477,intermolecular:383,intern:[],internal_element_set:210,internal_quadratur:210,internet:247,interpenetr:431,interpentr:[456,457,459],interpol:[6,15,38,57,106,193,200,201,210,236,251,289,366,367,376,387,436,445,458,464,465],interpret:[2,6,11,200,216,411,454,477,480,496,509],interrupt:298,intersect:[3,6,125,201,345,347,485],intersert:345,interspers:374,interstiti:[171,434],intertia:[3,99],interv:[3,6,96,199,214,248,264,298,303,304,316,452,458,477,496,509],intestieti:125,intial:[6,381,383],intiial:[42,487],intiti:[3,323],intra:308,intra_energi:240,intramolecular:[29,240],introduc:[6,9,97,113,200,264,298,303,308,359,366,382,397,407,419,423,427,463,496,509],introduct:[],intsal:[],intuit:369,inv:[125,172,309],invalid:[3,12,74,94,176,278,376,428,429,484],invari:[113,140,145,147],invent:311,invers:[],invert:[1,6,177,290],invis:345,invoc:[171,224,381,449,451,480],invok:[1,3,6,7,8,9,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,61,65,68,74,77,78,84,92,93,94,95,99,109,110,112,116,117,118,119,124,126,150,160,167,168,171,173,174,176,177,179,180,182,183,184,185,187,188,190,191,193,197,198,200,201,202,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,227,228,229,230,232,233,234,237,238,239,240,241,243,244,245,246,248,249,250,251,252,253,254,255,256,257,258,260,261,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,299,300,301,302,303,304,305,306,308,309,310,311,313,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,33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446,449,451,452,491,501,504],recompil:[1,3,9,12,202,311],recomput:[108,135,177,232,313,404,494],reconstruct:[3,226,452],record:[202,226,313],recov:[225,264],recreat:348,rectangl:[42,221,369],rectangular:[7,42,64,175,221,240,369,482,484,486],rectilinear:[125,172,198],rector:54,recurs:[42,221,387,469],recust:42,recv:479,red:[2,200,201,224,291],redefin:[3,484,490,509],redirect:12,redo:12,reduc:[],reduct:[18,19,124,125,172,262,298,366],redund:408,ree:457,reed:[262,298],rees:[7,9,13],ref:[333,334,373],refactor:6,refer:[],referenc:[3,6,12,65,70,74,121,126,197,198,204,214,240,297,338,367,397,413,438,446,480,500,509],reflect:[],refman:9,reformat:7,refresh:210,reg:485,regard:[6,61,261,311,312,317,441,445],regardless:[15,74,173,176,196,216,217,227,248,264,266,267,268,270,271,272,295,308,318,324,381,479,485,492],regim:[6,332,339,398,491],region:[],region_spher:8,region_styl:345,regist:[8,123,149,320,444,445],regoin:6,regress:509,regspher:173,regstrip:347,regul:6,regular:[1,3,42,64,93,171,175,197,200,211,221,240,336,367,398,417,479,482,484,486],reigon:509,reinhardt:[333,334],reject:[173,224,444,497],rel:[1,6,14,27,36,42,61,74,97,109,129,137,147,151,155,156,158,173,182,201,204,211,217,221,227,228,231,240,246,249,260,261,285,289,294,303,305,306,313,321,324,326,331,332,336,343,347,366,367,374,407,410,411,428,429,431,446,473,483,491,496,500,503,510],relat:[],relatic:[],relationship:[6,236,299,349,366,452,473,503,509],relax:[],releas:[0,5,7,8,13,222],relect:[3,436],reles:43,relev:[2,6,12,42,81,83,118,135,173,177,201,205,206,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,227,228,229,232,234,237,239,240,241,244,245,251,252,253,255,256,257,258,260,261,263,273,274,275,276,277,278,279,280,281,282,288,292,293,294,296,297,300,302,304,305,306,309,310,311,313,318,322,324,325,326,331,332,335,336,337,338,339,340,341,342,343,344,346,347,366,374,384,385,389,395,397,398,400,401,404,407,409,410,411,412,413,418,420,421,422,424,425,426,428,429,436,437,441,446,454,461,464,472,473,474,479,495,510],reli:[3,12,300,407,445,474,482,492],reloc:12,remain:[7,12,33,37,42,51,56,61,74,92,110,153,154,155,156,160,161,162,163,165,176,186,192,193,197,205,206,211,213,214,217,218,225,227,248,249,256,264,265,270,271,272,283,284,285,287,292,293,316,324,327,328,329,335,336,347,349,357,360,375,387,407,414,427,434,436,462,477,482,483,487,492,494,496,500,503,504,509,510],remaina:387,remaind:[9,173,197,228,294,324,337,467,482],remap:[3,6,12,61,63,74,156,173,196,217,227,246,261,285,366,482,483,484],remedi:[6,503],rememb:[2,504],remot:504,remov:[2,3,6,8,13,55,74,75,80,97,113,121,123,147,151,152,153,154,155,156,160,161,162,163,165,166,173,176,177,198,204,213,217,222,237,248,249,254,260,262,264,270,271,272,283,284,285,287,293,299,308,309,311,324,327,328,329,331,347,366,376,400,429,434,482,485,493,494,504,509,510],remove_bia:8,remove_bias_al:8,remove_molecul:210,remove_sourc:210,remove_speci:210,ren:172,renam:[12,348,493,504],render:[12,13,197,200,201],rendon:[264,265],reneighbor:[3,8,12,40,59,74,217,221,240,324,337,347,401,499,500],renssela:293,renumb:74,reorder:[3,12,40,479],rep:497,repeat:[2,6,200,201,217,224,225,240,317,369,387,465,467,469,477,496],repeatedli:2,repel:246,repes:197,replac:[2,3,6,11,12,42,65,94,95,124,150,151,152,153,154,155,156,159,160,161,162,163,165,166,197,198,200,201,202,213,214,216,217,218,219,221,224,228,248,269,296,303,305,397,421,464,483,484,489,490,500,509,510,511,513],replic:[],replica:[],replica_fil:12,report:[],repositori:[],reprens:336,repres:[1,3,6,8,9,12,15,41,42,43,61,69,74,95,120,123,185,193,197,198,200,213,214,215,216,217,218,219,225,231,241,243,248,251,264,291,293,295,303,308,309,313,321,336,338,345,367,376,382,387,410,417,427,428,429,431,432,433,439,442,444,445,468,469,477,479,482,492,494,497,503,509,511],represent:[3,6,8,9,59,61,141,175,197,241,242,291,336,387,407,410,434,446,482,485,503],reprocess:487,reproduc:[3,264,342,397,405,411],repul:431,repuls:[6,7,36,41,46,47,115,246,299,341,342,345,383,387,395,397,401,407,411,413,427,431,435,452,461,467,470,473,474,492],reqir:[299,301],request:[3,6,8,12,42,109,176,193,197,245,251,306,312,324,326,364,366,436,444,445,477,487,492,496,504,509,510,511],requir:[],rerun:[],rescal:[],research:[5,7,85,86,235,251,255,312,434,477,496],resembl:[303,504],resepct:6,reserv:[12,245,503],reservoir:[96,240,244,248,336],reset:[],reset_atomic_reference_posit:210,reset_dt:8,reset_target:8,reset_tim:210,reset_timestep:[],resid:13,residu:245,residue1:377,resist:[6,245],resolut:[215,452,464],resolv:[225,291,324,429,504],resort:3,resourc:[7,382,405],respa:[3,16,232,245,264,379,382,383,384,385,386,387,388,389,390,391,392,393,395,396,397,398,400,401,404,405,406,407,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,428,429,430,431,432,433,434,435,437,439,441,443,444,445,446,447,452,453,454,455,456,457,458,459,460,461,463,464,465,466,467,469,470,472,473,474,475,490,491,502,509],respecifi:434,respect:[1,6,9,13,14,15,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,46,47,48,49,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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying &amp; extending LAMMPS","4. Packages","8. Performance &amp; scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","&lt;no title&gt;","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","&lt;no title&gt;","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":222,"default":[37,40,41,56,59,60,61,63,64,71,74,92,93,97,108,109,111,113,114,125,129,130,147,153,161,162,166,172,173,176,178,192,195,196,197,198,200,201,202,203,205,206,207,209,210,211,213,217,218,219,222,223,225,226,227,228,232,237,240,241,246,248,249,250,251,252,254,259,262,264,265,269,285,286,290,291,294,295,296,297,298,300,303,305,306,308,309,324,326,331,332,333,334,337,339,341,343,347,360,364,366,367,369,370,372,373,375,377,378,379,381,384,387,389,407,428,429,434,436,444,445,461,462,477,478,479,482,483,485,487,489,490,491,494,496,498,499,500,501,502,508,510,511,512],"function":509,"long":[215,388,390,391,392,393,397,399,400,419,423,427,439,447],"new":8,"static":12,acceler:1,account:504,ackland:66,acknowledg:7,adapt:[205,206],addforc:207,addit:[12,13,504],addtorqu:208,adiabat:6,adjust_dt:314,adp:382,after:504,airebo:383,alloi:405,amber2lmp:13,amber:6,angl:[8,67],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:68,append:209,arrai:6,aspher:[6,9,87,151,266,270,274,275,283],atc:[9,210],atom:[6,7,8,66,69,73,74,75,76,79,80,81,83,84,86,90,97,101,102,105,106,107,113,117,118,120,147,148,171,209,211,212,297,509],atom_modifi:40,atom_styl:41,attract:5,aug:[],aveforc:220,awpmd:[9,384],balanc:[42,221],barostat:6,basal:69,beck:385,berendsen:[295,327],between:6,binary2txt:13,bodi:[6,8,9,43,70,152,267,271,276,284,386],bond:[8,13,71,72,222,223,224,304],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,58],bop:387,born:[388,399],boundari:[7,59],box:[6,60,225],branch:504,brownian:389,buck:[390,391,399,430],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:73,ch2lmp:13,chain:13,chang:504,change_box:61,charmm:[6,20,179,392,427],chunk:[6,68,74,78,95,99,110,112,121,153,168,170,213],citat:7,class2:[9,21,44,180,350,393],clear:62,cluster:75,cmm:9,cna:76,code:6,coeffici:6,colloid:[9,341,395,473],colvar:[9,13,226],com:[77,78,154],comb3:396,comb:[300,396],come:5,comm_modifi:63,comm_styl:64,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,505,506,507,508,509,510,511,512,513],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,509],compute_modifi:108,condit:7,conduct:[6,332],conserv:402,constant:[6,509],constraint:7,contact:[79,127],contact_radiu:[],coord:80,core:6,coreshel:9,correl:[214,215],cosin:[23,24,25,26,27,28,182],cossq:352,coul:[388,390,391,392,393,397,398,399,412,419,423,427,439,447],coupl:6,creat:223,create_atom:173,create_bond:174,create_box:175,createatom:13,creation:7,csld:328,csvr:328,cubic:421,cuda:[9,14,116,119,150,160,207,220,234,239,243,264,273,310,311,327,329,340,388,390,392,393,405,411,412,419,420,422,425,437,463,465],custom:[8,197,198],cut:[50,384,390,393,397,400,407,409,419,420,427,435,439],cvff:353,damag:[81,128],data2xmovi:13,data:6,data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