diff --git a/doc/Section_packages.html b/doc/Section_packages.html
index 865e1cd1b..b85c1b4ec 100644
--- a/doc/Section_packages.html
+++ b/doc/Section_packages.html
@@ -1,2737 +1,2737 @@
<!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>4. Packages — 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"/>
<link rel="next" title="5. Accelerating LAMMPS performance" href="Section_accelerate.html"/>
<link rel="prev" title="3. Commands" href="Section_commands.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 class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">4. Packages</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#standard-packages">4.1. Standard packages</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#asphere-package">4.1.1. ASPHERE package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#body-package">4.1.2. BODY package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#class2-package">4.1.3. CLASS2 package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#colloid-package">4.1.4. COLLOID package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#compress-package">4.1.5. COMPRESS package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#coreshell-package">4.1.6. CORESHELL package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#dipole-package">4.1.7. DIPOLE package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#fld-package">4.1.8. FLD package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#gpu-package">4.1.9. GPU package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#granular-package">4.1.10. GRANULAR package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#kim-package">4.1.11. KIM package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#kokkos-package">4.1.12. KOKKOS package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#kspace-package">4.1.13. KSPACE package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#manybody-package">4.1.14. MANYBODY package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#mc-package">4.1.15. MC package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#meam-package">4.1.16. MEAM package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#misc-package">4.1.17. MISC package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#molecule-package">4.1.18. MOLECULE package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#mpiio-package">4.1.19. MPIIO package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#opt-package">4.1.20. OPT package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#peri-package">4.1.21. PERI package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#poems-package">4.1.22. POEMS package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#python-package">4.1.23. PYTHON package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#qeq-package">4.1.24. QEQ package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#reax-package">4.1.25. REAX package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#replica-package">4.1.26. REPLICA package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#rigid-package">4.1.27. RIGID package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#shock-package">4.1.28. SHOCK package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#snap-package">4.1.29. SNAP package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#srd-package">4.1.30. SRD package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#voronoi-package">4.1.31. VORONOI package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#xtc-package">4.1.32. XTC package</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#user-packages">4.2. User packages</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#user-atc-package">4.2.1. USER-ATC package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-awpmd-package">4.2.2. USER-AWPMD package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-cg-cmm-package">4.2.3. USER-CG-CMM package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-colvars-package">4.2.4. USER-COLVARS package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-cuda-package">4.2.5. USER-CUDA package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-diffraction-package">4.2.6. USER-DIFFRACTION package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-dpd-package">4.2.7. USER-DPD package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-drude-package">4.2.8. USER-DRUDE package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-eff-package">4.2.9. USER-EFF package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-fep-package">4.2.10. USER-FEP package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-h5md-package">4.2.11. USER-H5MD package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-intel-package">4.2.12. USER-INTEL package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-lb-package">4.2.13. USER-LB package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-mgpt-package">4.2.14. USER-MGPT package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-misc-package">4.2.15. USER-MISC package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-molfile-package">4.2.16. USER-MOLFILE package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-omp-package">4.2.17. USER-OMP package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-phonon-package">4.2.18. USER-PHONON package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-qmmm-package">4.2.19. USER-QMMM package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-qtb-package">4.2.20. USER-QTB package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-quip-package">4.2.21. USER-QUIP package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-reaxc-package">4.2.22. USER-REAXC package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-smd-package">4.2.23. USER-SMD package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-smtbq-package">4.2.24. USER-SMTBQ package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-sph-package">4.2.25. USER-SPH package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-tally-package">4.2.26. USER-TALLY package</a></li>
<li class="toctree-l3"><a class="reference internal" href="#user-vtk-package">4.2.27. USER-VTK package</a></li>
</ul>
</li>
</ul>
</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 & 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 & 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>
</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> »</li>
<li>4. Packages</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 class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
<a href="Section_accelerate.html" class="btn btn-neutral float-right" title="5. Accelerating LAMMPS performance" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="Section_commands.html" class="btn btn-neutral" title="3. Commands" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="packages">
<h1>4. Packages<a class="headerlink" href="#packages" title="Permalink to this headline">¶</a></h1>
<p>This section gives an overview of the add-on optional packages that
extend LAMMPS functionality. Packages are groups of files that enable
a specific set of features. For example, force fields for molecular
systems or granular systems are in packages. You can see the list of
all packages by typing “make package” from within the src directory of
the LAMMPS distribution.</p>
<p>Here are links for two tables below, which list standard and user
packages.</p>
<div class="line-block">
<div class="line">4.1 <a class="reference internal" href="#pkg-1"><span>Standard packages</span></a></div>
<div class="line">4.2 <a class="reference internal" href="#pkg-2"><span>User packages</span></a></div>
<div class="line"><br /></div>
</div>
<p><a class="reference internal" href="Section_start.html#start-3"><span>Section_start 3</span></a> of the manual describes
the difference between standard packages and user packages. It also
has general details on how to include/exclude specific packages as
part of the LAMMPS build process, and on how to build auxiliary
libraries or modify a machine Makefile if a package requires it.</p>
<p>Following the two tables below, is a sub-section for each package. It
has a summary of what the package contains. It has specific
instructions on how to install it, build or obtain any auxiliary
library it requires, and any Makefile.machine changes it requires. It
also lists pointers to examples of its use or documentation provided
in the LAMMPS distribution.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The sub-sections below are still being filled in, as of Feb
2016.</p>
</div>
<p>Unless otherwise noted below, every package is independent of all the
others. I.e. any package can be included or excluded in a LAMMPS
build, independent of all other packages. However, note that some
packages include commands derived from commands in other packages. If
the other package is not installed, the derived command from the new
package will also not be installed when you include the new one.
E.g. the pair lj/cut/coul/long/omp command from the USER-OMP package
will not be installed as part of the USER-OMP package if the KSPACE
package is not also installed, since it contains the pair
lj/cut/coul/long command. If you later install the KSPACE package and
the USER-OMP package is already installed, both the pair
lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed.</p>
<hr class="docutils" />
<div class="section" id="standard-packages">
<span id="pkg-1"></span><h2>4.1. Standard packages<a class="headerlink" href="#standard-packages" title="Permalink to this headline">¶</a></h2>
<p>The current list of standard packages is as follows. Each package
name links to a sub-section below with more details.</p>
<table border="1" class="docutils">
<colgroup>
<col width="16%" />
<col width="21%" />
<col width="22%" />
<col width="28%" />
<col width="6%" />
<col width="7%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>Package</td>
<td>Description</td>
<td>Author(s)</td>
<td>Doc page</td>
<td>Example</td>
<td>Library</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#asphere"><span>ASPHERE</span></a></td>
<td>aspherical particles</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="Section_howto.html#howto-14"><span>Section_howto 6.14</span></a></td>
<td>ellipse</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#body"><span>BODY</span></a></td>
<td>body-style particles</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="body.html"><em>body</em></a></td>
<td>body</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#class2"><span>CLASS2</span></a></td>
<td>class 2 force fields</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="pair_class2.html"><em>pair_style lj/class2</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#colloid"><span>COLLOID</span></a></td>
<td>colloidal particles</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="atom_style.html"><em>atom_style colloid</em></a></td>
<td>colloid</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#compress"><span>COMPRESS</span></a></td>
<td>I/O compression</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><a class="reference internal" href="dump.html"><em>dump */gz</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#coreshell"><span>CORESHELL</span></a></td>
<td>adiabatic core/shell model</td>
<td>Hendrik Heenen (Technical U of Munich)</td>
<td><a class="reference internal" href="Section_howto.html#howto-25"><span>Section_howto 6.25</span></a></td>
<td>coreshell</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#dipole"><span>DIPOLE</span></a></td>
<td>point dipole particles</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="pair_dipole.html"><em>pair_style dipole/cut</em></a></td>
<td>dipole</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#fld"><span>FLD</span></a></td>
<td>Fast Lubrication Dynamics</td>
<td>Kumar & Bybee & Higdon (1)</td>
<td><a class="reference internal" href="pair_lubricateU.html"><em>pair_style lubricateU</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#gpu"><span>GPU</span></a></td>
<td>GPU-enabled styles</td>
<td>Mike Brown (ORNL)</td>
<td><a class="reference internal" href="accelerate_gpu.html"><em>Section accelerate</em></a></td>
<td>gpu</td>
<td>lib/gpu</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#granular"><span>GRANULAR</span></a></td>
<td>granular systems</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="Section_howto.html#howto-6"><span>Section_howto 6.6</span></a></td>
<td>pour</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#kim"><span>KIM</span></a></td>
<td>openKIM potentials</td>
<td>Smirichinski & Elliot & Tadmor (3)</td>
<td><a class="reference internal" href="pair_kim.html"><em>pair_style kim</em></a></td>
<td>kim</td>
<td>KIM</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#kokkos"><span>KOKKOS</span></a></td>
<td>Kokkos-enabled styles</td>
<td>Trott & Edwards (4)</td>
<td><a class="reference internal" href="accelerate_kokkos.html"><em>Section_accelerate</em></a></td>
<td>kokkos</td>
<td>lib/kokkos</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#kspace"><span>KSPACE</span></a></td>
<td>long-range Coulombic solvers</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a></td>
<td>peptide</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#manybody"><span>MANYBODY</span></a></td>
<td>many-body potentials</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="pair_tersoff.html"><em>pair_style tersoff</em></a></td>
<td>shear</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#meam"><span>MEAM</span></a></td>
<td>modified EAM potential</td>
<td>Greg Wagner (Sandia)</td>
<td><a class="reference internal" href="pair_meam.html"><em>pair_style meam</em></a></td>
<td>meam</td>
<td>lib/meam</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#mc"><span>MC</span></a></td>
<td>Monte Carlo options</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="fix_gcmc.html"><em>fix gcmc</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#molecule"><span>MOLECULE</span></a></td>
<td>molecular system force fields</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="Section_howto.html#howto-3"><span>Section_howto 6.3</span></a></td>
<td>peptide</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#opt"><span>OPT</span></a></td>
<td>optimized pair styles</td>
<td>Fischer & Richie & Natoli (2)</td>
<td><a class="reference internal" href="accelerate_opt.html"><em>Section accelerate</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#peri"><span>PERI</span></a></td>
<td>Peridynamics models</td>
<td>Mike Parks (Sandia)</td>
<td><a class="reference internal" href="pair_peri.html"><em>pair_style peri</em></a></td>
<td>peri</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#poems"><span>POEMS</span></a></td>
<td>coupled rigid body motion</td>
<td>Rudra Mukherjee (JPL)</td>
<td><a class="reference internal" href="fix_poems.html"><em>fix poems</em></a></td>
<td>rigid</td>
<td>lib/poems</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#python"><span>PYTHON</span></a></td>
<td>embed Python code in an input script</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="python.html"><em>python</em></a></td>
<td>python</td>
<td>lib/python</td>
</tr>
-<tr class="row-odd"><td><a class="reference internal" href="#reax"><span>REAX</span></a></td>
+<tr class="row-odd"><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>
<td>reax</td>
<td>lib/reax</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#replica"><span>REPLICA</span></a></td>
<td>multi-replica methods</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="Section_howto.html#howto-5"><span>Section_howto 6.5</span></a></td>
<td>tad</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#rigid"><span>RIGID</span></a></td>
<td>rigid bodies</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a></td>
<td>rigid</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#shock"><span>SHOCK</span></a></td>
<td>shock loading methods</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="fix_msst.html"><em>fix msst</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#snap"><span>SNAP</span></a></td>
<td>quantum-fit potential</td>
<td>Aidan Thompson (Sandia)</td>
<td><a class="reference internal" href="pair_snap.html"><em>pair snap</em></a></td>
<td>snap</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#srd"><span>SRD</span></a></td>
<td>stochastic rotation dynamics</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="fix_srd.html"><em>fix srd</em></a></td>
<td>srd</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#voronoi"><span>VORONOI</span></a></td>
<td>Voronoi tesselations</td>
<td>Daniel Schwen (LANL)</td>
<td><a class="reference internal" href="compute_voronoi_atom.html"><em>compute voronoi/atom</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>Voro++</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#xtc"><span>XTC</span></a></td>
<td>dumps in XTC format</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><a class="reference internal" href="dump.html"><em>dump</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
<p>The “Authors” column lists a name(s) if a specific person is
responible for creating and maintaining the package.</p>
<p>(1) The FLD package was created by Amit Kumar and Michael Bybee from
Jonathan Higdon’s group at UIUC.</p>
<p>(2) The OPT package was created by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technolgy).</p>
<p>(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott,
and Ellad Tadmor (U Minn).</p>
<p>(4) The KOKKOS package was created primarily by Christian Trott
(Sandia). It uses the Kokkos library which was developed by Carter
Edwards, Christian, and collaborators at Sandia.</p>
<p>The “Doc page” column links to either a sub-section of the
<a class="reference internal" href="Section_howto.html"><em>Section_howto</em></a> of the manual, or an input script
command implemented as part of the package, or to additional
documentation provided within the package.</p>
<p>The “Example” column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. “peptide” refers to the examples/peptide directory.</p>
<p>The “Library” column lists an external library which must be built
first and which LAMMPS links to when it is built. If it is listed as
lib/package, then the code for the library is under the lib directory
of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution.
See details on all of this below for individual packages.
p.s.: are we ever going to get commit messages from you? ;-)</p>
<hr class="docutils" />
<div class="section" id="asphere-package">
<span id="asphere"></span><h3>4.1.1. ASPHERE package<a class="headerlink" href="#asphere-package" title="Permalink to this headline">¶</a></h3>
<p>Contents: Aspherical particle models for ellipsoids, 2d lines, 3d
triangles.</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-asphere
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p asphere -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-asphere
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^asphere -a machine
</pre></div>
</div>
<p>Supporting info: examples/ASPHERE, examples/ellipse, Section howto
6.14, pair gayberne</p>
<hr class="docutils" />
</div>
<div class="section" id="body-package">
<span id="body"></span><h3>4.1.2. BODY package<a class="headerlink" href="#body-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
</pre></div>
</div>
<p>Supporting info: examples/body</p>
<hr class="docutils" />
</div>
<div class="section" id="class2-package">
<span id="class2"></span><h3>4.1.3. CLASS2 package<a class="headerlink" href="#class2-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-class2
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p class2 -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-class2
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^class2 -a machine
</pre></div>
</div>
<p>Supporting info:</p>
<hr class="docutils" />
</div>
<div class="section" id="colloid-package">
<span id="colloid"></span><h3>4.1.4. COLLOID package<a class="headerlink" href="#colloid-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-colloid
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p colloid -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-colloid
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^colloid -a machine
</pre></div>
</div>
<p>Supporting info: examples/colloid, examples/srd</p>
<hr class="docutils" />
</div>
<div class="section" id="compress-package">
<span id="compress"></span><h3>4.1.5. COMPRESS package<a class="headerlink" href="#compress-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-compress
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p compress -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-compress
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^compress -a machine
</pre></div>
</div>
<p>Supporting info:</p>
<hr class="docutils" />
</div>
<div class="section" id="coreshell-package">
<span id="coreshell"></span><h3>4.1.6. CORESHELL package<a class="headerlink" href="#coreshell-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-coreshell
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p coreshell -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-coreshell
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^coreshell -a machine
</pre></div>
</div>
<p>Supporting info: examples/coreshell, Section howto 6.26</p>
<hr class="docutils" />
</div>
<div class="section" id="dipole-package">
<span id="dipole"></span><h3>4.1.7. DIPOLE package<a class="headerlink" href="#dipole-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-dipole
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p dipole -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-dipole
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^dipole -a machine
</pre></div>
</div>
<p>Supporting info: examples/dipole</p>
<hr class="docutils" />
</div>
<div class="section" id="fld-package">
<span id="fld"></span><h3>4.1.8. FLD package<a class="headerlink" href="#fld-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-fld
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p fld -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-fld
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^fld -a machine
</pre></div>
</div>
<p>Supporting info:</p>
<hr class="docutils" />
</div>
<div class="section" id="gpu-package">
<span id="gpu"></span><h3>4.1.9. GPU package<a class="headerlink" href="#gpu-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-gpu
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p gpu -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-gpu
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^gpu -a machine
</pre></div>
</div>
<p>Supporting info: examples/accelerate, bench/FERMI, bench/KEPLER</p>
<hr class="docutils" />
</div>
<div class="section" id="granular-package">
<span id="granular"></span><h3>4.1.10. GRANULAR package<a class="headerlink" href="#granular-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-granular
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p granular -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-granular
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^granular -a machine
</pre></div>
</div>
<p>Supporting info: examples/pour, bench/in.chute, Section howto 6.6</p>
<hr class="docutils" />
</div>
<div class="section" id="kim-package">
<span id="kim"></span><h3>4.1.11. KIM package<a class="headerlink" href="#kim-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-kim
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p kim -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-kim
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^kim -a machine
</pre></div>
</div>
<p>Supporting info: examples/kim</p>
<hr class="docutils" />
</div>
<div class="section" id="kokkos-package">
<span id="kokkos"></span><h3>4.1.12. KOKKOS package<a class="headerlink" href="#kokkos-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-kokkow
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p kokkow -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-kokkow
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^kokkow -a machine
</pre></div>
</div>
<p>Supporting info:</p>
<p>For the KOKKOS package, you have 3 choices when building. You can
build with OMP or Cuda or Phi support. Phi support uses Xeon Phi
chips in “native” mode. This can be done by setting the following
variables in your Makefile.machine:</p>
<ul class="simple">
<li>for OMP support, set OMP = yes</li>
<li>for Cuda support, set OMP = yes and CUDA = yes</li>
<li>for Phi support, set OMP = yes and MIC = yes</li>
</ul>
<p>These can also be set as additional arguments to the make command, e.g.</p>
<div class="highlight-python"><div class="highlight"><pre>make g++ OMP=yes MIC=yes
</pre></div>
</div>
<p>Building the KOKKOS package with CUDA support requires a Makefile
machine that uses the NVIDIA “nvcc” compiler, as well as an
appropriate “arch” setting appropriate to the GPU hardware and NVIDIA
software you have on your machine. See
src/MAKE/OPTIONS/Makefile.kokkos_cuda for an example of such a machine
Makefile.</p>
<p>Examples: examples/accelerate, bench/FERMI, bench/KEPLER</p>
<hr class="docutils" />
</div>
<div class="section" id="kspace-package">
<span id="kspace"></span><h3>4.1.13. KSPACE package<a class="headerlink" href="#kspace-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-kspace
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p kspace -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-kspace
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^kspace -a machine
</pre></div>
</div>
<p>Supporting info:</p>
<p>Examples: examples/peptide, bench/in.rhodo</p>
<p>Doc: Section howto 6.7, Section howto 6.8, Section howto 6.9</p>
<hr class="docutils" />
</div>
<div class="section" id="manybody-package">
<span id="manybody"></span><h3>4.1.14. MANYBODY package<a class="headerlink" href="#manybody-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-manybody
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p manybody -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-manybody
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^manybody -a machine
</pre></div>
</div>
<p>Supporting info:</p>
<p>Examples: examples/comb, examples/eim, examples/nb3d, examples/vashishta</p>
<hr class="docutils" />
</div>
<div class="section" id="mc-package">
<span id="mc"></span><h3>4.1.15. MC package<a class="headerlink" href="#mc-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-mc
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p mc -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-mc
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^mc -a machine
</pre></div>
</div>
<p>Supporting info:</p>
<hr class="docutils" />
</div>
<div class="section" id="meam-package">
<span id="meam"></span><h3>4.1.16. MEAM package<a class="headerlink" href="#meam-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-meam
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p meam -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-meam
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^meam -a machine
</pre></div>
</div>
<p>Supporting info: examples/meam</p>
<hr class="docutils" />
</div>
<div class="section" id="misc-package">
<span id="misc"></span><h3>4.1.17. MISC package<a class="headerlink" href="#misc-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-misc
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p misc -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-misc
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^misc -a machine
</pre></div>
</div>
<p>Supporting info: examples/misc</p>
<hr class="docutils" />
</div>
<div class="section" id="molecule-package">
<span id="molecule"></span><h3>4.1.18. MOLECULE package<a class="headerlink" href="#molecule-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-molecule
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p molecule -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-molecule
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^molecule -a machine
</pre></div>
</div>
<p>Supporting info: examples/micelle, examples/peptide, bench/in.chain, bench/in.rhodo, Section howto 6.3</p>
<hr class="docutils" />
</div>
<div class="section" id="mpiio-package">
<span id="mpiio"></span><h3>4.1.19. MPIIO package<a class="headerlink" href="#mpiio-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-mpiio
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p mpiio -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-mpiio
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^mpiio -a machine
</pre></div>
</div>
<p>Supporting info:</p>
<hr class="docutils" />
</div>
<div class="section" id="opt-package">
<span id="opt"></span><h3>4.1.20. OPT package<a class="headerlink" href="#opt-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-opt
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p opt -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-opt
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^opt -a machine
</pre></div>
</div>
<p>Supporting info: examples/accelerate, bench/KEPLER</p>
<p>For the OPT package, your Makefile.machine needs an additional
settings for CCFLAGS.</p>
<ul class="simple">
<li>CCFLAGS: add -restrict</li>
</ul>
<hr class="docutils" />
</div>
<div class="section" id="peri-package">
<span id="peri"></span><h3>4.1.21. PERI package<a class="headerlink" href="#peri-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-peri
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p peri -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-peri
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^peri -a machine
</pre></div>
</div>
<p>Supporting info: examples/peri</p>
<hr class="docutils" />
</div>
<div class="section" id="poems-package">
<span id="poems"></span><h3>4.1.22. POEMS package<a class="headerlink" href="#poems-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-poems
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p poems -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-poems
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^poems -a machine
</pre></div>
</div>
<p>Supporting info: examples/rigid</p>
<hr class="docutils" />
</div>
<div class="section" id="python-package">
<span id="python"></span><h3>4.1.23. PYTHON package<a class="headerlink" href="#python-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-python
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p python -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-python
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^python -a machine
</pre></div>
</div>
<p>Supporting info: examples/python</p>
<hr class="docutils" />
</div>
<div class="section" id="qeq-package">
<span id="qeq"></span><h3>4.1.24. QEQ package<a class="headerlink" href="#qeq-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-qeq
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p qeq -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-qeq
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^qeq -a machine
</pre></div>
</div>
<p>Supporting info: examples/qeq</p>
<hr class="docutils" />
</div>
<div class="section" id="reax-package">
<span id="reax"></span><h3>4.1.25. REAX package<a class="headerlink" href="#reax-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-reax
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p reax -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-reax
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^reax -a machine
</pre></div>
</div>
<p>Supporting info: examples/reax</p>
<hr class="docutils" />
</div>
<div class="section" id="replica-package">
<span id="replica"></span><h3>4.1.26. REPLICA package<a class="headerlink" href="#replica-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-replica
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p replica -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-replica
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^replica -a machine
</pre></div>
</div>
<p>Supporting info: examples/neb, examples/prd, examples/tad, Section howto 6.5</p>
<hr class="docutils" />
</div>
<div class="section" id="rigid-package">
<span id="rigid"></span><h3>4.1.27. RIGID package<a class="headerlink" href="#rigid-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-rigid
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p rigid -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-rigid
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^rigid -a machine
</pre></div>
</div>
<p>Supporting info: examples/ASPHERE, examples/rigid</p>
<hr class="docutils" />
</div>
<div class="section" id="shock-package">
<span id="shock"></span><h3>4.1.28. SHOCK package<a class="headerlink" href="#shock-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-shock
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p shock -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-shock
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^shock -a machine
</pre></div>
</div>
<p>Supporting info: examples/hugoniostat, examples/msst</p>
<hr class="docutils" />
</div>
<div class="section" id="snap-package">
<span id="snap"></span><h3>4.1.29. SNAP package<a class="headerlink" href="#snap-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-snap
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p snap -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-snap
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^snap -a machine
</pre></div>
</div>
<p>Supporting info: examples/snap</p>
<hr class="docutils" />
</div>
<div class="section" id="srd-package">
<span id="srd"></span><h3>4.1.30. SRD package<a class="headerlink" href="#srd-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-srd
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p srd -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-srd
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^srd -a machine
</pre></div>
</div>
<p>Supporting info:</p>
<hr class="docutils" />
</div>
<div class="section" id="voronoi-package">
<span id="voronoi"></span><h3>4.1.31. VORONOI package<a class="headerlink" href="#voronoi-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-voronoi
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p voronoi -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-voronoi
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^voronoi -a machine
</pre></div>
</div>
<p>Supporting info: examples/voronoi</p>
<hr class="docutils" />
</div>
<div class="section" id="xtc-package">
<span id="xtc"></span><h3>4.1.32. XTC package<a class="headerlink" href="#xtc-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-xtc
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p xtc -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-xtc
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^xtc -a machine
</pre></div>
</div>
<p>Supporting info:</p>
<hr class="docutils" />
</div>
</div>
<div class="section" id="user-packages">
<span id="pkg-2"></span><h2>4.2. User packages<a class="headerlink" href="#user-packages" title="Permalink to this headline">¶</a></h2>
<p>The current list of user-contributed packages is as follows:</p>
<table border="1" class="docutils">
<colgroup>
<col width="18%" />
<col width="19%" />
<col width="20%" />
<col width="23%" />
<col width="7%" />
<col width="9%" />
<col width="5%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>Package</td>
<td>Description</td>
<td>Author(s)</td>
<td>Doc page</td>
<td>Example</td>
<td>Pic/movie</td>
<td>Library</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#user-atc"><span>USER-ATC</span></a></td>
<td>atom-to-continuum coupling</td>
<td>Jones & Templeton & Zimmerman (1)</td>
<td><a class="reference internal" href="fix_atc.html"><em>fix atc</em></a></td>
<td>USER/atc</td>
<td><a class="reference external" href="http://lammps.sandia.gov/pictures.html#atc">atc</a></td>
<td>lib/atc</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#user-awpmd"><span>USER-AWPMD</span></a></td>
<td>wave-packet MD</td>
<td>Ilya Valuev (JIHT)</td>
<td><a class="reference internal" href="pair_awpmd.html"><em>pair_style awpmd/cut</em></a></td>
<td>USER/awpmd</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>lib/awpmd</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#user-cg-cmm"><span>USER-CG-CMM</span></a></td>
<td>coarse-graining model</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><a class="reference internal" href="pair_sdk.html"><em>pair_style lj/sdk</em></a></td>
<td>USER/cg-cmm</td>
<td><a class="reference external" href="http://lammps.sandia.gov/pictures.html#cg">cg</a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#user-colvars"><span>USER-COLVARS</span></a></td>
<td>collective variables</td>
<td>Fiorin & Henin & Kohlmeyer (2)</td>
<td><a class="reference internal" href="fix_colvars.html"><em>fix colvars</em></a></td>
<td>USER/colvars</td>
<td><a class="reference external" href="colvars">colvars</a></td>
<td>lib/colvars</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#user-cuda"><span>USER-CUDA</span></a></td>
<td>NVIDIA GPU styles</td>
<td>Christian Trott (U Tech Ilmenau)</td>
<td><a class="reference internal" href="accelerate_cuda.html"><em>Section accelerate</em></a></td>
<td>USER/cuda</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>lib/cuda</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#user-diffraction"><span>USER-DIFFRACTION</span></a></td>
<td>virutal x-ray and electron diffraction</td>
<td>Shawn Coleman (ARL)</td>
<td><a class="reference internal" href="compute_xrd.html"><em>compute xrd</em></a></td>
<td>USER/diffraction</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#user-dpd"><span>USER-DPD</span></a></td>
<td>dissipative particle dynamics (DPD)</td>
<td>Larentzos & Mattox & Brennan (5)</td>
<td>src/USER-DPD/README</td>
<td>USER/dpd</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#user-drude"><span>USER-DRUDE</span></a></td>
<td>Drude oscillators</td>
<td>Dequidt & Devemy & Padua (3)</td>
<td><a class="reference internal" href="tutorial_drude.html"><em>tutorial</em></a></td>
<td>USER/drude</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#user-eff"><span>USER-EFF</span></a></td>
<td>electron force field</td>
<td>Andres Jaramillo-Botero (Caltech)</td>
<td><a class="reference internal" href="pair_eff.html"><em>pair_style eff/cut</em></a></td>
<td>USER/eff</td>
<td><a class="reference external" href="http://lammps.sandia.gov/movies.html#eff">eff</a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#user-fep"><span>USER-FEP</span></a></td>
<td>free energy perturbation</td>
<td>Agilio Padua (U Blaise Pascal Clermont-Ferrand)</td>
<td><a class="reference internal" href="compute_fep.html"><em>compute fep</em></a></td>
<td>USER/fep</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#user-h5md"><span>USER-H5MD</span></a></td>
<td>dump output via HDF5</td>
<td>Pierre de Buyl (KU Leuven)</td>
<td><a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>lib/h5md</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#user-intel"><span>USER-INTEL</span></a></td>
<td>Vectorized CPU and Intel(R) coprocessor styles</td>
<td><ol class="first last upperalpha simple" start="23">
<li>Michael Brown (Intel)</li>
</ol>
</td>
<td><a class="reference internal" href="accelerate_intel.html"><em>Section accelerate</em></a></td>
<td>examples/intel</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#user-lb"><span>USER-LB</span></a></td>
<td>Lattice Boltzmann fluid</td>
<td>Colin Denniston (U Western Ontario)</td>
<td><a class="reference internal" href="fix_lb_fluid.html"><em>fix lb/fluid</em></a></td>
<td>USER/lb</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#user-mgpt"><span>USER-MGPT</span></a></td>
<td>fast MGPT multi-ion potentials</td>
<td>Tomas Oppelstrup & John Moriarty (LLNL)</td>
<td><a class="reference internal" href="pair_mgpt.html"><em>pair_style mgpt</em></a></td>
<td>USER/mgpt</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#user-misc"><span>USER-MISC</span></a></td>
<td>single-file contributions</td>
<td>USER-MISC/README</td>
<td>USER-MISC/README</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#user-molfile"><span>USER-MOLFILE</span></a></td>
<td><a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a> molfile plug-ins</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><a class="reference internal" href="dump_molfile.html"><em>dump molfile</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>VMD-MOLFILE</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#user-omp"><span>USER-OMP</span></a></td>
<td>OpenMP threaded styles</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><a class="reference internal" href="accelerate_omp.html"><em>Section accelerate</em></a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#user-phonon"><span>USER-PHONON</span></a></td>
<td>phonon dynamical matrix</td>
<td>Ling-Ti Kong (Shanghai Jiao Tong U)</td>
<td><a class="reference internal" href="fix_phonon.html"><em>fix phonon</em></a></td>
<td>USER/phonon</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#user-qmmm"><span>USER-QMMM</span></a></td>
<td>QM/MM coupling</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><a class="reference internal" href="fix_qmmm.html"><em>fix qmmm</em></a></td>
<td>USER/qmmm</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>lib/qmmm</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#user-qtb"><span>USER-QTB</span></a></td>
<td>quantum nuclear effects</td>
<td>Yuan Shen (Stanford)</td>
<td><a class="reference internal" href="fix_qtb.html"><em>fix qtb</em></a> <a class="reference internal" href="fix_qbmsst.html"><em>fix_qbmsst</em></a></td>
<td>qtb</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#user-quip"><span>USER-QUIP</span></a></td>
<td>QUIP/libatoms interface</td>
<td>Albert Bartok-Partay (U Cambridge)</td>
<td><a class="reference internal" href="pair_quip.html"><em>pair_style quip</em></a></td>
<td>USER/quip</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>lib/quip</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#user-reaxc"><span>USER-REAXC</span></a></td>
<td>C version of ReaxFF</td>
<td>Metin Aktulga (LBNL)</td>
<td><a class="reference internal" href="pair_reax_c.html"><em>pair_style reaxc</em></a></td>
<td>reax</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#user-smd"><span>USER-SMD</span></a></td>
<td>smoothed Mach dynamics</td>
<td>Georg Ganzenmuller (EMI)</td>
<td><a class="reference external" href="PDF/SMD_LAMMPS_userguide.pdf">userguide.pdf</a></td>
<td>USER/smd</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#user-smtbq"><span>USER-SMTBQ</span></a></td>
<td>Second Moment Tight Binding - QEq potential</td>
<td>Salles & Maras & Politano & Tetot (4)</td>
<td><a class="reference internal" href="pair_smtbq.html"><em>pair_style smtbq</em></a></td>
<td>USER/smtbq</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#user-sph"><span>USER-SPH</span></a></td>
<td>smoothed particle hydrodynamics</td>
<td>Georg Ganzenmuller (EMI)</td>
<td><a class="reference external" href="PDF/SPH_LAMMPS_userguide.pdf">userguide.pdf</a></td>
<td>USER/sph</td>
<td><a class="reference external" href="http://lammps.sandia.gov/movies.html#sph">sph</a></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#user-tally"><span>USER-TALLY</span></a></td>
<td>Pairwise tallied computes</td>
<td>Axel Kohlmeyer (Temple U)</td>
<td><code class="xref doc docutils literal"><span class="pre">compute</span></code></td>
<td>USER/tally</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#user-vtk"><span>USER-VTK</span></a></td>
<td>VTK-style dumps</td>
<td>Berger and Queteschiner (6)</td>
<td><code class="xref doc docutils literal"><span class="pre">compute</span> <span class="pre">custom/vtk</span></code></td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td><ul class="first last simple">
<li></li>
</ul>
</td>
<td>lib/vtk</td>
</tr>
<tr class="row-odd"><td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
<p>The “Authors” column lists a name(s) if a specific person is
responible for creating and maintaining the package.</p>
<p>(1) The ATC package was created by Reese Jones, Jeremy Templeton, and
Jon Zimmerman (Sandia).</p>
<p>(2) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
the colvars module library written by Giacomo Fiorin (Temple U) and
Jerome Henin (LISM, Marseille, France).</p>
<p>(3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal
Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
(U Blaise Pascal).</p>
<p>(4) The SMTBQ package was created by Nicolas Salles, Emile Maras,
Olivier Politano, and Robert Tetot (LAAS-CNRS, France).</p>
<p>(5) The USER-DPD package was created by James Larentzos (ARL), Timothy
Mattox (Engility), and John Brennan (ARL).</p>
<p>(6) The USER-VTK package was created by Richard Berger (JKU) and
Daniel Queteschiner (DCS Computing).</p>
<p>The “Doc page” column links to either a sub-section of the
<a class="reference internal" href="Section_howto.html"><em>Section_howto</em></a> of the manual, or an input script
command implemented as part of the package, or to additional
documentation provided within the package.</p>
<p>The “Example” column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. “peptide” refers to the examples/peptide directory. USER/cuda
refers to the examples/USER/cuda directory.</p>
<p>The “Library” column lists an external library which must be built
first and which LAMMPS links to when it is built. If it is listed as
lib/package, then the code for the library is under the lib directory
of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution.
See details on all of this below for individual packages.</p>
<hr class="docutils" />
<div class="section" id="user-atc-package">
<span id="user-atc"></span><h3>4.2.1. USER-ATC package<a class="headerlink" href="#user-atc-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<p>This package implements a “fix atc” command which can be used in a
LAMMPS input script. This fix can be employed to either do concurrent
coupling of MD with FE-based physics surrogates or on-the-fly
post-processing of atomic information to continuum fields.</p>
<p>See the doc page for the fix atc command to get started. At the
bottom of the doc page are many links to additional documentation
contained in the doc/USER/atc directory.</p>
<p>There are example scripts for using this package in examples/USER/atc.</p>
<p>This package uses an external library in lib/atc which must be
compiled before making LAMMPS. See the lib/atc/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.</p>
<p>The primary people who created this package are Reese Jones (rjones at
sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if
you have questions.</p>
<p>Examples: examples/USER/atc</p>
<hr class="docutils" />
</div>
<div class="section" id="user-awpmd-package">
<span id="user-awpmd"></span><h3>4.2.2. USER-AWPMD package<a class="headerlink" href="#user-awpmd-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<p>This package contains a LAMMPS implementation of the Antisymmetrized
Wave Packet Molecular Dynamics (AWPMD) method.</p>
<p>See the doc page for the pair_style awpmd/cut command to get started.</p>
<p>There are example scripts for using this package in examples/USER/awpmd.</p>
<p>This package uses an external library in lib/awpmd which must be
compiled before making LAMMPS. See the lib/awpmd/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.</p>
<p>The person who created this package is Ilya Valuev at the JIHT in
Russia (valuev at physik.hu-berlin.de). Contact him directly if you
have questions.</p>
<p>Examples: examples/USER/awpmd</p>
<hr class="docutils" />
</div>
<div class="section" id="user-cg-cmm-package">
<span id="user-cg-cmm"></span><h3>4.2.3. USER-CG-CMM package<a class="headerlink" href="#user-cg-cmm-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
</pre></div>
</div>
<p>Supporting info:</p>
<p>This package implements 3 commands which can be used in a LAMMPS input
script:</p>
<ul class="simple">
<li>pair_style lj/sdk</li>
<li>pair_style lj/sdk/coul/long</li>
<li>angle_style sdk</li>
</ul>
<p>These styles allow coarse grained MD simulations with the
parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
(SDK), with extensions to simulate ionic liquids, electrolytes, lipids
and charged amino acids.</p>
<p>See the doc pages for these commands for details.</p>
<p>There are example scripts for using this package in
examples/USER/cg-cmm.</p>
<p>This is the second generation implementation reducing the the clutter
of the previous version. For many systems with electrostatics, it will
be faster to use pair_style hybrid/overlay with lj/sdk and coul/long
instead of the combined lj/sdk/coul/long style. since the number of
charged atom types is usually small. For any other coulomb
interactions this is now required. To exploit this property, the use
of the kspace_style pppm/cg is recommended over regular pppm. For all
new styles, input file backward compatibility is provided. The old
implementation is still available through appending the /old
suffix. These will be discontinued and removed after the new
implementation has been fully validated.</p>
<p>The current version of this package should be considered beta
quality. The CG potentials work correctly for “normal” situations, but
have not been testing with all kinds of potential parameters and
simulation systems.</p>
<p>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
<p>Examples: examples/USER/cg-cmm</p>
<hr class="docutils" />
</div>
<div class="section" id="user-colvars-package">
<span id="user-colvars"></span><h3>4.2.4. USER-COLVARS package<a class="headerlink" href="#user-colvars-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<p>This package implements the “fix colvars” command which can be
used in a LAMMPS input script.</p>
<p>This fix allows to use “collective variables” to implement
Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
Sampling and Restraints. This code consists of two parts:</p>
<ul class="simple">
<li>A portable collective variable module library written and maintained</li>
<li>by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and</li>
<li>Jerome Henin (LISM, CNRS, Marseille, France). This code is located in</li>
<li>the directory lib/colvars and needs to be compiled first. The colvars</li>
<li>fix and an interface layer, exchanges information between LAMMPS and</li>
<li>the collective variable module.</li>
</ul>
<p>See the doc page of <a class="reference internal" href="fix_colvars.html"><em>fix colvars</em></a> for more details.</p>
<p>There are example scripts for using this package in
examples/USER/colvars</p>
<p>This is a very new interface that does not yet support all
features in the module and will see future optimizations
and improvements. The colvars module library is also available
in NAMD has been thoroughly used and tested there. Bugs and
problems are likely due to the interface layers code.
Thus the current version of this package should be considered
beta quality.</p>
<p>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
<p>Examples: examples/USER/colvars</p>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<hr class="docutils" />
</div>
<div class="section" id="user-cuda-package">
<span id="user-cuda"></span><h3>4.2.5. USER-CUDA package<a class="headerlink" href="#user-cuda-package" title="Permalink to this headline">¶</a></h3>
<p>This package provides acceleration of various LAMMPS pair styles, fix
styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
GPUs.</p>
<p>See this section of the manual to get started:</p>
<p><span class="xref std std-ref">Section_accelerate</span></p>
<p>There are example scripts for using this package in
examples/USER/cuda.</p>
<p>This package uses an external library in lib/cuda which must be
compiled before making LAMMPS. See the lib/cuda/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.</p>
<p>The person who created this package is Christian Trott at the
University of Technology Ilmenau, Germany (christian.trott at
tu-ilmenau.de). Contact him directly if you have questions.</p>
<p>Examples: examples/accelerate, bench/FERMI, bench/KEPLER</p>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<hr class="docutils" />
</div>
<div class="section" id="user-diffraction-package">
<span id="user-diffraction"></span><h3>4.2.6. USER-DIFFRACTION package<a class="headerlink" href="#user-diffraction-package" title="Permalink to this headline">¶</a></h3>
<p>This package contains the commands neeed to calculate x-ray and
electron diffraction intensities based on kinematic diffraction
theory.</p>
<p>See these doc pages and their related commands to get started:</p>
<ul class="simple">
<li><a class="reference internal" href="compute_xrd.html"><em>compute xrd</em></a></li>
<li><a class="reference internal" href="compute_saed.html"><em>compute saed</em></a></li>
<li><a class="reference internal" href="fix_saed_vtk.html"><em>fix saed/vtk</em></a></li>
</ul>
<p>The person who created this package is Shawn P. Coleman
(shawn.p.coleman8.ctr at mail.mil) while at the University of
Arkansas. Contact him directly if you have questions.</p>
<p>Examples: examples/USER/diffraction</p>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
</pre></div>
</div>
<p>Supporting info:</p>
<hr class="docutils" />
</div>
<div class="section" id="user-dpd-package">
<span id="user-dpd"></span><h3>4.2.7. USER-DPD package<a class="headerlink" href="#user-dpd-package" title="Permalink to this headline">¶</a></h3>
<p>This package implements the dissipative particle dynamics (DPD) method
under isothermal, isoenergetic, isobaric and isenthalpic conditions.
The DPD equations of motion are integrated efficiently through the
Shardlow splitting algorithm.</p>
<p>See these doc pages and their related commands to get started:</p>
<ul class="simple">
<li><a class="reference internal" href="compute_dpd.html"><em>compute dpd</em></a></li>
<li><a class="reference internal" href="compute_dpd_atom.html"><em>compute dpd/atom</em></a></li>
<li><a class="reference internal" href="fix_eos_table.html"><em>fix_eos/cv</em></a></li>
<li><a class="reference internal" href="fix_eos_table.html"><em>fix_eos/table</em></a></li>
<li><a class="reference internal" href="fix_shardlow.html"><em>fix_shardlow</em></a></li>
<li><a class="reference internal" href="pair_dpd_conservative.html"><em>pair_dpd/conservative</em></a></li>
<li><a class="reference internal" href="pair_dpd_fdt.html"><em>pair_dpd/fdt</em></a></li>
<li><a class="reference internal" href="pair_dpd_fdt.html"><em>pair_dpd/fdt/energy</em></a></li>
</ul>
<p>There are example scripts for using this package in examples/USER/dpd.</p>
<p>The people who created this package are James Larentzos
(james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at
engilitycorp.com) and John Brennan (john.k.brennan.civ at mail.mil).
Contact them directly if you have questions.</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
</pre></div>
</div>
<p>Examples: examples/USER/dpd</p>
<hr class="docutils" />
</div>
<div class="section" id="user-drude-package">
<span id="user-drude"></span><h3>4.2.8. USER-DRUDE package<a class="headerlink" href="#user-drude-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<p>This package implements methods for simulating polarizable systems
in LAMMPS using thermalized Drude oscillators.</p>
<p>See these doc pages and their related commands to get started:</p>
<ul class="simple">
<li><a class="reference internal" href="tutorial_drude.html"><em>Drude tutorial</em></a></li>
<li><a class="reference internal" href="fix_drude.html"><em>fix drude</em></a></li>
<li><a class="reference internal" href="compute_temp_drude.html"><em>compute temp/drude</em></a></li>
<li><a class="reference internal" href="fix_langevin_drude.html"><em>fix langevin/drude</em></a></li>
<li><a class="reference internal" href="fix_drude_transform.html"><em>fix drude/transform/...</em></a></li>
<li><a class="reference internal" href="pair_thole.html"><em>pair thole</em></a></li>
</ul>
<p>There are auxiliary tools for using this package in tools/drude.</p>
<p>The person who created this package is Alain Dequidt at Universite
Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr)
Contact him directly if you have questions. Co-authors: Julien Devemy,
Agilio Padua.</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
</pre></div>
</div>
<p>Examples: examples/USER/drude</p>
<p>Doc: Section howto 6.27</p>
<hr class="docutils" />
</div>
<div class="section" id="user-eff-package">
<span id="user-eff"></span><h3>4.2.9. USER-EFF package<a class="headerlink" href="#user-eff-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<p>This package contains a LAMMPS implementation of the electron Force
Field (eFF) currently under development at Caltech, as described in
A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
2010. The eFF potential was first introduced by Su and Goddard, in
2007.</p>
<p>eFF can be viewed as an approximation to QM wave packet dynamics and
Fermionic molecular dynamics, combining the ability of electronic
structure methods to describe atomic structure, bonding, and chemistry
in materials, and of plasma methods to describe nonequilibrium
dynamics of large systems with a large number of highly excited
electrons. We classify it as a mixed QM-classical approach rather than
a conventional force field method, which introduces QM-based terms (a
spin-dependent repulsion term to account for the Pauli exclusion
principle and the electron wavefunction kinetic energy associated with
the Heisenberg principle) that reduce, along with classical
electrostatic terms between nuclei and electrons, to the sum of a set
of effective pairwise potentials. This makes eFF uniquely suited to
simulate materials over a wide range of temperatures and pressures
where electronically excited and ionized states of matter can occur
and coexist.</p>
<p>The necessary customizations to the LAMMPS core are in place to
enable the correct handling of explicit electron properties during
minimization and dynamics.</p>
<p>See the doc page for the pair_style eff/cut command to get started.</p>
<p>There are example scripts for using this package in
examples/USER/eff.</p>
<p>There are auxiliary tools for using this package in tools/eff.</p>
<p>The person who created this package is Andres Jaramillo-Botero at
CalTech (ajaramil at wag.caltech.edu). Contact him directly if you
have questions.</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
</pre></div>
</div>
<p>Examples: examples/USER/eff</p>
<hr class="docutils" />
</div>
<div class="section" id="user-fep-package">
<span id="user-fep"></span><h3>4.2.10. USER-FEP package<a class="headerlink" href="#user-fep-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<p>This package provides methods for performing free energy perturbation
simulations with soft-core pair potentials in LAMMPS.</p>
<p>See these doc pages and their related commands to get started:</p>
<ul class="simple">
<li><a class="reference internal" href="fix_adapt_fep.html"><em>fix adapt/fep</em></a></li>
<li><a class="reference internal" href="compute_fep.html"><em>compute fep</em></a></li>
<li><a class="reference internal" href="pair_lj_soft.html"><em>soft pair styles</em></a></li>
</ul>
<p>The person who created this package is Agilio Padua at Universite
Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr)
Contact him directly if you have questions.</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
</pre></div>
</div>
<p>Examples: examples/USER/fep</p>
<hr class="docutils" />
</div>
<div class="section" id="user-h5md-package">
<span id="user-h5md"></span><h3>4.2.11. USER-H5MD package<a class="headerlink" href="#user-h5md-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<p>This package contains a <a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a> command for
performing a dump of atom properties in HDF5 format. <a class="reference external" href="http://www.hdfgroup.org/HDF5/">HDF5 files</a> are binary, portable and self-describing and can be
examined and used by a variety of auxiliary tools. The output HDF5
files are structured in a format called H5MD, which was designed to
store molecular data, and can be used and produced by various MD and
MD-related codes. The <code class="xref doc docutils literal"><span class="pre">dump</span> <span class="pre">h5md</span></code> command gives a
citation to a paper describing the format.</p>
<p>The person who created this package and the underlying H5MD format is
Pierre de Buyl at KU Leuven (see <a class="reference external" href="http://pdebuyl.be">http://pdebuyl.be</a>). Contact him
directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-intel-package">
<span id="user-intel"></span><h3>4.2.12. USER-INTEL package<a class="headerlink" href="#user-intel-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<p>This package provides options for performing neighbor list and
non-bonded force calculations in single, mixed, or double precision
and also a capability for accelerating calculations with an
Intel(R) Xeon Phi(TM) coprocessor.</p>
<p>See this section of the manual to get started:</p>
<p><span class="xref std std-ref">Section_accelerate</span></p>
<p>The person who created this package is W. Michael Brown at Intel
(michael.w.brown at intel.com). Contact him directly if you have questions.</p>
<p>For the USER-INTEL package, you have 2 choices when building. You can
build with CPU or Phi support. The latter uses Xeon Phi chips in
“offload” mode. Each of these modes requires additional settings in
your Makefile.machine for CCFLAGS and LINKFLAGS.</p>
<p>For CPU mode (if using an Intel compiler):</p>
<ul class="simple">
<li>CCFLAGS: add -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits</li>
<li>LINKFLAGS: add -fopenmp</li>
</ul>
<p>For Phi mode add the following in addition to the CPU mode flags:</p>
<ul class="simple">
<li>CCFLAGS: add -DLMP_INTEL_OFFLOAD and</li>
<li>LINKFLAGS: add -offload</li>
</ul>
<p>And also add this to CCFLAGS:</p>
<pre class="literal-block">
-offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs="gather_scatter_loop_unroll=4""
</pre>
<p>Examples: examples/accelerate, bench/KEPLER</p>
<hr class="docutils" />
</div>
<div class="section" id="user-lb-package">
<span id="user-lb"></span><h3>4.2.13. USER-LB package<a class="headerlink" href="#user-lb-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<p>This package contains a LAMMPS implementation of a background
Lattice-Boltzmann fluid, which can be used to model MD particles
influenced by hydrodynamic forces.</p>
<p>See this doc page and its related commands to get started:</p>
<p><a class="reference internal" href="fix_lb_fluid.html"><em>fix lb/fluid</em></a></p>
<p>The people who created this package are Frances Mackay (fmackay at
uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of
Western Ontario. Contact them directly if you have questions.</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
</pre></div>
</div>
<p>Examples: examples/USER/lb</p>
<hr class="docutils" />
</div>
<div class="section" id="user-mgpt-package">
<span id="user-mgpt"></span><h3>4.2.14. USER-MGPT package<a class="headerlink" href="#user-mgpt-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<p>This package contains a fast implementation for LAMMPS of
quantum-based MGPT multi-ion potentials. The MGPT or model GPT method
derives from first-principles DFT-based generalized pseudopotential
theory (GPT) through a series of systematic approximations valid for
mid-period transition metals with nearly half-filled d bands. The
MGPT method was originally developed by John Moriarty at Lawrence
Livermore National Lab (LLNL).</p>
<p>In the general matrix representation of MGPT, which can also be
applied to f-band actinide metals, the multi-ion potentials are
evaluated on the fly during a simulation through d- or f-state matrix
multiplication, and the forces that move the ions are determined
analytically. The <em>mgpt</em> pair style in this package calculates forces
and energies using an optimized matrix-MGPT algorithm due to Tomas
Oppelstrup at LLNL.</p>
<p>See this doc page to get started:</p>
<p><a class="reference internal" href="pair_mgpt.html"><em>pair_style mgpt</em></a></p>
<p>The persons who created the USER-MGPT package are Tomas Oppelstrup
(<a class="reference external" href="mailto:oppelstrup2%40llnl.gov">oppelstrup2<span>@</span>llnl<span>.</span>gov</a>) and John Moriarty (<a class="reference external" href="mailto:moriarty2%40llnl.gov">moriarty2<span>@</span>llnl<span>.</span>gov</a>)
Contact them directly if you have any questions.</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
</pre></div>
</div>
<p>Examples: examples/USER/mgpt</p>
<hr class="docutils" />
</div>
<div class="section" id="user-misc-package">
<span id="user-misc"></span><h3>4.2.15. USER-MISC package<a class="headerlink" href="#user-misc-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<p>The files in this package are a potpourri of (mostly) unrelated
features contributed to LAMMPS by users. Each feature is a single
pair of files (<a href="#id2"><span class="problematic" id="id3">*</span></a>.cpp and <a href="#id4"><span class="problematic" id="id5">*</span></a>.h).</p>
<p>More information about each feature can be found by reading its doc
page in the LAMMPS doc directory. The doc page which lists all LAMMPS
input script commands is as follows:</p>
<p><a class="reference internal" href="Section_commands.html#cmd-5"><span>Section_commands</span></a></p>
<p>User-contributed features are listed at the bottom of the fix,
compute, pair, etc sections.</p>
<p>The list of features and author of each is given in the
src/USER-MISC/README file.</p>
<p>You should contact the author directly if you have specific questions
about the feature or its coding.</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
</pre></div>
</div>
<p>Examples: examples/USER/misc</p>
<hr class="docutils" />
</div>
<div class="section" id="user-molfile-package">
<span id="user-molfile"></span><h3>4.2.16. USER-MOLFILE package<a class="headerlink" href="#user-molfile-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<p>This package contains a dump molfile command which uses molfile
plugins that are bundled with the
<a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a> molecular visualization and
analysis program, to enable LAMMPS to dump its information in formats
compatible with various molecular simulation tools.</p>
<p>The package only provides the interface code, not the plugins. These
can be obtained from a VMD installation which has to match the
platform that you are using to compile LAMMPS for. By adding plugins
to VMD, support for new file formats can be added to LAMMPS (or VMD or
other programs that use them) without having to recompile the
application itself.</p>
<p>See this doc page to get started:</p>
<p><span class="xref std std-ref">dump molfile</span></p>
<p>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-omp-package">
<span id="user-omp"></span><h3>4.2.17. USER-OMP package<a class="headerlink" href="#user-omp-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<p>This package provides OpenMP multi-threading support and
other optimizations of various LAMMPS pair styles, dihedral
styles, and fix styles.</p>
<p>See this section of the manual to get started:</p>
<p><span class="xref std std-ref">Section_accelerate</span></p>
<p>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
<p>For the USER-OMP package, your Makefile.machine needs additional
settings for CCFLAGS and LINKFLAGS.</p>
<ul class="simple">
<li>CCFLAGS: add -fopenmp and -restrict</li>
<li>LINKFLAGS: add -fopenmp</li>
</ul>
<p>Examples: examples/accelerate, bench/KEPLER</p>
<hr class="docutils" />
</div>
<div class="section" id="user-phonon-package">
<span id="user-phonon"></span><h3>4.2.18. USER-PHONON package<a class="headerlink" href="#user-phonon-package" title="Permalink to this headline">¶</a></h3>
<p>This package contains a fix phonon command that calculates dynamical
matrices, which can then be used to compute phonon dispersion
relations, directly from molecular dynamics simulations.</p>
<p>See this doc page to get started:</p>
<p><a class="reference internal" href="fix_phonon.html"><em>fix phonon</em></a></p>
<p>The person who created this package is Ling-Ti Kong (konglt at
sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly
if you have questions.</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
</pre></div>
</div>
<p>Examples: examples/USER/phonon</p>
<hr class="docutils" />
</div>
<div class="section" id="user-qmmm-package">
<span id="user-qmmm"></span><h3>4.2.19. USER-QMMM package<a class="headerlink" href="#user-qmmm-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<p>This package provides a fix qmmm command which allows LAMMPS to be
used in a QM/MM simulation, currently only in combination with pw.x
code from the <a class="reference external" href="http://www.quantum-espresso.org">Quantum ESPRESSO</a> package.</p>
<p>The current implementation only supports an ONIOM style mechanical
coupling to the Quantum ESPRESSO plane wave DFT package.
Electrostatic coupling is in preparation and the interface has been
written in a manner that coupling to other QM codes should be possible
without changes to LAMMPS itself.</p>
<p>See this doc page to get started:</p>
<p><a class="reference internal" href="fix_qmmm.html"><em>fix qmmm</em></a></p>
<p>as well as the lib/qmmm/README file.</p>
<p>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.</p>
<hr class="docutils" />
</div>
<div class="section" id="user-qtb-package">
<span id="user-qtb"></span><h3>4.2.20. USER-QTB package<a class="headerlink" href="#user-qtb-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<p>This package provides a self-consistent quantum treatment of the
vibrational modes in a classical molecular dynamics simulation. By
coupling the MD simulation to a colored thermostat, it introduces zero
point energy into the system, alter the energy power spectrum and the
heat capacity towards their quantum nature. This package could be of
interest if one wants to model systems at temperatures lower than
their classical limits or when temperatures ramp up across the
classical limits in the simulation.</p>
<p>See these two doc pages to get started:</p>
<p><a class="reference internal" href="fix_qtb.html"><em>fix qtb</em></a> provides quantum nulcear correction through a
colored thermostat and can be used with other time integration schemes
like <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a> or <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a>.</p>
<p><a class="reference internal" href="fix_qbmsst.html"><em>fix qbmsst</em></a> enables quantum nuclear correction of a
multi-scale shock technique simulation by coupling the quantum thermal
bath with the shocked system.</p>
<p>The person who created this package is Yuan Shen (sy0302 at
stanford.edu) at Stanford University. Contact him directly if you
have questions.</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
</pre></div>
</div>
<p>Examples: examples/USER/qtb</p>
<hr class="docutils" />
</div>
<div class="section" id="user-quip-package">
<span id="user-quip"></span><h3>4.2.21. USER-QUIP package<a class="headerlink" href="#user-quip-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<p>Examples: examples/USER/quip</p>
<hr class="docutils" />
</div>
<div class="section" id="user-reaxc-package">
<span id="user-reaxc"></span><h3>4.2.22. USER-REAXC package<a class="headerlink" href="#user-reaxc-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
</pre></div>
</div>
<p>Supporting info:</p>
<p>This package contains a implementation for LAMMPS of the ReaxFF force
field. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. It was originally developed by Adri van Duin and the Goddard
group at CalTech.</p>
<p>The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in
C, should give identical or very similar results to pair_style reax,
which is a ReaxFF implementation on top of a Fortran library, a
version of which library was originally authored by Adri van Duin.</p>
<p>The reax/c version should be somewhat faster and more scalable,
particularly with respect to the charge equilibration calculation. It
should also be easier to build and use since there are no complicating
issues with Fortran memory allocation or linking to a Fortran library.</p>
<p>For technical details about this implemention of ReaxFF, see
this paper:</p>
<p>Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty,
S. A. Pandit, A. Y. Grama, Parallel Computing, in press (2011).</p>
<p>See the doc page for the pair_style reax/c command for details
of how to use it in LAMMPS.</p>
<p>The person who created this package is Hasan Metin Aktulga (hmaktulga
at lbl.gov), while at Purdue University. Contact him directly, or
Aidan Thompson at Sandia (athomps at sandia.gov), if you have
questions.</p>
<p>Examples: examples/reax</p>
<hr class="docutils" />
</div>
<div class="section" id="user-smd-package">
<span id="user-smd"></span><h3>4.2.23. USER-SMD package<a class="headerlink" href="#user-smd-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<p>This package implements smoothed Mach dynamics (SMD) in
LAMMPS. Currently, the package has the following features:</p>
<ul class="simple">
<li>Does liquids via traditional Smooth Particle Hydrodynamics (SPH)</li>
<li>Also solves solids mechanics problems via a state of the art
stabilized meshless method with hourglass control.</li>
<li>Can specify hydrostatic interactions independently from material
strength models, i.e. pressure and deviatoric stresses are separated.</li>
<li>Many material models available (Johnson-Cook, plasticity with
hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new
material models.</li>
<li>Rigid boundary conditions (walls) can be loaded as surface geometries
from <a href="#id7"><span class="problematic" id="id8">*</span></a>.STL files.</li>
</ul>
<p>See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started.</p>
<p>There are example scripts for using this package in examples/USER/smd.</p>
<p>The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.</p>
<p>Examples: examples/USER/smd</p>
<hr class="docutils" />
</div>
<div class="section" id="user-smtbq-package">
<span id="user-smtbq"></span><h3>4.2.24. USER-SMTBQ package<a class="headerlink" href="#user-smtbq-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
</pre></div>
</div>
<p>Supporting info:</p>
<p>This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
potential for the description of ionocovalent bonds in oxides.</p>
<p>There are example scripts for using this package in
examples/USER/smtbq.</p>
<p>See this doc page to get started:</p>
<p><a class="reference internal" href="pair_smtbq.html"><em>pair_style smtbq</em></a></p>
<p>The persons who created the USER-SMTBQ package are Nicolas Salles,
Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at
these email addreses: <a class="reference external" href="mailto:lammps%40u-bourgogne.fr">lammps<span>@</span>u-bourgogne<span>.</span>fr</a>, <a class="reference external" href="mailto:nsalles%40laas.fr">nsalles<span>@</span>laas<span>.</span>fr</a>. Contact
them directly if you have any questions.</p>
<p>Examples: examples/USER/smtbq</p>
<hr class="docutils" />
</div>
<div class="section" id="user-sph-package">
<span id="user-sph"></span><h3>4.2.25. USER-SPH package<a class="headerlink" href="#user-sph-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
</pre></div>
</div>
<p>Supporting info:</p>
<p>This package implements smoothed particle hydrodynamics (SPH) in
LAMMPS. Currently, the package has the following features:</p>
<ul class="simple">
<li>Tait, ideal gas, Lennard-Jones equation of states, full support for
complete (i.e. internal-energy dependent) equations of state</li>
<li>Plain or Monaghans XSPH integration of the equations of motion</li>
<li>Density continuity or density summation to propagate the density field</li>
<li>Commands to set internal energy and density of particles from the
input script</li>
<li>Output commands to access internal energy and density for dumping and
thermo output</li>
</ul>
<p>See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.</p>
<p>There are example scripts for using this package in examples/USER/sph.</p>
<p>The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.</p>
<p>Examples: examples/USER/sph</p>
<hr class="docutils" />
</div>
<div class="section" id="user-tally-package">
<span id="user-tally"></span><h3>4.2.26. USER-TALLY package<a class="headerlink" href="#user-tally-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
</pre></div>
</div>
<p>To un-install via make or Make.py:</p>
<div class="highlight-python"><div class="highlight"><pre>make no-body
make machine
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
</pre></div>
</div>
<p>Supporting info:</p>
<p>Examples: examples/USER/tally</p>
<hr class="docutils" />
</div>
<div class="section" id="user-vtk-package">
<span id="user-vtk"></span><h3>4.2.27. USER-VTK package<a class="headerlink" href="#user-vtk-package" title="Permalink to this headline">¶</a></h3>
<p>Contents:</p>
<p>To install via make or Make.py:</p>
<p>To un-install via make or Make.py:</p>
<p>Supporting info:</p>
<p>Examples: examples/USER/tally</p>
</div>
</div>
</div>
</div>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="Section_accelerate.html" class="btn btn-neutral float-right" title="5. Accelerating LAMMPS performance" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="Section_commands.html" class="btn btn-neutral" title="3. Commands" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
<hr/>
<div role="contentinfo">
<p>
© 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>
<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/_sources/Manual.txt b/doc/_sources/Manual.txt
index 736ad34cd..3f7f92f7d 100644
--- a/doc/_sources/Manual.txt
+++ b/doc/_sources/Manual.txt
@@ -1,104 +1,104 @@
.. raw:: html
<H1></H1>
LAMMPS Documentation
====================
-17 Feb 2016 version
+22 Feb 2016 version
-------------------
Version info:
-------------
The LAMMPS "version" is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it immediately, and post a notice on `this page of the WWW site <bug_>`_. Each dated copy of LAMMPS contains all the
features and bug-fixes up to and including that version date. The
version date is printed to the screen and logfile every time you run
LAMMPS. It is also in the file src/version.h and in the LAMMPS
directory name created when you unpack a tarball, and at the top of
the first page of the manual (this page).
* If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of LAMMPS.
* If you browse the HTML doc pages included in your tarball, they
describe the version you have.
* The `PDF file <Manual.pdf>`_ on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don't want
it to be part of every patch.
* There is also a `Developer.pdf <Developer.pdf>`_ file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS.
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).
The primary developers of LAMMPS are `Steve Plimpton <sjp_>`_, Aidan
Thompson, and Paul Crozier who can be contacted at
sjplimp,athomps,pscrozi at sandia.gov. The `LAMMPS WWW Site <lws_>`_ at
http://lammps.sandia.gov has more information about the code and its
uses.
.. _bug: http://lammps.sandia.gov/bug.html
.. _sjp: http://www.sandia.gov/~sjplimp
----------
The LAMMPS documentation is organized into the following sections. If
you find errors or omissions in this manual or have suggestions for
useful information to add, please send an email to the developers so
we can improve the LAMMPS documentation.
Once you are familiar with LAMMPS, you may want to bookmark :ref:`this page <comm>` at Section_commands.html#comm since
it gives quick access to documentation for all LAMMPS commands.
`PDF file <Manual.pdf>`_ of the entire manual, generated by
`htmldoc <http://freecode.com/projects/htmldoc>`_
.. toctree::
:maxdepth: 2
:numbered:
Section_intro
Section_start
Section_commands
Section_packages
Section_accelerate
Section_howto
Section_example
Section_perf
Section_tools
Section_modify
Section_python
Section_errors
Section_history
Indices and tables
==================
* :ref:`genindex`
* :ref:`search`
.. raw:: html
</BODY>
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
diff --git a/doc/_sources/angle_none.txt b/doc/_sources/angle_none.txt
index b67cd3d5f..a53a50ac0 100644
--- a/doc/_sources/angle_none.txt
+++ b/doc/_sources/angle_none.txt
@@ -1,41 +1,44 @@
.. index:: angle_style none
angle_style none command
========================
Syntax
""""""
.. parsed-literal::
angle_style none
Examples
""""""""
.. parsed-literal::
angle_style none
Description
"""""""""""
-Using an angle style of none means angle forces are not computed, even
-if triplets of angle atoms were listed in the data file read by the
-:doc:`read_data <read_data>` command.
+Using an angle style of none means angle forces and energies are not
+computed, even if triplets of angle atoms were listed in the data file
+read by the :doc:`read_data <read_data>` command.
+
+See the :doc:`angle_style zero <angle_zero>` command for a way to
+calculate angle statistics, but compute no angle interactions.
Restrictions
""""""""""""
none
Related commands
""""""""""""""""
:doc:`angle_style zero <angle_zero>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
diff --git a/doc/_sources/dihedral_style.txt b/doc/_sources/dihedral_style.txt
index a32c12e50..c5e806406 100644
--- a/doc/_sources/dihedral_style.txt
+++ b/doc/_sources/dihedral_style.txt
@@ -1,136 +1,136 @@
.. index:: dihedral_style
dihedral_style command
======================
Syntax
""""""
.. parsed-literal::
dihedral_style style
* style = *none* or *hybrid* or *charmm* or *class2* or *harmonic* or *helix* or *multi/harmonic* or *opls*
Examples
""""""""
.. parsed-literal::
dihedral_style harmonic
dihedral_style multi/harmonic
dihedral_style hybrid harmonic charmm
Description
"""""""""""
Set the formula(s) LAMMPS uses to compute dihedral interactions
between quadruplets of atoms, which remain in force for the duration
of the simulation. The list of dihedral quadruplets is read in by a
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` command
from a data or restart file.
Hybrid models where dihedrals are computed using different dihedral
potentials can be setup using the *hybrid* dihedral style.
The coefficients associated with a dihedral style can be specified in
a data or restart file or via the :doc:`dihedral_coeff <dihedral_coeff>`
command.
All dihedral potentials store their coefficient data in binary restart
files which means dihedral_style and
:doc:`dihedral_coeff <dihedral_coeff>` commands do not need to be
re-specified in an input script that restarts a simulation. See the
:doc:`read_restart <read_restart>` command for details on how to do
this. The one exception is that dihedral_style *hybrid* only stores
the list of sub-styles in the restart file; dihedral coefficients need
to be re-specified.
.. note::
When both a dihedral and pair style is defined, the
:doc:`special_bonds <special_bonds>` command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 4 bonded atoms.
In the formulas listed for each dihedral style, *phi* is the torsional
angle defined by the quadruplet of atoms. This angle has a sign
convention as shown in this diagram:
.. image:: Eqs/dihedral_sign.jpg
:align: center
where the I,J,K,L ordering of the 4 atoms that define the dihedral
is from left to right.
This sign convention effects several of the dihedral styles listed
below (e.g. charmm, helix) in the sense that the energy formula
depends on the sign of phi, which may be reflected in the value of the
coefficients you specify.
.. note::
When comparing the formulas and coefficients for various LAMMPS
dihedral styles with dihedral equations defined by other force fields,
note that some force field implementations divide/multiply the energy
prefactor *K* by the multiple number of torsions that contain the J-K
bond in an I-J-K-L torsion. LAMMPS does not do this, i.e. the listed
dihedral equation applies to each individual dihedral. Thus you need
to define *K* appropriately via the
:doc:`dihedral_coeff <dihedral_coeff>` command to account for this
difference if necessary.
----------
Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated :doc:`dihedral_coeff <dihedral_coeff>` command.
Note that there are also additional dihedral styles submitted by users
which are included in the LAMMPS distribution. The list of these with
links to the individual styles are given in the dihedral section of
:ref:`this page <cmd_5>`.
* :doc:`dihedral_style none <dihedral_none>` - turn off dihedral interactions
-* :doc:`dihedral_style hybrid <dihedral_hybrid>` - define multiple styles of dihedral interactions
* :doc:`dihedral_style zero <dihedral_zero>` - topology but no interactions
+* :doc:`dihedral_style hybrid <dihedral_hybrid>` - define multiple styles of dihedral interactions
* :doc:`dihedral_style charmm <dihedral_charmm>` - CHARMM dihedral
* :doc:`dihedral_style class2 <dihedral_class2>` - COMPASS (class 2) dihedral
* :doc:`dihedral_style harmonic <dihedral_harmonic>` - harmonic dihedral
* :doc:`dihedral_style helix <dihedral_helix>` - helix dihedral
* :doc:`dihedral_style multi/harmonic <dihedral_multi_harmonic>` - multi-harmonic dihedral
* :doc:`dihedral_style opls <dihedral_opls>` - OPLS dihedral
----------
Restrictions
""""""""""""
Dihedral styles can only be set for atom styles that allow dihedrals
to be defined.
Most dihedral styles are part of the MOLECULE package. They are only
enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info on packages.
The doc pages for individual dihedral potentials tell if it is part of
a package.
Related commands
""""""""""""""""
:doc:`dihedral_coeff <dihedral_coeff>`
Default
"""""""
dihedral_style none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
diff --git a/doc/_sources/dihedral_zero.txt b/doc/_sources/dihedral_zero.txt
index 7e048fc1f..97d3283ad 100644
--- a/doc/_sources/dihedral_zero.txt
+++ b/doc/_sources/dihedral_zero.txt
@@ -1,50 +1,51 @@
.. index:: dihedral_style zero
dihedral_style zero command
===========================
Syntax
""""""
.. parsed-literal::
dihedral_style zero
Examples
""""""""
.. parsed-literal::
dihedral_style zero
dihedral_coeff *
Description
"""""""""""
Using a dihedral style of zero means dihedral forces and energies are
not computed, but the geometry of dihedral quadruplets is still
accessible to other commands.
As an example, the :doc:`compute dihedral/local <compute_dihedral_local>` command can be used to
-compute the theta values for the list of quadruplets of dihderal atoms
+compute the theta values for the list of quadruplets of dihedral atoms
listed in the data file read by the :doc:`read_data <read_data>`
-command. If no dihedral style is defined, this command cannot be used.
+command. If no dihedral style is defined, this command cannot be
+used.
Note that the :doc:`dihedral_coeff <dihedral_coeff>` command must be
used for all dihedral types, though no additional values are
specified.
Restrictions
""""""""""""
none
**Related commands:** none
:doc:`dihedral_style none <dihedral_none>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
diff --git a/doc/_sources/pair_none.txt b/doc/_sources/pair_none.txt
index 98de4e85c..5f784a7fe 100644
--- a/doc/_sources/pair_none.txt
+++ b/doc/_sources/pair_none.txt
@@ -1,55 +1,56 @@
.. index:: pair_style none
pair_style none command
=======================
Syntax
""""""
.. parsed-literal::
pair_style none
Examples
""""""""
.. parsed-literal::
pair_style none
Description
"""""""""""
-Using a pair style of none means pair forces are not computed.
+Using a pair style of none means pair forces and energies are not
+computed.
With this choice, the force cutoff is 0.0, which means that only atoms
within the neighbor skin distance (see the :doc:`neighbor <neighbor>`
command) are communicated between processors. You must insure the
skin distance is large enough to acquire atoms needed for computing
bonds, angles, etc.
A pair style of *none* will also prevent pairwise neighbor lists from
being built. However if the :doc:`neighbor <neighbor>` style is *bin*,
data structures for binning are still allocated. If the neighbor skin
distance is small, then these data structures can consume a large
amount of memory. So you should either set the neighbor style to
*nsq* or set the skin distance to a larger value.
See the :doc:`pair_style zero <pair_zero>` for a way to trigger the
building of a neighbor lists, but compute no pairwise interactions.
Restrictions
""""""""""""
none
Related commands
""""""""""""""""
:doc:`pair_style zero <pair_zero>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
diff --git a/doc/_sources/pair_zero.txt b/doc/_sources/pair_zero.txt
index 26410cbc0..88c19af00 100644
--- a/doc/_sources/pair_zero.txt
+++ b/doc/_sources/pair_zero.txt
@@ -1,65 +1,65 @@
.. index:: pair_style zero
pair_style zero command
=======================
Syntax
""""""
.. parsed-literal::
pair_style zero cutoff
* zero = style name of this pair style
cutoff = global cutoff (distance units)
Examples
""""""""
.. parsed-literal::
pair_style zero
pair_coeff * *
pair_coeff 1 2 3.0
Description
"""""""""""
Define a global cutoff length for the purpose of building a neighbor
-list and acquiring ghost atoms, but do not compute any pairwise
-forces.
+list and acquiring ghost atoms, but do not compute any pairwise forces
+or energies.
This can be useful for fixes or computes which require a neighbor list
to enumerate pairs of atoms within some cutoff distance, but when
pairwise forces are not otherwise needed. Examples are the :doc:`fix bond/create <fix_bond_create>`, :doc:`compute rdf <compute_rdf>`,
:doc:`compute voronoi/atom <compute_voronoi_atom>` commands.
Note that the :doc:`comm_modify cutoff <comm_modify>` command can be
used to insure communication of ghost atoms even when a pair style is
not defined, but it will not trigger neighbor list generation.
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands, or by mixing as described below:
* cutoff (distance units)
This coefficient is optional. If not specified, the global cutoff
specified in the pair_style command is used.
Restrictions
""""""""""""
none
Related commands
""""""""""""""""
:doc:`pair_style none <pair_none>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
diff --git a/doc/angle_none.html b/doc/angle_none.html
index 796a9482d..3a9dea282 100644
--- a/doc/angle_none.html
+++ b/doc/angle_none.html
@@ -1,221 +1,223 @@
<!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>angle_style none command — 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 & 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 & 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>
</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> »</li>
<li>angle_style none 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="angle-style-none-command">
<span id="index-0"></span><h1>angle_style none command<a class="headerlink" href="#angle-style-none-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>angle_style none
</pre></div>
</div>
</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>angle_style none
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
-<p>Using an angle style of none means angle forces are not computed, even
-if triplets of angle atoms were listed in the data file read by the
-<a class="reference internal" href="read_data.html"><em>read_data</em></a> command.</p>
+<p>Using an angle style of none means angle forces and energies are not
+computed, even if triplets of angle atoms were listed in the data file
+read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command.</p>
+<p>See the <a class="reference internal" href="angle_zero.html"><em>angle_style zero</em></a> command for a way to
+calculate angle statistics, but compute no angle interactions.</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="angle_zero.html"><em>angle_style zero</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
© 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>
<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/angle_none.txt b/doc/angle_none.txt
index e8eee85ef..a4a9b07c7 100644
--- a/doc/angle_none.txt
+++ b/doc/angle_none.txt
@@ -1,31 +1,34 @@
"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
angle_style none command :h3
[Syntax:]
angle_style none :pre
[Examples:]
angle_style none :pre
[Description:]
-Using an angle style of none means angle forces are not computed, even
-if triplets of angle atoms were listed in the data file read by the
-"read_data"_read_data.html command.
+Using an angle style of none means angle forces and energies are not
+computed, even if triplets of angle atoms were listed in the data file
+read by the "read_data"_read_data.html command.
+
+See the "angle_style zero"_angle_zero.html command for a way to
+calculate angle statistics, but compute no angle interactions.
[Restrictions:] none
[Related commands:]
"angle_style zero"_angle_zero.html
[Default:] none
diff --git a/doc/dihedral_style.html b/doc/dihedral_style.html
index ff669a414..ed133f64b 100644
--- a/doc/dihedral_style.html
+++ b/doc/dihedral_style.html
@@ -1,297 +1,297 @@
<!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>dihedral_style command — 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 & 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 & 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>
</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> »</li>
<li>dihedral_style 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="dihedral-style-command">
<span id="index-0"></span><h1>dihedral_style command<a class="headerlink" href="#dihedral-style-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>dihedral_style style
</pre></div>
</div>
<ul class="simple">
<li>style = <em>none</em> or <em>hybrid</em> or <em>charmm</em> or <em>class2</em> or <em>harmonic</em> or <em>helix</em> or <em>multi/harmonic</em> or <em>opls</em></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>dihedral_style harmonic
dihedral_style multi/harmonic
dihedral_style hybrid harmonic charmm
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Set the formula(s) LAMMPS uses to compute dihedral interactions
between quadruplets of atoms, which remain in force for the duration
of the simulation. The list of dihedral quadruplets is read in by a
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command
from a data or restart file.</p>
<p>Hybrid models where dihedrals are computed using different dihedral
potentials can be setup using the <em>hybrid</em> dihedral style.</p>
<p>The coefficients associated with a dihedral style can be specified in
a data or restart file or via the <a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a>
command.</p>
<p>All dihedral potentials store their coefficient data in binary restart
files which means dihedral_style and
<a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a> commands do not need to be
re-specified in an input script that restarts a simulation. See the
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command for details on how to do
this. The one exception is that dihedral_style <em>hybrid</em> only stores
the list of sub-styles in the restart file; dihedral coefficients need
to be re-specified.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">When both a dihedral and pair style is defined, the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 4 bonded atoms.</p>
</div>
<p>In the formulas listed for each dihedral style, <em>phi</em> is the torsional
angle defined by the quadruplet of atoms. This angle has a sign
convention as shown in this diagram:</p>
<img alt="_images/dihedral_sign.jpg" class="align-center" src="_images/dihedral_sign.jpg" />
<p>where the I,J,K,L ordering of the 4 atoms that define the dihedral
is from left to right.</p>
<p>This sign convention effects several of the dihedral styles listed
below (e.g. charmm, helix) in the sense that the energy formula
depends on the sign of phi, which may be reflected in the value of the
coefficients you specify.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">When comparing the formulas and coefficients for various LAMMPS
dihedral styles with dihedral equations defined by other force fields,
note that some force field implementations divide/multiply the energy
prefactor <em>K</em> by the multiple number of torsions that contain the J-K
bond in an I-J-K-L torsion. LAMMPS does not do this, i.e. the listed
dihedral equation applies to each individual dihedral. Thus you need
to define <em>K</em> appropriately via the
<a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a> command to account for this
difference if necessary.</p>
</div>
<hr class="docutils" />
<p>Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated <a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a> command.</p>
<p>Note that there are also additional dihedral styles submitted by users
which are included in the LAMMPS distribution. The list of these with
links to the individual styles are given in the dihedral section of
<a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
<ul class="simple">
<li><a class="reference internal" href="dihedral_none.html"><em>dihedral_style none</em></a> - turn off dihedral interactions</li>
-<li><a class="reference internal" href="dihedral_hybrid.html"><em>dihedral_style hybrid</em></a> - define multiple styles of dihedral interactions</li>
<li><a class="reference internal" href="dihedral_zero.html"><em>dihedral_style zero</em></a> - topology but no interactions</li>
+<li><a class="reference internal" href="dihedral_hybrid.html"><em>dihedral_style hybrid</em></a> - define multiple styles of dihedral interactions</li>
<li><a class="reference internal" href="dihedral_charmm.html"><em>dihedral_style charmm</em></a> - CHARMM dihedral</li>
<li><a class="reference internal" href="dihedral_class2.html"><em>dihedral_style class2</em></a> - COMPASS (class 2) dihedral</li>
<li><a class="reference internal" href="dihedral_harmonic.html"><em>dihedral_style harmonic</em></a> - harmonic dihedral</li>
<li><a class="reference internal" href="dihedral_helix.html"><em>dihedral_style helix</em></a> - helix dihedral</li>
<li><a class="reference internal" href="dihedral_multi_harmonic.html"><em>dihedral_style multi/harmonic</em></a> - multi-harmonic dihedral</li>
<li><a class="reference internal" href="dihedral_opls.html"><em>dihedral_style opls</em></a> - OPLS dihedral</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<p>Dihedral styles can only be set for atom styles that allow dihedrals
to be defined.</p>
<p>Most dihedral styles are part of the MOLECULE package. They are only
enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info on packages.
The doc pages for individual dihedral potentials tell if it is part of
a package.</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="dihedral_coeff.html"><em>dihedral_coeff</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
<p>dihedral_style none</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
© 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>
<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/dihedral_style.txt b/doc/dihedral_style.txt
index 6e76d887a..1e0d9a83f 100644
--- a/doc/dihedral_style.txt
+++ b/doc/dihedral_style.txt
@@ -1,118 +1,118 @@
"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
dihedral_style command :h3
[Syntax:]
dihedral_style style :pre
style = {none} or {hybrid} or {charmm} or {class2} or {harmonic} or {helix} or \
{multi/harmonic} or {opls} :ul
[Examples:]
dihedral_style harmonic
dihedral_style multi/harmonic
dihedral_style hybrid harmonic charmm :pre
[Description:]
Set the formula(s) LAMMPS uses to compute dihedral interactions
between quadruplets of atoms, which remain in force for the duration
of the simulation. The list of dihedral quadruplets is read in by a
"read_data"_read_data.html or "read_restart"_read_restart.html command
from a data or restart file.
Hybrid models where dihedrals are computed using different dihedral
potentials can be setup using the {hybrid} dihedral style.
The coefficients associated with a dihedral style can be specified in
a data or restart file or via the "dihedral_coeff"_dihedral_coeff.html
command.
All dihedral potentials store their coefficient data in binary restart
files which means dihedral_style and
"dihedral_coeff"_dihedral_coeff.html commands do not need to be
re-specified in an input script that restarts a simulation. See the
"read_restart"_read_restart.html command for details on how to do
this. The one exception is that dihedral_style {hybrid} only stores
the list of sub-styles in the restart file; dihedral coefficients need
to be re-specified.
NOTE: When both a dihedral and pair style is defined, the
"special_bonds"_special_bonds.html command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 4 bonded atoms.
In the formulas listed for each dihedral style, {phi} is the torsional
angle defined by the quadruplet of atoms. This angle has a sign
convention as shown in this diagram:
:c,image(Eqs/dihedral_sign.jpg)
where the I,J,K,L ordering of the 4 atoms that define the dihedral
is from left to right.
This sign convention effects several of the dihedral styles listed
below (e.g. charmm, helix) in the sense that the energy formula
depends on the sign of phi, which may be reflected in the value of the
coefficients you specify.
NOTE: When comparing the formulas and coefficients for various LAMMPS
dihedral styles with dihedral equations defined by other force fields,
note that some force field implementations divide/multiply the energy
prefactor {K} by the multiple number of torsions that contain the J-K
bond in an I-J-K-L torsion. LAMMPS does not do this, i.e. the listed
dihedral equation applies to each individual dihedral. Thus you need
to define {K} appropriately via the
"dihedral_coeff"_dihedral_coeff.html command to account for this
difference if necessary.
:line
Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "dihedral_coeff"_dihedral_coeff.html command.
Note that there are also additional dihedral styles submitted by users
which are included in the LAMMPS distribution. The list of these with
links to the individual styles are given in the dihedral section of
"this page"_Section_commands.html#cmd_5.
"dihedral_style none"_dihedral_none.html - turn off dihedral interactions
-"dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions
-"dihedral_style zero"_dihedral_zero.html - topology but no interactions :ul
+"dihedral_style zero"_dihedral_zero.html - topology but no interactions
+"dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul
"dihedral_style charmm"_dihedral_charmm.html - CHARMM dihedral
"dihedral_style class2"_dihedral_class2.html - COMPASS (class 2) dihedral
"dihedral_style harmonic"_dihedral_harmonic.html - harmonic dihedral
"dihedral_style helix"_dihedral_helix.html - helix dihedral
"dihedral_style multi/harmonic"_dihedral_multi_harmonic.html - multi-harmonic dihedral
"dihedral_style opls"_dihedral_opls.html - OPLS dihedral :ul
:line
[Restrictions:]
Dihedral styles can only be set for atom styles that allow dihedrals
to be defined.
Most dihedral styles are part of the MOLECULE package. They are only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
The doc pages for individual dihedral potentials tell if it is part of
a package.
[Related commands:]
"dihedral_coeff"_dihedral_coeff.html
[Default:]
dihedral_style none
diff --git a/doc/dihedral_zero.html b/doc/dihedral_zero.html
index ba12edcff..2d2b416d6 100644
--- a/doc/dihedral_zero.html
+++ b/doc/dihedral_zero.html
@@ -1,227 +1,228 @@
<!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>dihedral_style zero command — 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 & 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 & 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>
</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> »</li>
<li>dihedral_style zero 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="dihedral-style-zero-command">
<span id="index-0"></span><h1>dihedral_style zero command<a class="headerlink" href="#dihedral-style-zero-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>dihedral_style zero
</pre></div>
</div>
</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>dihedral_style zero
dihedral_coeff *
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Using a dihedral style of zero means dihedral forces and energies are
not computed, but the geometry of dihedral quadruplets is still
accessible to other commands.</p>
<p>As an example, the <a class="reference internal" href="compute_dihedral_local.html"><em>compute dihedral/local</em></a> command can be used to
-compute the theta values for the list of quadruplets of dihderal atoms
+compute the theta values for the list of quadruplets of dihedral atoms
listed in the data file read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
-command. If no dihedral style is defined, this command cannot be used.</p>
+command. If no dihedral style is defined, this command cannot be
+used.</p>
<p>Note that the <a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a> command must be
used for all dihedral types, though no additional values are
specified.</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>
<p><strong>Related commands:</strong> none</p>
<p><a class="reference internal" href="dihedral_none.html"><em>dihedral_style none</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
© 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>
<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/dihedral_zero.txt b/doc/dihedral_zero.txt
index 85523847b..efa04f528 100644
--- a/doc/dihedral_zero.txt
+++ b/doc/dihedral_zero.txt
@@ -1,42 +1,43 @@
"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
dihedral_style zero command :h3
[Syntax:]
dihedral_style zero :pre
[Examples:]
dihedral_style zero
dihedral_coeff * :pre
[Description:]
Using a dihedral style of zero means dihedral forces and energies are
not computed, but the geometry of dihedral quadruplets is still
accessible to other commands.
As an example, the "compute
dihedral/local"_compute_dihedral_local.html command can be used to
-compute the theta values for the list of quadruplets of dihderal atoms
+compute the theta values for the list of quadruplets of dihedral atoms
listed in the data file read by the "read_data"_read_data.html
-command. If no dihedral style is defined, this command cannot be used.
+command. If no dihedral style is defined, this command cannot be
+used.
Note that the "dihedral_coeff"_dihedral_coeff.html command must be
used for all dihedral types, though no additional values are
specified.
[Restrictions:] none
[Related commands:] none
"dihedral_style none"_dihedral_none.html
[Default:] none
diff --git a/doc/fix_langevin.html b/doc/fix_langevin.html
index a3192dc1e..5a289e8fe 100644
--- a/doc/fix_langevin.html
+++ b/doc/fix_langevin.html
@@ -1,490 +1,490 @@
<!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>fix langevin command — 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 & 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 & 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>
</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> »</li>
<li>fix langevin 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="fix-langevin-command">
<span id="index-0"></span><h1>fix langevin command<a class="headerlink" href="#fix-langevin-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="fix-langevin-kk-command">
<h1>fix langevin/kk command<a class="headerlink" href="#fix-langevin-kk-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>fix ID group-ID langevin Tstart Tstop damp seed keyword values ...
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
<li>langevin = style name of this fix command</li>
<li>Tstart,Tstop = desired temperature at start/end of run (temperature units)</li>
<li>Tstart can be a variable (see below)</li>
<li>damp = damping parameter (time units)</li>
<li>seed = random number seed to use for white noise (positive integer)</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>angmom</em> or <em>omega</em> or <em>scale</em> or <em>tally</em> or <em>zero</em></li>
</ul>
<pre class="literal-block">
<em>angmom</em> value = <em>no</em> or factor
<em>no</em> = do not thermostat rotational degrees of freedom via the angular momentum
factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below
<em>gjf</em> value = <em>no</em> or <em>yes</em>
<em>no</em> = use standard formulation
<em>yes</em> = use Gronbech-Jensen/Farago formulation
<em>omega</em> value = <em>no</em> or <em>yes</em>
<em>no</em> = do not thermostat rotational degrees of freedom via the angular velocity
<em>yes</em> = do thermostat rotational degrees of freedom via the angular velocity
<em>scale</em> values = type ratio
type = atom type (1-N)
ratio = factor by which to scale the damping coefficient
<em>tally</em> value = <em>no</em> or <em>yes</em>
<em>no</em> = do not tally the energy added/subtracted to atoms
<em>yes</em> = do tally the energy added/subtracted to atoms
<em>zero</em> value = <em>no</em> or <em>yes</em>
<em>no</em> = do not set total random force to zero
<em>yes</em> = set total random force to zero
</pre>
</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>fix 3 boundary langevin 1.0 1.0 1000.0 699483
fix 1 all langevin 1.0 1.1 100.0 48279 scale 3 1.5
fix 1 all langevin 1.0 1.1 100.0 48279 angmom 3.333
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
-<p>Apply a Langevin thermostat as described in <a class="reference internal" href="#schneider"><span>(Schneider)</span></a>
+<p>Apply a Langevin thermostat as described in <a class="reference internal" href="fix_langevin_eff.html#schneider"><span>(Schneider)</span></a>
to a group of atoms which models an interaction with a background
implicit solvent. Used with <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a>, this command
performs Brownian dynamics (BD), since the total force on each atom
will have the form:</p>
<div class="highlight-python"><div class="highlight"><pre>F = Fc + Ff + Fr
Ff = - (m / damp) v
Fr is proportional to sqrt(Kb T m / (dt damp))
</pre></div>
</div>
<p>Fc is the conservative force computed via the usual inter-particle
interactions (<a class="reference internal" href="pair_style.html"><em>pair_style</em></a>,
<a class="reference internal" href="bond_style.html"><em>bond_style</em></a>, etc).</p>
<p>The Ff and Fr terms are added by this fix on a per-particle basis.
See the <a class="reference internal" href="pair_dpd.html"><em>pair_style dpd/tstat</em></a> command for a
thermostatting option that adds similar terms on a pairwise basis to
pairs of interacting particles.</p>
<p>Ff is a frictional drag or viscous damping term proportional to the
particle’s velocity. The proportionality constant for each atom is
computed as m/damp, where m is the mass of the particle and damp is
the damping factor specified by the user.</p>
<p>Fr is a force due to solvent atoms at a temperature T randomly bumping
into the particle. As derived from the fluctuation/dissipation
theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
dt damp), where Kb is the Boltzmann constant, T is the desired
temperature, m is the mass of the particle, dt is the timestep size,
and damp is the damping factor. Random numbers are used to randomize
the direction and magnitude of this force as described in
-<a class="reference internal" href="#dunweg"><span>(Dunweg)</span></a>, where a uniform random number is used (instead of
+<a class="reference internal" href="fix_langevin_eff.html#dunweg"><span>(Dunweg)</span></a>, where a uniform random number is used (instead of
a Gaussian random number) for speed.</p>
<p>Note that unless you use the <em>omega</em> or <em>angmom</em> keywords, the
thermostat effect of this fix is applied to only the translational
degrees of freedom for the particles, which is an important
consideration for finite-size particles, which have rotational degrees
of freedom, are being thermostatted. The translational degrees of
freedom can also have a bias velocity removed from them before
thermostatting takes place; see the description below.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Unlike the <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a> command which performs
Nose/Hoover thermostatting AND time integration, this fix does NOT
perform time integration. It only modifies forces to effect
thermostatting. Thus you must use a separate time integration fix,
like <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a> to actually update the velocities and
positions of atoms using the modified forces. Likewise, this fix
should not normally be used on atoms that also have their temperature
controlled by another fix - e.g. by <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a> or <a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></a> commands.</p>
</div>
<p>See <a class="reference internal" href="Section_howto.html#howto-16"><span>this howto section</span></a> of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.</p>
<p>The desired temperature at each timestep is a ramped value during the
run from <em>Tstart</em> to <em>Tstop</em>.</p>
<p><em>Tstart</em> can be specified as an equal-style or atom-style
<a class="reference internal" href="variable.html"><em>variable</em></a>. In this case, the <em>Tstop</em> setting is
ignored. If the value is a variable, it should be specified as
v_name, where name is the variable name. In this case, the variable
will be evaluated each timestep, and its value used to determine the
target temperature.</p>
<p>Equal-style variables can specify formulas with various mathematical
functions, and include <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent temperature.</p>
<p>Atom-style variables can specify the same formulas as equal-style
variables but can also include per-atom values, such as atom
coordinates. Thus it is easy to specify a spatially-dependent
temperature with optional time-dependence as well.</p>
<p>Like other fixes that perform thermostatting, this fix can be used
with <a class="reference internal" href="compute.html"><em>compute commands</em></a> that remove a “bias” from the
atom velocities. E.g. removing the center-of-mass velocity from a
group of atoms or removing the x-component of velocity from the
calculation. This is not done by default, but only if the
<a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> command is used to assign a temperature
compute to this fix that includes such a bias term. See the doc pages
for individual <a class="reference internal" href="compute.html"><em>compute commands</em></a> to determine which ones
include a bias. In this case, the thermostat works in the following
manner: bias is removed from each atom, thermostatting is performed on
the remaining thermal degrees of freedom, and the bias is added back
in.</p>
<p>The <em>damp</em> parameter is specified in time units and determines how
rapidly the temperature is relaxed. For example, a value of 100.0
means to relax the temperature in a timespan of (roughly) 100 time
units (tau or fmsec or psec - see the <a class="reference internal" href="units.html"><em>units</em></a> command).
The damp factor can be thought of as inversely related to the
viscosity of the solvent. I.e. a small relaxation time implies a
hi-viscosity solvent and vice versa. See the discussion about gamma
and viscosity in the documentation for the <a class="reference internal" href="fix_viscous.html"><em>fix viscous</em></a> command for more details.</p>
<p>The random # <em>seed</em> must be a positive integer. A Marsaglia random
number generator is used. Each processor uses the input seed to
generate its own unique seed and its own stream of random numbers.
Thus the dynamics of the system will not be identical on two runs on
different numbers of processors.</p>
<hr class="docutils" />
<p>The keyword/value option pairs are used in the following ways.</p>
<p>The keyword <em>angmom</em> and <em>omega</em> keywords enable thermostatting of
rotational degrees of freedom in addition to the usual translational
degrees of freedom. This can only be done for finite-size particles.</p>
<p>A simulation using atom_style sphere defines an omega for finite-size
spheres. A simulation using atom_style ellipsoid defines a finite
size and shape for aspherical particles and an angular momentum.
The Langevin formulas for thermostatting the rotational degrees of
freedom are the same as those above, where force is replaced by
torque, m is replaced by the moment of inertia I, and v is replaced by
omega (which is derived from the angular momentum in the case of
aspherical particles).</p>
<p>The rotational temperature of the particles can be monitored by the
<a class="reference internal" href="compute_temp_sphere.html"><em>compute temp/sphere</em></a> and <a class="reference internal" href="compute_temp_asphere.html"><em>compute temp/asphere</em></a> commands with their rotate
options.</p>
<p>For the <em>omega</em> keyword there is also a scale factor of 10.0/3.0 that
is applied as a multiplier on the Ff (damping) term in the equation
above and of sqrt(10.0/3.0) as a multiplier on the Fr term. This does
not affect the thermostatting behaviour of the Langevin formalism but
insures that the randomized rotational diffusivity of spherical
particles is correct.</p>
<p>For the <em>angmom</em> keyword a similar scale factor is needed which is
10.0/3.0 for spherical particles, but is anisotropic for aspherical
particles (e.g. ellipsoids). Currently LAMMPS only applies an
isotropic scale factor, and you can choose its magnitude as the
specified value of the <em>angmom</em> keyword. If your aspherical particles
are (nearly) spherical than a value of 10.0/3.0 = 3.333 is a good
choice. If they are highly aspherical, a value of 1.0 is as good a
choice as any, since the effects on rotational diffusivity of the
particles will be incorrect regardless. Note that for any reasonable
scale factor, the thermostatting effect of the <em>angmom</em> keyword on the
rotational temperature of the aspherical particles should still be
valid.</p>
<p>The keyword <em>scale</em> allows the damp factor to be scaled up or down by
the specified factor for atoms of that type. This can be useful when
different atom types have different sizes or masses. It can be used
multiple times to adjust damp for several atom types. Note that
specifying a ratio of 2 increases the relaxation time which is
equivalent to the solvent’s viscosity acting on particles with 1/2 the
diameter. This is the opposite effect of scale factors used by the
<a class="reference internal" href="fix_viscous.html"><em>fix viscous</em></a> command, since the damp factor in fix
<em>langevin</em> is inversely related to the gamma factor in fix <em>viscous</em>.
Also note that the damping factor in fix <em>langevin</em> includes the
particle mass in Ff, unlike fix <em>viscous</em>. Thus the mass and size of
different atom types should be accounted for in the choice of ratio
values.</p>
<p>The keyword <em>tally</em> enables the calculation of the cumulative energy
added/subtracted to the atoms as they are thermostatted. Effectively
it is the energy exchanged between the infinite thermal reservoir and
the particles. As described below, this energy can then be printed
out or added to the potential energy of the system to monitor energy
conservation.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">this accumulated energy does NOT include kinetic energy removed
by the <em>zero</em> flag. LAMMPS will print a warning when both options are
active.</p>
</div>
<p>The keyword <em>zero</em> can be used to eliminate drift due to the
thermostat. Because the random forces on different atoms are
independent, they do not sum exactly to zero. As a result, this fix
applies a small random force to the entire system, and the
center-of-mass of the system undergoes a slow random walk. If the
keyword <em>zero</em> is set to <em>yes</em>, the total random force is set exactly
to zero by subtracting off an equal part of it from each atom in the
group. As a result, the center-of-mass of a system with zero initial
momentum will not drift over time.</p>
<p>The keyword <em>gjf</em> can be used to run the <a class="reference internal" href="#gronbech-jensen"><span>Gronbech-Jensen/Farago</span></a> time-discretization of the Langevin model. As
described in the papers cited below, the purpose of this method is to
enable longer timesteps to be used (up to the numerical stability
limit of the integrator), while still producing the correct Boltzmann
distribution of atom positions. It is implemented within LAMMPS, by
changing how the the random force is applied so that it is composed of
the average of two random forces representing half-contributions from
the previous and current time intervals.</p>
<p>In common with all methods based on Verlet integration, the
discretized velocities generated by this method in conjunction with
velocity-Verlet time integration are not exactly conjugate to the
positions. As a result the temperature (computed from the discretized
velocities) will be systematically lower than the target temperature,
by a small amount which grows with the timestep. Nonetheless, the
distribution of atom positions will still be consistent with the
target temperature.</p>
<p>As an example of using the <em>gjf</em> keyword, for molecules containing C-H
bonds, configurational properties generated with dt = 2.5 fs and tdamp
= 100 fs are indistinguishable from dt = 0.5 fs. Because the velocity
distribution systematically decreases with increasing timestep, the
method should not be used to generate properties that depend on the
velocity distribution, such as the velocity autocorrelation function
(VACF). In this example, the velocity distribution at dt = 2.5fs
generates an average temperature of 220 K, instead of 300 K.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. Because the state of the random number generator
is not saved in restart files, this means you cannot do “exact”
restarts with this fix, where the simulation continues on the same as
if no restart had taken place. However, in a statistical sense, a
restarted simulation should produce the same behavior.</p>
<p>The <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>temp</em> option is supported by this
fix. You can use it to assign a temperature <a class="reference internal" href="compute.html"><em>compute</em></a>
you have defined to this fix which will be used in its thermostatting
procedure, as described above. For consistency, the group used by
this fix and by the compute should be the same.</p>
<p>The <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>energy</em> option is supported by this
fix to add the energy change induced by Langevin thermostatting to the
system’s potential energy as part of <a class="reference internal" href="thermo_style.html"><em>thermodynamic output</em></a>. Note that use of this option requires
setting the <em>tally</em> keyword to <em>yes</em>.</p>
<p>This fix computes a global scalar which can be accessed by various
<a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The scalar is the
cummulative energy change due to this fix. The scalar value
calculated by this fix is “extensive”. Note that calculation of this
quantity requires setting the <em>tally</em> keyword to <em>yes</em>.</p>
<p>This fix can ramp its target temperature over multiple runs, using the
<em>start</em> and <em>stop</em> keywords of the <a class="reference internal" href="run.html"><em>run</em></a> command. See the
<a class="reference internal" href="run.html"><em>run</em></a> command for details of how to do this.</p>
<p>This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</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="fix_nh.html"><em>fix nvt</em></a>, <a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></a>, <a class="reference internal" href="fix_viscous.html"><em>fix viscous</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, <a class="reference internal" href="pair_dpd.html"><em>pair_style dpd/tstat</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 option defaults are angmom = no, omega = no, scale = 1.0 for all
types, tally = no, zero = no, gjf = no.</p>
<hr class="docutils" />
<p id="dunweg"><strong>(Dunweg)</strong> Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).</p>
<p id="schneider"><strong>(Schneider)</strong> Schneider and Stoll, Phys Rev B, 17, 1302 (1978).</p>
<p id="gronbech-jensen"><strong>(Gronbech-Jensen)</strong> Gronbech-Jensen and Farago, Mol Phys, 111, 983
(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm,
185, 524 (2014)</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
© 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>
<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/kspace_modify.html b/doc/kspace_modify.html
index eb55acd0a..cba6aeaa7 100644
--- a/doc/kspace_modify.html
+++ b/doc/kspace_modify.html
@@ -1,491 +1,491 @@
<!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>kspace_modify command — 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 & 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 & 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>
</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> »</li>
<li>kspace_modify 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="kspace-modify-command">
<span id="index-0"></span><h1>kspace_modify command<a class="headerlink" href="#kspace-modify-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>kspace_modify keyword value ...
</pre></div>
</div>
<ul class="simple">
<li>one or more keyword/value pairs may be listed</li>
</ul>
<pre class="literal-block">
keyword = <em>mesh</em> or <em>order</em> or <em>order/disp</em> or <em>mix/disp</em> or <em>overlap</em> or <em>minorder</em> or <em>force</em> or <em>gewald</em> or <em>gewald/disp</em> or <em>slab</em> or (nozforce* or <em>compute</em> or <em>cutoff/adjust</em> or <em>fftbench</em> or <em>collective</em> or <em>diff</em> or <em>kmax/ewald</em> or <em>force/disp/real</em> or <em>force/disp/kspace</em> or <em>splittol</em> or <em>disp/auto</em>:l
<em>mesh</em> value = x y z
x,y,z = grid size in each dimension for long-range Coulombics
<em>mesh/disp</em> value = x y z
x,y,z = grid size in each dimension for 1/r^6 dispersion
<em>order</em> value = N
N = extent of Gaussian for PPPM or MSM mapping of charge to grid
<em>order/disp</em> value = N
N = extent of Gaussian for PPPM mapping of dispersion term to grid
<em>mix/disp</em> value = <em>pair</em> or <em>geom</em> or <em>none</em>
<em>overlap</em> = <em>yes</em> or <em>no</em> = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor
<em>minorder</em> value = M
M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication
<em>force</em> value = accuracy (force units)
<em>gewald</em> value = rinv (1/distance units)
rinv = G-ewald parameter for Coulombics
<em>gewald/disp</em> value = rinv (1/distance units)
rinv = G-ewald parameter for dispersion
<em>slab</em> value = volfactor or <em>nozforce</em>
volfactor = ratio of the total extended volume used in the
2d approximation compared with the volume of the simulation domain
<em>nozforce</em> turns off kspace forces in the z direction
<em>compute</em> value = <em>yes</em> or <em>no</em>
<em>cutoff/adjust</em> value = <em>yes</em> or <em>no</em>
<em>pressure/scalar</em> value = <em>yes</em> or <em>no</em>
<em>fftbench</em> value = <em>yes</em> or <em>no</em>
<em>collective</em> value = <em>yes</em> or <em>no</em>
<em>diff</em> value = <em>ad</em> or <em>ik</em> = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode
<em>kmax/ewald</em> value = kx ky kz
kx,ky,kz = number of Ewald sum kspace vectors in each dimension
<em>force/disp/real</em> value = accuracy (force units)
<em>force/disp/kspace</em> value = accuracy (force units)
<em>splittol</em> value = tol
tol = relative size of two eigenvalues (see discussion below)
<em>disp/auto</em> value = yes or no
</pre>
</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>kspace_modify mesh 24 24 30 order 6
kspace_modify slab 3.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Set parameters used by the kspace solvers defined by the
<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command. Not all parameters are
relevant to all kspace styles.</p>
<p>The <em>mesh</em> keyword sets the grid size for kspace style <em>pppm</em> or
<em>msm</em>. In the case of PPPM, this is the FFT mesh, and each dimension
must be factorizable into powers of 2, 3, and 5. In the case of MSM,
this is the finest scale real-space mesh, and each dimension must be
factorizable into powers of 2. When this option is not set, the PPPM
or MSM solver chooses its own grid size, consistent with the
user-specified accuracy and pairwise cutoff. Values for x,y,z of
0,0,0 unset the option.</p>
<p>The <em>mesh/disp</em> keyword sets the grid size for kspace style
<em>pppm/disp</em>. This is the FFT mesh for long-range dispersion and ach
dimension must be factorizable into powers of 2, 3, and 5. When this
option is not set, the PPPM solver chooses its own grid size,
consistent with the user-specified accuracy and pairwise cutoff.
Values for x,y,z of 0,0,0 unset the option.</p>
<p>The <em>order</em> keyword determines how many grid spacings an atom’s charge
extends when it is mapped to the grid in kspace style <em>pppm</em> or <em>msm</em>.
The default for this parameter is 5 for PPPM and 8 for MSM, which
means each charge spans 5 or 8 grid cells in each dimension,
respectively. For the LAMMPS implementation of MSM, the order can
range from 4 to 10 and must be even. For PPPM, the minimum allowed
setting is 2 and the maximum allowed setting is 7. The larger the
value of this parameter, the smaller that LAMMPS will set the grid
size, to achieve the requested accuracy. Conversely, the smaller the
order value, the larger the grid size will be. Note that there is an
inherent trade-off involved: a small grid will lower the cost of FFTs
or MSM direct sum, but a larger order parameter will increase the cost
of interpolating charge/fields to/from the grid.</p>
<p>The <em>order/disp</em> keyword determines how many grid spacings an atom’s
dispersion term extends when it is mapped to the grid in kspace style
<em>pppm/disp</em>. It has the same meaning as the <em>order</em> setting for
Coulombics.</p>
<p>The <em>overlap</em> keyword can be used in conjunction with the <em>minorder</em>
keyword with the PPPM styles to adjust the amount of communication
that occurs when values on the FFT grid are exchangeed between
processors. This communication is distinct from the communication
inherent in the parallel FFTs themselves, and is required because
processors interpolate charge and field values using grid point values
owned by neighboring processors (i.e. ghost point communication). If
the <em>overlap</em> keyword is set to <em>yes</em> then this communication is
allowed to extend beyond nearest-neighbor processors, e.g. when using
lots of processors on a small problem. If it is set to <em>no</em> then the
communication will be limited to nearest-neighbor processors and the
<em>order</em> setting will be reduced if necessary, as explained by the
<em>minorder</em> keyword discussion. The <em>overlap</em> keyword is always set to
<em>yes</em> in MSM.</p>
<p>The <em>minorder</em> keyword allows LAMMPS to reduce the <em>order</em> setting if
necessary to keep the communication of ghost grid point limited to
exchanges between nearest-neighbor processors. See the discussion of
the <em>overlap</em> keyword for details. If the <em>overlap</em> keyword is set to
<em>yes</em>, which is the default, this is never needed. If it set to <em>no</em>
and overlap occurs, then LAMMPS will reduce the order setting, one
step at a time, until the ghost grid overlap only extends to nearest
neighbor processors. The <em>minorder</em> keyword limits how small the
<em>order</em> setting can become. The minimum allowed value for PPPM is 2,
which is the default. If <em>minorder</em> is set to the same value as
<em>order</em> then no reduction is allowed, and LAMMPS will generate an
error if the grid communcation is non-nearest-neighbor and <em>overlap</em>
is set to <em>no</em>. The <em>minorder</em> keyword is not currently supported in
MSM.</p>
<p>The PPPM order parameter may be reset by LAMMPS when it sets up the
FFT grid if the implied grid stencil extends beyond the grid cells
owned by neighboring processors. Typically this will only occur when
small problems are run on large numbers of processors. A warning will
be generated indicating the order parameter is being reduced to allow
LAMMPS to run the problem. Automatic adjustment of the order parameter
is not supported in MSM.</p>
<p>The <em>force</em> keyword overrides the relative accuracy parameter set by
the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command with an absolute
accuracy. The accuracy determines the RMS error in per-atom forces
calculated by the long-range solver and is thus specified in force
units. A negative value for the accuracy setting means to use the
relative accuracy parameter. The accuracy setting is used in
conjunction with the pairwise cutoff to determine the number of
K-space vectors for style <em>ewald</em>, the FFT grid size for style
<em>pppm</em>, or the real space grid size for style <em>msm</em>.</p>
<p>The <em>gewald</em> keyword sets the value of the Ewald or PPPM G-ewald
parameter for charge as <em>rinv</em> in reciprocal distance units. Without
this setting, LAMMPS chooses the parameter automatically as a function
of cutoff, precision, grid spacing, etc. This means it can vary from
one simulation to the next which may not be desirable for matching a
KSpace solver to a pre-tabulated pairwise potential. This setting can
also be useful if Ewald or PPPM fails to choose a good grid spacing
and G-ewald parameter automatically. If the value is set to 0.0,
LAMMPS will choose the G-ewald parameter automatically. MSM does not
use the <em>gewald</em> parameter.</p>
<p>The <em>gewald/disp</em> keyword sets the value of the Ewald or PPPM G-ewald
parameter for dispersion as <em>rinv</em> in reciprocal distance units. It
has the same meaning as the <em>gewald</em> setting for Coulombics.</p>
<p>The <em>slab</em> keyword allows an Ewald or PPPM solver to be used for a
systems that are periodic in x,y but non-periodic in z - a
<a class="reference internal" href="boundary.html"><em>boundary</em></a> setting of “boundary p p f”. This is done by
treating the system as if it were periodic in z, but inserting empty
volume between atom slabs and removing dipole inter-slab interactions
so that slab-slab interactions are effectively turned off. The
volfactor value sets the ratio of the extended dimension in z divided
by the actual dimension in z. The recommended value is 3.0. A larger
value is inefficient; a smaller value introduces unwanted slab-slab
interactions. The use of fixed boundaries in z means that the user
must prevent particle migration beyond the initial z-bounds, typically
by providing a wall-style fix. The methodology behind the <em>slab</em>
option is explained in the paper by <a class="reference internal" href="#yeh"><span>(Yeh)</span></a>. The <em>slab</em> option
is also extended to non-neutral systems
<a class="reference internal" href="#ballenegger"><span>(Ballenegger)</span></a>. An alternative slab option can be
invoked with the <em>nozforce</em> keyword in lieu of the volfactor. This
turns off all kspace forces in the z direction. The <em>nozforce</em> option
is not supported by MSM. For MSM, any combination of periodic,
non-periodic, or shrink-wrapped boundaries can be set using
<a class="reference internal" href="boundary.html"><em>boundary</em></a> (the slab approximation in not needed). The
<em>slab</em> keyword is not currently supported by Ewald or PPPM when using
a triclinic simulation cell. The slab correction has also been
extended to point dipole interactions <a class="reference internal" href="#klapp"><span>(Klapp)</span></a> in
<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> <em>ewald/disp</em>.</p>
<p>The <em>compute</em> keyword allows Kspace computations to be turned off,
even though a <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> is defined. This is
not useful for running a real simulation, but can be useful for
debugging purposes or for computing only partial forces that do not
include the Kspace contribution. You can also do this by simply not
defining a <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a>, but a Kspace-compatible
<a class="reference internal" href="pair_style.html"><em>pair_style</em></a> requires a kspace style to be defined.
This keyword gives you that option.</p>
<p>The <em>cutoff/adjust</em> keyword applies only to MSM. If this option is
turned on, the Coulombic cutoff will be automatically adjusted at the
beginning of the run to give the desired estimated error. Other
cutoffs such as LJ will not be affected. If the grid is not set using
the <em>mesh</em> command, this command will also attempt to use the optimal
grid that minimizes cost using an estimate given by
-<a class="reference internal" href="#hardy"><span>(Hardy)</span></a>. Note that this cost estimate is not exact, somewhat
+<a class="reference internal" href="kspace_style.html#hardy"><span>(Hardy)</span></a>. Note that this cost estimate is not exact, somewhat
experimental, and still may not yield the optimal parameters.</p>
<p>The <em>pressure/scalar</em> keyword applies only to MSM. If this option is
turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will
be computed, which can be used, for example, to run an isotropic barostat.
Computing the full pressure tensor with MSM is expensive, and this option
provides a faster alternative. The scalar pressure is computed using a
relationship between the Coulombic energy and pressure <a class="reference internal" href="#hummer"><span>(Hummer)</span></a>
instead of using the virial equation. This option cannot be used to access
individual components of the pressure tensor, to compute per-atom virial,
or with suffix kspace/pair styles of MSM, like OMP or GPU.</p>
<p>The <em>fftbench</em> keyword applies only to PPPM. It is on by default. If
this option is turned off, LAMMPS will not take the time at the end
of a run to give FFT benchmark timings, and will finish a few seconds
faster than it would if this option were on.</p>
<p>The <em>collective</em> keyword applies only to PPPM. It is set to <em>no</em> by
default, except on IBM BlueGene machines. If this option is set to
<em>yes</em>, LAMMPS will use MPI collective operations to remap data for
3d-FFT operations instead of the default point-to-point communication.
This is faster on IBM BlueGene machines, and may also be faster on
other machines if they have an efficient implementation of MPI
collective operations and adequate hardware.</p>
<p>The <em>diff</em> keyword specifies the differentiation scheme used by the
PPPM method to compute forces on particles given electrostatic
potentials on the PPPM mesh. The <em>ik</em> approach is the default for
-PPPM and is the original formulation used in <a class="reference internal" href="#hockney"><span>(Hockney)</span></a>. It
+PPPM and is the original formulation used in <a class="reference internal" href="kspace_style.html#hockney"><span>(Hockney)</span></a>. It
performs differentiation in Kspace, and uses 3 FFTs to transfer each
component of the computed fields back to real space for total of 4
FFTs per timestep.</p>
<p>The analytic differentiation <em>ad</em> approach uses only 1 FFT to transfer
information back to real space for a total of 2 FFTs per timestep. It
then performs analytic differentiation on the single quantity to
generate the 3 components of the electric field at each grid point.
This is sometimes referred to as “smoothed” PPPM. This approach
requires a somewhat larger PPPM mesh to achieve the same accuracy as
the <em>ik</em> method. Currently, only the <em>ik</em> method (default) can be
used for a triclinic simulation cell with PPPM. The <em>ad</em> method is
always used for MSM.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Currently, not all PPPM styles support the <em>ad</em> option. Support
for those PPPM variants will be added later.</p>
</div>
<p>The <em>kmax/ewald</em> keyword sets the number of kspace vectors in each
dimension for kspace style <em>ewald</em>. The three values must be positive
integers, or else (0,0,0), which unsets the option. When this option
is not set, the Ewald sum scheme chooses its own kspace vectors,
consistent with the user-specified accuracy and pairwise cutoff. In
any case, if kspace style <em>ewald</em> is invoked, the values used are
printed to the screen and the log file at the start of the run.</p>
<p>With the <em>mix/disp</em> keyword one can select the mixing rule for the
dispersion coefficients. With <em>pair</em>, the dispersion coefficients of
unlike types are computed as indicated with
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>. With <em>geom</em>, geometric mixing is
enforced on the dispersion coefficients in the kspace
coefficients. When using the arithmetic mixing rule, this will
speed-up the simulations but introduces some error in the force
computations, as shown in <a class="reference internal" href="#wennberg"><span>(Wennberg)</span></a>. With <em>none</em>, it is
assumed that no mixing rule is applicable. Splitting of the dispersion
coefficients will be performed as described in
-<a class="reference internal" href="#isele-holder"><span>(Isele-Holder)</span></a>. This splitting can be influenced with
+<a class="reference internal" href="kspace_style.html#isele-holder"><span>(Isele-Holder)</span></a>. This splitting can be influenced with
the <em>splittol</em> keywords. Only the eigenvalues that are larger than tol
compared to the largest eigenvalues are included. Using this keywords
the original matrix of dispersion coefficients is approximated. This
leads to faster computations, but the accuracy in the reciprocal space
computations of the dispersion part is decreased.</p>
<p>The <em>force/disp/real</em> and <em>force/disp/kspace</em> keywords set the force
accuracy for the real and space computations for the dispersion part
-of pppm/disp. As shown in <a class="reference internal" href="#isele-holder"><span>(Isele-Holder)</span></a>, optimal
+of pppm/disp. As shown in <a class="reference internal" href="kspace_style.html#isele-holder"><span>(Isele-Holder)</span></a>, optimal
performance and accuracy in the results is obtained when these values
are different.</p>
<p>The <em>disp/auto</em> option controlls whether the pppm/disp is allowed to
generate PPPM parameters automatically. If set to <em>no</em>, parameters have
to be specified using the <em>gewald/disp</em>, <em>mesh/disp</em>,
<em>force/disp/real</em> or <em>force/disp/kspace</em> keywords, or
the code will stop with an error message. When this option is set to
<em>yes</em>, the error message will not appear and the simulation will start.
For a typical application, using the automatic parameter generation will provide
simulations that are either inaccurate or slow. Using this option is thus not
recommended. For guidelines on how to obtain good parameters, see the <a class="reference internal" href="Section_howto.html#howto-23"><span>How-To</span></a> discussion.</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="kspace_style.html"><em>kspace_style</em></a>, <a class="reference internal" href="boundary.html"><em>boundary</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 option defaults are mesh = mesh/disp = 0 0 0, order = order/disp =
5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0,
gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust =
yes (MSM), pressure/scalar = yes (MSM), fftbench = yes (PPPM), diff = ik
(PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0,
split = 0, tol = 1.0e-6, and disp/auto = no.</p>
<hr class="docutils" />
<p id="hockney"><strong>(Hockney)</strong> Hockney and Eastwood, Computer Simulation Using Particles,
Adam Hilger, NY (1989).</p>
<p id="yeh"><strong>(Yeh)</strong> Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999).</p>
<p id="ballenegger"><strong>(Ballenegger)</strong> Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107
(2009).</p>
<p id="klapp"><strong>(Klapp)</strong> Klapp, Schoen, J Chem Phys, 117, 8050 (2002).</p>
<p id="hardy"><strong>(Hardy)</strong> David Hardy thesis: Multilevel Summation for the Fast
Evaluation of Forces for the Simulation of Biomolecules, University of
Illinois at Urbana-Champaign, (2006).</p>
<p id="hummer"><strong>(Hummer)</strong> Hummer, Gronbech-Jensen, Neumann, J Chem Phys, 109, 2791 (1998)</p>
<p id="isele-holder"><strong>(Isele-Holder)</strong> Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J
Chem Theory Comput, 9, 5412 (2013).</p>
<p id="wennberg"><strong>(Wennberg)</strong> Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput,
9, 3527 (2013).</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
© 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>
<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/pair_modify.html b/doc/pair_modify.html
index 6e5b07287..a73d2889c 100644
--- a/doc/pair_modify.html
+++ b/doc/pair_modify.html
@@ -1,434 +1,434 @@
<!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>pair_modify command — 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 & 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 & 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>
</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> »</li>
<li>pair_modify 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="pair-modify-command">
<span id="index-0"></span><h1>pair_modify command<a class="headerlink" href="#pair-modify-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>pair_modify keyword values ...
</pre></div>
</div>
<ul class="simple">
<li>one or more keyword/value pairs may be listed</li>
<li>keyword = <em>pair</em> or <em>shift</em> or <em>mix</em> or <em>table</em> or <em>table/disp</em> or <em>tabinner</em> or <em>tabinner/disp</em> or <em>tail</em> or <em>compute</em></li>
</ul>
<pre class="literal-block">
<em>pair</em> values = sub-style N <em>special</em> which wt1 wt2 wt3
sub-style = sub-style of <a class="reference internal" href="pair_hybrid.html"><em>pair hybrid</em></a>
N = which instance of sub-style (only if sub-style is used multiple times)
<em>special</em> which wt1 wt2 wt3 = override <em>special_bonds</em> settings (optional)
which = <em>lj/coul</em> or <em>lj</em> or <em>coul</em>
w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
<em>mix</em> value = <em>geometric</em> or <em>arithmetic</em> or <em>sixthpower</em>
<em>shift</em> value = <em>yes</em> or <em>no</em>
<em>table</em> value = N
2^N = # of values in table
<em>table/disp</em> value = N
2^N = # of values in table
<em>tabinner</em> value = cutoff
cutoff = inner cutoff at which to begin table (distance units)
<em>tabinner/disp</em> value = cutoff
cutoff = inner cutoff at which to begin table (distance units)
<em>tail</em> value = <em>yes</em> or <em>no</em>
<em>compute</em> value = <em>yes</em> or <em>no</em>
</pre>
</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>pair_modify shift yes mix geometric
pair_modify tail yes
pair_modify table 12
pair_modify pair lj/cut compute no
pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Modify the parameters of the currently defined pair style. Not all
parameters are relevant to all pair styles.</p>
<p>If used, the <em>pair</em> keyword must appear first in the list of keywords.
It can only be used with the <a class="reference internal" href="pair_hybrid.html"><em>hybrid and hybrid/overlay</em></a> pair styles. It means that all the
following parameters will only be modified for the specified
sub-style. If the sub-style is defined multiple times, then an
additional numeric argument <em>N</em> must also be specified, which is a
number from 1 to M where M is the number of times the sub-style was
listed in the <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> command. The extra
number indicates which instance of the sub-style the remaining
keywords will be applied to. Note that if the <em>pair</em> keyword is not
used, and the pair style is <em>hybrid</em> or <em>hybrid/overlay</em>, then all the
specified keywords will be applied to all sub-styles.</p>
<p>The <em>special</em> keyword can only be used in conjunction with the <em>pair</em>
keyword and must directly follow it. It allows to override the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> settings for the specified sub-style.
More details are given below.</p>
<p>The <em>mix</em> keyword affects pair coefficients for interactions between
atoms of type I and J, when I != J and the coefficients are not
explicitly set in the input script. Note that coefficients for I = J
must be set explicitly, either in the input script via the
“pair_coeff” command or in the “Pair Coeffs” section of the <a class="reference internal" href="read_data.html"><em>data file</em></a>. For some pair styles it is not necessary to
specify coefficients when I != J, since a “mixing” rule will create
them from the I,I and J,J settings. The pair_modify <em>mix</em> value
determines what formulas are used to compute the mixed coefficients.
In each case, the cutoff distance is mixed the same way as sigma.</p>
<p>Note that not all pair styles support mixing. Also, some mix options
are not available for certain pair styles. See the doc page for
individual pair styles for those restrictions. Note also that the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command also can be to directly set
coefficients for a specific I != J pairing, in which case no mixing is
performed.</p>
<p>mix <em>geometric</em></p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">epsilon_ij</span> <span class="o">=</span> <span class="n">sqrt</span><span class="p">(</span><span class="n">epsilon_i</span> <span class="o">*</span> <span class="n">epsilon_j</span><span class="p">)</span>
<span class="n">sigma_ij</span> <span class="o">=</span> <span class="n">sqrt</span><span class="p">(</span><span class="n">sigma_i</span> <span class="o">*</span> <span class="n">sigma_j</span><span class="p">)</span>
</pre></div>
</div>
<p>mix <em>arithmetic</em></p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">epsilon_ij</span> <span class="o">=</span> <span class="n">sqrt</span><span class="p">(</span><span class="n">epsilon_i</span> <span class="o">*</span> <span class="n">epsilon_j</span><span class="p">)</span>
<span class="n">sigma_ij</span> <span class="o">=</span> <span class="p">(</span><span class="n">sigma_i</span> <span class="o">+</span> <span class="n">sigma_j</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span>
</pre></div>
</div>
<p>mix <em>sixthpower</em></p>
<div class="highlight-python"><div class="highlight"><pre>epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
(sigma_i^6 + sigma_j^6)
sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)
</pre></div>
</div>
<p>The <em>shift</em> keyword determines whether a Lennard-Jones potential is
shifted at its cutoff to 0.0. If so, this adds an energy term to each
pairwise interaction which will be included in the thermodynamic
output, but does not affect pair forces or atom trajectories. See the
doc page for individual pair styles to see which ones support this
option.</p>
<p>The <em>table</em> and <em>table/disp</em> keywords apply to pair styles with a
long-range Coulombic term or long-range dispersion term respectively;
see the doc page for individual styles to see which potentials support
these options. If N is non-zero, a table of length 2^N is
pre-computed for forces and energies, which can shrink their
computational cost by up to a factor of 2. The table is indexed via a
-bit-mapping technique <a class="reference internal" href="#wolff"><span>(Wolff)</span></a> and a linear interpolation is
+bit-mapping technique <a class="reference internal" href="pair_table.html#wolff"><span>(Wolff)</span></a> and a linear interpolation is
performed between adjacent table values. In our experiments with
different table styles (lookup, linear, spline), this method typically
gave the best performance in terms of speed and accuracy.</p>
<p>The choice of table length is a tradeoff in accuracy versus speed. A
larger N yields more accurate force computations, but requires more
memory which can slow down the computation due to cache misses. A
reasonable value of N is between 8 and 16. The default value of 12
(table of length 4096) gives approximately the same accuracy as the
no-table (N = 0) option. For N = 0, forces and energies are computed
directly, using a polynomial fit for the needed erfc() function
evaluation, which is what earlier versions of LAMMPS did. Values
greater than 16 typically slow down the simulation and will not
improve accuracy; values from 1 to 8 give unreliable results.</p>
<p>The <em>tabinner</em> and <em>tabinner/disp</em> keywords set an inner cutoff above
which the pairwise computation is done by table lookup (if tables are
invoked), for the corresponding Coulombic and dispersion tables
discussed with the <em>table</em> and <em>table/disp</em> keywords. The smaller the
cutoff is set, the less accurate the table becomes (for a given number
of table values), which can require use of larger tables. The default
cutoff value is sqrt(2.0) distance units which means nearly all
pairwise interactions are computed via table lookup for simulations
with “real” units, but some close pairs may be computed directly
(non-table) for simulations with “lj” units.</p>
<p>When the <em>tail</em> keyword is set to <em>yes</em>, certain pair styles will add
a long-range VanderWaals tail “correction” to the energy and pressure.
These corrections are bookkeeping terms which do not affect dynamics,
unless a constant-pressure simulation is being performed. See the doc
page for individual styles to see which support this option. These
corrections are included in the calculation and printing of
thermodynamic quantities (see the <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a>
command). Their effect will also be included in constant NPT or NPH
simulations where the pressure influences the simulation box
dimensions (e.g. the <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> and <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a>
commands). The formulas used for the long-range corrections come from
equation 5 of <a class="reference internal" href="#sun"><span>(Sun)</span></a>.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The tail correction terms are computed at the beginning of each
run, using the current atom counts of each atom type. If atoms are
deleted (or lost) or created during a simulation, e.g. via the <a class="reference internal" href="fix_gcmc.html"><em>fix gcmc</em></a> command, the correction factors are not
re-computed. If you expect the counts to change dramatically, you can
break a run into a series of shorter runs so that the correction
factors are re-computed more frequently.</p>
</div>
<p>Several additional assumptions are inherent in using tail corrections,
including the following:</p>
<ul class="simple">
<li>The simulated system is a 3d bulk homogeneous liquid. This option
should not be used for systems that are non-liquid, 2d, have a slab
geometry (only 2d periodic), or inhomogeneous.</li>
<li>G(r), the radial distribution function (rdf), is unity beyond the
cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an
LJ fluid), and it is probably a good idea to verify this assumption by
checking the rdf. The rdf is not exactly unity beyond the cutoff for
each pair of interaction types, so the tail correction is necessarily
an approximation.</li>
</ul>
<p>The tail corrections are computed at the beginning of each simulation
run. If the number of atoms changes during the run, e.g. due to atoms
leaving the simulation domain, or use of the <a class="reference internal" href="fix_gcmc.html"><em>fix gcmc</em></a>
command, then the corrections are not updates to relect the changed
atom count. If this is a large effect in your simulation, you should
break the long run into several short runs, so that the correction
factors are re-computed multiple times.</p>
<ul class="simple">
<li>Thermophysical properties obtained from calculations with this option
enabled will not be thermodynamically consistent with the truncated
force-field that was used. In other words, atoms do not feel any LJ
pair interactions beyond the cutoff, but the energy and pressure
reported by the simulation include an estimated contribution from
those interactions.</li>
</ul>
<p>The <em>compute</em> keyword allows pairwise computations to be turned off,
even though a <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> is defined. This is not
useful for running a real simulation, but can be useful for debugging
purposes or for performing a <a class="reference internal" href="rerun.html"><em>rerun</em></a> simulation, when you
only wish to compute partial forces that do not include the pairwise
contribution.</p>
<p>Two examples are as follows. First, this option allows you to perform
a simulation with <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> with only a
subset of the hybrid sub-styles enabled. Second, this option allows
you to perform a simulation with only long-range interactions but no
short-range pairwise interactions. Doing this by simply not defining
a pair style will not work, because the
<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command requires a Kspace-compatible
pair style be defined.</p>
<hr class="docutils" />
<div class="section" id="use-of-special-keyword">
<h3>Use of <em>special</em> keyword<a class="headerlink" href="#use-of-special-keyword" title="Permalink to this headline">¶</a></h3>
<p>The <em>special</em> keyword allows to override the 1-2, 1-3, and 1-4
exclusion settings for individual sub-styles of a
<a class="reference internal" href="pair_hybrid.html"><em>hybrid pair style</em></a>. It requires 4 arguments similar
to the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command, <em>which</em> and
wt1,wt2,wt3. The <em>which</em> argument can be <em>lj</em> to change the
Lennard-Jones settings, <em>coul</em> to change the Coulombic settings,
or <em>lj/coul</em> to change both to the same set of 3 values. The wt1,wt2,wt3
values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
1-3, and 1-4 bond topology neighbors, respectively. The <em>special</em>
keyword can only be used in conjunction with the <em>pair</em> keyword
and has to directly follow it.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The global settings specified by the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command affect the construction of
neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
exclude those pairs from the neighbor list entirely. Weights of 1.0
store the neighbor with no weighting applied. Thus only global values
different from exactly 0.0 or 1.0 can be overridden and an error is
generated if the requested setting is not compatible with the global
setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for 1.0 is
usually a sufficient workaround in this case without causing a
significant error.</p>
</div>
</div>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div>none</div></blockquote>
<p>You cannot use <em>shift</em> yes with <em>tail</em> yes, since those are
conflicting options. You cannot use <em>tail</em> yes with 2d simulations.</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="pair_style.html"><em>pair_style</em></a>, <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>,
<a class="reference internal" href="thermo_style.html"><em>thermo_style</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 option defaults are mix = geometric, shift = no, table = 12,
tabinner = sqrt(2.0), tail = no, and compute = yes.</p>
<p>Note that some pair styles perform mixing, but only a certain style of
mixing. See the doc pages for individual pair styles for details.</p>
<hr class="docutils" />
<p id="wolff"><strong>(Wolff)</strong> Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).</p>
<p id="sun"><strong>(Sun)</strong> Sun, J Phys Chem B, 102, 7338-7364 (1998).</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
© 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>
<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/pair_none.html b/doc/pair_none.html
index f3edd46ae..fb2246af3 100644
--- a/doc/pair_none.html
+++ b/doc/pair_none.html
@@ -1,232 +1,233 @@
<!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>pair_style none command — 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 & 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 & 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>
</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> »</li>
<li>pair_style none 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="pair-style-none-command">
<span id="index-0"></span><h1>pair_style none command<a class="headerlink" href="#pair-style-none-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>pair_style none
</pre></div>
</div>
</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>pair_style none
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
-<p>Using a pair style of none means pair forces are not computed.</p>
+<p>Using a pair style of none means pair forces and energies are not
+computed.</p>
<p>With this choice, the force cutoff is 0.0, which means that only atoms
within the neighbor skin distance (see the <a class="reference internal" href="neighbor.html"><em>neighbor</em></a>
command) are communicated between processors. You must insure the
skin distance is large enough to acquire atoms needed for computing
bonds, angles, etc.</p>
<p>A pair style of <em>none</em> will also prevent pairwise neighbor lists from
being built. However if the <a class="reference internal" href="neighbor.html"><em>neighbor</em></a> style is <em>bin</em>,
data structures for binning are still allocated. If the neighbor skin
distance is small, then these data structures can consume a large
amount of memory. So you should either set the neighbor style to
<em>nsq</em> or set the skin distance to a larger value.</p>
<p>See the <a class="reference internal" href="pair_zero.html"><em>pair_style zero</em></a> for a way to trigger the
building of a neighbor lists, but compute no pairwise interactions.</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="pair_zero.html"><em>pair_style zero</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
© 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>
<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/pair_none.txt b/doc/pair_none.txt
index c3ba80e9a..f4e952519 100644
--- a/doc/pair_none.txt
+++ b/doc/pair_none.txt
@@ -1,45 +1,46 @@
"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
pair_style none command :h3
[Syntax:]
pair_style none :pre
[Examples:]
pair_style none :pre
[Description:]
-Using a pair style of none means pair forces are not computed.
+Using a pair style of none means pair forces and energies are not
+computed.
With this choice, the force cutoff is 0.0, which means that only atoms
within the neighbor skin distance (see the "neighbor"_neighbor.html
command) are communicated between processors. You must insure the
skin distance is large enough to acquire atoms needed for computing
bonds, angles, etc.
A pair style of {none} will also prevent pairwise neighbor lists from
being built. However if the "neighbor"_neighbor.html style is {bin},
data structures for binning are still allocated. If the neighbor skin
distance is small, then these data structures can consume a large
amount of memory. So you should either set the neighbor style to
{nsq} or set the skin distance to a larger value.
See the "pair_style zero"_pair_zero.html for a way to trigger the
building of a neighbor lists, but compute no pairwise interactions.
[Restrictions:] none
[Related commands:]
"pair_style zero"_pair_zero.html
[Default:] none
diff --git a/doc/pair_zero.html b/doc/pair_zero.html
index 612eb8e39..a32f40036 100644
--- a/doc/pair_zero.html
+++ b/doc/pair_zero.html
@@ -1,244 +1,244 @@
<!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>pair_style zero command — 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 & 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 & 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>
</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> »</li>
<li>pair_style zero 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="pair-style-zero-command">
<span id="index-0"></span><h1>pair_style zero command<a class="headerlink" href="#pair-style-zero-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>pair_style zero cutoff
</pre></div>
</div>
<ul class="simple">
<li>zero = style name of this pair style
cutoff = global cutoff (distance units)</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>pair_style zero
pair_coeff * *
pair_coeff 1 2 3.0
</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 global cutoff length for the purpose of building a neighbor
-list and acquiring ghost atoms, but do not compute any pairwise
-forces.</p>
+list and acquiring ghost atoms, but do not compute any pairwise forces
+or energies.</p>
<p>This can be useful for fixes or computes which require a neighbor list
to enumerate pairs of atoms within some cutoff distance, but when
pairwise forces are not otherwise needed. Examples are the <a class="reference internal" href="fix_bond_create.html"><em>fix bond/create</em></a>, <a class="reference internal" href="compute_rdf.html"><em>compute rdf</em></a>,
<a class="reference internal" href="compute_voronoi_atom.html"><em>compute voronoi/atom</em></a> commands.</p>
<p>Note that the <a class="reference internal" href="comm_modify.html"><em>comm_modify cutoff</em></a> command can be
used to insure communication of ghost atoms even when a pair style is
not defined, but it will not trigger neighbor list generation.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>cutoff (distance units)</li>
</ul>
<p>This coefficient is optional. If not specified, the global cutoff
specified in the pair_style command is used.</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="pair_none.html"><em>pair_style none</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
© 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>
<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/pair_zero.txt b/doc/pair_zero.txt
index a891a392b..3664acaa8 100644
--- a/doc/pair_zero.txt
+++ b/doc/pair_zero.txt
@@ -1,57 +1,58 @@
"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
pair_style zero command :h3
[Syntax:]
pair_style zero cutoff :pre
zero = style name of this pair style
cutoff = global cutoff (distance units) :l
[Examples:]
pair_style zero
pair_coeff * *
pair_coeff 1 2 3.0 :pre
[Description:]
Define a global cutoff length for the purpose of building a neighbor
-list and acquiring ghost atoms, but do not compute any pairwise
-forces.
+list and acquiring ghost atoms, but do not compute any pairwise forces
+or energies.
This can be useful for fixes or computes which require a neighbor list
to enumerate pairs of atoms within some cutoff distance, but when
pairwise forces are not otherwise needed. Examples are the "fix
bond/create"_fix_bond_create.html, "compute rdf"_compute_rdf.html,
"compute voronoi/atom"_compute_voronoi_atom.html commands.
Note that the "comm_modify cutoff"_comm_modify.html command can be
used to insure communication of ghost atoms even when a pair style is
not defined, but it will not trigger neighbor list generation.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
cutoff (distance units) :ul
This coefficient is optional. If not specified, the global cutoff
specified in the pair_style command is used.
[Restrictions:] none
[Related commands:]
"pair_style none"_pair_none.html
[Default:] none
+
diff --git a/doc/searchindex.js b/doc/searchindex.js
index 0ffb7e361..ac22941b0 100644
--- a/doc/searchindex.js
+++ b/doc/searchindex.js
@@ -1 +1 @@
-Search.setIndex({envversion:47,filenames:["Manual","Section_accelerate","Section_commands","Section_errors","Section_example","Section_history","Section_howto","Section_intro","Section_modify","Section_packages","Section_perf","Section_python","Section_start","Section_tools","accelerate_cuda","accelerate_gpu","accelerate_intel","accelerate_kokkos","accelerate_omp","accelerate_opt","angle_charmm","angle_class2","angle_coeff","angle_cosine","angle_cosine_delta","angle_cosine_periodic","angle_cosine_shift","angle_cosine_shift_exp","angle_cosine_squared","angle_dipole","angle_fourier","angle_fourier_simple","angle_harmonic","angle_hybrid","angle_none","angle_quartic","angle_sdk","angle_style","angle_table","angle_zero","atom_modify","atom_style","balance","body","bond_class2","bond_coeff","bond_fene","bond_fene_expand","bond_harmonic","bond_harmonic_shift","bond_harmonic_shift_cut","bond_hybrid","bond_morse","bond_none","bond_nonlinear","bond_quartic","bond_style","bond_table","bond_zero","boundary","box","change_box","clear","comm_modify","comm_style","compute","compute_ackland_atom","compute_angle_local","compute_angmom_chunk","compute_basal_atom","compute_body_local","compute_bond_local","compute_centro_atom","compute_chunk_atom","compute_cluster_atom","compute_cna_atom","compute_com","compute_com_chunk","compute_contact_atom","compute_coord_atom","compute_damage_atom","compute_dihedral_local","compute_dilatation_atom","compute_displace_atom","compute_dpd","compute_dpd_atom","compute_erotate_asphere","compute_erotate_rigid","compute_erotate_sphere","compute_erotate_sphere_atom","compute_event_displace","compute_fep","compute_group_group","compute_gyration","compute_gyration_chunk","compute_heat_flux","compute_hexorder_atom","compute_improper_local","compute_inertia_chunk","compute_ke","compute_ke_atom","compute_ke_atom_eff","compute_ke_eff","compute_ke_rigid","compute_meso_e_atom","compute_meso_rho_atom","compute_meso_t_atom","compute_modify","compute_msd","compute_msd_chunk","compute_msd_nongauss","compute_omega_chunk","compute_orientorder_atom","compute_pair","compute_pair_local","compute_pe","compute_pe_atom","compute_plasticity_atom","compute_pressure","compute_property_atom","compute_property_chunk","compute_property_local","compute_rdf","compute_reduce","compute_saed","compute_slice","compute_smd_contact_radius","compute_smd_damage","compute_smd_hourglass_error","compute_smd_internal_energy","compute_smd_plastic_strain","compute_smd_plastic_strain_rate","compute_smd_rho","compute_smd_tlsph_defgrad","compute_smd_tlsph_dt","compute_smd_tlsph_num_neighs","compute_smd_tlsph_shape","compute_smd_tlsph_strain","compute_smd_tlsph_strain_rate","compute_smd_tlsph_stress","compute_smd_triangle_mesh_vertices","compute_smd_ulsph_num_neighs","compute_smd_ulsph_strain","compute_smd_ulsph_strain_rate","compute_smd_ulsph_stress","compute_smd_vol","compute_sna_atom","compute_stress_atom","compute_tally","compute_temp","compute_temp_asphere","compute_temp_body","compute_temp_chunk","compute_temp_com","compute_temp_cs","compute_temp_deform","compute_temp_deform_eff","compute_temp_drude","compute_temp_eff","compute_temp_partial","compute_temp_profile","compute_temp_ramp","compute_temp_region","compute_temp_region_eff","compute_temp_rotate","compute_temp_sphere","compute_ti","compute_torque_chunk","compute_vacf","compute_vcm_chunk","compute_voronoi_atom","compute_xrd","create_atoms","create_bonds","create_box","delete_atoms","delete_bonds","dielectric","dihedral_charmm","dihedral_class2","dihedral_coeff","dihedral_cosine_shift_exp","dihedral_fourier","dihedral_harmonic","dihedral_helix","dihedral_hybrid","dihedral_multi_harmonic","dihedral_nharmonic","dihedral_none","dihedral_opls","dihedral_quadratic","dihedral_style","dihedral_table","dihedral_zero","dimension","displace_atoms","dump","dump_custom_vtk","dump_h5md","dump_image","dump_modify","dump_molfile","echo","fix","fix_adapt","fix_adapt_fep","fix_addforce","fix_addtorque","fix_append_atoms","fix_atc","fix_atom_swap","fix_ave_atom","fix_ave_chunk","fix_ave_correlate","fix_ave_correlate_long","fix_ave_histo","fix_ave_spatial","fix_ave_spatial_sphere","fix_ave_time","fix_aveforce","fix_balance","fix_bond_break","fix_bond_create","fix_bond_swap","fix_box_relax","fix_colvars","fix_deform","fix_deposit","fix_drag","fix_drude","fix_drude_transform","fix_dt_reset","fix_efield","fix_enforce2d","fix_eos_cv","fix_eos_table","fix_evaporate","fix_external","fix_freeze","fix_gcmc","fix_gld","fix_gle","fix_gravity","fix_heat","fix_imd","fix_indent","fix_ipi","fix_langevin","fix_langevin_drude","fix_langevin_eff","fix_lb_fluid","fix_lb_momentum","fix_lb_pc","fix_lb_rigid_pc_sphere","fix_lb_viscous","fix_lineforce","fix_meso","fix_meso_stationary","fix_modify","fix_momentum","fix_move","fix_msst","fix_neb","fix_nh","fix_nh_eff","fix_nph_asphere","fix_nph_body","fix_nph_sphere","fix_nphug","fix_npt_asphere","fix_npt_body","fix_npt_sphere","fix_nve","fix_nve_asphere","fix_nve_asphere_noforce","fix_nve_body","fix_nve_eff","fix_nve_limit","fix_nve_line","fix_nve_noforce","fix_nve_sphere","fix_nve_tri","fix_nvt_asphere","fix_nvt_body","fix_nvt_sllod","fix_nvt_sllod_eff","fix_nvt_sphere","fix_oneway","fix_orient_fcc","fix_phonon","fix_pimd","fix_planeforce","fix_poems","fix_pour","fix_press_berendsen","fix_print","fix_property_atom","fix_qbmsst","fix_qeq","fix_qeq_comb","fix_qeq_reax","fix_qmmm","fix_qtb","fix_reax_bonds","fix_reaxc_species","fix_recenter","fix_restrain","fix_rigid","fix_saed_vtk","fix_setforce","fix_shake","fix_shardlow","fix_smd","fix_smd_adjust_dt","fix_smd_integrate_tlsph","fix_smd_integrate_ulsph","fix_smd_move_triangulated_surface","fix_smd_setvel","fix_smd_tlsph_reference_configuration","fix_smd_wall_surface","fix_spring","fix_spring_rg","fix_spring_self","fix_srd","fix_store_force","fix_store_state","fix_temp_berendsen","fix_temp_csvr","fix_temp_rescale","fix_temp_rescale_eff","fix_tfmc","fix_thermal_conductivity","fix_ti_rs","fix_ti_spring","fix_tmd","fix_ttm","fix_tune_kspace","fix_vector","fix_viscosity","fix_viscous","fix_wall","fix_wall_gran","fix_wall_piston","fix_wall_reflect","fix_wall_region","fix_wall_srd","group","group2ndx","if","improper_class2","improper_coeff","improper_cossq","improper_cvff","improper_distance","improper_fourier","improper_harmonic","improper_hybrid","improper_none","improper_ring","improper_style","improper_umbrella","improper_zero","include","info","jump","kspace_modify","kspace_style","label","lattice","log","mass","min_modify","min_style","minimize","molecule","neb","neigh_modify","neighbor","newton","next","package","pair_adp","pair_airebo","pair_awpmd","pair_beck","pair_body","pair_bop","pair_born","pair_brownian","pair_buck","pair_buck_long","pair_charmm","pair_class2","pair_coeff","pair_colloid","pair_comb","pair_coul","pair_coul_diel","pair_cs","pair_dipole","pair_dpd","pair_dpd_conservative","pair_dpd_fdt","pair_dsmc","pair_eam","pair_edip","pair_eff","pair_eim","pair_gauss","pair_gayberne","pair_gran","pair_gromacs","pair_hbond_dreiding","pair_hybrid","pair_kim","pair_lcbop","pair_line_lj","pair_list","pair_lj","pair_lj96","pair_lj_cubic","pair_lj_expand","pair_lj_long","pair_lj_sf","pair_lj_smooth","pair_lj_smooth_linear","pair_lj_soft","pair_lubricate","pair_lubricateU","pair_mdf","pair_meam","pair_meam_spline","pair_meam_sw_spline","pair_mgpt","pair_mie","pair_modify","pair_morse","pair_nb3b_harmonic","pair_nm","pair_none","pair_peri","pair_polymorphic","pair_quip","pair_reax","pair_reax_c","pair_resquared","pair_sdk","pair_smd_hertz","pair_smd_tlsph","pair_smd_triangulated_surface","pair_smd_ulsph","pair_smtbq","pair_snap","pair_soft","pair_sph_heatconduction","pair_sph_idealgas","pair_sph_lj","pair_sph_rhosum","pair_sph_taitwater","pair_sph_taitwater_morris","pair_srp","pair_style","pair_sw","pair_table","pair_tersoff","pair_tersoff_mod","pair_tersoff_zbl","pair_thole","pair_tri_lj","pair_vashishta","pair_write","pair_yukawa","pair_yukawa_colloid","pair_zbl","pair_zero","partition","prd","print","processors","python","quit","read_data","read_dump","read_restart","region","replicate","rerun","reset_timestep","restart","run","run_style","set","shell","special_bonds","suffix","tad","temper","thermo","thermo_modify","thermo_style","timer","timestep","tutorial_drude","uncompute","undump","unfix","units","variable","velocity","write_data","write_dump","write_restart"],objects:{},objnames:{},objtypes:{},terms:{"00a":332,"00b":332,"02214e23":95,"03275e":506,"0892e":12,"0b1":11,"0e20":[348,484,507],"0e4":[261,341,410],"0e5":261,"0x98b5e0":199,"100k":1,"1024x1024":199,"10e":398,"10f":3,"10g":507,"10th":[476,482,495],"10x":[3,372,373,375,376,386],"10x10x10":160,"10x20x20":368,"11e":10,"15g":[200,507],"16g":[212,218],"16x":1,"18986e":373,"18e":10,"1_12":368,"1_3":368,"1_6":368,"1_prop":6,"1st":[2,6,8,12,20,22,38,45,57,59,60,62,73,91,166,178,180,192,204,205,212,213,214,215,216,217,218,222,226,235,263,295,305,334,346,350,370,376,381,382,386,393,395,404,406,407,414,415,424,425,430,431,432,437,441,452,462,463,464,465,466,469,475,481,489,490,493,507],"1x2x2":478,"2000k":199,"20x":386,"23899e":373,"2400k":199,"256k":10,"25x":10,"298k":397,"2_3":368,"2k_ss":406,"2nd":[2,3,6,11,12,15,17,38,46,47,57,59,62,73,79,92,154,161,192,200,212,213,214,215,216,217,218,222,224,226,235,263,307,312,320,346,349,356,364,373,374,375,376,380,382,395,406,412,413,430,452,461,462,463,464,465,466,469,481,488,490,493,507],"2pi":192,"2theta":171,"2x1x2":478,"2x2x1":478,"2x2x2":478,"2x4x10":478,"2x5":406,"300k":[241,307,496,508],"310k":496,"32k":10,"3419e":261,"3806504e":[6,95],"38e":10,"3n_k":240,"3nk":297,"3nkb":302,"3rd":[15,17,20,38,57,73,110,120,192,212,213,215,216,217,218,222,235,307,308,346,374,378,380,395,406,412,413,452,462,463,464,465,466,469,481,488,493,507],"3x3":[95,368],"4857990943e":406,"4_94":11,"4th":[6,38,57,83,108,109,122,168,178,192,200,320,346,366,379,381,382,386,404,407,414,430,437,441,452,462,463,464,466,469,481,488,493,496,511],"4x10":364,"4x2x10":478,"4x6x10":478,"50k":1,"53xx":18,"54xx":18,"55e":10,"5_1":386,"5_12":368,"5_6":368,"5kx":[206,232],"5nlog_2":12,"5th":[122,373,498],"6021765e":506,"6863e22":440,"6x6":6,"72360e":261,"7797e":261,"7842e":12,"8032044e":506,"8706e":451,"8706q":451,"8730m":451,"8730n":451,"8e12":214,"8x1":6,"8x2":[6,12],"948q":451,"9e18":[12,40],"9e9":440,"9jan09":[341,410],"9th":375,"__main__":479,"__pthread_key_cr":12,"_boundingbox":197,"_compute_group_group":148,"_compute_heat_flux":148,"_compute_t":8,"_j1m1m1":146,"_j2m2m2":146,"_serial":12,"abstract":17,"boolean":[3,346,348],"break":[],"byte":[3,12,214,498],"case":[1,2,3,6,8,11,12,13,15,16,17,18,40,41,42,46,47,61,63,65,73,75,108,109,114,120,122,123,149,150,151,152,153,155,158,159,160,161,162,164,165,166,170,172,174,175,176,178,195,196,197,198,199,200,206,207,211,212,213,215,216,217,218,219,220,222,224,226,230,232,236,239,242,243,245,246,247,248,250,261,263,264,265,266,267,268,269,270,271,282,283,284,286,288,289,293,294,296,297,298,299,306,307,309,312,314,315,317,320,323,326,327,328,330,331,335,337,338,340,341,343,344,345,346,348,364,365,366,368,370,372,373,374,375,377,379,380,382,391,394,396,398,404,406,409,410,412,413,414,426,427,428,430,433,435,437,441,444,447,449,453,460,463,464,466,473,476,479,481,483,484,488,489,491,493,495,497,498,499,500,502,506,507,508,510,511],"catch":[1,3,479],"char":[6,8,451],"class":[1,3,5,6,7,8,9,11,12,13,22,37,45,56,180,191,237,296,350,359,392,413,443,444,461,469,479,481],"default":[],"export":[199,393],"final":[3,5,6,7,8,11,12,17,42,61,91,147,200,211,212,213,215,216,217,218,220,224,226,239,262,263,268,297,301,307,308,312,332,334,335,342,348,373,375,381,382,386,404,407,414,426,430,437,441,442,462,463,464,466,469,476,489,495,502,507,509],"float":[3,6,8,12,41,43,73,119,196,200,212,218,244,296,308,325,406,448,450,479,481,491,498,507],"function":[],"import":[1,2,3,6,11,17,73,110,172,183,203,224,239,242,247,248,263,302,326,327,328,330,335,345,347,426,433,479,481,490,498,502],"int":[3,6,8,11,106,237,239,247,249,302,335,498],"long":[],"new":[],"null":[3,6,95,96,112,118,147,172,203,219,225,228,231,260,296,305,309,312,316,317,320,321,341,381,382,395,404,407,410,413,414,415,430,431,432,437,441,443,444,452,462,464,465,466,469,481,484,489,491,508],"public":[0,7,8,12,237,246,407,442,451],"return":[2,3,6,8,11,14,15,16,17,18,19,42,73,114,123,140,141,145,170,172,200,212,216,217,226,237,263,348,362,364,410,478,479,480,488,491,497,507],"short":[1,3,6,7,13,16,170,263,307,323,336,366,376,377,380,382,386,387,389,390,391,395,396,398,406,413,416,418,422,426,429,430,435,438,446,451,463,467,476,479,489,491,495,502],"static":[],"switch":[1,3,6,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,44,46,47,48,49,50,52,54,55,57,95,115,118,146,149,159,171,178,179,181,182,183,184,186,187,189,190,192,199,202,206,210,219,226,233,238,242,246,247,250,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,299,307,309,310,326,328,332,333,339,343,349,351,352,354,355,358,360,362,364,366,369,375,379,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,404,405,407,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,433,436,437,438,440,443,445,446,453,462,463,464,465,466,469,471,472,473,475,476,478,481,483,484,488,490,494,496,507,509,511],"throw":498,"true":[6,12,13,17,114,121,196,197,212,220,222,226,263,264,288,289,290,294,307,330,334,346,348,380,406,410,451,462,479,483,491,507],"try":[1,3,8,12,17,19,212,244,250,331,332,333,338,479,507],"var":[3,11,12,172,346,364,492,507],"void":[4,6,7,8,42,175,220,237,484],"while":[1,3,9,10,11,12,13,14,18,73,110,146,155,170,183,196,201,210,217,224,226,230,240,241,246,247,248,250,263,284,297,298,302,304,336,366,373,380,386,397,404,444,464,466,469,476,479,490,495,502],a10:348,a123:348,a12:445,a2m:[6,95],a_0:[250,335,386],a_0_real:250,a_1:335,a_2:335,a_3:335,a_4:335,a_c:394,a_cc:394,a_f:466,a_i:[],a_ij:386,a_j:[],a_pi:386,a_sigma:386,a_ss:394,aacut:289,aat:179,aatom1:121,aatom2:121,aatom3:121,ab_23_cd:348,abbrevi:12,abc:[3,12,348,479,507],aberdeen:[84,85,234,311],abf:225,abf_integr:13,abi:201,abil:[3,9,224,263,294,307,406],abl:[3,8,11,12,40,90,196,201,223,232,238,331,338,380,479,507,510],ablat:335,about:[0,1,3,4,6,8,9,10,11,12,13,17,40,42,43,63,65,80,114,121,122,124,166,172,196,197,199,200,201,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,228,230,231,232,233,236,237,238,239,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,259,262,268,272,273,274,275,276,277,278,279,280,281,287,288,289,291,292,293,294,295,296,298,299,300,301,302,303,304,305,306,307,308,309,310,320,321,323,324,326,327,328,329,330,331,332,333,334,335,337,338,339,340,342,343,344,345,346,363,366,372,373,375,380,385,391,396,413,440,444,472,479,482,483,488,489,491,496,500,507,509,511],abov:[1,2,6,7,8,10,11,12,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,38,41,42,43,44,45,46,47,48,49,50,51,52,54,55,57,59,65,66,70,72,73,74,75,78,79,90,91,93,94,95,98,99,101,102,118,120,122,124,146,147,149,150,151,152,153,154,155,158,159,160,161,162,164,165,166,170,171,172,174,175,178,179,180,181,182,183,184,185,186,187,189,190,192,196,197,198,199,200,203,204,205,206,207,212,213,215,216,217,218,220,223,224,226,227,232,235,237,239,243,245,247,248,249,253,262,263,268,290,293,295,300,306,307,312,320,323,326,327,328,329,346,348,349,350,351,352,353,354,355,356,358,360,366,368,370,374,375,379,380,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,416,418,419,420,421,422,423,424,425,426,427,428,429,430,433,434,435,436,438,440,441,443,444,445,446,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,468,469,471,472,473,474,475,476,477,478,479,481,482,483,484,485,488,489,490,491,492,495,496,499,502,507,508,510,511],abscissa:463,absenc:207,absent:502,absolut:[3,200,210,225,226,230,312,325,365,366,373,410,418,482],absorb:335,absoult:366,ac3:171,academ:239,acc:330,acceler:[],accelri:[6,13],accept:[7,12,91,170,172,200,210,223,226,239,330,390,422,489,496],acceptor:412,access:[0,3,6,7,8,9,11,12,16,39,41,58,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,89,92,93,94,95,96,97,98,100,101,104,105,106,108,109,110,111,112,113,114,116,117,118,119,120,121,123,124,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,159,160,161,162,163,164,165,167,168,169,170,171,193,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,220,221,222,223,224,225,226,227,228,231,232,233,236,237,238,239,240,241,242,243,244,245,247,249,250,251,252,253,254,255,256,257,259,260,261,262,263,268,272,273,274,275,276,277,278,279,280,281,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,317,320,321,322,323,324,325,326,327,328,329,331,332,333,334,335,337,338,339,340,341,342,343,344,345,361,365,380,408,410,412,413,430,443,444,453,478,479,482,487,499,507],accidenti:358,accler:16,accommod:208,accomod:263,accompani:8,accomplish:[16,226,251,279],accord:[6,66,73,84,127,133,136,154,199,210,221,222,250,263,289,297,312,314,332,333,335,340,341,343,344,345,376,380,406,410,421,424,441,448,450,451,453,455,456,458,459,460,495,507],accordingli:[11,14,150,151,165,170,176,376,427,428,460],account:[3,6,9,91,124,154,170,171,180,191,213,215,231,244,245,247,263,269,270,271,282,283,284,286,288,292,298,307,308,310,320,321,322,323,326,327,328,331,335,338,354,374,396,402,410,418,422,427,428,430,433,451,478,495,508],accuml:[3,307,331,338],accumul:[1,6,8,15,73,84,148,203,213,214,247,307,312,337,363,380,487,506],accur:[1,3,6,15,17,38,42,57,155,220,261,302,307,310,323,331,338,344,346,366,386,406,409,410,435,445,461,463,464,466,495,500,507],accuraci:[1,3,6,12,42,195,196,200,220,241,263,299,310,336,346,365,366,372,406,435,443,444,463,470,490,495,500,502,507,510],accuractli:500,ach:365,achiev:[1,3,6,16,17,18,29,42,220,239,241,263,264,289,290,297,365,413,490],achiv:18,acid:9,ackland1:404,ackland2:404,ackland:[],acknowledg:[],acml:12,aco:507,acolor:[199,200],acoust:289,acquir:[3,6,60,63,64,175,176,222,224,226,263,439,474,486,502],across:[1,2,3,6,9,12,13,15,42,59,63,67,70,71,73,81,97,113,114,121,123,160,174,176,212,215,216,217,220,231,243,307,308,313,331,335,338,344,348,375,380,476,481,484,485,489,498,500],act:[3,6,114,157,230,242,245,246,247,248,250,253,262,307,317,330,332,333,335,344,345,346,373,388,399,409,410,412,445,460],acta:[124,171,381],actinid:[9,433],action:[2,6,11,12,73,240,245,333,502],activ:[5,8,11,12,13,14,56,61,91,170,225,240,244,247,253,262,287,307,315,334,363,426,461,475,504,507],actual:[1,3,6,8,12,57,64,128,155,196,197,200,204,205,219,221,222,230,247,248,284,288,293,294,302,312,323,325,326,327,328,330,336,345,346,365,376,409,411,416,421,427,428,460,478,479,490,491,499,507],adam:[365,366],adapt:[],add:[0,1,3,5,6,7,8,9,11,12,13,14,15,16,17,18,19,41,43,73,91,95,107,120,123,125,170,172,173,196,197,198,199,203,204,205,206,207,209,211,212,213,215,216,217,218,222,225,230,232,237,241,242,243,245,247,249,250,254,261,262,263,264,265,266,267,268,269,270,271,282,283,284,285,286,288,296,306,307,309,310,320,322,326,328,329,333,334,335,337,339,340,344,346,366,368,372,374,382,387,389,392,396,406,413,418,430,435,438,444,446,479,481,482,487,489,491,493,500,502],add_molecul:209,add_speci:209,add_to_nodeset:209,addforc:[],addit:[],addition:[6,8,16,145,323,345,409,445],additionali:197,addres:9,address:[7,8,11,199,246],addtorqu:[],adequ:[323,336,365,375,490],adher:29,adhikari:250,adiabat:[],adiam:[199,200],adjac:[40,170,172,375,435,463,464,495,496],adjiman:434,adjust:[2,3,6,16,17,42,61,124,134,150,151,152,155,156,159,160,165,166,171,176,196,199,212,220,224,226,244,247,251,255,259,260,263,264,268,284,288,291,293,294,297,298,299,300,305,307,315,323,327,331,336,338,339,340,342,343,345,365,366,373,375,380,382,403,427,428,451,466,491,508],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:[295,489,507],afshar:400,after:[2,3,5,6,8,9,11,12,15,21,22,33,40,41,42,45,51,59,60,61,63,65,73,150,151,152,153,154,155,156,159,160,161,162,164,165,172,173,175,176,179,180,185,195,196,197,198,199,200,201,203,204,205,209,210,212,213,220,221,222,223,224,226,230,239,250,251,252,253,254,259,260,261,263,269,270,271,277,282,283,284,286,289,293,297,305,307,310,319,324,326,327,328,330,331,332,333,334,338,340,342,346,349,350,356,364,370,371,373,374,376,378,379,380,381,382,386,393,395,404,405,406,407,413,414,415,426,427,428,430,431,432,433,437,441,443,444,451,452,461,462,464,465,466,469,476,478,480,481,482,483,484,486,487,489,491,493,495,498,499,502,506,507,508,509,510,511],afterrun:489,afterward:3,afterword:42,ag1:171,ag2:171,again:[6,11,12,16,17,64,146,152,158,166,196,200,226,243,293,349,364,375,427,428,476,478,479,481,483,488,495,497,507,509],against:[11,12,13,66,227,375,443,444],aggreg:[6,12,67,70,71,81,97,114,121,243,259,305,307,321,476,508],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:[6,12,29,42,73,174,192,216,220,245,368,481,484,502],alkali:406,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,165,166,167,168,169,170,171,172,173,174,175,176,178,180,185,191,192,193,196,197,198,199,200,201,203,204,205,206,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,256,258,259,261,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,319,320,322,323,324,325,326,327,330,331,332,333,334,335,336,337,338,340,341,342,343,344,345,346,347,348,349,350,354,359,361,363,364,365,366,367,368,370,373,374,375,376,377,379,380,381,382,383,385,386,387,389,390,391,392,393,395,396,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,422,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,472,473,475,476,478,479,480,481,482,483,484,485,486,488,489,490,491,492,493,494,495,496,498,499,500,502,506,507,508,509,510,511],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:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,56,59,60,61,63,64,65,79,96,112,114,148,150,151,152,165,170,171,172,174,180,191,192,196,197,199,200,201,203,204,206,208,209,210,212,213,214,215,216,217,218,220,222,223,224,225,226,227,231,232,237,239,240,241,242,244,247,250,253,254,258,260,263,264,288,292,293,294,295,296,297,301,307,308,310,312,314,315,319,323,330,331,332,333,335,336,337,338,339,340,346,348,350,359,365,366,368,373,374,375,376,379,380,383,386,387,388,389,390,391,396,404,406,410,411,412,413,418,422,427,428,433,435,441,444,445,448,450,451,460,470,472,476,479,481,483,484,485,486,487,488,491,493,494,495,498,499,507,508],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:[6,8,9,12,29,41,73,91,124,170,171,172,195,196,199,212,223,245,250,251,255,260,262,297,307,310,312,316,320,321,330,334,335,341,344,346,368,371,372,373,375,396,399,410,413,416,418,422,430,443,444,463,481,484,491,492,507],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:[3,65,203,296,304,348,374,507],alreadi:[3,7,8,9,12,16,17,18,43,172,173,175,198,208,212,216,217,220,222,226,254,295,297,323,346,347,374,375,400,411,413,420,428,460,470,473,477,481,482,486,491,507],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,40,41,42,43,45,55,56,57,60,61,63,65,68,73,74,75,77,79,83,91,93,94,96,98,108,109,110,111,112,113,118,120,122,123,125,146,147,148,149,150,151,152,153,154,155,156,158,159,160,161,162,164,165,166,167,168,169,172,173,174,175,176,178,180,191,192,194,195,196,197,198,199,200,201,203,204,205,206,208,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,232,237,238,239,240,241,243,244,247,248,249,250,260,261,263,264,265,266,267,268,269,270,271,276,279,280,282,283,284,285,286,288,289,290,292,293,294,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,316,317,320,321,323,326,327,328,329,330,334,335,336,337,339,341,344,346,347,348,350,356,359,363,365,366,368,369,370,373,374,375,376,377,379,380,386,390,391,393,397,398,399,400,404,405,406,409,410,412,413,414,422,426,427,430,433,435,437,439,440,441,442,445,446,448,455,456,458,459,461,462,463,464,465,466,467,469,476,478,479,480,481,482,483,484,485,486,488,489,490,491,493,494,495,496,499,500,501,502,503,505,506,507,508,509,511],alter:[3,6,8,9,11,12,42,61,149,150,151,152,153,155,158,159,160,161,164,165,172,176,196,197,199,201,204,205,212,221,222,223,224,226,262,263,302,305,307,309,317,323,331,338,345,372,375,413,481,486,488,491,507,508,511],altern:[1,6,8,11,12,17,18,95,172,196,203,213,226,234,244,248,263,296,307,330,331,338,351,355,365,372,373,381,382,396,401,402,404,405,407,415,418,426,430,431,432,437,441,442,452,462,464,466,469,479,481,482,494,496,499],although:[29,43,192,253,263,294,298,307,330,364,488,502,511],aluminum:473,alwai:[0,6,11,12,17,18,55,59,65,73,170,200,212,213,214,216,217,218,222,225,239,241,245,299,302,307,323,340,344,345,349,365,366,371,373,374,376,377,380,389,392,404,421,433,443,444,451,453,463,464,466,473,476,481,482,484,486,493,495,498,502,507,508],amap:200,amatrix:241,amaz:11,amazingli:13,amber2lmp:[],amber:[],ambient:199,ambigu:[3,65,203,507],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:[226,260,316,341,358,484,507],amu:239,amzallag:451,analag:[6,507],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:[6,8,13,375,433],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:[6,10,61,73,124,161,171,172,195,196,197,199,200,208,216,217,226,227,239,244,245,260,300,305,340,342,343,345,366,368,371,377,381,382,391,404,426,430,437,442,443,444,466,473,484,490,506,508],angular:[6,29,41,63,65,68,86,87,88,89,111,119,146,150,151,164,165,172,196,197,203,247,253,259,260,265,266,267,269,270,271,273,274,275,278,280,281,282,283,286,305,307,310,316,325,381,386,395,410,427,428,430,433,441,461,464,465,481,491,507,508],angularm:274,anharmon:[27,54,181,302,495],ani:[1,3,6,7,8,9,10,11,12,13,14,15,16,17,22,29,38,40,41,42,43,45,56,57,60,61,63,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,175,176,178,180,192,195,196,197,198,199,200,203,206,207,208,210,212,213,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,232,236,239,242,243,245,247,250,253,259,260,263,268,288,290,292,293,294,296,298,299,300,302,304,305,307,309,310,312,316,317,320,322,323,324,325,334,335,340,341,342,343,344,345,346,347,348,350,364,365,366,368,370,371,373,374,375,377,378,379,380,382,386,390,391,395,396,399,400,404,405,407,409,413,414,415,422,433,435,441,443,444,445,452,460,461,462,463,464,465,466,467,468,469,474,475,476,478,479,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,499,500,502,503,505,506,507,508,509,510,511],anihil:426,anim:[2,4,7,11,13,199,375],anion:[407,451],aniso:[3,224,226,263,264,265,266,267,268,269,270,271,294,307],anisotrop:[247,409,445],ann:434,annot:[7,462,464,465,466,469,481],annual:[476,495],anoth:[1,3,4,6,7,8,11,12,17,29,41,65,73,74,91,122,125,198,199,203,204,210,212,215,216,217,218,223,226,227,240,243,247,248,253,263,264,268,293,296,307,308,326,327,328,335,345,348,371,373,375,376,379,396,400,406,407,409,412,413,417,418,426,443,445,453,460,463,464,465,466,475,476,479,482,488,490,496,502,507,511],ansi:[9,12,16],answer:[3,4,8,12,307,377,378],anthoni:333,antiquewhit:200,antisymmetr:[9,41,383],antisymmetri:406,antonelli:[332,333],antonio:440,anymor:333,anyon:7,anyparticl:90,anyth:[8,11,172,226,246,462,464,466,492],anywai:[175,380,502,509],anywher:[12,172,393,430,452,507],aoff:[374,481],aparam:[91,204,205],apart:[3,173,253,320,376,385,453,481,490],aperiod:289,api:[11,12,201,414,479],appar:3,appear:[2,3,6,11,12,13,40,41,42,74,79,91,96,112,114,121,122,146,155,172,173,175,196,197,199,200,212,216,217,220,224,227,230,239,244,293,304,305,334,346,348,349,365,373,374,375,394,404,430,435,451,463,469,477,478,479,481,482,483,486,488,502,507,511],append:[],appendix:[29,399,451],appl:[224,263,264,469],appli:[2,3,4,5,6,8,9,12,17,18,29,33,42,51,59,61,63,65,73,74,91,92,110,122,146,147,152,158,160,162,166,171,172,174,178,180,185,191,195,196,197,199,200,203,204,205,206,207,209,212,219,220,224,225,226,228,231,232,234,235,237,238,239,240,241,242,244,245,247,248,249,250,254,263,264,268,269,270,271,277,282,283,286,287,288,290,294,297,305,306,307,309,310,312,313,316,320,321,322,324,326,327,328,329,331,333,334,335,338,346,365,368,373,374,375,385,387,389,391,396,399,406,410,411,412,413,415,416,418,424,428,433,435,438,443,446,447,448,449,450,460,467,472,481,482,484,485,486,490,491,493,498,502,507,508,509,510],applic:[1,6,9,12,17,201,209,223,227,228,237,239,241,244,288,293,306,312,320,331,338,365,380,466,491,502],applyt:3,appopri:17,approach:[6,7,9,14,196,209,240,289,290,302,307,330,331,333,335,338,365,386,396,398,402,403,409,413,433,445,447,449,460,470],appropri:[1,2,3,6,8,9,11,12,13,15,17,33,38,43,51,57,63,75,92,95,122,123,150,151,152,180,185,191,192,195,196,197,200,212,213,216,217,218,223,224,226,237,238,241,250,258,260,261,263,265,266,267,268,269,270,271,282,283,284,286,290,293,294,297,302,307,311,323,326,327,328,331,338,340,341,343,344,345,356,366,375,382,386,390,394,395,396,405,410,413,415,422,426,433,442,443,444,462,463,464,465,466,469,470,481,482,483,485,486,494,495,498,507,508],approri:242,approxim:[6,9,124,128,171,239,241,250,290,308,310,330,365,371,372,373,388,398,406,409,427,428,433,435,442,445,451,472,495,502],april:11,aprpopri:476,apu:[427,428],aqua:[199,200],aquamarin:200,ar_therm:209,ar_ttm:209,ara:13,arbitrari:[6,41,60,122,196,197,199,201,225,226,242,263,290,298,462,479,492,507],arbitrarili:[11,61,122,146,195,224,263,396,507],arcco:3,arch:[1,9,12,14,15,17],architect:363,architectur:[16,380,433],archiv:[6,7,11,12,325,393,488],arcsin:3,area:[6,42,95,118,122,170,220,226,250,331,338,403,410,440,468,478,491],aren:[122,296,348],arflag:12,arg:[3,11,12,22,41,42,45,56,61,65,73,91,123,160,166,170,172,175,176,180,195,196,197,198,200,203,204,205,206,208,210,212,213,214,215,216,217,218,219,220,221,222,225,226,227,232,237,239,242,243,244,245,253,260,265,266,267,293,306,307,308,309,313,316,317,319,330,333,340,341,342,343,345,346,350,363,375,380,387,388,389,391,392,393,398,399,402,406,411,413,418,422,426,427,428,429,438,446,448,450,461,478,479,481,484,486,488,490,492,494,499,500,507,508,510,511],argon:239,argonn:12,argument:[2,3,6,8,9,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,42,43,44,45,46,47,48,49,50,52,54,55,57,61,65,75,91,95,112,115,118,122,146,147,149,154,159,160,161,166,170,172,173,174,176,178,179,180,181,182,183,184,186,187,189,190,192,196,197,200,203,204,205,206,208,211,212,213,214,215,216,217,218,219,220,224,225,226,233,235,237,238,239,241,242,246,247,253,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,292,293,295,299,304,307,308,309,310,323,326,328,335,337,339,341,343,346,348,349,350,351,352,354,355,356,358,360,363,364,366,367,368,370,375,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,398,399,400,402,404,405,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,429,430,431,432,435,436,437,438,440,441,443,444,445,446,451,452,453,461,462,463,464,465,466,467,469,471,472,473,475,476,477,478,479,480,481,482,484,486,489,490,491,492,496,498,499,507,508,510],aris:[12,472],arithmet:[3,6,108,365,391,394,421,435,467,468],arkansa:9,arl:[9,84,85,234,311],armi:[84,85,234,311],armv8:17,arnold:365,around:[1,3,4,6,12,43,59,60,61,68,72,73,74,75,79,122,146,150,167,170,172,174,195,199,200,207,208,224,226,227,245,260,263,296,298,302,307,316,320,323,340,341,344,364,374,451,481,484,491,492,502,507],aroung:3,arrai:[],arrang:146,arrheniu:495,art:[9,476,495],artefact:241,articl:[6,451],articul:[7,292],artifact:[92,170,502],artifici:[261,297,455,456,458],arun:13,arxiv:[146,198,452],ascend:[42,200,244,253,307,486],asci:7,ascii:[13,197,308,334,375,404,407,430,481],ash:[427,428],asid:[8,172,430],asin:507,ask:[3,11],askari:440,askoos:13,asoci:199,aspect:[6,7,61,226,239,409,445,468,481,491,495],aspect_ratio:308,asper:4,aspher:[],asq:[427,428],assembl:4,assign:[1,2,3,6,7,11,12,14,15,17,18,33,40,41,42,51,59,61,63,65,68,73,74,77,94,98,109,111,116,119,120,124,146,147,152,167,169,171,172,175,185,195,196,197,198,199,200,201,203,204,205,208,212,215,220,222,223,224,227,229,239,244,247,248,249,250,260,263,265,266,267,268,269,270,271,280,282,283,284,285,286,290,293,294,296,298,304,307,308,326,327,328,329,346,356,366,368,370,374,375,379,380,386,404,407,409,412,413,444,445,473,478,479,481,482,483,484,485,490,491,496,499,507,508],assignemnt:[6,490],assing:296,assingn:463,assist:[7,261],associ:[3,5,6,8,9,12,22,37,40,41,45,56,61,68,76,77,83,91,93,94,98,104,106,108,109,111,136,167,180,191,196,197,199,200,204,205,206,210,224,226,232,237,239,240,246,250,260,263,292,302,306,307,308,321,323,347,348,350,359,368,373,375,379,380,393,396,400,402,403,404,406,412,413,415,418,422,447,449,460,461,463,479,482,489,501,502,504,507],associd:69,assum:[2,3,4,6,11,12,16,17,18,40,61,69,73,92,101,107,109,149,150,151,152,153,154,155,157,158,159,160,161,162,164,165,166,170,172,175,200,204,205,210,212,213,215,216,217,218,224,226,236,244,246,250,253,265,266,267,269,270,271,273,275,278,280,281,282,283,286,288,289,293,294,295,298,307,309,312,320,331,334,335,340,343,346,353,365,366,374,375,380,386,388,390,393,394,403,406,412,413,417,422,427,428,468,476,478,479,481,483,486,491,495,498,499,502,508],assumpt:[170,244,381,435],astar:430,astart:453,asterisk:[22,45,63,79,91,122,166,176,180,200,204,205,253,307,350,370,393,412,460,475,478,491,506],astop:[373,453],asu:404,asub:430,asubrama:13,asymmetr:[133,343,386,404],asynchron:[15,16],atan2:507,atan:507,atc:[],atc_fe_output:209,athomp:[0,7,9,13],atm2pa:6,atmospher:506,atol:12,atom1:[292,306,374,481],atom2:[292,306,374,481],atom3:[292,306,374,481],atom4:[306,374,481],atom:[],atom_element_map:209,atom_forc:444,atom_info:444,atom_modifi:[],atom_styl:[],atom_vec:8,atom_vec_atom:8,atom_vec_electron:8,atom_veloc:444,atom_weight:209,atomey:[6,7,11,13,196,199,200],atomfil:[3,73,296,346,379,491,507],atomic_charg:209,atomic_numb:441,atomid:481,atomist:[6,209,330,433],atomperbin:3,atomt:200,atomvec:8,attach:[6,217,290,312,320,481],attatch:333,attempt:[3,6,42,61,73,195,210,220,221,222,223,227,239,293,294,323,343,365,369,375,413,479,496,499,507],attend:209,attent:[15,18],attogram:506,attrac:430,attract:[],attribut:[3,6,7,8,11,40,41,43,60,65,73,91,119,120,121,123,150,166,196,197,199,200,203,204,205,211,212,215,216,217,223,224,263,265,266,267,268,269,270,271,273,274,282,283,284,286,294,307,308,325,326,327,328,368,374,386,406,413,481,482,483,491,499,507],atw:[427,428],atwat:465,atwt:430,atyp:[121,166,222,396,418,422,426],au1:171,au3:171,aug:[],augment:[12,119,224,296,430],augt1:430,auo:304,auoh:304,author:[3,8,9,13,198,404,405,502],auto:[3,6,8,11,12,95,168,203,213,214,312,337,365,374,380,478],autocorrel:[65,95,247],autom:[12,199],automag:7,automat:[3,6,12,14,15,16,17,18,19,36,134,192,208,214,239,241,250,307,312,336,365,380,395,404,413,430,433,447,448,449,450,473,481,494,502,507],auxiliari:[1,6,9,11,12,13,196,289,307,482,486,509],avail:[1,3,5,6,7,8,9,11,12,13,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,63,65,84,85,91,115,118,119,146,149,159,170,178,179,181,182,183,184,186,187,189,190,192,196,199,203,206,212,215,216,217,218,219,224,225,226,233,234,235,238,240,242,244,247,263,264,265,266,267,268,269,270,271,272,273,280,282,283,284,286,299,301,307,308,309,310,311,326,328,333,339,343,349,351,352,354,355,358,360,363,366,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,430,431,435,436,437,438,440,441,443,444,445,446,452,453,462,463,464,465,466,469,471,472,473,482,484,490,494,507],availab:[],avalo:[311,402],ave_chunk:6,aveforc:[],avendano:434,averag:[3,6,7,12,15,42,65,66,73,84,85,91,95,96,108,110,122,124,148,152,160,168,171,196,197,200,203,205,209,211,212,213,214,215,216,217,218,219,220,224,239,241,243,247,253,263,264,268,289,294,297,303,304,307,308,312,349,382,402,406,430,467,482,486,499,502,507],averi:323,avesq:123,avg:12,avi:199,avoid:[1,3,6,12,36,40,61,172,173,192,199,208,213,215,218,230,239,241,248,288,290,298,302,307,308,337,344,378,386,406,426,430,444,463,483,489,490,502],awai:[3,6,63,122,196,199,212,223,227,242,245,262,288,312,320,334,340,376,396,418,422,486],awar:[380,405,478],awpmd:[],axel:[7,9,13,18],axi:[3,6,42,73,96,124,136,150,171,172,174,195,199,212,220,239,242,245,260,293,316,320,335,341,354,360,368,481,484,491],axial:268,azimuth:[199,242],azur:200,b_k:452,ba2:171,babadi:445,back:[1,6,7,11,12,13,14,15,17,153,154,155,159,160,161,162,164,172,176,196,197,200,201,204,205,225,230,237,244,245,247,248,263,269,270,271,282,283,284,286,305,307,326,327,328,332,333,342,343,345,364,365,366,375,410,479,481,482,483,484,485,488,494,495,507,508],backbon:[223,310,358],backcolor:[200,510],backend:17,background:[9,91,92,118,147,200,220,226,247,323,331,335,338,375,394,427,428,430],backtrack:[371,373],backward:[9,12,201,375,495,507],baczewski:240,bad:[3,12,61,63,245,375,481,486,498],badli:[3,224,263],bal:330,balanc:[],balasubramanian:285,ball:[146,427,428],ballenegg:365,bammann:209,band:[4,6,7,9,146,203,262,372,375,386,433,451],bandwidth:[1,10,18,41],bandwith:199,bar:[91,199,506],barashev:404,bare:[230,246,248],barost:[230,502],barostat:[],barostt:6,barr:395,barrat:302,barrett:69,barrier:[3,4,6,262,360,375,395,408,495],bartel:289,bartok2010:452,bartok2013:452,bartok:[9,146,442,452],bartok_2010:442,bartok_phd:442,bary:506,barycent:319,basal:[],base:[3,4,6,8,9,11,12,13,14,15,20,65,66,73,80,91,95,108,117,124,152,154,171,172,174,196,198,199,200,203,209,216,217,220,221,222,226,227,231,239,244,247,251,253,277,289,290,293,296,298,300,307,308,312,313,323,330,366,380,382,384,386,400,406,409,412,413,414,416,418,427,431,432,438,440,441,451,462,465,466,469,476,478,481,482,483,485,488,491,492,495,496,499,506,507,508,511],bash:393,bashford:[6,20,178,391,493],basi:[3,6,12,41,146,152,172,208,247,249,289,323,340,368,416,491,507],basic:[6,7,8,12,17,42,119,147,199,200,209,220,263,264,288,344,381,383,433,475,483,502],basin:[90,375,476,495],bask:[404,430,441],bath:[9,297,302],batom1:[71,121,123,196,200],batom2:[71,121,123,196,200],bayli:[6,178,493],bb13:179,bcc:[3,4,7,66,72,75,368,430,432],bcolor:[3,199,200],bdiam:[3,199,200],be2:171,bead:[5,7,10,13,41,46,47,164,207,223,290,460],beam:227,bear:[6,240],becau:13,becaus:[0,1,3,6,8,12,16,17,18,41,42,43,61,66,73,74,79,96,112,122,134,146,152,157,162,172,173,174,178,196,197,198,199,200,201,206,212,220,221,222,223,224,226,232,238,239,240,241,246,247,248,249,260,263,264,277,284,293,297,298,302,307,320,325,330,331,334,335,338,342,343,344,345,346,352,365,371,373,375,376,379,380,391,393,396,398,400,406,407,409,410,411,412,413,417,426,427,428,430,435,445,460,461,463,467,468,478,479,481,483,484,485,488,490,491,493,495,496,502,507,508,509,511],beck:[],becker:[381,404],beckman:244,becom:[1,2,3,6,7,8,18,40,42,55,59,61,73,174,196,197,199,200,220,221,222,223,226,239,241,250,262,263,304,305,326,327,340,341,343,344,345,365,366,371,375,382,394,396,404,406,409,418,435,441,445,462,469,472,481,482,484,491,507],been:[1,2,3,6,7,8,9,11,12,13,16,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,43,44,46,47,48,49,50,52,54,55,57,59,61,62,65,67,71,73,91,115,118,119,120,121,123,125,149,150,151,152,153,154,155,159,160,161,162,164,165,173,174,175,176,178,179,181,182,183,184,186,187,189,190,192,195,196,197,199,200,201,206,208,210,211,212,213,215,216,217,218,219,220,223,224,225,226,227,233,238,239,242,244,245,247,248,250,251,252,253,254,258,260,261,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,292,293,294,297,299,301,304,305,307,309,310,319,324,326,327,328,335,336,337,339,340,341,342,343,345,346,349,351,352,354,355,358,360,364,365,366,373,376,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,403,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,431,432,433,436,437,438,440,443,444,445,446,453,460,462,463,464,465,466,468,469,471,472,473,476,478,479,481,482,483,484,485,487,491,495,498,499,507,508,509,510],befor:[1,2,3,6,8,9,12,14,17,22,29,40,41,42,45,61,68,73,76,77,83,93,94,98,108,109,110,111,120,152,155,160,161,167,172,173,175,176,180,194,195,200,204,205,206,207,208,210,212,215,216,217,218,219,220,224,229,230,238,239,244,246,247,248,250,253,260,263,269,270,271,282,283,286,289,296,297,298,301,302,307,308,309,324,326,327,328,334,340,341,342,346,350,370,371,373,375,380,407,410,426,430,433,461,470,476,478,479,482,483,484,485,486,488,489,491,495,498,499,502,507,508,509,510,511],began:[5,12],begin:[3,8,12,38,40,57,73,123,125,173,192,195,196,200,204,205,209,211,212,213,215,216,217,218,220,226,235,277,292,305,308,323,325,328,337,342,345,346,362,364,365,366,367,369,372,374,375,376,379,380,404,433,435,441,448,450,451,453,460,463,473,476,481,488,495,497,499,506,507,509],behalf:3,behav:[3,27,181,372,373],behavior:[3,176,192,196,197,199,201,223,224,227,239,240,241,244,247,248,249,263,293,297,302,323,326,327,335,372,386,406,430,473,475,483,487,507,509],behaviour:[6,247],behind:[8,246,261,297,323,365],beig:200,belak:7,believ:11,bellott:[6,20,178,391,493],bellow:354,belong:[2,3,41,73,126,175,210,212,216,239,253,307,346,374,447,481],below:[1,2,3,5,6,8,9,11,12,15,16,17,22,38,40,41,42,43,45,55,57,61,62,65,67,70,71,73,79,81,95,97,118,119,122,123,124,146,147,152,158,160,166,170,171,172,175,176,178,180,191,192,195,196,197,199,200,203,204,206,207,209,212,213,214,215,216,217,219,220,222,223,224,226,227,232,235,237,239,242,243,245,247,248,253,260,261,263,268,269,270,271,282,283,286,288,293,296,297,298,305,306,307,309,310,317,320,323,324,325,326,327,328,331,332,333,335,338,340,341,346,348,350,363,365,368,370,371,373,374,375,377,380,381,382,383,386,387,388,391,392,393,394,396,399,404,406,407,409,410,411,412,413,416,418,419,420,421,422,423,424,425,426,427,428,429,430,434,435,440,443,444,445,446,452,453,460,461,463,468,469,471,472,473,474,475,476,479,481,482,483,484,486,488,489,491,493,494,495,497,498,499,501,502,507,508,511],bench:[1,6,9,11,12],benchmark:[1,7,10,11,12,13,14,15,16,17,18,42,220,365,494],beneath:227,benedict:433,benefici:[63,377],benefit:[1,240,490],bennet:91,beowulf:7,berardi:[409,445],beraun:335,berendsen:[],berensen:307,berger:9,berkelei:170,berkowitz:365,berlin:[7,9,312],bern:[3,290,298,299,395,409,451,461,490],bernendsen:6,beryllium:406,besid:[8,309,484],best:[1,6,8,14,15,16,17,18,19,263,284,285,306,307,380,386,396,418,422,435,463,482,490,495],beta:[6,9,289,297,381,384,404,405,407,430,464,465,466,499,507],beta_:386,beta_k:452,beta_pi:386,beta_sigma:386,beta_t:465,better:[3,6,7,8,12,14,16,27,146,181,205,220,239,250,263,277,298,305,307,323,366,375,380,464],betwe:385,between:[],beutler:426,bewteen:[114,213,323,331,338,413,416,478],beyon:490,beyond:[3,5,6,12,17,63,73,91,170,196,200,215,216,239,263,365,377,408,424,435,495,499,507],bflag1:[43,199],bflag2:[43,199],bgq:[17,433],bi3:171,bi5:171,bia:[3,6,8,118,147,150,151,152,153,154,155,159,160,161,162,164,165,203,212,225,226,239,247,248,263,269,270,271,282,283,284,286,302,326,327,328,330,508],bias:[6,9,225,508],biaxial:150,biersack:[430,461,466,473],big:[3,4,12,196,297,302,323,376,394],bigbig:[3,12],bigger:3,bigint:[3,237],bilay:[4,10,320],bilayer1:320,bilayer2:320,bill:7,billion:[3,7,10,12,40,239,489],bin2d:73,bin3d:73,bin:[3,6,11,12,40,65,68,73,77,94,98,109,111,120,122,152,160,167,169,196,200,212,215,216,217,289,297,302,323,376,377,380,403,439,482,510],binari:[3,6,7,9,12,13,16,33,37,51,56,185,191,196,197,198,199,200,201,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,312,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345,356,359,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,436,438,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,468,469,471,472,473,482,483,488,509,511],binary2txt:[],binchunk:212,bind:[9,17,18,198,216,386,451],binsiz:[40,200,376,380],binstyl:160,bio:[41,376],biolog:[6,7],biologi:184,biomolecul:[292,307,365,366,391],biomolecular:490,biophys:244,biosym:13,bird:403,bisect:[42,220,468],bisector:[6,396,418,422],bispectrum:[65,146,452],bisqu:200,bit:[3,11,12,17,40,237,248,435,463,489,502],bitmap:[3,463,470],bitrat:[199,200],bitzek:372,bkgd_dyn:430,bla:12,black:200,blais:[9,13],blanchedalmond:200,blank:[2,3,12,38,57,113,192,199,235,292,307,374,375,386,405,430,437,452,462,463,464,465,466,469,478,479,481,507],blast:335,blend:430,block:[2,3,6,95,146,172,174,175,293,344,368,380,386,406,441,452,484,495,502],blocksiz:380,blow:[3,277,340,344,453],blown:3,blue:[2,199,200,223],bluegen:[196,365,433],blueviolet:200,bni:73,board:[366,399],bodi:[],body_nparticl:8,bodyflag:481,bodyforc:250,bodyforcei:250,bodyforcex:250,bodyforcez:250,bodystyl:[253,307],boff:[374,481],bogaert:330,bogu:[3,155,224],bogusz:92,bohr:[404,406,433,466,506],boltzmann:[6,7,9,91,95,118,149,152,153,154,155,158,159,160,161,162,164,212,223,247,250,251,252,253,254,268,339,400,496,506],bond:[],bond_coeff:[],bond_graph_cutoff:444,bond_harmon:[8,49,50],bond_harmonicshift:50,bond_info:444,bond_interact:209,bond_styl:[],bond_typ:176,bondangl:[3,21,33,481],bondbond13:[3,179,481],bondbond:[3,21,33,481],bondchk:444,bondcoeff:3,bondtyp:[221,222,374],bonet:[311,402],bonu:[3,509],book:472,bookkeep:435,bookmark:0,boost:[1,3,12,66,376],bop:[],border:[3,7,16,63,335,508],boresch:91,boreschkarplu:91,born:[],boron:406,borrow:312,bose:302,botero:[7,9,13,406],both:[1,3,6,7,8,9,11,12,14,15,16,17,27,37,40,41,55,56,59,61,63,64,65,70,71,73,87,91,92,114,119,121,122,134,148,150,151,152,157,160,162,165,170,172,174,175,176,181,191,192,196,199,202,203,204,205,210,212,213,216,217,218,221,222,223,224,225,226,231,239,241,243,245,247,248,250,251,259,260,263,264,269,270,271,277,282,283,286,292,293,296,297,304,307,310,312,320,323,327,331,332,333,335,338,340,341,343,344,345,348,349,359,366,370,373,374,375,376,378,380,382,386,387,388,389,390,391,392,394,399,400,404,405,406,409,410,412,413,414,418,420,422,423,424,426,427,428,433,434,435,438,445,446,462,464,465,466,469,476,478,479,481,482,483,484,488,493,498,499,502,507,509,510,511],bottleneck:[1,3,479,500],bottom:[8,9,155,170,200,226,238,250,284,331,338,368,493],bottomwal:219,bounc:[3,323],bound:[3,6,17,26,27,42,43,59,61,73,161,174,181,195,196,197,200,215,216,220,226,227,231,239,248,263,293,323,340,341,342,343,344,345,365,373,406,481,484,495,502,507,508],boundar:3,boundari:[],boundary_dynam:209,boundary_faceset:209,boundary_integr:209,bount:11,bourgogn:9,box:[],boxcolor:[199,200],boxxlo:11,bpa:380,bpclermont:[9,13],bptype:460,br1:171,bracket:[2,3,6,42,65,73,123,125,203,211,212,213,215,216,217,218,220,337,499,507],bragg:[124,171],branc:[],branch:11,branicio2009:469,branicio:[75,469],breakabl:[7,45,56],breakag:[80,221],breakdown:[1,12,15,92,113,443,444,476,495],brennan:[9,84,85,234,311,402,460],brenner:[382,461],brick:[3,42,63,64,160,174,220,481,483,485,507],brief:[1,5,6,7,8,12,246,263,382,386,444,495],briefli:[6,10,290,395,451],brilliantov:410,bristol:[5,7],brittl:440,broader:479,broadli:8,broken:[2,55,67,71,72,80,108,113,121,176,221,263,386,483,493,500,509],brook:6,brought:195,brown:[7,9,13,15,16,124,147,200],brownain:388,brownian:[],brownw:7,brows:0,browser:[4,199],bryantsev:412,bsd:12,bstyle:[41,43],btype:[71,121,173,196,396,418,422,426,460],buc:389,buck:[],buckingham:[7,204,205,298,366,387,389,390,398,429,461],buckplusattr:451,buffer:[3,8,197,199,200,498],bufi:199,bug:[],bui:199,build:[],builder:[7,13],built:[1,2,3,4,6,8,9,11,12,13,14,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,41,44,46,47,48,49,50,51,52,54,55,56,57,66,69,80,82,84,85,87,90,91,101,102,103,104,105,106,110,115,117,118,124,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,156,158,159,163,164,166,170,171,178,179,181,182,183,184,185,186,187,189,190,191,192,196,197,198,201,203,206,207,208,210,214,219,221,222,223,225,226,227,232,233,234,235,236,238,239,240,241,242,244,246,247,249,250,251,252,253,254,256,257,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,278,280,281,282,283,284,285,286,288,289,290,292,293,296,297,298,299,300,301,302,303,304,307,309,310,311,312,313,314,315,316,317,319,323,326,328,329,330,331,332,333,335,336,338,339,341,342,343,347,348,349,351,352,353,354,355,356,358,359,360,366,375,376,377,380,381,382,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,476,479,482,484,490,494,495,496],bulatov:[431,432],bulk:[4,6,10,72,250,288,294,397,430,433,435,440,447,449,451,485],bullet:7,bump:247,bunch:8,bundl:[9,199,201],burlywood:200,bussi1:327,bussi2:327,bussi:[241,327],buyl:[9,198],bybe:9,bypass:6,c1060:14,c11:[213,430],c12:213,c13:213,c1n:213,c2050:14,c21:213,c22:213,c23:213,c2n:213,c31:213,c32:213,c33:213,c34:213,c3n:213,c41:213,c42:213,c43:213,c44:213,c_0:[335,458,459],c_1:[70,71,123,124,171,196,200,240,296,308,346],c_2:[71,123,124,168,170,171,196,308,337,346],c_3:[123,308],c_6:170,c_cluster:6,c_cstherm:6,c_dist:123,c_doubl:11,c_e:335,c_flux:95,c_forc:123,c_gauss:408,c_hb:412,c_id:[6,65,73,91,123,125,196,197,211,212,213,214,215,216,217,218,308,325,337,499,507],c_ij:6,c_ijkl:6,c_index:123,c_k:240,c_ke:331,c_msdmol:125,c_my_stress:211,c_mycentro:[212,216],c_mychunk1:120,c_mychunk2:120,c_mychunk:[6,68,77,94,98,109,111,152,167,169],c_mycom:215,c_mycomput:212,c_myd:197,c_myf:[196,510],c_myrdf:[122,218],c_mytemp:[8,213,214,215,218,337,499,507],c_n:[],c_n_k:240,c_p:147,c_pe:116,c_peratom:[116,147],c_pi:386,c_press:123,c_prop:6,c_radiu:170,c_reax:[443,444],c_sa:308,c_sigma:386,c_size:6,c_stress:196,c_tatom:[],c_tdrude:[230,248,502],c_thermo_press:[8,213,214,215,218],c_thermo_temp:218,c_xrd:215,ca2:171,cach:[17,40,435,494],cacul:310,cadetblu:200,cai:502,calcforc:250,calclat:95,calcluat:[110,116,118,147,396],calcualt:[95,212],calcul:[],caldwel:[6,178,493],calhoun:290,call:[],callabl:[3,11],callback:[3,8,11,148,203,237,479],caller:3,calori:506,caltech:[6,7,9,13,406],calucl:6,calul:[11,12,152,366],cambridg:[9,442],campa:289,can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,178,179,180,181,182,183,184,185,186,187,189,190,191,192,193,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,233,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,358,359,360,361,362,363,364,365,366,368,369,370,371,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,488,489,490,491,492,493,494,495,496,497,498,499,500,502,506,507,508,509,510,511],cancel:[203,307,508],candid:[176,210,239],cannot:[1,2,3,6,11,12,13,15,16,17,39,40,41,42,55,58,59,60,61,70,73,86,88,92,123,125,148,150,152,173,175,176,193,195,196,197,198,199,200,211,212,213,215,216,217,218,220,223,224,226,227,239,240,241,247,248,249,253,260,263,265,267,269,271,273,274,275,280,282,286,293,294,297,302,304,307,308,309,313,323,331,335,337,338,340,341,344,345,346,348,361,365,368,373,375,378,379,380,389,390,392,404,409,411,418,422,424,426,435,438,443,445,446,447,449,460,461,463,476,478,479,481,482,484,485,487,490,491,493,495,498,506,507],canon:[203,210,239,241,263,264,282,283,284,285,286,290,327,330,333,433,440],cao1:290,cao2:290,cao:290,capabl:[5,7,9,11,14,17,18,342,348,366,380,382,392],capac:[9,41,106,158,234,302,335,455,481,491],capit:[229,481],capolungo:[124,171,308],captur:[6,336,382,390,406,410,422,430,502],carbid:396,carbon:[7,199,358,382,395,415,430],card:[12,14,16,22,45,79,91,122,180,204,205,307,350,370,393,412,475,483,488,509,511],care:[3,6,61,73,172,175,195,212,216,217,221,222,227,241,246,250,263,293,307,330,385,479,481,484,485,490,491],carefulli:[11,12,55,304,346,413,415,486],carlo:[6,7,9,203,210,223,239,307,330,403,461],caro:[210,404],carpent:[7,13],carri:[16,256,296,335,410,444],cart:[3,478],carter:[9,17],cartesian:[3,64,381,478],carv:175,cascad:[231,335],cash:7,cast:[241,507],cat:[15,199],catastroph:298,cate:250,categori:[],cation:[407,451],cauchi:[139,144],caus:[1,2,3,6,8,12,16,17,172,174,175,176,196,200,208,224,231,239,263,277,288,293,305,307,310,340,342,343,344,345,348,364,366,373,375,379,412,418,424,427,428,435,475,479,480,481,482,485,486,488,489,507,511],caution:[1,366],cautiou:[221,222],cautious:382,caveat:[382,490],cbecker:[381,404],cc1:[6,14,68,77,94,98,109,111,120,152,167,169,212,216],cc2:14,ccc:[405,462,464,466,469],ccflag:[9,12,16,17,18,19,196],ccm6:404,ccsi:[405,462,464,466,469],ccu:386,cd2:171,cdeam:404,cdennist:9,cdll:11,cdof:[6,152,212],cdte:386,cdte_bop:386,cdtese:386,cdzn:386,cdznte:386,ce3:171,ce4:171,ceas:372,ceil:507,cell:[3,6,61,92,122,124,170,171,172,196,208,224,225,239,244,261,263,264,268,289,297,300,311,335,365,366,368,403,406,433,499],cella:[6,499],cellalpha:[6,499],cellb:[6,499],cellbeta:[6,499],cellc:[6,499],cellgamma:[6,499],center:[3,6,25,43,65,68,73,76,77,90,93,94,103,108,109,110,120,122,124,152,153,154,157,160,164,167,169,172,199,200,203,204,205,207,212,215,216,217,224,226,227,228,230,239,240,245,247,248,253,259,263,269,270,271,282,283,284,286,289,293,298,304,305,307,308,312,320,321,323,325,326,327,328,330,331,333,340,344,349,368,374,385,405,406,409,410,416,427,428,430,431,432,462,464,465,466,468,469,484,491,502,507],centimet:506,central:[3,63,72,78,79,96,112,122,128,146,170,253,288,310,321,353,374,433,437,443,444,469,481],centro:[],centroid:[3,290,468,491],cerda:365,ceriotti2:241,ceriotti:[13,241,246],certain:[1,2,3,6,8,12,17,40,73,119,123,125,176,196,197,199,211,212,213,215,216,217,218,223,237,238,307,309,324,337,348,356,364,376,413,435,444,467,483,487,502,507],certainli:245,cerutti:366,cfg:[3,6,7,13,196,198,199,200,201],cfile:444,cfl:[134,313],cfor:312,cg_type:446,cgiko:2,cgikot:2,cgkio:2,cgko:2,cgkot:2,cgo:2,cgot:2,ch2:310,ch2lmp:[],ch3:310,ch5md:198,chain3:376,chain:[],challeng:[6,312],chalopin:302,champaign:[244,365,366,427],chan:433,chandler:[381,404],chandrasekhar:[6,418],chang:[1,2,3,6,8,9,11,12,14,15,16,17,40,41,42,47,56,59,61,64,73,82,91,108,122,132,134,154,155,156,172,173,174,176,192,195,196,197,198,199,200,201,203,204,205,206,207,209,210,216,217,219,220,221,222,223,224,225,226,227,231,232,236,238,239,241,243,244,245,247,249,250,251,253,259,260,261,263,264,265,266,267,268,269,270,271,277,282,283,284,285,286,288,289,293,294,296,297,298,301,304,305,306,307,309,310,312,323,326,327,328,329,331,332,333,334,335,336,338,341,344,346,366,371,373,375,378,380,400,406,410,413,427,428,430,433,435,443,444,451,460,461,476,477,478,479,481,482,483,484,485,486,487,489,490,491,492,493,496,499,503,505,506,507,508,509],change_box:[],changeabl:196,channel:[4,206],chapter:[290,366],charact:[2,3,6,12,38,42,57,65,192,196,197,199,200,201,203,220,235,296,304,348,374,379,406,417,441,443,444,451,463,478,479,483,488,489,507,509,510,511],character:[6,69,72,112,122,146,452,476,495],characterist:[248,323,332],charg:[1,3,4,5,6,7,9,11,15,41,91,92,119,124,171,172,196,197,201,203,204,205,210,227,232,239,296,298,299,300,304,325,338,365,366,374,387,389,395,396,398,399,404,406,407,413,418,422,426,438,443,444,451,461,466,467,469,470,472,473,481,482,486,491,493,502,506,507],charmm2lammp:13,charmm:[],chartreus:200,cheap:323,cheaper:[231,409,445],check:[3,6,8,11,12,15,17,40,42,73,95,192,210,216,220,221,222,227,236,239,245,246,293,306,310,323,331,333,338,346,348,364,373,374,375,376,377,380,403,414,417,435,444,476,478,479,481,489,495,498,499,507],checkf:192,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:[9,297,298,300,386,406,443,444],chen:335,cheng:395,chenoweth:[443,444],chenoweth_2008:[443,444],chi:[97,161,195,288,298,300,361,407,409,508],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:[3,6,9,12,15,16,18,41,42,55,91,147,150,151,165,176,192,212,216,217,220,223,226,227,241,247,250,261,263,290,298,307,330,359,366,371,372,375,377,380,413,426,435,439,481,490,491,494,495,501,502,506],choos:[1,3,6,7,8,12,16,17,18,29,40,55,91,123,162,163,199,221,222,223,224,227,236,247,250,261,263,265,266,267,268,269,270,271,293,294,311,323,327,341,365,366,372,470,476,478,490,496],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:[9,461,469],claus:479,clean:[6,12,14,15,17,489],cleanli:[480,510],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],client:[244,246],climb:[262,375,495],clinic:[7,13],clo:[161,195,508],clock:[12,476,495],clockwis:341,close:[3,6,11,12,13,40,42,69,73,147,175,196,222,223,224,241,248,250,263,284,307,310,341,344,364,366,369,371,372,375,380,382,386,396,397,416,430,435,447,449,463,466,485,491,502,504],closer:[3,42,122,170,195,196,220,224,228,332,375],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:[3,9],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:[7,9,29,36,41,55,184,292,307,323,411,446,490,493],coarser:[366,507],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:[9,239,406],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:[7,8,9,15],collect:[3,6,7,8,9,13,41,43,68,77,87,94,98,103,109,111,120,152,160,167,169,172,196,197,200,212,225,253,259,292,302,305,307,346,365,374,376,394,481,488,494,500,511],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:[3,6,9,12,13,43,65,67,68,69,70,71,73,77,79,81,83,85,94,96,97,98,109,111,112,114,116,119,120,121,122,123,125,146,147,152,160,167,169,170,171,192,196,197,200,203,211,212,213,215,216,217,218,253,260,261,297,307,324,325,335,345,408,412,443,444,482,496,498,507],columnar:170,colvar:[],colvarmodul:12,com:[],comamnd:226,comand:223,comannd:380,comb3:[],comb:[],comb_1:299,comb_2:299,combiant:397,combin:[3,6,7,9,11,13,36,41,65,67,71,81,91,97,108,114,121,150,151,165,196,199,209,215,244,253,263,290,296,311,327,336,344,347,349,365,366,368,372,380,394,396,397,402,406,407,413,425,426,452,462,464,466,469,472,484,489,494,502,507],come:[],comfort:[12,13],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:[2,7,11,12,38,57,178,192,196,235,248,307,335,374,375,381,404,405,407,417,430,437,444,451,452,462,463,464,465,466,469,478,479,481,502,507],commerci:7,commit:9,commmand:[3,6,12,61,113,285,416,475,476,478,495,510],common:[],commonli:[3,6,12,17,25,59,61,110,112,174,196,199,201,360,411,420,452,464,466,481,484,493],commun:[1,3,6,7,8,10,11,12,14,15,16,18,41,42,60,63,64,73,170,175,176,199,200,220,221,222,224,225,226,244,246,250,252,253,254,263,289,296,298,299,300,307,311,323,335,346,363,365,376,377,378,380,402,403,439,474,478,479,490,491,507,509,511],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:[1,3,4,6,8,12,17,40,90,116,124,155,171,180,191,200,230,298,346,348,365,366,373,375,430,451,476,495,496,502,506],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,44,45,56,179,180,191,349,350,359,392,461],compat:[3,5,7,8,9,11,12,13,17,18,42,73,123,125,183,196,201,205,211,212,213,215,216,217,218,220,289,301,327,330,337,340,343,365,380,414,433,435,463,478,479,507],compens:[6,221,222,305,376,406],compet:334,competit:366,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,170,196,198,199,201,244,334,366,380,433,481,482,486,507],compl:17,complain:[11,12,17],complement:430,complementari:[7,396,418],complet:[3,6,9,11,12,15,42,61,73,200,216,220,225,253,290,293,296,323,334,336,347,348,364,375,380,407,448,450,468,476,481,486,489,493,495,498,502,507],complex:[6,8,11,12,13,25,41,43,64,96,112,146,148,160,172,173,250,319,344,363,375,406,433,463,479,481,484,507],compli:[330,334],complic:[6,7,9,12,13,210,239,479],complier:12,compon:[3,6,8,12,63,65,68,69,75,83,92,93,94,95,96,98,99,102,109,110,111,112,113,114,115,116,118,119,123,133,136,137,138,139,142,143,144,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,167,168,169,195,196,197,199,200,206,207,211,212,213,214,215,216,217,218,219,223,224,226,227,232,237,242,246,247,250,253,255,259,260,262,263,264,268,269,270,271,282,283,284,286,287,289,290,291,294,305,307,309,310,312,316,317,320,323,326,327,328,330,337,338,343,344,345,365,368,372,373,374,375,380,400,406,410,427,428,448,450,451,452,481,482,491,499,507,508],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:[2,3,510],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:[9,16,366,507],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],confin:[481,495],conflict:[3,12,41,197,435,479],conform:[3,6,13,61,223,224,262,306,312,334,358,375,406,493],confus:[3,469],conjuct:400,conjug:[7,8,247,372,406,443,444],conjunct:[6,7,73,90,91,120,155,160,166,172,176,200,204,205,247,250,254,277,293,294,298,299,300,302,307,311,323,331,338,343,365,366,375,387,389,393,396,400,406,412,418,435,438,446,467,481,484,488,502,511],connect:[3,6,91,157,175,223,244,292,307,310,320,375,397,410,460,466,478,479,481,485,502],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:[6,9,72,73,80,91,121,154,157,158,175,196,197,200,204,205,211,213,216,220,222,223,227,251,264,289,307,330,331,334,335,338,366,393,406,413,444,445,451,460,476,477,479,482,483,484,486,489,491,499,502,507],consider:[6,8,247,248,326,327,328,380,490],consist:[3,6,8,9,11,12,41,43,67,71,81,97,109,114,117,118,121,152,155,157,172,184,195,201,206,207,212,226,227,230,232,237,240,247,248,249,260,263,265,266,267,268,269,270,271,272,273,275,276,277,278,280,281,282,283,284,285,286,294,297,302,304,306,307,326,327,328,329,339,365,366,368,374,375,380,382,386,388,394,396,406,409,413,416,427,428,430,433,435,445,448,450,451,463,470,479,481,482,483,484,485,486,493,502,507],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:[6,8,12,14,38,55,57,63,66,69,72,74,75,79,96,112,124,146,171,224,263,289,306,344,376,380,399,433,435,460,462,463,484,485,500,507],constructor:[8,11],consult:444,consum:[1,302,439,507],consumpt:363,contact:[],contact_stiff:[447,449],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,65,91,95,122,124,146,152,160,170,171,172,174,178,180,191,192,196,197,199,200,201,203,204,205,209,211,212,213,215,216,217,218,220,225,227,232,235,241,245,246,247,250,261,277,288,289,292,293,295,297,300,304,307,308,313,323,330,334,335,344,345,348,364,366,374,375,378,379,381,382,383,386,395,396,399,404,405,406,413,414,430,433,437,441,442,443,444,452,462,463,464,465,466,467,469,476,477,478,479,481,482,483,484,486,488,490,493,495,496,498,499,502,507,509,511],content:[9,12,18,444,497,499],context:[3,6,8,12,17,122,123,200,221,222,227,292,304,339,372,472,481,488,497,506,507,508],contibut:72,contigu:478,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,73,83,108,109,168,200,203,204,205,210,212,213,214,215,216,217,218,220,223,224,225,226,227,239,240,241,243,244,245,247,248,249,255,260,261,263,265,266,267,268,269,270,271,282,283,284,285,286,291,293,296,297,307,308,312,322,323,325,332,333,335,341,344,348,364,379,380,386,400,403,420,423,443,444,445,448,450,465,476,479,481,483,484,489,495,496,498,499,507,509],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:[1,6,43,56,66,154,157,197,226,346,448,450,472,510],contrib:335,contribut:[3,5,6,7,8,9,12,13,17,65,68,70,72,73,76,77,79,82,88,91,92,93,94,95,98,107,109,111,113,114,115,116,118,120,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,205,210,211,212,213,215,216,217,218,224,239,247,250,253,254,258,264,284,285,292,293,301,304,307,308,310,337,365,373,375,383,400,403,404,406,413,427,428,433,435,443,444,451,493,499,502],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:[6,12,29,196,201,218,308,368,452,507],convent:[3,8,9,29,183,190,191,197,200,306,320,347,404,406,507],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:[3,8,146,199,200,210,213,294,365,396,397,398,406,418,422,426,438,479,495,506],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,61,65,73,95,172,179,196,199,200,218,261,293,346,349,351,355,358,368,375,381,404,433,464,466,473,479,481,482,483,488,498,502,506,507,509,511],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:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,61,63,64,65,68,70,73,76,77,79,83,91,93,94,98,108,109,111,119,120,122,140,146,155,161,167,169,170,172,176,195,196,197,198,199,200,201,203,206,211,212,215,216,217,220,221,222,223,224,225,226,227,230,232,233,237,239,242,243,244,245,246,247,248,260,262,263,265,266,267,269,270,271,284,287,288,289,292,293,294,304,305,307,309,310,312,317,320,321,322,323,325,333,334,335,342,343,345,346,368,373,374,375,380,381,382,385,405,451,476,481,482,483,484,486,489,491,495,502,507,508],coordn:[120,212],coorind:[],copi:[0,3,4,8,11,12,15,17,41,125,199,335,375,393,443,479],copper:473,coproccesor:16,coprocessor:[1,4,7,9,16,17,380,494],coproprocessor:17,copy_arrai:8,copyright:[7,8,292],coral:200,core:[],core_shel:154,coreshel:[6,389,396,398],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],cornflowerblu:200,cornsilk:200,corp:[],corpor:16,corr:395,correct:[3,6,9,11,12,16,17,61,91,92,107,108,116,122,154,159,166,197,199,226,239,241,247,263,264,284,292,294,297,334,340,344,365,375,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,471,472,473,481,496,499,502],correction_max_iter:209,correctli:[3,8,9,11,17,73,83,107,108,109,149,150,151,153,155,157,158,159,160,161,164,165,168,196,200,206,227,232,237,248,257,263,264,300,307,310,320,322,341,344,375,376,380,398,428,433,478,479,481,491,506,508],correl:[],correpond:235,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,72,73,91,101,102,115,118,119,120,121,124,125,133,136,137,138,139,140,142,143,144,146,149,150,159,166,170,171,178,179,180,181,182,183,184,186,187,189,190,192,195,196,197,199,200,204,205,206,212,214,215,216,217,219,222,224,226,233,237,238,242,247,250,251,259,260,261,263,265,266,267,268,269,270,271,272,273,277,280,282,283,284,286,289,290,294,299,307,309,310,326,328,330,339,340,341,343,344,345,347,349,350,351,352,354,355,358,360,366,370,372,374,375,381,382,384,387,388,389,390,391,392,393,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,416,418,419,420,421,422,423,424,425,426,427,430,431,433,435,436,437,438,440,441,443,444,445,446,451,452,453,462,463,464,465,466,469,471,472,473,476,478,479,481,482,484,494,495,496,498,499,502,507],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:[2,3,6,9,11,12,17,33,42,51,61,68,73,77,91,94,98,109,111,115,118,120,152,162,167,169,185,196,197,199,200,204,205,212,213,216,220,226,237,246,296,297,298,302,305,307,309,323,324,330,334,335,336,340,344,346,348,356,362,364,371,373,376,380,383,408,412,413,416,443,444,477,478,479,481,483,485,488,489,496,497,502,507,508],coulomb:[3,5,6,7,8,9,10,12,14,15,18,74,92,113,114,122,147,173,177,298,300,336,365,366,373,380,387,389,390,391,392,395,396,397,398,399,406,410,411,413,418,422,426,429,435,438,443,444,446,451,461,466,467,469,472,486,493,499,502,506],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,42,65,70,79,95,120,122,123,160,170,176,206,207,210,212,215,216,217,219,220,227,232,236,239,245,263,277,293,310,326,327,344,366,373,374,375,377,380,408,412,435,499,507],counter:[3,341,476,487,489,495],counteract:239,counterbal:243,counterbalanc:29,counterpart:[196,307,476],counterproduct:18,coupl:[],courant:313,cours:[3,8,132,134,166,196,204,205,240,306,320,334,340,342,343,345,346,366,427,453,478,481,494,502,507,509],courtesi:368,cov:451,coval:[6,29,406,430,451,502],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:[1,3,4,9,10,12,14,15,16,17,18,65,73,200,214,230,248,336,363,366,380,393,461,476,494,495,498,499,500,507],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:[3,122,173,199,200,221,222,223,258,373,440,468,483,486,507],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:[3,12,22,73,93,150,170,180,196,197,199,211,216,222,226,260,262,284,307,316,320,322,331,338,350,368,375,391,400,403,404,411,412,413,418,420,422,441,446,448,450,464,466,473,481,485,491,509],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:15,cuda_get:15,cuda_hom:15,cuda_prec: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:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,41,42,43,61,63,65,73,75,83,91,107,108,114,122,123,136,147,152,160,162,168,170,173,176,195,196,197,198,199,200,201,204,205,209,212,216,217,218,220,221,222,223,224,225,226,227,231,232,237,239,241,244,245,247,253,260,263,264,269,270,271,277,282,283,284,286,292,293,298,299,301,304,305,306,307,310,311,312,313,314,315,316,317,319,321,322,323,326,327,328,334,335,338,339,340,341,342,343,345,346,348,363,364,365,366,369,370,372,373,374,375,380,386,393,395,399,404,406,407,410,413,414,417,427,428,430,431,432,435,441,443,444,447,448,449,450,453,464,466,467,470,476,477,478,479,481,482,483,484,485,487,488,489,491,493,495,496,498,499,507,508,509,510,511],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:[3,6,10,16,18,40,46,47,55,56,63,72,74,75,79,91,96,112,114,121,122,146,170,173,175,176,222,223,228,235,288,297,298,300,302,304,307,311,323,336,340,344,346,363,365,366,373,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,394,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,444,445,446,451,452,453,454,455,456,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,479,483,486,490,502,507],cutoff_glob:[],cutoff_inn:[],cutoffa:405,cutoffc:405,cuu3:404,cval:171,cvd:330,cvel:312,cvff:[],cwiggl:[3,260,340,343,345,507],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:[0,6,12,13,195,443,444,507],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:[6,7,11,12,13,14,17,124,128,171,172,290,295,363,365,380,414,435,470,479,480,488,491,498,507],deby:[],decai:[96,396,473],decid:[3,6,12,16,73,260,296,307,336,496],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:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,178,179,180,181,182,183,184,186,187,189,190,191,192,193,194,195,196,197,198,199,200,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,220,221,222,223,224,226,227,230,231,232,234,237,238,239,242,245,246,247,248,249,250,258,260,262,263,264,265,266,267,268,269,270,271,273,274,275,278,280,281,282,283,284,285,286,288,289,290,292,293,294,296,298,300,305,307,308,309,310,313,317,321,323,325,326,327,328,329,331,332,333,335,337,338,340,341,342,343,344,345,346,348,349,350,351,352,353,354,355,358,359,360,361,363,365,366,368,370,372,373,374,375,376,377,378,379,380,382,383,384,385,387,388,389,390,391,392,393,394,396,397,399,400,401,402,403,405,406,408,409,410,411,412,413,414,416,418,419,420,421,422,423,424,425,426,427,428,429,433,434,435,436,437,438,440,441,443,444,445,446,447,448,449,450,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,481,482,484,485,486,487,490,491,492,493,495,496,498,499,502,503,504,505,506,507,508],definit:[2,3,6,8,12,13,80,82,122,146,200,212,213,214,215,216,217,218,226,234,245,268,308,325,337,340,343,345,347,359,363,374,383,386,394,401,402,406,416,441,448,450,452,468,479,481,483,490,492,506,507],defint:499,deform:[],deg2theta:171,deg:502,degener:[3,292],degrad:[8,18,289,366,490],degre:[3,6,8,20,21,24,28,29,32,35,36,38,67,81,96,97,99,101,102,104,106,107,112,118,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,171,172,178,179,182,183,190,192,195,199,212,223,230,239,241,242,247,248,253,263,264,268,269,270,271,282,283,284,286,290,292,306,307,310,326,327,328,333,349,351,355,358,360,373,399,404,412,491,499,502,508],degress:[152,212],del:495,delai:[3,6,12,376,403,499],deleg:413,delet:[2,3,7,8,12,55,59,62,65,170,175,176,203,212,213,215,216,217,218,221,223,236,239,263,308,326,327,346,348,364,374,376,379,435,460,481,482,483,484,492,493,498,503,505,507,508],delete_atom:[],delete_bond:[],delete_el:209,deli:195,delimit:[479,507],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:[3,6,7,9,18,41,42,61,105,122,132,146,158,170,172,204,205,209,212,216,217,220,226,237,250,253,256,257,289,293,294,298,335,340,368,370,374,381,386,404,430,431,432,441,445,451,455,457,458,459,481,490,491,499,506],density_continu:450,density_summ:450,depart:[0,7],departur:[261,297],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,63,65,67,70,71,72,73,81,96,97,108,114,115,118,119,120,121,125,146,149,155,159,160,166,172,173,178,179,180,181,182,183,184,186,187,189,190,191,192,195,196,197,199,200,203,204,205,206,207,210,212,214,215,216,218,219,220,222,224,226,232,233,238,241,242,243,245,247,248,250,252,253,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,288,299,302,304,307,309,310,311,317,323,326,327,328,330,332,334,335,337,339,340,343,344,345,346,348,349,350,351,352,354,355,358,360,366,368,373,374,376,377,378,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,430,431,433,434,436,437,438,440,441,443,444,445,446,451,452,453,461,462,463,464,465,466,467,469,471,472,473,476,478,481,483,484,487,491,493,495,498,499,501,507,508],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:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,64,65,70,72,73,75,92,116,119,122,124,136,146,147,150,151,152,156,157,160,163,165,166,170,171,172,174,175,184,189,192,196,197,198,203,204,205,212,213,214,215,216,217,218,220,223,224,225,226,227,229,230,235,240,241,244,245,246,247,248,249,250,252,253,254,258,262,263,264,268,276,285,288,290,295,296,297,298,299,300,307,312,320,323,324,325,326,327,328,329,330,331,332,333,338,340,341,343,348,365,366,368,371,372,373,374,375,379,382,383,385,387,388,389,391,392,393,394,395,396,399,404,406,407,409,410,411,413,416,418,419,420,421,422,423,424,425,426,427,428,429,430,433,434,440,441,442,443,444,445,446,451,452,453,460,461,462,463,464,465,466,467,469,471,472,473,474,476,478,479,481,482,483,484,485,491,494,495,498,507,508,509],descript:[],descriptor:[146,196,414],deserno:366,design:[0,3,6,7,8,9,11,13,14,15,17,124,154,157,171,209,223,229,230,263,264,288,289,308,330,335,383,384,385,388,391,396,398,406,426,427,428,431,432,441,444,463],desir:[2,3,6,7,11,12,14,15,16,33,41,51,61,73,92,95,118,123,147,154,172,185,195,212,218,224,226,237,239,240,247,248,249,253,263,284,292,293,294,295,298,302,307,310,323,326,327,328,329,334,341,356,362,365,366,368,371,373,374,375,400,404,412,427,428,462,464,466,477,478,479,481,485,490,495,496,498,499,507,508,509],desk:7,desktop:[4,6,7,10,12,199],despit:502,destabil:386,destre:358,destroi:[11,40,221,222],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,65,68,69,70,73,77,80,94,95,98,107,109,111,113,115,117,118,120,123,125,146,147,149,150,151,152,155,165,166,167,169,172,173,176,177,180,191,195,196,197,199,200,203,204,205,209,212,213,214,215,216,218,220,222,223,224,225,226,227,237,239,240,241,242,244,245,247,249,250,254,260,261,262,263,264,265,266,267,268,269,270,271,275,277,282,283,284,285,286,289,292,293,294,296,297,299,300,301,307,310,311,323,326,327,328,329,330,331,333,334,335,336,337,338,339,346,348,350,359,365,366,369,373,374,376,377,380,381,382,383,385,386,388,390,391,392,393,394,395,396,399,400,406,407,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,429,430,434,435,440,443,444,445,451,452,453,461,468,471,472,479,481,482,483,484,486,487,490,491,493,496,499,500,507,508,511],detect:[2,3,12,43,63,65,90,96,238,293,334,375,395,412,417,476,478,481,492,495,507],determ:380,determin:[1,3,6,8,9,12,15,40,41,43,52,59,60,61,63,64,70,73,91,107,113,115,118,124,125,133,147,160,161,170,171,172,195,196,197,199,200,201,202,206,207,208,211,212,213,214,215,216,217,218,219,220,224,226,227,230,232,239,242,243,245,247,248,253,258,260,261,263,269,270,271,282,283,284,286,288,290,293,294,297,304,305,306,307,308,309,313,315,317,323,326,327,328,330,336,337,340,341,342,343,344,345,346,359,365,366,368,374,376,377,380,382,383,390,395,399,403,404,408,410,413,414,422,430,433,435,444,445,451,460,463,467,472,478,481,482,484,486,488,491,495,497,498,500,506,507,508],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_singl:[3,12,366],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,301,433],dhi:[61,195,226,293],dhug:[261,297],dhugoniot:[261,297],dia:430,diagnost:[],diagon:[3,6,87,146,147,148,224,263,294,307,338,448,450],diagonalstyl:452,diagram:[42,124,171,191,220,290],diallo:412,diam:[199,200,293,374],diamet:[3,6,41,43,119,172,196,197,199,200,204,205,247,293,307,323,325,339,341,374,394,409,410,420,445,468,472,481,482,491],diamond:[368,406,430],diamter:[41,293],dick:6,dicsuss:260,dictat:[210,261],did:[3,12,373,400,403,404,410,435,464,466,489],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,168,337,365],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,63,66,70,72,73,91,96,99,101,102,126,146,149,150,151,152,153,155,158,159,160,161,162,164,165,166,172,173,175,180,191,192,195,196,199,200,203,205,208,210,212,215,220,221,222,223,224,225,226,230,235,238,239,240,241,242,243,244,247,248,250,260,263,264,265,266,267,269,270,271,273,275,278,280,281,282,283,286,288,290,292,294,297,298,299,302,305,307,310,312,320,321,323,326,327,328,331,332,333,335,338,339,340,341,344,348,349,359,362,364,365,366,368,369,371,372,374,375,377,378,379,380,381,382,386,390,391,393,394,395,400,401,402,404,406,409,410,411,413,416,418,419,421,422,429,430,431,432,434,435,437,441,443,444,445,446,447,448,450,451,452,453,461,462,463,464,466,468,469,472,475,476,478,479,481,483,484,485,486,489,490,491,493,495,496,498,499,500,502,506,507,508,509],differenti:[1,3,6,29,192,365,396,441,465],difficult:[224,290,380,412,490],difficulti:[96,112,310,443],diffract:[],diffus:[],digit:[2,3,200,348,433],dih_table1:192,dih_table2:192,dihder:193,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:222,dihydrid:406,dij:310,dilat:[],dim1:3,dim2:3,dim:[3,61,73,149,153,154,155,158,159,160,161,162,164,172,195,216,226,245,341,368,430,484,506,507,508],dimdim:507,dimems:289,dimens:[],dimensinon:73,dimension:[3,40,96,118,124,146,149,152,153,154,155,158,159,160,161,162,164,171,194,212,216,262,289,335,368,371,375,441,481,491],dimensionless:[110,127,128,130,133,135,137,142,146,335,366,452,472],diment:3,dimentionless:141,dimer:[6,307,430],dimgrai:200,dimstr:[42,220],dinola:[294,326],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,41,196,197,325,502],dir1:492,dir2:492,dir:[1,3,4,8,11,12,261,288,297,322,441,443,444,479,492,507],dirac:146,direc:441,direct:[],directli:[3,6,8,9,11,12,91,119,146,148,196,197,198,199,206,232,241,245,250,289,308,327,339,341,342,343,344,368,372,380,381,382,387,389,390,396,399,404,406,418,422,435,438,446,460,479,491,492,493,499,507],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,62,197,201,225,246,292,298,301,311,319,323,332,333,375,379,381,382,386,393,395,396,404,405,407,414,415,426,430,431,432,433,437,441,442,443,444,451,452,462,464,465,466,469,479,481,482,483,492,507],disabl:[3,12,16,335,417,479,494,507],disadvantag:[6,220],disallow:[196,226,263],disappear:483,discard:[2,3,42,73,214,216,220,336,344,478,483,484],discontinu:[9,192,373,424],discourag:430,discov:[13,336],discret:[6,8,41,43,199,200,247,250],discuss:[],disk:[6,88,89,96,165,194,227,239,293,479],disloc:[72,433],disord:[40,72,433],disp:[],dispar:445,disperion:[399,422],dispers:[3,6,7,9,170,289,365,366,390,399,422,427,435,444,463,469],displac:[],displace_atom:[],displace_box:61,displacemet:484,displai:[11,13,22,37,45,56,180,191,196,199,350,359,393,461],dispters:3,disregard:433,dissip:[6,9,41,84,85,234,240,247,289,311,332,333,388,400,401,402,410,427,428,461],dissolut:221,dist:[6,71,95,114,123,196,290,306,403,460,476,508],distanc:[],distinct:[6,230,304,365,445],distinguish:[6,90,146,253,406,480],distort:[170,381],distrbut:381,distribut:[],distro:[117,393,440,441],ditto:[8,12,14,15,16,17,18,43,121,222,473,479],div:8,divd:123,diverg:[3,12,40,307,333,483,502,509],divid:[3,6,16,42,95,118,123,132,134,147,169,170,180,191,200,212,213,215,220,226,288,331,338,343,365,373,375,407,444,451,469,490,498,507],divis:[6,250,386,416,426,478,499,507],dl_poli:[6,7],dlambda:166,dlammps_async_imd:244,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,199],dlammps_gzip:[3,12,196,199,334,481,482,486],dlammps_jpeg:[3,12,199],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,199],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,196],dlen:491,dlmp_intel_offload:[9,12,16],dlo:[61,195,226,293],dlopen:6,dlvo:[7,394,472],dm_lb:250,dmax:[323,371],dmpvtk:197,dmpvtp:197,dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,41,43,56,59,61,65,68,70,77,91,94,98,107,109,110,111,113,115,117,118,120,123,125,147,150,151,152,165,167,169,172,173,174,180,191,195,196,197,198,199,200,201,203,204,205,210,211,212,213,214,215,216,217,218,227,239,247,248,258,263,264,269,270,271,275,282,283,284,285,286,293,296,307,320,323,326,327,328,337,341,344,346,348,350,359,364,373,374,375,380,381,382,385,393,395,396,404,405,407,412,413,415,416,430,431,432,435,437,440,441,442,452,461,462,464,466,468,469,479,481,482,483,484,486,489,490,491,498,499,507,508,509,510],docuement:445,dodd:43,dodgerblu:200,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,40,42,43,51,55,57,61,64,65,69,72,73,74,91,92,95,109,116,122,123,124,148,150,152,154,155,160,162,166,171,172,173,174,176,178,180,185,191,192,195,196,197,198,199,200,203,209,210,212,216,219,220,222,223,224,226,230,232,235,236,239,240,243,245,247,248,250,253,259,263,264,265,266,267,269,270,271,282,283,284,285,286,294,295,296,300,302,305,307,323,326,328,330,331,335,338,339,340,343,344,345,346,351,352,353,355,356,358,364,365,366,367,368,374,375,376,381,382,383,384,385,386,388,390,391,392,394,395,396,397,399,400,403,404,405,406,408,409,410,411,413,414,415,416,417,420,421,423,424,425,427,428,430,431,432,433,435,441,442,443,444,445,447,448,449,450,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,468,469,471,472,473,476,477,478,479,481,482,483,484,485,488,489,491,492,493,494,495,498,499,502,507,511],doegenomestolif:7,doesn:[3,7,8,12,172,196,197,210,216,217,320,374,376,380,382,395,405,415,443,444,462,464,465,466,469,481,483],dof:[3,8,118,150,151,152,165,212,307,508],dof_per_atom:[152,212],dof_per_chunk:[152,212],doff:[374,481],doi:[6,225],domain:[3,6,7,12,13,18,40,42,43,60,63,64,73,124,161,171,174,195,198,199,200,203,210,220,224,226,227,243,246,250,263,264,290,302,307,311,335,340,341,365,366,375,380,403,435,476,478,481,485,498],domin:[1,406,495],don:[0,8,12,13,122,175,206,232,248,296,344,430,451,479,481],donadio:327,done:[1,3,6,7,8,9,12,14,15,16,17,18,38,40,42,57,61,64,73,166,169,172,175,192,196,199,200,209,210,212,214,215,216,217,218,220,221,222,223,224,226,227,235,237,239,244,245,247,248,255,263,269,270,271,282,283,284,286,287,289,290,291,293,296,304,307,308,310,323,326,327,328,330,332,333,346,348,364,365,366,373,375,376,379,380,382,390,404,413,414,415,422,428,429,430,435,443,460,463,468,476,477,478,479,482,485,486,489,499,500,502,507,508],donor:412,dot:[147,168,206,232,242,262],doti:[386,441],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,40,91,226,237,295,344,348,364,366,379,380,386,407,411,433,443,444,477,481,485,489,494,507,508],dover:209,down:[3,6,7,8,11,40,73,224,239,247,323,339,380,406,435,451,480,500],downhil:[371,372],download:[5,7,8,11,12,13,17,244,414,442],downsid:6,downward:304,dozen:[8,12,113,203,443,444],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:256,dpdtheta:[41,84,85,402],dpdtheta_i:[234,235],dproduct:383,dr_ewald:[124,308],drag:[],dragforc:250,drai:[261,297],drain:[243,339,373],dramat:[61,195,221,222,223,224,226,263,323,326,327,366,380,435,451,478],drautz:386,draw:199,drawback:296,drawn:[43,196,199,200,240,476],drayleigh:[261,297],dreid:[],drfourth:110,drho:[119,381,404],drift:[6,108,110,240,241,247,248,259,305,323,490,498,502],drive:[11,12,207,224,226,242,263,288,294,307,342,375],driven:[6,184],driver:[6,12,14,15,203,237,244],drop:[3,200,400],droplet:413,drsquar:110,drude:[],dry:236,dsecriptor:414,dsf:[],dsmc:[],dstyle:293,dt_collis:250,dt_lb:250,dt_md:250,dt_srd:323,dtilt:[61,226],dtneb:495,dtqm:297,dtype:[121,222],dual:[16,17,323,380],dudarev:171,due:[1,3,6,9,10,12,16,17,19,41,55,59,60,63,68,72,73,76,77,83,90,92,93,94,98,107,108,109,110,111,116,122,124,132,146,147,149,150,151,153,155,158,159,160,161,162,164,165,167,171,172,175,176,196,197,199,203,206,207,215,219,221,222,223,224,225,226,227,232,233,236,237,240,241,244,245,247,248,249,250,253,254,255,259,260,261,262,263,268,277,288,291,293,305,306,307,309,320,322,323,324,326,327,328,329,330,332,333,335,339,340,342,343,344,346,366,371,373,375,376,377,397,400,401,402,404,408,409,413,427,428,435,441,443,445,446,460,463,464,466,470,472,473,476,478,481,482,483,490,495,498,499,500,502,507,508],duffi:335,duin:[9,298,303,443,444],duke:366,dummi:[12,29,465],dump0:197,dump10000:197,dump1:486,dump20000:197,dump2:486,dump2vtk_tri:140,dump:[],dump_0:197,dump_1:197,dump_atom:8,dump_custom:8,dump_h5md:198,dump_modifi:[],dump_p:197,dumpcustom:8,dumptimestep:486,dunbrack:[6,20,178,391,493],dunweg:[247,249],duplic:[2,3,14,15,17,42,43,173,197,220,241,288,481,506],dupont:[5,7,13],durat:[37,56,149,150,151,153,154,155,157,158,159,160,161,164,165,191,200,212,239,302,335,359,410,461],dure:[2,3,6,8,9,12,16,17,38,40,42,57,73,91,132,134,148,154,173,176,192,196,197,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,228,231,232,233,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,259,260,262,263,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,312,316,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,366,373,375,379,380,400,426,433,435,444,463,476,477,479,481,484,486,488,489,491,493,495,496,499,500,507,510,511],dvector:8,dvlo:472,dvx:6,dx_lb:250,dy3:171,dyamic:12,dyanam:6,dyanmic:495,dynam:[],dynamo:[5,381,404,430],dyne:506,dyre:423,dysam:484,e28637:29,e_1:386,e_2:386,e_b:407,e_data:197,e_e:406,e_hbond:412,e_i:[6,386,407],e_j:[6,386],e_k:[386,406],e_kl:6,e_lj:[382,399],e_n:[386,406],e_nn:406,e_pr:406,e_rebo:382,e_tors:382,e_tot:433,e_vol:433,eaa:349,eaat:179,each:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,42,43,44,46,47,48,49,50,51,52,54,55,56,57,59,61,63,64,65,66,68,69,70,72,73,74,75,76,77,78,79,80,82,83,85,87,89,91,93,94,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,115,116,117,118,119,120,121,122,123,124,125,126,140,146,147,148,150,151,152,153,154,155,156,159,160,161,162,164,165,166,167,168,169,170,171,172,175,176,178,179,180,181,182,183,184,185,186,187,189,190,191,192,195,196,197,198,199,200,201,202,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,235,236,237,239,240,241,242,243,244,245,246,247,248,249,250,251,253,254,255,256,257,259,260,261,262,263,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,298,299,300,302,304,307,308,309,310,311,312,316,317,319,320,321,322,323,324,325,326,327,328,330,333,334,335,336,337,338,339,340,341,343,344,345,346,348,349,351,352,353,354,355,356,358,359,360,364,365,366,368,372,373,374,375,376,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,413,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,433,434,435,436,437,438,440,441,443,444,445,446,447,451,452,453,454,455,456,457,458,459,460,461,462,463,466,467,468,469,470,471,472,473,474,475,476,478,479,481,482,483,484,485,486,488,489,490,491,493,495,496,498,499,500,501,502,506,507,508,509,511],eacn:[42,220],eam0d:289,eam3d:289,eam:[],eam_databas:13,eam_gener:13,eangl:499,earli:[42,212,215,216,217,218,220,301,308],earlier:[7,8,12,61,200,375,410,430,435,495],earliest:495,earth:406,easi:[6,7,8,9,11,13,91,147,196,204,205,206,207,216,219,232,242,243,245,247,248,309,317,326,327,328,340,343,345,374,481,484,489,491,508],easier:[8,9,13,16,196,197,199,289],easili:[8,11,199,200,339,375,478,488,497,507],eastwood:[365,366],eat:179,eatom:346,eaxmpl:6,eba:21,ebb13:179,ebb:21,ebond:[230,248,498,499],ebt:179,ec_ii:430,ec_ij:430,ec_jj:430,echo:[],eco:[443,444],ecoa:[443,444],ecoul:[113,230,248,443,444,499],ecp:[406,481],edg:[2,3,6,42,43,61,73,124,170,171,174,175,198,199,208,216,245,309,340,343,344,345,346,368,481,484,491],edge_histo:170,edge_threshold:170,edih:499,edim:331,edip:[],edit:[3,8,12,13,14,15,16,17,18,19,502],editor:13,edu:[7,9,11,13,404,427,440,443,444],edward:[9,17],eebt:179,eff:[],effect:[1,2,3,6,8,9,11,12,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,44,46,47,48,49,50,52,54,55,57,68,73,76,77,83,93,94,98,108,109,110,111,115,118,147,149,154,159,160,167,170,176,178,179,181,182,183,184,186,187,189,190,191,192,195,196,197,199,200,204,205,206,209,210,213,217,218,219,221,222,223,224,226,227,233,235,238,239,240,241,242,243,244,245,247,248,262,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,287,288,290,293,294,296,297,298,299,302,306,307,309,310,322,323,326,327,328,330,331,333,335,338,339,340,341,342,343,344,345,346,349,351,352,354,355,358,360,365,366,368,372,373,374,375,376,381,382,384,386,387,388,389,390,391,392,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,433,435,436,437,438,440,445,446,447,449,451,453,461,462,463,464,465,466,468,469,471,472,473,476,478,479,483,484,486,490,491,493,499,500,506,507,509],efffect:485,efficaci:40,effici:[0,1,3,6,7,8,9,10,12,15,17,18,40,60,63,69,118,148,196,197,198,199,200,213,214,224,226,230,241,263,290,292,293,302,307,310,323,365,366,371,376,380,386,394,396,413,418,422,433,445,463,488,511],effort:[5,7,482],efftemp:[101,102,158],efi:[443,444],efield:[],eflux:243,eforc:197,eggebrecht:[396,451],ehb:[443,444],eigensolv:3,eigenvalu:[289,290,365],eigtol:3,eik:166,eim:[],eimp:499,einstein:[302,333],either:[1,2,3,4,6,8,9,11,12,14,15,16,17,22,33,42,45,51,61,65,73,108,113,119,122,124,146,147,152,154,155,170,171,172,175,180,185,192,196,197,198,199,200,203,211,213,215,217,218,220,223,224,225,226,227,239,245,246,250,254,260,261,263,264,268,284,288,304,307,309,310,312,320,323,330,337,341,344,348,350,363,365,366,368,372,373,377,380,386,388,394,404,413,414,416,427,428,430,433,435,439,441,460,464,466,468,476,479,481,483,484,485,488,490,493,496,498,507],ejtehadi:[394,409,445],elaplong:[204,205,245,484,499,507],elaps:[3,195,204,205,206,207,219,226,232,242,243,245,247,248,260,293,309,317,326,327,328,340,341,343,345,453,476,484,486,487,491,495,499,507],elast:[],elastic_t:4,elba:29,electr:[6,203,209,232,248,365,366,407,443,444,473,502,506],electrolyt:[9,472],electron:[3,6,7,9,13,41,101,102,119,124,156,158,163,197,203,209,229,230,248,249,264,276,285,300,329,335,372,374,381,383,395,399,404,406,407,430,433,441,442,451,466,469,473,481,501,502,506],electron_integr:209,electron_temperatur:209,electron_unit:406,electroneg:[6,298,299,300,395,407,451],electroneg_compon:451,electronic_dens:3,electronic_specific_heat:3,electronic_thermal_conduct:3,electrostat:[6,9,16,18,210,239,298,300,301,336,365,366,394,399,406,418,426,428,444,451,472],eleftheri:307,elem1:[407,430,452],elem2:[407,430,452],elem:451,element1:[304,381,404,451],element2:[304,381,404,451],element:[3,6,7,8,12,13,43,65,83,93,108,110,118,123,125,140,146,147,148,149,150,151,152,153,154,155,159,160,161,162,164,165,168,196,197,198,199,200,201,203,209,213,215,218,289,304,330,337,381,382,386,395,404,405,406,407,413,414,415,430,431,432,433,437,441,442,443,444,451,452,462,464,465,466,469,502,507,510],elementn:[381,404],elementset:209,elev:495,elif:[146,348],elig:[3,210,221,222,236,239,412],elimin:[3,6,73,170,240,247,248,307,310,332,333,476],elj:399,ellad:9,elliot:9,elliott:9,ellips:[4,6,9,73,86,150,194],ellipsoid:[3,4,6,7,9,13,41,43,73,86,119,136,150,172,194,195,196,197,247,260,265,269,273,274,282,307,323,370,373,409,428,445,461,481,491,509],ellipsoidflag:481,elong:[230,248,499],elp:[443,444],els:[3,7,8,12,73,113,122,123,125,198,199,211,212,213,215,216,217,218,239,263,307,323,335,336,337,346,348,365,413,480,492,507,510],elsewher:[8,260,323,430,442,443,444,493,499,507],elt:430,emac:[],email:[0,3,5,7,8,9,11,407],emb:[3,9,344],emb_lin_neg:430,embed:[3,5,7,11,12,13,29,92,148,170,335,381,404,407,426,430,431,432,441,461,470,479],embt:179,emi:[7,9],emil:9,emol:[443,444,499],emphas:410,empir:[209,327,382,406],emploi:[9,289,298,302,465],empti:[3,59,73,170,174,307,365,376,417,481,492,493,507],enabl:[3,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,40,41,44,46,47,48,49,50,51,52,54,55,56,57,62,63,64,66,69,80,82,87,91,101,102,103,104,105,106,110,115,117,118,124,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,154,156,158,159,163,164,166,170,171,178,179,181,182,183,184,185,186,187,189,190,191,192,196,197,198,200,201,203,204,205,206,207,208,210,214,217,219,221,222,223,225,226,227,232,233,236,237,238,239,240,241,242,244,245,246,247,248,249,250,251,252,253,254,256,257,259,261,263,264,265,266,267,268,269,270,271,272,273,274,275,276,278,280,281,282,283,284,285,286,288,289,290,292,293,297,298,299,300,301,302,303,304,306,307,309,310,312,313,314,315,316,317,319,320,322,323,326,328,329,330,331,332,333,335,336,338,339,340,341,342,343,344,347,349,351,352,354,355,356,358,359,360,366,373,375,379,380,381,382,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,435,436,437,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,479,482,483,484,488,490,500,507,511],enclos:[2,6,12,174,196,295,348,430,451,477,479,489,507],encod:[13,40,43,196,199,200,296,413],encompass:[3,6,41,43,59,61,122,173,319,337,461,484],encount:[3,8,12,61,112,215,379,486,507],encourag:[7,8,301,321],end12i:119,end12x:119,end12z:119,end1i:119,end1x:119,end1z:119,end2i:119,end2x:119,end2z:119,end:[1,2,3,5,6,8,11,12,15,16,17,18,19,38,41,42,43,59,61,73,119,175,176,179,195,196,197,199,200,201,204,205,213,215,217,218,223,226,240,245,247,249,262,263,264,277,294,306,307,312,323,326,327,328,329,331,334,335,338,342,345,346,364,365,374,375,379,380,400,404,409,416,429,433,445,448,450,452,453,470,476,479,481,482,483,484,486,488,489,493,497,499,502,507,511],end_of_step:8,endbondtors:[3,179,185,481],endif:8,energet:[223,382,444],energi:[],energy_compon:451,energy_update_freq:444,enforc:[6,59,60,109,195,196,197,198,199,201,203,210,223,226,263,287,289,299,307,310,348,365,418,478,507,508],enforce2d:[],eng:[11,67,71,114,196,237,346,348,395,432],eng_previ:348,engil:9,engilitycorp:9,engin:[209,226,292,312,332,404,431],engr:[443,444],enhanc:[205,209,476],enlarg:[61,199],enough:[3,41,63,90,172,173,175,176,220,248,293,297,302,307,336,340,341,344,376,380,396,439,481,485,486],enpub:404,enrti:[],ensembl:[],ensight:6,ensur:[3,6,146,196,197,210,214,224,239,240,263,313,334,366,386,403,426,462,469],enter:[59,162,407,433,469,495],enthalpi:[129,265,266,267,404,498,499,507],entir:[0,2,3,6,11,14,15,42,43,65,84,85,92,115,116,118,122,124,147,152,171,172,200,203,204,205,212,216,217,220,223,225,236,239,240,243,247,248,259,263,265,266,267,268,269,270,271,288,290,292,305,307,321,335,337,348,380,399,422,435,463,481,489,490],entireti:468,entiti:[6,8,41,43,196,307],entri:[3,8,12,38,43,57,67,71,81,97,114,121,124,133,136,137,138,139,140,142,143,144,170,192,197,200,215,216,217,225,235,297,346,374,386,405,430,437,444,452,462,463,464,465,466,469,507],entropi:495,entry1:[38,57,200,393,463],entry2:200,entryn:200,enumer:[173,196,474],enumuer:6,env:380,environ:[1,3,6,11,12,16,17,18,199,241,246,288,380,381,386,393,395,405,406,441,464,478,492,507],epair:[113,200,408,412,443,444,499],epen:[443,444],epfl:[241,246],epp:399,epq:399,eps0:472,eps14:426,epsilon0:466,epsilon:[3,6,36,46,47,51,54,55,91,178,204,205,239,307,323,340,344,371,373,385,391,392,394,396,397,398,399,409,411,412,413,416,417,418,419,420,421,422,423,424,425,426,429,434,438,445,446,456,462,468,471,472,490,502,506],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:[2,3,6,8,11,12,17,40,42,55,65,67,70,71,73,78,81,90,91,95,97,114,116,121,123,125,147,150,166,168,170,172,195,199,200,203,204,205,206,207,210,213,214,215,218,219,220,224,226,227,232,239,240,242,243,245,247,248,250,253,254,260,261,268,279,288,290,293,295,297,298,299,302,304,306,307,309,312,317,319,326,327,328,331,332,333,335,337,338,340,343,345,346,348,364,368,373,375,376,377,379,380,395,400,402,408,409,412,416,427,433,434,441,443,444,445,447,448,449,451,452,453,463,468,469,473,477,478,479,481,483,484,488,489,492,495,497,499,507,508],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:[3,298,369,488,511],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:506,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:506,esub:430,eta:[6,250,263,297,298,300,339,405,407,409,441,465,469,506],eta_dot:263,eta_ij:441,eta_ji:407,etag:[41,481],etail:499,etap:263,etap_dot:263,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,40,41,43,55,63,70,93,94,95,99,115,116,119,121,147,149,152,153,154,155,156,158,159,160,161,162,164,166,172,174,175,176,185,196,197,199,200,203,204,209,210,211,212,215,216,217,218,221,222,226,227,237,239,240,247,263,293,304,308,335,336,344,348,364,365,373,374,375,376,378,404,405,413,426,428,433,439,443,444,462,464,466,469,476,479,481,482,483,488,490,491,495,496,497,498,499,500,502,506,507,509,511],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:[2,3,9,11,12,38,57,73,91,92,95,113,123,146,148,152,162,170,172,195,196,197,199,200,204,205,206,207,209,211,212,213,214,215,216,217,218,219,226,232,240,242,243,245,246,247,248,289,295,298,309,313,317,326,327,328,337,340,343,345,346,348,365,366,371,373,380,433,435,441,447,449,451,463,476,477,479,483,484,486,488,489,490,491,495,497,499,507,508],evalut:[348,479],evan:[160,284],evanseck:[6,20,178,391,493],evapor:[],evaul:[8,373],evdwl:[113,443,444,499],even:[3,6,8,12,15,17,18,34,40,42,53,59,61,63,65,72,73,125,170,173,174,188,192,196,197,200,203,204,205,210,211,212,215,216,217,218,220,221,222,224,226,227,230,245,248,261,263,264,289,293,302,304,307,308,319,323,331,335,338,340,344,346,357,365,371,373,375,380,385,406,407,410,413,416,435,445,469,470,474,481,482,484,486,487,488,490,491,493,496,498,499,500,502,511],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:[0,1,2,3,6,8,9,11,12,15,16,40,42,73,74,95,119,125,134,160,175,196,197,198,199,200,201,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,231,236,237,239,241,243,244,245,250,251,259,263,264,268,287,288,289,293,294,295,296,297,298,299,300,302,304,305,307,308,310,312,323,325,326,327,328,329,330,331,334,335,336,337,338,346,348,364,366,375,376,377,380,400,403,413,426,443,444,451,457,475,476,477,481,483,485,486,488,489,490,495,496,497,499,507,511],everyth:[8,113],everywher:[122,420],eviri:406,evolut:[241,250,290,476],evolv:[250,290,336],ewald:[2,3,5,6,7,8,12,92,116,124,147,336,365,366,373,387,389,390,396,399,406,418,422,438,446,461,463],ewald_disp:399,ewalddisp:3,exact:[22,42,45,73,128,166,175,180,220,223,240,241,247,248,249,293,302,303,323,335,350,365,393,483,488,495,507,509,511],exactli:[3,6,12,14,17,38,42,43,57,61,73,74,95,122,150,156,163,172,192,204,205,215,220,226,231,235,240,247,248,249,264,276,277,285,289,297,323,328,329,342,380,393,400,404,410,413,427,435,463,483,484,491,495,507],exager:502,examin:[6,8,9,17,223,289],examp:[479,507],exampl:[],exce:[3,6,16,17,18,42,60,73,174,211,212,215,216,217,218,220,224,226,231,236,263,289,304,308,314,315,323,373,380,481,507],exceed:[3,42,61,220,226,263,323,489],excel:406,except:[1,2,5,6,8,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,61,62,65,73,93,94,114,115,118,123,147,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,172,176,178,179,180,181,182,183,184,186,187,189,190,191,192,195,196,197,200,203,206,212,213,215,219,220,224,226,233,238,239,242,245,247,249,263,264,265,266,267,268,269,270,271,272,273,276,277,280,282,283,284,285,286,290,299,300,307,309,310,320,323,326,328,329,335,339,343,346,347,348,349,350,351,352,354,355,358,359,360,365,366,368,370,374,375,376,378,379,380,381,382,384,387,388,389,390,391,392,393,394,395,396,398,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,431,436,437,438,440,443,444,445,446,453,461,462,463,464,465,466,469,471,472,473,476,478,479,481,483,484,486,489,490,491,492,493,495,499,502,506,507,508,510],excess:[214,406],exchang:[2,3,6,8,9,63,64,203,209,210,239,247,299,307,331,335,338,365,380,406,496],exchange:365,excit:[9,406],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:[1,3,9,12,16,91,380,395,433,435,490,500],excurs:[263,476],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,62,173,199,244,301,348,364,367,379,477,479,489,492,495,507],exempl:451,exemplari:240,exemplifi:406,exert:[6,245,248,302,342,343,344,366],exhaust:[209,379,507],exhibit:[96,263,372,406,490],exist:[3,6,7,8,11,12,13,16,37,56,61,70,72,128,172,173,191,198,199,200,203,208,219,222,224,227,239,292,293,295,346,347,349,351,352,353,355,359,369,374,380,401,402,413,443,460,470,477,479,481,482,483,492,493,494,507,508,509],exit:[2,3,11,12,42,59,196,220,235,364,379,479,480,489,498,507],exlanatori:3,exp:[],expand:[],expans:[12,146,196,492,507],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,73,107,153,164,170,192,220,232,239,241,260,288,294,296,297,302,307,346,366,376,393,430,433,435,476,479,481,483,486,490,495,507],expens:[6,10,73,200,288,292,307,335,346,365,366,376,380,479],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:[1,3,6,8,11,12,16,18,42,61,65,67,70,71,73,74,75,78,79,81,90,97,152,160,192,196,197,199,200,203,212,213,218,220,222,224,226,263,288,296,307,320,346,348,364,365,368,374,375,379,385,404,416,451,453,468,479,482,483,486,488,491,502,507,511],explan:[3,6,61,119,146,196,197,212,262,288,413,475,478,479,481,490],explanatori:[3,8,123,196,197,211,212,215,216,217,307,374,478,507],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],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],explictli:[16,494],exploit:[9,15,17,290],explor:[124,171],expon:[3,298,300,404,409,412,426,434,446],exponenti:[91,441,462,469,473,495,507],expos:11,exposit:[209,400,403],express:[6,146,158,172,204,205,224,260,288,298,335,341,348,386,404,406,420,430,451,452,461,507],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:[3,6,8,11,12,16,17,41,42,47,63,73,107,115,116,118,124,147,149,150,151,153,155,158,159,160,161,162,164,165,171,172,173,174,178,200,215,220,222,263,295,296,297,307,323,373,374,377,378,399,410,413,416,430,435,478,479,481,484,493,502,507],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_harm:333,f_i:[29,441],f_id:[6,73,123,125,196,197,203,211,212,213,214,215,216,217,218,258,325,337,499,507],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:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,59,60,61,74,91,95,107,114,121,122,124,146,166,171,174,178,189,195,196,199,200,204,205,213,220,224,226,227,239,244,247,249,250,261,263,264,268,290,294,298,306,310,313,315,323,327,331,338,339,340,344,355,366,368,374,380,382,383,386,387,389,391,396,397,398,400,401,402,406,410,413,417,418,430,433,435,437,438,444,446,453,462,467,478,481,484,485,490,493,495,496,499,502,506,507],factori:[3,479],factoriz:365,fail:[3,11,12,61,176,224,227,365,373,375,398,444,479],failur:[127,448,480,507],fairli:[11,435,490,495],faken:75,falcon:244,fall:[3,6,200,215,293,479,507],fals:[90,346,348,451,507],fame:8,famili:[469,478],familiar:[0,11],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:[6,8,42,73,172,200,203,204,205,210,216,220,222,227,239,241,245,260,261,263,265,266,267,268,269,270,271,279,282,283,284,285,286,296,297,299,307,312,316,322,325,333,335,339,340,341,343,345,375,413,427,484,493,507,510],fasolino:415,fast:[6,7,9,12,13,17,40,196,197,274,297,336,365,366,388,427,428,433,461,463,483,488,490,499,508,511],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,63,65,110,115,118,149,159,178,179,181,182,183,184,186,187,189,190,192,196,197,200,206,219,220,226,233,238,242,246,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,294,298,299,307,309,310,323,326,328,330,332,335,339,343,349,351,352,354,355,358,360,365,366,377,378,380,381,382,384,386,387,388,389,390,391,392,393,394,395,396,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,436,437,438,440,445,446,453,461,462,463,464,465,466,469,471,472,473,476,484,490,494,502],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:[279,507],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:506,fene:[],fennel:[396,418],fep:[],ferguson:[6,178,493],fermi:[1,9,12,15,158,380,466],fermion:[9,406],fernando:429,ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,18,40,65,201,211,212,213,215,216,217,218,248,263,293,296,298,310,337,365,373,374,375,382,451,478,481,486,490,492,500,507,509],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:[1,3,7,11,12,14,15,92,115,116,147,289,365,366,490],fft_inc:[12,366],fft_lib:12,fft_path:12,fftbench:[365,500],fftw2:12,fftw3:12,fftw: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],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:[3,12,13,38,42,57,192,196,197,199,200,201,209,212,213,214,215,216,217,218,220,225,235,288,292,295,298,299,300,303,304,307,308,334,335,362,363,364,374,375,381,382,386,396,404,405,407,415,430,431,432,437,441,442,443,444,451,452,462,463,464,465,466,469,477,478,479,482,483,488,492,499,507,509,510,511],filennam:488,filep:[3,196,197,200,483,488,511],filepo:304,fill:[7,9,172,199,293,335,368,376,386,433,444,484],filter:[200,209],final_integr:8,final_integrate_respa:8,finchham:[6,154,398],find:[0,3,4,6,7,8,11,12,13,14,16,38,40,57,63,73,75,91,123,175,192,201,210,223,224,235,236,239,262,288,293,294,302,306,371,373,375,376,396,413,418,422,430,451,461,463,502,507],find_custom:8,fine:[16,17,176,206,232,333,376,380,507],finer:[146,172,507],finest:365,finger:[172,195,260,484],finish:[6,11,42,220,348,362,364,365,377,379,380,468,486,507,508],finit:[],finni:[7,404,461],finvers:230,fiorin:[9,225],fire:[],firebrick:200,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,59,61,63,64,73,83,92,95,108,109,110,112,118,122,123,133,136,139,140,144,147,157,160,166,168,170,171,173,174,175,179,192,196,197,198,199,200,201,203,204,212,213,215,216,217,218,220,223,226,235,239,240,245,250,260,261,262,263,288,290,295,296,297,299,304,307,310,312,320,321,323,324,325,332,333,334,335,337,341,346,348,349,356,368,373,374,375,376,379,380,381,382,385,386,387,389,391,393,395,396,404,406,407,410,411,413,414,415,416,417,418,422,427,428,430,432,433,435,437,441,443,444,451,452,460,462,463,464,465,466,469,473,476,477,478,479,481,482,483,486,488,490,493,494,495,498,499,502,507,508,509,511],fischer:[6,9,19,20,178,391,493],fit:[3,6,9,12,38,57,192,235,306,323,382,386,415,430,435,456,463,465,489,507],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_modifi:[],fix_mov:[195,341],fix_nh:8,fix_npt:241,fix_nvt:[210,239],fix_poem:[3,6],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:[3,8,9,11,12,14,15,16,17,41,68,76,77,83,90,93,94,98,108,109,111,124,167,171,175,196,197,199,200,201,218,223,225,229,244,247,251,253,259,260,289,296,307,320,322,323,330,334,343,346,363,366,374,378,379,380,382,412,417,430,433,460,476,478,479,481,482,483,485,486,487,491,507],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:[340,388,427,428],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:507,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:[2,200,247,248,260,263,294,307,326,327,490,501,506,508],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:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,61,65,66,72,73,75,84,95,96,101,102,112,119,122,123,125,146,147,150,151,152,158,160,165,168,170,172,173,178,181,182,183,184,186,187,189,190,192,196,198,199,200,203,209,210,211,212,213,214,215,216,217,218,220,225,226,227,230,231,234,235,237,239,240,241,244,246,247,248,250,253,261,263,268,269,270,271,282,283,284,286,289,290,292,295,296,297,298,300,302,304,306,307,308,310,325,326,327,328,331,332,333,334,335,337,338,346,347,351,352,353,354,355,358,360,363,368,370,373,374,375,380,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,435,436,437,438,440,441,442,443,444,445,446,448,450,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,468,469,471,472,473,474,476,478,479,481,482,484,486,488,489,490,493,495,496,497,502,507,508,510],foo:[4,8,11,12,196,199,237,479,492,507],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:[2,3,6,8,12,19,22,45,55,65,68,76,77,79,83,91,93,94,96,98,108,109,111,122,146,147,166,167,176,180,200,203,204,205,222,240,241,247,249,253,260,284,289,300,302,306,307,335,340,344,349,350,353,358,370,372,374,375,382,383,386,393,401,402,404,406,408,412,413,417,429,430,432,433,437,438,441,443,444,445,451,452,453,461,463,464,465,466,472,475,478,479,481,486,491,498,502,507],formal:[6,80,82,95,240,241,247,263,290,323,331,451],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,70,79,180,192,196,197,198,199,200,201,212,215,216,217,218,220,222,235,289,292,296,298,300,303,307,308,319,334,335,346,347,350,370,374,375,381,382,386,393,404,407,417,430,432,442,443,444,446,452,463,469,470,478,479,481,482,483,486,497,498,499,507,509],former:[6,12,16,40,42,200,220,335,339,386,388,487,493,507],formerli:[7,13],formul:[1,41,66,147,206,232,247,263,284,298,300,306,310,334,365,382,386,404,406,409,430,440],formula:[2,3,6,7,13,21,22,37,45,55,56,72,75,91,93,94,95,99,101,102,111,118,124,147,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,171,172,177,179,180,191,195,196,204,205,206,207,212,213,214,215,218,219,226,232,242,243,245,247,248,260,288,289,295,304,309,317,321,323,326,327,328,337,340,343,345,346,348,349,350,352,359,368,374,382,383,385,386,391,392,393,394,399,400,404,405,409,410,411,412,414,417,418,420,421,422,424,425,427,428,430,434,435,436,445,446,453,461,462,463,464,465,466,469,471,472,477,481,484,491,498,499,506,507,508],forth:[1,6,11,12,13,14,15,379,479,484,488],fortran:[3,6,9,11,12,13,237,404,413,430,443,444],fortun:8,forward:[3,8,91,364,375,380],foster:[386,440,441],foul:175,found:[3,6,9,12,75,166,196,223,225,239,244,250,289,330,336,348,364,376,393,396,399,476,482,483,498],four:[6,11,55,83,108,109,146,168,261,335,358,374,375,433,476],fourier:[],fourth:[6,110,306,320,330,391,437,451],fox:[6,124,178,459,493],fphi:[38,57,463],fpic:12,fplo:[38,57,463],fprime:463,fqdn:246,fqq:399,frac:[],fraction:[1,3,6,8,12,16,40,42,82,115,147,175,195,199,200,210,221,222,223,224,261,293,297,304,305,323,328,329,368,375,380,386,388,410,427,428,486,491],fragment:[43,244,304],fraig:43,frame:[87,146,200,209,261,297,342,409],framer:[199,200],framework:[5,241,381,452],franc:9,fraunhof:9,free:[5,6,7,9,13,29,62,65,72,91,166,205,288,323,332,333,334,335,372,375,383,406,426,433,441,472,478],freedom:[3,6,8,99,101,102,104,106,107,118,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,212,223,230,239,241,247,248,253,263,264,268,269,270,271,282,283,284,286,290,292,307,310,326,327,328,333,373,399,499,502,508],freeli:[0,6,7,12,150,151,165,170,199],freez:[],frenkel:[239,333],freq:208,frequenc:[3,6,16,40,108,200,214,277,289,290,297,302,363,400,406,444,451,476,490,495,507,510],frequent:[3,66,69,72,74,75,79,92,96,112,146,200,221,222,236,331,338,435,488],fri:[261,297],friction:[4,5,6,10,43,203,241,247,297,302,307,335,339,341,410,491],friedrich:313,from:[],front:[261,297,342],frontend:[199,301],frozen:[6,118,176,238,240,248,376,408],fs2:[6,95],fscale:244,fstr:507,fstring:479,ftol:[373,375,476,495],fuchsia:200,fuction:396,fudg:310,fugac:239,fugacity_coeff:239,fulfil:6,full:[1,2,3,6,9,12,17,38,40,41,95,199,213,214,225,250,288,365,366,380,386,404,406,407,409,467,481,483,488,489,493,495,500,502,510],full_energi:[3,239],fuller:373,fulli:[3,6,9,80,241,246,288,373,375,396,441,442,481,509],fulton:404,fumi:387,func:[479,507],funcfl:404,functino:[],functionaliri:225,fund:[0,7],fundament:[323,506],funnel_flow:319,funrol:433,further:[3,6,8,12,13,63,65,73,90,110,113,122,199,200,203,212,215,216,217,218,221,227,231,250,254,290,298,308,311,313,323,335,337,346,366,371,373,374,375,376,381,385,395,433,451,476,495,496,507],furthermor:[27,181,402,406],furthest:63,futher:3,futur:[],g_ewald:3,g_ewald_6:3,g_ewald_disp:3,g_jik:441,g_p:335,ga3:171,gaa:386,gahler:372,gai:[3,409,461],gain:330,gainsboro:200,galindo:434,game:244,gamma0:29,gamma:[3,6,29,247,250,254,289,297,298,300,302,339,400,402,405,409,430,434,455,458,459,462,464,466,469,499],gamma_:[3,335,341],gamma_ijk:464,gamma_n:[341,410],gamma_p:[3,335],gamma_t:[341,410],gammaa:434,gammafactor:250,gammar:434,gan:[441,462,464,466,469],gan_sw:441,gan_tersoff:441,ganzenmuel:[7,9],ganzenmul:9,gao:[6,20,178,391,493],gap:[192,427,428,442,452],gap_2014_5_8_60_17_10_38_466:442,gap_exampl:442,gaseou:7,gass:239,gather:[11,489],gather_atom:11,gather_scatter_loop_unrol:[9,12],gathert_atom:11,gauch:184,gaug:12,gauss:[],gaussian:[6,41,65,95,108,110,240,241,247,290,306,323,327,345,365,400,403,406,408,442,461,476,507,508],gave:[3,435],gaybern:[],gcc:17,gcmc:[],gcore:230,gd3:171,gdot:428,gdrude:230,ge4:171,gec:[464,466],gen:[263,264],gener:[],genom:7,gentler:[340,343,345],gentli:405,geom:[6,365,403,476,508],geometr:[3,6,7,8,43,59,61,73,162,163,172,174,196,200,206,216,217,219,220,227,232,243,263,269,270,271,282,283,284,286,307,309,317,326,327,328,344,346,365,368,375,385,388,392,394,396,399,406,409,411,418,419,420,421,422,423,424,425,426,427,428,429,434,435,445,453,467,468,471,472,481,484,491,499,507],geometri:[3,6,7,9,13,25,39,42,58,73,160,172,193,216,220,221,222,224,227,245,311,361,368,435,481,484],georg:[7,9],georgia:13,gerber:426,germani:[9,14],germann:[268,420,476,495],germano:409,gerolf:13,get:[],get_natom:[11,479],get_rank:11,get_siz:11,getenv:507,gettimeofdai:12,gewald:[6,365],gezelt:[396,418],gf100:14,gf104:14,gf200:14,gflop:12,gflp:12,ghost:[3,6,7,12,16,60,63,64,75,170,175,176,224,226,248,263,296,307,308,363,365,376,380,400,402,403,406,410,417,474,486,491,502],ghostwhit:200,ghz:10,giacomo:9,gif:[4,199],gifsicl:199,gigabit:18,gillan:452,gingold:[455,456,458],gio:2,git:[7,12],github:[13,17,225,241,246,442],give:[0,1,2,3,5,6,7,8,9,10,11,12,14,15,16,17,18,55,73,96,112,119,152,155,159,172,196,197,200,206,208,212,213,215,218,224,226,241,263,284,288,289,294,302,304,307,337,365,366,373,376,377,380,382,386,403,406,412,413,430,433,435,445,464,465,466,476,478,479,481,491,495,502,508],given:[3,5,6,7,9,10,11,12,16,17,22,27,37,45,56,63,65,66,69,73,112,119,129,130,131,133,134,137,138,139,140,141,142,143,144,145,146,147,166,170,174,180,181,191,192,196,197,198,200,203,210,212,214,216,221,222,224,226,227,231,239,240,241,242,244,250,257,260,262,263,268,287,288,289,290,297,298,304,306,310,319,320,321,323,325,330,335,336,339,340,341,344,350,359,365,366,380,381,382,386,387,389,390,392,393,394,395,396,397,400,401,402,403,404,406,407,409,412,418,419,420,422,430,431,432,433,434,435,437,438,441,445,446,448,450,451,452,461,473,476,479,481,483,484,491,495,506,510,511],gjf:247,gjwagn:7,gko:2,gld:[],gle4md:[241,246],gle:[],glitch:3,glob:492,global:[],glosli:[366,433],glotzer:[307,400],glue:11,gmail:[7,9,13],gmake:[12,17],gmask:[3,507],gnu:[0,7,12,17],gnuplot:[11,13],goal:[5,12,40],goddard:[6,9,25,298,299,300,360,406,412,443,444,493],goe:[12,55,146,172,195,260,316,373,376,399,405,411,420,423,453,473,484,488],gold:[72,200],goldenrod:200,goldman:297,gone:3,good:[1,3,6,12,17,42,75,124,170,171,220,247,261,263,298,304,310,330,365,375,376,381,394,403,404,433,435,463,469,476,490,495,499],googl:244,gordan:146,gordon:6,gould:[6,178,493],gov:[0,7,9,13,381,404,407,506],govern:250,gpl:[0,7,8,12],gpt:[9,433],gpu1:380,gpu:[],gpuid:380,gpun:380,grab:[3,6],gracefulli:3,grad:[6,206,232,262],gradient:[6,7,8,12,13,128,133,224,232,242,243,262,284,299,331,335,371,372,375,428,444,463],gradient_correct:450,graduat:292,graft:223,grai:200,grain:[5,6,7,9,29,36,41,55,69,172,175,184,203,288,292,307,323,411,433,446,490,493],gram:[212,216,217,404,506],grama:[9,300,444],gran:[],grand:[3,203,210,239],granflow:5,granular:[],graph:11,graphen:485,graphic:11,grasp:5,gravit:242,graviti:[],grdient:209,great:[3,13,297],greater:[1,3,10,63,73,90,170,200,224,240,263,288,328,342,380,385,387,389,390,416,435,476,478,481,484,490,495,507,508],greathous:13,greatli:[124,495],green:[2,6,95,136,137,199,200,289,290,331,386],green_kubo:6,greenyellow:200,greffet:302,greg:[7,9],grest:[46,47,223,323,366,390,410,422,493],grew:73,grid:[3,12,42,64,124,160,171,174,197,220,250,302,323,335,336,363,365,366,475,478,481,483,485,490],grigera:6,grime:41,grmask:[3,507],gromac:[],gronbech:[247,365],groot:400,ground:[6,84,85,234,311,406],group1:[154,175,376],group2:[92,148,154,173,175,376],group2ndx:[],group:[],group_id:11,groupbig:323,groupid1:[253,307],groupid2:[253,307],groupid:481,groupnam:376,grouptyp:239,grow:[3,6,8,208,226,227,245,247,263,288,337,410,481,493],grow_arrai:8,grow_reset:8,growth:[6,330],grueneisen:9,gsmooth_factor:430,gstyle:[3,478],gtl:7,gtx285:14,gtx450:14,gtx460:14,gtx470:14,gtx560:14,gtx580:14,guarante:[67,71,81,97,114,121,172,175,196,231,298,364,368,491],guess:[3,196,294,482],gui:[7,11],guid:[1,17,41,80,82,104,105,106,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,203,256,257,313,314,315,316,319,336,440,448,450,454,455,456,457,458,459,491],guidelin:[1,8,14,15,16,17,18,19,365,463],guidlin:17,gullet:430,gulp:6,gumbsch:372,gunnel:433,gunsteren:[294,326,426],gunzenmul:7,gunzip:12,guo:[6,20,178,184,391,493],gwald:3,gyrat:[],gzip:[3,12,196,197,199,200,334,375,481,482,486],h12:409,h2o:[41,374],h5cc:198,h5md1:198,haak:[294,326],had:[3,6,11,13,61,65,196,197,200,201,215,218,223,224,240,241,243,247,248,249,261,263,265,266,267,268,269,270,271,282,283,284,286,293,294,323,326,327,328,335,400,403,410,460,483,487,490,496,499],hafskjold:6,half:[1,3,6,8,9,16,17,40,42,60,61,174,199,211,220,226,247,263,335,340,344,376,380,383,386,394,406,433,447,449,481,483,484,491,502],halfwai:[42,199,200,416],halperin:96,halsei:410,halt:[42,200,220,243,348,498],halv:199,ham:[38,57],hamak:[340,344,394,445],hamilton:72,hamiltonian:[203,241,263,264,327,406,490],hammond:[365,366],han:404,hand:[3,6,19,55,148,172,190,195,199,250,260,368,396,406,481,484,491,494],handl:[3,9,16,199,225,300,380,383,406,427,444,469,479,495],hang:[3,12,478,479],happen:[3,6,8,12,15,18,63,122,176,200,210,213,376,380,479,482,489],happi:8,haptic:244,hara:465,hard:[1,253,300,306,307,403,451,484],harden:[9,453],harder:[340,344,502],hardi:[209,248,365,366,502],hardwar:[1,9,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,115,118,149,159,178,179,181,182,183,184,186,187,189,190,192,206,219,226,233,238,242,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,299,307,309,310,326,328,339,343,349,351,352,354,355,358,360,365,366,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,436,437,438,440,445,446,453,462,463,464,465,466,469,471,472,473,484,494],hardwir:[3,17,341],hardy2:366,harm:383,harmon:[],harmonic_fix_wal:428,harpertown:18,harrison:382,hart:323,hartre:[383,404,406,433,506],hasan:9,hash:[40,481],hassl:306,hat:[6,10,262],have:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,43,44,46,47,48,49,50,52,54,55,57,59,61,65,66,67,68,69,71,72,73,74,75,77,79,83,90,94,95,96,98,108,109,110,111,112,115,118,119,120,121,122,136,146,147,148,149,150,151,152,153,155,159,161,164,165,167,168,169,170,172,173,174,175,176,178,179,181,182,183,184,186,187,189,190,192,195,196,197,198,199,200,201,206,208,210,211,212,213,216,217,218,219,220,221,222,223,224,226,227,232,233,236,238,239,240,241,242,243,244,245,247,248,249,250,253,258,260,261,263,265,266,267,268,269,270,271,272,273,277,280,282,283,284,285,286,288,290,292,293,294,296,297,298,299,302,305,307,309,310,317,319,323,324,326,327,328,329,330,334,335,336,337,339,340,341,342,343,344,345,346,347,348,349,351,352,354,355,356,358,360,365,366,368,371,372,373,374,375,376,377,380,381,382,383,384,386,387,388,389,390,391,392,394,395,396,399,400,401,402,403,404,405,407,408,409,410,411,412,413,414,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,435,436,437,438,440,441,443,444,445,446,450,451,453,462,463,464,465,466,468,469,471,472,473,475,476,478,479,481,482,483,484,485,486,487,488,489,490,491,493,495,496,498,499,500,502,506,507,508,509,510,511],haven:479,hayoun:302,hayr:247,hbcut:443,hbnewflag:443,hbond:[],hbond_cutoff:444,hcp:[66,69,75,368,430],hdf5:[9,198],he1:171,head:[6,21,179,349,408,412,443,444,496],header:[3,6,7,8,12,173,196,199,200,201,212,213,215,216,217,218,261,297,304,308,335,374,381,386,404,460,478,481,491,498],heal:490,heat:[],heatconduct:[],heavi:323,heavili:[42,220],heavisid:335,hecht:323,heenen:9,height:[199,227,293,375,408],heisenberg:9,held:[6,73,323,375,410],helic:184,helium:384,helix:[],hello:479,help:[3,8,12,14,15,16,17,18,19,196,224,226,261,363,386,464,466,509],henc:[1,3,13,20,21,26,32,35,36,72,73,114,152,154,162,179,212,263,300,323,339,340,344,346,349,351,355,358,366,396,408,426,441],henderson:54,hendrik:9,henin:[9,225],henkelman1:[262,375],henkelman2:[262,375],henkelman:[262,372,375],here:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,22,37,41,42,45,56,65,70,71,72,73,124,152,170,171,180,183,191,196,199,200,203,212,220,223,226,239,240,248,250,288,297,300,302,308,335,340,343,345,346,348,350,359,364,373,375,379,380,382,383,386,393,407,409,412,413,417,429,433,441,445,448,450,451,461,463,473,479,483,486,502,507],herist:336,herrmann:323,hertizian:341,hertz:[],hertzian:[6,341,410,461],hertzsch:410,hess:365,hessian:[5,372],heterogen:110,heurist:[336,482],hex:[3,172,368],hexagon:[69,96,430],hexahedron:197,hexat:96,hexord:[],hey:[116,147],hf4:171,hfo:395,hftn:[372,373,375],hg1:171,hg2:171,hgrid:323,hibb:290,hidden:[17,479],hienergi:346,hierarch:[7,490],hierarchi:[366,390,391,418,419,422,429,434,490],higdon:[9,427,428],high:[1,3,6,7,9,12,19,42,112,192,196,199,220,224,231,248,261,331,335,338,366,372,373,380,386,406,409,433,445,463,473,478,490,495,502],higher:[1,14,146,175,200,212,218,221,222,227,245,293,302,330,343,345,373,406,414,451,507],highest:[227,348,374,375,507],highli:[3,6,7,9,172,199,226,247,263,277,297,307,371,373,406,476,495],highlight:[6,7,10,13],hight:408,hilger:[365,366],hill:290,hill_height:13,him:9,hint:12,histo:[],histogram:[1,3,6,12,65,122,170,203,213,215,218],histor:407,histori:[],hit:[3,323,342],hmaktulga:[7,9],ho3:171,hoc:358,hocknei:[365,366],hofl:198,hoh:[6,396,418,422],hold:[6,33,61,73,185,212,226,255,291,306,307,320,373,375,410,426,472,492],holdem:306,holder2:366,holder:[365,366],hole:320,holian:[268,420],holm:[288,366],holonom:334,home:[11,12,201],homebrew:12,homepag:[197,199,244],homogen:[284,435],hone:290,honeydew:200,honor:201,hood:433,hook:[],hookean:410,hoomd:201,hoover:[6,7,8,162,203,230,247,248,263,264,265,266,267,268,269,270,271,282,283,284,285,286,290,294,302,307,326,327,328,333,400,502],hop:[223,375,386,451],hope:[5,13,17,42,43,220,489],hopefulli:[8,373],horizon:440,horn:6,host:[3,12,16,17,225,380],hot:[6,243,264],hotpink:200,hottest:331,hour:12,hourglass:[],hove:430,how:[],howev:[1,2,3,6,7,9,11,12,15,16,17,36,40,42,73,92,95,109,124,146,171,192,196,199,200,213,214,218,220,223,224,227,230,239,240,241,246,247,248,249,250,253,263,288,290,293,296,297,302,307,308,323,324,326,327,330,331,335,336,337,338,339,366,368,370,371,375,380,392,394,404,405,410,413,430,433,439,441,450,462,463,466,476,478,479,482,483,489,495,498,499,502,507,508],howto:[6,9,65,73,149,150,151,153,155,158,159,160,161,162,164,165,203,247,248,263,294,326,327,328,396,412,418,422,508],hoyt:209,hpc:[1,15],hsw:17,htm:404,html:[0,4,8,11,12,15,148,246,408,428,490,491],htmldoc:0,htst:495,http:[0,6,7,9,11,13,14,15,225,241,244,246,381,404,427,442,443,444],htype:[396,418,422,426],hubbard:397,huge:[12,174,277,323,481,486,498],huggin:[7,387,389,461],hugh:209,hugoniostat:[4,9,203,268],hugoniot:[261,268,297],hull:170,hummer:365,hundr:[7,14],hura:6,hwloc:[12,17],hybrid:[],hydrat:408,hydrocarbon:[382,395,406],hydrodyanm:41,hydrodynam:[7,9,41,104,106,250,252,253,254,388,427,428,448,450,461,491],hydrogen:[3,6,7,236,302,382,386,396,406,412,418,422,426,443,444,461,481,490,502],hydrostat:[3,9,224,263,268,294,307],hynninen:[397,408],hyoungki:432,hyper:290,hyperbol:397,hyperspher:146,hyperthread:[16,17],i_0:335,i_1:441,i_csid:6,i_flag1:296,i_mpi_pin_domain:16,i_myflag1:296,i_myflag2:296,i_n:441,i_nam:[119,196,296,325,491],ialloi:430,iatom1:121,iatom2:121,iatom3:121,iatom4:121,ibar:430,ibead:290,ibm:[196,365,433],icc:[10,12,433],icm:[9,244],ico:66,icosohedr:75,ictp:13,id1:[307,375,417,481,484],id2:[307,312,320,375,417,481,484],id_press:[224,261,263,265,266,267,268,269,270,271,294],id_temp:[223,224,261,263,265,266,267,268,269,270,271,282,283,284,286,294,326,327,328],idea:[1,3,6,11,12,42,147,199,200,220,245,288,312,323,331,366,435,489,502],ideal:[6,9,12,41,75,122,128,230,239,288,368,427,455,502],idealga:[],ident:[1,3,9,12,40,41,73,146,196,200,215,224,225,240,241,247,248,260,263,288,290,294,302,304,307,366,374,375,380,387,389,396,398,404,418,420,426,437,443,444,451,452,469,473,476,479,482,495,506,507,508,510],identi:380,identif:69,identifi:[1,3,6,12,38,41,57,72,170,172,192,235,304,323,346,412,417,430,463,476,478,481,484,495,496,498,500],idflag:293,idl:[18,495],idn:[307,375],idr:507,ielement:430,ieni:13,ifdef:[8,12],iff:248,iffp:479,ignor:[3,6,11,16,42,43,63,73,87,91,103,113,125,176,196,197,199,200,204,205,213,214,215,216,218,220,224,225,226,227,239,242,246,247,260,263,268,274,279,293,294,295,296,306,307,308,323,326,327,328,334,335,337,340,344,345,346,356,367,370,374,375,380,381,392,393,394,404,405,407,409,416,417,430,437,441,445,462,463,464,465,466,468,469,476,478,481,482,486,491,493,495,498,507],ihl:323,iii:[6,9,25,298,300,360,412,493],ijj:469,ijk:[354,358,360,386,441,469,478],ijl:358,ikeshoji:6,ikj:469,iko:2,ill:[152,162,212,298],illeg:3,illinoi:[244,365,366,427],illog:479,illustr:[1,6,8,11,12,16,17,18,19,288,290,375,413,479,507],ilmenau:[7,9,14],ilya:[7,9],imag:[],image2pip:199,imageint:3,imagemagick:[4,199],imagin:[320,334,386,405,413,414,416,431,432,437,441,462,464,465,466,469,493],imaginari:[6,96,239,290,481],imbal:[1,12,42,220,380,500],imbalanc:[42,220],imbu:323,imd:[],img:199,immedi:[0,2,3,8,12,172,221,222,227,310,319,324,325,342,478,479,481,483,495,507,510],immens:3,immers:[250,307],impact:[1,4,6,8,231,330,500],impart:[3,6,242,323,345],impei:[6,418],implement:[1,3,6,8,9,12,17,18,27,80,84,85,91,112,124,154,160,171,172,180,181,191,212,225,229,234,241,244,247,250,252,253,254,261,263,284,287,289,290,296,297,300,301,302,310,311,312,323,330,335,339,358,364,365,366,373,375,380,381,383,386,395,396,398,400,401,402,404,405,406,413,418,422,426,430,440,443,444,445,464,466,478,479,490,495,502,507,509],impli:[3,6,41,61,91,147,195,199,204,205,206,226,232,247,306,326,328,329,365,368,393,479],implicit:[],implicitli:8,implict:397,imporop:374,importannt:[],important:333,important_not:[],impos:[2,6,73,118,161,195,203,206,207,219,232,233,237,242,245,254,255,262,277,288,291,309,317,320,322,323,330,331,332,333,338,339,340,343,344,345,373,375,377,475,489],imposs:[1,3,481],improp:[],improper_coeff:[],improper_styl:[],impropercoeff:3,impropertyp:222,imprort:102,improt:[204,205],improv:[0,1,9,16,40,42,200,220,263,289,380,412,418,433,435,444,462,465],imrop:357,in3:171,inaccur:[1,3,6,175,261,365],inaccuraci:344,inact:412,inappropri:172,incid:[124,171,227],includ:[],includig:[348,364],inclus:[],incom:244,incompat:[3,11,414],incomplet:[3,11,481],incompress:[264,406],inconsist:[3,176,223,482],inconveni:368,incorpor:[297,386,397],incorrect:[3,155,247,430],incorrectli:[3,368,410,507],increas:[1,3,6,10,18,38,57,59,61,115,124,147,192,196,197,199,200,214,221,222,223,226,235,239,247,294,305,306,307,331,334,338,365,366,375,380,406,409,444,463,465,479,490,495,507],increasingli:406,increment:[3,11,134,206,207,219,220,227,232,236,263,293,312,313,346,364,379,416,451,476,479,493,495,507],incur:[14,17,212,216,217,236,335,478],inde:155,indefatig:7,indefinit:332,indent:[],independ:[4,6,9,11,12,16,17,42,61,65,95,123,125,158,172,195,203,211,212,213,215,216,217,218,220,223,224,225,226,227,240,242,247,248,250,253,263,289,294,298,302,307,308,312,322,333,335,368,410,433,476,479,498,508],indetermin:[196,197,200],index:[0,3,6,8,11,12,38,40,41,57,70,71,123,125,170,192,196,200,211,213,235,244,246,290,308,335,346,347,348,370,379,435,443,444,463,470,481,496,507],indianr:200,indigo:200,indirectli:[6,507],indistinguish:247,indium:452,individu:[],induc:[],industri:7,ineffici:[3,6,41,66,69,72,74,75,79,96,112,146,160,199,226,263,289,365,377],inelig:210,inerti:428,inertia:[],inexpens:[241,490],inf:[2,3,12,338,484],infer:[3,99,101,102,166,206,207,220,221,222,232,244,292,323,331,338,368,393,407,481,493,499],infil:[3,13,307,478],infin:[3,373,486,499],infininti:199,infinit:[3,227,238,245,247,250,289,323,335,341,342,366,368,406,481,485,506],infinitesim:6,inflect:[397,420,461],influenc:[3,9,42,82,154,260,293,365,366,435,464,465,466],inform:[0,1,2,3,6,7,8,9,11,12,13,15,17,40,42,43,61,63,64,65,70,92,121,123,124,171,172,178,196,197,198,199,200,201,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,236,237,238,239,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,262,272,273,274,275,276,277,278,279,280,281,287,288,289,291,292,293,294,295,296,298,299,300,301,302,303,304,305,306,307,308,309,310,313,320,321,323,324,326,327,328,329,330,331,332,334,337,338,339,340,342,343,344,345,347,363,365,366,369,372,373,374,375,376,378,380,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,436,438,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,471,472,473,478,479,481,482,483,485,486,488,493,495,496,498,500,507,509,510,511],infrequ:[6,263,400,476,495],infti:[397,427,428],ingtegr:386,inher:[365,373,435],inherit:[6,467],inhomogen:[18,335,435],inidividu:373,init:[3,8,305,451],init_fil:335,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,38,40,41,42,57,59,61,64,73,82,83,90,91,108,109,136,168,173,174,192,195,196,197,199,200,201,204,205,208,209,213,220,222,223,224,226,233,235,239,240,244,245,246,247,248,250,255,259,260,261,262,263,268,277,289,290,291,296,297,302,305,306,307,309,311,322,323,325,330,332,333,334,335,336,337,340,341,342,343,345,346,348,365,369,372,373,375,382,383,399,400,403,433,442,443,444,451,463,476,478,479,481,483,484,486,488,489,491,495,496,499,502,507,508,509,511],initial_integr:8,initial_integrate_respa:8,initialis:442,initialt:335,inlclud:11,inlcud:507,inlin:479,inner2:[391,411],inner:[3,8,16,196,245,348,364,371,372,373,375,379,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,440,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,468,469,470,471,472,473,490,495,507],inner_distance_cutoff:412,innergroup:253,innermost:[38,57,73,378,463,490],innernod:253,innner:424,inordin:336,inorgan:[6,469],inp:[225,348,452,469],input1:[67,70,71,81,97,114,119,120,121,123,125,325],input2:[67,70,71,81,97,114,119,120,121,123,125,325],input:[],input_doubl:3,inquir:313,insensit:12,insert:[3,5,7,8,12,61,172,203,227,239,245,293,365,452,460,479,485,502],insid:[2,3,6,8,11,73,135,141,172,196,197,200,211,216,217,227,228,236,239,245,250,253,293,307,323,340,342,343,344,345,346,363,368,420,479,480,481,483,484,491,495,507],insight:[6,13],instabl:[250,399,450],instal:[],instanc:[6,11,204,225,241,342,408,413,435,441,479,502],instantan:[6,65,223,224,240,241,263,268,289,294,297,302,304,307,330,487,499],instanti:[6,11,12,209,413,478],instead:[1,3,6,8,9,11,12,13,17,18,41,42,61,63,65,72,73,94,108,123,150,154,176,192,196,197,205,212,215,216,217,218,220,224,225,239,247,250,253,254,289,295,305,307,325,343,363,365,366,369,376,380,389,390,404,417,419,426,430,433,476,484,488,495,497,502,507],institut:[9,244,292],instruct:[],insuffici:[3,6,12],insult:263,insur:[3,6,11,12,17,40,41,63,75,107,109,172,173,192,196,197,199,200,206,221,222,227,232,233,236,237,239,242,247,259,295,296,305,307,323,335,340,344,345,346,348,364,374,376,380,394,409,413,439,445,463,474,478,479,481,482,486,489,490,498,499,507,508],int_max:3,integ:[3,6,8,11,12,40,41,43,66,70,72,73,112,119,121,123,125,146,170,172,175,176,178,182,183,187,192,195,196,199,200,210,212,216,217,221,222,223,227,229,237,239,240,241,244,247,248,249,250,289,292,293,296,297,302,307,323,325,327,330,334,335,354,365,368,388,400,402,403,416,430,443,444,448,450,452,476,478,479,480,481,489,490,491,495,498,507,508],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,214,240,442,481],intens:[1,3,6,9,65,68,76,77,90,93,94,95,98,108,109,110,111,118,120,122,123,124,125,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,167,168,169,171,203,212,213,215,216,217,218,220,221,222,223,231,236,243,253,261,263,268,304,307,308,323,331,335,337,338,498,499],intepol:507,inter:[14,18,43,63,64,152,175,176,196,223,247,249,262,299,307,365,375,386,491,502,507,509,511],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,40,41,43,45,51,53,55,56,59,63,65,67,71,74,79,81,91,92,96,97,112,113,114,116,118,121,122,128,129,130,131,133,134,135,136,137,138,139,141,142,143,144,146,147,148,150,151,165,166,170,173,174,175,176,177,178,180,184,185,188,191,196,197,203,204,205,221,222,223,238,239,244,245,247,249,253,277,288,290,292,293,298,300,306,307,314,315,323,324,330,335,339,340,341,344,345,350,351,352,353,355,357,359,365,366,373,374,375,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,439,440,441,444,445,446,448,450,451,452,453,460,461,462,463,464,465,466,467,468,469,470,471,472,473,476,479,481,483,485,486,490,491,493,498,499,502,509],interatom:[3,4,7,172,196,262,332,333,381,386,404,406,414,430,433,451,465,507],intercept:124,interchang:6,interconnect:18,interconvert:406,intereract:40,interesect:344,interest:[1,5,7,8,9,11,13,73,171,290,330,333,366,405,428,443,444,479,507],interf:380,interfac:[],interfer:[12,263,382],interg:[6,502],intergr:[490,494],interi:428,interior:[3,6,42,344,484],interlac:430,interleav:[6,172,489],intermedi:[6,12,61,199,262,288,358,375,479,480,489,493],intermix:476,intermolecular:382,intern:[],internal_element_set:209,internal_quadratur:209,internet:246,interpenetr:430,interpentr:[455,456,458],interpol:[6,15,38,57,105,192,199,200,209,235,250,288,365,366,375,386,435,444,457,463,464],interpret:[2,6,11,199,215,410,453,476,479,495,507],interrupt:297,intersect:[3,6,124,200,344,346,484],intersert:344,interspers:373,interstiti:[170,433],intertia:[3,98],interv:[3,6,95,198,213,247,263,297,302,303,315,451,457,476,495,507],intestieti:124,intial:[6,380,382],intiial:[42,486],intiti:[3,322],intra:307,intra_energi:239,intramolecular:[29,239],introduc:[6,9,96,112,199,263,297,302,307,358,365,381,396,406,418,422,426,462,495,507],introduct:[],intsal:[],intuit:368,inv:[124,171,308],invalid:[3,12,73,93,175,277,375,427,428,483],invari:[112,139,144,146],invent:310,invers:[],invert:[1,6,176,289],invis:344,invoc:[170,223,380,448,450,479],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,61,65,68,73,76,77,83,91,92,93,94,98,108,109,111,115,116,117,118,123,149,159,166,167,170,172,173,175,176,178,179,181,182,183,184,186,187,189,190,192,196,197,199,200,201,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,228,229,231,232,233,236,237,238,239,240,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,259,260,262,263,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,298,299,300,301,302,303,304,305,307,308,309,310,312,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,349,351,352,354,355,358,360,364,365,366,367,368,373,375,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,404,405,407,408,409,410,411,412,413,414,418,419,420,421,422,423,424,425,426,427,428,431,435,436,437,438,440,445,446,448,450,452,453,462,463,464,465,466,469,470,471,472,473,475,478,479,480,482,484,486,489,490,492,493,495,498,499,502,507,508],invokd:3,involv:[3,6,7,8,12,65,114,121,122,123,152,176,203,210,221,239,250,292,295,300,323,365,372,373,375,385,403,409,416,462,464,466,477,478,484,486,490,495,496],ioff:[374,481],ion:[6,7,9,154,287,320,335,366,386,397,407,408,430,433,451,461,466,473,481,502],ionic:[6,9,387,389,397,406,407,438,451,502],ioniz:[9,395,406],ionocoval:9,iparam:[3,222],ipi:[],ipp:[],ir3:171,ir4:171,irregular:[6,42,60,220,224,226,263,307],irrelev:437,irrespect:[427,428],irrevers:230,is_act:[3,507],is_avail:[3,507],is_defin:[3,507],isbn:472,isel:[365,366],isenthalp:[9,263,264,265,266,267],ismail:[365,366,390,422],isn:[3,8,11,12,243],iso:[3,224,230,248,263,264,265,266,267,268,269,270,271,294,302,307,502],isobar:[9,263,264,269,270,271,311,402],isodem:406,isoenerget:[9,311,402],isoenthalp:[311,402],isol:[3,175,346],isomorph:290,isotherm:[9,239,263,264,269,270,271,294,311,402],isotrop:[6,96,247,294,365,366,388,409,427,428],isovolum:308,isralewitz:312,issu:[1,3,6,9,11,12,13,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,61,73,75,83,108,115,118,149,159,178,179,181,182,183,184,186,187,189,190,192,199,206,209,219,223,224,226,227,232,233,238,239,242,247,261,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,290,294,296,299,307,309,310,322,326,327,328,333,339,343,345,348,349,351,352,354,355,358,360,366,374,375,378,381,382,384,387,388,389,390,391,392,394,395,396,399,400,404,405,407,408,409,410,411,412,418,419,420,421,422,423,424,425,426,427,431,436,437,438,440,445,446,453,460,462,463,464,465,466,469,471,472,473,481,483,484,490,493,498,499,507,508],ital:[443,444],itali:13,item:[6,7,8,42,196,200,220],iter:[3,6,12,40,42,65,198,206,207,219,220,224,230,232,237,245,289,298,299,307,310,330,346,348,364,371,372,373,375,379,451,476,486,490,495,499,507],ith:[73,123,125,211,212,213,214,215,216,217,218,325,337,499,507],itself:[2,3,4,6,7,8,9,11,12,13,18,43,61,95,113,163,196,198,199,200,201,213,214,225,230,248,258,262,301,307,335,346,348,374,375,396,407,409,413,414,463,479,485,488,489,493,507,511],itset:491,ityp:[3,121,122,172,208,222,300,470],itype1:122,itype2:122,itypen:122,ivector:8,ivori:200,ixcm:307,ixi:[43,98,307,374,507],ixx:[43,98,307,374,507],ixz:[43,98,307,374,507],iycm:307,iyi:[43,98,307,374,507],iyz:[43,98,307,374,507],izcm:307,izrailev:312,izumi:465,izz:[43,98,307,374,507],j0jt:95,j20:213,j_m:146,jac:[6,178,493],jackson:434,jacobi:3,jacobsen:372,jagreat:13,jame:[9,19],janssen:288,januari:430,jaramillo:[7,9,13,406],jarzynski:312,jatempl:9,jcc:9,jcp:340,jec:13,jeff:13,jello:263,jensen:[247,365],jeremi:[9,432],jerom:9,jewett:13,jiang:[248,502],jiao:[9,13],jiht:[7,9],jik:386,jim:7,jku:[7,9],jmake:12,jmm:146,joannopoulo:261,job:[12,62,310,489],jochim:[263,264],john:[7,9,13,198],johnson:[9,13],join:[6,484],joint:[3,292,412],jon:[9,72],jonathan:9,jone:[1,3,6,7,9,10,12,13,46,47,66,91,113,116,203,209,294,323,340,344,366,368,373,382,385,389,390,391,392,394,399,409,411,412,413,416,417,418,419,420,422,423,425,426,429,434,435,441,445,446,456,461,468,493,502],jonsson:[75,262,372,375,451],jorgensen:[6,189,396,418,422],joul:506,journal:[166,184,209,300,366,404,433,443,444,455,456,458],jparam:[3,222],jpeg:[3,12,199],jpeglib:12,jpg:[4,8,12,196,199,200,510],jpg_inc:12,jpg_lib:12,jpg_path:12,jpl:[7,9],jth:507,jtype1:122,jtype2:122,jtype:[3,122,222,470],jtypen:122,judg:495,judici:6,julien:9,jump:[],june:201,just:[3,6,8,11,12,13,17,19,22,29,43,45,61,63,95,113,116,122,147,150,151,165,176,180,196,199,212,216,217,226,230,236,253,260,294,296,307,330,335,346,348,350,374,375,380,382,385,393,413,441,468,479,483,485,486,488,489,500,502,507,510,511],justo:405,jusufi:[397,408],jut:344,jzimmer:9,k11:95,k22:95,k33:95,k_2:353,k_4:353,k_b:[],k_d:502,k_n:[],k_na:[],k_sigma:386,k_ub:20,kadiri:69,kalia:469,kamberaj:307,kapfer:112,kappa:[6,95,311,331,396,402,418,471,472],kappa_:335,karplu:91,karttunen:250,kate:[],kayser:397,kbit:200,kboltz:323,kbp:200,kbt:302,kcal2j:95,kcal:[244,490,502,506],kde:13,ke_eta_dot:263,ke_etap_dot:263,ke_omega_dot:263,keblinski:[396,451],kecom:152,keef:124,keep:[3,7,12,61,73,190,216,222,226,245,289,305,333,338,365,373,396,426,452,476,481,487,489,495,499,507],keflag:3,kei:[6,17,61,323,469,495],keir:13,kelchner:72,kelkar:338,kelvin:506,kemper:[299,395],kepler30:17,kepler32:17,kepler35:17,kepler37:17,kepler:[1,9,12,14,15,17,380],kept:[6,203,268,332,333,502],kernel:[7,13,17,41,105,135,141,209,240,241,315,433,454,455,456,457,458,459,481,491],kernel_radiu:[],keword:199,keyboard:12,keyword:[],keywrod:406,kforc:502,khaki:200,khersonskii:146,kick:[206,207,208,232,342],kilogram:506,kim:[],kimviri:[3,414],kind:[1,2,3,6,7,8,9,11,12,17,40,41,42,43,63,64,65,75,123,125,152,196,197,199,203,210,212,213,215,220,223,225,229,239,242,260,307,310,323,330,345,375,377,379,386,406,443,444,470,476,480,481,486,487,494,495,502,507],kinemat:[9,427,428],kinet:[3,6,8,9,65,86,87,88,89,91,95,99,100,101,102,103,118,147,149,150,151,152,153,154,155,157,158,159,160,161,162,164,165,203,210,212,224,230,239,243,247,259,261,263,264,265,266,267,268,269,270,271,294,297,323,331,338,339,373,406,476,495,499,502],kiss:12,kjl:358,klahn:334,klapp:365,klein:[6,9,209,225,263,264,285,307,418,446],kloss:7,kmax:[3,124,308,365],knc:17,knock:335,know:[3,11,12,42,65,113,122,203,230,246,248,277,323,373,405,414,467,479,482,485,490,502],knowledg:[4,8,199,414],known:[3,12,146,199,289,298,307,332,478,495,508],kohlmey:[7,9,13,18,365,366],kokko:[],kokkos_arch:17,kokkos_cuda:[9,12,17],kokkos_cuda_opt:17,kokkos_debug:17,kokkos_devic:17,kokkos_omp:[12,17],kokkos_pg:17,kokkos_phi:[12,17],kokkos_use_tpl:17,kokkow:9,kolafa:366,kollman:[6,178,493],kondor:442,kone:[332,333],kong2011:289,kong:[9,13,289],konglt:9,koning00a:332,koning00b:332,koning96:[332,333],koning97:333,koning99:332,kooser:13,koskinen:372,kosztin:312,krau:13,kremer:[46,47,493],kress:[431,432],kspace:[],kspace_modifi:[],kspace_styl:[],kspce:12,kspring:262,kstart:306,kstop:306,kth:[240,290],kub:20,kubo:[6,95,331],kumagai:465,kumar:[9,427,428],kuronen:441,kurt:292,l12:430,l_box:406,l_skin:335,la3:171,laa:9,lab:[5,7,9,12,117,440],label:[],laboratori:[0,84,85,234,261,297,311],lack:[3,261,406],lackmann:386,ladd:[284,333],lafitt:434,lag:335,lagrang:[136,137],lagrangian:[6,128,129,130,131,133,134,135,136,137,138,139,141,142,143,144,209,261,297,298,314,315,448,450,502],lagrangian_posit:[261,297],lagrangian_spe:[261,297],lai:475,lambda1:[464,465,466,469],lambda2:[464,465,466],lambda3:[464,466],lambda4:469,lambda:[91,117,124,166,171,250,308,332,333,335,381,405,426,462],lambda_fin:332,lambda_initi:332,lamda:[3,54,323],laminar:459,lamm:6,lammps2pdb:[6,13],lammps_clos:6,lammps_command:6,lammps_extract_atom:6,lammps_extract_comput:6,lammps_extract_fix:6,lammps_extract_glob:6,lammps_extract_vari:6,lammps_fil:6,lammps_gather_atom:3,lammps_get_coord:6,lammps_get_natom:6,lammps_n:[6,12],lammps_open:6,lammps_potenti:[393,395,492],lammps_put_coord:6,lammps_quest:[6,237],lammps_scatter_atom:3,lammps_set_vari:6,lammps_sppark:6,lammps_vers:6,lammpsplot:13,lammpspotenti:393,lammpstrj:[482,486,502],lammpsviri:[3,414],lamoureux:[6,230,467,502],landron:451,lane:1,lang:502,langevin:[],langevin_drud:[],langston:43,languag:[6,11,12,17,479,507],lanl:9,lapack:12,laps:336,laptop:7,larentzo:[9,84,85,234,311],larg:[0,1,3,5,6,7,8,9,10,12,13,14,16,18,40,41,42,60,61,72,73,115,122,147,152,155,160,172,173,174,184,192,195,196,197,199,200,212,216,217,220,223,224,226,227,231,239,250,263,277,284,289,292,293,297,302,304,305,306,307,310,320,323,331,335,336,338,340,344,358,365,366,371,373,376,380,394,400,406,409,410,417,433,435,439,445,463,476,479,481,483,484,488,490,495,498,500,502,508,511],larger:[1,2,3,6,11,12,13,40,42,57,61,72,73,122,172,174,199,213,215,218,227,243,250,263,284,285,293,298,302,306,307,308,311,319,323,330,335,339,340,341,344,365,366,371,372,373,375,376,377,380,386,394,396,397,406,410,418,422,428,435,439,460,461,468,481,485,486,489,490,495,507],largest:[3,6,12,40,73,170,172,231,365,373,377,460,463,481,483,489,490,501,507],laroch:302,laser:335,last:[1,2,3,5,6,11,12,15,38,43,57,61,63,73,116,123,147,170,192,196,197,199,200,201,202,212,213,215,216,217,218,220,231,262,305,308,320,323,348,363,373,374,375,376,380,384,385,386,387,394,395,400,401,402,404,408,409,411,412,416,419,421,423,424,425,428,434,436,445,451,453,460,463,467,468,471,472,476,477,479,482,486,488,489,493,495,496,499,500,507],lat:430,late:5,latenc:[10,244],later:[6,9,11,12,16,17,41,61,73,109,174,176,213,227,268,284,292,312,330,346,348,365,373,374,379,380,382,386,479,481,483,485,495,498,507,509],latest:[7,212,213,214,215,216,217,218,308,483],latex:8,latgen:289,latitud:146,lattc:430,latter:[2,6,9,11,12,14,15,16,17,42,43,91,150,200,204,205,211,212,216,217,220,224,245,254,263,265,266,267,269,270,271,292,294,296,300,307,323,339,344,364,374,386,388,389,390,391,392,399,416,418,422,426,433,438,446,451,467,476,478,479,484,487,498,507,510],lattic:[],launch:[1,3,6,11,12,17,18,380,478,479],laupretr:358,lavend:200,lavenderblush:200,lavgevin:226,law:[6,261,378,448,450],lawngreen:200,lawrenc:9,layer:[6,9,73,203,216,331,335,338],layout:[1,3,17,174,363,478,481,490],lb_fluid:250,lbl:[7,9,170],lbnl:9,lbtype:250,lcbop:[],ld_library_path:[11,12],ldfftw:12,ldrd:7,lead:[2,3,6,12,22,25,40,42,45,61,63,79,91,122,166,170,176,180,200,204,205,215,220,227,241,250,268,297,307,310,323,330,331,338,350,358,365,370,375,380,393,396,418,422,424,433,450,475,481,491,502,507,508],least:[3,6,12,18,73,124,171,198,210,216,241,292,296,339,376,380,413,463,468,479,507],leav:[3,7,11,12,17,21,42,59,147,162,179,220,224,227,263,265,266,267,269,270,271,293,294,307,310,349,435,481,485,493],lechman:323,lectur:312,led:[3,5],lee2:430,lee:[209,430],left:[6,11,12,42,113,148,191,199,200,223,245,287,323,346,348,368,481,483,488,507,511],leftmost:[42,220],legaci:[12,197],legal:7,lehoucq:440,leimkuhl:343,leiu:400,lemonchiffon:200,len:491,lenart:[397,408],length:[3,6,8,11,12,18,21,38,40,41,42,43,45,54,55,56,57,60,61,63,67,70,71,73,76,81,82,84,86,91,92,93,94,95,97,108,110,113,114,118,120,121,123,124,125,134,136,149,150,151,152,153,154,155,156,157,159,160,161,162,163,164,165,168,170,171,174,179,192,196,197,199,200,203,210,214,215,217,218,220,221,222,223,224,226,235,239,242,250,261,262,263,264,268,277,288,294,304,307,308,310,311,320,323,330,334,335,337,340,344,366,368,371,373,375,376,378,383,386,387,389,396,397,403,406,408,412,416,418,430,435,443,444,454,463,464,471,472,474,481,484,489,491,498,499,502,507],lengthi:239,lennard:[],lenoski:[431,432],less:[1,3,6,13,14,15,16,17,18,38,42,57,59,60,61,73,78,96,112,114,121,122,150,151,165,192,200,212,215,216,217,218,220,222,223,224,226,227,236,245,261,263,288,300,302,308,323,342,343,345,366,368,373,377,380,386,391,409,410,416,427,428,435,445,462,463,466,472,481,507,508],let:[1,12,38,57,155,183,192,213,235,310,323,341,380,394,463,490,494,502,509],lett:[146,160,241,248,250,261,302,312,332,333,372,386,404,406,409,426,452,502],letter:[2,12,42,59,61,200,220,229,230,248,290,348,379,442],leuven:9,level:[2,3,8,11,12,14,17,196,199,204,205,214,244,260,262,263,348,363,366,379,386,390,391,418,419,422,429,433,434,443,444,478,490,495,500,507],lever:460,levin:410,lewi:313,lexicon:7,lgr_po:[261,297],lgr_vel:[261,297],lgvdw:444,li1:171,liang:395,lib:[1,3,9,11,12,14,15,17,197,301,380,395,414,479,482],libatom:[9,442],libcolvar:12,libdir:11,libfftw3:12,libgpu:15,libjpeg:12,liblammp:[11,12],liblammps_foo:[11,12],liblammps_g:[11,12],liblammpscuda:14,libmpi:11,libmpi_stub:12,libmpich:12,libpackag:12,libpng:12,librari:[],librt:17,licens:[0,7,8,12,199],lie:[6,308],lieu:365,life:7,lifo:8,ligand:320,liggght:7,lightblu:200,lightcor:200,lightcyan:200,lightest:330,lightgoldenrodyellow:200,lightgreen:200,lightgrei:200,lightli:320,lightpink:200,lightsalmon:200,lightseagreen:200,lightskyblu:200,lightslategrai:200,lightsteelblu:200,lightweight:323,lightyellow:200,like:[3,4,6,7,8,9,11,12,14,16,17,18,40,43,55,61,156,163,199,201,206,224,225,227,230,232,244,247,248,249,261,263,264,269,270,271,276,277,282,283,284,285,286,288,294,296,297,298,302,307,308,311,323,325,326,327,328,329,330,331,338,339,340,343,344,345,348,365,368,372,375,380,386,394,399,400,402,406,407,410,412,413,423,424,430,452,463,466,471,472,478,479,481,482,483,484,486,491,496,499,500,502,507,508],likelihood:[124,171,223],likewis:[1,6,10,12,15,16,18,40,42,73,92,121,209,220,221,222,239,247,248,263,264,268,285,302,323,326,327,328,366,375,381,385,386,396,404,407,433,461,479,481,483,493,507],likhtman:214,lime:200,limegreen:200,limit:[],limit_eradiu:406,limit_veloc:[314,315],lindahl:365,line:[],linear:[],linearli:[10,123,200,226,289,340,342,343,345,374,375,377,481,507],lineflag:[6,481],lineforc:[],linen:200,linesearch:[8,12,371],ling:[9,13],lingo:[11,414],link:[5,6,7,8,9,11,12,13,14,15,17,22,37,45,56,65,180,191,197,199,203,222,244,248,292,301,303,312,320,350,359,383,393,430,442,443,444,461,467,479],linker:12,linkflag:[9,12,16,18],linux:[10,11,12,15,199,201,244],linuxamd64:482,liouvil:263,lip:13,lipid:[4,9,10,13,29,307],lipton:292,liquid:[6,7,9,29,40,41,42,61,91,96,147,158,170,220,224,226,239,263,294,297,302,330,399,433,435,438,465,490],lisal:[311,402,460],lism:9,list:[],listen:[244,246],listfil:417,liter:[481,492],literatur:[6,8,430,451,462],lithium:406,littl:[1,3,12,66,263,376,476,484],littmark:[430,461,466,473],liu:[412,444],livermor:9,lj1043:[],lj126:[],lj12_4:446,lj12_6:446,lj1d:289,lj6:3,lj93:[],lj96:[],lj9_6:446,lj_flag:382,llnl:[5,7,9],lmp1:11,lmp2:11,lmp2arc:[],lmp2cfg:[],lmp2vmd:[],lmp:[11,479,502],lmp_auto:12,lmp_cuda:[14,17],lmp_foo:12,lmp_g:[6,11,12,13,17,364],lmp_gpu:15,lmp_ibm:[12,364],lmp_inc:12,lmp_intel_cpu:[],lmp_intel_phi:[],lmp_kokkos_cuda:17,lmp_kokkos_omp:17,lmp_kokkos_phi:17,lmp_linux:[4,6,12],lmp_mac:12,lmp_machin:[1,12,14,15,16,380],lmp_mpi:[12,17,18,19,290],lmp_mvapich:17,lmp_omp:[],lmp_openmpi:17,lmp_opt:[],lmp_win_mpi:12,lmp_win_no:12,lmpptr:[11,479],lmpqst:237,lmpsdata:13,lmptype:[3,12,237],load:[1,3,4,6,7,9,11,12,16,17,18,42,199,201,203,220,244,297,380,395,478,479,500],loadabl:11,loca:200,local:[],localhost:244,localized_lambda:209,localonli:12,localvector:65,locat:[3,6,8,9,11,12,27,63,122,124,170,171,181,192,196,227,228,250,322,333,344,371,393,396,407,408,418,420,422,467,478,481,482,484,491,493],lock:[3,379,507],lockstep:[224,263,294,307],log:[],logarithm:[142,143,507],logfil:[0,3,6,12,295,369,477],logfreq2:507,logfreq:[200,488,497,507],logic:[7,11,12,17,42,172,220,346,348,476,478,479,482,490,495,507],lomdahl:[268,420],london:[13,239,444],lone:[443,444],longer:[1,3,6,8,12,13,55,122,196,200,211,212,213,214,215,216,217,218,221,239,247,288,292,297,307,310,330,340,344,346,371,380,382,410,451,478,486,490,495,504],longest:[42,220,221,376,468],longitudin:320,look:[1,3,6,8,11,12,18,55,63,196,199,202,393,452,463,502,507],lookup:[3,40,192,435,463],lookup_t:308,loop:[3,4,6,7,11,12,18,40,43,67,70,71,81,92,97,114,121,122,147,199,212,216,217,221,222,231,330,346,348,364,367,373,375,376,378,379,403,433,451,476,477,479,485,486,489,490,495,500,501,507,508],loopa:[348,364,379],loopb:[348,364,379],loopmax:451,loopvar:507,lopez:[263,264],lorant:298,lorentz:171,lose:[6,60,61,174,224,226,248,263,410,481],loss:[6,506],lossi:199,lossless:199,lost:[3,12,13,59,107,227,305,313,323,435,481,482,483,490,498],lot:[18,312,365],low:[1,3,6,7,12,42,155,170,196,199,220,230,248,284,302,307,331,338,366,433,444,463,472,495,502],lower:[2,3,6,9,11,12,42,59,61,73,92,148,161,195,199,200,213,214,215,216,217,220,224,230,244,247,248,250,263,297,302,331,338,340,341,346,347,365,368,379,397,430,495,503,505,508],lowercas:199,lowest:[146,348,374,491,495,496,507],ls_:140,lsfftw:12,lsurfac:335,lu3:171,lubric:[],lubricateu:[],lubricuteu:274,lucki:12,luigi:13,lumped_lambda_solv:209,lussetti:331,lustig:[7,13],lybrand:366,lyulin:358,m4v:199,m_c:[],m_d:502,m_eff:[341,410],m_fill:3,m_i:321,m_lambdai:440,m_taubi:440,m_u:250,m_v:250,m_yield_stress:440,mac:[12,14],mac_mpi:12,mach:[9,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,313,314,315,316,319,491],machin:[1,3,4,6,7,9,10,11,12,14,15,16,17,18,19,196,197,199,244,263,336,365,371,373,378,380,433,478,483,488,489,490,508,511],mackai:[9,250,252,253,254],mackerel:[6,20,178,248,391,493,502],maco:199,macro:17,macroparticl:403,macroscop:[7,242,261,440],made:[3,6,11,12,15,16,33,42,43,51,66,173,185,196,199,201,203,204,205,210,220,227,231,244,253,293,301,305,307,333,346,356,376,380,409,410,413,443,445,453,478,485,491,494,503,505,508,509],madura:[6,418],magazin:404,magda:340,magenta:200,magic:[3,11],maginn:[166,338],magnitu:325,magnitud:[6,72,110,114,119,148,172,195,196,197,200,227,228,242,243,245,247,312,320,322,323,330,341,366,373,399,410,491],mai:[0,1,2,3,6,7,8,11,12,13,14,15,16,17,18,29,38,40,41,42,57,60,61,63,65,67,70,71,73,81,90,91,92,93,94,96,97,107,108,110,112,113,114,115,116,118,119,120,121,123,124,125,146,147,150,151,152,160,161,165,166,170,171,172,173,174,175,176,191,192,195,196,197,198,199,200,201,203,204,205,206,208,210,212,213,214,215,216,217,218,219,220,221,222,224,226,227,230,231,232,235,236,239,240,241,243,244,245,247,248,249,250,251,253,258,259,260,261,263,264,268,277,280,289,290,293,294,295,296,297,298,299,302,304,305,306,307,308,309,310,312,314,315,317,323,325,326,327,330,331,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,363,364,365,366,368,371,372,373,374,375,376,377,378,380,383,385,386,394,400,406,410,413,414,416,424,426,428,430,431,432,433,435,443,444,446,452,460,463,469,473,476,477,478,479,481,482,483,484,485,486,487,488,489,490,491,493,495,496,498,499,502,507,508,509,511],mail:[3,7,9,12,346],main:[3,6,8,11,12,197,244,250,307,332,333,404,451,467,479,496],mainboard:1,mainli:[380,438],maintain:[8,9,13,40,157,222,226,284,323,336,372,381,404,490,493],major:12,make:[],makefil:[3,7,9,11,12,13,14,15,16,17,18,19,196,197,366,380,433,479],makelist:12,maks:410,malloc:[3,12],manag:[5,8,12,196,244,290,325,490],manbi:452,mandadapu:209,mandatori:[8,196,225],manh:386,mani:[1,2,3,4,5,6,7,8,9,12,13,14,15,16,17,18,38,40,41,42,43,57,63,65,70,73,92,95,107,108,122,148,152,172,173,192,195,196,197,198,199,200,201,203,204,205,206,210,211,212,213,214,215,216,217,218,220,221,222,223,224,226,227,235,236,239,240,243,244,250,251,259,261,263,264,268,277,287,288,289,293,296,298,299,300,302,304,307,308,310,323,334,335,337,346,348,365,373,375,376,378,380,393,395,403,406,408,412,413,451,452,461,463,464,466,479,481,483,485,486,488,489,490,491,493,494,495,496,500,507,508,511],manipul:[12,42,220,244,396,441,492],manner:[2,3,6,9,11,17,42,147,168,199,204,205,206,207,215,220,226,231,232,237,243,247,248,263,269,270,271,282,283,284,286,301,326,327,328,331,332,333,338,340,344,348,366,374,375,379,380,404,406,413,416,427,468,476,478,481,482,483,484,486,490,495,496],manolopoulo:246,mantissa:3,manual:[0,1,3,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,44,46,47,48,49,50,52,54,55,57,60,65,70,73,115,118,124,149,150,151,153,154,155,158,159,160,161,162,164,165,171,178,179,181,182,183,184,186,187,189,190,192,196,197,199,201,206,216,219,226,233,238,242,246,247,248,262,263,265,266,267,268,269,270,271,272,273,275,278,280,281,282,283,284,286,294,296,299,307,308,309,310,326,327,328,338,339,343,348,349,351,352,354,355,358,360,366,375,379,380,381,382,384,385,387,388,389,390,391,392,394,395,396,398,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,436,437,438,440,445,446,453,462,463,464,465,466,469,471,472,473,476,484,490,494,495,496,499,507],manybodi:[7,8,147,148,373,381,382,386,395,404,407,413,415,437,441,462,464,465,466,469,493,507],map:[2,3,11,12,17,18,40,61,66,73,124,128,146,160,171,172,195,199,200,209,216,289,306,365,366,368,375,381,382,386,395,404,405,407,413,414,415,430,431,432,435,437,441,442,443,444,451,452,460,462,463,464,465,466,469,478,481,483,495,507],map_fil:289,mapflag:12,mara:[9,451],march:430,margin:495,mari:13,mark:[411,426,448,450,451],marker:295,maroon:200,maroonmpi:11,marrink:411,marsaglia:[3,240,241,247,248,302],marseil:9,martin:[289,430],martinez:210,martyna:[263,264,307,490],mashayak:17,mask:[3,288,507],mask_direct:209,mass:[],mass_matrix:209,massdelta:310,massiv:[0,199,250,290,331,338],massless:[6,248,366,396,418,422,426,502],masstot:307,master:[3,375,476,495],mat:[69,209,395,465],match:[3,6,8,9,11,12,17,38,42,57,61,73,122,155,192,200,201,220,223,226,235,244,263,264,284,304,308,323,330,365,366,386,412,424,430,442,443,444,463,475,479,481,482,483,486,490,495,502,507],matchett:43,mater:[75,381,432,441,451],materi:[6,7,9,61,72,130,131,175,208,209,226,239,245,261,288,294,302,331,335,341,396,404,405,406,410,414,430,431,433,440,443,444,447,448,449,450,476,481,495,502,506],material_fil:209,math:[],mathemat:[124,146,171,172,195,204,205,206,207,219,224,232,240,242,243,245,247,248,295,309,317,326,327,328,340,343,345,452,477,484,491,508],mathrm:[],mathtt:[],matlab:[],matric:[9,146,241,289,409],matrix:[3,6,9,95,170,213,224,241,289,298,365,368,433],matter:[6,9,12,40,59,61,73,154,216,335,376,382,398,404,406,430,446,451,464,466,469,473],mattox:9,mattson:[84,85,118,147,234,311],max2theta:171,max:[3,6,8,12,15,18,73,123,200,215,220,222,224,227,293,310,323,348,368,371,373,375,376,380,451,476,481,495,499,507],max_alpha:8,max_cell_s:403,max_group:3,max_nn:315,max_travel:316,max_vel:[314,315],max_veloc:315,maxangl:239,maxbodi:3,maxbond:[3,222],maxedg:170,maxev:[373,476,495],maxfoo:8,maxim:[330,375],maximum:[3,6,8,12,15,17,25,42,43,46,54,55,59,61,63,96,112,122,123,124,127,170,171,173,174,195,196,208,213,214,215,220,222,226,227,231,239,277,288,293,298,310,313,314,315,323,336,365,366,371,375,376,380,383,386,403,408,427,428,451,481,484,489,499,507,508],maxit:[298,373,476,495,499],maxsize_restart:8,maxspeci:3,maxwel:[17,287],maxwell50:17,maxwell52:17,maxwell53:17,maxx:441,mayb:13,mayer:[7,387,389,451,461],mayo:[6,7,13,25,360,412,493],mbt:179,mbyte:[12,302],mcdlt:[162,243],mcgraw:290,mdash:502,mdatom:239,mdf:[],mdnvt:239,mdregion:209,mdtemp:239,mdump:[42,220],meain:[],meam:[],meam_sw_splin:432,meamf:430,mean:[1,2,3,4,6,7,8,10,11,12,17,22,34,37,38,39,40,42,43,45,53,55,56,57,58,59,61,63,65,70,73,74,78,79,86,88,89,91,95,96,108,109,110,112,118,119,120,121,122,123,146,147,149,150,151,153,154,155,158,159,160,161,162,164,165,166,172,173,175,176,178,180,188,191,192,193,194,195,196,197,199,200,201,203,204,205,208,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,232,235,237,239,240,241,242,243,245,247,248,249,253,260,263,265,266,267,268,269,270,271,277,282,283,284,286,288,290,292,293,294,296,302,304,305,307,309,310,312,317,320,323,325,326,327,328,330,331,334,335,337,338,339,340,341,342,343,344,345,346,350,351,352,353,355,357,359,361,365,366,368,370,371,373,374,375,376,378,380,383,387,389,390,391,393,396,400,403,404,406,409,410,412,413,416,418,419,422,429,430,434,435,438,439,441,443,444,445,446,460,462,463,464,465,466,468,472,475,476,478,479,481,482,483,484,485,486,487,488,489,490,491,492,493,495,496,498,499,502,506,507,508,509,511],meaning:[122,130,131,133,136,140,413],meaningless:[69,330],meant:[6,307,467,485],measur:[],meaur:500,mech:440,mechan:[6,8,9,11,12,16,17,41,84,85,132,148,209,234,243,290,301,386,406,414,420,433,448,450,475,479,481],mechanic:301,mechanim:128,meck:112,media:199,medium:472,mediumaquamarin:200,mediumblu:200,mediumorchid:200,mediumpurpl:200,mediumseagreen:200,mediumslateblu:200,mediumspringgreen:200,mediumturquois:200,mediumvioletr:200,mee:330,meet:[3,12,173,199,200,222,223,336,486],mehl:381,mei:429,meloni:40,melros:[427,428],melt1:201,melt2:201,melt3:201,melt:[4,10,223,289,386,433,465],mem:15,member:[175,292,386],membran:[29,287,472],memori:[1,3,5,6,7,8,9,12,15,16,17,18,40,41,62,73,200,212,214,216,217,240,241,302,335,363,376,380,386,435,439,444,478,481],memory_usag:8,mendelev:404,mention:[1,6,7,11,41,43,226,243,250,268,340,368,375,382,443,444,483,507],menu:[199,244],mep:[262,375],mer:[4,10,223],meremianin:146,merg:[5,481],merz:[6,178,493],mescscop:440,mesh:[],meshless:9,meso:[],meso_:[],meso_cv:[],meso_rho:[],meso_t:[],mesocop:41,mesoparticl:[234,235,402],mesoscal:7,mesoscop:[7,104,105,106,256],mess:[3,491],messag:[],met:[8,42,122,220,348,364,366,373,375,379,468,489],metadynam:[9,13,225],metal:[3,5,7,9,10,41,61,73,161,172,208,209,216,217,226,227,243,245,297,298,302,339,340,342,343,345,366,368,377,381,382,386,395,404,405,406,407,413,415,430,431,432,433,441,442,451,462,464,465,466,469,484,498,499,501,506],meter:[377,506],methan:[297,302],methanol:4,methin:358,method:[1,3,5,6,7,8,9,11,12,13,16,17,19,38,40,41,42,57,66,91,95,116,147,192,203,204,205,209,213,214,220,225,235,237,247,250,254,258,261,263,289,290,297,298,299,300,302,307,310,311,312,330,331,332,333,338,365,366,371,372,373,375,380,381,383,386,395,396,404,406,407,430,431,432,435,441,451,461,463,469,476,478,479,481,482,484,495,502],methodolog:[6,75,147,290,365],metin:[7,9],metric:[3,10,66,484,499],metropoli:[210,239,496],mezei:91,mf1:201,mf2:201,mf3:201,mg2:171,mglob_default_function_attr:[9,12],mgoh:437,mgpt:[],miai:302,mic:[9,12,17],micel:[4,9,13,321],micelle2d:[],michael:[9,13,432],michel:13,mickel:112,micro:[3,501,506],microcanon:[272,273,275,276,278,280,281],microelast:440,micromet:506,micropor:239,microscal:427,microsec:506,microsecond:506,mid:[5,9,61,226,433,460],middl:[3,6,8,16,22,42,45,79,91,122,161,166,176,179,180,200,204,205,211,220,293,305,306,307,331,338,349,350,370,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,428,429,430,431,432,433,434,436,438,440,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,468,469,471,472,473,475,479,489,490,491,507],middlebondtors:[3,179,481],midnightblu:200,midpoint:460,mie:[],might:[3,4,6,7,8,12,14,25,73,154,237,239,241,307,451,479,489,507],migrat:[3,8,17,42,43,61,63,67,71,81,97,114,121,196,203,220,288,296,302,323,365,377,380,489,509,511],mikami:[6,263,264],mike:[7,9,13,15,16],mil:[9,404],mill:372,miller:307,million:[3,7,10,40,42,73,220],mimic:[6,43,55,248,261,293,396,408,418],mimim:[224,375],min2theta:171,min:[3,4,6,8,12,123,146,200,215,365,368,451,460,476,495,507],min_cap:3,min_cg:8,min_clearstor:8,min_dof:8,min_modifi:[],min_nn:315,min_popstor:8,min_post_forc:8,min_pre_forc:8,min_pushstor:8,min_setup:8,min_setup_pre_forc:8,min_step:8,min_stor:8,min_styl:[],minarea:170,mincap:444,mind:[7,240,289],mine:[12,92,162,163,203,346,504],minim:[],minima:[184,360],minimi:[375,468],minimizaiton:375,minimizi:302,minimum:[3,12,25,26,27,43,46,59,61,73,90,110,123,170,171,173,175,181,195,196,199,208,215,224,225,231,246,262,304,306,308,313,315,319,323,340,344,348,360,365,368,371,372,373,375,376,391,406,409,411,412,418,420,422,427,428,444,446,460,476,489,495,507,508],minlength:170,minmiz:[8,224],minn:9,minord:[3,365],mintcream:200,mintmir:[7,298,396,461],minu:[12,61,152,226,348,375,507],minut:[4,8],mirror:[63,342],misc:[],miscellan:[2,209],mise:[139,144],mishin:[381,461],mismatch:3,miss:[3,5,12,175,215,239,277,302,323,417,435,498,499],mistak:[3,507],mistakenli:3,mistyp:3,mistyros:200,mitchel:[6,117,154,365,366,398,440],mitchell2011:440,mitchell2011a:440,mitig:263,mitur:[],mivi2:302,mix:[1,3,6,9,14,15,16,73,121,154,215,216,336,365,366,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,474,479,481,494,502,509],mixtur:[6,41,263,307,323,345,394,430,481],mixture_ref_t:430,mjpeg:199,mkdir:492,mkl:12,mkmk:289,mkv:199,mldivide3:3,mlpark:7,mlutipl:218,mn2:171,mn3:171,mn4:171,mo3:171,mo5:[171,433],mo6:171,mobil:[6,110,147,149,150,151,153,158,165,199,307,346,347],moccasin:200,mod:[],mode:[1,3,6,9,11,12,13,14,15,16,17,18,63,68,77,92,94,98,109,111,120,122,123,148,152,167,169,170,171,196,197,199,200,215,218,225,226,237,241,263,290,302,312,323,363,365,377,380,396,406,433,451,478,483,488,490,499,506,507,511],model:[],model_ar_p_mors:414,modern:[12,247,249],modest:[1,378],modif:[6,13,91,430,433,445,466,502],modifi:[],modify_param:8,modin:209,modul:[3,9,11,12,13,225,302,479],modular:8,modulo:[3,507],modulu:[294,410,430,440,447,449],moementum:260,mofil:482,mol1:507,mol:[3,9,73,119,172,174,175,196,197,200,225,227,239,244,247,293,296,307,310,319,325,399,409,446,490,491,502,507],molchunk:[68,77,94,98,109,111,152,167,169,212],mole:[210,404,506],moleclu:[221,222,227,236],molecul:[],molecular:[0,2,3,5,6,7,8,9,12,13,40,41,54,73,114,119,121,149,150,151,153,155,158,159,160,161,164,165,172,173,174,175,176,184,196,197,198,201,209,222,225,239,246,289,290,297,301,302,306,312,334,335,366,374,383,384,386,390,403,406,413,461,481,482,483,485,486,490,491,493,499,501,502,507],molfil:[],molfrac:[227,293],molnar:312,molp:115,moltempl:[],molybdenum:433,mom:[6,95,306,508],momementum:[150,151,265,266,269,270,273,274,275,282,283],momemtum:68,moment:[3,6,9,41,43,86,88,89,111,119,150,165,172,194,196,197,247,250,253,263,280,293,307,321,325,374,399,405,451,481,491,502,506],momenta:[241,274,338,406],momentum:[],momon:223,monaghan:[9,455,456,458],monitor:[3,6,12,101,102,155,224,226,227,236,244,247,261,263,293,295,297,307,310,323,373,375,399,499],mono:[75,427],monodispers:[3,341,388,410,427,428],monom:[13,55,223],monoton:[3,235,312,334,375,495],monoval:366,mont:[6,7,9,203,210,223,239,307,330,403,461],montalenti:[476,495],month:0,moor:[17,84,85,147,234,311],more:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,42,43,44,45,46,47,48,49,50,51,52,54,55,56,57,60,61,63,64,65,66,67,69,70,71,72,73,74,79,80,81,82,87,90,91,92,94,96,97,101,102,103,104,105,106,107,108,110,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,154,155,156,158,159,160,161,163,164,165,166,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,189,190,191,192,195,196,197,198,199,200,201,203,204,205,206,207,208,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,235,236,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,278,280,281,282,283,284,285,286,288,289,290,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,309,310,311,312,313,314,315,316,317,319,323,325,326,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,358,359,360,363,365,366,368,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,436,437,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,476,477,478,479,481,482,484,485,486,487,488,489,490,491,492,493,494,495,496,498,500,502,507,508,509,510,511],morefoo:8,moreov:[221,222],moriarti:[9,433],moriarty1:433,moriarty2:[9,433],moriarty3:433,morri:[],morriss:[160,284],mors:[],morse_f:463,mosel:372,mosi2:430,moskalev:146,most:[0,1,2,3,4,5,6,7,8,10,11,12,15,17,18,19,37,40,42,56,73,108,114,160,191,196,197,199,200,212,215,216,217,218,220,221,222,224,243,263,264,290,295,296,297,298,307,308,336,338,346,348,359,366,372,376,378,380,382,406,409,430,442,443,444,466,476,477,478,490,495,499,500,507,509],mostli:[8,9,11,13,73,174,199,376,481,490,493,507,510],motiion:6,motion:[3,6,7,9,43,90,102,108,149,150,151,153,155,157,158,159,160,161,162,164,165,226,230,241,250,253,254,260,263,264,268,284,288,290,292,302,306,307,311,331,335,341,344,375,399,406,427,428,484,490,502],motiv:288,mous:244,mov:199,move:[],move_tri_surf:[],movement:[3,6,12,260,330,373,499],movi:[],mp4:199,mpeg:199,mpg:199,mpi4pi:11,mpi:[],mpi_allreduc:[307,479],mpi_barri:1,mpi_cart:478,mpi_cart_cr:478,mpi_cart_get:478,mpi_cart_rank:478,mpi_cart_shift:478,mpi_comm:6,mpi_comm_world:[],mpi_fastmgpt:433,mpi_get_processor_nam:478,mpi_inc:12,mpi_lib:12,mpi_lmp_bigint:3,mpi_lmp_tagint:3,mpi_path:12,mpi_wtim:12,mpicc:11,mpich2:12,mpich:[12,14,15,16,17,18,380],mpich_icc:16,mpicxx:[12,17],mpiexec:[12,14,15,16,17,18,380],mpiio:[196,200,483,488,511],mpirun:[1,6,11,12,14,15,16,17,18,19,290,364,380],mplayer:199,msd:[],msi2lmp:[],msi:13,msm:[],msmse:[124,171,308],msse3:433,msst:[],mtchell2011:440,mtchell2011a:440,mtd:225,mth:[8,125,200,498],mtk:[263,264,268],mtotal:374,mu_j:29,muccioli:409,much:[1,3,6,11,40,148,196,197,199,214,224,297,330,376,377,380,409,445,476,479,495,500,502,507],mui:[119,196,197,232,325,481],mukherje:[7,9,292],mulder:334,muller:[6,95,203,331,338,434],mult:8,multi:[],multibodi:[3,63,292],multicent:406,multicor:[1,478,494],multidimension:13,multielectron:383,multilevel:[365,366],multiphys:11,multipl:[],multipli:[3,91,95,122,180,191,204,205,213,247,250,288,294,368,373,382,481,507],multiprocessor:380,multiscal:11,multisect:[42,220],multistag:91,multitud:7,mundi:285,munich:9,murdick:386,murti:465,murtola:365,must:[1,2,3,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,54,55,57,58,59,61,63,64,73,86,88,90,91,109,113,115,118,121,122,123,124,125,150,154,161,165,170,171,172,173,174,175,176,178,179,180,181,182,183,184,185,186,187,189,190,192,193,194,195,196,197,198,199,200,201,204,205,206,208,209,210,211,212,213,215,216,217,218,219,220,221,222,223,224,226,227,230,232,235,237,239,240,241,243,244,245,246,247,248,250,251,252,253,254,258,259,260,261,262,263,264,265,267,268,269,271,273,274,275,277,280,282,286,288,292,293,294,295,296,297,298,300,302,304,305,306,307,308,309,310,311,317,319,320,322,323,326,327,328,330,331,333,334,335,337,338,340,341,342,343,344,345,346,348,349,350,351,352,353,354,355,356,358,360,361,365,366,368,370,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,476,477,478,479,481,482,483,484,486,488,489,490,491,492,495,496,498,499,502,506,507,508,509,511],mutli:6,mutlipl:481,mutual:[3,368,500],mutut:490,muvt:239,mux:[119,196,197,199,232,325,481],muz:[119,196,197,232,325,481],mv2_comm_world_local_rank:12,mvapich2:[17,380],mvapich:12,mxn:[12,290],my_ga:239,my_one_wat:239,my_post_process:492,my_qeq:298,my_setup:492,my_swap_region:210,myblock:[227,293],mybox:174,mychunk1:120,mychunk2:120,mychunk:[6,68,77,94,98,109,111,152,167,169],mycmap:481,mycom:215,mydump:[196,200],myer:[5,7],myfil:[478,507],myfix:[210,496],myflux:95,myforc:[196,197,510],myhug:268,myke:95,mymol:[41,310,374],mympi:11,mymultipli:[479,507],myn:479,mype:95,mypi:507,mypress:258,myramp:147,myrdf:[122,218],myreg:368,myregion:346,myrigid:[87,103,293],mysocket:246,myspher:[200,344],mystr:348,mystress:95,mytemp:[2,107,149,150,151,153,155,156,158,160,165,258,348,364,379,498,508],myz:481,n_dephas:476,n_element:198,n_f:[297,302],n_hbond:412,n_ij:410,n_ion:335,n_k:240,n_particl:84,na1:171,nabla:335,nacl:[4,6,430],nacl_cs_x0:6,nakano:[298,300,375,469],namd:[7,9,196,244],name1:[166,226],name2:[166,226],name:[0,1,2,3,5,6,8,9,11,12,13,33,43,51,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,185,195,196,197,198,199,200,201,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,265,266,267,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,336,337,338,339,340,341,342,343,344,345,346,347,348,356,363,364,366,367,369,374,375,379,381,382,386,389,404,405,407,409,410,413,414,415,417,430,431,432,437,441,443,444,451,452,462,464,465,466,467,469,470,474,478,479,481,482,483,484,488,491,494,496,497,499,502,507,508,509,510,511],namespac:[6,8,12],nan:3,nangl:[3,481],nangletyp:[374,481,491],nano:[307,501,506],nanoindent:72,nanolett:307,nanomet:[196,200,506],nanoparticl:[220,307],nanosec:506,nanosecond:506,nappli:237,narea:3,narrow:[6,192],narulkar:[464,466],nasa:7,nasr:289,natdef:3,nation:[0,7,9,12,117,440],nativ:[1,6,7,9,12,16,17,196,201,482],natoli:[9,19],natom1:121,natom2:121,natom:[3,6,11,40,374,479,481,498,499,507],nattempt:293,natur:[6,9,146,226,263,288,302,341,404,406,407,430,441,478,507],navajowhit:200,navi:[200,404],navier:250,nb3:171,nb3b:[],nb3bharmon:437,nb3d:9,nb5:171,nbin:[122,215,216,217,331,338],nbodi:[253,307,433],nbond:[3,119,481],nbondtyp:[200,374,481,491],nbot:386,nbounc:323,nbrhood_cutoff:444,nbtype:121,nbuild:499,ncall:237,ncbin:73,nchar:200,nchunk:[3,6,68,73,77,94,98,109,111,120,152,167,169,212],ncoeff:452,ncorr:214,ncorrel:214,ncount:[212,213,214],nd3:171,ndanger:499,nden:[6,95],ndihedr:[3,481],ndihedraltyp:[374,481],ndim:216,ndirango:307,ndof:[263,268],ndoubl:481,ndp:502,ndx2group:[],ndx:347,neal:307,nearbi:[7,64,173,227,260,299,323,344,376,382,427,428,461,472,502],nearest:[3,72,73,75,96,112,170,173,250,262,288,330,344,365,417,430,451,463,507],nearli:[6,9,18,55,61,220,247,323,406,433,435,476,479,485,493],neb:[],neb_combin:375,neb_fin:375,neb_log:495,neb_step:495,neb_styl:495,necessari:[6,9,11,12,13,15,17,33,63,91,180,185,191,201,220,224,225,239,240,301,311,323,336,346,365,380,426,433,435,451,481,482,486,489,490,491,495,502,510],necessarili:[12,302,330,351,352,353,355,368,435,508],necessit:296,need:[1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,33,37,38,40,41,42,43,51,55,56,57,60,63,65,66,69,72,74,75,79,86,95,96,107,109,112,115,118,134,146,147,149,150,151,152,153,155,158,159,160,161,162,164,165,172,174,176,178,180,185,191,192,195,196,198,199,200,204,205,206,207,209,210,212,213,214,215,216,217,218,220,221,222,224,225,226,230,232,235,237,238,239,243,244,246,247,248,250,256,257,263,277,289,293,294,296,302,306,307,312,319,323,331,334,335,337,338,339,340,346,356,359,365,366,374,375,376,377,380,381,382,383,384,386,387,388,389,390,391,392,394,395,396,398,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,468,469,471,472,474,476,479,481,482,483,484,486,488,489,491,493,494,495,496,502,507,509,510,511],needless:[6,376],neeed:9,neelov:366,neg:[3,6,12,27,47,67,71,93,107,114,121,146,147,174,176,181,183,192,199,224,226,227,240,268,288,312,320,334,338,340,345,365,372,407,421,430,461,481,484,500],neglect:[412,428],neglig:[6,11,91,263,462],neigh:[],neigh_modifi:[],neighbor:[],neighborhood:[26,96,128,452],neighbour:248,neighobr:[6,396,418,422],neither:[2,3,12,42,65,197,209,223,226,227,382,388,406,427,428,486],nelem:452,nelement:[381,404],nelson:[96,112],nemd:[],nest:[2,348,362,379,507],net:[3,6,11,40,90,92,153,164,243,288,298,307,428,444],netpbm:199,network:[12,196,221,222,244,478],neumann:365,neutral:[3,92,239,365,396,418,451],never:[7,12,65,73,203,213,224,239,263,288,310,325,336,340,343,345,365,376,404,430,452,469,478,481,495,498,507],neveri:[3,8,73,206,211,212,213,214,215,216,217,218,221,222,223,250,251,289,298,299,300,303,304,308,331,337,338,375,451,486,495],newatom:227,newer:[12,212,430,507],newfil:[362,364],newli:[227,293,502,508],newlin:200,newn:307,newt:159,newtemp:[65,107],newtion:[386,433,441],newton:[],newtonian:240,newtyp:[3,222],next:[],neyt:330,nfile:[3,38,57,192,196,197,200,235,463,483,488,511],nfirst:486,nfirt:486,nfreak:308,nfreq:[40,73,211,212,213,214,215,216,217,218,220,304,308,486],nghost:[3,12],ngp:110,ngpu:380,nguyen:[15,386],nharmon:[],nhc:290,nht:307,ni2:171,ni3:171,ni_000:[124,308],nialh_jea:404,nialhjea:[393,413],nice:[6,8],nickla:432,nicola:9,nimprop:[3,481],nimpropertyp:[374,481],nine:[133,140,407,451],ninteg:481,nissila:[250,451],nist:[381,404,506],niter:[42,220],nitrid:396,niu3:[393,404,413],nkb:297,nlast:486,nlen:214,nline:374,nlocal:[3,8,11,12,237],nlog:366,nlvalu:112,nmax:43,nmin:43,nmol:481,nmpimd:290,nn2:430,nneighmaxdef:3,nnn:[96,112],no_affin:[16,380],no_gradient_correct:450,no_histori:6,no_velocity_gradi:450,noced:373,nocheck:417,nocit:12,nocoeff:509,nodal:[6,38,57,192,209,235,335,463],node:[1,3,12,14,15,16,17,18,42,124,128,171,198,220,244,250,335,380,417,478,494],node_area:250,node_group:209,nodeless:406,nodeset:209,nodeset_to_elementset:209,nodess:16,nof:192,noforc:[],nois:[6,240,241,247,248,249,250,297,302,307,327,335],nomenclatur:[6,73,216,368],nomin:[196,263],non:[],nonbond:[4,12,437,461],none:[],noneq:241,nonequilibrium:[9,332,333,406],nonetheless:247,nongauss:[],nongaussian:110,nonlinear:[],nonloc:[440,491],nonperiod:3,nonzero:3,noordhoek:395,nopreliminari:192,nor:[2,3,42,61,197,209,313,314,315,316,317,319,395,447,448,449,450,481,484],nord:[441,464,466],norder:478,nordlund:[441,464,466],norm:[6,12,65,123,203,212,216,217,308,314,315,373,375,460,498,499,506],normal:[3,6,9,10,11,12,40,42,60,63,65,69,72,73,75,92,95,107,108,118,122,123,157,160,170,172,173,174,192,200,203,212,213,215,216,217,220,224,226,227,238,239,243,247,248,260,263,277,288,290,291,298,302,304,305,312,323,324,326,327,328,335,340,341,344,345,349,351,352,353,355,370,372,373,375,380,394,395,409,410,413,433,460,473,475,476,479,481,483,484,486,487,491,495,498,499,500,502,506,507,510],norman:335,nornal:3,nose:[6,7,8,162,203,230,247,248,263,264,265,266,267,268,269,270,271,282,283,284,285,286,290,294,302,307,326,327,328,333,400,502],noskov:[467,502],noslip:[323,345],nosync:500,notabl:[5,40],notat:[6,63,65,72,146,166,203,260,263,404,469,507],note:[1,2,3,6,7,8,9,11,12,13,14,15,16,17,18,19,22,24,25,28,32,33,35,36,37,38,39,40,41,42,43,45,48,55,56,57,58,60,61,62,63,64,65,67,68,70,71,73,75,77,81,91,93,94,95,97,98,102,108,109,110,111,114,116,118,119,120,121,122,123,124,125,146,147,152,154,155,156,160,162,166,167,169,170,171,172,173,174,175,176,178,180,183,185,189,191,192,193,195,196,197,198,199,200,201,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,230,231,232,234,235,236,237,239,241,242,243,245,246,247,248,249,250,258,259,260,261,263,265,266,267,268,269,270,271,277,282,283,284,286,290,292,293,294,296,297,298,300,305,306,307,308,311,312,320,321,323,326,327,328,331,334,335,337,338,339,340,341,344,345,346,348,349,350,351,352,353,355,359,361,364,365,366,368,370,373,374,375,376,380,381,382,386,387,389,390,391,393,394,396,397,399,400,401,402,403,404,407,409,410,411,412,413,417,418,420,422,426,427,428,430,431,432,433,434,435,437,441,443,444,445,446,448,450,451,452,453,456,460,462,463,464,466,468,469,472,473,474,476,478,479,481,482,483,484,485,486,488,489,491,493,495,496,498,499,502,506,507,508,510,511],noth:[210,246,367,380,479,492],notic:[0,6,7,8,12,333,335,502],noutcol:8,noutput:289,noutrow:8,novemb:430,novik:13,novint:244,now:[2,3,6,9,11,12,13,47,63,64,73,196,204,205,222,240,244,245,307,341,344,366,368,404,406,410,443,444,453,477,482,502,508],nowait:244,nozforc:365,np3:171,np4:171,np6:171,npair:[122,213],nparticl:[3,41,43,385],npartit:499,npernod:[14,15,16,17,18,380],nph:[],nphi:[16,380],nphug:[],npoli:293,nproc:[3,11,196],npt:[],npt_aspher:[265,271,282],npt_bodi:[266,283],npt_sphere:[267,286],nrbin:[],nrecomput:403,nrepeat:[73,211,212,213,214,215,216,217,218,304,308,486],nreset:[224,263,264,268],nreset_ref:224,nrho:[381,404],nrl:404,nsall:9,nsampl:403,nsbin:73,nsbmax_most:3,nsec:501,nskip:[125,486],nsq:[3,377,439],nstart:[125,213,214,215,218,308,481,486],nstat:288,nstep:[3,13,224,263,346,457,479,482],nsteplast:479,nstop:[125,486],nswap:[331,338],nswaptyp:3,ntabl:[38,57,192,235,463],nterm:312,nth:[12,79,122,123,196,197,200,215,226,486,496],ntheta:386,nthread:[3,380],ntild:289,ntpc:380,ntptask:380,ntype1:121,ntype2:121,ntype:[3,146,172,196,200,298,300,406,412,441,481,491],nuclear:[9,101,102,158,241,264,297,302,374,406,473],nuclei:[9,101,102,156,158,163,197,249,264,276,285,329,383,406,481],nucleu:[101,102,298,466,502],nudg:[4,6,7,203,262,372,375],nulcear:9,num:[],num_of_collis:3,numa:[1,3,12,380,478],numactl:16,number:[1,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,27,38,40,41,42,43,45,57,65,66,67,68,70,71,72,73,74,75,77,78,79,80,81,82,84,91,94,95,96,97,98,107,108,109,111,112,114,117,118,119,120,121,122,123,124,125,135,141,146,149,150,151,152,153,154,155,157,158,159,160,161,162,164,165,166,167,169,170,171,172,173,174,175,176,180,181,191,192,195,196,197,198,199,200,201,203,204,205,208,210,212,213,214,215,216,217,218,220,221,222,223,225,226,227,235,236,237,239,240,241,243,244,245,246,247,248,249,250,253,260,263,264,268,277,288,289,290,292,293,296,297,298,302,304,307,310,311,315,323,324,325,327,330,331,332,333,335,336,337,338,340,342,343,345,346,348,350,363,365,366,368,370,371,373,374,375,376,377,380,381,382,386,388,393,395,400,403,404,405,406,407,412,413,414,415,416,430,431,432,433,435,437,441,442,443,444,445,448,450,451,452,460,462,463,464,465,466,468,469,470,473,475,476,478,479,481,482,483,484,485,487,488,489,490,491,493,495,496,498,499,500,502,506,507,508,511],number_of_a:3,number_of_b:3,number_of_typ:[],numbond:3,numer:[1,2,3,6,9,11,12,22,38,42,43,45,57,73,79,91,112,122,166,176,180,192,196,199,200,204,205,206,208,209,212,216,218,232,240,243,247,260,263,290,307,310,311,335,340,342,343,345,346,350,370,373,374,393,399,413,430,435,443,444,450,463,473,475,479,480,481,488,491,497,498,499,507],numpi:11,nvalu:[212,216,217,218,479],nvaluelast:479,nvc_get_devic:15,nvcc:[1,9,12,17],nve:[],nve_aspher:[265,269,282],nve_bodi:[266,270,283],nve_spher:[267,271,286],nvida:17,nvidia:[1,3,9,12,14,15,17,380,494],nvt1:502,nvt2:502,nvt:[],nvt_aspher:[265,269,286],nvt_bodi:[266,270],nvt_sphere:[267,271],nvtfe:209,nwait:289,nwchem:7,nxnode:335,o_cor:154,o_shel:154,oascr:7,obei:[3,226,368,476],ober:7,obj_shared_foo:12,obj_target:12,object:[6,8,11,12,15,41,43,199,224,244,250,253,293,312,319,373,374,479,484],observ:[263,297,326,327,330,331,338],obsolet:13,obstacl:[4,245],obtain:[1,3,9,12,29,75,91,108,112,170,201,205,238,241,250,268,289,290,330,365,382,399,430,435,442,451,464,466,490],obviou:[12,473,507],obvious:[199,293,496,507],occ:408,occasion:[3,263,476],occlus:199,occup:[3,170,380,408],occur:[1,3,6,9,11,12,14,17,40,59,61,63,64,73,90,110,170,173,175,192,196,197,200,210,220,223,224,226,235,239,242,245,253,261,277,298,307,323,332,345,346,348,365,376,380,403,406,426,444,463,476,478,479,484,486,490,495,498,507],occurr:[358,481,495,507],oct:11,octahedr:25,octant:478,odd:[42,112,200,220,263,307,326,327,335,496],off:[1,3,6,12,14,15,17,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,37,38,40,41,44,45,46,47,48,49,50,51,52,54,55,56,57,61,63,67,71,73,113,114,115,118,119,121,146,147,149,155,159,170,171,176,178,179,180,181,182,183,184,185,186,187,189,190,191,192,196,197,199,200,203,206,210,218,219,222,223,226,233,238,239,240,242,244,247,248,253,263,265,266,267,268,269,270,271,272,273,277,280,282,283,284,286,292,294,295,299,307,309,310,323,326,328,338,339,340,343,344,349,350,351,352,354,355,356,358,359,360,365,366,373,375,376,378,380,381,382,384,387,388,389,390,391,392,394,395,396,398,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,430,431,435,436,437,438,440,444,445,446,448,450,451,453,460,461,462,463,464,465,466,469,471,472,473,476,477,478,481,483,484,488,490,493,494,495,500,504,506,507,509,511],offend:[3,479],offer:[6,14,18,175,372,396,451,476,490],offic:7,offload:[1,9,12,16,17,244,380],offset:[3,6,59,172,199,226,227,293,374,396,418,422,461,481],offsit:8,often:[1,3,6,7,12,13,14,15,16,17,18,37,56,73,166,191,199,206,215,218,220,224,237,244,263,290,308,359,368,372,373,375,376,377,380,395,400,418,463,464,466,476,495,502,506],ohio:432,old:[3,6,9,203,224,227,263,430,443,453,482,485,489,492,506,509],older:[3,5,12,13,17,200,212,224,263,453,507],oldlac:200,oleinik:386,olfason:[6,25,360,412,493],oliv:200,olivedrab:200,olivi:9,ollila:[250,252,253,254],olmst:[209,288],omega0:360,omega:[],omega_dot:263,omega_ij:[401,402],omega_ijk:466,omega_ik:464,omegai:[119,196,197,325],omegax:[119,196,197,325],omegaz:[119,196,197,325],omgea:6,omiss:[0,7],omit:[192,200,342,390,399,422],omp:[],omp_num_thread:[3,16,18,380],omp_proc_bind:17,ompi_comm_world_local_rank:12,ompi_icc:16,on_the_fli:209,onc:[0,1,2,3,6,11,12,16,41,42,61,62,65,73,95,109,178,198,199,200,203,204,205,220,221,222,227,237,239,241,248,289,293,296,307,323,331,336,338,346,371,374,375,376,409,411,413,414,441,445,478,479,488,495,498,502,507],onelevel:478,onewai:[],ongo:244,oniom:[9,301],onli:[1,2,3,6,7,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,42,43,44,46,47,48,49,50,51,52,54,55,56,57,61,62,63,65,66,67,68,69,70,71,72,73,74,75,77,80,81,82,84,85,87,90,91,92,94,96,97,98,101,102,103,104,105,106,107,108,109,110,111,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,155,156,158,159,160,162,163,164,165,166,167,169,170,171,172,175,176,178,179,181,182,183,184,185,186,187,189,190,191,192,196,197,198,199,200,201,203,204,205,206,207,208,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,230,232,233,234,235,236,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,278,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,296,297,298,299,300,301,302,303,304,307,308,309,310,311,312,313,314,315,316,317,319,323,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,351,352,353,354,355,356,358,359,360,363,365,366,368,370,373,374,375,376,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,478,479,481,482,484,485,486,488,489,490,491,492,493,495,496,497,498,499,500,502,507,508,509],only_group:170,onn:490,onset:[297,358],ontario:9,onto:[146,174,223,227,250,460],onward:2,open:[],opencl:[1,3,7,15,380],opengl:6,openkim:9,openmp:[1,3,7,9,12,16,17,18,363,380,494],openmpi:[12,14,15,16,17,18,380],opensourc:7,oper:[],opl:[],oppelstrup2:9,oppelstrup:[9,433],oppos:[6,40,194,196,197,306,342,366,374,481],opposit:[6,29,72,208,247,254,288,307,338,375,396,426,467,479],opt:[],optic:150,optim:[],option:[],optionn:17,orang:[2,199,200],orbit:[298,300,386,396,406,451,461],orchid:200,order:[1,2,3,6,9,11,12,14,27,29,38,40,42,57,61,65,67,71,73,81,91,93,94,96,97,98,112,114,118,121,136,146,147,149,150,151,152,153,154,155,158,159,160,161,162,164,165,176,181,191,192,196,197,199,200,203,206,211,213,215,216,217,218,219,221,222,223,224,225,230,232,239,241,243,244,246,250,251,253,261,263,288,296,297,301,304,305,306,307,308,309,310,312,317,319,324,330,334,335,336,337,347,348,349,351,352,353,355,358,359,365,374,375,381,382,383,386,395,402,403,404,406,407,409,410,413,415,418,426,430,433,443,444,445,451,461,462,463,464,465,466,467,469,470,476,478,479,481,482,486,488,490,491,495,498,502,507,511],orderomg:3,ordinari:[117,412,440],org:[6,7,11,12,13,14,442],organ:[0,3,6,7,8,395],organis:[448,450],organometal:25,orien:491,orient:[],orienti:[],orientord:[],origid:212,origin:[3,6,7,9,12,73,83,108,109,120,124,168,172,174,195,199,200,203,204,205,212,216,217,221,222,226,230,248,260,263,284,290,293,303,307,308,316,322,333,362,364,365,368,372,381,382,384,386,396,399,400,403,404,412,415,430,440,443,444,464,466,467,468,478,481,482,483,484,485,486,506,509],origin_i:217,origin_x:217,origin_z:217,orlikowski:433,ornl:[7,9,15],orsi:29,ortho:[3,61,174,481],orthogon:[],orthograph:199,orthong:61,orthongon:[61,307],orthonorm:227,orthorhomb:297,os4:171,oscil:[6,9,157,222,226,229,230,248,260,261,263,297,302,307,340,341,343,345,374,383,467,502,507],oscillatori:[260,316],oserror:11,other:[],otherswis:16,otherwis:[1,3,9,12,14,16,17,18,37,40,56,73,107,117,124,150,151,152,165,173,191,197,200,201,210,212,221,222,226,237,239,241,248,263,307,359,360,373,380,388,413,417,427,428,441,470,474,476,479,481,482,502,507],otyp:[396,418,422,426],ouml:502,our:[5,6,7,8,13,250,310,435,464,466,502],out:[1,2,3,6,7,8,11,12,13,14,18,19,21,42,66,68,73,77,94,95,98,99,102,108,109,110,111,113,120,121,149,150,151,152,153,155,156,158,159,160,161,162,164,165,167,169,175,179,196,197,199,200,201,203,216,220,221,222,225,233,238,239,245,247,250,255,277,289,291,292,293,302,303,304,307,320,335,344,346,347,348,349,351,355,363,364,368,371,375,379,406,413,429,461,475,476,478,479,484,485,486,488,489,490,492,495,497,498,499,503,505,507,508,509,510,511],outcom:[307,508],outer2:[391,411],outer:[3,8,16,73,231,245,348,364,371,373,379,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,436,438,440,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,468,469,470,471,472,473,476,489,490,495,501,507],outer_distance_cutoff:412,outermost:[38,57,73,204,205,260,263,376,463,490],outfil:[13,478],outlin:[6,199],outmost:244,outpt:[],output:[],output_frequ:209,outputss:133,outsid:[3,59,61,73,162,172,195,196,197,198,199,200,201,215,216,227,239,245,307,308,323,328,329,342,343,344,345,346,363,375,387,389,396,406,418,420,438,446,479,481,482,484,491,498,508],outuput:[],outut:6,outward:[73,170,340,344,345,481,490],over:[1,3,5,6,7,9,12,16,18,27,40,42,43,56,62,67,70,71,73,81,82,91,92,93,94,96,97,106,108,110,112,114,121,122,131,132,138,143,146,147,152,155,158,166,168,181,192,199,201,203,204,205,211,212,213,214,215,216,217,218,219,220,221,222,226,227,237,240,241,245,247,248,249,253,260,261,262,263,264,265,266,267,269,270,271,282,283,284,285,286,288,293,294,297,304,305,306,307,308,312,320,323,326,327,328,329,331,334,337,338,340,342,343,344,345,346,349,364,367,375,376,377,380,394,400,404,405,406,407,412,427,430,433,441,452,453,461,462,463,464,465,466,469,477,478,479,484,486,487,489,490,495,496,498,499,507,508],overal:[6,18,25,61,166,224,230,263,264,290,310,323,348,371,406,412,413,452],overalap:307,overcom:[277,323],overflow:[3,374,376],overhead:[6,11,19,42,200,212,214,216,217,220,236,296,376,377,484,500],overkil:307,overlai:[],overlaid:7,overlap:[3,13,16,64,78,172,175,192,200,208,211,212,215,216,217,218,227,231,277,293,298,304,307,308,323,341,345,365,368,371,373,374,380,400,406,410,413,416,426,447,449,453,468,481,484,490],overload:1,overrid:[3,9,12,14,16,17,22,45,73,158,172,180,199,200,204,205,224,231,258,263,350,365,376,393,412,413,430,435,443,478,479,491,493,498,507],overridden:[6,172,199,268,307,416,427,435,453,461,489,507,509],overview:[],overwrit:[11,12,22,45,180,200,212,213,214,215,216,217,218,308,350,363,369,393,430,479,482],overwritten:[197,295,334,363,412,413,476,477,482],own:[3,4,6,7,8,11,12,13,15,17,40,42,61,63,65,67,68,71,73,75,77,81,94,97,98,109,111,119,120,121,123,125,152,155,167,169,170,196,197,200,203,209,211,212,213,214,215,216,217,218,220,223,224,226,237,240,241,247,248,250,258,261,263,265,266,267,268,269,270,271,282,283,284,286,290,294,302,307,308,326,327,328,337,365,375,380,382,386,395,405,415,441,443,444,462,464,465,466,469,478,491,496,498,508],oxford:[29,91,399],oxid:[9,395,396,451],oxygen:[6,41,236,396,418,422,451,481],oxygen_c:154,p_e:335,p_ik:441,p_pi:386,pacakg:380,pack:[5,8,69,341,380,386,430],pack_bord:8,pack_border_bodi:8,pack_border_hybrid:8,pack_border_vel:8,pack_comm:8,pack_comm_bodi:8,pack_comm_hybrid:8,pack_comm_vel:8,pack_exchang:8,pack_restart:8,pack_revers:8,pack_reverse_comm:8,pack_reverse_hybrid:8,packaag:380,packag:[],packakg:15,packet:[7,9,41,199,383,406],pad:[3,196,197,199,200,290,507],padua:[9,13],page:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,45,56,59,61,65,68,70,77,91,94,98,107,109,110,111,113,115,118,120,123,125,147,150,151,152,165,167,169,172,173,174,180,191,195,196,197,198,199,200,201,203,204,205,210,211,212,213,214,215,216,217,218,227,239,246,247,248,258,263,264,269,270,271,275,282,283,284,285,286,293,296,307,320,323,326,327,328,337,341,344,346,348,350,359,364,373,374,375,376,380,381,382,385,393,395,396,404,405,407,412,413,415,416,430,431,432,435,437,441,442,452,461,462,464,466,468,469,479,481,482,483,484,486,489,490,491,493,498,499,507,508,509,510],pai:[15,18],pair:[],pair_:[91,204,205],pair_airebo:415,pair_charmm:426,pair_class:8,pair_coeff:[],pair_dpd:[9,401],pair_eam:381,pair_eff:158,pair_foo:8,pair_hybrid:[413,467],pair_interact:209,pair_list:417,pair_lj:426,pair_lj_cut:8,pair_lj_soft_coul_soft:91,pair_modifi:[],pair_sph:[454,455,456,457,458,459],pair_styl:[],pair_tally_callback:8,pair_writ:[],paircoeff:3,pairfoo:8,pairij:[3,481],pairkim:3,pairstyl:8,pairwis:[],palegoldenrod:200,palegreen:200,paleturquois:200,palevioletr:200,pan:199,panagiotopoulo:[397,408],pandit:[9,300,444],papaconstantopoulo:381,papayawhip:200,paper:[3,6,7,8,9,13,40,41,66,146,160,166,184,247,250,254,262,292,298,300,307,323,331,335,338,365,372,375,382,390,396,410,412,415,420,422,440,443,444,464,466,476,495],paradyn:5,paraemt:445,paragraph:[73,160,340,368,463,482,483],parallel:[],parallelepip:[6,174,368,481,484],parallelipip:[174,289],paralleliz:292,param:[3,298,300,416,478,484],paramet:[],parameter:[124,171,382,386,395,396,404,405,406,407,415,430,431,432,441,443,444,451,462,464,465,466,469],parameter_fil:209,parameterizaion:396,parametr:[6,9,36,405,442,446],paramt:[110,298,342,445],paramter:395,paratem:426,paraview:[197,308],parent:[3,8,346],parenthes:[38,57,192,235,410,463,507],parenthesi:[2,212,348,507],parinello:[6,7],pariticl:220,paritlc:3,park:[3,7,9,209,312,432,440],parmin:433,parrinello1981:224,parrinello:[224,241,261,263,264,297,327],pars:[],parser:[12,507],part:[0,1,2,3,6,7,8,9,11,12,17,20,21,23,24,25,26,27,28,29,30,31,32,35,36,37,38,41,42,44,46,47,48,49,50,52,54,55,56,57,66,69,72,73,74,80,82,87,96,101,102,103,104,105,106,108,110,113,114,115,117,118,121,124,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,154,156,158,159,163,164,166,170,171,175,178,179,181,182,183,184,186,187,189,190,191,192,196,197,198,200,201,203,206,207,208,210,214,217,219,220,221,222,223,224,225,226,227,229,232,233,236,237,238,239,240,241,242,244,245,246,247,248,249,250,251,252,253,254,256,257,258,261,263,264,265,266,267,268,269,270,271,272,273,274,275,276,278,280,281,282,283,284,285,286,288,289,290,292,293,297,298,299,300,301,302,303,304,306,307,309,310,312,313,314,315,316,317,319,320,322,323,326,328,329,330,331,332,333,334,335,336,338,339,340,341,342,343,344,346,347,348,349,351,352,354,355,358,359,360,365,366,373,374,375,376,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,403,404,405,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,436,437,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,478,479,481,482,483,484,488,489,490,493,499,507,511],partai:[9,442],parti:9,partial:[],partic:6,particip:[222,385,416,468],particl:[],particleenergi:3,particleviri:3,particular:[1,3,6,8,10,12,41,65,67,71,72,73,81,97,114,119,121,122,146,172,195,196,197,203,208,216,220,223,239,240,245,246,250,260,263,288,293,306,307,310,330,341,346,349,366,368,371,374,380,385,386,387,389,391,392,394,398,402,405,406,409,411,413,418,422,426,429,437,438,445,446,461,462,464,465,466,469,476,478,481,482,483,488,489,491,499,507,508,510,511],particularli:[6,7,9,12,15,16,25,40,199,224,307,366,406],particuolog:43,partilc:323,partit:[],partitoin:64,partner:[3,7,63,221,222,223,248,323,338,467,491,496,502],pascal:[9,13,506],pass:[6,7,8,11,68,76,77,83,93,94,98,108,109,110,111,167,196,197,199,200,201,224,225,237,239,260,261,263,296,323,340,364,376,380,413,416,443,460,479,481,482,486,492,507,510],passphras:12,past:[],patch:[0,12],patchi:307,patel:433,path:[3,6,7,11,12,13,15,201,246,262,290,312,323,330,335,375,381,382,386,393,404,405,407,415,430,431,432,437,441,442,443,451,452,462,464,466,469,482],pathtolammp:451,patient:12,patom1:121,patom2:121,patrick:465,pattern:[3,7,12,64,75,483],pattnaik:307,paul:[0,7,13,247,249],pauli:[9,406,451],paus:489,paves:290,payn:[146,442,452],pb2:171,pb4:171,pbc:[73,340,383],pchain:[263,264,268,307],pcie:1,pd2:171,pd4:171,pdamp:[263,264,268,294,307],pdb:[6,13,201],pdebuyl:9,pdf:[0,8,9,13,17,41,104,105,106,117,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,225,246,256,257,313,314,315,316,319,440,454,455,456,457,458,459,491],pdim:338,pdlammp:[80,82,440],pdlammps_ep:[117,440],pdlammps_v:440,pe_eta:263,pe_etap:263,pe_omega:263,pe_strain:263,peachei:13,peachpuff:200,peak:408,pearlman:91,peculiar:12,pedersen:366,peform:[40,299],penalti:[14,443,444],pencil:[6,73,160,216],pend:3,penetr:[43,126,447,449,491],penetret:41,peng:171,penn:13,pentium:10,peopl:[7,8,9,12],peptid:[4,9,225],per:[],peratom:[3,116,147,170],perceiv:199,percent:[3,12,16,224,380,462],percentag:[1,12,224,263,293,294,307],percol:222,perfect:[6,42,72,75,96,220,288,375],perfectli:[42,220,482],perfom:[6,375],perform:[],performac:1,pergamon:[430,466,473],perhap:368,peri:[],peridyma:80,peridynam:[3,4,6,7,9,41,65,80,82,117,440,461,481,491],perimitt:397,period:[],perioid:340,perl:[6,13],perm0:506,perman:[3,40,55,73,176,221,222,244,306,346,380,412,485,493],permeabl:287,permiss:[222,479],permit:[6,250,433],permitt:[397,466,472,473],permut:[12,405,462,464,466,469],perpendicular:[6,73,150,199,226,245,255,260,262,288,291,316,340,341,372,481],perram:[366,409],persepct:199,persist:[3,8,73,237,307,380,478,479,483,487,507],person:9,persp:[3,199],perspect:199,pertain:[393,461],perturb:[9,13,72,91,259,305,340,343,345,486],peru:200,peskin:250,pessimist:366,petersen:[323,366],pettifor:[386,461],pettifor_1:386,pettifor_2:386,pettifor_3:386,pfactor:199,pforc:479,phantom:244,pharmaceut:7,phase:[3,12,16,263,330,338,386,418,465,478],phd:442,phenol:502,phenomena:406,phi0:[190,306],phi1:179,phi2:[179,405,462],phi3:[179,405,462],phi:[1,3,4,7,9,12,16,17,81,96,112,146,191,192,199,242,289,306,352,380,381,386,404,407,430,431,432,494],phi_ij:[386,407,441],philadelphia:9,phillip:[248,400,502],phillpot:[299,395,396,451],philosoph:404,philosophi:[6,7,246],phonon:[],phophor:452,phosphid:452,phy:[6,7,13,20,21,25,40,44,46,47,66,72,75,91,92,96,112,116,118,146,147,154,160,178,179,189,198,210,214,224,225,230,240,241,246,247,248,249,250,261,262,263,264,268,284,285,289,290,294,297,299,302,307,310,311,312,323,326,327,330,331,332,333,335,338,340,349,358,360,365,366,372,375,382,386,387,391,392,394,395,396,397,398,399,400,402,404,405,406,408,409,410,411,412,415,418,420,422,423,426,427,428,429,430,432,434,435,438,440,441,445,451,452,460,462,463,464,465,466,467,469,476,490,493,495,502],physic:[3,6,9,12,14,16,17,18,41,43,54,61,126,154,166,209,226,241,247,249,250,252,253,254,261,289,298,300,334,335,366,368,375,380,382,384,390,394,404,412,413,433,442,443,444,447,455,456,458,459,476,478,490,491,496,506],physica:[427,428],physik:[7,9],pic:9,picki:8,picocoulomb:506,picogram:506,picosecond:[200,226,499,506],picosend:406,pictur:7,pie:[],piec:[3,11,146,200,263,488,511],pierr:9,pieter:13,pimd:[],pin:16,pink:200,pipe:[6,196,199],pipelin:[3,6],pisarev:335,pishevar:400,piston:[],pitera:6,pixel:199,pizza:[4,6,7,11,13,42,196,199,220],pjintv:13,pka:335,place:[3,6,7,9,11,12,33,42,51,73,91,166,172,176,185,192,196,199,200,202,203,204,205,222,223,226,239,240,241,243,246,247,248,249,251,253,254,263,269,270,271,282,283,286,293,296,305,307,326,327,328,335,340,343,345,364,393,412,461,468,478,479,482,489,491,496,499,507],placehold:[33,185,381,382,395,404,407,414,415,430,431,432,437,441,443,444,452,460,462,464,465,466,469],placement:[368,418],plai:[199,330],plain:[9,426,479],plan:[3,5,6,17,174,481],planar:[6,41,43,245,288,341,358,360],planck:[239,290],plane:[3,6,9,42,43,59,61,69,73,96,199,203,209,216,220,242,245,255,288,291,301,320,322,335,341,349,351,352,353,354,355,360,368,428,468,484,491],planeforc:[],plasma:[9,92,264,335,406],plastic:[],plastic_strain:[],plastic_strain_r:[],platform:[1,3,7,9,12,13,15,17,196,199,201,483,488,511],plath:[6,95,203,331,338],player:199,pleas:[0,3,7,11,12,13,209,241,250,254,289,292,303,330,346,405,407,440,448,450,451],plen:383,plimpton:[0,5,7,72,118,147,223,288,298,323,410,440],plo:29,plog:[3,12,490],ploop:[263,264,268],plot:[7,11,13,297,424,426,463,470],plu:[3,11,12,40,61,70,101,170,175,200,219,224,226,227,268,307,377,406,416],plug:9,plugin:[9,13,201,482],plum:200,pm3:171,pmb:[],pme:366,pmf:[225,312,320],png:[3,12,196,199],pni:199,poariz:6,poem:[],point1:481,point2:481,point3:481,point:[],point_data:308,pointer:[3,7,8,9,11,237,479],pois:506,poiseuil:[4,206,242],poisson:[61,226,366,410],poisson_solv:209,polak:372,polar:[6,7,112,146,154,171,209,229,395,396,418,467,502],polar_off:395,polar_on:395,polariz:[],poli:[],politano:[9,451],pollock:[7,366],polya:346,polybond:13,polychain:307,polydispers:[3,374,388,394,410,427,428,461,472],polygon:[],polyhedron:170,polym:[],polymer:7,polymorph:[],polynomi:[9,38,57,192,404,424,435,451,456,463],polytechn:292,poor:[16,17,42,220,284,285,310,380,424],poorli:[372,373],pop:[3,8],popen:12,popul:[12,302,368,403,481],popular:[12,196,405],pore:320,poros:175,porou:[250,253],port:[244,246],portabl:[7,9,12,196,198,225,443,483],portion:[1,3,11,12,15,16,42,55,73,92,95,113,114,116,119,147,148,162,196,197,200,211,212,215,216,217,218,220,224,236,250,263,265,266,267,269,270,271,299,304,305,307,308,348,364,376,380,387,389,390,391,392,396,397,399,400,406,408,409,411,412,418,422,426,429,438,445,446,466,470,480,481,486,490,491,500,507],poschel:410,posfreq:304,posit:[3,6,14,27,40,41,42,43,47,59,61,72,73,83,93,94,108,109,114,123,124,128,146,147,155,170,171,172,174,175,176,181,183,192,195,197,198,199,200,203,204,206,208,210,211,212,215,216,217,220,221,222,223,224,225,226,227,230,232,239,240,241,242,244,245,247,248,249,250,252,253,256,257,260,261,263,264,265,266,267,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,288,289,290,292,293,294,297,298,302,304,305,307,310,312,316,319,320,322,323,325,326,327,328,330,332,333,334,335,338,340,341,342,343,344,345,346,349,365,368,375,382,383,385,388,400,402,403,406,408,421,444,451,460,463,468,476,481,484,491,502,507,508],posix:244,posix_memalign:12,possibl:[1,3,6,8,9,11,12,15,38,41,42,56,61,65,72,73,91,119,121,146,147,150,151,165,195,196,197,198,200,203,205,209,210,216,220,221,222,223,227,229,234,241,248,288,293,301,302,304,307,319,323,325,335,336,354,364,366,373,376,377,380,403,412,430,444,448,450,451,463,469,479,485,494,495,496,499,502,507,508,510],post:[],post_forc:8,post_force_integr:8,post_force_respa:8,post_integrate_respa:8,postit:[216,217,277],postiv:90,postma:[294,326],postprocess:13,pot:[410,444],potentail:407,potenti:[],potentiel:426,potetni:413,potin:433,potpourri:9,pour:[],pourtoi:330,pow:226,powderblu:200,power7:17,power8:17,power:[3,9,11,110,146,200,302,365,380,386,479],pparam:[91,204,205],ppm:[12,196,199],ppn:[14,15,16,17,18,380],pppm:[],pppm_disp:3,pppmdisp:3,pproni:[3,240],pr3:171,pr4:171,practic:[3,12,224,263,264,289,296,469,478],prb:[464,466],prd:[],pre:[],pre_exchang:8,pre_forc:8,pre_force_respa:8,pre_neighbor:8,prec:451,prec_tim:14,prece:450,preced:[2,6,61,197,211,212,213,214,215,216,217,218,246,304,308,348,368,375,380,386,412,495,498,499,507],preceed:[11,12,73,160,213,340,479,507],precipit:170,precis:[1,3,9,12,13,14,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,44,46,47,48,49,50,52,54,55,57,108,115,118,149,159,172,178,179,181,182,183,184,186,187,189,190,192,196,200,206,212,218,219,224,226,233,238,242,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,298,299,300,307,309,310,326,328,339,343,349,351,352,354,355,358,360,365,366,373,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,404,405,407,408,409,410,411,412,418,419,420,421,422,423,424,425,426,427,431,433,436,437,438,440,443,445,446,451,453,462,463,464,465,466,469,471,472,473,483,484,490,491,494,499,502,506,507,508],precv:478,predefin:[190,200,346,406],predict:[1,6,10,12,277,307,380],preexponenti:495,prefactor:[24,25,28,32,35,36,166,180,191,204,205,213,340,351,355,358,373,394,408,437,445,446,453,472],prefer:[7,8,12,306,336,382],prefix:[11,12,199,225,289,475,478],preliminari:[38,57,192,235,463],prematur:373,prepar:[9,298,301,323,492,502],prepend:443,preprint:[146,452],preprocessor:244,prerecord:225,prescrib:[6,8,150,151,152,165,203,204,209,212,227,260,279,336],presenc:[196,221,222,250,253,427,428,433,472,509],present:[1,3,12,18,170,192,198,199,227,240,241,246,250,251,253,254,302,319,341,344,347,395,406,417,426,433,444,445,451,478,502],preserv:[3,61,224,226,263,310,323,345,482],press:[],pressdown:219,pressur:[],pressure_with_eviri:406,presum:[75,161,203,204,205,226,375,413,484],prevent:[2,3,6,41,126,227,238,293,323,334,358,365,371,373,375,380,400,413,439,455,456,458,460,479,483,489,491,502,507],previou:[],previouli:227,previous:[3,11,61,63,73,90,107,123,125,161,172,174,176,195,196,197,198,200,208,210,211,212,213,215,216,217,218,226,227,239,245,258,260,293,305,307,309,310,335,337,340,341,342,343,345,346,367,410,461,476,479,483,484,494,496,498,499,503,504,505,507,508],prevoiu:341,price:[6,399],primari:[0,6,9,335],primarili:[5,7,9,17,148],primaritli:[],prime:[230,248,411,433,464,466,478],primit:[3,6,343,344,368],princip:[3,244,451],principl:[6,9,11,244,264,298,406,414,433,462,478],prinicp:[43,307,374],print:[],printabl:2,printflag:414,printfluid:250,prior:[170,194,311,367,510],priori:490,prioriz:380,prism:[3,6,160,174,484],priveleg:3,privileg:[11,12,244],prob:[221,222],probab:453,probabl:[3,8,12,41,73,162,175,176,178,210,220,221,222,223,227,239,248,263,293,340,346,373,435,463,476,495,502],probe:507,problem:[],problemat:239,proc:[1,3,8,11,12,15,119,196,197,364,478],proce:[42,55,176,220,231,375,433,488,496,499],procedur:[6,12,40,42,200,210,220,239,247,248,249,263,265,266,267,268,269,270,271,282,283,284,285,286,289,326,327,328,329,332,333,373,375,382,388,482,502],proceed:[12,433],procesor:[42,478],process:[],processor:[],processsor:[42,220,478],procp1:[196,197],procsessor:500,procssor:490,produc:[1,3,4,6,7,9,12,13,14,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,43,44,46,47,48,49,50,52,54,55,57,65,67,70,71,73,81,97,114,115,116,118,119,120,121,123,125,147,149,159,170,178,179,181,182,183,184,186,187,189,190,192,196,197,200,203,206,211,212,213,215,216,217,218,219,220,223,226,233,237,238,240,241,242,247,248,249,258,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,293,297,298,299,302,307,308,309,310,324,325,326,328,335,336,337,339,340,343,348,349,351,352,354,355,358,360,366,373,375,378,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,436,437,438,440,441,444,445,446,453,462,463,464,465,466,469,471,472,473,476,478,483,484,486,487,490,495,496,507,508],product:[6,16,17,18,146,170,226,284,298,336,380,383,406,444,478,507],proessor:380,prof:292,profi:161,profil:[],program:[3,4,6,7,9,11,12,13,17,148,196,199,200,201,203,225,237,244,250,301,404,479,480,492,507],programm:[13,17],progress:[1,42,220,244,261,297,372,373,375,499,502],prohibit:491,project:[6,7,13,14,372,461],promis:7,promot:386,prompt:[8,11,12,244,492],proni:[3,240,241],proofread:8,prop:[6,296],propag:[4,9,208,263,297,313,406,413],propens:6,proper:[223,288,430,479],properati:296,properli:[206,232,307,311,319,374,375,402,479,508],properti:[],propoerti:323,proport:[6,40,42,91,108,109,168,220,247,248,249,297,331,338,339,410],proportion:247,propos:[6,146,210,224,239,263,284,302,418,432,465,467],prospect:7,protect:323,protein:[7,10,172,305,307,321,481,489],protocol:244,proton:[466,473,506],prototyp:[10,43,440],prouduc:[218,337],prove:[84,85,234,250,311],proven:284,provid:[1,3,4,6,7,8,9,11,12,13,14,15,16,17,18,29,41,43,63,69,72,124,145,148,166,170,171,172,198,199,201,211,212,218,223,224,225,226,237,239,244,246,250,254,261,263,289,297,298,301,302,307,311,312,330,332,333,336,337,348,363,365,366,371,375,380,382,386,388,393,395,396,400,405,406,410,412,415,417,426,427,430,432,433,441,442,443,444,451,452,460,461,462,464,465,466,469,478,483,489,491,494,495,499,500,507],proxim:195,psa:343,pscreen:[3,12,490],pscrozi:[0,7,13],psec:[200,226,243,247,248,263,294,307,326,327,501,506],psend:478,pseudo:[406,476,481,486],pseudodynam:330,pseudopotenti:[9,433],psf:6,psi:[407,472],psi_ij:407,pstart:[3,263,264,268,294,307],pstop:[3,263,264,268,294,307],pstyle:[91,113,204,205],psu:[443,444],psuedo:486,pt2:171,pt4:171,ptarget:224,pthread:[12,17],ptr:[6,11,237,479],ptype1:121,ptype2:121,pu3:171,pu4:171,pu6:171,publicli:5,publish:[7,250,254,298,396,430,433,464,466],pull:[312,320],puls:335,pump:[427,428],punctuat:[2,476,495],purchas:199,purdu:[9,13],pure:[11,323,413,431,432,464,466,490],purg:[3,482],purpl:[2,200],purport:11,purpos:[3,6,7,12,43,63,73,124,134,140,155,156,171,172,174,176,192,196,216,218,223,224,247,288,290,293,295,306,323,365,380,390,416,422,433,435,468,474,481,484,488,491,493,494,507,511],push:[3,8,206,219,226,245,262,288,305,312,373,410,453],pushd:245,put:[3,6,8,11,12,13,40,61,160,172,196,227,231,342,343,346,368,443,479,481,485],putenv:[492,507],px1:490,px2:490,pxx:[224,263,294,307,365,366,498,499],pxy:[3,6,499],pxz:[3,6,499],py1:490,py2:490,pydir:11,pyi:[224,263,294,307,365,366,499],pymol:[7,11,13],pymol_aspher:[],pympi:11,pypar:11,python:[],pythonpath:11,pyz:[3,6,499],pz1:490,pz2:490,pzz:[224,261,263,294,297,307,365,366,499],q_1:451,q_2:451,q_3:451,q_c:[],q_d:502,q_i:[407,426],q_j:426,qbmsst:[],qcore:298,qdamp:298,qdist:[396,418,422,426],qeq1:298,qeq2:298,qeq:[],qeqal:451,qeqallparallel:451,qfile:[298,396],qin:243,qinitmod:451,qmin:372,qmmm:[],qmol:301,qout:243,qstep:298,qtb:[],quad:[12,18,380,478],quadrat:[],quadratur:[91,209],quadrupl:381,quadruplet:[188,191,193,349,351,352,353,355,357,358,359,361],qualifi:[3,246],qualiti:[7,9,199,200],quantic:451,quantit:[76,83,108,109,110,168,410],quantiti:[],quantum:[6,9,146,237,241,290,297,301,302,386,406,433,451,461],quantum_temperatur:297,quartic:[],quartic_spher:209,quartz:[297,302],quasi:290,quat:[3,491],quaternion:[3,6,41,86,119,136,150,151,172,265,266,269,270,273,274,275,282,283,409,481,491],quati:[119,481],quatj:[119,481],quatk:[119,481],quatw:[119,481],queen:13,quench:[346,476,495],queri:[3,11,55,279,479,507],quest:[6,237],question:[8,9,12,13,288,346,440,507],queteschin:9,quick:[0,12,14,15,16,17,18,19],quickli:[3,4,8,12,13,40,96,220,226,239,244,323,372,373,375],quickmin:[371,372,373,375,495],quicktim:[4,199],quip:[],quit:[],quot:[2,3,12,198,253,295,348,430,476,477,479,489,507],quotat:451,r10:386,r12:409,r_1:146,r_2:146,r_c:[397,399,408,466],r_cut:[386,429],r_d:502,r_e:407,r_ewald:308,r_fu:[427,428],r_i:[29,146],r_ii:146,r_ij:[29,386,406,441,473],r_ik:441,r_j:29,r_jik:441,r_m:429,r_max:217,r_me:397,r_mh:408,r_min:[217,398],r_ub:20,r_x86_64_32:12,ra2:171,rad2theta:171,rad:346,radhi:484,radial:[65,73,101,102,119,122,146,156,158,163,212,217,249,264,276,285,320,329,373,406,412,435,481,484],radian:[20,21,24,28,32,35,36,38,171,179,190,192,306,349,351,355,358,481,484,491],radiat:[124,171,335],radic:[174,481],radii:[73,78,146,223,227,394,404,409,410,427,428,433,447,449,472,484],radit:406,radiu:[],radlo:484,rafferti:338,rahman:[6,7,224,261,263,264,297,440],rai:[9,17,171],ram:466,ramirez:214,ramp:[],ran:[3,4,6,10,11],random:[3,6,40,172,175,195,199,208,210,221,222,223,225,227,236,239,240,241,247,248,249,250,259,263,290,293,297,302,305,307,311,323,327,330,335,339,342,388,400,401,402,403,476,491,496,502,507,508],random_se:476,randomli:[172,175,210,227,239,247,293,323,345,495,496],rang:[1,3,6,7,8,9,10,12,14,15,16,18,38,40,57,63,73,74,79,92,112,114,115,116,118,122,123,127,146,147,158,166,171,173,176,177,184,192,196,197,199,200,209,210,222,226,227,239,241,293,308,323,324,330,331,336,338,365,366,373,376,377,380,382,384,386,387,388,389,390,391,392,394,396,397,398,399,400,403,404,406,409,411,412,413,415,418,419,420,421,422,423,424,425,426,427,428,429,430,433,434,435,436,438,441,444,445,446,451,460,461,463,466,471,472,473,475,479,490,491,499,510],rangecoulomb:[],rank:[6,11,12,244,336,363,478],rankin:268,raphson:3,rapid:[4,6,11],rapidli:[3,8,12,73,223,247,261,263,307,326,327,339,396,400],rapp:[298,299,300],rappe_and_goddard:299,rare:6,rasmol:[6,7],rasmussen:409,raster3d:[6,7],rate:[],rather:[1,2,6,9,12,41,42,64,118,155,199,220,226,240,241,307,327,335,339,341,342,343,346,406,443,463,482,486,491,493,498,507],ratio:[6,10,61,91,106,146,210,220,226,247,249,323,331,338,339,365,378,409,410,445,455,468,478,481,491,495],rational:[336,493],rattl:[],rattle_debug:310,ravelo:[268,420],rayleigh:[261,297],rb1:171,rbb:451,rbg:200,rcb:[3,42,220],rcm:[93,94],rcmx:[93,94],rcmy:[93,94],rcut:63,rcutfac:[146,452],rd1:375,rdc:17,rdf:[],rdn:375,rdt:375,rdx:4,reach:[6,12,42,125,214,220,222,224,248,268,316,323,330,348,364,379,397,502,507],react:6,reactant:406,reaction:[312,321,334,345,375,406],reactiv:[9,304,382],read:[2,3,6,7,8,9,11,12,13,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,37,38,39,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,61,121,170,172,173,175,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,195,196,197,199,200,201,202,203,209,210,223,224,226,227,235,239,241,244,260,261,263,265,266,267,268,269,270,271,282,283,284,285,286,289,290,292,293,295,296,300,307,310,312,316,319,322,325,333,334,335,341,347,349,350,351,352,353,354,355,357,358,359,360,361,362,364,370,374,375,379,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,401,402,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,436,438,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,472,473,474,476,478,481,482,483,485,486,487,488,489,491,492,493,495,507,508,509,511],read_data:[],read_dump:[],read_restart:[],read_restart_set:8,readabl:[197,199,374,488,511],reader:[3,13,482],readi:[11,12,173,175,176,244,491,502,509,510,511],readm:[1,4,6,8,9,11,12,13,170,196,197,201,301,414,433,443,444,479],real:[3,6,7,11,27,30,31,61,73,95,96,112,146,161,172,181,195,200,208,216,217,226,227,230,244,245,248,260,290,297,302,305,339,340,342,343,345,354,365,366,368,371,377,396,433,435,443,444,466,481,484,490,498,501,506,508],realist:[3,227,485],realiz:[73,203,479],realli:[1,3,8,12,118,128,147,200,245,376,413,493],realloc:3,realtim:244,reamin:[340,344],rearrang:[197,375],reason:[3,6,7,11,12,19,40,153,164,172,212,216,217,247,294,307,332,333,336,346,374,375,380,393,397,406,407,408,428,435,468,470,485,490,508],reax:[],reax_def:3,reaxc:[],reaxff:[3,4,5,7,9,13,203,298,300,303,304,413,443,444,461,493],rebal:[42,220],rebalanc:[42,220],rebo:[],rebuild:[11,12,14,15,16,239,376,400,499],rebuilt:[3,12,196,197,198,199,201,376,380],recalcul:[73,91,323],receiv:[3,219,244,246,288,478],recent:[],reciproc:[6,12,124,170,171,289,365,387,389,390,396,399,406,418,422,438,446,495],recog:12,recoginz:3,recogn:[3,12,16,75,174,221,222,263,374,404,430,443,479,481,488,489,502],recomend:6,recommend:[7,9,12,14,16,199,200,297,333,365,406,413,427,428,433,444,445,448,450,451,490,500],recompil:[1,3,9,12,201,310],recomput:[107,134,176,231,312,403,493],reconstruct:[3,225,451],record:[201,225,312],recov:[224,263],recreat:347,rectangl:[42,220,368],rectangular:[7,42,64,174,220,239,368,481,483,485],rectilinear:[124,171,197],rector:54,recurs:[42,220,386,468],recust:42,recv:478,red:[2,10,199,200,223,290],redefin:[3,483,489,507],redirect:12,redo:12,reduc:[],reduct:[18,19,123,124,171,261,297,365],redund:407,ree:456,reed:[261,297],rees:[7,9,13],ref:[332,333,372],refactor:6,refer:[],referenc:[3,6,12,65,70,73,120,196,197,203,213,218,239,296,337,366,396,412,437,445,479,499,507],reflect:[],reformat:7,refresh:209,reg:484,regard:[6,61,260,310,311,316,440,444],regardless:[15,73,172,175,195,215,216,226,247,263,265,266,267,269,270,271,294,307,317,323,380,478,484,491],regim:[6,331,338,397,490],region:[],region_spher:8,region_styl:344,regist:[8,122,148,319,443,444],regoin:6,regress:507,regspher:172,regstrip:346,regul:6,regular:[1,3,9,42,64,92,170,174,196,199,210,220,239,335,366,397,416,478,481,483,485],reigon:507,reinhardt:[332,333],reject:[172,223,443,496],rel:[1,6,14,27,36,42,61,73,96,108,128,136,146,150,154,155,157,172,181,200,203,210,216,220,226,227,230,239,245,248,259,260,284,288,293,302,304,305,312,320,323,325,330,331,335,342,346,365,366,373,406,409,410,427,428,430,445,472,482,490,495,499,502,508],relat:[],relatic:[],relationship:[6,235,298,348,365,451,472,502,507],relax:[],releas:[0,5,7,8,13,221],relect:[3,435],reles:43,relev:[2,6,12,42,80,82,117,134,172,176,200,204,205,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,226,227,228,231,233,236,238,239,240,243,244,250,251,252,254,255,256,257,259,260,262,272,273,274,275,276,277,278,279,280,281,287,291,292,293,295,296,299,301,303,304,305,308,309,310,312,317,321,323,324,325,330,331,334,335,336,337,338,339,340,341,342,343,345,346,365,373,383,384,388,394,396,397,399,400,403,406,408,409,410,411,412,417,419,420,421,423,424,425,427,428,435,436,440,445,453,460,463,471,472,473,478,494,508],reli:[3,12,299,406,444,473,481,491],reloc:12,remain:[7,12,33,37,42,51,56,61,73,91,109,152,153,154,155,159,160,161,162,164,175,185,191,192,196,204,205,210,212,213,216,217,224,226,247,248,255,263,264,269,270,271,282,283,284,286,291,292,315,323,326,327,328,334,335,346,348,356,359,374,386,406,413,426,433,435,461,476,481,482,486,491,493,495,499,502,507,508],remaina:386,remaind:[172,196,227,293,323,336,466,481],remap:[3,6,12,61,63,73,155,172,195,216,226,245,260,284,365,481,482,483],remedi:[6,502],rememb:2,remov:[2,3,6,8,9,13,55,73,74,79,96,112,120,122,146,150,151,152,153,154,155,159,160,161,162,164,165,172,175,176,197,203,212,216,221,236,247,248,253,259,261,263,269,270,271,282,283,284,286,292,298,307,308,310,323,326,327,328,330,346,365,375,399,428,433,481,484,492,493,507,508],remove_bia:8,remove_bias_al:8,remove_molecul:209,remove_sourc:209,remove_speci:209,ren:171,renam:[12,347,492],render:[12,13,196,199,200],rendon:[263,264],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:[2,3,6,11,12,42,65,93,94,123,149,150,151,152,153,154,155,158,159,160,161,162,164,165,196,197,199,200,201,212,213,215,216,217,218,220,223,227,247,268,295,302,304,396,420,463,482,483,488,489,499,507,508,509,511],replic:[],replica:[],replica_fil:12,report:[],repositori:[7,12,414,442,443,444],reprens:335,repres:[1,3,6,8,9,12,15,41,42,43,61,69,73,94,119,122,184,192,196,197,199,212,213,214,215,216,217,218,224,230,240,242,247,250,263,290,292,294,302,307,308,312,320,335,337,344,366,375,381,386,409,416,426,427,428,430,431,432,438,441,443,444,467,468,476,478,481,491,493,496,502,507,509],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:[6,7,9,36,41,46,47,114,245,298,340,341,344,382,386,394,396,400,406,410,412,426,430,434,451,460,466,469,472,473,491],reqir:[298,300],request:[3,6,8,12,42,108,175,192,196,244,250,305,311,323,325,363,365,435,443,444,476,486,491,495,507,508,509],requir:[],rerun:[],rescal:[],research:[5,7,84,85,234,250,254,311,433,476,495],resembl:302,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],resort:3,resourc:[7,381,404],respa:[3,16,231,244,263,378,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,428,429,430,431,432,433,434,436,438,440,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,468,469,471,472,473,489,490,501,507],respecifi:433,respect:[1,6,9,10,13,14,15,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,46,47,48,49,50,52,54,55,57,61,72,73,91,93,101,102,115,118,124,128,149,154,157,159,166,170,171,178,179,181,182,183,184,186,187,189,190,192,197,199,200,216,217,222,223,224,226,242,245,247,248,250,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,298,299,307,308,312,320,322,335,340,343,349,351,352,354,355,358,360,363,365,366,370,373,374,379,380,381,382,384,386,387,388,389,390,391,392,394,395,396,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,430,431,433,435,436,437,438,440,445,446,450,451,452,453,462,463,464,465,466,467,469,471,472,473,478,482,491,494,502,507,509,511],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:[1,2,3,6,7,9,11,12,13,15,16,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,46,47,48,49,50,52,54,55,57,65,66,68,69,73,77,91,94,95,98,108,109,111,115,116,118,120,121,122,123,124,125,147,149,152,155,159,166,167,169,171,172,175,178,179,181,182,183,184,186,187,189,190,192,195,196,197,199,200,203,206,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,230,233,235,238,239,240,242,247,248,250,254,261,263,265,266,267,268,269,270,271,272,273,280,282,283,284,285,286,289,290,298,299,304,305,307,309,310,323,326,328,331,332,333,335,336,337,339,340,341,343,345,348,349,351,352,354,355,358,360,365,366,375,378,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,430,431,433,435,436,437,438,440,444,445,446,453,462,463,464,465,466,467,469,471,472,473,476,478,481,483,484,485,486,490,491,492,493,495,506,507,508],resum:507,retain:[2,221,222,386,433,478],retart:[33,51,185,356],retir:[3,443],retreiv:8,retriev:[6,8,237,431,432,507],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],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:[3,6,11,12,42,148,172,190,191,195,197,220,223,245,250,260,287,348,368,396,481,484,491,507],rightmost:[42,220],rigid:[],rigidifi:307,rii:[93,94],rij:[96,112,221,222,288,400,401,402,460],rin:[412,423,424],ring:[],rino:[75,469],rinv:365,rirj:[341,410],rise:[],risi:[146,452],risk:[8,306,490],rix:[93,94],rjk:[221,222],rjone:[7,9,13],rlo:463,rmask:[3,507],rmass:3,rmax:[73,173,221],rmdir:492,rmin0:[146,452],rmin:[73,173,222,420],rmsd:334,rnemd:6,robert:9,robin:200,robust:[371,372,373],rock:430,rockett:441,rod:307,rodata:12,rodnei:302,roi:7,role:330,roll:12,ronchetti:112,room:[59,61],root:[11,91,93,94,198,330,334,380,404,488],rosati:40,rose:430,ross:430,rosski:290,rosybrown:200,rot:[6,95,290,306,330,508],rotat:[],rotation:112,rotaton:484,rough:[6,172,199,345],roughli:[7,10,12,42,155,199,214,239,247,248,262,263,277,294,307,323,326,327,330,366,375,380,447,449,483,490],round:[],rous:240,rout:[91,412,426],routin:[5,6,8,11,15,16,38,40,57,92,176,178,250,433,442,463,494],roux:[6,230,248,467,502],row:[6,67,68,70,71,77,81,94,97,98,109,111,114,120,121,122,125,152,160,167,169,170,171,212,213,215,216,217,218,253,307,335,337,345,406],royalblu:200,rozero:430,rperp:[260,316],rpi:292,rpm:12,rrespa:[1,3,5,7,8,16,204,205,260,263,376,381,382,383,384,385,387,388,389,390,391,392,394,395,396,397,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,428,429,430,431,432,434,436,438,440,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,468,469,471,472,473,490],rspace:3,rsq:[463,470],rsurfac:335,ru3:171,ru4:171,rub:20,rubia:[431,432],rudd:[435,463],rudra:[7,9],rudranarayan:[7,292],ruiz:210,rule:[],run1:[6,379,507],run2:[6,362,364,379,507],run3:[6,379,507],run4:[6,379,507],run5:[6,379,507],run6:[6,379,507],run7:[6,379,481,482,486,507],run8:[6,379,507],run:[],run_styl:[],runloop:364,runtim:[12,17,199,380],russia:9,rutherford:335,rutuparna:[464,466],ryan:9,ryckaert:[310,358],rycroft:170,rydberg:433,s00:440,s0st:6,s2050:1,s2629:404,s319:209,s_fact:313,s_i:[6,406],s_ij:6,sack:7,saddl:[262,375],saddlebrown:200,sadigh:[210,404,431,432],saed_vtk:124,safe:[12,199,230,248,380],safe_zon:3,safest:[3,323],safeti:313,safezon:444,safran:472,sagui:[366,399],sai:[1,3,12,13,200,443,444,479],said:373,sakai:465,sall:[9,451],salmon:200,salt:[397,408,430,481],salter:451,same:[1,2,3,4,6,8,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,38,40,41,42,44,45,46,47,48,49,50,51,52,54,55,57,59,61,64,65,67,71,73,74,79,81,83,86,88,89,91,92,93,94,95,96,97,99,102,108,109,110,112,114,115,116,118,119,121,122,123,146,147,148,149,150,151,152,153,154,155,158,159,160,161,162,164,165,166,168,170,172,173,174,175,176,178,179,180,181,182,183,184,185,186,187,189,190,192,194,195,196,197,198,199,200,203,204,205,206,209,210,212,215,216,217,218,219,220,221,222,223,224,226,227,231,232,233,238,239,240,241,242,243,244,245,246,247,248,249,250,253,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,285,286,288,289,290,292,293,294,297,298,299,300,302,303,304,305,306,307,309,310,312,317,320,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,341,342,343,344,346,347,348,349,350,351,352,354,355,358,360,365,366,368,369,370,374,375,376,377,378,379,380,381,382,384,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,403,404,405,406,407,408,409,410,411,412,413,414,417,418,419,420,421,422,423,424,425,426,427,428,430,431,434,435,436,437,438,440,441,445,446,451,453,460,461,462,463,464,465,466,469,471,472,473,476,478,479,481,482,483,484,486,489,490,491,492,493,494,495,499,502,506,507,508,510],sampl:[1,2,4,6,9,10,11,12,14,95,108,150,151,165,170,195,199,203,212,213,216,217,225,227,237,239,241,243,263,264,290,293,302,304,308,320,321,323,327,330,333,345,376,386,403,481,495],sample_frequ:209,san:440,sandia:[0,5,7,9,13,14,17,72,117,407,430,440],sandybrown:200,saniti:[306,376],satellit:[6,154],satifsi:507,satisfi:[3,12,75,124,146,171,224,250,268,310,343,373,376,410,495],satur:397,save:[6,8,12,19,41,61,192,197,199,214,223,240,241,247,248,249,293,302,335,347,366,376,378,386,483,486,493],sb3:171,sb5:171,sc3:171,scalabl:[],scalar:[],scale:[0,1,3,4,5,6,9,10,13,18,41,61,65,73,74,95,119,122,123,146,158,166,192,195,196,197,199,200,203,204,205,209,210,213,224,226,239,243,244,245,247,249,250,261,263,265,266,267,268,269,270,271,290,294,297,298,307,314,315,323,325,327,330,332,333,335,339,346,365,366,368,374,377,381,382,383,397,403,406,410,413,427,428,430,433,440,447,449,467,482,484,486,490,493,495,498,499,507,508],scale_factor:[447,449],scalegamma:250,scalexi:[3,224,263,268],scalexz:[224,263,268],scaleyz:[224,263,268],scan:[200,222,364,482],scatter:[11,124,171],scatter_atom:11,scatter_coord:11,scenario:[6,41,63,223,296,305,323,336,344,376,485,486,490,498],scf:502,schaik:426,schedul:476,schell:465,schemat:223,scheme:[6,9,18,240,241,263,290,302,310,335,365,467],schlitter1:334,schlitter2:334,schlitter:334,schmid:400,schneider:[247,249],schoen:365,schr:502,schroding:406,schroeder:[112,502],schulten:[248,312,366,502],schunk:323,schwen:9,sci:[75,343,395,432,441,451],scienc:[8,209,223,244,312,332,404,431,451,465],scientif:[146,404],scm:11,scratch:[12,42,220],screen:[],screenshot:11,scripe:11,script:[],scripta:69,scsl:12,sdk:[],sea:11,seagreen:200,seamlessli:296,search:[0,2,3,8,12,96,112,173,175,200,201,323,371,372,373,375,377,476,482,483,495,507],seashel:200,sec:[12,501,506],second:[1,3,6,9,10,11,12,16,55,59,61,63,73,92,95,108,110,112,118,139,140,144,147,148,160,166,170,171,173,174,175,195,196,200,203,204,212,213,215,216,217,218,223,239,240,245,260,262,290,304,306,307,310,312,320,321,323,332,333,335,346,365,368,372,373,375,376,380,385,386,387,389,390,395,396,404,406,407,410,411,413,416,417,420,430,435,437,451,462,465,466,467,469,473,476,477,478,479,481,483,488,490,494,495,499,502,506,507,508,509,511],second_mo:451,secondari:[3,184],sectinn:510,section:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,42,43,44,45,46,47,48,49,50,51,52,54,55,56,57,60,61,65,66,67,68,69,70,71,73,76,77,80,81,82,83,84,87,90,91,92,93,94,95,97,98,101,102,103,104,105,106,108,109,110,111,113,114,115,117,118,119,120,121,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,178,179,180,181,182,183,184,185,186,187,189,190,191,192,195,196,197,198,199,201,203,206,207,208,209,210,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,229,230,232,233,235,236,238,239,240,241,242,244,246,247,248,249,250,251,252,253,254,256,257,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,278,280,281,282,283,284,285,286,288,289,290,292,293,294,296,297,298,299,300,301,302,303,304,307,309,310,311,312,313,314,315,316,317,319,323,326,327,328,329,330,331,332,333,334,335,336,338,339,341,342,343,346,347,349,350,351,352,353,354,355,356,358,359,360,366,367,368,370,374,375,377,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,436,437,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,476,477,478,479,481,482,484,486,489,490,491,492,494,495,496,499,500,502,507,508],section_acceler:[9,12,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,115,118,149,159,178,179,181,182,183,184,186,187,189,190,192,206,219,226,233,238,242,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,299,307,309,310,326,328,339,343,349,351,352,354,355,358,360,366,381,382,384,387,389,390,391,392,394,395,396,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,431,436,437,438,440,445,446,453,462,463,464,465,466,469,471,472,473,484,490],section_accerl:404,section_command:[0,1,9,348],section_error:[7,12],section_exampl:[2,6],section_histori:[7,12],section_howto15:85,section_howto:[6,8,9,11,12,41,43,59,61,66,68,69,70,72,73,74,75,77,78,79,80,82,83,86,87,88,89,90,91,93,94,96,98,99,100,101,102,103,104,105,106,109,111,112,115,116,117,120,122,123,126,141,142,143,144,146,147,152,154,166,167,169,170,174,194,212,262,275,278,281,338,385,398,476,481,484,495],section_modifi:[6,7,43,196,197,199,499],section_packag:12,section_perf:7,section_python:[6,12],section_start:[3,4,6,9,11,369,375,475,476,490,496,499],section_tool:[6,7],see:[1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,59,60,61,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,232,233,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,256,257,258,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,280,281,282,283,284,285,286,288,289,290,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,309,310,311,312,313,314,315,316,317,319,320,322,323,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,362,365,366,368,369,370,372,373,374,375,376,377,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,475,476,477,478,479,481,482,483,484,486,487,488,489,490,491,493,494,495,496,497,498,499,500,501,502,507,508,509,510,511],seed1:496,seed2:496,seed:[3,172,175,195,199,208,210,221,222,223,225,227,236,239,240,241,247,248,249,250,290,293,297,302,307,323,327,330,335,342,388,400,402,403,476,491,496,502,507,508],seed_com:248,seed_drud:248,seek:[42,220],seem:[6,224,336,372,430,490],seen:[12,250,344],segement:3,segment:[3,4,6,7,12,41,43,86,119,199,203,278,293,307,323,400,416,444,460,461,481,489,491],select:[3,6,12,15,61,63,73,123,124,161,166,171,172,192,199,201,208,210,216,217,226,227,236,239,244,245,260,312,322,330,331,336,338,340,342,343,345,363,365,371,375,377,380,412,417,430,451,478,482,484,490,491,495,500,507],self:[],sellerio:13,semi:[3,201,209,210,287,289,482],semiax:150,semimet:406,send:[0,3,5,7,8,11,12,200,244,478],sender:[3,478],sens:[1,3,6,7,18,40,42,43,61,73,108,191,196,212,215,216,217,218,220,223,226,240,241,246,247,248,249,293,297,302,308,323,330,331,335,338,346,375,396,418,422,464,465,466,476,481,486,490,493,498],sensabl:244,sensibl:109,sensit:[2,6,75,224,302,508],sent:[200,244,363],sep:[6,11,507],separ:[2,3,6,7,9,12,13,41,42,78,122,128,146,172,175,197,199,200,201,209,213,220,221,222,223,224,227,230,239,247,248,263,277,290,293,294,296,298,302,307,310,323,326,327,328,331,338,346,366,380,387,389,396,397,399,401,402,418,427,428,430,437,442,452,461,462,463,466,472,479,481,482,483,490,493,498,502,508,509,510],seper:397,sequec:507,sequenc:[2,3,12,42,61,196,197,199,200,201,220,241,262,346,368,375,413,441,496,507],sequenti:[61,62,200,441,482],sequestr:7,ser:289,seri:[3,4,6,9,13,18,146,196,197,199,200,213,218,240,241,293,379,382,409,430,433,435,445,453,463,479,488,489,496,498,499,507],serial:[],serial_icc:12,serious:8,serv:[6,134,174,323,460],server:[1,246,380],set:[],set_callback:237,set_energi:237,set_vari:[6,11,479],setarea:250,sete:[212,223],setenv:[11,12,393],setfl:[13,381,404],setforc:[],setgamma:250,setmask:8,settl:224,setup:[3,4,6,7,8,11,12,13,16,37,41,56,61,73,91,95,160,173,174,175,176,191,200,209,223,226,323,336,359,376,377,380,461,478,481,489,509,511],setup_pre_exchang:8,setup_pre_forc:8,setup_pre_force_respa:8,setvel:[],seven:432,seventh:[139,144],sever:[1,4,5,6,7,8,10,11,12,13,15,18,40,41,65,73,91,166,173,176,191,196,197,198,201,203,209,221,222,224,241,247,250,254,263,292,294,296,307,312,323,330,339,363,368,373,380,383,386,390,403,404,413,422,426,430,435,441,443,444,450,451,476,479,483,487,495,499,502,507,508],sexton:433,sfactor:[3,199,200,374],sfftw:12,sgi:12,sgmc:210,sgrid:323,sgroup:170,shade:199,shake:[],shan:[17,298,299,395],shanghai:[9,13],shape:[],shapei:[119,481],shapex:[119,481],shapez:[119,481],shapshot:486,shardlow:[],share:[],shared0:[],sharon:307,sharp:[344,430,466],shawn:9,shear:[3,4,5,6,7,9,61,63,155,195,224,226,250,263,284,323,338,341,410,427,428,440,448,450],sheet:485,shell:[],shen:9,shenderova:382,sheppard:372,shflag:12,shield:[],shift:[],shiftse:323,shiga:[6,263,264],shini:[199,510],shinoda:[6,9,263,264,446],shiny:199,ship:201,shlib:[11,12],shlibflag:12,shock:[203,208,261,268,297,342,420],shockvel:[261,297],shortcut:[224,263,294,307],shorter:[3,125,239,288,377,435,489],shortest:[199,377,383,490],shorthand:200,shoul:468,should:[1,2,3,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,43,44,45,46,47,48,49,50,52,54,55,57,61,63,72,73,75,83,87,91,95,101,102,103,107,108,109,115,116,118,147,149,150,151,154,155,158,159,160,162,165,168,172,174,176,178,179,180,181,182,183,184,186,187,189,190,192,194,195,196,197,199,200,204,205,206,207,210,214,219,220,221,222,223,224,226,227,229,230,232,233,235,236,237,238,239,240,241,242,243,245,247,248,249,250,252,253,254,255,260,263,265,266,267,268,269,270,271,272,273,277,280,282,283,284,286,288,289,290,291,292,293,294,295,297,298,299,300,301,302,303,304,305,306,307,309,310,317,320,323,324,326,327,328,329,330,331,334,335,336,338,339,340,341,342,343,344,345,346,348,349,350,351,352,354,355,358,360,366,368,369,371,373,374,375,376,377,378,380,381,382,384,385,387,388,389,390,391,392,393,394,395,396,398,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,430,431,433,435,436,437,438,439,440,442,443,445,446,447,449,451,453,460,462,463,464,465,466,467,469,471,472,473,476,477,478,479,481,482,483,484,485,486,488,489,490,491,493,497,498,499,502,507,508,509],shouldn:[3,8],show:[6,11,12,122,288,375,412,430,433,463],shown:[1,12,16,17,42,101,102,124,146,158,171,191,220,223,247,263,284,290,293,302,330,365,406,407,409,410,426,433,445,451,481],shrank:73,shrink:[3,6,42,59,61,73,174,195,196,199,204,205,208,220,226,227,245,250,288,323,342,346,365,366,373,396,418,422,435,481,482],shrunk:73,shut:[6,11,376,480],si4:171,siam:343,sic:[4,396,413,430,437,462,464,466,469],sic_tersoff:441,sicc:[405,462,464,466,469],sicg:[464,466],sicsi:[405,462,464,466,469],side1:484,side2:484,side3:484,side4:484,side:[3,8,42,59,63,73,162,172,210,211,220,223,227,239,245,250,260,288,293,301,320,340,344,345,346,375,396,409,410,445,468,479,481,484,491],sidewai:4,sienna:200,siepmann:338,sigam:394,sigam_ii:[],sige:[464,466],sigma0:386,sigma14:426,sigma1:386,sigma2:386,sigma:[3,6,10,46,47,51,55,91,178,196,197,200,204,205,239,250,288,311,323,339,340,344,368,377,380,382,385,386,387,391,392,394,399,400,402,403,405,406,409,411,412,416,417,418,419,420,421,422,423,424,425,426,429,434,435,445,446,456,462,468,490,506,507,508],sigma_14:391,sigma_:397,sigma_c:394,sigma_cc:[382,394],sigma_h:408,sigma_i:[407,435],sigma_ii:468,sigma_ij:[435,468],sigma_j:435,sigma_max:403,sigma_ss:394,sign:[3,6,12,183,191,287,320,343,348,433,489,498,507],signal:480,signicantli:17,signifi:[3,68,77,94,98,109,111,120,152,167,169],signific:[7,12,18,90,240,261,264,302,323,336,406,409,430,433,435,509],significantli:[1,6,40,147,170,250,263,306,406,462],sij:213,sikandar:17,silbert:410,silent:[200,479,492],silicon:[405,430,462,481],sill:440,silver:200,sim:[9,446],similar:[5,6,7,8,9,11,12,17,18,41,42,43,47,61,70,74,91,118,121,122,147,148,172,173,196,197,200,203,204,205,212,214,220,237,238,240,247,253,254,264,296,297,302,306,307,327,330,340,341,343,345,366,371,372,374,382,385,386,400,404,406,410,426,427,435,440,441,450,463,478,483,488,490,495,497,499,502,507,508,509,511],similarli:[3,6,7,8,61,118,168,174,176,195,196,199,200,211,212,215,216,217,218,222,226,232,245,263,265,266,267,269,270,271,292,294,307,308,310,323,330,331,338,344,349,366,368,375,378,390,410,422,462,478,481,484,485,490,491,495,510],simluat:[6,40,200,323,427,482,483],simlul:[307,335],simmul:338,simpl:[],simpler:[8,11,43,200,307],simplest:[3,8,41,68,77,94,98,109,111,120,122,152,167,169,298,502],simpli:[1,3,6,8,11,12,14,17,68,73,77,92,94,98,100,109,111,119,120,125,152,167,169,175,176,200,203,204,205,212,215,216,217,218,222,224,226,230,237,246,248,253,263,290,294,305,307,308,331,337,338,365,366,368,374,375,380,390,399,413,422,430,435,478,479,486,489,496,499,506,507],simplif:406,simplifi:[210,306,433],simplist:11,simualt:366,simul:[],simulatan:380,simulation_nam:444,simulationub:451,simulatoin:[12,482],simult:380,simultan:[6,7,15,16,226],sin:[226,260,340,343,345,441,481,484,491,507],sinc:[0,1,2,3,6,8,9,10,11,12,13,15,16,21,22,33,40,42,45,55,61,63,66,69,73,75,93,94,116,122,124,150,152,162,170,174,175,177,178,180,185,196,197,199,200,203,204,205,206,207,210,211,212,213,214,215,216,217,218,219,220,223,224,225,226,227,231,232,239,241,243,246,247,249,250,260,263,265,266,267,268,269,270,271,274,277,284,288,290,293,295,296,302,305,307,312,322,323,331,335,336,337,338,340,341,344,345,346,347,349,350,364,366,373,374,375,376,379,380,381,382,386,389,390,391,392,394,395,399,400,403,404,405,409,410,411,413,414,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,438,441,442,443,444,445,446,451,452,453,462,463,464,465,466,469,473,476,478,479,481,482,484,486,489,490,491,492,493,495,499,502,506,507,508,510],sinclair:[7,404,461],sine:441,singapor:146,singh:381,singl:[1,2,3,6,7,8,9,11,12,14,15,16,17,18,41,42,43,59,61,63,65,67,68,70,71,77,79,81,91,92,94,97,98,108,109,111,114,119,120,121,122,123,125,148,152,167,169,170,172,196,197,199,200,201,203,208,211,212,213,215,216,217,218,220,222,223,224,227,230,236,238,243,250,253,260,263,264,268,277,290,292,293,295,306,307,308,310,313,319,323,325,335,337,340,341,343,345,346,348,365,366,371,374,375,376,377,379,380,381,382,386,391,393,395,403,404,405,406,407,410,411,412,413,414,415,430,431,432,433,437,438,441,442,443,444,445,451,452,453,462,464,465,466,469,476,477,479,481,488,489,490,491,492,493,494,495,496,498,507,510,511],singleel:386,singular:[426,427,428],sinnott:[299,382,395],sinusoid:[172,226,340,341,343,345],sio2:469,sio:395,sirk:[147,460],sisic:[405,462,464,466,469],sisisi:[405,462,464,465,466,469],sister:393,sit:[289,481],site:[0,1,2,3,4,5,6,7,8,10,11,12,13,14,15,16,17,69,72,91,244,250,251,310,366,381,386,396,404,408,418,422,426,438,443,444,467],situat:[9,170,224,239,250,263,290,308,372,386],sival:171,six:[6,139,144,146,213,215,437,441],sixth:437,sixthpow:[392,435],size:[],size_restart:8,sizei:416,sizej:416,sizescal:3,sizex:271,sjplimp:[0,7,11,12],sjtu:9,skew:[3,6,60,61,174,199,226,263,481,484],skin:[3,12,40,63,75,121,173,175,239,277,307,311,335,376,377,380,416,439,499,506],skip:[12,16,33,185,292,293,364,374,379,417,481,486,489,498,507],skyblu:200,slab:[3,6,73,160,216,293,320,365,366,376,435],slateblu:200,slategrai:200,slater:[],sleight:55,slepoi:430,slice:[],slider:11,slight:[3,12,335],slightli:[1,6,40,41,196,197,198,199,201,302,307,366,382,396,418,422,464,466,469,476,489,509],sligthli:399,sliozberg:460,slip:[3,203,323,339,345],sllod:[],slope:[6,108,109,331,333,338,397,507],slot:1,slow:[3,6,7,12,40,240,244,247,248,261,263,323,330,365,375,380,435,451,490,500,502,508],slower:[1,10,17,40,248,366,380,386],slowest:[335,478],slowli:[12,73,220,339,373,433,453,483],slurm:12,slurm_localid:12,sm3:171,small:[],smallbig:3,smaller:[1,3,6,12,16,17,40,57,61,63,73,125,174,196,197,199,200,210,227,231,239,250,289,307,323,333,348,365,366,371,380,435,461,468,470,481,488,490,507,511],smallest:[3,43,72,73,74,170,261,304,507],smallint:3,smallq:366,smallsmal:[3,12],smart:241,smd:[],smd_contact_radiu:[],smd_lammps_userguid:9,smd_mass_dens:[],smd_user_guid:[],smi:[3,380],smirichinski:9,smit:239,smith:438,smmoth:491,smooth:[],smoother:172,smoothli:[55,146,331,338,391,411,424,426,429,466,473],smpd:12,smtb:[9,451],smtbq:[],smulat:433,sn2:171,sn4:171,sna:[],snad:[],snap:[],snapcoeff:452,snaphot:486,snapparam:452,snapshot:[],snav:[],snb:17,snow:200,soc:412,socket:[12,17,18,246,478],soderlind:433,soft:[],softer:[340,344],softwar:[1,6,9,11,12,14,15,16,17,18,19,170,244,292,308],sole:[221,222,375,441,448,450],solid:[4,6,7,9,10,40,41,42,61,72,75,95,108,147,170,209,220,224,226,231,253,263,265,266,267,269,270,271,288,289,294,307,330,333,366,368,387,420,433,440,448,450,481],solut:[3,6,13,170,224,231,261,305,310,323,344,507],solv:[3,9,12,18,250,298,310,333,335,366,372,428],solvat:[4,10,172],solvent:[4,7,13,63,73,173,175,220,236,240,241,247,263,305,307,320,323,331,338,339,391,394,396,397,408,418,427,428,445,461,481,491],solver:[],some:[1,2,3,4,6,7,8,9,10,11,12,13,16,17,18,40,41,42,56,63,65,73,107,110,113,119,123,125,150,151,152,153,164,165,166,170,172,175,180,183,191,194,196,197,199,200,203,204,205,208,210,211,212,213,215,216,217,218,220,222,223,224,225,236,239,261,263,264,293,295,296,298,300,307,312,324,330,335,336,337,339,340,346,363,364,365,366,371,372,373,374,375,376,377,380,383,385,386,393,396,404,406,413,416,433,435,443,444,461,463,474,476,478,479,480,481,483,486,487,488,489,490,491,493,495,498,499,506,507,508,511],somehow:3,someindex:347,someon:[7,373],someth:[2,3,7,8,11,12,61,224,263,340,343,345,376,413,479,488],sometim:[2,3,6,8,12,18,216,224,263,331,338,365,377],somewhat:[7,9,12,72,108,152,162,212,263,365],somewher:[17,264,406],soon:[3,43,210,223,236,239,244,443],sophist:[7,148],sorensen:495,sort:[3,13,16,40,73,196,197,200,201,244,375,376,380,403,482,483,510],sound:[134,250,261,313,458,459],soundspe:[458,459],sourc:[],source_integr:209,sourceforg:11,south:146,souza:331,space:[2,3,6,8,11,12,18,42,61,73,124,146,161,166,171,172,192,195,199,204,205,208,215,216,217,220,222,226,227,245,250,257,260,263,289,290,305,308,313,323,340,342,343,345,348,365,366,368,374,375,376,387,389,390,396,399,404,406,416,418,422,430,433,438,441,446,463,470,472,478,481,484,493,499,502,507,508],spahn:410,span:[2,12,38,73,204,205,216,245,307,365,381,382,386,395,404,407,414,415,430,431,432,437,441,452,462,464,465,466,469,475,476,484,485,507],spars:[73,192],spatial:[],spawn:244,spc:[],spcpu:499,speak:[17,323,330],spearot:[124,171,308],specfi:[12,113,245,484],speci:[],special:[],special_bond:[],specif:[1,2,3,6,7,8,9,10,12,13,15,16,17,18,22,29,33,41,42,43,51,65,73,114,119,121,122,152,154,157,170,172,180,185,196,197,199,200,201,203,204,205,208,209,212,213,215,216,217,218,220,223,225,236,237,239,240,244,250,258,293,295,296,299,307,330,335,336,340,346,350,366,373,375,380,382,385,386,398,404,409,410,413,414,415,430,433,435,443,444,445,461,462,467,468,478,481,482,486,487,488,490,491,497,498,499,506,507,508,509],specifi:[2,3,6,7,8,9,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,54,55,56,57,58,59,61,63,65,67,68,70,71,72,73,75,77,78,79,80,81,82,83,87,89,90,91,92,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,147,149,152,154,159,160,161,166,167,168,169,170,171,172,173,174,175,176,178,179,180,181,182,183,184,185,186,187,189,190,191,192,193,195,196,197,198,199,200,201,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,235,238,239,240,241,242,243,245,246,247,248,250,251,252,253,255,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,277,280,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,316,317,320,321,322,323,324,325,326,327,328,330,333,334,335,337,339,340,341,342,343,344,345,346,347,348,349,350,351,352,354,355,356,358,359,360,361,364,365,366,368,369,370,373,374,375,376,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,502,506,507,508,509,510,511],specifii:[241,250],speciti:490,spectral:452,spectrum:[9,146,297,302],sped:[40,261],speed:[1,3,6,9,12,14,15,16,17,18,19,40,42,134,196,200,220,247,250,261,297,313,323,330,336,342,365,366,375,380,386,396,433,435,458,459,464,476,490,496],speedup:[1,18,366,490],spefici:[172,199,412],speicifi:[],spell:484,spellmey:[6,178,493],spend:[12,211],spent:[1,12,13,15,476,495,500],sperhic:481,sph:[],sph_lammps_userguid:9,sph_user_guid:[],sphere1:250,sphere:[],spheric:[],spheriod:[3,6],spherioid:323,spheroid:[6,263,280,307,323],spike:122,spin:[9,41,119,197,341,383,406,481],spirit:[7,214],spit:3,spline:[],split:[1,3,6,9,11,12,18,42,212,216,220,248,263,311,343,365,380,402,468,475,478,490],splittol:[6,365],sppark:6,spread:[1,6,12,348,489],spring:[],springer:312,springgreen:200,sptial:73,sputter:227,sq2:[3,368],sqrt:[2,3,43,61,83,93,112,239,247,249,288,323,339,341,368,394,400,404,408,410,430,435,507],squar:[],squeez:[224,245,427,428],squibb:[5,7],sr2:171,src:[0,1,3,4,6,7,8,9,11,12,14,15,16,17,18,19,170,196,237,310,433],srd:[],srmax:73,srmin:73,srolovitz:404,srp:[],srtio:451,srun:12,ssa:311,ssao:[199,510],stabil:[6,9,247,263,386,443],stabl:[6,66,134,250,268,306,313,386,502],stabli:240,stack:[3,8,72],stage:[3,8,91,203,237,262,301,346,375,476,495,507],stagger:[1,2,3,200,366,488,497,507],stai:[3,14,17,204,205,261,279,297,380,481],stamp:[203,330,482],stamped:12,stan:17,stand:[0,6,7,12,13,303,443,444,479],standard:[],stanford:9,starikov:335,start:[],start_6:408,start_7:490,startstep:507,stat:[12,55,176,288,302,373,400],statcoul:506,statcoulomb:506,state:[],statement:[3,479,480],stationari:[],statist:[3,6,12,40,42,53,66,188,214,221,222,223,240,241,247,248,249,292,293,297,302,307,310,323,334,335,336,357,373,375,382,400,403,410,427,472,476,483,489,491,495,498,499],statu:[3,12,55,62,127,176,225,230,248,395,480,495],statvolt:506,std:12,stdin:[3,12,364],steadi:[6,261,268,297],steelblu:200,steep:463,steepest:[7,372],steer:[7,9,225,228,312],stegailov:335,steinhardt:[65,112],steinhaus:502,stencil:[3,250,365],step:[1,2,3,6,8,10,11,12,13,14,15,16,17,18,19,40,73,95,101,102,116,122,123,134,147,158,168,170,196,198,199,200,201,203,204,205,209,210,212,213,214,215,216,217,218,220,221,222,223,224,226,227,230,231,236,237,239,241,244,245,248,261,277,288,289,293,295,296,297,298,299,300,308,310,311,312,313,323,325,328,329,330,331,332,333,334,335,336,337,338,345,346,348,364,365,371,373,375,376,400,408,412,430,433,443,444,451,476,478,479,483,485,486,488,489,490,495,496,498,499,502,507,511],stepani:312,stepwis:91,stesman:330,steve:[0,5,7,13],steven:223,stiff:[6,41,52,221,222,289,290,373,440,502],stile:397,still:[1,3,6,9,11,12,13,14,17,38,39,42,58,63,73,96,114,122,170,176,192,193,194,196,197,200,204,205,220,243,247,277,298,302,323,335,348,361,365,366,371,392,404,409,410,413,417,427,439,443,445,453,461,481,483,489],stilling:[3,5,7,15,92,148,405,432,441,461,462,469,493],stipul:244,stl:[9,73,316,319],stl_surf:319,stochast:[4,7,9,203,241,311,323,330,345,402,403],stockmay:41,stoddard:399,stoichiometri:451,stoke:[250,339],stoll:[247,249],stone:[9,19,366,399],stop:[],stopstep:507,stopthresh:[42,220],storag:[3,12,15,337,380,493],store:[],store_st:324,storm:12,stouch:7,str:507,straatsma:6,straddl:[3,61,63,162,245,307,320,346,481,485,491],straight:307,straightforward:[13,406,502],strain:[],strang:[192,199,507],strategi:[],stratford:250,strcmp:348,stream:[3,6,118,147,152,155,156,199,209,226,240,241,247,248,284,293,302,323,508],streamlin:[12,489],streitz:[],streiz:396,strength:[3,9,146,166,177,199,306,340,344,413,444,445,493],stress:[],stretch:[3,55,61,123,221,312],strict:452,strictli:[6,42,192,220,261,297,330,481],stride2:507,stride:[200,241,488,497,507],strietz:396,strike:227,string:[2,3,6,11,12,42,172,196,197,198,200,212,213,214,215,216,217,218,220,239,295,308,348,367,379,430,441,442,443,452,477,479,481,491,492,498,499,507],strip:507,strong:[298,382],stronger:6,strongest:[427,428],strongli:[1,6,13,227,307,310,335,433,502],structrur:3,structur:[],structured_point:308,strucur:75,stuart:[298,299,382,395,451,461],stub:12,stuck:224,student:292,studi:[6,110,420,451],studio:[],stukowski:[210,404],style1:[33,51,185,356,413,481],style2:[33,51,185,356,413,481],style:[],style_nam:[263,264],stylecomput:451,stylist:8,sub1:492,sub:[1,3,4,6,7,8,9,11,12,13,18,33,37,40,41,42,43,51,56,60,63,65,70,91,95,113,146,166,174,185,191,198,199,200,204,205,220,224,226,263,264,268,289,297,302,307,310,311,335,336,344,346,356,359,368,370,380,385,395,403,409,410,412,413,416,435,443,444,445,451,467,468,473,478,481,484,490,498],subbox:[123,199,200],subcutoff:416,subdirectori:4,subdivis:250,subdomain:250,subequ:11,subgroup:[196,510],subinterv:198,subject:[6,42,175,220,467],submit:[],subramaniyan:13,subroutin:380,subscript:[11,335,349,407,469,507],subsequ:[3,6,11,12,42,61,108,173,200,214,220,224,239,330,335,336,337,368,379,404,461,479,481,482,488,491,492,501,507,511],subset:[6,11,12,16,42,82,146,196,197,200,220,259,263,265,266,267,268,269,270,271,293,294,298,307,375,380,382,386,413,435,475,478,481,483,486,490,507],substanti:[6,16,462,490],substep:263,substitut:[1,2,3,12,196,246,375,379,406,435,479,492,507],substract:396,substrat:[174,224,263,265,266,267,269,270,271,294,307,481],substyl:[426,490],subsystem:335,subtl:[99,101,102,241],subtleti:158,subtract:[3,6,55,65,73,95,99,102,107,108,110,118,147,149,150,151,152,153,154,155,156,158,159,160,161,162,164,165,196,197,203,212,239,240,243,247,248,249,251,255,259,284,291,307,346,376,425,481,491,499,507,508],succe:12,succeed:[213,214],succes:214,succesfulli:3,success:[2,6,11,12,14,15,122,196,200,210,213,224,227,239,277,293,307,323,330,348,373,375,479,480,488,489,496],successfulli:[3,11,196,227,479,492],successulli:11,successv:486,sucessfulli:3,sudden:36,suddenli:344,sudo:[11,12],sufac:43,suffer:[16,17,18,338,344,380],suffici:[2,3,7,17,18,42,63,73,198,216,220,261,263,289,323,330,337,340,348,417,435,481,502],suffix2:12,suffix:[],suggest:[0,6,7,12,261,297,479,502],suit:[7,9,13,205,250,406],suitabl:[4,12,13,17,55,91,196,223,296,327,386,393,410,426,430,443,444,476,495],sukumaran:214,sum:[3,6,8,9,12,41,72,73,78,82,87,92,93,94,96,99,103,108,110,112,113,115,116,118,122,123,129,145,146,147,149,152,153,154,155,158,159,160,161,162,164,166,168,169,170,212,213,215,216,217,218,227,237,240,247,248,253,288,289,293,297,302,307,308,312,322,333,335,337,340,344,346,365,366,373,385,396,400,406,407,416,418,421,430,443,444,452,468,479,499,502,507,508],summar:[6,407,451],summari:[],summat:[6,9,43,72,92,112,365,366,390,396,404,405,418,422,433,451,462,464,465,466,469],summer:[3,13,216,443,444],sumsq:123,sun:[21,44,179,349,392,435,444],sunderland:17,sup:[289,297,302,395,451,502],supercomput:[12,18,479],superpos:[413,461],superposit:7,supinski:433,supplement:[241,443,444],supplementari:[225,409,445],suppli:[12,192,239,261,335],support:[1,3,6,7,8,9,11,12,13,14,15,16,17,18,19,41,42,43,63,91,92,107,113,196,197,198,199,200,201,204,205,206,207,212,220,223,224,225,232,237,241,242,245,247,248,249,250,258,261,263,265,266,267,268,269,270,271,282,283,284,285,286,288,289,294,297,299,301,306,307,309,313,314,315,316,317,319,320,322,326,327,328,329,333,338,340,344,363,364,365,366,372,373,374,380,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,468,469,471,472,473,478,482,483,484,488,490,491,492,494,495,501,502,506,507,510,511],suppos:[3,8,407,507],suppress:[6,12,170],sure:[6,8,11,13,14,192,204,205,224,293,307,310,345,404,463],surf:[140,173],surfac:[2,3,4,6,8,9,41,43,59,72,124,140,146,170,172,175,199,203,227,236,245,250,253,288,299,306,316,319,320,323,330,335,340,344,345,375,386,413,427,428,433,449,451,468,472,478,484],surface_mov:335,surfact:[397,408],surpris:406,surrog:9,surround:[38,57,72,172,192,200,224,235,263,265,266,267,269,270,271,288,294,307,463,502],suspect:3,suspens:[427,428],sustain:[196,197,224,410],suzuki:[263,307],svg:6,svn:[7,11,12],sw_exampl:442,swamp:307,swap:[],swegat:334,swiggl:[3,260,340,343,345,484,507],swiler:[146,452],switch7_section_start:408,switchflag:[146,452],swm4:502,swol:54,swope:6,sxx:200,sy0302:9,symbol:[6,12,124,171,304,386,406,452],symmetr:[6,72,91,98,118,137,138,139,142,143,144,147,204,205,224,263,264,331,338,381,393,399,404,464,466,507],symmetri:[3,5,6,7,8,65,66,72,96,112,174,196,197,261,288,349,366,381,481,502],sync:[3,6,500],synchron:[1,241,375,500],synechococcu:7,syntax:[],sysdim:289,sysmt:17,sysstem:386,syst:451,system:[],system_:290,systemat:[6,9,214,239,247,433],systemx:3,t10:496,t11:496,t12:496,t13:496,t14:496,t15:496,t3e:12,t_chain:3,t_corr:3,t_correl:476,t_dephas:476,t_e:335,t_e_min:335,t_equil:[332,333],t_event:[3,476,495],t_hi:495,t_infil:335,t_init:[297,335],t_iter:3,t_j:29,t_lb:250,t_lo:495,t_order:3,t_oufil:335,t_out:335,t_outfil:335,t_qm:297,t_switch:[332,333],t_target:388,ta06a:452,ta4:433,ta5:171,ta6:433,tab:[2,481],tabbernor:124,tabinn:435,tabul:[3,7,13,22,37,38,45,56,57,67,73,81,97,192,235,323,365,381,386,387,389,390,391,392,393,396,404,406,418,422,429,438,441,444,446,461,463,464,470,483],tabular:441,tabulate_long_rang:444,tad:[],tadmor:9,tag:[209,502],tagint:3,tail:[3,91,116,166,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,471,472,473,499,507],tailor:[73,336],tait:[9,458,459],taitwat:[],take:[1,2,3,6,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,43,44,45,46,47,48,49,50,52,54,55,57,61,79,91,93,95,115,118,119,122,123,147,149,159,166,170,176,178,179,180,181,182,183,184,186,187,189,190,192,196,199,200,204,205,206,219,220,224,226,233,238,242,246,247,248,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,299,307,309,310,320,321,322,323,325,326,327,328,336,339,343,346,349,350,351,352,354,355,358,360,365,366,370,380,381,382,384,386,387,388,389,390,391,392,393,394,395,396,399,400,404,405,407,408,409,410,411,412,418,419,420,421,422,423,424,425,426,427,431,433,436,437,438,440,443,444,445,446,451,453,460,462,463,464,465,466,467,469,471,472,473,475,479,482,484,489,490,491,496,498,499,500,507],taken:[6,61,154,172,195,223,227,239,240,241,247,248,249,250,293,297,300,335,354,404,406,409,462,469,476,490,491],talk:[6,7],talli:[],tan:[200,507],tandem:[4,16,307],tang:433,tangent:[43,262],tangenti:[6,114,323,341,345,410],tanh:335,tantalum:[4,433,452],taper:[3,300,429],tar:12,tarbal:[0,8,11,12],target:[3,6,7,8,11,12,17,40,42,200,208,220,224,225,227,239,240,241,247,248,249,263,264,265,266,267,268,269,270,271,282,283,284,285,286,290,294,297,302,307,312,321,326,327,328,329,334,335,338,339,342,363,366,388,400,476,487,489,508],target_fil:334,task:[1,6,7,12,13,14,15,16,17,18,55,200,244,290,336,380,479,500],taskset:16,tatb:[4,303],tatom:502,tau:[3,161,214,247,248,250,263,294,307,326,327,332,333,335,501,506],tau_1:240,tau_k:240,tau_n_k:240,tb3:171,tbead:164,tbp:386,tchain:[263,264,268,284,285,307],tcl:302,tcom:248,tcsh:[11,12,393],tdamp:[247,263,264,268,307,326,327],tdephas:476,tdrude:[157,230,248,502],teal:200,tech:[7,9,13],technic:[6,7,9,250,300,323,444],techniqu:[6,7,9,91,203,224,261,297,307,339,342,366,435,463,502],technolgi:9,technolog:[9,14,19,244],tell:[2,6,11,12,37,56,191,203,289,359,376,443,444,461,479,483,502],telsa:17,temeperatur:11,temp:[],temp_drud:502,temp_eff:102,tempcom:[150,151,165],temper:[],temperar:290,temperatur:[],temperature_definit:209,tempfix:496,templ:[7,9,18],templat:[3,8,13,17,19,41,172,173,175,227,239,293,307,310,374,481],templeton2010:209,templeton2011:209,templeton:[9,209],tempor:240,temporari:[2,3,488],temporarili:[192,306,494,495],ten:14,tend:[29,263,288],tensil:[7,226],tensor:[3,6,8,65,86,87,93,94,95,98,111,118,133,136,137,138,139,142,143,144,146,147,148,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,224,250,253,263,264,268,292,294,307,338,365,366,374,406,427,428,433,448,450,499,507],tenth:[133,364],term:[0,1,3,5,6,7,8,9,12,20,21,22,27,38,41,46,47,63,91,92,93,95,116,118,147,148,150,151,160,165,166,179,180,181,192,200,204,205,211,213,215,218,226,232,240,241,242,247,248,249,250,262,263,264,265,266,267,268,269,270,271,282,283,284,286,290,294,297,306,307,321,326,327,328,335,337,339,341,349,350,360,365,373,376,381,382,386,387,388,389,390,391,392,394,395,396,397,398,399,400,401,402,404,405,406,407,409,410,411,418,422,425,426,427,428,430,431,432,433,435,438,445,451,460,462,464,465,466,469,472,490,491,493,499,502],termin:[124,263,373,375,448,450,480,489],termostat:327,terrel:372,terri:7,tersoff:[],tersoff_1:[464,465,466],tersoff_2:[464,465,466],tersoff_mod:465,tertiari:184,tessel:[9,170],test:[],test_descriptor_str:3,testf:192,testu:192,tether:[6,305,312,320,322,333,408],tetot:[9,451],tex:8,texa:440,texas_holdem:306,text:[2,3,4,6,7,8,12,13,38,42,57,192,196,197,199,200,203,209,212,213,214,215,216,217,218,220,225,235,244,295,334,335,347,366,368,375,404,407,417,430,452,463,477,481,482,498,507,509],textur:17,tfac_insert:239,tfactor:[3,200],tfinal:507,tfix:306,tflag:199,tfmc:[],th4:171,than:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,27,38,40,41,42,43,57,59,60,61,63,65,70,73,78,90,92,96,110,112,114,118,121,122,125,147,170,173,174,175,181,192,195,196,198,200,203,208,210,212,215,216,217,218,220,221,222,223,224,226,227,228,231,235,236,239,240,241,242,245,246,247,250,261,288,289,293,294,295,296,297,298,300,302,305,306,307,308,311,312,313,319,320,321,323,327,328,330,331,335,338,339,340,341,342,343,344,345,346,348,365,366,371,372,373,374,375,376,377,380,385,386,387,389,390,391,404,406,409,410,416,427,428,430,435,443,444,445,451,453,460,461,462,463,466,468,470,472,473,476,477,478,479,481,482,483,484,485,486,489,490,493,495,496,498,507,508,509],thank:[244,464,466],thb:444,thb_cutoff:444,thb_cutoff_sq:444,thei:[0,1,2,3,4,6,7,8,11,12,13,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,42,43,44,46,47,48,49,50,52,54,55,56,57,59,61,63,65,66,68,70,72,73,76,77,83,86,88,91,93,94,95,98,108,109,111,114,115,118,120,121,122,123,125,146,149,150,152,154,155,158,159,165,167,169,170,172,174,175,176,178,179,181,182,183,184,186,187,189,190,191,192,196,197,199,200,203,204,205,206,208,211,212,213,215,216,217,218,219,220,221,222,223,224,226,227,232,233,238,239,240,242,243,244,247,248,250,253,260,263,265,266,267,268,269,270,271,272,273,274,275,280,282,283,284,286,292,293,294,295,296,298,299,306,307,308,309,310,323,324,326,327,328,330,334,335,337,338,339,341,343,344,346,347,348,349,351,352,353,354,355,358,359,360,363,365,366,368,370,372,373,374,375,376,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,398,399,400,403,404,405,406,407,408,409,410,411,412,413,414,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,436,437,438,440,441,443,444,445,446,451,452,453,460,461,462,463,464,465,466,467,468,469,470,471,472,473,477,479,481,482,483,484,485,486,490,491,493,494,499,502,507,509,510],them:[1,2,3,4,6,7,8,9,11,12,13,14,17,40,41,42,55,61,73,95,108,113,120,123,125,148,174,179,196,199,200,201,211,212,213,215,216,217,218,220,223,224,226,236,244,247,248,259,263,265,266,267,268,269,270,271,282,283,286,288,294,296,304,305,306,307,310,323,326,327,328,330,334,335,337,341,342,343,345,346,349,366,368,374,375,376,380,381,386,393,404,407,409,413,416,435,445,453,468,476,479,481,488,493,496,502,507,508],themselv:[6,11,175,204,205,220,248,365,366,375,377,381,386,396,404,426,430,431,432,452,507],theor:330,theorem:[240,247,311,386,402],theoret:[110,244,297,462],theori:[3,6,9,12,41,146,209,225,241,263,289,365,366,386,433,472,495],thereaft:[73,255,291,307,331,338,479],therebi:[336,427,428],therefor:[3,6,12,66,91,157,230,239,248,250,310,330,366,398,442,444,462,467,490,502],therein:[6,430],thereof:91,thermal:[],thermo:[],thermo_modifi:[],thermo_p:[3,65,115,479,499],thermo_press:[65,118,224,230,263,265,266,267,268,269,270,271,294,498,499,502],thermo_styl:[],thermo_temp:[65,118,149,223,224,239,263,265,266,267,268,269,270,271,282,283,284,286,289,294,326,327,328,498,499,502],thermoberendsen:6,thermochem:506,thermochemistri:406,thermodyam:[499,506],thermodyanm:[65,223,323,346,490],thermodynam:[],thermophys:435,thermost:[6,154,208,225,230,248,342,502],thermostat:[],thermostatequ:6,thesi:[365,366,427,442],thess:387,theta0:[20,21,24,26,27,28,32,33,35,36,146,181,306,358],theta0max:146,theta10:386,theta1:[179,349,386],theta2:[179,349,386],theta3:[349,386],theta4:386,theta5:386,theta6:386,theta7:386,theta8:386,theta9:386,theta:[3,6,26,27,37,38,39,65,67,82,96,112,146,171,172,181,193,195,199,242,302,306,335,349,358,412,441,465,481,484,491],theta_0:437,theta_:[358,386],theta_c:412,theta_ijk:386,theta_ijl:349,theta_jik:[431,432],theta_pi:386,theta_sigma:386,thex:298,thi:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,434,435,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,502,503,504,505,506,507,508,509,510,511],thick:[73,124,199,216,484],thie:116,thijss:330,thin:[122,199],thing:[3,6,11,12,55,70,73,224,263,294,307,323,478,479,483,507],think:[3,6,7,8,11,13,200,307,346,351,355,368,373,413,443,444,463,479,483,486,507],third:[6,9,12,29,95,140,146,147,170,212,213,215,216,217,218,240,304,320,321,335,395,407,430,437,467,469,476,477,479,481,484],thirumalai:184,thistl:200,tho:405,thole:[],thompson:[0,5,7,9,13,118,146,147,298,368,452],thoroughli:9,those:[1,2,3,4,5,6,7,8,12,13,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,38,40,41,43,44,46,47,48,49,50,51,52,54,55,57,63,73,74,79,91,95,96,112,114,115,116,118,122,146,147,149,152,159,162,170,172,176,178,179,181,182,183,184,185,186,187,189,190,192,195,196,197,199,200,210,211,212,213,216,217,218,224,226,227,236,242,244,245,246,247,253,260,262,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,293,296,299,307,325,332,333,337,341,342,343,346,347,349,351,352,354,355,356,358,360,365,366,373,375,376,380,381,382,384,387,388,389,390,391,392,393,394,395,396,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,430,431,435,436,437,438,440,443,444,445,446,452,453,461,462,463,464,465,466,469,471,472,473,476,478,479,481,483,484,485,486,488,490,491,493,495,498,499,500,502,507,510,511],though:[6,8,12,39,40,41,58,65,73,95,109,172,193,196,200,210,216,221,222,224,226,231,264,305,307,309,319,331,338,348,361,365,368,375,400,403,404,406,407,409,410,426,427,435,469,476,481,483,484,489,493,500,507],thought:[155,247,284,307,339,340,372,410,417,502],thread:[1,3,9,12,16,17,18,244,336,363,380,494,500],threads_per_atom:3,three:[1,3,6,55,65,76,91,95,96,110,123,124,125,136,146,150,171,172,184,203,223,224,229,251,263,268,289,294,298,307,323,330,332,335,353,354,358,365,366,374,380,381,382,386,404,405,407,409,410,414,417,430,431,432,433,437,441,444,445,451,452,462,464,465,466,469,479,481,484,507],threebodi:462,thresh:[42,196,197,199,200,220,479],threshhold:[3,42,199,220,346,479],threshold:[3,42,90,170,200,220,288,376,444,476,495],thrid:479,through:[3,6,7,9,11,12,65,172,176,196,197,201,224,237,239,244,245,250,252,253,254,263,264,290,298,316,330,335,340,344,364,371,382,402,405,406,410,416,418,433,446,451,453,460,467,476,479,482,492,498,502],throughout:[6,16,122,124,336,380,433,481],thru:[3,6,7,11,12,68,76,77,83,93,94,98,108,109,110,111,167,195,196,200,215,260,323,343,348,364,373,379,484],thrust:1,thu:[1,2,3,6,8,9,11,12,18,33,38,40,42,43,51,61,63,65,66,68,69,72,73,74,75,77,79,83,92,94,95,96,98,108,109,111,112,114,115,119,120,121,122,123,146,147,148,152,155,160,162,167,168,169,172,174,175,176,180,185,191,192,195,196,197,199,200,201,203,204,205,206,207,211,212,213,215,216,217,218,219,220,221,222,223,224,226,227,230,232,236,240,241,242,243,244,245,247,248,253,258,263,268,279,288,294,296,298,302,305,307,308,309,310,312,316,317,320,321,322,323,324,326,327,328,330,331,334,335,337,338,339,340,343,344,345,346,348,349,356,365,366,368,371,373,374,375,379,380,381,382,385,386,387,388,389,390,391,392,393,394,395,396,400,402,403,404,405,406,407,408,409,410,413,414,415,416,418,422,426,427,428,430,431,432,433,435,436,438,440,441,442,443,444,445,451,452,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,473,476,478,479,481,482,483,484,485,486,488,489,490,491,493,495,496,497,498,499,500,502,506,507,508,509,510],thumb:[8,10,17,172,195,260,307,380,394,484,490],thz:302,ti2:171,ti3:171,ti4:171,tight:[9,386,451],tightli:296,tij:399,tildeslei:[29,91,399],tile:[3,6,42,64,172,220,416,468,478,507],tilt:[3,6,59,60,61,73,160,174,196,197,200,216,224,226,227,242,261,263,264,288,297,366,368,469,481,484,499],time:[],time_integr:209,timedelta:213,timelin:5,timer:[],timescal:[3,211,212,213,215,216,217,218,261,297,302,406,476,490],timespan:[247,248,263,294,307,326,327],timestamp:[3,486],timestep:[],timesteppnig:310,timothi:9,tin:[395,396],tine:[],tinfoil:366,tini:[74,122,172,373,386,508],tinker:7,tio2:451,tio:451,tip3p:[],tip4:6,tip4p:[],tip:[],tirrel:340,titan:15,titer:307,titl:[212,213,214,215,216,217,218,295,444],title1:[212,213,214,215,216,217,218],title2:[212,213,214,215,216,217,218],title3:[212,213,215,216,217,218],tji:399,tl1:171,tl3:171,tlbr_msw:441,tlo:495,tloop:[263,264,268],tlsph:[],tlsph_defgrad:[],tlsph_strain:[],tlsph_strain_rat:[],tlsph_stress:[],tm3:171,tmax:[3,231,495],tmd:[],tmd_dump_fil:334,tmdatom:334,tmin:231,tmp1:[215,218,492],tmp2:[215,218,492],tmp3:492,tmp:[6,12,42,68,70,71,77,94,98,109,111,120,122,152,167,169,196,197,199,200,220,296,307,331,338,379,488,492,507],tobia:[263,264,307],todd:284,toe:166,toff:[374,481],togeth:[2,3,6,11,12,17,40,42,73,121,147,152,166,173,196,197,204,205,212,215,220,224,230,241,248,263,294,307,312,317,320,323,341,345,346,408,413,479,484,489,502,510],toggl:[61,176,488],togheth:[],togther:3,tol:[310,323,365,462],toler:[3,224,298,299,300,310,323,373,375,462,476,495],toma:9,tomato:200,tong:[9,13],too:[1,3,6,7,40,42,66,69,72,74,75,79,92,96,112,146,160,173,175,199,214,220,221,222,224,227,236,239,243,263,289,294,298,302,304,310,323,330,331,335,338,366,375,376,380,400,416,476,484,495,498,502,507],took:[73,453],tool:[],toolkit:[6,7,13,14,15,197],top:[0,3,8,9,11,12,13,61,155,170,195,203,219,226,243,250,262,284,308,342,343,345,375,380,443,444,452,481,485,491],top_group:317,top_veloc:317,topic:[507,510],toplog:[3,478],topolgi:41,topolog:[2,3,6,7,8,12,13,37,40,41,56,91,114,121,175,176,191,200,221,222,244,292,359,374,413,435,478,481,482,483,485,486,493],topwal:219,torder:307,torqu:[],torsion:[6,179,180,191,382,443,444],torsion_flag:382,tosi:387,tot:[302,451],total:[3,6,11,12,14,15,16,17,18,40,42,43,65,73,83,84,85,92,93,94,95,103,107,108,109,110,113,115,116,123,128,129,130,131,133,134,135,136,137,138,139,146,147,149,152,153,154,155,158,159,160,161,162,164,166,168,169,170,196,203,206,207,210,212,214,215,216,217,219,220,222,228,230,232,237,238,239,240,245,247,248,249,250,251,253,261,263,264,268,279,289,290,292,293,297,302,304,306,307,308,309,312,314,317,320,322,331,332,333,335,338,340,344,365,373,374,375,376,377,380,381,383,385,386,395,404,406,410,430,431,432,433,441,443,444,448,451,452,468,476,478,479,481,483,489,490,495,496,499,500,507],touch:[12,245,341,483],toukmaji:[366,399],toward:[9,29,170,199,203,227,228,245,250,262,268,288,305,320,334,336,358,375],toxvaerd:423,tpa:380,tparam:307,tpartial:152,tpc:380,tpcpu:499,tperiod:307,tptask:[16,380],tqx:[119,196,197,325],tqy:[119,196,197,325],tqz:[119,196,197,325],trace:406,track:[3,7,12,222,226,250,335,345,476,481,487,495,499,507],track_displac:209,tracker:244,trade:[6,12,299,365,366,396,418,422,490,495],tradeoff:435,tradit:[6,9,366],traffic:12,trail:[2,22,45,79,91,122,166,176,180,200,204,205,307,350,370,374,375,393,407,430,444,452,475,481,489,491],train:444,traingul:319,traj:225,traj_titl:444,trajectori:[3,6,12,40,91,196,244,263,265,266,267,269,270,271,272,273,275,276,278,280,281,282,283,284,285,286,290,307,310,312,316,336,345,400,435,444,483,491,496,502,506],tran:[183,184],transfer:[1,6,16,209,230,244,246,331,335,338,365,380,386,433,502],transform:[],transit:[6,9,90,262,312,334,375,397,426,432,433,466,476,495],translat:[3,6,63,65,99,100,101,102,103,150,151,152,156,165,212,239,243,247,248,253,263,269,270,271,282,283,286,290,307,326,327,328,330,368,406,481,499],transmiss:244,transmit:[6,244],transpar:[14,17],transport:[209,335,454],transpos:12,trap:[3,6,95,168,213,245,337,507],trapezoid:[213,507],trate:[3,226,244],travel:323,treat:[2,3,6,8,17,41,43,73,86,88,89,147,150,154,165,176,194,212,213,215,218,227,238,264,289,292,293,307,323,335,337,344,348,364,365,373,374,376,385,398,406,407,409,412,416,431,432,433,445,468,481,484,486,489,491,502,507],treatment:[9,302,398],tree:[3,292,426],tref:403,tri:[],tri_surfac:[],trial:[227,239,383,490],triangl:[],triangleflag:481,triangul:[2,6,13,319,449],triangular:[4,6,43,86,119,224,281,319,449,481],tricki:[478,502],triclin:[],triflag:6,trigger:[3,11,12,64,90,220,223,239,373,439,474,499],trigon:25,trilinear:250,trilino:17,trim:[3,482],tringl:199,tripflag:443,tripl:[2,146,226,386,443,477,479],triplet:[3,34,37,39,405,437,441,462,464,465,466,469],trivial:[8,11,298],trj:444,trott:[7,9,14,17,146,452],troubl:[11,12],truli:8,truncat:[3,5,6,12,73,296,302,340,344,372,384,396,406,410,418,420,423,435,440,451,491],trung:15,tscale:[3,261,297],tschopp:69,tsige:390,tsrd:[323,345],tstart:[240,241,247,249,263,264,307,326,327,328,329,400,487],tstat:[],tstop:[240,241,247,249,263,264,307,326,327,328,329,400,487,495],tsuzuki:[75,469],tthi:133,ttm:[],ttm_mod:335,tucker:[146,452],tuckerman2006:[],tuckerman:[263,264,285,290,307,490],tune:[],tunnel:290,turkand:112,turn:[3,4,6,12,22,33,37,40,45,51,55,56,61,67,71,73,114,121,146,170,171,176,180,185,191,199,200,203,210,221,222,223,224,239,244,263,277,292,295,296,307,323,350,356,359,365,373,375,376,378,380,382,398,412,413,430,435,444,460,461,477,481,483,488,493,494,499,500,504,509],turquois:200,tutein:382,tutori:[6,9],tweak:[12,172,244,380],twice:[3,6,16,17,65,92,178,200,203,204,205,224,260,263,300,311,380,413,479,481,488],twin:69,twist:[427,428],two:[1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,22,38,40,42,43,45,55,57,59,61,63,65,67,70,71,73,78,79,81,91,92,96,97,108,113,114,119,120,121,122,123,124,146,148,150,154,155,157,158,160,166,170,171,172,173,175,180,195,196,197,198,199,200,203,204,205,210,211,212,213,215,216,217,218,220,221,222,223,224,227,230,236,239,240,241,243,245,246,247,248,250,253,262,263,264,268,288,289,290,293,294,296,297,298,302,304,307,312,320,323,330,331,333,335,338,341,344,346,348,350,360,365,366,368,370,371,373,374,375,378,380,381,382,383,385,386,387,388,389,390,393,394,395,396,398,399,400,403,404,405,406,407,409,410,413,416,417,418,422,426,427,428,430,433,435,438,441,442,443,444,445,447,451,452,453,460,461,462,464,465,466,467,468,469,472,473,475,476,478,479,481,482,483,484,485,488,491,493,494,495,496,498,499,502,506,507,508,509,510,511],two_temperatur:209,twobodi:[464,466,469],twogrid:3,twojmax:[146,452],twolevel:[3,478],txt2html:8,txt:[8,13,196,201,295,296,335,363,374,417,451,470,486,507],typcial:[42,220],type1:[79,124,171],type2:[79,124,171],type:[],typei:416,typej:416,typen:[79,124,171],typic:[1,2,3,6,7,8,10,11,12,13,14,15,16,17,18,29,40,41,42,46,47,56,59,61,63,65,72,73,90,91,107,113,125,134,166,172,173,175,196,197,198,199,200,203,204,205,206,208,209,212,214,220,221,222,223,224,226,227,232,236,237,239,242,248,263,277,289,292,293,296,298,300,306,307,310,313,315,323,330,338,339,345,365,368,372,373,374,375,376,377,380,391,393,394,396,408,409,412,413,417,418,422,427,428,430,435,445,448,450,461,463,466,476,477,479,481,482,483,484,490,493,495,496,498,506,507,509,511],typicali:12,tzou:335,u_cond:[84,85,234],u_f:250,u_i:[234,235],u_ij:441,u_mech:[84,85,234],u_prom:386,uberuaga:[262,375],ubiquit:[11,386],ucond:41,uhf:383,uiuc:[9,17],uloop:[3,290,375,379,507],ulpsh:[],ulsph:[],ulsph_num_neigh:[],ultim:495,ultra:170,umbrella:[],umech:41,umin:[26,27,49,50,181],unabl:[3,11,42,220],unaffect:[196,224,263,307,482,493,498],unalt:[204,205,277],unambigu:[73,216,469],unari:[348,507],unbalanc:3,unbias:[160,406],unbond:[222,481],unbroken:82,uncertainti:41,unchang:[61,224,227,262,263,265,266,267,269,270,271,279,294,307,481,482,485,491],uncharg:[41,366],uncom:[1,4],uncompress:[12,73,199],uncomput:[],uncorrel:[240,330,476],uncoupl:290,undefin:[3,12],under:[0,5,6,7,8,9,10,12,18,21,22,45,146,179,180,199,244,261,263,293,297,298,311,349,350,370,402,406,426,444,452,479,495,502],underestim:170,underflow:199,undergo:[6,90,91,108,160,240,247,248,263,312,323],undergon:[223,323],underli:[6,9,12,17,72,199,263,335,368],undermin:40,underpredict:6,underscor:[2,3,65,197,203,223,224,261,263,265,266,267,268,269,270,271,282,283,284,286,294,296,326,327,328,348,374,507],understand:[1,6,8,239,264,433],understood:[196,386],undesir:[61,224,226,263,307],undetermin:323,undisturb:[427,428],undo:[176,244],undump:[],unexpect:[3,487],unfix:[],unfix_flux:209,unfold:321,unfortun:[336,489,490],uniaxi:[3,150,268],uniform:[7,16,42,92,122,209,220,221,222,247,250,253,264,330,403,409,445,476,478,507,508],uniformli:[61,122,195,250,293,335,441,463,508],uninstal:12,uninterrupt:[210,227,239,260,261,263,265,266,267,268,269,270,271,282,283,284,285,286,296,297,307,312,322,325,333,335,341],union:[3,6,41,200,344,346,481,484],uniqu:[3,6,7,8,9,12,40,73,128,214,240,241,247,248,268,296,302,304,375,404,406,481,507,508],unit:[],unit_styl:3,uniti:[405,435,456],unitless:[66,69,72,73,120,177,212,216,217,226,239,261,263,297,341,373,383,410,438,440,462,464,465,466,469,506],unitlesss:[80,82,117],univ:[9,13],univers:[3,6,9,12,13,18,91,244,365,366,375,379,427,432,440,442,466,475,478,507],universit:[9,13],unix:[12,17,246,492],unknown:[3,12,66,75,481],unless:[2,3,9,11,12,15,16,56,59,69,108,124,157,171,172,196,197,200,201,208,224,227,239,247,263,265,266,267,269,270,271,293,294,307,323,334,367,373,394,435,463,479,484,488,493,507],unlik:[12,33,51,61,93,162,172,185,196,214,247,263,268,294,300,302,326,327,328,356,364,365,381,386,404,407,412,413,417,430,431,432,444,452,461,478,483,488,493,507,511],unlimit:441,unlucki:3,unmark:7,unmodifi:324,unnecessari:16,unoccupi:335,unoptim:199,unpack:[0,8,11,380],unpack_bord:8,unpack_border_bodi:8,unpack_border_hybrid:8,unpack_border_vel:8,unpack_comm:8,unpack_comm_bodi:8,unpack_comm_hybrid:8,unpack_comm_vel:8,unpack_exchang:8,unpack_restart:8,unpack_revers:8,unpack_reverse_comm:8,unpack_reverse_hybrid:8,unpad:200,unperturb:91,unphys:[3,6,248,263,307,481],unpredict:[305,491],unpublish:433,unrecogn:3,unrel:[8,9,13,178],unreli:435,unrestrain:306,unrestrict:383,unscal:[3,119,166,196,197,325,482],unset:[3,365,406],unshift:399,unsmooth:424,unsolv:[377,391],unsort:200,unspecifi:[226,481],unsplit:502,unstabl:[3,250],unstrain:226,unsuccess:[3,293],unsuffici:[],unsupport:3,untar:12,until:[2,3,6,12,14,38,40,42,57,73,125,192,199,220,224,227,235,239,244,293,316,323,325,332,348,364,365,376,379,380,386,410,463,476,481,482,486,487,489,495,506,507],untilt:484,unus:386,unusu:[3,8,376],unwant:[3,172,365],unwrap:[3,68,76,77,83,93,94,98,108,109,111,119,147,167,196,197,200,201,211,223,225,244,260,307,320,325,481,482,485,491],unwrapexpand:196,unzip:12,up_intern:199,updat:[0,3,6,8,12,13,129,130,131,141,142,143,144,195,196,197,203,210,221,222,230,237,240,247,248,250,252,253,256,257,260,261,263,264,265,266,267,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,292,294,296,297,302,307,315,316,325,326,327,328,330,335,346,347,380,386,399,433,435,443,444,450,476,481,483,491,492,495,502],upenn:[11,13],upgrad:12,upon:[6,210,244,386,467,495],upper:[2,3,42,59,61,73,92,108,110,148,161,168,195,200,213,214,216,217,220,224,230,248,250,263,297,302,340,341,346,347,373,410,451,484,508],upsid:6,upsilon:409,upto:[3,483,489],upward:227,urbana:[244,365,366,427],urey_bradlei:20,usa:9,usabl:[12,239,404],usag:[3,6,8,248,288,302,323,413,426,481],use_ldg:17,usec:501,useful:380,user:[],user_misc:[30,31,35,182,187,190,354],userguid:9,usr:[11,12,14,482],usual:[2,3,6,9,12,14,17,18,24,28,32,35,36,48,63,73,91,123,150,151,152,157,165,170,189,196,197,199,204,205,210,212,223,224,225,226,239,242,247,249,261,268,289,297,298,304,306,307,323,331,335,338,340,344,348,355,363,375,376,380,391,394,397,399,409,413,414,417,426,427,428,435,437,447,448,449,450,452,460,462,467,476,480,482,486,490,492,495,498,499,507,511],util:[8,12,17,18,380,409,500],utilizi:12,utilz:[12,500],utsa:440,utsph_strain_r:[],uttormark:13,uuml:289,uwo:9,v11:6,v22:6,v33:6,v_0:[3,335],v_2:433,v_3:433,v_4:433,v_a:[8,226],v_abc:[479,499,507],v_area:[2,507],v_atomfil:491,v_c:166,v_cluster:296,v_dc:166,v_delta:91,v_dhug:[261,297],v_diff:[168,337],v_displac:226,v_dk:166,v_dlj:166,v_drai:[261,297],v_dx:[260,484],v_dy:[260,484],v_dz:260,v_e_hbond:412,v_ea:[443,444],v_eb:[443,444],v_eqeq:[443,444],v_espac:206,v_f:479,v_fac:479,v_flux:243,v_foo:[479,507],v_ij:441,v_increas:242,v_integr:337,v_jx:95,v_jy:95,v_jz:95,v_k11:95,v_k22:95,v_k33:95,v_k:166,v_ke:[196,197,510],v_left:484,v_lgr_po:[261,297],v_lgr_vel:[261,297],v_linear:[340,343,345],v_lj:166,v_mol:200,v_mu:427,v_myi:260,v_myindex:507,v_myke:123,v_mystep:488,v_myvar:[8,200],v_myx:260,v_n:[250,433],v_name1:[166,226],v_name2:[166,226],v_name:[3,6,73,91,123,195,196,197,199,200,204,205,206,207,211,212,213,214,215,216,217,218,219,232,242,243,245,247,248,260,309,317,325,326,327,328,337,340,343,345,479,484,488,491,497,499,507,508],v_nstep:346,v_occ:408,v_omega:260,v_oscil:[206,207,219,232,309],v_phi:242,v_prefactor:[204,205,453],v_press:147,v_pressdown:[343,345],v_push:206,v_pxy:6,v_pxz:6,v_pyz:6,v_r0:245,v_r1:170,v_r2:170,v_r:[170,245],v_rad:346,v_radiu:245,v_ramp:[340,343,345],v_rate:[226,245],v_scale1:[204,205],v_scale2:[204,205],v_size:[204,205],v_t_qm:297,v_temp:331,v_theta:[242,484],v_tp:226,v_up:484,v_v0:507,v_v11:6,v_v22:6,v_v33:6,v_v:[260,507],v_valu:[199,479],v_vx:260,v_vy:260,v_vz:[260,508],v_wiggl:[340,343,345],v_x:[2,172,245,260,340,343,345,479,484,507],v_xave:6,v_xmax:6,v_xx:172,v_y:[172,245,484],v_yi:172,v_z:484,vacanc:[4,170,332,433],vacf:[],vacuum:[335,366,397,466,473],valanc:386,vale:3,valenc:[300,386,406,443,444],valent:386,valeriu:9,valid:[2,3,6,9,11,12,73,124,158,171,200,224,239,247,288,307,323,346,348,363,368,404,406,409,433,441,481,482,489,491,507],vallon:430,valon:430,valu:[],valuabl:500,value0:507,value1:[12,152,211,212,213,214,215,216,217,218,268,337,346,492],value2:[12,152,211,212,213,214,215,216,217,218,268,337,346,492],valuei:213,valuej:213,valuev:[7,9],valus:296,van:[9,54,91,113,294,298,303,326,394,395,426,430,443,444,472,508],vanadium:433,vanderwa:[435,499],vanilla:[6,8,12],vanillia:43,vanish:[230,302,310],vapor:[42,220,239,498],vapour:330,var1:492,var2:492,varaibl:[3,484],varavg:12,vare:335,vari:[1,18,42,63,64,73,91,124,160,162,171,204,205,209,212,213,216,220,224,226,261,263,294,306,307,326,327,335,340,365,391,400,401,402,411,424,427,440,453,463,478,496],variabl:[],variable_hill_factor:13,variable_nam:444,varianc:[123,400,507],variant:[1,3,6,12,87,103,263,268,307,311,365,372,380,431,432,464,466,490,494,508],variat:[12,42,220,507],varieti:[1,2,6,7,9,13,15,73,199,244,363,368,413,430,443,444,461,469,507],variou:[],varreturn:479,varshalovich:146,varshnei:13,vartiabl:3,vashishta1990:469,vashishta2007:469,vashishta:[],vbia:6,vcm:[],vdim:[161,331,338,508],vdisplac:[3,245,260,340,343,345,507],vdw:[3,395,444],vec1:[123,296],vec2:[123,296],vec:288,vector:[],vel:[3,6,63,212,216,217,226,248,293,312,342,400,402,406,410,476,483,484,486,502,507],veld:[13,323,366,390,422],veloc:[],velocit:[243,400,402,406,410],velocity_bottom:250,velocity_gradi:450,velocity_temp:508,velocity_top:250,vendor:12,verbatim:479,verbos:[12,451],veri:[1,3,6,7,8,9,10,12,13,17,42,73,74,91,122,123,196,197,199,200,211,212,213,214,215,216,217,218,220,221,222,224,239,253,263,264,277,290,305,310,326,327,337,375,376,377,380,406,410,427,428,440,452,453,463,489,499,500,502,506,509],verifi:[8,380,435,490,496],verlag:312,verlet:[1,3,7,8,12,18,209,247,263,277,284,290,310,324,335,343,346,475,478,490],versa:[3,6,13,61,166,174,223,235,245,247,248,307,481,482,502],versu:[6,14,15,16,18,40,42,82,108,109,122,168,200,220,307,310,366,390,399,410,422,435,499,507],vertex:[43,140,319],vertic:[],vfinal:507,vfrac:119,vhi:[161,508],via:[],vibrat:[6,9,227,241,288,297,302,358,406,476,490],vice:[3,6,13,61,166,174,223,235,245,247,248,307,481,482,502],video:199,view:[4,6,7,9,13,196,199,323,386,406,407,451],viewer:[196,199],viewpoint:199,vij:400,vika:13,vim:[],vincent:[9,19],violat:330,violet:200,virial:[3,65,95,118,146,147,166,204,205,224,230,263,264,265,266,267,268,269,270,271,292,294,307,310,365,380,383,400,401,402,403,406,414],virialmod:414,virtual:[6,7,8,12,462],virut:9,visa:7,viscoelast:[117,410,440],viscoelsat:440,viscos:[],viscou:[],viscous:307,vision:451,visit:[308,443,444],vista:196,visual:[],viz:[11,13],viz_tool:11,vizplotgui_tool:11,vizualiziton:308,vlo:[161,508],vmax:[224,323],vmd:[6,7,9,11,13,196,201,244,482],vmdarch:201,vmdhome:201,vname:[172,507],voigt:[6,146],vol:[],volfactor:365,volpress:433,volt:[442,506],volum:[2,3,6,41,42,60,61,65,82,91,95,105,118,122,124,132,136,145,147,170,171,172,175,210,212,216,217,220,224,226,227,234,239,250,261,263,264,268,272,273,275,276,278,280,281,282,283,284,285,286,293,294,297,307,312,335,340,344,346,365,368,374,388,427,428,433,440,458,459,473,477,478,481,484,491,499,502,506,507],volumetr:82,von:[139,144],voro:[3,9,170],vorobyov:502,voronoi:[],vorselaar:214,voter2:[476,495],voter:[431,432,476,495],voth:[41,290],vpz:342,vratio:507,vri:411,vrpn:244,vshear:341,vstream:6,vtarget:[3,338],vtk:[],vtp:197,vtr:197,vtu:197,vv0210:13,vx0:168,vxcm:307,vxhi:[227,293],vxlo:[227,293],vy0:168,vycm:307,vyhi:[227,293],vylo:[227,293],vz0:168,vzcm:307,vzhi:227,vzi:342,vzlo:227,w_1:146,w_2:146,w_i:146,w_ik:441,waal:[91,113,394,395,426,443,444,472],wadlei:[13,386],wag:[7,9,13],wagner:[7,9,209,250,430],wai:[1,2,3,6,7,8,11,12,15,18,22,45,53,61,65,67,68,71,73,74,77,79,81,91,94,95,96,97,98,109,111,112,114,120,121,122,146,147,149,150,151,152,153,154,155,158,159,160,161,162,164,165,166,167,169,172,175,180,188,192,195,196,197,199,200,203,204,205,212,215,216,218,219,222,223,224,226,237,240,245,247,248,250,261,263,268,277,290,293,294,296,305,307,308,312,320,323,325,326,327,328,331,334,335,337,340,343,345,346,350,351,352,353,355,357,358,366,368,370,373,375,376,380,381,382,393,396,397,400,403,404,405,407,409,412,413,415,418,430,431,432,435,437,439,441,442,445,451,452,453,460,462,464,466,469,475,476,479,481,482,483,484,485,486,489,490,491,507,508],wait:[1,12,244,289,476,478],walk:[3,240,247,248,263],wall:[],wall_surac:140,wall_surfac:[],wallhi:340,wallstyl:341,wander:320,wang:[366,430,441],want:[0,1,2,3,5,6,7,8,9,11,12,17,38,41,57,65,68,70,73,77,83,84,85,94,98,108,109,111,113,115,116,118,120,122,147,152,167,168,169,170,172,175,178,192,196,197,199,200,203,204,205,206,211,212,220,223,226,227,230,232,235,237,239,245,248,258,279,288,293,296,306,307,309,320,322,324,331,333,338,340,344,346,348,366,368,375,381,382,386,394,395,400,404,407,413,414,415,416,430,437,441,443,444,451,453,462,463,464,466,468,469,477,479,481,482,483,484,486,488,489,496,499,502,507,509,511],ward:386,warm:[16,406],warn:[],warner:381,warp:[5,430],warranti:7,warren:400,wasn:3,wast:3,watanab:[332,333],watch:375,water:[],watkin:189,wave:[7,9,41,208,261,301,342,383,406],wavefunct:[9,383,406],wavelength:[124,171],wavepacket:[41,383,406,481],wavevector:289,wbodi:87,weak:[96,298],web:[1,8,14,15,16,17,393],webb:209,weber:[3,5,7,15,92,148,405,432,441,461,462,469,493],websit:8,weckner:440,wedg:[],weight:[],welcom:479,well:[1,3,6,7,8,9,11,12,13,15,16,17,18,27,41,52,69,73,96,112,118,147,150,158,172,181,199,200,206,210,212,218,220,221,222,224,227,232,239,243,247,250,254,260,263,268,293,307,309,317,330,333,341,373,375,380,385,408,409,412,413,414,427,428,430,433,445,453,464,465,466,479,481,483,485,490,495,500,502,506,510],wennberg:365,went:[3,11],were:[3,4,5,6,7,11,12,13,15,16,19,34,42,43,53,57,62,72,73,108,112,115,118,122,149,152,172,175,176,188,196,199,200,203,206,212,215,216,217,218,220,226,232,236,243,244,277,284,308,341,342,346,357,365,377,379,406,410,413,417,440,444,463,476,478,479,481,482,483,484,486,488,496,499,507,508,510,511],weren:486,western:9,westview:472,what:[],whatev:[8,12,14,15,114,119,122,123,125,199,200,204,205,224,263,294,296,341,368,372,373,375,380,392,394,433,443,444,495,502,507],wheat:200,whelan:171,when:[0,1,2,3,4,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,40,41,42,43,44,46,47,48,49,50,51,52,54,55,56,57,61,63,64,65,73,74,83,90,92,96,108,109,110,112,113,115,118,119,122,123,125,148,149,150,155,159,160,162,168,170,172,173,174,175,176,178,179,180,181,182,183,184,185,186,187,189,190,191,192,196,197,198,199,200,201,203,204,205,206,207,208,210,211,212,213,215,216,217,218,219,220,221,222,223,224,225,226,227,231,232,233,235,236,237,238,239,241,242,244,247,250,251,253,254,258,263,264,265,266,267,268,269,270,271,272,273,277,279,280,282,283,284,286,288,292,293,294,295,296,297,299,300,301,302,306,307,308,309,310,312,320,321,323,324,325,326,328,330,331,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,351,352,354,355,356,358,359,360,362,363,364,365,366,368,371,372,373,374,375,376,377,379,380,381,382,384,387,388,389,390,391,392,393,394,395,396,398,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,435,436,437,438,440,441,443,444,445,446,452,453,460,462,463,464,465,466,468,469,471,472,473,474,476,478,479,481,482,483,484,485,486,487,488,489,490,491,492,493,495,496,498,499,500,501,506,507,508,509,511],whenev:[0,8,12,14,73,200,211,217,307,368,412,479,490,494,507,511],whenth:3,where:[1,3,6,8,9,10,11,12,14,15,18,21,23,24,25,26,27,28,29,32,35,36,37,40,41,42,44,48,49,50,52,56,63,65,67,68,70,71,72,73,75,77,81,82,84,86,87,88,89,91,92,93,94,96,97,98,99,100,101,102,103,109,111,114,118,119,120,121,122,123,124,125,147,149,150,151,152,153,154,155,158,159,160,161,162,164,165,166,167,169,171,173,175,176,179,181,191,195,196,199,200,203,204,205,206,207,212,213,216,219,220,223,224,226,227,231,232,234,236,237,239,240,241,242,243,245,247,248,249,250,253,254,256,258,260,261,263,264,268,277,280,287,288,289,290,293,295,296,297,300,302,307,308,309,310,312,316,317,320,322,325,326,327,328,331,332,333,335,338,339,340,341,343,344,345,346,349,351,352,353,354,355,358,359,360,363,366,368,372,373,374,375,376,377,380,381,382,385,386,387,389,393,394,395,396,397,398,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,418,422,427,428,429,430,431,432,433,435,437,438,440,441,442,443,444,445,451,452,455,458,459,460,461,462,463,464,465,466,469,472,473,475,476,478,479,480,481,483,484,485,486,488,490,491,493,495,496,497,498,499,502,506,507,508,509,511],wherea:[6,11,96,210,240,263,298,330,335,502],wherebi:299,wherev:243,whether:[6,8,11,12,17,40,41,55,61,63,65,72,73,107,113,115,159,160,192,199,200,202,203,204,205,212,218,221,222,223,224,225,226,230,236,239,248,260,263,268,296,310,323,331,337,338,346,348,363,365,366,374,378,380,389,391,395,411,413,417,427,428,430,435,444,451,461,476,479,481,482,484,486,493,494,495,498,507,508],which:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,28,29,32,33,37,38,40,41,42,43,45,46,47,48,51,52,54,55,56,57,60,61,63,65,66,68,69,72,73,74,75,76,77,78,79,80,82,83,84,85,86,87,89,91,92,93,94,95,98,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,116,117,118,119,120,122,123,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,178,179,180,183,184,185,186,189,191,192,195,196,197,199,200,201,203,204,205,206,207,208,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,253,254,257,258,260,261,262,263,264,265,266,267,268,269,270,271,273,275,277,278,280,281,282,283,284,285,286,288,289,290,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,312,313,314,315,317,319,320,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,340,341,342,343,344,345,346,348,349,350,352,355,356,359,360,363,364,365,366,368,370,371,372,373,374,375,376,377,379,380,381,382,383,385,386,387,389,390,391,393,394,395,396,397,398,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,422,424,426,427,428,430,431,432,433,435,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,453,456,460,461,462,463,464,465,466,467,468,469,472,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,502,507,508,509,510,511],whichev:[12,379,476,495],white:[200,240,247,248,249,307,327,335,481,507,510],whitesmok:200,whitespac:[2,3,200,374,481],who:[0,3,6,7,8,9,13,381,404],whole:[230,244,289,302,312,502],wholli:227,whose:[3,6,7,8,18,19,38,40,43,57,61,78,91,157,175,192,199,200,210,226,235,245,246,260,263,265,266,267,269,270,271,288,289,305,306,310,323,337,344,346,368,375,376,406,420,447,449,462,463,464,466,502,507,508],why:[3,6,248,331,338],wide:[1,6,7,9,63,65,203,331,338,368,377,391,394,406,443,444],wider:1,width:[199,200,383,408],wiggl:[3,226,260,316,340,341,343,345,484],wigner:146,wih:6,wiki:14,wikipedia:[6,14],wild:[3,12,22,45,79,91,122,180,204,205,307,350,370,393,412,475,483,488,509,511],wildcard:[3,12,166,176,196,197,199,200,304,393,460,488,491,510,511],wildli:263,win:380,window:[3,4,12,13,73,196,199,201,212,213,214,215,216,217,218,244,308,328,329,393,482],wipe:[203,413,461,503,505],wire:306,wirt:200,wisconsin:13,wise:[3,12,400,462,490],wish:[2,3,5,6,7,8,11,12,14,17,41,43,59,60,61,73,123,147,152,173,174,176,178,196,197,200,204,211,212,213,216,217,218,222,226,227,236,239,245,250,254,293,296,307,310,323,324,340,341,368,375,380,389,412,413,430,435,443,463,479,481,482,483,489,493,499,507,508,511],within:[1,2,3,6,8,9,11,12,13,15,16,17,29,40,41,42,43,56,61,63,65,67,71,72,73,74,75,79,81,96,97,112,114,118,121,122,123,125,128,146,163,172,175,198,199,200,204,205,210,211,212,215,216,217,218,220,221,222,223,227,229,235,236,239,245,247,288,292,293,294,296,298,307,308,310,313,315,319,320,324,335,338,340,344,346,348,364,368,373,374,375,376,377,380,385,387,389,396,401,402,403,404,405,406,408,413,414,417,418,430,433,438,439,440,445,446,461,462,464,465,466,467,469,474,476,478,479,481,489,490,493,495,502,506,507],without:[1,2,3,4,6,7,8,9,11,12,14,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,61,91,115,118,149,154,159,173,178,179,181,182,183,184,186,187,189,190,192,196,199,200,201,203,206,212,214,215,216,217,218,219,224,226,233,235,238,240,242,244,247,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,285,286,293,296,298,299,301,305,307,308,309,310,316,323,326,328,339,343,347,349,351,352,354,355,358,360,364,365,366,375,376,380,381,382,384,387,388,389,390,391,392,393,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,433,435,436,437,438,440,444,445,446,453,461,462,463,464,465,466,469,471,472,473,479,481,484,489,490,499,502,506,507],witht:[],witi:15,wolf:[],wolff:[435,463],won:[3,305,428],wong:[209,386],word:[2,3,6,8,12,29,65,200,203,210,211,212,213,216,217,218,225,245,274,279,295,300,306,337,348,364,394,435,477,479,481,507,508],work:[1,3,6,7,8,9,11,12,14,16,18,40,55,61,62,92,123,124,150,151,153,154,155,159,160,161,162,164,165,170,171,196,199,201,204,205,212,216,217,223,237,246,247,248,250,254,260,263,269,270,271,282,283,284,285,286,304,306,308,310,326,327,328,333,364,376,380,393,395,398,400,413,427,428,430,433,435,451,476,478,479,482,483,485,489,490,492,495,507],workaround:[74,122,307,435,508],worker:[12,443,444,469],workhors:8,workstat:[380,479],world:[3,12,146,364,375,379,475,478,479,496,507],worlei:400,worri:17,worsen:18,worst:344,worth:[212,213,215,216,217,218,297,308],would:[1,3,4,5,6,7,8,11,12,22,29,37,42,43,45,56,72,73,74,93,95,122,147,152,160,172,173,174,175,176,180,191,196,197,199,200,201,203,204,205,207,210,212,220,223,225,226,230,231,236,239,242,243,244,248,260,263,264,277,288,290,294,296,298,302,305,323,330,334,342,343,346,348,349,350,351,352,353,355,356,359,365,368,370,372,373,375,376,379,380,381,382,386,393,394,395,396,400,401,402,403,404,405,407,413,414,415,416,430,431,432,433,437,441,443,444,448,450,452,460,462,464,465,466,469,476,479,481,484,485,486,488,489,490,491,492,496,498,499,502,507,508,510,511],wrap:[1,3,6,11,12,59,61,172,174,195,196,197,198,200,201,211,217,225,226,227,244,250,260,307,320,323,340,342,344,365,366,375,479,481,482,484,489],wrapper:[],wrigger:312,wright:373,writabl:3,write:[],write_atom_weight:209,write_data:[],write_dump:[],write_freq:444,write_head:8,write_restart:[],writen:308,written:[3,5,6,7,8,9,12,13,14,17,67,71,121,146,170,196,197,198,199,200,201,203,204,205,206,207,208,209,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,228,230,231,232,233,236,237,238,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,259,262,272,273,274,275,276,277,278,279,280,281,287,288,289,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,320,321,323,324,326,327,328,329,330,331,332,334,335,337,338,339,340,342,343,344,345,347,363,368,376,404,413,429,433,470,472,476,477,479,482,483,487,488,495,496,497,498,507,509,510,511],wrong:[3,11,224,263,287,340,344,345,376,444,483,488],wrote:[3,483],wt1:435,wt2:435,wt3:435,wurtzit:368,www:[0,2,3,4,5,6,7,8,10,11,12,13,15,381,404,427,442,443,444,506],x86:[12,433],x_ij:441,x_ijkl:349,x_kjli:349,x_ljik:349,xave:6,xavx:16,xcm:[8,307,507],xdr:[12,196],xeon:[1,4,7,9,12,16,17,18,380,494],xflag:[159,160,251,253,259,307,330],xhe:[],xhi:[2,6,59,61,174,196,226,334,340,343,345,481,484,499,507],xhi_bound:[6,196],xhi_new:481,xhost:[9,12,16],xi_ij:441,xiaowang:[13,407,464,466],xiij:288,xlat:[172,226,245,499],xlo:[2,6,11,59,61,174,196,226,245,334,340,343,345,481,484,499,507],xlo_bound:[6,196],xlo_new:481,xmax:[6,208,231,277,507],xmgrace:[],xmin:507,xml:[197,201,442],xml_label:442,xmovi:[],xmu:[341,410],xorig:73,xplane:341,xplor:196,xpo:172,xrd:[],xsph:9,xsu:[3,196,197,325,482],xt3:196,xt4:[18,196],xt5:[18,196],xtc:[],xtcdump:200,xvf:12,xwall:[342,343,345],xxx:12,xyz:[3,6,7,13,43,68,73,111,114,160,167,172,196,198,199,200,201,216,224,253,263,264,268,294,304,305,307,320,322,341,343,345,367,374,478,482,508,510],xzhou:[13,407],xzy:478,yang:[433,441],yate:433,yb2:171,yb3:171,ybox:226,ycm:307,year:[5,7],yeh:365,yellow:[199,200],yellowgreen:200,yet:[3,7,9,17,40,43,199,204,304,340,366,372,373,380,392,394,395,406,472,479,481,482,507,509,510],yflag:[159,160,251,253,259,307,330],yhi:[6,61,174,196,226,334,340,343,345,481,484,499],yhi_bound:[6,196],yield:[6,95,116,123,147,155,160,200,213,224,230,263,284,298,331,337,338,341,346,365,385,400,410,435,440,499,507],yip:332,ylat:[172,226,245,499],ylo:[6,61,174,196,226,334,340,343,345,481,484,499],ylo_bound:[6,196],ymax:[208,507],ymin:507,yorig:73,york:[290,366],yoshida:[263,307],you:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,33,35,38,40,41,42,43,44,46,47,48,49,50,51,52,54,55,57,59,60,61,63,65,68,70,73,74,75,76,77,79,83,84,85,91,92,93,94,95,96,98,107,108,109,111,112,113,115,116,118,120,122,123,146,147,149,150,151,152,155,159,160,165,166,167,168,169,170,172,173,174,175,176,178,179,180,181,182,183,184,185,186,187,189,190,191,192,195,196,197,199,200,201,203,204,205,206,207,210,211,212,213,215,216,217,218,219,220,221,222,223,224,226,227,230,232,233,235,236,237,238,239,240,241,242,243,244,245,247,248,249,258,260,263,265,266,267,268,269,270,271,272,273,277,279,280,282,283,284,285,286,289,290,292,293,294,296,298,299,302,305,306,307,309,310,312,320,322,323,324,326,327,328,329,331,332,333,334,335,337,338,339,340,341,343,344,345,346,348,349,351,352,354,355,356,358,360,364,365,366,368,370,372,373,374,375,376,379,380,381,382,384,386,387,388,389,390,391,392,393,394,395,396,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,430,431,432,433,435,436,437,438,439,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,469,471,472,473,475,476,477,478,479,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,502,506,507,508,509,511],young:[410,447,449],your:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,44,46,47,48,49,50,52,54,55,57,61,63,113,115,118,122,149,150,151,155,159,165,170,172,173,174,175,176,178,179,181,182,183,184,186,187,189,190,192,195,196,197,198,199,206,209,213,215,218,219,221,222,223,224,226,227,233,238,239,242,244,247,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,293,296,299,305,307,309,310,312,325,326,328,331,335,337,338,339,340,341,343,344,345,346,349,351,352,354,355,358,360,366,368,374,375,376,379,380,381,382,384,386,387,388,389,390,391,392,393,394,395,396,399,400,403,404,405,407,408,409,410,411,412,413,414,415,418,419,420,421,422,423,424,425,426,427,430,431,432,433,435,436,437,438,440,441,443,444,445,446,453,460,462,463,464,465,466,469,471,472,473,475,478,479,481,483,484,485,488,489,490,491,492,493,494,498,499,506,507,509,511],yourself:[6,8,12,13,224,374],yplane:341,ypo:172,ysu:[3,196,197,325,482],yuan:9,yukawa:[],yukawa_1_1:470,yxz:478,yzx:478,z_i:[406,466,473],z_j:[466,473],z_meam:430,zachari:13,zannoni:409,zbl:[],zblcut:466,zblcutinn:452,zblcutout:452,zblexpscal:466,zblz:452,zcm:307,zcylind:341,zepeda:210,zero:[2,3,4,6,9,11,12,26,27,34,37,40,42,49,50,61,63,65,68,73,74,77,91,92,94,96,98,107,108,109,110,111,112,114,115,116,118,119,120,121,122,123,124,127,146,147,150,151,152,153,160,161,164,165,167,169,170,171,172,174,175,176,178,181,190,192,195,196,199,200,203,204,205,206,208,210,211,212,213,214,215,216,217,218,219,220,221,222,224,226,231,232,233,236,238,239,240,241,243,247,248,249,250,251,253,259,260,261,263,268,277,280,290,295,296,297,298,299,302,304,305,307,308,309,310,314,315,317,323,325,330,331,333,335,338,339,340,341,342,343,345,346,347,348,354,368,371,373,374,375,376,380,383,386,387,389,390,391,394,396,399,400,401,402,406,409,411,412,413,414,418,420,422,423,426,428,429,430,433,435,440,444,445,446,451,460,463,467,469,473,476,477,478,481,482,484,486,488,489,490,491,495,496,499,502,507,508,509,511],zeta:[3,250,298,407],zfactor:199,zflag:[159,160,251,253,259,307,330],zhang:[307,331,410],zhi:[3,6,174,196,208,334,340,343,345,481,484,499],zhi_bound:[6,196],zhou:[13,386,407,441,464,466],zhu:459,ziegenhain:13,ziegler:[292,430,461,466,473],zimmerman2004:209,zimmerman2010:209,zimmerman:[9,72,209,386],zlat:[226,245,499],zlib:196,zlim:451,zlo:[3,6,174,196,208,334,340,342,343,345,481,484,499],zlo_bound:[6,196],zmax:[208,250,507],zmin:[250,507],zn2:171,zone:[124,308],zoom:[3,196,199,200],zorig:73,zplane:341,zr4:171,zrest:322,zsu:[3,196,197,325,482],zwall:340,zwall_veloc:250,zxy:478,zybin:444,zyx:478},titles:["LAMMPS Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & 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","<no title>","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","<no title>","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":[37,40,41,56,59,60,61,63,64,73,91,92,96,107,108,110,112,113,124,128,129,146,152,160,161,165,171,172,175,177,191,194,195,196,197,199,200,201,202,204,205,206,208,209,210,212,216,217,218,221,222,224,225,226,227,231,236,239,240,245,247,248,249,250,251,253,258,261,263,264,268,284,285,289,290,293,294,295,296,297,299,302,304,305,307,308,323,325,330,331,332,333,336,338,340,342,346,359,363,365,366,368,369,371,372,374,376,377,378,380,383,386,388,406,427,428,433,435,443,444,460,461,476,477,478,481,482,484,486,488,489,490,493,495,497,498,499,500,501,506,508,509,510],"function":507,"long":[214,387,389,390,391,392,396,398,399,418,422,426,438,446],"new":8,"static":12,acceler:1,ackland:66,acknowledg:7,adapt:[204,205],addforc:206,addit:[12,13],addtorqu:207,adiabat:6,adjust_dt:313,adp:381,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:[6,7,8,66,69,72,73,74,75,78,79,80,82,83,85,89,96,100,101,104,105,106,112,116,117,119,146,147,170,208,210,211,296,507],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],brownian:388,buck:[389,390,398,429],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:72,ch2lmp:13,chain:13,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:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,507],compute_modifi:107,condit:7,conduct:[6,331],conserv:401,constant:6,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:[396,418],dec:[],defgrad:133,deform:[155,156,226],delete_atom:175,delete_bond:176,delta:24,deposit:227,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],diagnost:7,diel:397,dielectr:177,diffract:9,diffus:6,dihedr:[8,81],dihedral_coeff:180,dihedral_styl:[2,178,179,181,182,183,184,185,186,187,188,189,190,191,192,193],dilat:82,dimens:194,dipol:[6,9,29,399],direct:230,discuss:6,disp:6,displac:[83,90],displace_atom:195,distanc:353,distribut:[7,12],document:0,dpd:[9,84,85,400,401,402],drag:228,dreid:[6,412],drude:[6,9,157,229,230,248],dsf:[396,418],dsmc:403,dump:[6,8,196,197,198,199,201],dump_modifi:200,dynam:298,eam:[13,404],echo:202,edip:405,eff:[9,13,101,102,156,158,163,249,264,276,285,329,406],efield:232,eim:407,elast:6,emac:13,energi:[129,402],enforce2d:233,ensembl:7,erot:[86,87,88,89],error:[3,128],evapor:236,event:90,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],exp:[27,181],expand:[47,421],extend:[8,11],extern:237,fcc:288,fdt:402,featur:[7,8,507],feb:0,fene:[46,47],fep:[9,13,91,205],field:[6,7],file:6,finit:6,fire:298,fix:[2,6,8,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,507],fix_modifi:[204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345],fld:9,flow:6,fluid:250,flux:[95,148],forc:[6,7,148,324],fourier:[30,31,182,354],freez:238,from:[6,11],futur:5,gauss:408,gaybern:409,gcmc:239,gener:[1,6,7,13],get:12,gld:240,gle:241,global:6,gpu:[9,15,384,387,389,391,392,394,396,399,400,404,408,409,411,418,419,420,421,434,436,445,446,453,462,463,464,471,472,473],gran:[341,410],granular:[6,9],graviti:242,gromac:411,group2ndx:347,group:[92,346,507],gyrat:[93,94],h5md:[9,196,198],harmon:[32,48,49,50,183,186,340,355,437],hbond:412,heat:[95,148,243],heatconduct:454,helix:184,hertz:[410,447],hexord:96,histo:215,histori:[5,410],hook:410,hourglass:128,hourglass_error:[],how:6,hybrid:[33,51,185,356,413],idealga:455,imag:[196,199],imd:244,implicit:391,improp:[8,97],improper_coeff:350,improper_styl:[2,349,351,352,353,354,355,356,357,358,359,360,361],includ:362,inclus:8,indent:245,indic:0,individu:2,induc:6,inertia:98,info:[0,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345,363],input:[2,6,8],instal:11,instruct:[],integr:[6,7],integrate_tlsph:314,integrate_ulsph:315,intel:[9,16,20,32,48,178,183,189,263,272,273,284,352,355,389,391,409,418,462,464],interfac:[6,11],intern:129,internal_energi:[],introduct:7,invers:230,ipi:246,ipp:13,jan:[],jul:[],jump:364,kate:13,keyword:435,kim:[9,414],kokko:[9,17],kspace:[2,8,9,336],kspace_modifi:365,kspace_styl:[6,366],label:367,lammp:[0,1,2,6,7,8,11,12],langevin:[247,248,249],lattic:368,lcbop:415,lennard:429,librari:[6,11,12],limit:[277,328],line:[12,278,416],linear:425,lineforc:255,list:[2,417],lj1043:340,lj126:340,lj93:340,lj96:419,lmp2arc:13,lmp2cfg:13,lmp2vmd:13,local:[6,67,70,71,81,97,114,121],log:369,lubric:427,lubricateu:428,make:12,manybodi:9,mass:370,math:507,matlab:13,mdf:429,meam:[9,430,431,432],measur:1,mesh:140,meso:[104,105,106,256,257],meso_:[],meso_rho:[],meso_t:[],messag:3,mgpt:[9,433],micelle2d:13,mie:434,min_modifi:371,min_styl:372,minim:[8,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345,373],misc:9,mod:[335,465],model:[6,7],modifi:8,molecul:[9,374],molfil:[9,196,201],moltempl:13,momentum:[251,259],morri:459,mors:[52,412,436],move:260,move_tri_surf:316,movi:[196,199],mpi:11,mpiio:9,msd:[108,109,110],msi2lmp:13,msm:[387,389,391,396,418],msst:261,multi:[6,7,186],multipl:6,nb3b:437,ndx2group:347,neb:[262,375],neigh:[135,141],neigh_modifi:376,neighbor:377,nemd:6,newton:378,next:379,nharmon:187,noforc:[274,279],non:[6,7],none:[34,53,188,357,439],nongauss:110,nonlinear:54,nph:[263,264,265,266,267,307],nphug:268,npt:[263,264,269,270,271,307],num:[135,141],nve:[272,273,274,275,276,277,278,279,280,281,307],nvt:[263,264,282,283,284,285,286,307],omega:111,omp:[9,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,44,46,47,48,49,50,52,54,55,57,178,179,181,182,183,184,186,187,189,190,192,242,263,265,267,268,269,271,272,280,282,284,286,299,349,351,352,354,355,358,360,381,382,384,387,388,389,390,391,392,394,395,396,397,399,400,404,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,432,436,437,438,440,445,446,453,462,463,464,465,466,469,471,472,473],onewai:287,open:7,oper:507,opl:189,opt:[9,19,391,404,418,422,436],optim:1,option:[6,8,12],orient:288,orientord:112,orthogon:6,other:6,output:[6,7,8,12,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345],overlai:413,overview:11,packag:[1,9,12,14,15,16,17,18,19,380],pair:[6,113,114],pair_coeff:393,pair_modifi:435,pair_styl:[2,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,474],pair_writ:470,pairwis:8,parallel:11,paramet:6,pars:2,partial:159,particl:[6,7,43],partit:475,past:5,per:6,perform:[1,10],peri:[9,440],period:25,phonon:[9,13,289],pimd:290,piston:342,planeforc:291,plastic:[117,130,131],plastic_strain:[],plastic_strain_r:[],pmb:440,poem:[9,292],point:298,polariz:6,poli:[388,427,428],polygon:[],polym:13,polymorph:441,post:7,potenti:[2,6,8],pour:293,pppm:6,prd:476,pre:7,press:294,pressur:118,previou:12,print:[295,477],problem:[3,4],process:[6,7],processor:478,profil:160,properti:[6,119,120,121,296],pymol_aspher:13,python:[9,11,13,479],qbmsst:297,qeq:[9,298,299,300],qmmm:[9,301],qtb:[9,302],quadrat:190,quantiti:6,quartic:[35,55],quip:[9,442],quit:480,radiu:126,ramp:161,rate:[131,138,143],rattl:310,rdf:122,read_data:481,read_dump:482,read_restart:483,reax:[9,13,300,303,304,443,444],reaxc:9,rebo:382,recent:305,reduc:123,refer:507,reflect:343,region:[8,123,162,163,344,484,507],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,41,42,44,45,46,47,48,49,50,51,52,54,55,56,57,58,59,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,87,88,89,90,91,93,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,196,197,198,199,200,201,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,238,239,240,241,242,243,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,302,303,304,305,307,308,309,311,312,313,314,315,316,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,362,363,364,365,366,368,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,486,487,488,489,490,491,493,494,495,496,497,498,499,500,501,503,504,505,507,508,509,510,511],relax:224,replic:485,replica:[6,7,9],report:3,requir:12,rerun:486,rescal:[328,329],reset:231,reset_timestep:487,resquar:445,restart2data:13,restart:[6,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345,488],restrain:306,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],rho:[105,132],rhosum:457,rigid:[6,9,87,103,253,307],ring:358,rotat:164,round:[],rule:2,run:[6,11,12,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345,489],run_styl:490,scalabl:10,scalar:6,screen:12,script:[2,6,8,11],sdk:[36,446],self:322,serial:11,set:[6,491],setforc:309,setvel:317,shake:310,shape:136,shardlow:311,share:[11,12],shell:[6,492],shield:298,shift:[26,27,49,50,181],shock:9,simpl:31,simul:6,size:6,slater:298,slice:125,sllod:[284,285],small:307,smd:[9,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,312,313,314,315,316,317,319,447,448,449,450],smooth:[424,425],smtbq:[9,451],sna:146,snad:146,snap:[9,452],snapshot:6,snav:146,soft:[426,453],solver:2,sourc:7,spatial:[216,217],spc:6,speci:304,special:[7,435,507],special_bond:493,sph:[9,454,455,456,457,458,459],sphere:[88,89,165,217,253,267,271,280,286],spheric:6,spline:[431,432],spring:[320,321,322,333],squar:28,srd:[9,323,345],srp:460,standard:9,start:[12,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345],state:325,stationari:257,stop:[204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345],store:[324,325],strain:[130,131,137,138,142,143],strategi:1,streitz:396,stress:[139,144,147,148],structur:2,style:[1,2,6,8],submit:8,suffix:494,summari:6,swap:[210,223],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,289,290,291,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],system:6,tabl:[0,6,38,57,192,235,463,464],tad:495,taitwat:[458,459],talli:[9,148],temp:[149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,326,327,328,329],temper:496,temperatur:6,tersoff:[464,465,466],test:11,tfmc:330,thermal:[6,331],thermo:[6,497],thermo_modifi:498,thermo_styl:499,thermodynam:[6,8],thermostat:6,thole:467,time:[6,218],timer:500,timestep:501,tip3p:6,tip4p:[6,396,418,422,426],tip:12,tlsph:[133,134,135,136,137,138,139,448],tlsph_defgrad:[],tlsph_dt:[],tlsph_num_neigh:[],tlsph_shape:[],tlsph_strain:[],tlsph_strain_rat:[],tlsph_stress:[],tmd:334,tool:[12,13],torqu:167,transform:230,tri:[281,468],tri_surfac:449,triangl:140,triangle_mesh_vertic:[],triclin:6,tstat:400,ttm:335,tune:336,type:7,ulsph:[141,142,143,144,450],ulsph_num_neigh:[],ulsph_strain:[],ulsph_strain_r:[],ulsph_stress:[],umbrella:360,uncomput:503,undump:504,unfix:505,unit:506,user:[9,12,14,16,18],vacf:168,valu:[6,507],variabl:[6,8,507],variou:1,vashishta:469,vcm:169,vector:[6,337,507],veloc:508,version:[0,5,12],vertic:140,via:12,vim:13,viscos:[6,338],viscou:[254,339],visual:6,vol:145,voronoi:[9,170],vtk:[9,196,197,308],wall:[6,340,341,342,343,344,345],wall_surfac:319,warn:3,water:6,weight:215,what:[7,12],wolf:[387,396],wrapper:11,write:6,write_data:509,write_dump:510,write_restart:511,xmgrace:13,xmovi:13,xrd:171,xtc:9,yukawa:[471,472],zbl:[466,473],zero:[39,58,193,361,474]}})
\ No newline at end of file
+Search.setIndex({envversion:47,filenames:["Manual","Section_accelerate","Section_commands","Section_errors","Section_example","Section_history","Section_howto","Section_intro","Section_modify","Section_packages","Section_perf","Section_python","Section_start","Section_tools","accelerate_cuda","accelerate_gpu","accelerate_intel","accelerate_kokkos","accelerate_omp","accelerate_opt","angle_charmm","angle_class2","angle_coeff","angle_cosine","angle_cosine_delta","angle_cosine_periodic","angle_cosine_shift","angle_cosine_shift_exp","angle_cosine_squared","angle_dipole","angle_fourier","angle_fourier_simple","angle_harmonic","angle_hybrid","angle_none","angle_quartic","angle_sdk","angle_style","angle_table","angle_zero","atom_modify","atom_style","balance","body","bond_class2","bond_coeff","bond_fene","bond_fene_expand","bond_harmonic","bond_harmonic_shift","bond_harmonic_shift_cut","bond_hybrid","bond_morse","bond_none","bond_nonlinear","bond_quartic","bond_style","bond_table","bond_zero","boundary","box","change_box","clear","comm_modify","comm_style","compute","compute_ackland_atom","compute_angle_local","compute_angmom_chunk","compute_basal_atom","compute_body_local","compute_bond_local","compute_centro_atom","compute_chunk_atom","compute_cluster_atom","compute_cna_atom","compute_com","compute_com_chunk","compute_contact_atom","compute_coord_atom","compute_damage_atom","compute_dihedral_local","compute_dilatation_atom","compute_displace_atom","compute_dpd","compute_dpd_atom","compute_erotate_asphere","compute_erotate_rigid","compute_erotate_sphere","compute_erotate_sphere_atom","compute_event_displace","compute_fep","compute_group_group","compute_gyration","compute_gyration_chunk","compute_heat_flux","compute_hexorder_atom","compute_improper_local","compute_inertia_chunk","compute_ke","compute_ke_atom","compute_ke_atom_eff","compute_ke_eff","compute_ke_rigid","compute_meso_e_atom","compute_meso_rho_atom","compute_meso_t_atom","compute_modify","compute_msd","compute_msd_chunk","compute_msd_nongauss","compute_omega_chunk","compute_orientorder_atom","compute_pair","compute_pair_local","compute_pe","compute_pe_atom","compute_plasticity_atom","compute_pressure","compute_property_atom","compute_property_chunk","compute_property_local","compute_rdf","compute_reduce","compute_saed","compute_slice","compute_smd_contact_radius","compute_smd_damage","compute_smd_hourglass_error","compute_smd_internal_energy","compute_smd_plastic_strain","compute_smd_plastic_strain_rate","compute_smd_rho","compute_smd_tlsph_defgrad","compute_smd_tlsph_dt","compute_smd_tlsph_num_neighs","compute_smd_tlsph_shape","compute_smd_tlsph_strain","compute_smd_tlsph_strain_rate","compute_smd_tlsph_stress","compute_smd_triangle_mesh_vertices","compute_smd_ulsph_num_neighs","compute_smd_ulsph_strain","compute_smd_ulsph_strain_rate","compute_smd_ulsph_stress","compute_smd_vol","compute_sna_atom","compute_stress_atom","compute_tally","compute_temp","compute_temp_asphere","compute_temp_body","compute_temp_chunk","compute_temp_com","compute_temp_cs","compute_temp_deform","compute_temp_deform_eff","compute_temp_drude","compute_temp_eff","compute_temp_partial","compute_temp_profile","compute_temp_ramp","compute_temp_region","compute_temp_region_eff","compute_temp_rotate","compute_temp_sphere","compute_ti","compute_torque_chunk","compute_vacf","compute_vcm_chunk","compute_voronoi_atom","compute_xrd","create_atoms","create_bonds","create_box","delete_atoms","delete_bonds","dielectric","dihedral_charmm","dihedral_class2","dihedral_coeff","dihedral_cosine_shift_exp","dihedral_fourier","dihedral_harmonic","dihedral_helix","dihedral_hybrid","dihedral_multi_harmonic","dihedral_nharmonic","dihedral_none","dihedral_opls","dihedral_quadratic","dihedral_style","dihedral_table","dihedral_zero","dimension","displace_atoms","dump","dump_custom_vtk","dump_h5md","dump_image","dump_modify","dump_molfile","echo","fix","fix_adapt","fix_adapt_fep","fix_addforce","fix_addtorque","fix_append_atoms","fix_atc","fix_atom_swap","fix_ave_atom","fix_ave_chunk","fix_ave_correlate","fix_ave_correlate_long","fix_ave_histo","fix_ave_spatial","fix_ave_spatial_sphere","fix_ave_time","fix_aveforce","fix_balance","fix_bond_break","fix_bond_create","fix_bond_swap","fix_box_relax","fix_colvars","fix_deform","fix_deposit","fix_drag","fix_drude","fix_drude_transform","fix_dt_reset","fix_efield","fix_enforce2d","fix_eos_cv","fix_eos_table","fix_evaporate","fix_external","fix_freeze","fix_gcmc","fix_gld","fix_gle","fix_gravity","fix_heat","fix_imd","fix_indent","fix_ipi","fix_langevin","fix_langevin_drude","fix_langevin_eff","fix_lb_fluid","fix_lb_momentum","fix_lb_pc","fix_lb_rigid_pc_sphere","fix_lb_viscous","fix_lineforce","fix_meso","fix_meso_stationary","fix_modify","fix_momentum","fix_move","fix_msst","fix_neb","fix_nh","fix_nh_eff","fix_nph_asphere","fix_nph_body","fix_nph_sphere","fix_nphug","fix_npt_asphere","fix_npt_body","fix_npt_sphere","fix_nve","fix_nve_asphere","fix_nve_asphere_noforce","fix_nve_body","fix_nve_eff","fix_nve_limit","fix_nve_line","fix_nve_noforce","fix_nve_sphere","fix_nve_tri","fix_nvt_asphere","fix_nvt_body","fix_nvt_sllod","fix_nvt_sllod_eff","fix_nvt_sphere","fix_oneway","fix_orient_fcc","fix_phonon","fix_pimd","fix_planeforce","fix_poems","fix_pour","fix_press_berendsen","fix_print","fix_property_atom","fix_qbmsst","fix_qeq","fix_qeq_comb","fix_qeq_reax","fix_qmmm","fix_qtb","fix_reax_bonds","fix_reaxc_species","fix_recenter","fix_restrain","fix_rigid","fix_saed_vtk","fix_setforce","fix_shake","fix_shardlow","fix_smd","fix_smd_adjust_dt","fix_smd_integrate_tlsph","fix_smd_integrate_ulsph","fix_smd_move_triangulated_surface","fix_smd_setvel","fix_smd_tlsph_reference_configuration","fix_smd_wall_surface","fix_spring","fix_spring_rg","fix_spring_self","fix_srd","fix_store_force","fix_store_state","fix_temp_berendsen","fix_temp_csvr","fix_temp_rescale","fix_temp_rescale_eff","fix_tfmc","fix_thermal_conductivity","fix_ti_rs","fix_ti_spring","fix_tmd","fix_ttm","fix_tune_kspace","fix_vector","fix_viscosity","fix_viscous","fix_wall","fix_wall_gran","fix_wall_piston","fix_wall_reflect","fix_wall_region","fix_wall_srd","group","group2ndx","if","improper_class2","improper_coeff","improper_cossq","improper_cvff","improper_distance","improper_fourier","improper_harmonic","improper_hybrid","improper_none","improper_ring","improper_style","improper_umbrella","improper_zero","include","info","jump","kspace_modify","kspace_style","label","lattice","log","mass","min_modify","min_style","minimize","molecule","neb","neigh_modify","neighbor","newton","next","package","pair_adp","pair_airebo","pair_awpmd","pair_beck","pair_body","pair_bop","pair_born","pair_brownian","pair_buck","pair_buck_long","pair_charmm","pair_class2","pair_coeff","pair_colloid","pair_comb","pair_coul","pair_coul_diel","pair_cs","pair_dipole","pair_dpd","pair_dpd_conservative","pair_dpd_fdt","pair_dsmc","pair_eam","pair_edip","pair_eff","pair_eim","pair_gauss","pair_gayberne","pair_gran","pair_gromacs","pair_hbond_dreiding","pair_hybrid","pair_kim","pair_lcbop","pair_line_lj","pair_list","pair_lj","pair_lj96","pair_lj_cubic","pair_lj_expand","pair_lj_long","pair_lj_sf","pair_lj_smooth","pair_lj_smooth_linear","pair_lj_soft","pair_lubricate","pair_lubricateU","pair_mdf","pair_meam","pair_meam_spline","pair_meam_sw_spline","pair_mgpt","pair_mie","pair_modify","pair_morse","pair_nb3b_harmonic","pair_nm","pair_none","pair_peri","pair_polymorphic","pair_quip","pair_reax","pair_reax_c","pair_resquared","pair_sdk","pair_smd_hertz","pair_smd_tlsph","pair_smd_triangulated_surface","pair_smd_ulsph","pair_smtbq","pair_snap","pair_soft","pair_sph_heatconduction","pair_sph_idealgas","pair_sph_lj","pair_sph_rhosum","pair_sph_taitwater","pair_sph_taitwater_morris","pair_srp","pair_style","pair_sw","pair_table","pair_tersoff","pair_tersoff_mod","pair_tersoff_zbl","pair_thole","pair_tri_lj","pair_vashishta","pair_write","pair_yukawa","pair_yukawa_colloid","pair_zbl","pair_zero","partition","prd","print","processors","python","quit","read_data","read_dump","read_restart","region","replicate","rerun","reset_timestep","restart","run","run_style","set","shell","special_bonds","suffix","tad","temper","thermo","thermo_modify","thermo_style","timer","timestep","tutorial_drude","uncompute","undump","unfix","units","variable","velocity","write_data","write_dump","write_restart"],objects:{},objnames:{},objtypes:{},terms:{"00a":332,"00b":332,"02214e23":95,"03275e":506,"0892e":12,"0b1":11,"0e20":[348,484,507],"0e4":[261,341,410],"0e5":261,"0x98b5e0":199,"100k":1,"1024x1024":199,"10e":398,"10f":3,"10g":507,"10th":[476,482,495],"10x":[3,372,373,375,376,386],"10x10x10":160,"10x20x20":368,"11e":10,"15g":[200,507],"16g":[212,218],"16x":1,"18986e":373,"18e":10,"1_12":368,"1_3":368,"1_6":368,"1_prop":6,"1st":[2,6,8,12,20,22,38,45,57,59,60,62,73,91,166,178,180,192,204,205,212,213,214,215,216,217,218,222,226,235,263,295,305,334,346,350,370,376,381,382,386,393,395,404,406,407,414,415,424,425,430,431,432,437,441,452,462,463,464,465,466,469,475,481,489,490,493,507],"1x2x2":478,"2000k":199,"20x":386,"23899e":373,"2400k":199,"256k":10,"25x":10,"298k":397,"2_3":368,"2k_ss":406,"2nd":[2,3,6,11,12,15,17,38,46,47,57,59,62,73,79,92,154,161,192,200,212,213,214,215,216,217,218,222,224,226,235,263,307,312,320,346,349,356,364,373,374,375,376,380,382,395,406,412,413,430,452,461,462,463,464,465,466,469,481,488,490,493,507],"2pi":192,"2theta":171,"2x1x2":478,"2x2x1":478,"2x2x2":478,"2x4x10":478,"2x5":406,"300k":[241,307,496,508],"310k":496,"32k":10,"3419e":261,"3806504e":[6,95],"38e":10,"3n_k":240,"3nk":297,"3nkb":302,"3rd":[15,17,20,38,57,73,110,120,192,212,213,215,216,217,218,222,235,307,308,346,374,378,380,395,406,412,413,452,462,463,464,465,466,469,481,488,493,507],"3x3":[95,368],"4857990943e":406,"4_94":11,"4th":[6,38,57,83,108,109,122,168,178,192,200,320,346,366,379,381,382,386,404,407,414,430,437,441,452,462,463,464,466,469,481,488,493,496,511],"4x10":364,"4x2x10":478,"4x6x10":478,"50k":1,"53xx":18,"54xx":18,"55e":10,"5_1":386,"5_12":368,"5_6":368,"5kx":[206,232],"5nlog_2":12,"5th":[122,373,498],"6021765e":506,"6863e22":440,"6x6":6,"72360e":261,"7797e":261,"7842e":12,"8032044e":506,"8706e":451,"8706q":451,"8730m":451,"8730n":451,"8e12":214,"8x1":6,"8x2":[6,12],"948q":451,"9e18":[12,40],"9e9":440,"9jan09":[341,410],"9th":375,"__main__":479,"__pthread_key_cr":12,"_boundingbox":197,"_compute_group_group":148,"_compute_heat_flux":148,"_compute_t":8,"_j1m1m1":146,"_j2m2m2":146,"_serial":12,"abstract":17,"boolean":[3,346,348],"break":[],"byte":[3,12,214,498],"case":[1,2,3,6,8,11,12,13,15,16,17,18,40,41,42,46,47,61,63,65,73,75,108,109,114,120,122,123,149,150,151,152,153,155,158,159,160,161,162,164,165,166,170,172,174,175,176,178,195,196,197,198,199,200,206,207,211,212,213,215,216,217,218,219,220,222,224,226,230,232,236,239,242,243,245,246,247,248,250,261,263,264,265,266,267,268,269,270,271,282,283,284,286,288,289,293,294,296,297,298,299,306,307,309,312,314,315,317,320,323,326,327,328,330,331,335,337,338,340,341,343,344,345,346,348,364,365,366,368,370,372,373,374,375,377,379,380,382,391,394,396,398,404,406,409,410,412,413,414,426,427,428,430,433,435,437,441,444,447,449,453,460,463,464,466,473,476,479,481,483,484,488,489,491,493,495,497,498,499,500,502,506,507,508,510,511],"catch":[1,3,479],"char":[6,8,451],"class":[1,3,5,6,7,8,9,11,12,13,22,37,45,56,180,191,237,296,350,359,392,413,443,444,461,469,479,481],"default":[],"export":[199,393],"final":[3,5,6,7,8,11,12,17,42,61,91,147,200,211,212,213,215,216,217,218,220,224,226,239,262,263,268,297,301,307,308,312,332,334,335,342,348,373,375,381,382,386,404,407,414,426,430,437,441,442,462,463,464,466,469,476,489,495,502,507,509],"float":[3,6,8,12,41,43,73,119,196,200,212,218,244,296,308,325,406,448,450,479,481,491,498,507],"function":[],"import":[1,2,3,6,11,17,73,110,172,183,203,224,239,242,247,248,263,302,326,327,328,330,335,345,347,426,433,479,481,490,498,502],"int":[3,6,8,11,106,237,239,247,249,302,335,498],"long":[],"new":[],"null":[3,6,95,96,112,118,147,172,203,219,225,228,231,260,296,305,309,312,316,317,320,321,341,381,382,395,404,407,410,413,414,415,430,431,432,437,441,443,444,452,462,464,465,466,469,481,484,489,491,508],"public":[0,7,8,12,237,246,407,442,451],"return":[2,3,6,8,11,14,15,16,17,18,19,42,73,114,123,140,141,145,170,172,200,212,216,217,226,237,263,348,362,364,410,478,479,480,488,491,497,507],"short":[1,3,6,7,13,16,170,263,307,323,336,366,376,377,380,382,386,387,389,390,391,395,396,398,406,413,416,418,422,426,429,430,435,438,446,451,463,467,476,479,489,491,495,502],"static":[],"switch":[1,3,6,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,44,46,47,48,49,50,52,54,55,57,95,115,118,146,149,159,171,178,179,181,182,183,184,186,187,189,190,192,199,202,206,210,219,226,233,238,242,246,247,250,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,299,307,309,310,326,328,332,333,339,343,349,351,352,354,355,358,360,362,364,366,369,375,379,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,404,405,407,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,433,436,437,438,440,443,445,446,453,462,463,464,465,466,469,471,472,473,475,476,478,481,483,484,488,490,494,496,507,509,511],"throw":498,"true":[6,12,13,17,114,121,196,197,212,220,222,226,263,264,288,289,290,294,307,330,334,346,348,380,406,410,451,462,479,483,491,507],"try":[1,3,8,12,17,19,212,244,250,331,332,333,338,479,507],"var":[3,11,12,172,346,364,492,507],"void":[4,6,7,8,42,175,220,237,484],"while":[1,3,9,10,11,12,13,14,18,73,110,146,155,170,183,196,201,210,217,224,226,230,240,241,246,247,248,250,263,284,297,298,302,304,336,366,373,380,386,397,404,444,464,466,469,476,479,490,495,502],a10:348,a123:348,a12:445,a2m:[6,95],a_0:[250,335,386],a_0_real:250,a_1:335,a_2:335,a_3:335,a_4:335,a_c:394,a_cc:394,a_f:466,a_i:[],a_ij:386,a_j:[],a_pi:386,a_sigma:386,a_ss:394,aacut:289,aat:179,aatom1:121,aatom2:121,aatom3:121,ab_23_cd:348,abbrevi:12,abc:[3,12,348,479,507],aberdeen:[84,85,234,311],abf:225,abf_integr:13,abi:201,abil:[3,9,224,263,294,307,406],abl:[3,8,11,12,40,90,196,201,223,232,238,331,338,380,479,507,510],ablat:335,about:[0,1,3,4,6,8,9,10,11,12,13,17,40,42,43,63,65,80,114,121,122,124,166,172,196,197,199,200,201,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,228,230,231,232,233,236,237,238,239,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,259,262,268,272,273,274,275,276,277,278,279,280,281,287,288,289,291,292,293,294,295,296,298,299,300,301,302,303,304,305,306,307,308,309,310,320,321,323,324,326,327,328,329,330,331,332,333,334,335,337,338,339,340,342,343,344,345,346,363,366,372,373,375,380,385,391,396,413,440,444,472,479,482,483,488,489,491,496,500,507,509,511],abov:[1,2,6,7,8,10,11,12,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,38,41,42,43,44,45,46,47,48,49,50,51,52,54,55,57,59,65,66,70,72,73,74,75,78,79,90,91,93,94,95,98,99,101,102,118,120,122,124,146,147,149,150,151,152,153,154,155,158,159,160,161,162,164,165,166,170,171,172,174,175,178,179,180,181,182,183,184,185,186,187,189,190,192,196,197,198,199,200,203,204,205,206,207,212,213,215,216,217,218,220,223,224,226,227,232,235,237,239,243,245,247,248,249,253,262,263,268,290,293,295,300,306,307,312,320,323,326,327,328,329,346,348,349,350,351,352,353,354,355,356,358,360,366,368,370,374,375,379,380,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,416,418,419,420,421,422,423,424,425,426,427,428,429,430,433,434,435,436,438,440,441,443,444,445,446,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,468,469,471,472,473,474,475,476,477,478,479,481,482,483,484,485,488,489,490,491,492,495,496,499,502,507,508,510,511],abscissa:463,absenc:207,absent:502,absolut:[3,200,210,225,226,230,312,325,365,366,373,410,418,482],absorb:335,absoult:366,ac3:171,academ:239,acc:330,acceler:[],accelri:[6,13],accept:[7,12,91,170,172,200,210,223,226,239,330,390,422,489,496],acceptor:412,access:[0,3,6,7,8,9,11,12,16,39,41,58,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,89,92,93,94,95,96,97,98,100,101,104,105,106,108,109,110,111,112,113,114,116,117,118,119,120,121,123,124,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,159,160,161,162,163,164,165,167,168,169,170,171,193,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,220,221,222,223,224,225,226,227,228,231,232,233,236,237,238,239,240,241,242,243,244,245,247,249,250,251,252,253,254,255,256,257,259,260,261,262,263,268,272,273,274,275,276,277,278,279,280,281,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,317,320,321,322,323,324,325,326,327,328,329,331,332,333,334,335,337,338,339,340,341,342,343,344,345,361,365,380,408,410,412,413,430,443,444,453,478,479,482,487,499,507],accidenti:358,accler:16,accommod:208,accomod:263,accompani:8,accomplish:[16,226,251,279],accord:[6,66,73,84,127,133,136,154,199,210,221,222,250,263,289,297,312,314,332,333,335,340,341,343,344,345,376,380,406,410,421,424,441,448,450,451,453,455,456,458,459,460,495,507],accordingli:[11,14,150,151,165,170,176,376,427,428,460],account:[3,6,9,91,124,154,170,171,180,191,213,215,231,244,245,247,263,269,270,271,282,283,284,286,288,292,298,307,308,310,320,321,322,323,326,327,328,331,335,338,354,374,396,402,410,418,422,427,428,430,433,451,478,495,508],accuml:[3,307,331,338],accumul:[1,6,8,15,73,84,148,203,213,214,247,307,312,337,363,380,487,506],accur:[1,3,6,15,17,38,42,57,155,220,261,302,307,310,323,331,338,344,346,366,386,406,409,410,435,445,461,463,464,466,495,500,507],accuraci:[1,3,6,12,42,195,196,200,220,241,263,299,310,336,346,365,366,372,406,435,443,444,463,470,490,495,500,502,507,510],accuractli:500,ach:365,achiev:[1,3,6,16,17,18,29,42,220,239,241,263,264,289,290,297,365,413,490],achiv:18,acid:9,ackland1:404,ackland2:404,ackland:[],acknowledg:[],acml:12,aco:507,acolor:[199,200],acoust:289,acquir:[3,6,60,63,64,175,176,222,224,226,263,439,474,486,502],across:[1,2,3,6,9,12,13,15,42,59,63,67,70,71,73,81,97,113,114,121,123,160,174,176,212,215,216,217,220,231,243,307,308,313,331,335,338,344,348,375,380,476,481,484,485,489,498,500],act:[3,6,114,157,230,242,245,246,247,248,250,253,262,307,317,330,332,333,335,344,345,346,373,388,399,409,410,412,445,460],acta:[124,171,381],actinid:[9,433],action:[2,6,11,12,73,240,245,333,502],activ:[5,8,11,12,13,14,56,61,91,170,225,240,244,247,253,262,287,307,315,334,363,426,461,475,504,507],actual:[1,3,6,8,12,57,64,128,155,196,197,200,204,205,219,221,222,230,247,248,284,288,293,294,302,312,323,325,326,327,328,330,336,345,346,365,376,409,411,416,421,427,428,460,478,479,490,491,499,507],adam:[365,366],adapt:[],add:[0,1,3,5,6,7,8,9,11,12,13,14,15,16,17,18,19,41,43,73,91,95,107,120,123,125,170,172,173,196,197,198,199,203,204,205,206,207,209,211,212,213,215,216,217,218,222,225,230,232,237,241,242,243,245,247,249,250,254,261,262,263,264,265,266,267,268,269,270,271,282,283,284,285,286,288,296,306,307,309,310,320,322,326,328,329,333,334,335,337,339,340,344,346,366,368,372,374,382,387,389,392,396,406,413,418,430,435,438,444,446,479,481,482,487,489,491,493,500,502],add_molecul:209,add_speci:209,add_to_nodeset:209,addforc:[],addit:[],addition:[6,8,16,145,323,345,409,445],additionali:197,addres:9,address:[7,8,11,199,246],addtorqu:[],adequ:[323,336,365,375,490],adher:29,adhikari:250,adiabat:[],adiam:[199,200],adjac:[40,170,172,375,435,463,464,495,496],adjiman:434,adjust:[2,3,6,16,17,42,61,124,134,150,151,152,155,156,159,160,165,166,171,176,196,199,212,220,224,226,244,247,251,255,259,260,263,264,268,284,288,291,293,294,297,298,299,300,305,307,315,323,327,331,336,338,339,340,342,343,345,365,366,373,375,380,382,403,427,428,451,466,491,508],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:[295,489,507],afshar:400,after:[2,3,5,6,8,9,11,12,15,21,22,33,40,41,42,45,51,59,60,61,63,65,73,150,151,152,153,154,155,156,159,160,161,162,164,165,172,173,175,176,179,180,185,195,196,197,198,199,200,201,203,204,205,209,210,212,213,220,221,222,223,224,226,230,239,250,251,252,253,254,259,260,261,263,269,270,271,277,282,283,284,286,289,293,297,305,307,310,319,324,326,327,328,330,331,332,333,334,338,340,342,346,349,350,356,364,370,371,373,374,376,378,379,380,381,382,386,393,395,404,405,406,407,413,414,415,426,427,428,430,431,432,433,437,441,443,444,451,452,461,462,464,465,466,469,476,478,480,481,482,483,484,486,487,489,491,493,495,498,499,502,506,507,508,509,510,511],afterrun:489,afterward:3,afterword:42,ag1:171,ag2:171,again:[6,11,12,16,17,64,146,152,158,166,196,200,226,243,293,349,364,375,427,428,476,478,479,481,483,488,495,497,507,509],against:[11,12,13,66,227,375,443,444],aggreg:[6,12,67,70,71,81,97,114,121,243,259,305,307,321,476,508],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:[6,12,29,42,73,174,192,216,220,245,368,481,484,502],alkali:406,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,165,166,167,168,169,170,171,172,173,174,175,176,178,180,185,191,192,193,196,197,198,199,200,201,203,204,205,206,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,256,258,259,261,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,319,320,322,323,324,325,326,327,330,331,332,333,334,335,336,337,338,340,341,342,343,344,345,346,347,348,349,350,354,359,361,363,364,365,366,367,368,370,373,374,375,376,377,379,380,381,382,383,385,386,387,389,390,391,392,393,395,396,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,422,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,472,473,475,476,478,479,480,481,482,483,484,485,486,488,489,490,491,492,493,494,495,496,498,499,500,502,506,507,508,509,510,511],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:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,56,59,60,61,63,64,65,79,96,112,114,148,150,151,152,165,170,171,172,174,180,191,192,196,197,199,200,201,203,204,206,208,209,210,212,213,214,215,216,217,218,220,222,223,224,225,226,227,231,232,237,239,240,241,242,244,247,250,253,254,258,260,263,264,288,292,293,294,295,296,297,301,307,308,310,312,314,315,319,323,330,331,332,333,335,336,337,338,339,340,346,348,350,359,365,366,368,373,374,375,376,379,380,383,386,387,388,389,390,391,396,404,406,410,411,412,413,418,422,427,428,433,435,441,444,445,448,450,451,460,470,472,476,479,481,483,484,485,486,487,488,491,493,494,495,498,499,507,508],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:[6,8,9,12,29,41,73,91,124,170,171,172,195,196,199,212,223,245,250,251,255,260,262,297,307,310,312,316,320,321,330,334,335,341,344,346,368,371,372,373,375,396,399,410,413,416,418,422,430,443,444,463,481,484,491,492,507],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:[3,65,203,296,304,348,374,507],alreadi:[3,7,8,9,12,16,17,18,43,172,173,175,198,208,212,216,217,220,222,226,254,295,297,323,346,347,374,375,400,411,413,420,428,460,470,473,477,481,482,486,491,507],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,40,41,42,43,45,55,56,57,60,61,63,65,68,73,74,75,77,79,83,91,93,94,96,98,108,109,110,111,112,113,118,120,122,123,125,146,147,148,149,150,151,152,153,154,155,156,158,159,160,161,162,164,165,166,167,168,169,172,173,174,175,176,178,180,191,192,194,195,196,197,198,199,200,201,203,204,205,206,208,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,232,237,238,239,240,241,243,244,247,248,249,250,260,261,263,264,265,266,267,268,269,270,271,276,279,280,282,283,284,285,286,288,289,290,292,293,294,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,316,317,320,321,323,326,327,328,329,330,334,335,336,337,339,341,344,346,347,348,350,356,359,363,365,366,368,369,370,373,374,375,376,377,379,380,386,390,391,393,397,398,399,400,404,405,406,409,410,412,413,414,422,426,427,430,433,435,437,439,440,441,442,445,446,448,455,456,458,459,461,462,463,464,465,466,467,469,476,478,479,480,481,482,483,484,485,486,488,489,490,491,493,494,495,496,499,500,501,502,503,505,506,507,508,509,511],alter:[3,6,8,9,11,12,42,61,149,150,151,152,153,155,158,159,160,161,164,165,172,176,196,197,199,201,204,205,212,221,222,223,224,226,262,263,302,305,307,309,317,323,331,338,345,372,375,413,481,486,488,491,507,508,511],altern:[1,6,8,11,12,17,18,95,172,196,203,213,226,234,244,248,263,296,307,330,331,338,351,355,365,372,373,381,382,396,401,402,404,405,407,415,418,426,430,431,432,437,441,442,452,462,464,466,469,479,481,482,494,496,499],although:[29,43,192,253,263,294,298,307,330,364,488,502,511],aluminum:473,alwai:[0,6,11,12,17,18,55,59,65,73,170,200,212,213,214,216,217,218,222,225,239,241,245,299,302,307,323,340,344,345,349,365,366,371,373,374,376,377,380,389,392,404,421,433,443,444,451,453,463,464,466,473,476,481,482,484,486,493,495,498,502,507,508],amap:200,amatrix:241,amaz:11,amazingli:13,amber2lmp:[],amber:[],ambient:199,ambigu:[3,65,203,507],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:[226,260,316,341,358,484,507],amu:239,amzallag:451,analag:[6,507],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:[6,8,13,375,433],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:[6,10,61,73,124,161,171,172,195,196,197,199,200,208,216,217,226,227,239,244,245,260,300,305,340,342,343,345,366,368,371,377,381,382,391,404,426,430,437,442,443,444,466,473,484,490,506,508],angular:[6,29,41,63,65,68,86,87,88,89,111,119,146,150,151,164,165,172,196,197,203,247,253,259,260,265,266,267,269,270,271,273,274,275,278,280,281,282,283,286,305,307,310,316,325,381,386,395,410,427,428,430,433,441,461,464,465,481,491,507,508],angularm:274,anharmon:[27,54,181,302,495],ani:[1,3,6,7,8,9,10,11,12,13,14,15,16,17,22,29,38,40,41,42,43,45,56,57,60,61,63,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,175,176,178,180,192,195,196,197,198,199,200,203,206,207,208,210,212,213,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,232,236,239,242,243,245,247,250,253,259,260,263,268,288,290,292,293,294,296,298,299,300,302,304,305,307,309,310,312,316,317,320,322,323,324,325,334,335,340,341,342,343,344,345,346,347,348,350,364,365,366,368,370,371,373,374,375,377,378,379,380,382,386,390,391,395,396,399,400,404,405,407,409,413,414,415,422,433,435,441,443,444,445,452,460,461,462,463,464,465,466,467,468,469,474,475,476,478,479,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,499,500,502,503,505,506,507,508,509,510,511],anihil:426,anim:[2,4,7,11,13,199,375],anion:[407,451],aniso:[3,224,226,263,264,265,266,267,268,269,270,271,294,307],anisotrop:[247,409,445],ann:434,annot:[7,462,464,465,466,469,481],annual:[476,495],anoth:[1,3,4,6,7,8,11,12,17,29,41,65,73,74,91,122,125,198,199,203,204,210,212,215,216,217,218,223,226,227,240,243,247,248,253,263,264,268,293,296,307,308,326,327,328,335,345,348,371,373,375,376,379,396,400,406,407,409,412,413,417,418,426,443,445,453,460,463,464,465,466,475,476,479,482,488,490,496,502,507,511],ansi:[9,12,16],answer:[3,4,8,12,307,377,378],anthoni:333,antiquewhit:200,antisymmetr:[9,41,383],antisymmetri:406,antonelli:[332,333],antonio:440,anymor:333,anyon:7,anyparticl:90,anyth:[8,11,172,226,246,462,464,466,492],anywai:[175,380,502,509],anywher:[12,172,393,430,452,507],aoff:[374,481],aparam:[91,204,205],apart:[3,173,253,320,376,385,453,481,490],aperiod:289,api:[11,12,201,414,479],appar:3,appear:[2,3,6,11,12,13,40,41,42,74,79,91,96,112,114,121,122,146,155,172,173,175,196,197,199,200,212,216,217,220,224,227,230,239,244,293,304,305,334,346,348,349,365,373,374,375,394,404,430,435,451,463,469,477,478,479,481,482,483,486,488,502,507,511],append:[],appendix:[29,399,451],appl:[224,263,264,469],appli:[2,3,4,5,6,8,9,12,17,18,29,33,42,51,59,61,63,65,73,74,91,92,110,122,146,147,152,158,160,162,166,171,172,174,178,180,185,191,195,196,197,199,200,203,204,205,206,207,209,212,219,220,224,225,226,228,231,232,234,235,237,238,239,240,241,242,244,245,247,248,249,250,254,263,264,268,269,270,271,277,282,283,286,287,288,290,294,297,305,306,307,309,310,312,313,316,320,321,322,324,326,327,328,329,331,333,334,335,338,346,365,368,373,374,375,385,387,389,391,396,399,406,410,411,412,413,415,416,418,424,428,433,435,438,443,446,447,448,449,450,460,467,472,481,482,484,485,486,490,491,493,498,502,507,508,509,510],applic:[1,6,9,12,17,201,209,223,227,228,237,239,241,244,288,293,306,312,320,331,338,365,380,466,491,502],applyt:3,appopri:17,approach:[6,7,9,14,196,209,240,289,290,302,307,330,331,333,335,338,365,386,396,398,402,403,409,413,433,445,447,449,460,470],appropri:[1,2,3,6,8,9,11,12,13,15,17,33,38,43,51,57,63,75,92,95,122,123,150,151,152,180,185,191,192,195,196,197,200,212,213,216,217,218,223,224,226,237,238,241,250,258,260,261,263,265,266,267,268,269,270,271,282,283,284,286,290,293,294,297,302,307,311,323,326,327,328,331,338,340,341,343,344,345,356,366,375,382,386,390,394,395,396,405,410,413,415,422,426,433,442,443,444,462,463,464,465,466,469,470,481,482,483,485,486,494,495,498,507,508],approri:242,approxim:[6,9,124,128,171,239,241,250,290,308,310,330,365,371,372,373,388,398,406,409,427,428,433,435,442,445,451,472,495,502],april:11,aprpopri:476,apu:[427,428],aqua:[199,200],aquamarin:200,ar_therm:209,ar_ttm:209,ara:13,arbitrari:[6,41,60,122,196,197,199,201,225,226,242,263,290,298,462,479,492,507],arbitrarili:[11,61,122,146,195,224,263,396,507],arcco:3,arch:[1,9,12,14,15,17],architect:363,architectur:[16,380,433],archiv:[6,7,11,12,325,393,488],arcsin:3,area:[6,42,95,118,122,170,220,226,250,331,338,403,410,440,468,478,491],aren:[122,296,348],arflag:12,arg:[3,11,12,22,41,42,45,56,61,65,73,91,123,160,166,170,172,175,176,180,195,196,197,198,200,203,204,205,206,208,210,212,213,214,215,216,217,218,219,220,221,222,225,226,227,232,237,239,242,243,244,245,253,260,265,266,267,293,306,307,308,309,313,316,317,319,330,333,340,341,342,343,345,346,350,363,375,380,387,388,389,391,392,393,398,399,402,406,411,413,418,422,426,427,428,429,438,446,448,450,461,478,479,481,484,486,488,490,492,494,499,500,507,508,510,511],argon:239,argonn:12,argument:[2,3,6,8,9,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,42,43,44,45,46,47,48,49,50,52,54,55,57,61,65,75,91,95,112,115,118,122,146,147,149,154,159,160,161,166,170,172,173,174,176,178,179,180,181,182,183,184,186,187,189,190,192,196,197,200,203,204,205,206,208,211,212,213,214,215,216,217,218,219,220,224,225,226,233,235,237,238,239,241,242,246,247,253,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,292,293,295,299,304,307,308,309,310,323,326,328,335,337,339,341,343,346,348,349,350,351,352,354,355,356,358,360,363,364,366,367,368,370,375,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,398,399,400,402,404,405,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,429,430,431,432,435,436,437,438,440,441,443,444,445,446,451,452,453,461,462,463,464,465,466,467,469,471,472,473,475,476,477,478,479,480,481,482,484,486,489,490,491,492,496,498,499,507,508,510],aris:[12,472],arithmet:[3,6,108,365,391,394,421,435,467,468],arkansa:9,arl:[9,84,85,234,311],armi:[84,85,234,311],armv8:17,arnold:365,around:[1,3,4,6,12,43,59,60,61,68,72,73,74,75,79,122,146,150,167,170,172,174,195,199,200,207,208,224,226,227,245,260,263,296,298,302,307,316,320,323,340,341,344,364,374,451,481,484,491,492,502,507],aroung:3,arrai:[],arrang:146,arrheniu:495,art:[9,476,495],artefact:241,articl:[6,451],articul:[7,292],artifact:[92,170,502],artifici:[261,297,455,456,458],arun:13,arxiv:[146,198,452],ascend:[42,200,244,253,307,486],asci:7,ascii:[13,197,308,334,375,404,407,430,481],ash:[427,428],asid:[8,172,430],asin:507,ask:[3,11],askari:440,askoos:13,asoci:199,aspect:[6,7,61,226,239,409,445,468,481,491,495],aspect_ratio:308,asper:4,aspher:[],asq:[427,428],assembl:4,assign:[1,2,3,6,7,11,12,14,15,17,18,33,40,41,42,51,59,61,63,65,68,73,74,77,94,98,109,111,116,119,120,124,146,147,152,167,169,171,172,175,185,195,196,197,198,199,200,201,203,204,205,208,212,215,220,222,223,224,227,229,239,244,247,248,249,250,260,263,265,266,267,268,269,270,271,280,282,283,284,285,286,290,293,294,296,298,304,307,308,326,327,328,329,346,356,366,368,370,374,375,379,380,386,404,407,409,412,413,444,445,473,478,479,481,482,483,484,485,490,491,496,499,507,508],assignemnt:[6,490],assing:296,assingn:463,assist:[7,261],associ:[3,5,6,8,9,12,22,37,40,41,45,56,61,68,76,77,83,91,93,94,98,104,106,108,109,111,136,167,180,191,196,197,199,200,204,205,206,210,224,226,232,237,239,240,246,250,260,263,292,302,306,307,308,321,323,347,348,350,359,368,373,375,379,380,393,396,400,402,403,404,406,412,413,415,418,422,447,449,460,461,463,479,482,489,501,502,504,507],associd:69,assum:[2,3,4,6,11,12,16,17,18,40,61,69,73,92,101,107,109,149,150,151,152,153,154,155,157,158,159,160,161,162,164,165,166,170,172,175,200,204,205,210,212,213,215,216,217,218,224,226,236,244,246,250,253,265,266,267,269,270,271,273,275,278,280,281,282,283,286,288,289,293,294,295,298,307,309,312,320,331,334,335,340,343,346,353,365,366,374,375,380,386,388,390,393,394,403,406,412,413,417,422,427,428,468,476,478,479,481,483,486,491,495,498,499,502,508],assumpt:[170,244,381,435],astar:430,astart:453,asterisk:[22,45,63,79,91,122,166,176,180,200,204,205,253,307,350,370,393,412,460,475,478,491,506],astop:[373,453],asu:404,asub:430,asubrama:13,asymmetr:[133,343,386,404],asynchron:[15,16],atan2:507,atan:507,atc:[],atc_fe_output:209,athomp:[0,7,9,13],atm2pa:6,atmospher:506,atol:12,atom1:[292,306,374,481],atom2:[292,306,374,481],atom3:[292,306,374,481],atom4:[306,374,481],atom:[],atom_element_map:209,atom_forc:444,atom_info:444,atom_modifi:[],atom_styl:[],atom_vec:8,atom_vec_atom:8,atom_vec_electron:8,atom_veloc:444,atom_weight:209,atomey:[6,7,11,13,196,199,200],atomfil:[3,73,296,346,379,491,507],atomic_charg:209,atomic_numb:441,atomid:481,atomist:[6,209,330,433],atomperbin:3,atomt:200,atomvec:8,attach:[6,217,290,312,320,481],attatch:333,attempt:[3,6,42,61,73,195,210,220,221,222,223,227,239,293,294,323,343,365,369,375,413,479,496,499,507],attend:209,attent:[15,18],attogram:506,attrac:430,attract:[],attribut:[3,6,7,8,11,40,41,43,60,65,73,91,119,120,121,123,150,166,196,197,199,200,203,204,205,211,212,215,216,217,223,224,263,265,266,267,268,269,270,271,273,274,282,283,284,286,294,307,308,325,326,327,328,368,374,386,406,413,481,482,483,491,499,507],atw:[427,428],atwat:465,atwt:430,atyp:[121,166,222,396,418,422,426],au1:171,au3:171,aug:[],augment:[12,119,224,296,430],augt1:430,auo:304,auoh:304,author:[3,8,9,13,198,404,405,502],auto:[3,6,8,11,12,95,168,203,213,214,312,337,365,374,380,478],autocorrel:[65,95,247],autom:[12,199],automag:7,automat:[3,6,12,14,15,16,17,18,19,36,134,192,208,214,239,241,250,307,312,336,365,380,395,404,413,430,433,447,448,449,450,473,481,494,502,507],auxiliari:[1,6,9,11,12,13,196,289,307,482,486,509],avail:[1,3,5,6,7,8,9,11,12,13,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,63,65,84,85,91,115,118,119,146,149,159,170,178,179,181,182,183,184,186,187,189,190,192,196,199,203,206,212,215,216,217,218,219,224,225,226,233,234,235,238,240,242,244,247,263,264,265,266,267,268,269,270,271,272,273,280,282,283,284,286,299,301,307,308,309,310,311,326,328,333,339,343,349,351,352,354,355,358,360,363,366,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,430,431,435,436,437,438,440,441,443,444,445,446,452,453,462,463,464,465,466,469,471,472,473,482,484,490,494,507],availab:[],avalo:[311,402],ave_chunk:6,aveforc:[],avendano:434,averag:[3,6,7,12,15,42,65,66,73,84,85,91,95,96,108,110,122,124,148,152,160,168,171,196,197,200,203,205,209,211,212,213,214,215,216,217,218,219,220,224,239,241,243,247,253,263,264,268,289,294,297,303,304,307,308,312,349,382,402,406,430,467,482,486,499,502,507],averi:323,avesq:123,avg:12,avi:199,avoid:[1,3,6,12,36,40,61,172,173,192,199,208,213,215,218,230,239,241,248,288,290,298,302,307,308,337,344,378,386,406,426,430,444,463,483,489,490,502],awai:[3,6,63,122,196,199,212,223,227,242,245,262,288,312,320,334,340,376,396,418,422,486],awar:[380,405,478],awpmd:[],axel:[7,9,13,18],axi:[3,6,42,73,96,124,136,150,171,172,174,195,199,212,220,239,242,245,260,293,316,320,335,341,354,360,368,481,484,491],axial:268,azimuth:[199,242],azur:200,b_k:452,ba2:171,babadi:445,back:[1,6,7,11,12,13,14,15,17,153,154,155,159,160,161,162,164,172,176,196,197,200,201,204,205,225,230,237,244,245,247,248,263,269,270,271,282,283,284,286,305,307,326,327,328,332,333,342,343,345,364,365,366,375,410,479,481,482,483,484,485,488,494,495,507,508],backbon:[223,310,358],backcolor:[200,510],backend:17,background:[9,91,92,118,147,200,220,226,247,323,331,335,338,375,394,427,428,430],backtrack:[371,373],backward:[9,12,201,375,495,507],baczewski:240,bad:[3,12,61,63,245,375,481,486,498],badli:[3,224,263],bal:330,balanc:[],balasubramanian:285,ball:[146,427,428],ballenegg:365,bammann:209,band:[4,6,7,9,146,203,262,372,375,386,433,451],bandwidth:[1,10,18,41],bandwith:199,bar:[91,199,506],barashev:404,bare:[230,246,248],barost:[230,502],barostat:[],barostt:6,barr:395,barrat:302,barrett:69,barrier:[3,4,6,262,360,375,395,408,495],bartel:289,bartok2010:452,bartok2013:452,bartok:[9,146,442,452],bartok_2010:442,bartok_phd:442,bary:506,barycent:319,basal:[],base:[3,4,6,8,9,11,12,13,14,15,20,65,66,73,80,91,95,108,117,124,152,154,171,172,174,196,198,199,200,203,209,216,217,220,221,222,226,227,231,239,244,247,251,253,277,289,290,293,296,298,300,307,308,312,313,323,330,366,380,382,384,386,400,406,409,412,413,414,416,418,427,431,432,438,440,441,451,462,465,466,469,476,478,481,482,483,485,488,491,492,495,496,499,506,507,508,511],bash:393,bashford:[6,20,178,391,493],basi:[3,6,12,41,146,152,172,208,247,249,289,323,340,368,416,491,507],basic:[6,7,8,12,17,42,119,147,199,200,209,220,263,264,288,344,381,383,433,475,483,502],basin:[90,375,476,495],bask:[404,430,441],bath:[9,297,302],batom1:[71,121,123,196,200],batom2:[71,121,123,196,200],bayli:[6,178,493],bb13:179,bcc:[3,4,7,66,72,75,368,430,432],bcolor:[3,199,200],bdiam:[3,199,200],be2:171,bead:[5,7,10,13,41,46,47,164,207,223,290,460],beam:227,bear:[6,240],becau:13,becaus:[0,1,3,6,8,12,16,17,18,41,42,43,61,66,73,74,79,96,112,122,134,146,152,157,162,172,173,174,178,196,197,198,199,200,201,206,212,220,221,222,223,224,226,232,238,239,240,241,246,247,248,249,260,263,264,277,284,293,297,298,302,307,320,325,330,331,334,335,338,342,343,344,345,346,352,365,371,373,375,376,379,380,391,393,396,398,400,406,407,409,410,411,412,413,417,426,427,428,430,435,445,460,461,463,467,468,478,479,481,483,484,485,488,490,491,493,495,496,502,507,508,509,511],beck:[],becker:[381,404],beckman:244,becom:[1,2,3,6,7,8,18,40,42,55,59,61,73,174,196,197,199,200,220,221,222,223,226,239,241,250,262,263,304,305,326,327,340,341,343,344,345,365,366,371,375,382,394,396,404,406,409,418,435,441,445,462,469,472,481,482,484,491,507],been:[1,2,3,6,7,8,9,11,12,13,16,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,43,44,46,47,48,49,50,52,54,55,57,59,61,62,65,67,71,73,91,115,118,119,120,121,123,125,149,150,151,152,153,154,155,159,160,161,162,164,165,173,174,175,176,178,179,181,182,183,184,186,187,189,190,192,195,196,197,199,200,201,206,208,210,211,212,213,215,216,217,218,219,220,223,224,225,226,227,233,238,239,242,244,245,247,248,250,251,252,253,254,258,260,261,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,292,293,294,297,299,301,304,305,307,309,310,319,324,326,327,328,335,336,337,339,340,341,342,343,345,346,349,351,352,354,355,358,360,364,365,366,373,376,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,403,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,431,432,433,436,437,438,440,443,444,445,446,453,460,462,463,464,465,466,468,469,471,472,473,476,478,479,481,482,483,484,485,487,491,495,498,499,507,508,509,510],befor:[1,2,3,6,8,9,12,14,17,22,29,40,41,42,45,61,68,73,76,77,83,93,94,98,108,109,110,111,120,152,155,160,161,167,172,173,175,176,180,194,195,200,204,205,206,207,208,210,212,215,216,217,218,219,220,224,229,230,238,239,244,246,247,248,250,253,260,263,269,270,271,282,283,286,289,296,297,298,301,302,307,308,309,324,326,327,328,334,340,341,342,346,350,370,371,373,375,380,407,410,426,430,433,461,470,476,478,479,482,483,484,485,486,488,489,491,495,498,499,502,507,508,509,510,511],began:[5,12],begin:[3,8,12,38,40,57,73,123,125,173,192,195,196,200,204,205,209,211,212,213,215,216,217,218,220,226,235,277,292,305,308,323,325,328,337,342,345,346,362,364,365,366,367,369,372,374,375,376,379,380,404,433,435,441,448,450,451,453,460,463,473,476,481,488,495,497,499,506,507,509],behalf:3,behav:[3,27,181,372,373],behavior:[3,176,192,196,197,199,201,223,224,227,239,240,241,244,247,248,249,263,293,297,302,323,326,327,335,372,386,406,430,473,475,483,487,507,509],behaviour:[6,247],behind:[8,246,261,297,323,365],beig:200,belak:7,believ:11,bellott:[6,20,178,391,493],bellow:354,belong:[2,3,41,73,126,175,210,212,216,239,253,307,346,374,447,481],below:[1,2,3,5,6,8,9,11,12,15,16,17,22,38,40,41,42,43,45,55,57,61,62,65,67,70,71,73,79,81,95,97,118,119,122,123,124,146,147,152,158,160,166,170,171,172,175,176,178,180,191,192,195,196,197,199,200,203,204,206,207,209,212,213,214,215,216,217,219,220,222,223,224,226,227,232,235,237,239,242,243,245,247,248,253,260,261,263,268,269,270,271,282,283,286,288,293,296,297,298,305,306,307,309,310,317,320,323,324,325,326,327,328,331,332,333,335,338,340,341,346,348,350,363,365,368,370,371,373,374,375,377,380,381,382,383,386,387,388,391,392,393,394,396,399,404,406,407,409,410,411,412,413,416,418,419,420,421,422,423,424,425,426,427,428,429,430,434,435,440,443,444,445,446,452,453,460,461,463,468,469,471,472,473,474,475,476,479,481,482,483,484,486,488,489,491,493,494,495,497,498,499,501,502,507,508,511],bench:[1,6,9,11,12],benchmark:[1,7,10,11,12,13,14,15,16,17,18,42,220,365,494],beneath:227,benedict:433,benefici:[63,377],benefit:[1,240,490],bennet:91,beowulf:7,berardi:[409,445],beraun:335,berendsen:[],berensen:307,berger:9,berkelei:170,berkowitz:365,berlin:[7,9,312],bern:[3,290,298,299,395,409,451,461,490],bernendsen:6,beryllium:406,besid:[8,309,484],best:[1,6,8,14,15,16,17,18,19,263,284,285,306,307,380,386,396,418,422,435,463,482,490,495],beta:[6,9,289,297,381,384,404,405,407,430,464,465,466,499,507],beta_:386,beta_k:452,beta_pi:386,beta_sigma:386,beta_t:465,better:[3,6,7,8,12,14,16,27,146,181,205,220,239,250,263,277,298,305,307,323,366,375,380,464],betwe:385,between:[],beutler:426,bewteen:[114,213,323,331,338,413,416,478],beyon:490,beyond:[3,5,6,12,17,63,73,91,170,196,200,215,216,239,263,365,377,408,424,435,495,499,507],bflag1:[43,199],bflag2:[43,199],bgq:[17,433],bi3:171,bi5:171,bia:[3,6,8,118,147,150,151,152,153,154,155,159,160,161,162,164,165,203,212,225,226,239,247,248,263,269,270,271,282,283,284,286,302,326,327,328,330,508],bias:[6,9,225,508],biaxial:150,biersack:[430,461,466,473],big:[3,4,12,196,297,302,323,376,394],bigbig:[3,12],bigger:3,bigint:[3,237],bilay:[4,10,320],bilayer1:320,bilayer2:320,bill:7,billion:[3,7,10,12,40,239,489],bin2d:73,bin3d:73,bin:[3,6,11,12,40,65,68,73,77,94,98,109,111,120,122,152,160,167,169,196,200,212,215,216,217,289,297,302,323,376,377,380,403,439,482,510],binari:[3,6,7,9,12,13,16,33,37,51,56,185,191,196,197,198,199,200,201,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,312,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345,356,359,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,436,438,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,468,469,471,472,473,482,483,488,509,511],binary2txt:[],binchunk:212,bind:[9,17,18,198,216,386,451],binsiz:[40,200,376,380],binstyl:160,bio:[41,376],biolog:[6,7],biologi:184,biomolecul:[292,307,365,366,391],biomolecular:490,biophys:244,biosym:13,bird:403,bisect:[42,220,468],bisector:[6,396,418,422],bispectrum:[65,146,452],bisqu:200,bit:[3,11,12,17,40,237,248,435,463,489,502],bitmap:[3,463,470],bitrat:[199,200],bitzek:372,bkgd_dyn:430,bla:12,black:200,blais:[9,13],blanchedalmond:200,blank:[2,3,12,38,57,113,192,199,235,292,307,374,375,386,405,430,437,452,462,463,464,465,466,469,478,479,481,507],blast:335,blend:430,block:[2,3,6,95,146,172,174,175,293,344,368,380,386,406,441,452,484,495,502],blocksiz:380,blow:[3,277,340,344,453],blown:3,blue:[2,199,200,223],bluegen:[196,365,433],blueviolet:200,bni:73,board:[366,399],bodi:[],body_nparticl:8,bodyflag:481,bodyforc:250,bodyforcei:250,bodyforcex:250,bodyforcez:250,bodystyl:[253,307],boff:[374,481],bogaert:330,bogu:[3,155,224],bogusz:92,bohr:[404,406,433,466,506],boltzmann:[6,7,9,91,95,118,149,152,153,154,155,158,159,160,161,162,164,212,223,247,250,251,252,253,254,268,339,400,496,506],bond:[],bond_coeff:[],bond_graph_cutoff:444,bond_harmon:[8,49,50],bond_harmonicshift:50,bond_info:444,bond_interact:209,bond_styl:[],bond_typ:176,bondangl:[3,21,33,481],bondbond13:[3,179,481],bondbond:[3,21,33,481],bondchk:444,bondcoeff:3,bondtyp:[221,222,374],bonet:[311,402],bonu:[3,509],book:472,bookkeep:435,bookmark:0,boost:[1,3,12,66,376],bop:[],border:[3,7,16,63,335,508],boresch:91,boreschkarplu:91,born:[],boron:406,borrow:312,bose:302,botero:[7,9,13,406],both:[1,3,6,7,8,9,11,12,14,15,16,17,27,37,40,41,55,56,59,61,63,64,65,70,71,73,87,91,92,114,119,121,122,134,148,150,151,152,157,160,162,165,170,172,174,175,176,181,191,192,196,199,202,203,204,205,210,212,213,216,217,218,221,222,223,224,225,226,231,239,241,243,245,247,248,250,251,259,260,263,264,269,270,271,277,282,283,286,292,293,296,297,304,307,310,312,320,323,327,331,332,333,335,338,340,341,343,344,345,348,349,359,366,370,373,374,375,376,378,380,382,386,387,388,389,390,391,392,394,399,400,404,405,406,409,410,412,413,414,418,420,422,423,424,426,427,428,433,434,435,438,445,446,462,464,465,466,469,476,478,479,481,482,483,484,488,493,498,499,502,507,509,510,511],bottleneck:[1,3,479,500],bottom:[8,9,155,170,200,226,238,250,284,331,338,368,493],bottomwal:219,bounc:[3,323],bound:[3,6,17,26,27,42,43,59,61,73,161,174,181,195,196,197,200,215,216,220,226,227,231,239,248,263,293,323,340,341,342,343,344,345,365,373,406,481,484,495,502,507,508],boundar:3,boundari:[],boundary_dynam:209,boundary_faceset:209,boundary_integr:209,bount:11,bourgogn:9,box:[],boxcolor:[199,200],boxxlo:11,bpa:380,bpclermont:[9,13],bptype:460,br1:171,bracket:[2,3,6,42,65,73,123,125,203,211,212,213,215,216,217,218,220,337,499,507],bragg:[124,171],branc:[],branch:11,branicio2009:469,branicio:[75,469],breakabl:[7,45,56],breakag:[80,221],breakdown:[1,12,15,92,113,443,444,476,495],brennan:[9,84,85,234,311,402,460],brenner:[382,461],brick:[3,42,63,64,160,174,220,481,483,485,507],brief:[1,5,6,7,8,12,246,263,382,386,444,495],briefli:[6,10,290,395,451],brilliantov:410,bristol:[5,7],brittl:440,broader:479,broadli:8,broken:[2,55,67,71,72,80,108,113,121,176,221,263,386,483,493,500,509],brook:6,brought:195,brown:[7,9,13,15,16,124,147,200],brownain:388,brownian:[],brownw:7,brows:0,browser:[4,199],bryantsev:412,bsd:12,bstyle:[41,43],btype:[71,121,173,196,396,418,422,426,460],buc:389,buck:[],buckingham:[7,204,205,298,366,387,389,390,398,429,461],buckplusattr:451,buffer:[3,8,197,199,200,498],bufi:199,bug:[],bui:199,build:[],builder:[7,13],built:[1,2,3,4,6,8,9,11,12,13,14,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,41,44,46,47,48,49,50,51,52,54,55,56,57,66,69,80,82,84,85,87,90,91,101,102,103,104,105,106,110,115,117,118,124,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,156,158,159,163,164,166,170,171,178,179,181,182,183,184,185,186,187,189,190,191,192,196,197,198,201,203,206,207,208,210,214,219,221,222,223,225,226,227,232,233,234,235,236,238,239,240,241,242,244,246,247,249,250,251,252,253,254,256,257,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,278,280,281,282,283,284,285,286,288,289,290,292,293,296,297,298,299,300,301,302,303,304,307,309,310,311,312,313,314,315,316,317,319,323,326,328,329,330,331,332,333,335,336,338,339,341,342,343,347,348,349,351,352,353,354,355,356,358,359,360,366,375,376,377,380,381,382,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,476,479,482,484,490,494,495,496],bulatov:[431,432],bulk:[4,6,10,72,250,288,294,397,430,433,435,440,447,449,451,485],bullet:7,bump:247,bunch:8,bundl:[9,199,201],burlywood:200,bussi1:327,bussi2:327,bussi:[241,327],buyl:[9,198],bybe:9,bypass:6,c1060:14,c11:[213,430],c12:213,c13:213,c1n:213,c2050:14,c21:213,c22:213,c23:213,c2n:213,c31:213,c32:213,c33:213,c34:213,c3n:213,c41:213,c42:213,c43:213,c44:213,c_0:[335,458,459],c_1:[70,71,123,124,171,196,200,240,296,308,346],c_2:[71,123,124,168,170,171,196,308,337,346],c_3:[123,308],c_6:170,c_cluster:6,c_cstherm:6,c_dist:123,c_doubl:11,c_e:335,c_flux:95,c_forc:123,c_gauss:408,c_hb:412,c_id:[6,65,73,91,123,125,196,197,211,212,213,214,215,216,217,218,308,325,337,499,507],c_ij:6,c_ijkl:6,c_index:123,c_k:240,c_ke:331,c_msdmol:125,c_my_stress:211,c_mycentro:[212,216],c_mychunk1:120,c_mychunk2:120,c_mychunk:[6,68,77,94,98,109,111,152,167,169],c_mycom:215,c_mycomput:212,c_myd:197,c_myf:[196,510],c_myrdf:[122,218],c_mytemp:[8,213,214,215,218,337,499,507],c_n:[],c_n_k:240,c_p:147,c_pe:116,c_peratom:[116,147],c_pi:386,c_press:123,c_prop:6,c_radiu:170,c_reax:[443,444],c_sa:308,c_sigma:386,c_size:6,c_stress:196,c_tatom:[],c_tdrude:[230,248,502],c_thermo_press:[8,213,214,215,218],c_thermo_temp:218,c_xrd:215,ca2:171,cach:[17,40,435,494],cacul:310,cadetblu:200,cai:502,calcforc:250,calclat:95,calcluat:[110,116,118,147,396],calcualt:[95,212],calcul:[],caldwel:[6,178,493],calhoun:290,call:[],callabl:[3,11],callback:[3,8,11,148,203,237,479],caller:3,calori:506,caltech:[6,7,9,13,406],calucl:6,calul:[11,12,152,366],cambridg:[9,442],campa:289,can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,178,179,180,181,182,183,184,185,186,187,189,190,191,192,193,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,233,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,358,359,360,361,362,363,364,365,366,368,369,370,371,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,488,489,490,491,492,493,494,495,496,497,498,499,500,502,506,507,508,509,510,511],cancel:[203,307,508],candid:[176,210,239],cannot:[1,2,3,6,11,12,13,15,16,17,39,40,41,42,55,58,59,60,61,70,73,86,88,92,123,125,148,150,152,173,175,176,193,195,196,197,198,199,200,211,212,213,215,216,217,218,220,223,224,226,227,239,240,241,247,248,249,253,260,263,265,267,269,271,273,274,275,280,282,286,293,294,297,302,304,307,308,309,313,323,331,335,337,338,340,341,344,345,346,348,361,365,368,373,375,378,379,380,389,390,392,404,409,411,418,422,424,426,435,438,443,445,446,447,449,460,461,463,476,478,479,481,482,484,485,487,490,491,493,495,498,506,507],canon:[203,210,239,241,263,264,282,283,284,285,286,290,327,330,333,433,440],cao1:290,cao2:290,cao:290,capabl:[5,7,9,11,14,17,18,342,348,366,380,382,392],capac:[9,41,106,158,234,302,335,455,481,491],capit:[229,481],capolungo:[124,171,308],captur:[6,336,382,390,406,410,422,430,502],carbid:396,carbon:[7,199,358,382,395,415,430],card:[12,14,16,22,45,79,91,122,180,204,205,307,350,370,393,412,475,483,488,509,511],care:[3,6,61,73,172,175,195,212,216,217,221,222,227,241,246,250,263,293,307,330,385,479,481,484,485,490,491],carefulli:[11,12,55,304,346,413,415,486],carlo:[6,7,9,203,210,223,239,307,330,403,461],caro:[210,404],carpent:[7,13],carri:[16,256,296,335,410,444],cart:[3,478],carter:[9,17],cartesian:[3,64,381,478],carv:175,cascad:[231,335],cash:7,cast:[241,507],cat:[15,199],catastroph:298,cate:250,categori:[],cation:[407,451],cauchi:[139,144],caus:[1,2,3,6,8,12,16,17,172,174,175,176,196,200,208,224,231,239,263,277,288,293,305,307,310,340,342,343,344,345,348,364,366,373,375,379,412,418,424,427,428,435,475,479,480,481,482,485,486,488,489,507,511],caution:[1,366],cautiou:[221,222],cautious:382,caveat:[382,490],cbecker:[381,404],cc1:[6,14,68,77,94,98,109,111,120,152,167,169,212,216],cc2:14,ccc:[405,462,464,466,469],ccflag:[9,12,16,17,18,19,196],ccm6:404,ccsi:[405,462,464,466,469],ccu:386,cd2:171,cdeam:404,cdennist:9,cdll:11,cdof:[6,152,212],cdte:386,cdte_bop:386,cdtese:386,cdzn:386,cdznte:386,ce3:171,ce4:171,ceas:372,ceil:507,cell:[3,6,61,92,122,124,170,171,172,196,208,224,225,239,244,261,263,264,268,289,297,300,311,335,365,366,368,403,406,433,499],cella:[6,499],cellalpha:[6,499],cellb:[6,499],cellbeta:[6,499],cellc:[6,499],cellgamma:[6,499],center:[3,6,25,43,65,68,73,76,77,90,93,94,103,108,109,110,120,122,124,152,153,154,157,160,164,167,169,172,199,200,203,204,205,207,212,215,216,217,224,226,227,228,230,239,240,245,247,248,253,259,263,269,270,271,282,283,284,286,289,293,298,304,305,307,308,312,320,321,323,325,326,327,328,330,331,333,340,344,349,368,374,385,405,406,409,410,416,427,428,430,431,432,462,464,465,466,468,469,484,491,502,507],centimet:506,central:[3,63,72,78,79,96,112,122,128,146,170,253,288,310,321,353,374,433,437,443,444,469,481],centro:[],centroid:[3,290,468,491],cerda:365,ceriotti2:241,ceriotti:[13,241,246],certain:[1,2,3,6,8,12,17,40,73,119,123,125,176,196,197,199,211,212,213,215,216,217,218,223,237,238,307,309,324,337,348,356,364,376,413,435,444,467,483,487,502,507],certainli:245,cerutti:366,cfg:[3,6,7,13,196,198,199,200,201],cfile:444,cfl:[134,313],cfor:312,cg_type:446,cgiko:2,cgikot:2,cgkio:2,cgko:2,cgkot:2,cgo:2,cgot:2,ch2:310,ch2lmp:[],ch3:310,ch5md:198,chain3:376,chain:[],challeng:[6,312],chalopin:302,champaign:[244,365,366,427],chan:433,chandler:[381,404],chandrasekhar:[6,418],chang:[1,2,3,6,8,9,11,12,14,15,16,17,40,41,42,47,56,59,61,64,73,82,91,108,122,132,134,154,155,156,172,173,174,176,192,195,196,197,198,199,200,201,203,204,205,206,207,209,210,216,217,219,220,221,222,223,224,225,226,227,231,232,236,238,239,241,243,244,245,247,249,250,251,253,259,260,261,263,264,265,266,267,268,269,270,271,277,282,283,284,285,286,288,289,293,294,296,297,298,301,304,305,306,307,309,310,312,323,326,327,328,329,331,332,333,334,335,336,338,341,344,346,366,371,373,375,378,380,400,406,410,413,427,428,430,433,435,443,444,451,460,461,476,477,478,479,481,482,483,484,485,486,487,489,490,491,492,493,496,499,503,505,506,507,508,509],change_box:[],changeabl:196,channel:[4,206],chapter:[290,366],charact:[2,3,6,12,38,42,57,65,192,196,197,199,200,201,203,220,235,296,304,348,374,379,406,417,441,443,444,451,463,478,479,483,488,489,507,509,510,511],character:[6,69,72,112,122,146,452,476,495],characterist:[248,323,332],charg:[1,3,4,5,6,7,9,11,15,41,91,92,119,124,171,172,196,197,201,203,204,205,210,227,232,239,296,298,299,300,304,325,338,365,366,374,387,389,395,396,398,399,404,406,407,413,418,422,426,438,443,444,451,461,466,467,469,470,472,473,481,482,486,491,493,502,506,507],charmm2lammp:13,charmm:[],chartreus:200,cheap:323,cheaper:[231,409,445],check:[3,6,8,11,12,15,17,40,42,73,95,192,210,216,220,221,222,227,236,239,245,246,293,306,310,323,331,333,338,346,348,364,373,374,375,376,377,380,403,414,417,435,444,476,478,479,481,489,495,498,499,507],checkf:192,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:[9,297,298,300,386,406,443,444],chen:335,cheng:395,chenoweth:[443,444],chenoweth_2008:[443,444],chi:[97,161,195,288,298,300,361,407,409,508],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:[3,6,9,12,15,16,18,41,42,55,91,147,150,151,165,176,192,212,216,217,220,223,226,227,241,247,250,261,263,290,298,307,330,359,366,371,372,375,377,380,413,426,435,439,481,490,491,494,495,501,502,506],choos:[1,3,6,7,8,12,16,17,18,29,40,55,91,123,162,163,199,221,222,223,224,227,236,247,250,261,263,265,266,267,268,269,270,271,293,294,311,323,327,341,365,366,372,470,476,478,490,496],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:[9,461,469],claus:479,clean:[6,12,14,15,17,489],cleanli:[480,510],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],client:[244,246],climb:[262,375,495],clinic:[7,13],clo:[161,195,508],clock:[12,476,495],clockwis:341,close:[3,6,11,12,13,40,42,69,73,147,175,196,222,223,224,241,248,250,263,284,307,310,341,344,364,366,369,371,372,375,380,382,386,396,397,416,430,435,447,449,463,466,485,491,502,504],closer:[3,42,122,170,195,196,220,224,228,332,375],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:[3,9],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:[7,9,29,36,41,55,184,292,307,323,411,446,490,493],coarser:[366,507],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:[9,239,406],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:[7,8,9,15],collect:[3,6,7,8,9,13,41,43,68,77,87,94,98,103,109,111,120,152,160,167,169,172,196,197,200,212,225,253,259,292,302,305,307,346,365,374,376,394,481,488,494,500,511],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:[3,6,9,12,13,43,65,67,68,69,70,71,73,77,79,81,83,85,94,96,97,98,109,111,112,114,116,119,120,121,122,123,125,146,147,152,160,167,169,170,171,192,196,197,200,203,211,212,213,215,216,217,218,253,260,261,297,307,324,325,335,345,408,412,443,444,482,496,498,507],columnar:170,colvar:[],colvarmodul:12,com:[],comamnd:226,comand:223,comannd:380,comb3:[],comb:[],comb_1:299,comb_2:299,combiant:397,combin:[3,6,7,9,11,13,36,41,65,67,71,81,91,97,108,114,121,150,151,165,196,199,209,215,244,253,263,290,296,311,327,336,344,347,349,365,366,368,372,380,394,396,397,402,406,407,413,425,426,452,462,464,466,469,472,484,489,494,502,507],come:[],comfort:[12,13],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:[2,7,11,12,38,57,178,192,196,235,248,307,335,374,375,381,404,405,407,417,430,437,444,451,452,462,463,464,465,466,469,478,479,481,502,507],commerci:7,commit:9,commmand:[3,6,12,61,113,285,416,475,476,478,495,510],common:[],commonli:[3,6,12,17,25,59,61,110,112,174,196,199,201,360,411,420,452,464,466,481,484,493],commun:[1,3,6,7,8,10,11,12,14,15,16,18,41,42,60,63,64,73,170,175,176,199,200,220,221,222,224,225,226,244,246,250,252,253,254,263,289,296,298,299,300,307,311,323,335,346,363,365,376,377,378,380,402,403,439,474,478,479,490,491,507,509,511],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:[1,3,4,6,8,12,17,40,90,116,124,155,171,180,191,200,230,298,346,348,365,366,373,375,430,451,476,495,496,502,506],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,44,45,56,179,180,191,349,350,359,392,461],compat:[3,5,7,8,9,11,12,13,17,18,42,73,123,125,183,196,201,205,211,212,213,215,216,217,218,220,289,301,327,330,337,340,343,365,380,414,433,435,463,478,479,507],compens:[6,221,222,305,376,406],compet:334,competit:366,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,170,196,198,199,201,244,334,366,380,433,481,482,486,507],compl:17,complain:[11,12,17],complement:430,complementari:[7,396,418],complet:[3,6,9,11,12,15,42,61,73,200,216,220,225,253,290,293,296,323,334,336,347,348,364,375,380,407,448,450,468,476,481,486,489,493,495,498,502,507],complex:[6,8,11,12,13,25,41,43,64,96,112,146,148,160,172,173,250,319,344,363,375,406,433,463,479,481,484,507],compli:[330,334],complic:[6,7,9,12,13,210,239,479],complier:12,compon:[3,6,8,12,63,65,68,69,75,83,92,93,94,95,96,98,99,102,109,110,111,112,113,114,115,116,118,119,123,133,136,137,138,139,142,143,144,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,167,168,169,195,196,197,199,200,206,207,211,212,213,214,215,216,217,218,219,223,224,226,227,232,237,242,246,247,250,253,255,259,260,262,263,264,268,269,270,271,282,283,284,286,287,289,290,291,294,305,307,309,310,312,316,317,320,323,326,327,328,330,337,338,343,344,345,365,368,372,373,374,375,380,400,406,410,427,428,448,450,451,452,481,482,491,499,507,508],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:[2,3,510],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:[9,16,366,507],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],confin:[481,495],conflict:[3,12,41,197,435,479],conform:[3,6,13,61,223,224,262,306,312,334,358,375,406,493],confus:[3,469],conjuct:400,conjug:[7,8,247,372,406,443,444],conjunct:[6,7,73,90,91,120,155,160,166,172,176,200,204,205,247,250,254,277,293,294,298,299,300,302,307,311,323,331,338,343,365,366,375,387,389,393,396,400,406,412,418,435,438,446,467,481,484,488,502,511],connect:[3,6,91,157,175,223,244,292,307,310,320,375,397,410,460,466,478,479,481,485,502],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:[6,9,72,73,80,91,121,154,157,158,175,196,197,200,204,205,211,213,216,220,222,223,227,251,264,289,307,330,331,334,335,338,366,393,406,413,444,445,451,460,476,477,479,482,483,484,486,489,491,499,502,507],consider:[6,8,247,248,326,327,328,380,490],consist:[3,6,8,9,11,12,41,43,67,71,81,97,109,114,117,118,121,152,155,157,172,184,195,201,206,207,212,226,227,230,232,237,240,247,248,249,260,263,265,266,267,268,269,270,271,272,273,275,276,277,278,280,281,282,283,284,285,286,294,297,302,304,306,307,326,327,328,329,339,365,366,368,374,375,380,382,386,388,394,396,406,409,413,416,427,428,430,433,435,445,448,450,451,463,470,479,481,482,483,484,485,486,493,502,507],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:[6,8,12,14,38,55,57,63,66,69,72,74,75,79,96,112,124,146,171,224,263,289,306,344,376,380,399,433,435,460,462,463,484,485,500,507],constructor:[8,11],consult:444,consum:[1,302,439,507],consumpt:363,contact:[],contact_stiff:[447,449],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,65,91,95,122,124,146,152,160,170,171,172,174,178,180,191,192,196,197,199,200,201,203,204,205,209,211,212,213,215,216,217,218,220,225,227,232,235,241,245,246,247,250,261,277,288,289,292,293,295,297,300,304,307,308,313,323,330,334,335,344,345,348,364,366,374,375,378,379,381,382,383,386,395,396,399,404,405,406,413,414,430,433,437,441,442,443,444,452,462,463,464,465,466,467,469,476,477,478,479,481,482,483,484,486,488,490,493,495,496,498,499,502,507,509,511],content:[9,12,18,444,497,499],context:[3,6,8,12,17,122,123,200,221,222,227,292,304,339,372,472,481,488,497,506,507,508],contibut:72,contigu:478,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,73,83,108,109,168,200,203,204,205,210,212,213,214,215,216,217,218,220,223,224,225,226,227,239,240,241,243,244,245,247,248,249,255,260,261,263,265,266,267,268,269,270,271,282,283,284,285,286,291,293,296,297,307,308,312,322,323,325,332,333,335,341,344,348,364,379,380,386,400,403,420,423,443,444,445,448,450,465,476,479,481,483,484,489,495,496,498,499,507,509],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:[1,6,43,56,66,154,157,197,226,346,448,450,472,510],contrib:335,contribut:[3,5,6,7,8,9,12,13,17,65,68,70,72,73,76,77,79,82,88,91,92,93,94,95,98,107,109,111,113,114,115,116,118,120,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,205,210,211,212,213,215,216,217,218,224,239,247,250,253,254,258,264,284,285,292,293,301,304,307,308,310,337,365,373,375,383,400,403,404,406,413,427,428,433,435,443,444,451,493,499,502],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:[6,12,29,196,201,218,308,368,452,507],convent:[3,8,9,29,183,190,191,197,200,306,320,347,404,406,507],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:[3,8,146,199,200,210,213,294,365,396,397,398,406,418,422,426,438,479,495,506],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,61,65,73,95,172,179,196,199,200,218,261,293,346,349,351,355,358,368,375,381,404,433,464,466,473,479,481,482,483,488,498,502,506,507,509,511],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:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,61,63,64,65,68,70,73,76,77,79,83,91,93,94,98,108,109,111,119,120,122,140,146,155,161,167,169,170,172,176,195,196,197,198,199,200,201,203,206,211,212,215,216,217,220,221,222,223,224,225,226,227,230,232,233,237,239,242,243,244,245,246,247,248,260,262,263,265,266,267,269,270,271,284,287,288,289,292,293,294,304,305,307,309,310,312,317,320,321,322,323,325,333,334,335,342,343,345,346,368,373,374,375,380,381,382,385,405,451,476,481,482,483,484,486,489,491,495,502,507,508],coordn:[120,212],coorind:[],copi:[0,3,4,8,11,12,15,17,41,125,199,335,375,393,443,479],copper:473,coproccesor:16,coprocessor:[1,4,7,9,16,17,380,494],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],cornflowerblu:200,cornsilk:200,corp:[],corpor:16,corr:395,correct:[3,6,9,11,12,16,17,61,91,92,107,108,116,122,154,159,166,197,199,226,239,241,247,263,264,284,292,294,297,334,340,344,365,375,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,471,472,473,481,496,499,502],correction_max_iter:209,correctli:[3,8,9,11,17,73,83,107,108,109,149,150,151,153,155,157,158,159,160,161,164,165,168,196,200,206,227,232,237,248,257,263,264,300,307,310,320,322,341,344,375,376,380,398,428,433,478,479,481,491,506,508],correl:[],correpond:235,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,72,73,91,101,102,115,118,119,120,121,124,125,133,136,137,138,139,140,142,143,144,146,149,150,159,166,170,171,178,179,180,181,182,183,184,186,187,189,190,192,195,196,197,199,200,204,205,206,212,214,215,216,217,219,222,224,226,233,237,238,242,247,250,251,259,260,261,263,265,266,267,268,269,270,271,272,273,277,280,282,283,284,286,289,290,294,299,307,309,310,326,328,330,339,340,341,343,344,345,347,349,350,351,352,354,355,358,360,366,370,372,374,375,381,382,384,387,388,389,390,391,392,393,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,416,418,419,420,421,422,423,424,425,426,427,430,431,433,435,436,437,438,440,441,443,444,445,446,451,452,453,462,463,464,465,466,469,471,472,473,476,478,479,481,482,484,494,495,496,498,499,502,507],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:[2,3,6,9,11,12,17,33,42,51,61,68,73,77,91,94,98,109,111,115,118,120,152,162,167,169,185,196,197,199,200,204,205,212,213,216,220,226,237,246,296,297,298,302,305,307,309,323,324,330,334,335,336,340,344,346,348,356,362,364,371,373,376,380,383,408,412,413,416,443,444,477,478,479,481,483,485,488,489,496,497,502,507,508],coulomb:[3,5,6,7,8,9,10,12,14,15,18,74,92,113,114,122,147,173,177,298,300,336,365,366,373,380,387,389,390,391,392,395,396,397,398,399,406,410,411,413,418,422,426,429,435,438,443,444,446,451,461,466,467,469,472,486,493,499,502,506],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,42,65,70,79,95,120,122,123,160,170,176,206,207,210,212,215,216,217,219,220,227,232,236,239,245,263,277,293,310,326,327,344,366,373,374,375,377,380,408,412,435,499,507],counter:[3,341,476,487,489,495],counteract:239,counterbal:243,counterbalanc:29,counterpart:[196,307,476],counterproduct:18,coupl:[],courant:313,cours:[3,8,132,134,166,196,204,205,240,306,320,334,340,342,343,345,346,366,427,453,478,481,494,502,507,509],courtesi:368,cov:451,coval:[6,29,406,430,451,502],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:[1,3,4,9,10,12,14,15,16,17,18,65,73,200,214,230,248,336,363,366,380,393,461,476,494,495,498,499,500,507],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:[3,122,173,199,200,221,222,223,258,373,440,468,483,486,507],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:[3,12,22,73,93,150,170,180,196,197,199,211,216,222,226,260,262,284,307,316,320,322,331,338,350,368,375,391,400,403,404,411,412,413,418,420,422,441,446,448,450,464,466,473,481,485,491,509],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:15,cuda_get:15,cuda_hom:15,cuda_prec: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:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,41,42,43,61,63,65,73,75,83,91,107,108,114,122,123,136,147,152,160,162,168,170,173,176,195,196,197,198,199,200,201,204,205,209,212,216,217,218,220,221,222,223,224,225,226,227,231,232,237,239,241,244,245,247,253,260,263,264,269,270,271,277,282,283,284,286,292,293,298,299,301,304,305,306,307,310,311,312,313,314,315,316,317,319,321,322,323,326,327,328,334,335,338,339,340,341,342,343,345,346,348,363,364,365,366,369,370,372,373,374,375,380,386,393,395,399,404,406,407,410,413,414,417,427,428,430,431,432,435,441,443,444,447,448,449,450,453,464,466,467,470,476,477,478,479,481,482,483,484,485,487,488,489,491,493,495,496,498,499,507,508,509,510,511],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:[3,6,10,16,18,40,46,47,55,56,63,72,74,75,79,91,96,112,114,121,122,146,170,173,175,176,222,223,228,235,288,297,298,300,302,304,307,311,323,336,340,344,346,363,365,366,373,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,394,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,444,445,446,451,452,453,454,455,456,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,479,483,486,490,502,507],cutoff_glob:[],cutoff_inn:[],cutoffa:405,cutoffc:405,cuu3:404,cval:171,cvd:330,cvel:312,cvff:[],cwiggl:[3,260,340,343,345,507],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:[0,6,12,13,195,443,444,507],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:[6,7,11,12,13,14,17,124,128,171,172,290,295,363,365,380,414,435,470,479,480,488,491,498,507],deby:[],decai:[96,396,473],decid:[3,6,12,16,73,260,296,307,336,496],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:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,178,179,180,181,182,183,184,186,187,189,190,191,192,193,194,195,196,197,198,199,200,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,220,221,222,223,224,226,227,230,231,232,234,237,238,239,242,245,246,247,248,249,250,258,260,262,263,264,265,266,267,268,269,270,271,273,274,275,278,280,281,282,283,284,285,286,288,289,290,292,293,294,296,298,300,305,307,308,309,310,313,317,321,323,325,326,327,328,329,331,332,333,335,337,338,340,341,342,343,344,345,346,348,349,350,351,352,353,354,355,358,359,360,361,363,365,366,368,370,372,373,374,375,376,377,378,379,380,382,383,384,385,387,388,389,390,391,392,393,394,396,397,399,400,401,402,403,405,406,408,409,410,411,412,413,414,416,418,419,420,421,422,423,424,425,426,427,428,429,433,434,435,436,437,438,440,441,443,444,445,446,447,448,449,450,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,481,482,484,485,486,487,490,491,492,493,495,496,498,499,502,503,504,505,506,507,508],definit:[2,3,6,8,12,13,80,82,122,146,200,212,213,214,215,216,217,218,226,234,245,268,308,325,337,340,343,345,347,359,363,374,383,386,394,401,402,406,416,441,448,450,452,468,479,481,483,490,492,506,507],defint:499,deform:[],deg2theta:171,deg:502,degener:[3,292],degrad:[8,18,289,366,490],degre:[3,6,8,20,21,24,28,29,32,35,36,38,67,81,96,97,99,101,102,104,106,107,112,118,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,171,172,178,179,182,183,190,192,195,199,212,223,230,239,241,242,247,248,253,263,264,268,269,270,271,282,283,284,286,290,292,306,307,310,326,327,328,333,349,351,355,358,360,373,399,404,412,491,499,502,508],degress:[152,212],del:495,delai:[3,6,12,376,403,499],deleg:413,delet:[2,3,7,8,12,55,59,62,65,170,175,176,203,212,213,215,216,217,218,221,223,236,239,263,308,326,327,346,348,364,374,376,379,435,460,481,482,483,484,492,493,498,503,505,507,508],delete_atom:[],delete_bond:[],delete_el:209,deli:195,delimit:[479,507],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:[3,6,7,9,18,41,42,61,105,122,132,146,158,170,172,204,205,209,212,216,217,220,226,237,250,253,256,257,289,293,294,298,335,340,368,370,374,381,386,404,430,431,432,441,445,451,455,457,458,459,481,490,491,499,506],density_continu:450,density_summ:450,depart:[0,7],departur:[261,297],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,63,65,67,70,71,72,73,81,96,97,108,114,115,118,119,120,121,125,146,149,155,159,160,166,172,173,178,179,180,181,182,183,184,186,187,189,190,191,192,195,196,197,199,200,203,204,205,206,207,210,212,214,215,216,218,219,220,222,224,226,232,233,238,241,242,243,245,247,248,250,252,253,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,288,299,302,304,307,309,310,311,317,323,326,327,328,330,332,334,335,337,339,340,343,344,345,346,348,349,350,351,352,354,355,358,360,366,368,373,374,376,377,378,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,430,431,433,434,436,437,438,440,441,443,444,445,446,451,452,453,461,462,463,464,465,466,467,469,471,472,473,476,478,481,483,484,487,491,493,495,498,499,501,507,508],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:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,64,65,70,72,73,75,92,116,119,122,124,136,146,147,150,151,152,156,157,160,163,165,166,170,171,172,174,175,184,189,192,196,197,198,203,204,205,212,213,214,215,216,217,218,220,223,224,225,226,227,229,230,235,240,241,244,245,246,247,248,249,250,252,253,254,258,262,263,264,268,276,285,288,290,295,296,297,298,299,300,307,312,320,323,324,325,326,327,328,329,330,331,332,333,338,340,341,343,348,365,366,368,371,372,373,374,375,379,382,383,385,387,388,389,391,392,393,394,395,396,399,404,406,407,409,410,411,413,416,418,419,420,421,422,423,424,425,426,427,428,429,430,433,434,440,441,442,443,444,445,446,451,452,453,460,461,462,463,464,465,466,467,469,471,472,473,474,476,478,479,481,482,483,484,485,491,494,495,498,507,508,509],descript:[],descriptor:[146,196,414],deserno:366,design:[0,3,6,7,8,9,11,13,14,15,17,124,154,157,171,209,223,229,230,263,264,288,289,308,330,335,383,384,385,388,391,396,398,406,426,427,428,431,432,441,444,463],desir:[2,3,6,7,11,12,14,15,16,33,41,51,61,73,92,95,118,123,147,154,172,185,195,212,218,224,226,237,239,240,247,248,249,253,263,284,292,293,294,295,298,302,307,310,323,326,327,328,329,334,341,356,362,365,366,368,371,373,374,375,400,404,412,427,428,462,464,466,477,478,479,481,485,490,495,496,498,499,507,508,509],desk:7,desktop:[4,6,7,10,12,199],despit:502,destabil:386,destre:358,destroi:[11,40,221,222],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,65,68,69,70,73,77,80,94,95,98,107,109,111,113,115,117,118,120,123,125,146,147,149,150,151,152,155,165,166,167,169,172,173,176,177,180,191,195,196,197,199,200,203,204,205,209,212,213,214,215,216,218,220,222,223,224,225,226,227,237,239,240,241,242,244,245,247,249,250,254,260,261,262,263,264,265,266,267,268,269,270,271,275,277,282,283,284,285,286,289,292,293,294,296,297,299,300,301,307,310,311,323,326,327,328,329,330,331,333,334,335,336,337,338,339,346,348,350,359,365,366,369,373,374,376,377,380,381,382,383,385,386,388,390,391,392,393,394,395,396,399,400,406,407,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,429,430,434,435,440,443,444,445,451,452,453,461,468,471,472,479,481,482,483,484,486,487,490,491,493,496,499,500,507,508,511],detect:[2,3,12,43,63,65,90,96,238,293,334,375,395,412,417,476,478,481,492,495,507],determ:380,determin:[1,3,6,8,9,12,15,40,41,43,52,59,60,61,63,64,70,73,91,107,113,115,118,124,125,133,147,160,161,170,171,172,195,196,197,199,200,201,202,206,207,208,211,212,213,214,215,216,217,218,219,220,224,226,227,230,232,239,242,243,245,247,248,253,258,260,261,263,269,270,271,282,283,284,286,288,290,293,294,297,304,305,306,307,308,309,313,315,317,323,326,327,328,330,336,337,340,341,342,343,344,345,346,359,365,366,368,374,376,377,380,382,383,390,395,399,403,404,408,410,413,414,422,430,433,435,444,445,451,460,463,467,472,478,481,482,484,486,488,491,495,497,498,500,506,507,508],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_singl:[3,12,366],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,301,433],dhi:[61,195,226,293],dhug:[261,297],dhugoniot:[261,297],dia:430,diagnost:[],diagon:[3,6,87,146,147,148,224,263,294,307,338,448,450],diagonalstyl:452,diagram:[42,124,171,191,220,290],diallo:412,diam:[199,200,293,374],diamet:[3,6,41,43,119,172,196,197,199,200,204,205,247,293,307,323,325,339,341,374,394,409,410,420,445,468,472,481,482,491],diamond:[368,406,430],diamter:[41,293],dick:6,dicsuss:260,dictat:[210,261],did:[3,12,373,400,403,404,410,435,464,466,489],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,168,337,365],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,63,66,70,72,73,91,96,99,101,102,126,146,149,150,151,152,153,155,158,159,160,161,162,164,165,166,172,173,175,180,191,192,195,196,199,200,203,205,208,210,212,215,220,221,222,223,224,225,226,230,235,238,239,240,241,242,243,244,247,248,250,260,263,264,265,266,267,269,270,271,273,275,278,280,281,282,283,286,288,290,292,294,297,298,299,302,305,307,310,312,320,321,323,326,327,328,331,332,333,335,338,339,340,341,344,348,349,359,362,364,365,366,368,369,371,372,374,375,377,378,379,380,381,382,386,390,391,393,394,395,400,401,402,404,406,409,410,411,413,416,418,419,421,422,429,430,431,432,434,435,437,441,443,444,445,446,447,448,450,451,452,453,461,462,463,464,466,468,469,472,475,476,478,479,481,483,484,485,486,489,490,491,493,495,496,498,499,500,502,506,507,508,509],differenti:[1,3,6,29,192,365,396,441,465],difficult:[224,290,380,412,490],difficulti:[96,112,310,443],diffract:[],diffus:[],digit:[2,3,200,348,433],dih_table1:192,dih_table2:192,dihder:[],dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:222,dihydrid:406,dij:310,dilat:[],dim1:3,dim2:3,dim:[3,61,73,149,153,154,155,158,159,160,161,162,164,172,195,216,226,245,341,368,430,484,506,507,508],dimdim:507,dimems:289,dimens:[],dimensinon:73,dimension:[3,40,96,118,124,146,149,152,153,154,155,158,159,160,161,162,164,171,194,212,216,262,289,335,368,371,375,441,481,491],dimensionless:[110,127,128,130,133,135,137,142,146,335,366,452,472],diment:3,dimentionless:141,dimer:[6,307,430],dimgrai:200,dimstr:[42,220],dinola:[294,326],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,41,196,197,325,502],dir1:492,dir2:492,dir:[1,3,4,8,11,12,261,288,297,322,441,443,444,479,492,507],dirac:146,direc:441,direct:[],directli:[3,6,8,9,11,12,91,119,146,148,196,197,198,199,206,232,241,245,250,289,308,327,339,341,342,343,344,368,372,380,381,382,387,389,390,396,399,404,406,418,422,435,438,446,460,479,491,492,493,499,507],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,62,197,201,225,246,292,298,301,311,319,323,332,333,375,379,381,382,386,393,395,396,404,405,407,414,415,426,430,431,432,433,437,441,442,443,444,451,452,462,464,465,466,469,479,481,482,483,492,507],disabl:[3,12,16,335,417,479,494,507],disadvantag:[6,220],disallow:[196,226,263],disappear:483,discard:[2,3,42,73,214,216,220,336,344,478,483,484],discontinu:[9,192,373,424],discourag:430,discov:[13,336],discret:[6,8,41,43,199,200,247,250],discuss:[],disk:[6,88,89,96,165,194,227,239,293,479],disloc:[72,433],disord:[40,72,433],disp:[],dispar:445,disperion:[399,422],dispers:[3,6,7,9,170,289,365,366,390,399,422,427,435,444,463,469],displac:[],displace_atom:[],displace_box:61,displacemet:484,displai:[11,13,22,37,45,56,180,191,196,199,350,359,393,461],dispters:3,disregard:433,dissip:[6,9,41,84,85,234,240,247,289,311,332,333,388,400,401,402,410,427,428,461],dissolut:221,dist:[6,71,95,114,123,196,290,306,403,460,476,508],distanc:[],distinct:[6,230,304,365,445],distinguish:[6,90,146,253,406,480],distort:[170,381],distrbut:381,distribut:[],distro:[117,393,440,441],ditto:[8,12,14,15,16,17,18,43,121,222,473,479],div:8,divd:123,diverg:[3,12,40,307,333,483,502,509],divid:[3,6,16,42,95,118,123,132,134,147,169,170,180,191,200,212,213,215,220,226,288,331,338,343,365,373,375,407,444,451,469,490,498,507],divis:[6,250,386,416,426,478,499,507],dl_poli:[6,7],dlambda:166,dlammps_async_imd:244,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,199],dlammps_gzip:[3,12,196,199,334,481,482,486],dlammps_jpeg:[3,12,199],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,199],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,196],dlen:491,dlmp_intel_offload:[9,12,16],dlo:[61,195,226,293],dlopen:6,dlvo:[7,394,472],dm_lb:250,dmax:[323,371],dmpvtk:197,dmpvtp:197,dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,41,43,56,59,61,65,68,70,77,91,94,98,107,109,110,111,113,115,117,118,120,123,125,147,150,151,152,165,167,169,172,173,174,180,191,195,196,197,198,199,200,201,203,204,205,210,211,212,213,214,215,216,217,218,227,239,247,248,258,263,264,269,270,271,275,282,283,284,285,286,293,296,307,320,323,326,327,328,337,341,344,346,348,350,359,364,373,374,375,380,381,382,385,393,395,396,404,405,407,412,413,415,416,430,431,432,435,437,440,441,442,452,461,462,464,466,468,469,479,481,482,483,484,486,489,490,491,498,499,507,508,509,510],docuement:445,dodd:43,dodgerblu:200,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,40,42,43,51,55,57,61,64,65,69,72,73,74,91,92,95,109,116,122,123,124,148,150,152,154,155,160,162,166,171,172,173,174,176,178,180,185,191,192,195,196,197,198,199,200,203,209,210,212,216,219,220,222,223,224,226,230,232,235,236,239,240,243,245,247,248,250,253,259,263,264,265,266,267,269,270,271,282,283,284,285,286,294,295,296,300,302,305,307,323,326,328,330,331,335,338,339,340,343,344,345,346,351,352,353,355,356,358,364,365,366,367,368,374,375,376,381,382,383,384,385,386,388,390,391,392,394,395,396,397,399,400,403,404,405,406,408,409,410,411,413,414,415,416,417,420,421,423,424,425,427,428,430,431,432,433,435,441,442,443,444,445,447,448,449,450,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,468,469,471,472,473,476,477,478,479,481,482,483,484,485,488,489,491,492,493,494,495,498,499,502,507,511],doegenomestolif:7,doesn:[3,7,8,12,172,196,197,210,216,217,320,374,376,380,382,395,405,415,443,444,462,464,465,466,469,481,483],dof:[3,8,118,150,151,152,165,212,307,508],dof_per_atom:[152,212],dof_per_chunk:[152,212],doff:[374,481],doi:[6,225],domain:[3,6,7,12,13,18,40,42,43,60,63,64,73,124,161,171,174,195,198,199,200,203,210,220,224,226,227,243,246,250,263,264,290,302,307,311,335,340,341,365,366,375,380,403,435,476,478,481,485,498],domin:[1,406,495],don:[0,8,12,13,122,175,206,232,248,296,344,430,451,479,481],donadio:327,done:[1,3,6,7,8,9,12,14,15,16,17,18,38,40,42,57,61,64,73,166,169,172,175,192,196,199,200,209,210,212,214,215,216,217,218,220,221,222,223,224,226,227,235,237,239,244,245,247,248,255,263,269,270,271,282,283,284,286,287,289,290,291,293,296,304,307,308,310,323,326,327,328,330,332,333,346,348,364,365,366,373,375,376,379,380,382,390,404,413,414,415,422,428,429,430,435,443,460,463,468,476,477,478,479,482,485,486,489,499,500,502,507,508],donor:412,dot:[147,168,206,232,242,262],doti:[386,441],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,40,91,226,237,295,344,348,364,366,379,380,386,407,411,433,443,444,477,481,485,489,494,507,508],dover:209,down:[3,6,7,8,11,40,73,224,239,247,323,339,380,406,435,451,480,500],downhil:[371,372],download:[5,7,8,11,12,13,17,244,414,442],downsid:6,downward:304,dozen:[8,12,113,203,443,444],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:256,dpdtheta:[41,84,85,402],dpdtheta_i:[234,235],dproduct:383,dr_ewald:[124,308],drag:[],dragforc:250,drai:[261,297],drain:[243,339,373],dramat:[61,195,221,222,223,224,226,263,323,326,327,366,380,435,451,478],drautz:386,draw:199,drawback:296,drawn:[43,196,199,200,240,476],drayleigh:[261,297],dreid:[],drfourth:110,drho:[119,381,404],drift:[6,108,110,240,241,247,248,259,305,323,490,498,502],drive:[11,12,207,224,226,242,263,288,294,307,342,375],driven:[6,184],driver:[6,12,14,15,203,237,244],drop:[3,200,400],droplet:413,drsquar:110,drude:[],dry:236,dsecriptor:414,dsf:[],dsmc:[],dstyle:293,dt_collis:250,dt_lb:250,dt_md:250,dt_srd:323,dtilt:[61,226],dtneb:495,dtqm:297,dtype:[121,222],dual:[16,17,323,380],dudarev:171,due:[1,3,6,9,10,12,16,17,19,41,55,59,60,63,68,72,73,76,77,83,90,92,93,94,98,107,108,109,110,111,116,122,124,132,146,147,149,150,151,153,155,158,159,160,161,162,164,165,167,171,172,175,176,196,197,199,203,206,207,215,219,221,222,223,224,225,226,227,232,233,236,237,240,241,244,245,247,248,249,250,253,254,255,259,260,261,262,263,268,277,288,291,293,305,306,307,309,320,322,323,324,326,327,328,329,330,332,333,335,339,340,342,343,344,346,366,371,373,375,376,377,397,400,401,402,404,408,409,413,427,428,435,441,443,445,446,460,463,464,466,470,472,473,476,478,481,482,483,490,495,498,499,500,502,507,508],duffi:335,duin:[9,298,303,443,444],duke:366,dummi:[12,29,465],dump0:197,dump10000:197,dump1:486,dump20000:197,dump2:486,dump2vtk_tri:140,dump:[],dump_0:197,dump_1:197,dump_atom:8,dump_custom:8,dump_h5md:198,dump_modifi:[],dump_p:197,dumpcustom:8,dumptimestep:486,dunbrack:[6,20,178,391,493],dunweg:[247,249],duplic:[2,3,14,15,17,42,43,173,197,220,241,288,481,506],dupont:[5,7,13],durat:[37,56,149,150,151,153,154,155,157,158,159,160,161,164,165,191,200,212,239,302,335,359,410,461],dure:[2,3,6,8,9,12,16,17,38,40,42,57,73,91,132,134,148,154,173,176,192,196,197,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,228,231,232,233,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,259,260,262,263,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,312,316,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,366,373,375,379,380,400,426,433,435,444,463,476,477,479,481,484,486,488,489,491,493,495,496,499,500,507,510,511],dvector:8,dvlo:472,dvx:6,dx_lb:250,dy3:171,dyamic:12,dyanam:6,dyanmic:495,dynam:[],dynamo:[5,381,404,430],dyne:506,dyre:423,dysam:484,e28637:29,e_1:386,e_2:386,e_b:407,e_data:197,e_e:406,e_hbond:412,e_i:[6,386,407],e_j:[6,386],e_k:[386,406],e_kl:6,e_lj:[382,399],e_n:[386,406],e_nn:406,e_pr:406,e_rebo:382,e_tors:382,e_tot:433,e_vol:433,eaa:349,eaat:179,each:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,42,43,44,46,47,48,49,50,51,52,54,55,56,57,59,61,63,64,65,66,68,69,70,72,73,74,75,76,77,78,79,80,82,83,85,87,89,91,93,94,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,115,116,117,118,119,120,121,122,123,124,125,126,140,146,147,148,150,151,152,153,154,155,156,159,160,161,162,164,165,166,167,168,169,170,171,172,175,176,178,179,180,181,182,183,184,185,186,187,189,190,191,192,195,196,197,198,199,200,201,202,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,235,236,237,239,240,241,242,243,244,245,246,247,248,249,250,251,253,254,255,256,257,259,260,261,262,263,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,298,299,300,302,304,307,308,309,310,311,312,316,317,319,320,321,322,323,324,325,326,327,328,330,333,334,335,336,337,338,339,340,341,343,344,345,346,348,349,351,352,353,354,355,356,358,359,360,364,365,366,368,372,373,374,375,376,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,413,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,433,434,435,436,437,438,440,441,443,444,445,446,447,451,452,453,454,455,456,457,458,459,460,461,462,463,466,467,468,469,470,471,472,473,474,475,476,478,479,481,482,483,484,485,486,488,489,490,491,493,495,496,498,499,500,501,502,506,507,508,509,511],eacn:[42,220],eam0d:289,eam3d:289,eam:[],eam_databas:13,eam_gener:13,eangl:499,earli:[42,212,215,216,217,218,220,301,308],earlier:[7,8,12,61,200,375,410,430,435,495],earliest:495,earth:406,easi:[6,7,8,9,11,13,91,147,196,204,205,206,207,216,219,232,242,243,245,247,248,309,317,326,327,328,340,343,345,374,481,484,489,491,508],easier:[8,9,13,16,196,197,199,289],easili:[8,11,199,200,339,375,478,488,497,507],eastwood:[365,366],eat:179,eatom:346,eaxmpl:6,eba:21,ebb13:179,ebb:21,ebond:[230,248,498,499],ebt:179,ec_ii:430,ec_ij:430,ec_jj:430,echo:[],eco:[443,444],ecoa:[443,444],ecoul:[113,230,248,443,444,499],ecp:[406,481],edg:[2,3,6,42,43,61,73,124,170,171,174,175,198,199,208,216,245,309,340,343,344,345,346,368,481,484,491],edge_histo:170,edge_threshold:170,edih:499,edim:331,edip:[],edit:[3,8,12,13,14,15,16,17,18,19,502],editor:13,edu:[7,9,11,13,404,427,440,443,444],edward:[9,17],eebt:179,eff:[],effect:[1,2,3,6,8,9,11,12,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,44,46,47,48,49,50,52,54,55,57,68,73,76,77,83,93,94,98,108,109,110,111,115,118,147,149,154,159,160,167,170,176,178,179,181,182,183,184,186,187,189,190,191,192,195,196,197,199,200,204,205,206,209,210,213,217,218,219,221,222,223,224,226,227,233,235,238,239,240,241,242,243,244,245,247,248,262,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,287,288,290,293,294,296,297,298,299,302,306,307,309,310,322,323,326,327,328,330,331,333,335,338,339,340,341,342,343,344,345,346,349,351,352,354,355,358,360,365,366,368,372,373,374,375,376,381,382,384,386,387,388,389,390,391,392,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,433,435,436,437,438,440,445,446,447,449,451,453,461,462,463,464,465,466,468,469,471,472,473,476,478,479,483,484,486,490,491,493,499,500,506,507,509],efffect:485,efficaci:40,effici:[0,1,3,6,7,8,9,10,12,15,17,18,40,60,63,69,118,148,196,197,198,199,200,213,214,224,226,230,241,263,290,292,293,302,307,310,323,365,366,371,376,380,386,394,396,413,418,422,433,445,463,488,511],effort:[5,7,482],efftemp:[101,102,158],efi:[443,444],efield:[],eflux:243,eforc:197,eggebrecht:[396,451],ehb:[443,444],eigensolv:3,eigenvalu:[289,290,365],eigtol:3,eik:166,eim:[],eimp:499,einstein:[302,333],either:[1,2,3,4,6,8,9,11,12,14,15,16,17,22,33,42,45,51,61,65,73,108,113,119,122,124,146,147,152,154,155,170,171,172,175,180,185,192,196,197,198,199,200,203,211,213,215,217,218,220,223,224,225,226,227,239,245,246,250,254,260,261,263,264,268,284,288,304,307,309,310,312,320,323,330,337,341,344,348,350,363,365,366,368,372,373,377,380,386,388,394,404,413,414,416,427,428,430,433,435,439,441,460,464,466,468,476,479,481,483,484,485,488,490,493,496,498,507],ejtehadi:[394,409,445],elaplong:[204,205,245,484,499,507],elaps:[3,195,204,205,206,207,219,226,232,242,243,245,247,248,260,293,309,317,326,327,328,340,341,343,345,453,476,484,486,487,491,495,499,507],elast:[],elastic_t:4,elba:29,electr:[6,203,209,232,248,365,366,407,443,444,473,502,506],electrolyt:[9,472],electron:[3,6,7,9,13,41,101,102,119,124,156,158,163,197,203,209,229,230,248,249,264,276,285,300,329,335,372,374,381,383,395,399,404,406,407,430,433,441,442,451,466,469,473,481,501,502,506],electron_integr:209,electron_temperatur:209,electron_unit:406,electroneg:[6,298,299,300,395,407,451],electroneg_compon:451,electronic_dens:3,electronic_specific_heat:3,electronic_thermal_conduct:3,electrostat:[6,9,16,18,210,239,298,300,301,336,365,366,394,399,406,418,426,428,444,451,472],eleftheri:307,elem1:[407,430,452],elem2:[407,430,452],elem:451,element1:[304,381,404,451],element2:[304,381,404,451],element:[3,6,7,8,12,13,43,65,83,93,108,110,118,123,125,140,146,147,148,149,150,151,152,153,154,155,159,160,161,162,164,165,168,196,197,198,199,200,201,203,209,213,215,218,289,304,330,337,381,382,386,395,404,405,406,407,413,414,415,430,431,432,433,437,441,442,443,444,451,452,462,464,465,466,469,502,507,510],elementn:[381,404],elementset:209,elev:495,elif:[146,348],elig:[3,210,221,222,236,239,412],elimin:[3,6,73,170,240,247,248,307,310,332,333,476],elj:399,ellad:9,elliot:9,elliott:9,ellips:[4,6,9,73,86,150,194],ellipsoid:[3,4,6,7,9,13,41,43,73,86,119,136,150,172,194,195,196,197,247,260,265,269,273,274,282,307,323,370,373,409,428,445,461,481,491,509],ellipsoidflag:481,elong:[230,248,499],elp:[443,444],els:[3,7,8,12,73,113,122,123,125,198,199,211,212,213,215,216,217,218,239,263,307,323,335,336,337,346,348,365,413,480,492,507,510],elsewher:[8,260,323,430,442,443,444,493,499,507],elt:430,emac:[],email:[0,3,5,7,8,9,11,407],emb:[3,9,344],emb_lin_neg:430,embed:[3,5,7,11,12,13,29,92,148,170,335,381,404,407,426,430,431,432,441,461,470,479],embt:179,emi:[7,9],emil:9,emol:[443,444,499],emphas:410,empir:[209,327,382,406],emploi:[9,289,298,302,465],empti:[3,59,73,170,174,307,365,376,417,481,492,493,507],enabl:[3,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,40,41,44,46,47,48,49,50,51,52,54,55,56,57,62,63,64,66,69,80,82,87,91,101,102,103,104,105,106,110,115,117,118,124,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,154,156,158,159,163,164,166,170,171,178,179,181,182,183,184,185,186,187,189,190,191,192,196,197,198,200,201,203,204,205,206,207,208,210,214,217,219,221,222,223,225,226,227,232,233,236,237,238,239,240,241,242,244,245,246,247,248,249,250,251,252,253,254,256,257,259,261,263,264,265,266,267,268,269,270,271,272,273,274,275,276,278,280,281,282,283,284,285,286,288,289,290,292,293,297,298,299,300,301,302,303,304,306,307,309,310,312,313,314,315,316,317,319,320,322,323,326,328,329,330,331,332,333,335,336,338,339,340,341,342,343,344,347,349,351,352,354,355,356,358,359,360,366,373,375,379,380,381,382,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,435,436,437,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,479,482,483,484,488,490,500,507,511],enclos:[2,6,12,174,196,295,348,430,451,477,479,489,507],encod:[13,40,43,196,199,200,296,413],encompass:[3,6,41,43,59,61,122,173,319,337,461,484],encount:[3,8,12,61,112,215,379,486,507],encourag:[7,8,301,321],end12i:119,end12x:119,end12z:119,end1i:119,end1x:119,end1z:119,end2i:119,end2x:119,end2z:119,end:[1,2,3,5,6,8,11,12,15,16,17,18,19,38,41,42,43,59,61,73,119,175,176,179,195,196,197,199,200,201,204,205,213,215,217,218,223,226,240,245,247,249,262,263,264,277,294,306,307,312,323,326,327,328,329,331,334,335,338,342,345,346,364,365,374,375,379,380,400,404,409,416,429,433,445,448,450,452,453,470,476,479,481,482,483,484,486,488,489,493,497,499,502,507,511],end_of_step:8,endbondtors:[3,179,185,481],endif:8,energet:[223,382,444],energi:[],energy_compon:451,energy_update_freq:444,enforc:[6,59,60,109,195,196,197,198,199,201,203,210,223,226,263,287,289,299,307,310,348,365,418,478,507,508],enforce2d:[],eng:[11,67,71,114,196,237,346,348,395,432],eng_previ:348,engil:9,engilitycorp:9,engin:[209,226,292,312,332,404,431],engr:[443,444],enhanc:[205,209,476],enlarg:[61,199],enough:[3,41,63,90,172,173,175,176,220,248,293,297,302,307,336,340,341,344,376,380,396,439,481,485,486],enpub:404,enrti:[],ensembl:[],ensight:6,ensur:[3,6,146,196,197,210,214,224,239,240,263,313,334,366,386,403,426,462,469],enter:[59,162,407,433,469,495],enthalpi:[129,265,266,267,404,498,499,507],entir:[0,2,3,6,11,14,15,42,43,65,84,85,92,115,116,118,122,124,147,152,171,172,200,203,204,205,212,216,217,220,223,225,236,239,240,243,247,248,259,263,265,266,267,268,269,270,271,288,290,292,305,307,321,335,337,348,380,399,422,435,463,481,489,490],entireti:468,entiti:[6,8,41,43,196,307],entri:[3,8,12,38,43,57,67,71,81,97,114,121,124,133,136,137,138,139,140,142,143,144,170,192,197,200,215,216,217,225,235,297,346,374,386,405,430,437,444,452,462,463,464,465,466,469,507],entropi:495,entry1:[38,57,200,393,463],entry2:200,entryn:200,enumer:[173,196,474],enumuer:6,env:380,environ:[1,3,6,11,12,16,17,18,199,241,246,288,380,381,386,393,395,405,406,441,464,478,492,507],epair:[113,200,408,412,443,444,499],epen:[443,444],epfl:[241,246],epp:399,epq:399,eps0:472,eps14:426,epsilon0:466,epsilon:[3,6,36,46,47,51,54,55,91,178,204,205,239,307,323,340,344,371,373,385,391,392,394,396,397,398,399,409,411,412,413,416,417,418,419,420,421,422,423,424,425,426,429,434,438,445,446,456,462,468,471,472,490,502,506],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:[2,3,6,8,11,12,17,40,42,55,65,67,70,71,73,78,81,90,91,95,97,114,116,121,123,125,147,150,166,168,170,172,195,199,200,203,204,205,206,207,210,213,214,215,218,219,220,224,226,227,232,239,240,242,243,245,247,248,250,253,254,260,261,268,279,288,290,293,295,297,298,299,302,304,306,307,309,312,317,319,326,327,328,331,332,333,335,337,338,340,343,345,346,348,364,368,373,375,376,377,379,380,395,400,402,408,409,412,416,427,433,434,441,443,444,445,447,448,449,451,452,453,463,468,469,473,477,478,479,481,483,484,488,489,492,495,497,499,507,508],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:[3,298,369,488,511],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:506,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:506,esub:430,eta:[6,250,263,297,298,300,339,405,407,409,441,465,469,506],eta_dot:263,eta_ij:441,eta_ji:407,etag:[41,481],etail:499,etap:263,etap_dot:263,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,40,41,43,55,63,70,93,94,95,99,115,116,119,121,147,149,152,153,154,155,156,158,159,160,161,162,164,166,172,174,175,176,185,196,197,199,200,203,204,209,210,211,212,215,216,217,218,221,222,226,227,237,239,240,247,263,293,304,308,335,336,344,348,364,365,373,374,375,376,378,404,405,413,426,428,433,439,443,444,462,464,466,469,476,479,481,482,483,488,490,491,495,496,497,498,499,500,502,506,507,509,511],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:[2,3,9,11,12,38,57,73,91,92,95,113,123,146,148,152,162,170,172,195,196,197,199,200,204,205,206,207,209,211,212,213,214,215,216,217,218,219,226,232,240,242,243,245,246,247,248,289,295,298,309,313,317,326,327,328,337,340,343,345,346,348,365,366,371,373,380,433,435,441,447,449,451,463,476,477,479,483,484,486,488,489,490,491,495,497,499,507,508],evalut:[348,479],evan:[160,284],evanseck:[6,20,178,391,493],evapor:[],evaul:[8,373],evdwl:[113,443,444,499],even:[3,6,8,12,15,17,18,34,40,42,53,59,61,63,65,72,73,125,170,173,174,188,192,196,197,200,203,204,205,210,211,212,215,216,217,218,220,221,222,224,226,227,230,245,248,261,263,264,289,293,302,304,307,308,319,323,331,335,338,340,344,346,357,365,371,373,375,380,385,406,407,410,413,416,435,445,469,470,474,481,482,484,486,487,488,490,491,493,496,498,499,500,502,511],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:[0,1,2,3,6,8,9,11,12,15,16,40,42,73,74,95,119,125,134,160,175,196,197,198,199,200,201,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,231,236,237,239,241,243,244,245,250,251,259,263,264,268,287,288,289,293,294,295,296,297,298,299,300,302,304,305,307,308,310,312,323,325,326,327,328,329,330,331,334,335,336,337,338,346,348,364,366,375,376,377,380,400,403,413,426,443,444,451,457,475,476,477,481,483,485,486,488,489,490,495,496,497,499,507,511],everyth:[8,113],everywher:[122,420],eviri:406,evolut:[241,250,290,476],evolv:[250,290,336],ewald:[2,3,5,6,7,8,12,92,116,124,147,336,365,366,373,387,389,390,396,399,406,418,422,438,446,461,463],ewald_disp:399,ewalddisp:3,exact:[22,42,45,73,128,166,175,180,220,223,240,241,247,248,249,293,302,303,323,335,350,365,393,483,488,495,507,509,511],exactli:[3,6,12,14,17,38,42,43,57,61,73,74,95,122,150,156,163,172,192,204,205,215,220,226,231,235,240,247,248,249,264,276,277,285,289,297,323,328,329,342,380,393,400,404,410,413,427,435,463,483,484,491,495,507],exager:502,examin:[6,8,9,17,223,289],examp:[479,507],exampl:[],exce:[3,6,16,17,18,42,60,73,174,211,212,215,216,217,218,220,224,226,231,236,263,289,304,308,314,315,323,373,380,481,507],exceed:[3,42,61,220,226,263,323,489],excel:406,except:[1,2,5,6,8,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,61,62,65,73,93,94,114,115,118,123,147,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,172,176,178,179,180,181,182,183,184,186,187,189,190,191,192,195,196,197,200,203,206,212,213,215,219,220,224,226,233,238,239,242,245,247,249,263,264,265,266,267,268,269,270,271,272,273,276,277,280,282,283,284,285,286,290,299,300,307,309,310,320,323,326,328,329,335,339,343,346,347,348,349,350,351,352,354,355,358,359,360,365,366,368,370,374,375,376,378,379,380,381,382,384,387,388,389,390,391,392,393,394,395,396,398,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,431,436,437,438,440,443,444,445,446,453,461,462,463,464,465,466,469,471,472,473,476,478,479,481,483,484,486,489,490,491,492,493,495,499,502,506,507,508,510],excess:[214,406],exchang:[2,3,6,8,9,63,64,203,209,210,239,247,299,307,331,335,338,365,380,406,496],exchange:365,excit:[9,406],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:[1,3,9,12,16,91,380,395,433,435,490,500],excurs:[263,476],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,62,173,199,244,301,348,364,367,379,477,479,489,492,495,507],exempl:451,exemplari:240,exemplifi:406,exert:[6,245,248,302,342,343,344,366],exhaust:[209,379,507],exhibit:[96,263,372,406,490],exist:[3,6,7,8,11,12,13,16,37,56,61,70,72,128,172,173,191,198,199,200,203,208,219,222,224,227,239,292,293,295,346,347,349,351,352,353,355,359,369,374,380,401,402,413,443,460,470,477,479,481,482,483,492,493,494,507,508,509],exit:[2,3,11,12,42,59,196,220,235,364,379,479,480,489,498,507],exlanatori:3,exp:[],expand:[],expans:[12,146,196,492,507],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,73,107,153,164,170,192,220,232,239,241,260,288,294,296,297,302,307,346,366,376,393,430,433,435,476,479,481,483,486,490,495,507],expens:[6,10,73,200,288,292,307,335,346,365,366,376,380,479],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:[1,3,6,8,11,12,16,18,42,61,65,67,70,71,73,74,75,78,79,81,90,97,152,160,192,196,197,199,200,203,212,213,218,220,222,224,226,263,288,296,307,320,346,348,364,365,368,374,375,379,385,404,416,451,453,468,479,482,483,486,488,491,502,507,511],explan:[3,6,61,119,146,196,197,212,262,288,413,475,478,479,481,490],explanatori:[3,8,123,196,197,211,212,215,216,217,307,374,478,507],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],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],explictli:[16,494],exploit:[9,15,17,290],explor:[124,171],expon:[3,298,300,404,409,412,426,434,446],exponenti:[91,441,462,469,473,495,507],expos:11,exposit:[209,400,403],express:[6,146,158,172,204,205,224,260,288,298,335,341,348,386,404,406,420,430,451,452,461,507],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:[3,6,8,11,12,16,17,41,42,47,63,73,107,115,116,118,124,147,149,150,151,153,155,158,159,160,161,162,164,165,171,172,173,174,178,200,215,220,222,263,295,296,297,307,323,373,374,377,378,399,410,413,416,430,435,478,479,481,484,493,502,507],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_harm:333,f_i:[29,441],f_id:[6,73,123,125,196,197,203,211,212,213,214,215,216,217,218,258,325,337,499,507],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:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,59,60,61,74,91,95,107,114,121,122,124,146,166,171,174,178,189,195,196,199,200,204,205,213,220,224,226,227,239,244,247,249,250,261,263,264,268,290,294,298,306,310,313,315,323,327,331,338,339,340,344,355,366,368,374,380,382,383,386,387,389,391,396,397,398,400,401,402,406,410,413,417,418,430,433,435,437,438,444,446,453,462,467,478,481,484,485,490,493,495,496,499,502,506,507],factori:[3,479],factoriz:365,fail:[3,11,12,61,176,224,227,365,373,375,398,444,479],failur:[127,448,480,507],fairli:[11,435,490,495],faken:75,falcon:244,fall:[3,6,200,215,293,479,507],fals:[90,346,348,451,507],fame:8,famili:[469,478],familiar:[0,11],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:[6,8,42,73,172,200,203,204,205,210,216,220,222,227,239,241,245,260,261,263,265,266,267,268,269,270,271,279,282,283,284,285,286,296,297,299,307,312,316,322,325,333,335,339,340,341,343,345,375,413,427,484,493,507,510],fasolino:415,fast:[6,7,9,12,13,17,40,196,197,274,297,336,365,366,388,427,428,433,461,463,483,488,490,499,508,511],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,63,65,110,115,118,149,159,178,179,181,182,183,184,186,187,189,190,192,196,197,200,206,219,220,226,233,238,242,246,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,294,298,299,307,309,310,323,326,328,330,332,335,339,343,349,351,352,354,355,358,360,365,366,377,378,380,381,382,384,386,387,388,389,390,391,392,393,394,395,396,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,436,437,438,440,445,446,453,461,462,463,464,465,466,469,471,472,473,476,484,490,494,502],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:[279,507],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:506,fene:[],fennel:[396,418],fep:[],ferguson:[6,178,493],fermi:[1,9,12,15,158,380,466],fermion:[9,406],fernando:429,ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,18,40,65,201,211,212,213,215,216,217,218,248,263,293,296,298,310,337,365,373,374,375,382,451,478,481,486,490,492,500,507,509],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:[1,3,7,11,12,14,15,92,115,116,147,289,365,366,490],fft_inc:[12,366],fft_lib:12,fft_path:12,fftbench:[365,500],fftw2:12,fftw3:12,fftw: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],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:[3,12,13,38,42,57,192,196,197,199,200,201,209,212,213,214,215,216,217,218,220,225,235,288,292,295,298,299,300,303,304,307,308,334,335,362,363,364,374,375,381,382,386,396,404,405,407,415,430,431,432,437,441,442,443,444,451,452,462,463,464,465,466,469,477,478,479,482,483,488,492,499,507,509,510,511],filennam:488,filep:[3,196,197,200,483,488,511],filepo:304,fill:[7,9,172,199,293,335,368,376,386,433,444,484],filter:[200,209],final_integr:8,final_integrate_respa:8,finchham:[6,154,398],find:[0,3,4,6,7,8,11,12,13,14,16,38,40,57,63,73,75,91,123,175,192,201,210,223,224,235,236,239,262,288,293,294,302,306,371,373,375,376,396,413,418,422,430,451,461,463,502,507],find_custom:8,fine:[16,17,176,206,232,333,376,380,507],finer:[146,172,507],finest:365,finger:[172,195,260,484],finish:[6,11,42,220,348,362,364,365,377,379,380,468,486,507,508],finit:[],finni:[7,404,461],finvers:230,fiorin:[9,225],fire:[],firebrick:200,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,59,61,63,64,73,83,92,95,108,109,110,112,118,122,123,133,136,139,140,144,147,157,160,166,168,170,171,173,174,175,179,192,196,197,198,199,200,201,203,204,212,213,215,216,217,218,220,223,226,235,239,240,245,250,260,261,262,263,288,290,295,296,297,299,304,307,310,312,320,321,323,324,325,332,333,334,335,337,341,346,348,349,356,368,373,374,375,376,379,380,381,382,385,386,387,389,391,393,395,396,404,406,407,410,411,413,414,415,416,417,418,422,427,428,430,432,433,435,437,441,443,444,451,452,460,462,463,464,465,466,469,473,476,477,478,479,481,482,483,486,488,490,493,494,495,498,499,502,507,508,509,511],fischer:[6,9,19,20,178,391,493],fit:[3,6,9,12,38,57,192,235,306,323,382,386,415,430,435,456,463,465,489,507],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_modifi:[],fix_mov:[195,341],fix_nh:8,fix_npt:241,fix_nvt:[210,239],fix_poem:[3,6],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:[3,8,9,11,12,14,15,16,17,41,68,76,77,83,90,93,94,98,108,109,111,124,167,171,175,196,197,199,200,201,218,223,225,229,244,247,251,253,259,260,289,296,307,320,322,323,330,334,343,346,363,366,374,378,379,380,382,412,417,430,433,460,476,478,479,481,482,483,485,486,487,491,507],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:507,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:[2,200,247,248,260,263,294,307,326,327,490,501,506,508],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:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,61,65,66,72,73,75,84,95,96,101,102,112,119,122,123,125,146,147,150,151,152,158,160,165,168,170,172,173,178,181,182,183,184,186,187,189,190,192,196,198,199,200,203,209,210,211,212,213,214,215,216,217,218,220,225,226,227,230,231,234,235,237,239,240,241,244,246,247,248,250,253,261,263,268,269,270,271,282,283,284,286,289,290,292,295,296,297,298,300,302,304,306,307,308,310,325,326,327,328,331,332,333,334,335,337,338,346,347,351,352,353,354,355,358,360,363,368,370,373,374,375,380,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,435,436,437,438,440,441,442,443,444,445,446,448,450,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,468,469,471,472,473,474,476,478,479,481,482,484,486,488,489,490,493,495,496,497,502,507,508,510],foo:[4,8,11,12,196,199,237,479,492,507],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:[2,3,6,8,12,19,22,45,55,65,68,76,77,79,83,91,93,94,96,98,108,109,111,122,146,147,166,167,176,180,200,203,204,205,222,240,241,247,249,253,260,284,289,300,302,306,307,335,340,344,349,350,353,358,370,372,374,375,382,383,386,393,401,402,404,406,408,412,413,417,429,430,432,433,437,438,441,443,444,445,451,452,453,461,463,464,465,466,472,475,478,479,481,486,491,498,502,507],formal:[6,80,82,95,240,241,247,263,290,323,331,451],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,70,79,180,192,196,197,198,199,200,201,212,215,216,217,218,220,222,235,289,292,296,298,300,303,307,308,319,334,335,346,347,350,370,374,375,381,382,386,393,404,407,417,430,432,442,443,444,446,452,463,469,470,478,479,481,482,483,486,497,498,499,507,509],former:[6,12,16,40,42,200,220,335,339,386,388,487,493,507],formerli:[7,13],formul:[1,41,66,147,206,232,247,263,284,298,300,306,310,334,365,382,386,404,406,409,430,440],formula:[2,3,6,7,13,21,22,37,45,55,56,72,75,91,93,94,95,99,101,102,111,118,124,147,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,171,172,177,179,180,191,195,196,204,205,206,207,212,213,214,215,218,219,226,232,242,243,245,247,248,260,288,289,295,304,309,317,321,323,326,327,328,337,340,343,345,346,348,349,350,352,359,368,374,382,383,385,386,391,392,393,394,399,400,404,405,409,410,411,412,414,417,418,420,421,422,424,425,427,428,430,434,435,436,445,446,453,461,462,463,464,465,466,469,471,472,477,481,484,491,498,499,506,507,508],forth:[1,6,11,12,13,14,15,379,479,484,488],fortran:[3,6,9,11,12,13,237,404,413,430,443,444],fortun:8,forward:[3,8,91,364,375,380],foster:[386,440,441],foul:175,found:[3,6,9,12,75,166,196,223,225,239,244,250,289,330,336,348,364,376,393,396,399,476,482,483,498],four:[6,11,55,83,108,109,146,168,261,335,358,374,375,433,476],fourier:[],fourth:[6,110,306,320,330,391,437,451],fox:[6,124,178,459,493],fphi:[38,57,463],fpic:12,fplo:[38,57,463],fprime:463,fqdn:246,fqq:399,frac:[],fraction:[1,3,6,8,12,16,40,42,82,115,147,175,195,199,200,210,221,222,223,224,261,293,297,304,305,323,328,329,368,375,380,386,388,410,427,428,486,491],fragment:[43,244,304],fraig:43,frame:[87,146,200,209,261,297,342,409],framer:[199,200],framework:[5,241,381,452],franc:9,fraunhof:9,free:[5,6,7,9,13,29,62,65,72,91,166,205,288,323,332,333,334,335,372,375,383,406,426,433,441,472,478],freedom:[3,6,8,99,101,102,104,106,107,118,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,212,223,230,239,241,247,248,253,263,264,268,269,270,271,282,283,284,286,290,292,307,310,326,327,328,333,373,399,499,502,508],freeli:[0,6,7,12,150,151,165,170,199],freez:[],frenkel:[239,333],freq:208,frequenc:[3,6,16,40,108,200,214,277,289,290,297,302,363,400,406,444,451,476,490,495,507,510],frequent:[3,66,69,72,74,75,79,92,96,112,146,200,221,222,236,331,338,435,488],fri:[261,297],friction:[4,5,6,10,43,203,241,247,297,302,307,335,339,341,410,491],friedrich:313,from:[],front:[261,297,342],frontend:[199,301],frozen:[6,118,176,238,240,248,376,408],fs2:[6,95],fscale:244,fstr:507,fstring:479,ftol:[373,375,476,495],fuchsia:200,fuction:396,fudg:310,fugac:239,fugacity_coeff:239,fulfil:6,full:[1,2,3,6,9,12,17,38,40,41,95,199,213,214,225,250,288,365,366,380,386,404,406,407,409,467,481,483,488,489,493,495,500,502,510],full_energi:[3,239],fuller:373,fulli:[3,6,9,80,241,246,288,373,375,396,441,442,481,509],fulton:404,fumi:387,func:[479,507],funcfl:404,functino:[],functionaliri:225,fund:[0,7],fundament:[323,506],funnel_flow:319,funrol:433,further:[3,6,8,12,13,63,65,73,90,110,113,122,199,200,203,212,215,216,217,218,221,227,231,250,254,290,298,308,311,313,323,335,337,346,366,371,373,374,375,376,381,385,395,433,451,476,495,496,507],furthermor:[27,181,402,406],furthest:63,futher:3,futur:[],g_ewald:3,g_ewald_6:3,g_ewald_disp:3,g_jik:441,g_p:335,ga3:171,gaa:386,gahler:372,gai:[3,409,461],gain:330,gainsboro:200,galindo:434,game:244,gamma0:29,gamma:[3,6,29,247,250,254,289,297,298,300,302,339,400,402,405,409,430,434,455,458,459,462,464,466,469,499],gamma_:[3,335,341],gamma_ijk:464,gamma_n:[341,410],gamma_p:[3,335],gamma_t:[341,410],gammaa:434,gammafactor:250,gammar:434,gan:[441,462,464,466,469],gan_sw:441,gan_tersoff:441,ganzenmuel:[7,9],ganzenmul:9,gao:[6,20,178,391,493],gap:[192,427,428,442,452],gap_2014_5_8_60_17_10_38_466:442,gap_exampl:442,gaseou:7,gass:239,gather:[11,489],gather_atom:11,gather_scatter_loop_unrol:[9,12],gathert_atom:11,gauch:184,gaug:12,gauss:[],gaussian:[6,41,65,95,108,110,240,241,247,290,306,323,327,345,365,400,403,406,408,442,461,476,507,508],gave:[3,435],gaybern:[],gcc:17,gcmc:[],gcore:230,gd3:171,gdot:428,gdrude:230,ge4:171,gec:[464,466],gen:[263,264],gener:[],genom:7,gentler:[340,343,345],gentli:405,geom:[6,365,403,476,508],geometr:[3,6,7,8,43,59,61,73,162,163,172,174,196,200,206,216,217,219,220,227,232,243,263,269,270,271,282,283,284,286,307,309,317,326,327,328,344,346,365,368,375,385,388,392,394,396,399,406,409,411,418,419,420,421,422,423,424,425,426,427,428,429,434,435,445,453,467,468,471,472,481,484,491,499,507],geometri:[3,6,7,9,13,25,39,42,58,73,160,172,193,216,220,221,222,224,227,245,311,361,368,435,481,484],georg:[7,9],georgia:13,gerber:426,germani:[9,14],germann:[268,420,476,495],germano:409,gerolf:13,get:[],get_natom:[11,479],get_rank:11,get_siz:11,getenv:507,gettimeofdai:12,gewald:[6,365],gezelt:[396,418],gf100:14,gf104:14,gf200:14,gflop:12,gflp:12,ghost:[3,6,7,12,16,60,63,64,75,170,175,176,224,226,248,263,296,307,308,363,365,376,380,400,402,403,406,410,417,474,486,491,502],ghostwhit:200,ghz:10,giacomo:9,gif:[4,199],gifsicl:199,gigabit:18,gillan:452,gingold:[455,456,458],gio:2,git:[7,12],github:[13,17,225,241,246,442],give:[0,1,2,3,5,6,7,8,9,10,11,12,14,15,16,17,18,55,73,96,112,119,152,155,159,172,196,197,200,206,208,212,213,215,218,224,226,241,263,284,288,289,294,302,304,307,337,365,366,373,376,377,380,382,386,403,406,412,413,430,433,435,445,464,465,466,476,478,479,481,491,495,502,508],given:[3,5,6,7,9,10,11,12,16,17,22,27,37,45,56,63,65,66,69,73,112,119,129,130,131,133,134,137,138,139,140,141,142,143,144,145,146,147,166,170,174,180,181,191,192,196,197,198,200,203,210,212,214,216,221,222,224,226,227,231,239,240,241,242,244,250,257,260,262,263,268,287,288,289,290,297,298,304,306,310,319,320,321,323,325,330,335,336,339,340,341,344,350,359,365,366,380,381,382,386,387,389,390,392,393,394,395,396,397,400,401,402,403,404,406,407,409,412,418,419,420,422,430,431,432,433,434,435,437,438,441,445,446,448,450,451,452,461,473,476,479,481,483,484,491,495,506,510,511],gjf:247,gjwagn:7,gko:2,gld:[],gle4md:[241,246],gle:[],glitch:3,glob:492,global:[],glosli:[366,433],glotzer:[307,400],glue:11,gmail:[7,9,13],gmake:[12,17],gmask:[3,507],gnu:[0,7,12,17],gnuplot:[11,13],goal:[5,12,40],goddard:[6,9,25,298,299,300,360,406,412,443,444,493],goe:[12,55,146,172,195,260,316,373,376,399,405,411,420,423,453,473,484,488],gold:[72,200],goldenrod:200,goldman:297,gone:3,good:[1,3,6,12,17,42,75,124,170,171,220,247,261,263,298,304,310,330,365,375,376,381,394,403,404,433,435,463,469,476,490,495,499],googl:244,gordan:146,gordon:6,gould:[6,178,493],gov:[0,7,9,13,381,404,407,506],govern:250,gpl:[0,7,8,12],gpt:[9,433],gpu1:380,gpu:[],gpuid:380,gpun:380,grab:[3,6],gracefulli:3,grad:[6,206,232,262],gradient:[6,7,8,12,13,128,133,224,232,242,243,262,284,299,331,335,371,372,375,428,444,463],gradient_correct:450,graduat:292,graft:223,grai:200,grain:[5,6,7,9,29,36,41,55,69,172,175,184,203,288,292,307,323,411,433,446,490,493],gram:[212,216,217,404,506],grama:[9,300,444],gran:[],grand:[3,203,210,239],granflow:5,granular:[],graph:11,graphen:485,graphic:11,grasp:5,gravit:242,graviti:[],grdient:209,great:[3,13,297],greater:[1,3,10,63,73,90,170,200,224,240,263,288,328,342,380,385,387,389,390,416,435,476,478,481,484,490,495,507,508],greathous:13,greatli:[124,495],green:[2,6,95,136,137,199,200,289,290,331,386],green_kubo:6,greenyellow:200,greffet:302,greg:[7,9],grest:[46,47,223,323,366,390,410,422,493],grew:73,grid:[3,12,42,64,124,160,171,174,197,220,250,302,323,335,336,363,365,366,475,478,481,483,485,490],grigera:6,grime:41,grmask:[3,507],gromac:[],gronbech:[247,365],groot:400,ground:[6,84,85,234,311,406],group1:[154,175,376],group2:[92,148,154,173,175,376],group2ndx:[],group:[],group_id:11,groupbig:323,groupid1:[253,307],groupid2:[253,307],groupid:481,groupnam:376,grouptyp:239,grow:[3,6,8,208,226,227,245,247,263,288,337,410,481,493],grow_arrai:8,grow_reset:8,growth:[6,330],grueneisen:9,gsmooth_factor:430,gstyle:[3,478],gtl:7,gtx285:14,gtx450:14,gtx460:14,gtx470:14,gtx560:14,gtx580:14,guarante:[67,71,81,97,114,121,172,175,196,231,298,364,368,491],guess:[3,196,294,482],gui:[7,11],guid:[1,17,41,80,82,104,105,106,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,203,256,257,313,314,315,316,319,336,440,448,450,454,455,456,457,458,459,491],guidelin:[1,8,14,15,16,17,18,19,365,463],guidlin:17,gullet:430,gulp:6,gumbsch:372,gunnel:433,gunsteren:[294,326,426],gunzenmul:7,gunzip:12,guo:[6,20,178,184,391,493],gwald:3,gyrat:[],gzip:[3,12,196,197,199,200,334,375,481,482,486],h12:409,h2o:[41,374],h5cc:198,h5md1:198,haak:[294,326],had:[3,6,11,13,61,65,196,197,200,201,215,218,223,224,240,241,243,247,248,249,261,263,265,266,267,268,269,270,271,282,283,284,286,293,294,323,326,327,328,335,400,403,410,460,483,487,490,496,499],hafskjold:6,half:[1,3,6,8,9,16,17,40,42,60,61,174,199,211,220,226,247,263,335,340,344,376,380,383,386,394,406,433,447,449,481,483,484,491,502],halfwai:[42,199,200,416],halperin:96,halsei:410,halt:[42,200,220,243,348,498],halv:199,ham:[38,57],hamak:[340,344,394,445],hamilton:72,hamiltonian:[203,241,263,264,327,406,490],hammond:[365,366],han:404,hand:[3,6,19,55,148,172,190,195,199,250,260,368,396,406,481,484,491,494],handl:[3,9,16,199,225,300,380,383,406,427,444,469,479,495],hang:[3,12,478,479],happen:[3,6,8,12,15,18,63,122,176,200,210,213,376,380,479,482,489],happi:8,haptic:244,hara:465,hard:[1,253,300,306,307,403,451,484],harden:[9,453],harder:[340,344,502],hardi:[209,248,365,366,502],hardwar:[1,9,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,115,118,149,159,178,179,181,182,183,184,186,187,189,190,192,206,219,226,233,238,242,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,299,307,309,310,326,328,339,343,349,351,352,354,355,358,360,365,366,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,436,437,438,440,445,446,453,462,463,464,465,466,469,471,472,473,484,494],hardwir:[3,17,341],hardy2:366,harm:383,harmon:[],harmonic_fix_wal:428,harpertown:18,harrison:382,hart:323,hartre:[383,404,406,433,506],hasan:9,hash:[40,481],hassl:306,hat:[6,10,262],have:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,43,44,46,47,48,49,50,52,54,55,57,59,61,65,66,67,68,69,71,72,73,74,75,77,79,83,90,94,95,96,98,108,109,110,111,112,115,118,119,120,121,122,136,146,147,148,149,150,151,152,153,155,159,161,164,165,167,168,169,170,172,173,174,175,176,178,179,181,182,183,184,186,187,189,190,192,195,196,197,198,199,200,201,206,208,210,211,212,213,216,217,218,219,220,221,222,223,224,226,227,232,233,236,238,239,240,241,242,243,244,245,247,248,249,250,253,258,260,261,263,265,266,267,268,269,270,271,272,273,277,280,282,283,284,285,286,288,290,292,293,294,296,297,298,299,302,305,307,309,310,317,319,323,324,326,327,328,329,330,334,335,336,337,339,340,341,342,343,344,345,346,347,348,349,351,352,354,355,356,358,360,365,366,368,371,372,373,374,375,376,377,380,381,382,383,384,386,387,388,389,390,391,392,394,395,396,399,400,401,402,403,404,405,407,408,409,410,411,412,413,414,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,435,436,437,438,440,441,443,444,445,446,450,451,453,462,463,464,465,466,468,469,471,472,473,475,476,478,479,481,482,483,484,485,486,487,488,489,490,491,493,495,496,498,499,500,502,506,507,508,509,510,511],haven:479,hayoun:302,hayr:247,hbcut:443,hbnewflag:443,hbond:[],hbond_cutoff:444,hcp:[66,69,75,368,430],hdf5:[9,198],he1:171,head:[6,21,179,349,408,412,443,444,496],header:[3,6,7,8,12,173,196,199,200,201,212,213,215,216,217,218,261,297,304,308,335,374,381,386,404,460,478,481,491,498],heal:490,heat:[],heatconduct:[],heavi:323,heavili:[42,220],heavisid:335,hecht:323,heenen:9,height:[199,227,293,375,408],heisenberg:9,held:[6,73,323,375,410],helic:184,helium:384,helix:[],hello:479,help:[3,8,12,14,15,16,17,18,19,196,224,226,261,363,386,464,466,509],henc:[1,3,13,20,21,26,32,35,36,72,73,114,152,154,162,179,212,263,300,323,339,340,344,346,349,351,355,358,366,396,408,426,441],henderson:54,hendrik:9,henin:[9,225],henkelman1:[262,375],henkelman2:[262,375],henkelman:[262,372,375],here:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,22,37,41,42,45,56,65,70,71,72,73,124,152,170,171,180,183,191,196,199,200,203,212,220,223,226,239,240,248,250,288,297,300,302,308,335,340,343,345,346,348,350,359,364,373,375,379,380,382,383,386,393,407,409,412,413,417,429,433,441,445,448,450,451,461,463,473,479,483,486,502,507],herist:336,herrmann:323,hertizian:341,hertz:[],hertzian:[6,341,410,461],hertzsch:410,hess:365,hessian:[5,372],heterogen:110,heurist:[336,482],hex:[3,172,368],hexagon:[69,96,430],hexahedron:197,hexat:96,hexord:[],hey:[116,147],hf4:171,hfo:395,hftn:[372,373,375],hg1:171,hg2:171,hgrid:323,hibb:290,hidden:[17,479],hienergi:346,hierarch:[7,490],hierarchi:[366,390,391,418,419,422,429,434,490],higdon:[9,427,428],high:[1,3,6,7,9,12,19,42,112,192,196,199,220,224,231,248,261,331,335,338,366,372,373,380,386,406,409,433,445,463,473,478,490,495,502],higher:[1,14,146,175,200,212,218,221,222,227,245,293,302,330,343,345,373,406,414,451,507],highest:[227,348,374,375,507],highli:[3,6,7,9,172,199,226,247,263,277,297,307,371,373,406,476,495],highlight:[6,7,10,13],hight:408,hilger:[365,366],hill:290,hill_height:13,him:9,hint:12,histo:[],histogram:[1,3,6,12,65,122,170,203,213,215,218],histor:407,histori:[],hit:[3,323,342],hmaktulga:[7,9],ho3:171,hoc:358,hocknei:[365,366],hofl:198,hoh:[6,396,418,422],hold:[6,33,61,73,185,212,226,255,291,306,307,320,373,375,410,426,472,492],holdem:306,holder2:366,holder:[365,366],hole:320,holian:[268,420],holm:[288,366],holonom:334,home:[11,12,201],homebrew:12,homepag:[197,199,244],homogen:[284,435],hone:290,honeydew:200,honor:201,hood:433,hook:[],hookean:410,hoomd:201,hoover:[6,7,8,162,203,230,247,248,263,264,265,266,267,268,269,270,271,282,283,284,285,286,290,294,302,307,326,327,328,333,400,502],hop:[223,375,386,451],hope:[5,13,17,42,43,220,489],hopefulli:[8,373],horizon:440,horn:6,host:[3,12,16,17,225,380],hot:[6,243,264],hotpink:200,hottest:331,hour:12,hourglass:[],hove:430,how:[],howev:[1,2,3,6,7,9,11,12,15,16,17,36,40,42,73,92,95,109,124,146,171,192,196,199,200,213,214,218,220,223,224,227,230,239,240,241,246,247,248,249,250,253,263,288,290,293,296,297,302,307,308,323,324,326,327,330,331,335,336,337,338,339,366,368,370,371,375,380,392,394,404,405,410,413,430,433,439,441,450,462,463,466,476,478,479,482,483,489,495,498,499,502,507,508],howto:[6,9,65,73,149,150,151,153,155,158,159,160,161,162,164,165,203,247,248,263,294,326,327,328,396,412,418,422,508],hoyt:209,hpc:[1,15],hsw:17,htm:404,html:[0,4,8,11,12,15,148,246,408,428,490,491],htmldoc:0,htst:495,http:[0,6,7,9,11,13,14,15,225,241,244,246,381,404,427,442,443,444],htype:[396,418,422,426],hubbard:397,huge:[12,174,277,323,481,486,498],huggin:[7,387,389,461],hugh:209,hugoniostat:[4,9,203,268],hugoniot:[261,268,297],hull:170,hummer:365,hundr:[7,14],hura:6,hwloc:[12,17],hybrid:[],hydrat:408,hydrocarbon:[382,395,406],hydrodyanm:41,hydrodynam:[7,9,41,104,106,250,252,253,254,388,427,428,448,450,461,491],hydrogen:[3,6,7,236,302,382,386,396,406,412,418,422,426,443,444,461,481,490,502],hydrostat:[3,9,224,263,268,294,307],hynninen:[397,408],hyoungki:432,hyper:290,hyperbol:397,hyperspher:146,hyperthread:[16,17],i_0:335,i_1:441,i_csid:6,i_flag1:296,i_mpi_pin_domain:16,i_myflag1:296,i_myflag2:296,i_n:441,i_nam:[119,196,296,325,491],ialloi:430,iatom1:121,iatom2:121,iatom3:121,iatom4:121,ibar:430,ibead:290,ibm:[196,365,433],icc:[10,12,433],icm:[9,244],ico:66,icosohedr:75,ictp:13,id1:[307,375,417,481,484],id2:[307,312,320,375,417,481,484],id_press:[224,261,263,265,266,267,268,269,270,271,294],id_temp:[223,224,261,263,265,266,267,268,269,270,271,282,283,284,286,294,326,327,328],idea:[1,3,6,11,12,42,147,199,200,220,245,288,312,323,331,366,435,489,502],ideal:[6,9,12,41,75,122,128,230,239,288,368,427,455,502],idealga:[],ident:[1,3,9,12,40,41,73,146,196,200,215,224,225,240,241,247,248,260,263,288,290,294,302,304,307,366,374,375,380,387,389,396,398,404,418,420,426,437,443,444,451,452,469,473,476,479,482,495,506,507,508,510],identi:380,identif:69,identifi:[1,3,6,12,38,41,57,72,170,172,192,235,304,323,346,412,417,430,463,476,478,481,484,495,496,498,500],idflag:293,idl:[18,495],idn:[307,375],idr:507,ielement:430,ieni:13,ifdef:[8,12],iff:248,iffp:479,ignor:[3,6,11,16,42,43,63,73,87,91,103,113,125,176,196,197,199,200,204,205,213,214,215,216,218,220,224,225,226,227,239,242,246,247,260,263,268,274,279,293,294,295,296,306,307,308,323,326,327,328,334,335,337,340,344,345,346,356,367,370,374,375,380,381,392,393,394,404,405,407,409,416,417,430,437,441,445,462,463,464,465,466,468,469,476,478,481,482,486,491,493,495,498,507],ihl:323,iii:[6,9,25,298,300,360,412,493],ijj:469,ijk:[354,358,360,386,441,469,478],ijl:358,ikeshoji:6,ikj:469,iko:2,ill:[152,162,212,298],illeg:3,illinoi:[244,365,366,427],illog:479,illustr:[1,6,8,11,12,16,17,18,19,288,290,375,413,479,507],ilmenau:[7,9,14],ilya:[7,9],imag:[],image2pip:199,imageint:3,imagemagick:[4,199],imagin:[320,334,386,405,413,414,416,431,432,437,441,462,464,465,466,469,493],imaginari:[6,96,239,290,481],imbal:[1,12,42,220,380,500],imbalanc:[42,220],imbu:323,imd:[],img:199,immedi:[0,2,3,8,12,172,221,222,227,310,319,324,325,342,478,479,481,483,495,507,510],immens:3,immers:[250,307],impact:[1,4,6,8,231,330,500],impart:[3,6,242,323,345],impei:[6,418],implement:[1,3,6,8,9,12,17,18,27,80,84,85,91,112,124,154,160,171,172,180,181,191,212,225,229,234,241,244,247,250,252,253,254,261,263,284,287,289,290,296,297,300,301,302,310,311,312,323,330,335,339,358,364,365,366,373,375,380,381,383,386,395,396,398,400,401,402,404,405,406,413,418,422,426,430,440,443,444,445,464,466,478,479,490,495,502,507,509],impli:[3,6,41,61,91,147,195,199,204,205,206,226,232,247,306,326,328,329,365,368,393,479],implicit:[],implicitli:8,implict:397,imporop:374,importannt:[],important:333,important_not:[],impos:[2,6,73,118,161,195,203,206,207,219,232,233,237,242,245,254,255,262,277,288,291,309,317,320,322,323,330,331,332,333,338,339,340,343,344,345,373,375,377,475,489],imposs:[1,3,481],improp:[],improper_coeff:[],improper_styl:[],impropercoeff:3,impropertyp:222,imprort:102,improt:[204,205],improv:[0,1,9,16,40,42,200,220,263,289,380,412,418,433,435,444,462,465],imrop:357,in3:171,inaccur:[1,3,6,175,261,365],inaccuraci:344,inact:412,inappropri:172,incid:[124,171,227],includ:[],includig:[348,364],inclus:[],incom:244,incompat:[3,11,414],incomplet:[3,11,481],incompress:[264,406],inconsist:[3,176,223,482],inconveni:368,incorpor:[297,386,397],incorrect:[3,155,247,430],incorrectli:[3,368,410,507],increas:[1,3,6,10,18,38,57,59,61,115,124,147,192,196,197,199,200,214,221,222,223,226,235,239,247,294,305,306,307,331,334,338,365,366,375,380,406,409,444,463,465,479,490,495,507],increasingli:406,increment:[3,11,134,206,207,219,220,227,232,236,263,293,312,313,346,364,379,416,451,476,479,493,495,507],incur:[14,17,212,216,217,236,335,478],inde:155,indefatig:7,indefinit:332,indent:[],independ:[4,6,9,11,12,16,17,42,61,65,95,123,125,158,172,195,203,211,212,213,215,216,217,218,220,223,224,225,226,227,240,242,247,248,250,253,263,289,294,298,302,307,308,312,322,333,335,368,410,433,476,479,498,508],indetermin:[196,197,200],index:[0,3,6,8,11,12,38,40,41,57,70,71,123,125,170,192,196,200,211,213,235,244,246,290,308,335,346,347,348,370,379,435,443,444,463,470,481,496,507],indianr:200,indigo:200,indirectli:[6,507],indistinguish:247,indium:452,individu:[],induc:[],industri:7,ineffici:[3,6,41,66,69,72,74,75,79,96,112,146,160,199,226,263,289,365,377],inelig:210,inerti:428,inertia:[],inexpens:[241,490],inf:[2,3,12,338,484],infer:[3,99,101,102,166,206,207,220,221,222,232,244,292,323,331,338,368,393,407,481,493,499],infil:[3,13,307,478],infin:[3,373,486,499],infininti:199,infinit:[3,227,238,245,247,250,289,323,335,341,342,366,368,406,481,485,506],infinitesim:6,inflect:[397,420,461],influenc:[3,9,42,82,154,260,293,365,366,435,464,465,466],inform:[0,1,2,3,6,7,8,9,11,12,13,15,17,40,42,43,61,63,64,65,70,92,121,123,124,171,172,178,196,197,198,199,200,201,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,236,237,238,239,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,262,272,273,274,275,276,277,278,279,280,281,287,288,289,291,292,293,294,295,296,298,299,300,301,302,303,304,305,306,307,308,309,310,313,320,321,323,324,326,327,328,329,330,331,332,334,337,338,339,340,342,343,344,345,347,363,365,366,369,372,373,374,375,376,378,380,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,436,438,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,471,472,473,478,479,481,482,483,485,486,488,493,495,496,498,500,507,509,510,511],infrequ:[6,263,400,476,495],infti:[397,427,428],ingtegr:386,inher:[365,373,435],inherit:[6,467],inhomogen:[18,335,435],inidividu:373,init:[3,8,305,451],init_fil:335,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,38,40,41,42,57,59,61,64,73,82,83,90,91,108,109,136,168,173,174,192,195,196,197,199,200,201,204,205,208,209,213,220,222,223,224,226,233,235,239,240,244,245,246,247,248,250,255,259,260,261,262,263,268,277,289,290,291,296,297,302,305,306,307,309,311,322,323,325,330,332,333,334,335,336,337,340,341,342,343,345,346,348,365,369,372,373,375,382,383,399,400,403,433,442,443,444,451,463,476,478,479,481,483,484,486,488,489,491,495,496,499,502,507,508,509,511],initial_integr:8,initial_integrate_respa:8,initialis:442,initialt:335,inlclud:11,inlcud:507,inlin:479,inner2:[391,411],inner:[3,8,16,196,245,348,364,371,372,373,375,379,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,440,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,468,469,470,471,472,473,490,495,507],inner_distance_cutoff:412,innergroup:253,innermost:[38,57,73,378,463,490],innernod:253,innner:424,inordin:336,inorgan:[6,469],inp:[225,348,452,469],input1:[67,70,71,81,97,114,119,120,121,123,125,325],input2:[67,70,71,81,97,114,119,120,121,123,125,325],input:[],input_doubl:3,inquir:313,insensit:12,insert:[3,5,7,8,12,61,172,203,227,239,245,293,365,452,460,479,485,502],insid:[2,3,6,8,11,73,135,141,172,196,197,200,211,216,217,227,228,236,239,245,250,253,293,307,323,340,342,343,344,345,346,363,368,420,479,480,481,483,484,491,495,507],insight:[6,13],instabl:[250,399,450],instal:[],instanc:[6,11,204,225,241,342,408,413,435,441,479,502],instantan:[6,65,223,224,240,241,263,268,289,294,297,302,304,307,330,487,499],instanti:[6,11,12,209,413,478],instead:[1,3,6,8,9,11,12,13,17,18,41,42,61,63,65,72,73,94,108,123,150,154,176,192,196,197,205,212,215,216,217,218,220,224,225,239,247,250,253,254,289,295,305,307,325,343,363,365,366,369,376,380,389,390,404,417,419,426,430,433,476,484,488,495,497,502,507],institut:[9,244,292],instruct:[],insuffici:[3,6,12],insult:263,insur:[3,6,11,12,17,40,41,63,75,107,109,172,173,192,196,197,199,200,206,221,222,227,232,233,236,237,239,242,247,259,295,296,305,307,323,335,340,344,345,346,348,364,374,376,380,394,409,413,439,445,463,474,478,479,481,482,486,489,490,498,499,507,508],int_max:3,integ:[3,6,8,11,12,40,41,43,66,70,72,73,112,119,121,123,125,146,170,172,175,176,178,182,183,187,192,195,196,199,200,210,212,216,217,221,222,223,227,229,237,239,240,241,244,247,248,249,250,289,292,293,296,297,302,307,323,325,327,330,334,335,354,365,368,388,400,402,403,416,430,443,444,448,450,452,476,478,479,480,481,489,490,491,495,498,507,508],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,214,240,442,481],intens:[1,3,6,9,65,68,76,77,90,93,94,95,98,108,109,110,111,118,120,122,123,124,125,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,167,168,169,171,203,212,213,215,216,217,218,220,221,222,223,231,236,243,253,261,263,268,304,307,308,323,331,335,337,338,498,499],intepol:507,inter:[14,18,43,63,64,152,175,176,196,223,247,249,262,299,307,365,375,386,491,502,507,509,511],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,34,37,40,41,43,45,51,53,55,56,59,63,65,67,71,74,79,81,91,92,96,97,112,113,114,116,118,121,122,128,129,130,131,133,134,135,136,137,138,139,141,142,143,144,146,147,148,150,151,165,166,170,173,174,175,176,177,178,180,184,185,188,191,196,197,203,204,205,221,222,223,238,239,244,245,247,249,253,277,288,290,292,293,298,300,306,307,314,315,323,324,330,335,339,340,341,344,345,350,351,352,353,355,357,359,365,366,373,374,375,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,439,440,441,444,445,446,448,450,451,452,453,460,461,462,463,464,465,466,467,468,469,470,471,472,473,476,479,481,483,485,486,490,491,493,498,499,502,509],interatom:[3,4,7,172,196,262,332,333,381,386,404,406,414,430,433,451,465,507],intercept:124,interchang:6,interconnect:18,interconvert:406,intereract:40,interesect:344,interest:[1,5,7,8,9,11,13,73,171,290,330,333,366,405,428,443,444,479,507],interf:380,interfac:[],interfer:[12,263,382],interg:[6,502],intergr:[490,494],interi:428,interior:[3,6,42,344,484],interlac:430,interleav:[6,172,489],intermedi:[6,12,61,199,262,288,358,375,479,480,489,493],intermix:476,intermolecular:382,intern:[],internal_element_set:209,internal_quadratur:209,internet:246,interpenetr:430,interpentr:[455,456,458],interpol:[6,15,38,57,105,192,199,200,209,235,250,288,365,366,375,386,435,444,457,463,464],interpret:[2,6,11,199,215,410,453,476,479,495,507],interrupt:297,intersect:[3,6,124,200,344,346,484],intersert:344,interspers:373,interstiti:[170,433],intertia:[3,98],interv:[3,6,95,198,213,247,263,297,302,303,315,451,457,476,495,507],intestieti:124,intial:[6,380,382],intiial:[42,486],intiti:[3,322],intra:307,intra_energi:239,intramolecular:[29,239],introduc:[6,9,96,112,199,263,297,302,307,358,365,381,396,406,418,422,426,462,495,507],introduct:[],intsal:[],intuit:368,inv:[124,171,308],invalid:[3,12,73,93,175,277,375,427,428,483],invari:[112,139,144,146],invent:310,invers:[],invert:[1,6,176,289],invis:344,invoc:[170,223,380,448,450,479],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,61,65,68,73,76,77,83,91,92,93,94,98,108,109,111,115,116,117,118,123,149,159,166,167,170,172,173,175,176,178,179,181,182,183,184,186,187,189,190,192,196,197,199,200,201,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,228,229,231,232,233,236,237,238,239,240,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,259,260,262,263,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,298,299,300,301,302,303,304,305,307,308,309,310,312,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,349,351,352,354,355,358,360,364,365,366,367,368,373,375,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,404,405,407,408,409,410,411,412,413,414,418,419,420,421,422,423,424,425,426,427,428,431,435,436,437,438,440,445,446,448,450,452,453,462,463,464,465,466,469,470,471,472,473,475,478,479,480,482,484,486,489,490,492,493,495,498,499,502,507,508],invokd:3,involv:[3,6,7,8,12,65,114,121,122,123,152,176,203,210,221,239,250,292,295,300,323,365,372,373,375,385,403,409,416,462,464,466,477,478,484,486,490,495,496],ioff:[374,481],ion:[6,7,9,154,287,320,335,366,386,397,407,408,430,433,451,461,466,473,481,502],ionic:[6,9,387,389,397,406,407,438,451,502],ioniz:[9,395,406],ionocoval:9,iparam:[3,222],ipi:[],ipp:[],ir3:171,ir4:171,irregular:[6,42,60,220,224,226,263,307],irrelev:437,irrespect:[427,428],irrevers:230,is_act:[3,507],is_avail:[3,507],is_defin:[3,507],isbn:472,isel:[365,366],isenthalp:[9,263,264,265,266,267],ismail:[365,366,390,422],isn:[3,8,11,12,243],iso:[3,224,230,248,263,264,265,266,267,268,269,270,271,294,302,307,502],isobar:[9,263,264,269,270,271,311,402],isodem:406,isoenerget:[9,311,402],isoenthalp:[311,402],isol:[3,175,346],isomorph:290,isotherm:[9,239,263,264,269,270,271,294,311,402],isotrop:[6,96,247,294,365,366,388,409,427,428],isovolum:308,isralewitz:312,issu:[1,3,6,9,11,12,13,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,61,73,75,83,108,115,118,149,159,178,179,181,182,183,184,186,187,189,190,192,199,206,209,219,223,224,226,227,232,233,238,239,242,247,261,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,290,294,296,299,307,309,310,322,326,327,328,333,339,343,345,348,349,351,352,354,355,358,360,366,374,375,378,381,382,384,387,388,389,390,391,392,394,395,396,399,400,404,405,407,408,409,410,411,412,418,419,420,421,422,423,424,425,426,427,431,436,437,438,440,445,446,453,460,462,463,464,465,466,469,471,472,473,481,483,484,490,493,498,499,507,508],ital:[443,444],itali:13,item:[6,7,8,42,196,200,220],iter:[3,6,12,40,42,65,198,206,207,219,220,224,230,232,237,245,289,298,299,307,310,330,346,348,364,371,372,373,375,379,451,476,486,490,495,499,507],ith:[73,123,125,211,212,213,214,215,216,217,218,325,337,499,507],itself:[2,3,4,6,7,8,9,11,12,13,18,43,61,95,113,163,196,198,199,200,201,213,214,225,230,248,258,262,301,307,335,346,348,374,375,396,407,409,413,414,463,479,485,488,489,493,507,511],itset:491,ityp:[3,121,122,172,208,222,300,470],itype1:122,itype2:122,itypen:122,ivector:8,ivori:200,ixcm:307,ixi:[43,98,307,374,507],ixx:[43,98,307,374,507],ixz:[43,98,307,374,507],iycm:307,iyi:[43,98,307,374,507],iyz:[43,98,307,374,507],izcm:307,izrailev:312,izumi:465,izz:[43,98,307,374,507],j0jt:95,j20:213,j_m:146,jac:[6,178,493],jackson:434,jacobi:3,jacobsen:372,jagreat:13,jame:[9,19],janssen:288,januari:430,jaramillo:[7,9,13,406],jarzynski:312,jatempl:9,jcc:9,jcp:340,jec:13,jeff:13,jello:263,jensen:[247,365],jeremi:[9,432],jerom:9,jewett:13,jiang:[248,502],jiao:[9,13],jiht:[7,9],jik:386,jim:7,jku:[7,9],jmake:12,jmm:146,joannopoulo:261,job:[12,62,310,489],jochim:[263,264],john:[7,9,13,198],johnson:[9,13],join:[6,484],joint:[3,292,412],jon:[9,72],jonathan:9,jone:[1,3,6,7,9,10,12,13,46,47,66,91,113,116,203,209,294,323,340,344,366,368,373,382,385,389,390,391,392,394,399,409,411,412,413,416,417,418,419,420,422,423,425,426,429,434,435,441,445,446,456,461,468,493,502],jonsson:[75,262,372,375,451],jorgensen:[6,189,396,418,422],joul:506,journal:[166,184,209,300,366,404,433,443,444,455,456,458],jparam:[3,222],jpeg:[3,12,199],jpeglib:12,jpg:[4,8,12,196,199,200,510],jpg_inc:12,jpg_lib:12,jpg_path:12,jpl:[7,9],jth:507,jtype1:122,jtype2:122,jtype:[3,122,222,470],jtypen:122,judg:495,judici:6,julien:9,jump:[],june:201,just:[3,6,8,11,12,13,17,19,22,29,43,45,61,63,95,113,116,122,147,150,151,165,176,180,196,199,212,216,217,226,230,236,253,260,294,296,307,330,335,346,348,350,374,375,380,382,385,393,413,441,468,479,483,485,486,488,489,500,502,507,510,511],justo:405,jusufi:[397,408],jut:344,jzimmer:9,k11:95,k22:95,k33:95,k_2:353,k_4:353,k_b:[],k_d:502,k_n:[],k_na:[],k_sigma:386,k_ub:20,kadiri:69,kalia:469,kamberaj:307,kapfer:112,kappa:[6,95,311,331,396,402,418,471,472],kappa_:335,karplu:91,karttunen:250,kate:[],kayser:397,kbit:200,kboltz:323,kbp:200,kbt:302,kcal2j:95,kcal:[244,490,502,506],kde:13,ke_eta_dot:263,ke_etap_dot:263,ke_omega_dot:263,keblinski:[396,451],kecom:152,keef:124,keep:[3,7,12,61,73,190,216,222,226,245,289,305,333,338,365,373,396,426,452,476,481,487,489,495,499,507],keflag:3,kei:[6,17,61,323,469,495],keir:13,kelchner:72,kelkar:338,kelvin:506,kemper:[299,395],kepler30:17,kepler32:17,kepler35:17,kepler37:17,kepler:[1,9,12,14,15,17,380],kept:[6,203,268,332,333,502],kernel:[7,13,17,41,105,135,141,209,240,241,315,433,454,455,456,457,458,459,481,491],kernel_radiu:[],keword:199,keyboard:12,keyword:[],keywrod:406,kforc:502,khaki:200,khersonskii:146,kick:[206,207,208,232,342],kilogram:506,kim:[],kimviri:[3,414],kind:[1,2,3,6,7,8,9,11,12,17,40,41,42,43,63,64,65,75,123,125,152,196,197,199,203,210,212,213,215,220,223,225,229,239,242,260,307,310,323,330,345,375,377,379,386,406,443,444,470,476,480,481,486,487,494,495,502,507],kinemat:[9,427,428],kinet:[3,6,8,9,65,86,87,88,89,91,95,99,100,101,102,103,118,147,149,150,151,152,153,154,155,157,158,159,160,161,162,164,165,203,210,212,224,230,239,243,247,259,261,263,264,265,266,267,268,269,270,271,294,297,323,331,338,339,373,406,476,495,499,502],kiss:12,kjl:358,klahn:334,klapp:365,klein:[6,9,209,225,263,264,285,307,418,446],kloss:7,kmax:[3,124,308,365],knc:17,knock:335,know:[3,11,12,42,65,113,122,203,230,246,248,277,323,373,405,414,467,479,482,485,490,502],knowledg:[4,8,199,414],known:[3,12,146,199,289,298,307,332,478,495,508],kohlmey:[7,9,13,18,365,366],kokko:[],kokkos_arch:17,kokkos_cuda:[9,12,17],kokkos_cuda_opt:17,kokkos_debug:17,kokkos_devic:17,kokkos_omp:[12,17],kokkos_pg:17,kokkos_phi:[12,17],kokkos_use_tpl:17,kokkow:9,kolafa:366,kollman:[6,178,493],kondor:442,kone:[332,333],kong2011:289,kong:[9,13,289],konglt:9,koning00a:332,koning00b:332,koning96:[332,333],koning97:333,koning99:332,kooser:13,koskinen:372,kosztin:312,krau:13,kremer:[46,47,493],kress:[431,432],kspace:[],kspace_modifi:[],kspace_styl:[],kspce:12,kspring:262,kstart:306,kstop:306,kth:[240,290],kub:20,kubo:[6,95,331],kumagai:465,kumar:[9,427,428],kuronen:441,kurt:292,l12:430,l_box:406,l_skin:335,la3:171,laa:9,lab:[5,7,9,12,117,440],label:[],laboratori:[0,84,85,234,261,297,311],lack:[3,261,406],lackmann:386,ladd:[284,333],lafitt:434,lag:335,lagrang:[136,137],lagrangian:[6,128,129,130,131,133,134,135,136,137,138,139,141,142,143,144,209,261,297,298,314,315,448,450,502],lagrangian_posit:[261,297],lagrangian_spe:[261,297],lai:475,lambda1:[464,465,466,469],lambda2:[464,465,466],lambda3:[464,466],lambda4:469,lambda:[91,117,124,166,171,250,308,332,333,335,381,405,426,462],lambda_fin:332,lambda_initi:332,lamda:[3,54,323],laminar:459,lamm:6,lammps2pdb:[6,13],lammps_clos:6,lammps_command:6,lammps_extract_atom:6,lammps_extract_comput:6,lammps_extract_fix:6,lammps_extract_glob:6,lammps_extract_vari:6,lammps_fil:6,lammps_gather_atom:3,lammps_get_coord:6,lammps_get_natom:6,lammps_n:[6,12],lammps_open:6,lammps_potenti:[393,395,492],lammps_put_coord:6,lammps_quest:[6,237],lammps_scatter_atom:3,lammps_set_vari:6,lammps_sppark:6,lammps_vers:6,lammpsplot:13,lammpspotenti:393,lammpstrj:[482,486,502],lammpsviri:[3,414],lamoureux:[6,230,467,502],landron:451,lane:1,lang:502,langevin:[],langevin_drud:[],langston:43,languag:[6,11,12,17,479,507],lanl:9,lapack:12,laps:336,laptop:7,larentzo:[9,84,85,234,311],larg:[0,1,3,5,6,7,8,9,10,12,13,14,16,18,40,41,42,60,61,72,73,115,122,147,152,155,160,172,173,174,184,192,195,196,197,199,200,212,216,217,220,223,224,226,227,231,239,250,263,277,284,289,292,293,297,302,304,305,306,307,310,320,323,331,335,336,338,340,344,358,365,366,371,373,376,380,394,400,406,409,410,417,433,435,439,445,463,476,479,481,483,484,488,490,495,498,500,502,508,511],larger:[1,2,3,6,11,12,13,40,42,57,61,72,73,122,172,174,199,213,215,218,227,243,250,263,284,285,293,298,302,306,307,308,311,319,323,330,335,339,340,341,344,365,366,371,372,373,375,376,377,380,386,394,396,397,406,410,418,422,428,435,439,460,461,468,481,485,486,489,490,495,507],largest:[3,6,12,40,73,170,172,231,365,373,377,460,463,481,483,489,490,501,507],laroch:302,laser:335,last:[1,2,3,5,6,11,12,15,38,43,57,61,63,73,116,123,147,170,192,196,197,199,200,201,202,212,213,215,216,217,218,220,231,262,305,308,320,323,348,363,373,374,375,376,380,384,385,386,387,394,395,400,401,402,404,408,409,411,412,416,419,421,423,424,425,428,434,436,445,451,453,460,463,467,468,471,472,476,477,479,482,486,488,489,493,495,496,499,500,507],lat:430,late:5,latenc:[10,244],later:[6,9,11,12,16,17,41,61,73,109,174,176,213,227,268,284,292,312,330,346,348,365,373,374,379,380,382,386,479,481,483,485,495,498,507,509],latest:[7,212,213,214,215,216,217,218,308,483],latex:8,latgen:289,latitud:146,lattc:430,latter:[2,6,9,11,12,14,15,16,17,42,43,91,150,200,204,205,211,212,216,217,220,224,245,254,263,265,266,267,269,270,271,292,294,296,300,307,323,339,344,364,374,386,388,389,390,391,392,399,416,418,422,426,433,438,446,451,467,476,478,479,484,487,498,507,510],lattic:[],launch:[1,3,6,11,12,17,18,380,478,479],laupretr:358,lavend:200,lavenderblush:200,lavgevin:226,law:[6,261,378,448,450],lawngreen:200,lawrenc:9,layer:[6,9,73,203,216,331,335,338],layout:[1,3,17,174,363,478,481,490],lb_fluid:250,lbl:[7,9,170],lbnl:9,lbtype:250,lcbop:[],ld_library_path:[11,12],ldfftw:12,ldrd:7,lead:[2,3,6,12,22,25,40,42,45,61,63,79,91,122,166,170,176,180,200,204,205,215,220,227,241,250,268,297,307,310,323,330,331,338,350,358,365,370,375,380,393,396,418,422,424,433,450,475,481,491,502,507,508],least:[3,6,12,18,73,124,171,198,210,216,241,292,296,339,376,380,413,463,468,479,507],leav:[3,7,11,12,17,21,42,59,147,162,179,220,224,227,263,265,266,267,269,270,271,293,294,307,310,349,435,481,485,493],lechman:323,lectur:312,led:[3,5],lee2:430,lee:[209,430],left:[6,11,12,42,113,148,191,199,200,223,245,287,323,346,348,368,481,483,488,507,511],leftmost:[42,220],legaci:[12,197],legal:7,lehoucq:440,leimkuhl:343,leiu:400,lemonchiffon:200,len:491,lenart:[397,408],length:[3,6,8,11,12,18,21,38,40,41,42,43,45,54,55,56,57,60,61,63,67,70,71,73,76,81,82,84,86,91,92,93,94,95,97,108,110,113,114,118,120,121,123,124,125,134,136,149,150,151,152,153,154,155,156,157,159,160,161,162,163,164,165,168,170,171,174,179,192,196,197,199,200,203,210,214,215,217,218,220,221,222,223,224,226,235,239,242,250,261,262,263,264,268,277,288,294,304,307,308,310,311,320,323,330,334,335,337,340,344,366,368,371,373,375,376,378,383,386,387,389,396,397,403,406,408,412,416,418,430,435,443,444,454,463,464,471,472,474,481,484,489,491,498,499,502,507],lengthi:239,lennard:[],lenoski:[431,432],less:[1,3,6,13,14,15,16,17,18,38,42,57,59,60,61,73,78,96,112,114,121,122,150,151,165,192,200,212,215,216,217,218,220,222,223,224,226,227,236,245,261,263,288,300,302,308,323,342,343,345,366,368,373,377,380,386,391,409,410,416,427,428,435,445,462,463,466,472,481,507,508],let:[1,12,38,57,155,183,192,213,235,310,323,341,380,394,463,490,494,502,509],lett:[146,160,241,248,250,261,302,312,332,333,372,386,404,406,409,426,452,502],letter:[2,12,42,59,61,200,220,229,230,248,290,348,379,442],leuven:9,level:[2,3,8,11,12,14,17,196,199,204,205,214,244,260,262,263,348,363,366,379,386,390,391,418,419,422,429,433,434,443,444,478,490,495,500,507],lever:460,levin:410,lewi:313,lexicon:7,lgr_po:[261,297],lgr_vel:[261,297],lgvdw:444,li1:171,liang:395,lib:[1,3,9,11,12,14,15,17,197,301,380,395,414,479,482],libatom:[9,442],libcolvar:12,libdir:11,libfftw3:12,libgpu:15,libjpeg:12,liblammp:[11,12],liblammps_foo:[11,12],liblammps_g:[11,12],liblammpscuda:14,libmpi:11,libmpi_stub:12,libmpich:12,libpackag:12,libpng:12,librari:[],librt:17,licens:[0,7,8,12,199],lie:[6,308],lieu:365,life:7,lifo:8,ligand:320,liggght:7,lightblu:200,lightcor:200,lightcyan:200,lightest:330,lightgoldenrodyellow:200,lightgreen:200,lightgrei:200,lightli:320,lightpink:200,lightsalmon:200,lightseagreen:200,lightskyblu:200,lightslategrai:200,lightsteelblu:200,lightweight:323,lightyellow:200,like:[3,4,6,7,8,9,11,12,14,16,17,18,40,43,55,61,156,163,199,201,206,224,225,227,230,232,244,247,248,249,261,263,264,269,270,271,276,277,282,283,284,285,286,288,294,296,297,298,302,307,308,311,323,325,326,327,328,329,330,331,338,339,340,343,344,345,348,365,368,372,375,380,386,394,399,400,402,406,407,410,412,413,423,424,430,452,463,466,471,472,478,479,481,482,483,484,486,491,496,499,500,502,507,508],likelihood:[124,171,223],likewis:[1,6,10,12,15,16,18,40,42,73,92,121,209,220,221,222,239,247,248,263,264,268,285,302,323,326,327,328,366,375,381,385,386,396,404,407,433,461,479,481,483,493,507],likhtman:214,lime:200,limegreen:200,limit:[],limit_eradiu:406,limit_veloc:[314,315],lindahl:365,line:[],linear:[],linearli:[10,123,200,226,289,340,342,343,345,374,375,377,481,507],lineflag:[6,481],lineforc:[],linen:200,linesearch:[8,12,371],ling:[9,13],lingo:[11,414],link:[5,6,7,8,9,11,12,13,14,15,17,22,37,45,56,65,180,191,197,199,203,222,244,248,292,301,303,312,320,350,359,383,393,430,442,443,444,461,467,479],linker:12,linkflag:[9,12,16,18],linux:[10,11,12,15,199,201,244],linuxamd64:482,liouvil:263,lip:13,lipid:[4,9,10,13,29,307],lipton:292,liquid:[6,7,9,29,40,41,42,61,91,96,147,158,170,220,224,226,239,263,294,297,302,330,399,433,435,438,465,490],lisal:[311,402,460],lism:9,list:[],listen:[244,246],listfil:417,liter:[481,492],literatur:[6,8,430,451,462],lithium:406,littl:[1,3,12,66,263,376,476,484],littmark:[430,461,466,473],liu:[412,444],livermor:9,lj1043:[],lj126:[],lj12_4:446,lj12_6:446,lj1d:289,lj6:3,lj93:[],lj96:[],lj9_6:446,lj_flag:382,llnl:[5,7,9],lmp1:11,lmp2:11,lmp2arc:[],lmp2cfg:[],lmp2vmd:[],lmp:[11,479,502],lmp_auto:12,lmp_cuda:[14,17],lmp_foo:12,lmp_g:[6,11,12,13,17,364],lmp_gpu:15,lmp_ibm:[12,364],lmp_inc:12,lmp_intel_cpu:[],lmp_intel_phi:[],lmp_kokkos_cuda:17,lmp_kokkos_omp:17,lmp_kokkos_phi:17,lmp_linux:[4,6,12],lmp_mac:12,lmp_machin:[1,12,14,15,16,380],lmp_mpi:[12,17,18,19,290],lmp_mvapich:17,lmp_omp:[],lmp_openmpi:17,lmp_opt:[],lmp_win_mpi:12,lmp_win_no:12,lmpptr:[11,479],lmpqst:237,lmpsdata:13,lmptype:[3,12,237],load:[1,3,4,6,7,9,11,12,16,17,18,42,199,201,203,220,244,297,380,395,478,479,500],loadabl:11,loca:200,local:[],localhost:244,localized_lambda:209,localonli:12,localvector:65,locat:[3,6,8,9,11,12,27,63,122,124,170,171,181,192,196,227,228,250,322,333,344,371,393,396,407,408,418,420,422,467,478,481,482,484,491,493],lock:[3,379,507],lockstep:[224,263,294,307],log:[],logarithm:[142,143,507],logfil:[0,3,6,12,295,369,477],logfreq2:507,logfreq:[200,488,497,507],logic:[7,11,12,17,42,172,220,346,348,476,478,479,482,490,495,507],lomdahl:[268,420],london:[13,239,444],lone:[443,444],longer:[1,3,6,8,12,13,55,122,196,200,211,212,213,214,215,216,217,218,221,239,247,288,292,297,307,310,330,340,344,346,371,380,382,410,451,478,486,490,495,504],longest:[42,220,221,376,468],longitudin:320,look:[1,3,6,8,11,12,18,55,63,196,199,202,393,452,463,502,507],lookup:[3,40,192,435,463],lookup_t:308,loop:[3,4,6,7,11,12,18,40,43,67,70,71,81,92,97,114,121,122,147,199,212,216,217,221,222,231,330,346,348,364,367,373,375,376,378,379,403,433,451,476,477,479,485,486,489,490,495,500,501,507,508],loopa:[348,364,379],loopb:[348,364,379],loopmax:451,loopvar:507,lopez:[263,264],lorant:298,lorentz:171,lose:[6,60,61,174,224,226,248,263,410,481],loss:[6,506],lossi:199,lossless:199,lost:[3,12,13,59,107,227,305,313,323,435,481,482,483,490,498],lot:[18,312,365],low:[1,3,6,7,12,42,155,170,196,199,220,230,248,284,302,307,331,338,366,433,444,463,472,495,502],lower:[2,3,6,9,11,12,42,59,61,73,92,148,161,195,199,200,213,214,215,216,217,220,224,230,244,247,248,250,263,297,302,331,338,340,341,346,347,365,368,379,397,430,495,503,505,508],lowercas:199,lowest:[146,348,374,491,495,496,507],ls_:140,lsfftw:12,lsurfac:335,lu3:171,lubric:[],lubricateu:[],lubricuteu:274,lucki:12,luigi:13,lumped_lambda_solv:209,lussetti:331,lustig:[7,13],lybrand:366,lyulin:358,m4v:199,m_c:[],m_d:502,m_eff:[341,410],m_fill:3,m_i:321,m_lambdai:440,m_taubi:440,m_u:250,m_v:250,m_yield_stress:440,mac:[12,14],mac_mpi:12,mach:[9,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,313,314,315,316,319,491],machin:[1,3,4,6,7,9,10,11,12,14,15,16,17,18,19,196,197,199,244,263,336,365,371,373,378,380,433,478,483,488,489,490,508,511],mackai:[9,250,252,253,254],mackerel:[6,20,178,248,391,493,502],maco:199,macro:17,macroparticl:403,macroscop:[7,242,261,440],made:[3,6,11,12,15,16,33,42,43,51,66,173,185,196,199,201,203,204,205,210,220,227,231,244,253,293,301,305,307,333,346,356,376,380,409,410,413,443,445,453,478,485,491,494,503,505,508,509],madura:[6,418],magazin:404,magda:340,magenta:200,magic:[3,11],maginn:[166,338],magnitu:325,magnitud:[6,72,110,114,119,148,172,195,196,197,200,227,228,242,243,245,247,312,320,322,323,330,341,366,373,399,410,491],mai:[0,1,2,3,6,7,8,11,12,13,14,15,16,17,18,29,38,40,41,42,57,60,61,63,65,67,70,71,73,81,90,91,92,93,94,96,97,107,108,110,112,113,114,115,116,118,119,120,121,123,124,125,146,147,150,151,152,160,161,165,166,170,171,172,173,174,175,176,191,192,195,196,197,198,199,200,201,203,204,205,206,208,210,212,213,214,215,216,217,218,219,220,221,222,224,226,227,230,231,232,235,236,239,240,241,243,244,245,247,248,249,250,251,253,258,259,260,261,263,264,268,277,280,289,290,293,294,295,296,297,298,299,302,304,305,306,307,308,309,310,312,314,315,317,323,325,326,327,330,331,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,363,364,365,366,368,371,372,373,374,375,376,377,378,380,383,385,386,394,400,406,410,413,414,416,424,426,428,430,431,432,433,435,443,444,446,452,460,463,469,473,476,477,478,479,481,482,483,484,485,486,487,488,489,490,491,493,495,496,498,499,502,507,508,509,511],mail:[3,7,9,12,346],main:[3,6,8,11,12,197,244,250,307,332,333,404,451,467,479,496],mainboard:1,mainli:[380,438],maintain:[8,9,13,40,157,222,226,284,323,336,372,381,404,490,493],major:12,make:[],makefil:[3,7,9,11,12,13,14,15,16,17,18,19,196,197,366,380,433,479],makelist:12,maks:410,malloc:[3,12],manag:[5,8,12,196,244,290,325,490],manbi:452,mandadapu:209,mandatori:[8,196,225],manh:386,mani:[1,2,3,4,5,6,7,8,9,12,13,14,15,16,17,18,38,40,41,42,43,57,63,65,70,73,92,95,107,108,122,148,152,172,173,192,195,196,197,198,199,200,201,203,204,205,206,210,211,212,213,214,215,216,217,218,220,221,222,223,224,226,227,235,236,239,240,243,244,250,251,259,261,263,264,268,277,287,288,289,293,296,298,299,300,302,304,307,308,310,323,334,335,337,346,348,365,373,375,376,378,380,393,395,403,406,408,412,413,451,452,461,463,464,466,479,481,483,485,486,488,489,490,491,493,494,495,496,500,507,508,511],manipul:[12,42,220,244,396,441,492],manner:[2,3,6,9,11,17,42,147,168,199,204,205,206,207,215,220,226,231,232,237,243,247,248,263,269,270,271,282,283,284,286,301,326,327,328,331,332,333,338,340,344,348,366,374,375,379,380,404,406,413,416,427,468,476,478,481,482,483,484,486,490,495,496],manolopoulo:246,mantissa:3,manual:[0,1,3,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,44,46,47,48,49,50,52,54,55,57,60,65,70,73,115,118,124,149,150,151,153,154,155,158,159,160,161,162,164,165,171,178,179,181,182,183,184,186,187,189,190,192,196,197,199,201,206,216,219,226,233,238,242,246,247,248,262,263,265,266,267,268,269,270,271,272,273,275,278,280,281,282,283,284,286,294,296,299,307,308,309,310,326,327,328,338,339,343,348,349,351,352,354,355,358,360,366,375,379,380,381,382,384,385,387,388,389,390,391,392,394,395,396,398,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,436,437,438,440,445,446,453,462,463,464,465,466,469,471,472,473,476,484,490,494,495,496,499,507],manybodi:[],map:[2,3,11,12,17,18,40,61,66,73,124,128,146,160,171,172,195,199,200,209,216,289,306,365,366,368,375,381,382,386,395,404,405,407,413,414,415,430,431,432,435,437,441,442,443,444,451,452,460,462,463,464,465,466,469,478,481,483,495,507],map_fil:289,mapflag:12,mara:[9,451],march:430,margin:495,mari:13,mark:[411,426,448,450,451],marker:295,maroon:200,maroonmpi:11,marrink:411,marsaglia:[3,240,241,247,248,302],marseil:9,martin:[289,430],martinez:210,martyna:[263,264,307,490],mashayak:17,mask:[3,288,507],mask_direct:209,mass:[],mass_matrix:209,massdelta:310,massiv:[0,199,250,290,331,338],massless:[6,248,366,396,418,422,426,502],masstot:307,master:[3,375,476,495],mat:[69,209,395,465],match:[3,6,8,9,11,12,17,38,42,57,61,73,122,155,192,200,201,220,223,226,235,244,263,264,284,304,308,323,330,365,366,386,412,424,430,442,443,444,463,475,479,481,482,483,486,490,495,502,507],matchett:43,mater:[75,381,432,441,451],materi:[6,7,9,61,72,130,131,175,208,209,226,239,245,261,288,294,302,331,335,341,396,404,405,406,410,414,430,431,433,440,443,444,447,448,449,450,476,481,495,502,506],material_fil:209,math:[],mathemat:[124,146,171,172,195,204,205,206,207,219,224,232,240,242,243,245,247,248,295,309,317,326,327,328,340,343,345,452,477,484,491,508],mathrm:[],mathtt:[],matlab:[],matric:[9,146,241,289,409],matrix:[3,6,9,95,170,213,224,241,289,298,365,368,433],matter:[6,9,12,40,59,61,73,154,216,335,376,382,398,404,406,430,446,451,464,466,469,473],mattox:9,mattson:[84,85,118,147,234,311],max2theta:171,max:[3,6,8,12,15,18,73,123,200,215,220,222,224,227,293,310,323,348,368,371,373,375,376,380,451,476,481,495,499,507],max_alpha:8,max_cell_s:403,max_group:3,max_nn:315,max_travel:316,max_vel:[314,315],max_veloc:315,maxangl:239,maxbodi:3,maxbond:[3,222],maxedg:170,maxev:[373,476,495],maxfoo:8,maxim:[330,375],maximum:[3,6,8,12,15,17,25,42,43,46,54,55,59,61,63,96,112,122,123,124,127,170,171,173,174,195,196,208,213,214,215,220,222,226,227,231,239,277,288,293,298,310,313,314,315,323,336,365,366,371,375,376,380,383,386,403,408,427,428,451,481,484,489,499,507,508],maxit:[298,373,476,495,499],maxsize_restart:8,maxspeci:3,maxwel:[17,287],maxwell50:17,maxwell52:17,maxwell53:17,maxx:441,mayb:13,mayer:[7,387,389,451,461],mayo:[6,7,13,25,360,412,493],mbt:179,mbyte:[12,302],mcdlt:[162,243],mcgraw:290,mdash:502,mdatom:239,mdf:[],mdnvt:239,mdregion:209,mdtemp:239,mdump:[42,220],meain:[],meam:[],meam_sw_splin:432,meamf:430,mean:[1,2,3,4,6,7,8,10,11,12,17,22,34,37,38,39,40,42,43,45,53,55,56,57,58,59,61,63,65,70,73,74,78,79,86,88,89,91,95,96,108,109,110,112,118,119,120,121,122,123,146,147,149,150,151,153,154,155,158,159,160,161,162,164,165,166,172,173,175,176,178,180,188,191,192,193,194,195,196,197,199,200,201,203,204,205,208,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,232,235,237,239,240,241,242,243,245,247,248,249,253,260,263,265,266,267,268,269,270,271,277,282,283,284,286,288,290,292,293,294,296,302,304,305,307,309,310,312,317,320,323,325,326,327,328,330,331,334,335,337,338,339,340,341,342,343,344,345,346,350,351,352,353,355,357,359,361,365,366,368,370,371,373,374,375,376,378,380,383,387,389,390,391,393,396,400,403,404,406,409,410,412,413,416,418,419,422,429,430,434,435,438,439,441,443,444,445,446,460,462,463,464,465,466,468,472,475,476,478,479,481,482,483,484,485,486,487,488,489,490,491,492,493,495,496,498,499,502,506,507,508,509,511],meaning:[122,130,131,133,136,140,413],meaningless:[69,330],meant:[6,307,467,485],measur:[],meaur:500,mech:440,mechan:[6,8,9,11,12,16,17,41,84,85,132,148,209,234,243,290,301,386,406,414,420,433,448,450,475,479,481],mechanic:301,mechanim:128,meck:112,media:199,medium:472,mediumaquamarin:200,mediumblu:200,mediumorchid:200,mediumpurpl:200,mediumseagreen:200,mediumslateblu:200,mediumspringgreen:200,mediumturquois:200,mediumvioletr:200,mee:330,meet:[3,12,173,199,200,222,223,336,486],mehl:381,mei:429,meloni:40,melros:[427,428],melt1:201,melt2:201,melt3:201,melt:[4,10,223,289,386,433,465],mem:15,member:[175,292,386],membran:[29,287,472],memori:[1,3,5,6,7,8,9,12,15,16,17,18,40,41,62,73,200,212,214,216,217,240,241,302,335,363,376,380,386,435,439,444,478,481],memory_usag:8,mendelev:404,mention:[1,6,7,11,41,43,226,243,250,268,340,368,375,382,443,444,483,507],menu:[199,244],mep:[262,375],mer:[4,10,223],meremianin:146,merg:[5,481],merz:[6,178,493],mescscop:440,mesh:[],meshless:9,meso:[],meso_:[],meso_cv:[],meso_rho:[],meso_t:[],mesocop:41,mesoparticl:[234,235,402],mesoscal:7,mesoscop:[7,104,105,106,256],mess:[3,491],messag:[],met:[8,42,122,220,348,364,366,373,375,379,468,489],metadynam:[9,13,225],metal:[3,5,7,9,10,41,61,73,161,172,208,209,216,217,226,227,243,245,297,298,302,339,340,342,343,345,366,368,377,381,382,386,395,404,405,406,407,413,415,430,431,432,433,441,442,451,462,464,465,466,469,484,498,499,501,506],meter:[377,506],methan:[297,302],methanol:4,methin:358,method:[1,3,5,6,7,8,9,11,12,13,16,17,19,38,40,41,42,57,66,91,95,116,147,192,203,204,205,209,213,214,220,225,235,237,247,250,254,258,261,263,289,290,297,298,299,300,302,307,310,311,312,330,331,332,333,338,365,366,371,372,373,375,380,381,383,386,395,396,404,406,407,430,431,432,435,441,451,461,463,469,476,478,479,481,482,484,495,502],methodolog:[6,75,147,290,365],metin:[7,9],metric:[3,10,66,484,499],metropoli:[210,239,496],mezei:91,mf1:201,mf2:201,mf3:201,mg2:171,mglob_default_function_attr:[9,12],mgoh:437,mgpt:[],miai:302,mic:[9,12,17],micel:[4,9,13,321],micelle2d:[],michael:[9,13,432],michel:13,mickel:112,micro:[3,501,506],microcanon:[272,273,275,276,278,280,281],microelast:440,micromet:506,micropor:239,microscal:427,microsec:506,microsecond:506,mid:[5,9,61,226,433,460],middl:[3,6,8,16,22,42,45,79,91,122,161,166,176,179,180,200,204,205,211,220,293,305,306,307,331,338,349,350,370,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,428,429,430,431,432,433,434,436,438,440,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,468,469,471,472,473,475,479,489,490,491,507],middlebondtors:[3,179,481],midnightblu:200,midpoint:460,mie:[],might:[3,4,6,7,8,12,14,25,73,154,237,239,241,307,451,479,489,507],migrat:[3,8,17,42,43,61,63,67,71,81,97,114,121,196,203,220,288,296,302,323,365,377,380,489,509,511],mikami:[6,263,264],mike:[7,9,13,15,16],mil:[9,404],mill:372,miller:307,million:[3,7,10,40,42,73,220],mimic:[6,43,55,248,261,293,396,408,418],mimim:[224,375],min2theta:171,min:[3,4,6,8,12,123,146,200,215,365,368,451,460,476,495,507],min_cap:3,min_cg:8,min_clearstor:8,min_dof:8,min_modifi:[],min_nn:315,min_popstor:8,min_post_forc:8,min_pre_forc:8,min_pushstor:8,min_setup:8,min_setup_pre_forc:8,min_step:8,min_stor:8,min_styl:[],minarea:170,mincap:444,mind:[7,240,289],mine:[12,92,162,163,203,346,504],minim:[],minima:[184,360],minimi:[375,468],minimizaiton:375,minimizi:302,minimum:[3,12,25,26,27,43,46,59,61,73,90,110,123,170,171,173,175,181,195,196,199,208,215,224,225,231,246,262,304,306,308,313,315,319,323,340,344,348,360,365,368,371,372,373,375,376,391,406,409,411,412,418,420,422,427,428,444,446,460,476,489,495,507,508],minlength:170,minmiz:[8,224],minn:9,minord:[3,365],mintcream:200,mintmir:[7,298,396,461],minu:[12,61,152,226,348,375,507],minut:[4,8],mirror:[63,342],misc:[],miscellan:[2,209],mise:[139,144],mishin:[381,461],mismatch:3,miss:[3,5,12,175,215,239,277,302,323,417,435,498,499],mistak:[3,507],mistakenli:3,mistyp:3,mistyros:200,mitchel:[6,117,154,365,366,398,440],mitchell2011:440,mitchell2011a:440,mitig:263,mitur:[],mivi2:302,mix:[1,3,6,9,14,15,16,73,121,154,215,216,336,365,366,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,474,479,481,494,502,509],mixtur:[6,41,263,307,323,345,394,430,481],mixture_ref_t:430,mjpeg:199,mkdir:492,mkl:12,mkmk:289,mkv:199,mldivide3:3,mlpark:7,mlutipl:218,mn2:171,mn3:171,mn4:171,mo3:171,mo5:[171,433],mo6:171,mobil:[6,110,147,149,150,151,153,158,165,199,307,346,347],moccasin:200,mod:[],mode:[1,3,6,9,11,12,13,14,15,16,17,18,63,68,77,92,94,98,109,111,120,122,123,148,152,167,169,170,171,196,197,199,200,215,218,225,226,237,241,263,290,302,312,323,363,365,377,380,396,406,433,451,478,483,488,490,499,506,507,511],model:[],model_ar_p_mors:414,modern:[12,247,249],modest:[1,378],modif:[6,13,91,430,433,445,466,502],modifi:[],modify_param:8,modin:209,modul:[3,9,11,12,13,225,302,479],modular:8,modulo:[3,507],modulu:[294,410,430,440,447,449],moementum:260,mofil:482,mol1:507,mol:[3,9,73,119,172,174,175,196,197,200,225,227,239,244,247,293,296,307,310,319,325,399,409,446,490,491,502,507],molchunk:[68,77,94,98,109,111,152,167,169,212],mole:[210,404,506],moleclu:[221,222,227,236],molecul:[],molecular:[0,2,3,5,6,7,8,9,12,13,40,41,54,73,114,119,121,149,150,151,153,155,158,159,160,161,164,165,172,173,174,175,176,184,196,197,198,201,209,222,225,239,246,289,290,297,301,302,306,312,334,335,366,374,383,384,386,390,403,406,413,461,481,482,483,485,486,490,491,493,499,501,502,507],molfil:[],molfrac:[227,293],molnar:312,molp:115,moltempl:[],molybdenum:433,mom:[6,95,306,508],momementum:[150,151,265,266,269,270,273,274,275,282,283],momemtum:68,moment:[3,6,9,41,43,86,88,89,111,119,150,165,172,194,196,197,247,250,253,263,280,293,307,321,325,374,399,405,451,481,491,502,506],momenta:[241,274,338,406],momentum:[],momon:223,monaghan:[9,455,456,458],monitor:[3,6,12,101,102,155,224,226,227,236,244,247,261,263,293,295,297,307,310,323,373,375,399,499],mono:[75,427],monodispers:[3,341,388,410,427,428],monom:[13,55,223],monoton:[3,235,312,334,375,495],monoval:366,mont:[6,7,9,203,210,223,239,307,330,403,461],montalenti:[476,495],month:0,moor:[17,84,85,147,234,311],more:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,42,43,44,45,46,47,48,49,50,51,52,54,55,56,57,60,61,63,64,65,66,67,69,70,71,72,73,74,79,80,81,82,87,90,91,92,94,96,97,101,102,103,104,105,106,107,108,110,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,154,155,156,158,159,160,161,163,164,165,166,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,189,190,191,192,195,196,197,198,199,200,201,203,204,205,206,207,208,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,235,236,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,278,280,281,282,283,284,285,286,288,289,290,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,309,310,311,312,313,314,315,316,317,319,323,325,326,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,358,359,360,363,365,366,368,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,436,437,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,476,477,478,479,481,482,484,485,486,487,488,489,490,491,492,493,494,495,496,498,500,502,507,508,509,510,511],morefoo:8,moreov:[221,222],moriarti:[9,433],moriarty1:433,moriarty2:[9,433],moriarty3:433,morri:[],morriss:[160,284],mors:[],morse_f:463,mosel:372,mosi2:430,moskalev:146,most:[0,1,2,3,4,5,6,7,8,10,11,12,15,17,18,19,37,40,42,56,73,108,114,160,191,196,197,199,200,212,215,216,217,218,220,221,222,224,243,263,264,290,295,296,297,298,307,308,336,338,346,348,359,366,372,376,378,380,382,406,409,430,442,443,444,466,476,477,478,490,495,499,500,507,509],mostli:[8,9,11,13,73,174,199,376,481,490,493,507,510],motiion:6,motion:[3,6,7,9,43,90,102,108,149,150,151,153,155,157,158,159,160,161,162,164,165,226,230,241,250,253,254,260,263,264,268,284,288,290,292,302,306,307,311,331,335,341,344,375,399,406,427,428,484,490,502],motiv:288,mous:244,mov:199,move:[],move_tri_surf:[],movement:[3,6,12,260,330,373,499],movi:[],mp4:199,mpeg:199,mpg:199,mpi4pi:11,mpi:[],mpi_allreduc:[307,479],mpi_barri:1,mpi_cart:478,mpi_cart_cr:478,mpi_cart_get:478,mpi_cart_rank:478,mpi_cart_shift:478,mpi_comm:6,mpi_comm_world:[],mpi_fastmgpt:433,mpi_get_processor_nam:478,mpi_inc:12,mpi_lib:12,mpi_lmp_bigint:3,mpi_lmp_tagint:3,mpi_path:12,mpi_wtim:12,mpicc:11,mpich2:12,mpich:[12,14,15,16,17,18,380],mpich_icc:16,mpicxx:[12,17],mpiexec:[12,14,15,16,17,18,380],mpiio:[],mpirun:[1,6,11,12,14,15,16,17,18,19,290,364,380],mplayer:199,msd:[],msi2lmp:[],msi:13,msm:[],msmse:[124,171,308],msse3:433,msst:[],mtchell2011:440,mtchell2011a:440,mtd:225,mth:[8,125,200,498],mtk:[263,264,268],mtotal:374,mu_j:29,muccioli:409,much:[1,3,6,11,40,148,196,197,199,214,224,297,330,376,377,380,409,445,476,479,495,500,502,507],mui:[119,196,197,232,325,481],mukherje:[7,9,292],mulder:334,muller:[6,95,203,331,338,434],mult:8,multi:[],multibodi:[3,63,292],multicent:406,multicor:[1,478,494],multidimension:13,multielectron:383,multilevel:[365,366],multiphys:11,multipl:[],multipli:[3,91,95,122,180,191,204,205,213,247,250,288,294,368,373,382,481,507],multiprocessor:380,multiscal:11,multisect:[42,220],multistag:91,multitud:7,mundi:285,munich:9,murdick:386,murti:465,murtola:365,must:[1,2,3,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,54,55,57,58,59,61,63,64,73,86,88,90,91,109,113,115,118,121,122,123,124,125,150,154,161,165,170,171,172,173,174,175,176,178,179,180,181,182,183,184,185,186,187,189,190,192,193,194,195,196,197,198,199,200,201,204,205,206,208,209,210,211,212,213,215,216,217,218,219,220,221,222,223,224,226,227,230,232,235,237,239,240,241,243,244,245,246,247,248,250,251,252,253,254,258,259,260,261,262,263,264,265,267,268,269,271,273,274,275,277,280,282,286,288,292,293,294,295,296,297,298,300,302,304,305,306,307,308,309,310,311,317,319,320,322,323,326,327,328,330,331,333,334,335,337,338,340,341,342,343,344,345,346,348,349,350,351,352,353,354,355,356,358,360,361,365,366,368,370,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,476,477,478,479,481,482,483,484,486,488,489,490,491,492,495,496,498,499,502,506,507,508,509,511],mutli:6,mutlipl:481,mutual:[3,368,500],mutut:490,muvt:239,mux:[119,196,197,199,232,325,481],muz:[119,196,197,232,325,481],mv2_comm_world_local_rank:12,mvapich2:[17,380],mvapich:12,mxn:[12,290],my_ga:239,my_one_wat:239,my_post_process:492,my_qeq:298,my_setup:492,my_swap_region:210,myblock:[227,293],mybox:174,mychunk1:120,mychunk2:120,mychunk:[6,68,77,94,98,109,111,152,167,169],mycmap:481,mycom:215,mydump:[196,200],myer:[5,7],myfil:[478,507],myfix:[210,496],myflux:95,myforc:[196,197,510],myhug:268,myke:95,mymol:[41,310,374],mympi:11,mymultipli:[479,507],myn:479,mype:95,mypi:507,mypress:258,myramp:147,myrdf:[122,218],myreg:368,myregion:346,myrigid:[87,103,293],mysocket:246,myspher:[200,344],mystr:348,mystress:95,mytemp:[2,107,149,150,151,153,155,156,158,160,165,258,348,364,379,498,508],myz:481,n_dephas:476,n_element:198,n_f:[297,302],n_hbond:412,n_ij:410,n_ion:335,n_k:240,n_particl:84,na1:171,nabla:335,nacl:[4,6,430],nacl_cs_x0:6,nakano:[298,300,375,469],namd:[7,9,196,244],name1:[166,226],name2:[166,226],name:[0,1,2,3,5,6,8,9,11,12,13,33,43,51,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,185,195,196,197,198,199,200,201,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,265,266,267,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,336,337,338,339,340,341,342,343,344,345,346,347,348,356,363,364,366,367,369,374,375,379,381,382,386,389,404,405,407,409,410,413,414,415,417,430,431,432,437,441,443,444,451,452,462,464,465,466,467,469,470,474,478,479,481,482,483,484,488,491,494,496,497,499,502,507,508,509,510,511],namespac:[6,8,12],nan:3,nangl:[3,481],nangletyp:[374,481,491],nano:[307,501,506],nanoindent:72,nanolett:307,nanomet:[196,200,506],nanoparticl:[220,307],nanosec:506,nanosecond:506,nappli:237,narea:3,narrow:[6,192],narulkar:[464,466],nasa:7,nasr:289,natdef:3,nation:[0,7,9,12,117,440],nativ:[1,6,7,9,12,16,17,196,201,482],natoli:[9,19],natom1:121,natom2:121,natom:[3,6,11,40,374,479,481,498,499,507],nattempt:293,natur:[6,9,146,226,263,288,302,341,404,406,407,430,441,478,507],navajowhit:200,navi:[200,404],navier:250,nb3:171,nb3b:[],nb3bharmon:437,nb3d:9,nb5:171,nbin:[122,215,216,217,331,338],nbodi:[253,307,433],nbond:[3,119,481],nbondtyp:[200,374,481,491],nbot:386,nbounc:323,nbrhood_cutoff:444,nbtype:121,nbuild:499,ncall:237,ncbin:73,nchar:200,nchunk:[3,6,68,73,77,94,98,109,111,120,152,167,169,212],ncoeff:452,ncorr:214,ncorrel:214,ncount:[212,213,214],nd3:171,ndanger:499,nden:[6,95],ndihedr:[3,481],ndihedraltyp:[374,481],ndim:216,ndirango:307,ndof:[263,268],ndoubl:481,ndp:502,ndx2group:[],ndx:347,neal:307,nearbi:[7,64,173,227,260,299,323,344,376,382,427,428,461,472,502],nearest:[3,72,73,75,96,112,170,173,250,262,288,330,344,365,417,430,451,463,507],nearli:[6,9,18,55,61,220,247,323,406,433,435,476,479,485,493],neb:[],neb_combin:375,neb_fin:375,neb_log:495,neb_step:495,neb_styl:495,necessari:[6,9,11,12,13,15,17,33,63,91,180,185,191,201,220,224,225,239,240,301,311,323,336,346,365,380,426,433,435,451,481,482,486,489,490,491,495,502,510],necessarili:[12,302,330,351,352,353,355,368,435,508],necessit:296,need:[1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,33,37,38,40,41,42,43,51,55,56,57,60,63,65,66,69,72,74,75,79,86,95,96,107,109,112,115,118,134,146,147,149,150,151,152,153,155,158,159,160,161,162,164,165,172,174,176,178,180,185,191,192,195,196,198,199,200,204,205,206,207,209,210,212,213,214,215,216,217,218,220,221,222,224,225,226,230,232,235,237,238,239,243,244,246,247,248,250,256,257,263,277,289,293,294,296,302,306,307,312,319,323,331,334,335,337,338,339,340,346,356,359,365,366,374,375,376,377,380,381,382,383,384,386,387,388,389,390,391,392,394,395,396,398,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,468,469,471,472,474,476,479,481,482,483,484,486,488,489,491,493,494,495,496,502,507,509,510,511],needless:[6,376],neeed:9,neelov:366,neg:[3,6,12,27,47,67,71,93,107,114,121,146,147,174,176,181,183,192,199,224,226,227,240,268,288,312,320,334,338,340,345,365,372,407,421,430,461,481,484,500],neglect:[412,428],neglig:[6,11,91,263,462],neigh:[],neigh_modifi:[],neighbor:[],neighborhood:[26,96,128,452],neighbour:248,neighobr:[6,396,418,422],neither:[2,3,12,42,65,197,209,223,226,227,382,388,406,427,428,486],nelem:452,nelement:[381,404],nelson:[96,112],nemd:[],nest:[2,348,362,379,507],net:[3,6,11,40,90,92,153,164,243,288,298,307,428,444],netpbm:199,network:[12,196,221,222,244,478],neumann:365,neutral:[3,92,239,365,396,418,451],never:[7,12,65,73,203,213,224,239,263,288,310,325,336,340,343,345,365,376,404,430,452,469,478,481,495,498,507],neveri:[3,8,73,206,211,212,213,214,215,216,217,218,221,222,223,250,251,289,298,299,300,303,304,308,331,337,338,375,451,486,495],newatom:227,newer:[12,212,430,507],newfil:[362,364],newli:[227,293,502,508],newlin:200,newn:307,newt:159,newtemp:[65,107],newtion:[386,433,441],newton:[],newtonian:240,newtyp:[3,222],next:[],neyt:330,nfile:[3,38,57,192,196,197,200,235,463,483,488,511],nfirst:486,nfirt:486,nfreak:308,nfreq:[40,73,211,212,213,214,215,216,217,218,220,304,308,486],nghost:[3,12],ngp:110,ngpu:380,nguyen:[15,386],nharmon:[],nhc:290,nht:307,ni2:171,ni3:171,ni_000:[124,308],nialh_jea:404,nialhjea:[393,413],nice:[6,8],nickla:432,nicola:9,nimprop:[3,481],nimpropertyp:[374,481],nine:[133,140,407,451],ninteg:481,nissila:[250,451],nist:[381,404,506],niter:[42,220],nitrid:396,niu3:[393,404,413],nkb:297,nlast:486,nlen:214,nline:374,nlocal:[3,8,11,12,237],nlog:366,nlvalu:112,nmax:43,nmin:43,nmol:481,nmpimd:290,nn2:430,nneighmaxdef:3,nnn:[96,112],no_affin:[16,380],no_gradient_correct:450,no_histori:6,no_velocity_gradi:450,noced:373,nocheck:417,nocit:12,nocoeff:509,nodal:[6,38,57,192,209,235,335,463],node:[1,3,12,14,15,16,17,18,42,124,128,171,198,220,244,250,335,380,417,478,494],node_area:250,node_group:209,nodeless:406,nodeset:209,nodeset_to_elementset:209,nodess:16,nof:192,noforc:[],nois:[6,240,241,247,248,249,250,297,302,307,327,335],nomenclatur:[6,73,216,368],nomin:[196,263],non:[],nonbond:[4,12,437,461],none:[],noneq:241,nonequilibrium:[9,332,333,406],nonetheless:247,nongauss:[],nongaussian:110,nonlinear:[],nonloc:[440,491],nonperiod:3,nonzero:3,noordhoek:395,nopreliminari:192,nor:[2,3,42,61,197,209,313,314,315,316,317,319,395,447,448,449,450,481,484],nord:[441,464,466],norder:478,nordlund:[441,464,466],norm:[6,12,65,123,203,212,216,217,308,314,315,373,375,460,498,499,506],normal:[3,6,9,10,11,12,40,42,60,63,65,69,72,73,75,92,95,107,108,118,122,123,157,160,170,172,173,174,192,200,203,212,213,215,216,217,220,224,226,227,238,239,243,247,248,260,263,277,288,290,291,298,302,304,305,312,323,324,326,327,328,335,340,341,344,345,349,351,352,353,355,370,372,373,375,380,394,395,409,410,413,433,460,473,475,476,479,481,483,484,486,487,491,495,498,499,500,502,506,507,510],norman:335,nornal:3,nose:[6,7,8,162,203,230,247,248,263,264,265,266,267,268,269,270,271,282,283,284,285,286,290,294,302,307,326,327,328,333,400,502],noskov:[467,502],noslip:[323,345],nosync:500,notabl:[5,40],notat:[6,63,65,72,146,166,203,260,263,404,469,507],note:[1,2,3,6,7,8,9,11,12,13,14,15,16,17,18,19,22,24,25,28,32,33,35,36,37,38,39,40,41,42,43,45,48,55,56,57,58,60,61,62,63,64,65,67,68,70,71,73,75,77,81,91,93,94,95,97,98,102,108,109,110,111,114,116,118,119,120,121,122,123,124,125,146,147,152,154,155,156,160,162,166,167,169,170,171,172,173,174,175,176,178,180,183,185,189,191,192,193,195,196,197,198,199,200,201,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,230,231,232,234,235,236,237,239,241,242,243,245,246,247,248,249,250,258,259,260,261,263,265,266,267,268,269,270,271,277,282,283,284,286,290,292,293,294,296,297,298,300,305,306,307,308,311,312,320,321,323,326,327,328,331,334,335,337,338,339,340,341,344,345,346,348,349,350,351,352,353,355,359,361,364,365,366,368,370,373,374,375,376,380,381,382,386,387,389,390,391,393,394,396,397,399,400,401,402,403,404,407,409,410,411,412,413,417,418,420,422,426,427,428,430,431,432,433,434,435,437,441,443,444,445,446,448,450,451,452,453,456,460,462,463,464,466,468,469,472,473,474,476,478,479,481,482,483,484,485,486,488,489,491,493,495,496,498,499,502,506,507,508,510,511],noth:[210,246,367,380,479,492],notic:[0,6,7,8,12,333,335,502],noutcol:8,noutput:289,noutrow:8,novemb:430,novik:13,novint:244,now:[2,3,6,9,11,12,13,47,63,64,73,196,204,205,222,240,244,245,307,341,344,366,368,404,406,410,443,444,453,477,482,502,508],nowait:244,nozforc:365,np3:171,np4:171,np6:171,npair:[122,213],nparticl:[3,41,43,385],npartit:499,npernod:[14,15,16,17,18,380],nph:[],nphi:[16,380],nphug:[],npoli:293,nproc:[3,11,196],npt:[],npt_aspher:[265,271,282],npt_bodi:[266,283],npt_sphere:[267,286],nrbin:[],nrecomput:403,nrepeat:[73,211,212,213,214,215,216,217,218,304,308,486],nreset:[224,263,264,268],nreset_ref:224,nrho:[381,404],nrl:404,nsall:9,nsampl:403,nsbin:73,nsbmax_most:3,nsec:501,nskip:[125,486],nsq:[3,377,439],nstart:[125,213,214,215,218,308,481,486],nstat:288,nstep:[3,13,224,263,346,457,479,482],nsteplast:479,nstop:[125,486],nswap:[331,338],nswaptyp:3,ntabl:[38,57,192,235,463],nterm:312,nth:[12,79,122,123,196,197,200,215,226,486,496],ntheta:386,nthread:[3,380],ntild:289,ntpc:380,ntptask:380,ntype1:121,ntype2:121,ntype:[3,146,172,196,200,298,300,406,412,441,481,491],nuclear:[9,101,102,158,241,264,297,302,374,406,473],nuclei:[9,101,102,156,158,163,197,249,264,276,285,329,383,406,481],nucleu:[101,102,298,466,502],nudg:[4,6,7,203,262,372,375],nulcear:9,num:[],num_of_collis:3,numa:[1,3,12,380,478],numactl:16,number:[1,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,27,38,40,41,42,43,45,57,65,66,67,68,70,71,72,73,74,75,77,78,79,80,81,82,84,91,94,95,96,97,98,107,108,109,111,112,114,117,118,119,120,121,122,123,124,125,135,141,146,149,150,151,152,153,154,155,157,158,159,160,161,162,164,165,166,167,169,170,171,172,173,174,175,176,180,181,191,192,195,196,197,198,199,200,201,203,204,205,208,210,212,213,214,215,216,217,218,220,221,222,223,225,226,227,235,236,237,239,240,241,243,244,245,246,247,248,249,250,253,260,263,264,268,277,288,289,290,292,293,296,297,298,302,304,307,310,311,315,323,324,325,327,330,331,332,333,335,336,337,338,340,342,343,345,346,348,350,363,365,366,368,370,371,373,374,375,376,377,380,381,382,386,388,393,395,400,403,404,405,406,407,412,413,414,415,416,430,431,432,433,435,437,441,442,443,444,445,448,450,451,452,460,462,463,464,465,466,468,469,470,473,475,476,478,479,481,482,483,484,485,487,488,489,490,491,493,495,496,498,499,500,502,506,507,508,511],number_of_a:3,number_of_b:3,number_of_typ:[],numbond:3,numer:[1,2,3,6,9,11,12,22,38,42,43,45,57,73,79,91,112,122,166,176,180,192,196,199,200,204,205,206,208,209,212,216,218,232,240,243,247,260,263,290,307,310,311,335,340,342,343,345,346,350,370,373,374,393,399,413,430,435,443,444,450,463,473,475,479,480,481,488,491,497,498,499,507],numpi:11,nvalu:[212,216,217,218,479],nvaluelast:479,nvc_get_devic:15,nvcc:[1,9,12,17],nve:[],nve_aspher:[265,269,282],nve_bodi:[266,270,283],nve_spher:[267,271,286],nvida:17,nvidia:[1,3,9,12,14,15,17,380,494],nvt1:502,nvt2:502,nvt:[],nvt_aspher:[265,269,286],nvt_bodi:[266,270],nvt_sphere:[267,271],nvtfe:209,nwait:289,nwchem:7,nxnode:335,o_cor:154,o_shel:154,oascr:7,obei:[3,226,368,476],ober:7,obj_shared_foo:12,obj_target:12,object:[6,8,11,12,15,41,43,199,224,244,250,253,293,312,319,373,374,479,484],observ:[263,297,326,327,330,331,338],obsolet:13,obstacl:[4,245],obtain:[1,3,9,12,29,75,91,108,112,170,201,205,238,241,250,268,289,290,330,365,382,399,430,435,442,451,464,466,490],obviou:[12,473,507],obvious:[199,293,496,507],occ:408,occasion:[3,263,476],occlus:199,occup:[3,170,380,408],occur:[1,3,6,9,11,12,14,17,40,59,61,63,64,73,90,110,170,173,175,192,196,197,200,210,220,223,224,226,235,239,242,245,253,261,277,298,307,323,332,345,346,348,365,376,380,403,406,426,444,463,476,478,479,484,486,490,495,498,507],occurr:[358,481,495,507],oct:11,octahedr:25,octant:478,odd:[42,112,200,220,263,307,326,327,335,496],off:[1,3,6,12,14,15,17,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,37,38,40,41,44,45,46,47,48,49,50,51,52,54,55,56,57,61,63,67,71,73,113,114,115,118,119,121,146,147,149,155,159,170,171,176,178,179,180,181,182,183,184,185,186,187,189,190,191,192,196,197,199,200,203,206,210,218,219,222,223,226,233,238,239,240,242,244,247,248,253,263,265,266,267,268,269,270,271,272,273,277,280,282,283,284,286,292,294,295,299,307,309,310,323,326,328,338,339,340,343,344,349,350,351,352,354,355,356,358,359,360,365,366,373,375,376,378,380,381,382,384,387,388,389,390,391,392,394,395,396,398,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,430,431,435,436,437,438,440,444,445,446,448,450,451,453,460,461,462,463,464,465,466,469,471,472,473,476,477,478,481,483,484,488,490,493,494,495,500,504,506,507,509,511],offend:[3,479],offer:[6,14,18,175,372,396,451,476,490],offic:7,offload:[1,9,12,16,17,244,380],offset:[3,6,59,172,199,226,227,293,374,396,418,422,461,481],offsit:8,often:[1,3,6,7,12,13,14,15,16,17,18,37,56,73,166,191,199,206,215,218,220,224,237,244,263,290,308,359,368,372,373,375,376,377,380,395,400,418,463,464,466,476,495,502,506],ohio:432,old:[3,6,9,203,224,227,263,430,443,453,482,485,489,492,506,509],older:[3,5,12,13,17,200,212,224,263,453,507],oldlac:200,oleinik:386,olfason:[6,25,360,412,493],oliv:200,olivedrab:200,olivi:9,ollila:[250,252,253,254],olmst:[209,288],omega0:360,omega:[],omega_dot:263,omega_ij:[401,402],omega_ijk:466,omega_ik:464,omegai:[119,196,197,325],omegax:[119,196,197,325],omegaz:[119,196,197,325],omgea:6,omiss:[0,7],omit:[192,200,342,390,399,422],omp:[],omp_num_thread:[3,16,18,380],omp_proc_bind:17,ompi_comm_world_local_rank:12,ompi_icc:16,on_the_fli:209,onc:[0,1,2,3,6,11,12,16,41,42,61,62,65,73,95,109,178,198,199,200,203,204,205,220,221,222,227,237,239,241,248,289,293,296,307,323,331,336,338,346,371,374,375,376,409,411,413,414,441,445,478,479,488,495,498,502,507],onelevel:478,onewai:[],ongo:244,oniom:[9,301],onli:[1,2,3,6,7,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,42,43,44,46,47,48,49,50,51,52,54,55,56,57,61,62,63,65,66,67,68,69,70,71,72,73,74,75,77,80,81,82,84,85,87,90,91,92,94,96,97,98,101,102,103,104,105,106,107,108,109,110,111,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,155,156,158,159,160,162,163,164,165,166,167,169,170,171,172,175,176,178,179,181,182,183,184,185,186,187,189,190,191,192,196,197,198,199,200,201,203,204,205,206,207,208,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,230,232,233,234,235,236,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,278,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,296,297,298,299,300,301,302,303,304,307,308,309,310,311,312,313,314,315,316,317,319,323,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,351,352,353,354,355,356,358,359,360,363,365,366,368,370,373,374,375,376,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,478,479,481,482,484,485,486,488,489,490,491,492,493,495,496,497,498,499,500,502,507,508,509],only_group:170,onn:490,onset:[297,358],ontario:9,onto:[146,174,223,227,250,460],onward:2,open:[],opencl:[1,3,7,15,380],opengl:6,openkim:9,openmp:[1,3,7,9,12,16,17,18,363,380,494],openmpi:[12,14,15,16,17,18,380],opensourc:7,oper:[],opl:[],oppelstrup2:9,oppelstrup:[9,433],oppos:[6,40,194,196,197,306,342,366,374,481],opposit:[6,29,72,208,247,254,288,307,338,375,396,426,467,479],opt:[],optic:150,optim:[],option:[],optionn:17,orang:[2,199,200],orbit:[298,300,386,396,406,451,461],orchid:200,order:[1,2,3,6,9,11,12,14,27,29,38,40,42,57,61,65,67,71,73,81,91,93,94,96,97,98,112,114,118,121,136,146,147,149,150,151,152,153,154,155,158,159,160,161,162,164,165,176,181,191,192,196,197,199,200,203,206,211,213,215,216,217,218,219,221,222,223,224,225,230,232,239,241,243,244,246,250,251,253,261,263,288,296,297,301,304,305,306,307,308,309,310,312,317,319,324,330,334,335,336,337,347,348,349,351,352,353,355,358,359,365,374,375,381,382,383,386,395,402,403,404,406,407,409,410,413,415,418,426,430,433,443,444,445,451,461,462,463,464,465,466,467,469,470,476,478,479,481,482,486,488,490,491,495,498,502,507,511],orderomg:3,ordinari:[117,412,440],org:[6,7,11,12,13,14,442],organ:[0,3,6,7,8,395],organis:[448,450],organometal:25,orien:491,orient:[],orienti:[],orientord:[],origid:212,origin:[3,6,7,9,12,73,83,108,109,120,124,168,172,174,195,199,200,203,204,205,212,216,217,221,222,226,230,248,260,263,284,290,293,303,307,308,316,322,333,362,364,365,368,372,381,382,384,386,396,399,400,403,404,412,415,430,440,443,444,464,466,467,468,478,481,482,483,484,485,486,506,509],origin_i:217,origin_x:217,origin_z:217,orlikowski:433,ornl:[7,9,15],orsi:29,ortho:[3,61,174,481],orthogon:[],orthograph:199,orthong:61,orthongon:[61,307],orthonorm:227,orthorhomb:297,os4:171,oscil:[6,9,157,222,226,229,230,248,260,261,263,297,302,307,340,341,343,345,374,383,467,502,507],oscillatori:[260,316],oserror:11,other:[],otherswis:16,otherwis:[1,3,9,12,14,16,17,18,37,40,56,73,107,117,124,150,151,152,165,173,191,197,200,201,210,212,221,222,226,237,239,241,248,263,307,359,360,373,380,388,413,417,427,428,441,470,474,476,479,481,482,502,507],otyp:[396,418,422,426],ouml:502,our:[5,6,7,8,13,250,310,435,464,466,502],out:[1,2,3,6,7,8,11,12,13,14,18,19,21,42,66,68,73,77,94,95,98,99,102,108,109,110,111,113,120,121,149,150,151,152,153,155,156,158,159,160,161,162,164,165,167,169,175,179,196,197,199,200,201,203,216,220,221,222,225,233,238,239,245,247,250,255,277,289,291,292,293,302,303,304,307,320,335,344,346,347,348,349,351,355,363,364,368,371,375,379,406,413,429,461,475,476,478,479,484,485,486,488,489,490,492,495,497,498,499,503,505,507,508,509,510,511],outcom:[307,508],outer2:[391,411],outer:[3,8,16,73,231,245,348,364,371,373,379,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,436,438,440,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,468,469,470,471,472,473,476,489,490,495,501,507],outer_distance_cutoff:412,outermost:[38,57,73,204,205,260,263,376,463,490],outfil:[13,478],outlin:[6,199],outmost:244,outpt:[],output:[],output_frequ:209,outputss:133,outsid:[3,59,61,73,162,172,195,196,197,198,199,200,201,215,216,227,239,245,307,308,323,328,329,342,343,344,345,346,363,375,387,389,396,406,418,420,438,446,479,481,482,484,491,498,508],outuput:[],outut:6,outward:[73,170,340,344,345,481,490],over:[1,3,5,6,7,9,12,16,18,27,40,42,43,56,62,67,70,71,73,81,82,91,92,93,94,96,97,106,108,110,112,114,121,122,131,132,138,143,146,147,152,155,158,166,168,181,192,199,201,203,204,205,211,212,213,214,215,216,217,218,219,220,221,222,226,227,237,240,241,245,247,248,249,253,260,261,262,263,264,265,266,267,269,270,271,282,283,284,285,286,288,293,294,297,304,305,306,307,308,312,320,323,326,327,328,329,331,334,337,338,340,342,343,344,345,346,349,364,367,375,376,377,380,394,400,404,405,406,407,412,427,430,433,441,452,453,461,462,463,464,465,466,469,477,478,479,484,486,487,489,490,495,496,498,499,507,508],overal:[6,18,25,61,166,224,230,263,264,290,310,323,348,371,406,412,413,452],overalap:307,overcom:[277,323],overflow:[3,374,376],overhead:[6,11,19,42,200,212,214,216,217,220,236,296,376,377,484,500],overkil:307,overlai:[],overlaid:7,overlap:[3,13,16,64,78,172,175,192,200,208,211,212,215,216,217,218,227,231,277,293,298,304,307,308,323,341,345,365,368,371,373,374,380,400,406,410,413,416,426,447,449,453,468,481,484,490],overload:1,overrid:[3,9,12,14,16,17,22,45,73,158,172,180,199,200,204,205,224,231,258,263,350,365,376,393,412,413,430,435,443,478,479,491,493,498,507],overridden:[6,172,199,268,307,416,427,435,453,461,489,507,509],overview:[],overwrit:[11,12,22,45,180,200,212,213,214,215,216,217,218,308,350,363,369,393,430,479,482],overwritten:[197,295,334,363,412,413,476,477,482],own:[3,4,6,7,8,11,12,13,15,17,40,42,61,63,65,67,68,71,73,75,77,81,94,97,98,109,111,119,120,121,123,125,152,155,167,169,170,196,197,200,203,209,211,212,213,214,215,216,217,218,220,223,224,226,237,240,241,247,248,250,258,261,263,265,266,267,268,269,270,271,282,283,284,286,290,294,302,307,308,326,327,328,337,365,375,380,382,386,395,405,415,441,443,444,462,464,465,466,469,478,491,496,498,508],oxford:[29,91,399],oxid:[9,395,396,451],oxygen:[6,41,236,396,418,422,451,481],oxygen_c:154,p_e:335,p_ik:441,p_pi:386,pacakg:380,pack:[5,8,69,341,380,386,430],pack_bord:8,pack_border_bodi:8,pack_border_hybrid:8,pack_border_vel:8,pack_comm:8,pack_comm_bodi:8,pack_comm_hybrid:8,pack_comm_vel:8,pack_exchang:8,pack_restart:8,pack_revers:8,pack_reverse_comm:8,pack_reverse_hybrid:8,packaag:380,packag:[],packakg:15,packet:[7,9,41,199,383,406],pad:[3,196,197,199,200,290,507],padua:[9,13],page:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,45,56,59,61,65,68,70,77,91,94,98,107,109,110,111,113,115,118,120,123,125,147,150,151,152,165,167,169,172,173,174,180,191,195,196,197,198,199,200,201,203,204,205,210,211,212,213,214,215,216,217,218,227,239,246,247,248,258,263,264,269,270,271,275,282,283,284,285,286,293,296,307,320,323,326,327,328,337,341,344,346,348,350,359,364,373,374,375,376,380,381,382,385,393,395,396,404,405,407,412,413,415,416,430,431,432,435,437,441,442,452,461,462,464,466,468,469,479,481,482,483,484,486,489,490,491,493,498,499,507,508,509,510],pai:[15,18],pair:[],pair_:[91,204,205],pair_airebo:415,pair_charmm:426,pair_class:8,pair_coeff:[],pair_dpd:[9,401],pair_eam:381,pair_eff:158,pair_foo:8,pair_hybrid:[413,467],pair_interact:209,pair_list:417,pair_lj:426,pair_lj_cut:8,pair_lj_soft_coul_soft:91,pair_modifi:[],pair_sph:[454,455,456,457,458,459],pair_styl:[],pair_tally_callback:8,pair_writ:[],paircoeff:3,pairfoo:8,pairij:[3,481],pairkim:3,pairstyl:8,pairwis:[],palegoldenrod:200,palegreen:200,paleturquois:200,palevioletr:200,pan:199,panagiotopoulo:[397,408],pandit:[9,300,444],papaconstantopoulo:381,papayawhip:200,paper:[3,6,7,8,9,13,40,41,66,146,160,166,184,247,250,254,262,292,298,300,307,323,331,335,338,365,372,375,382,390,396,410,412,415,420,422,440,443,444,464,466,476,495],paradyn:5,paraemt:445,paragraph:[73,160,340,368,463,482,483],parallel:[],parallelepip:[6,174,368,481,484],parallelipip:[174,289],paralleliz:292,param:[3,298,300,416,478,484],paramet:[],parameter:[124,171,382,386,395,396,404,405,406,407,415,430,431,432,441,443,444,451,462,464,465,466,469],parameter_fil:209,parameterizaion:396,parametr:[6,9,36,405,442,446],paramt:[110,298,342,445],paramter:395,paratem:426,paraview:[197,308],parent:[3,8,346],parenthes:[38,57,192,235,410,463,507],parenthesi:[2,212,348,507],parinello:[6,7],pariticl:220,paritlc:3,park:[3,7,9,209,312,432,440],parmin:433,parrinello1981:224,parrinello:[224,241,261,263,264,297,327],pars:[],parser:[12,507],part:[0,1,2,3,6,7,8,9,11,12,17,20,21,23,24,25,26,27,28,29,30,31,32,35,36,37,38,41,42,44,46,47,48,49,50,52,54,55,56,57,66,69,72,73,74,80,82,87,96,101,102,103,104,105,106,108,110,113,114,115,117,118,121,124,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,154,156,158,159,163,164,166,170,171,175,178,179,181,182,183,184,186,187,189,190,191,192,196,197,198,200,201,203,206,207,208,210,214,217,219,220,221,222,223,224,225,226,227,229,232,233,236,237,238,239,240,241,242,244,245,246,247,248,249,250,251,252,253,254,256,257,258,261,263,264,265,266,267,268,269,270,271,272,273,274,275,276,278,280,281,282,283,284,285,286,288,289,290,292,293,297,298,299,300,301,302,303,304,306,307,309,310,312,313,314,315,316,317,319,320,322,323,326,328,329,330,331,332,333,334,335,336,338,339,340,341,342,343,344,346,347,348,349,351,352,354,355,358,359,360,365,366,373,374,375,376,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,403,404,405,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,436,437,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,478,479,481,482,483,484,488,489,490,493,499,507,511],partai:[9,442],parti:9,partial:[],partic:6,particip:[222,385,416,468],particl:[],particleenergi:3,particleviri:3,particular:[1,3,6,8,10,12,41,65,67,71,72,73,81,97,114,119,121,122,146,172,195,196,197,203,208,216,220,223,239,240,245,246,250,260,263,288,293,306,307,310,330,341,346,349,366,368,371,374,380,385,386,387,389,391,392,394,398,402,405,406,409,411,413,418,422,426,429,437,438,445,446,461,462,464,465,466,469,476,478,481,482,483,488,489,491,499,507,508,510,511],particularli:[6,7,9,12,15,16,25,40,199,224,307,366,406],particuolog:43,partilc:323,partit:[],partitoin:64,partner:[3,7,63,221,222,223,248,323,338,467,491,496,502],pascal:[9,13,506],pass:[6,7,8,11,68,76,77,83,93,94,98,108,109,110,111,167,196,197,199,200,201,224,225,237,239,260,261,263,296,323,340,364,376,380,413,416,443,460,479,481,482,486,492,507,510],passphras:12,past:[],patch:[0,12],patchi:307,patel:433,path:[3,6,7,11,12,13,15,201,246,262,290,312,323,330,335,375,381,382,386,393,404,405,407,415,430,431,432,437,441,442,443,451,452,462,464,466,469,482],pathtolammp:451,patient:12,patom1:121,patom2:121,patrick:465,pattern:[3,7,12,64,75,483],pattnaik:307,paul:[0,7,13,247,249],pauli:[9,406,451],paus:489,paves:290,payn:[146,442,452],pb2:171,pb4:171,pbc:[73,340,383],pchain:[263,264,268,307],pcie:1,pd2:171,pd4:171,pdamp:[263,264,268,294,307],pdb:[6,13,201],pdebuyl:9,pdf:[0,8,9,13,17,41,104,105,106,117,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,225,246,256,257,313,314,315,316,319,440,454,455,456,457,458,459,491],pdim:338,pdlammp:[80,82,440],pdlammps_ep:[117,440],pdlammps_v:440,pe_eta:263,pe_etap:263,pe_omega:263,pe_strain:263,peachei:13,peachpuff:200,peak:408,pearlman:91,peculiar:12,pedersen:366,peform:[40,299],penalti:[14,443,444],pencil:[6,73,160,216],pend:3,penetr:[43,126,447,449,491],penetret:41,peng:171,penn:13,pentium:10,peopl:[7,8,9,12],peptid:[4,9,225],per:[],peratom:[3,116,147,170],perceiv:199,percent:[3,12,16,224,380,462],percentag:[1,12,224,263,293,294,307],percol:222,perfect:[6,42,72,75,96,220,288,375],perfectli:[42,220,482],perfom:[6,375],perform:[],performac:1,pergamon:[430,466,473],perhap:368,peri:[],peridyma:80,peridynam:[3,4,6,7,9,41,65,80,82,117,440,461,481,491],perimitt:397,period:[],perioid:340,perl:[6,13],perm0:506,perman:[3,40,55,73,176,221,222,244,306,346,380,412,485,493],permeabl:287,permiss:[222,479],permit:[6,250,433],permitt:[397,466,472,473],permut:[12,405,462,464,466,469],perpendicular:[6,73,150,199,226,245,255,260,262,288,291,316,340,341,372,481],perram:[366,409],persepct:199,persist:[3,8,73,237,307,380,478,479,483,487,507],person:9,persp:[3,199],perspect:199,pertain:[393,461],perturb:[9,13,72,91,259,305,340,343,345,486],peru:200,peskin:250,pessimist:366,petersen:[323,366],pettifor:[386,461],pettifor_1:386,pettifor_2:386,pettifor_3:386,pfactor:199,pforc:479,phantom:244,pharmaceut:7,phase:[3,12,16,263,330,338,386,418,465,478],phd:442,phenol:502,phenomena:406,phi0:[190,306],phi1:179,phi2:[179,405,462],phi3:[179,405,462],phi:[1,3,4,7,9,12,16,17,81,96,112,146,191,192,199,242,289,306,352,380,381,386,404,407,430,431,432,494],phi_ij:[386,407,441],philadelphia:9,phillip:[248,400,502],phillpot:[299,395,396,451],philosoph:404,philosophi:[6,7,246],phonon:[],phophor:452,phosphid:452,phy:[6,7,13,20,21,25,40,44,46,47,66,72,75,91,92,96,112,116,118,146,147,154,160,178,179,189,198,210,214,224,225,230,240,241,246,247,248,249,250,261,262,263,264,268,284,285,289,290,294,297,299,302,307,310,311,312,323,326,327,330,331,332,333,335,338,340,349,358,360,365,366,372,375,382,386,387,391,392,394,395,396,397,398,399,400,402,404,405,406,408,409,410,411,412,415,418,420,422,423,426,427,428,429,430,432,434,435,438,440,441,445,451,452,460,462,463,464,465,466,467,469,476,490,493,495,502],physic:[3,6,9,12,14,16,17,18,41,43,54,61,126,154,166,209,226,241,247,249,250,252,253,254,261,289,298,300,334,335,366,368,375,380,382,384,390,394,404,412,413,433,442,443,444,447,455,456,458,459,476,478,490,491,496,506],physica:[427,428],physik:[7,9],pic:9,picki:8,picocoulomb:506,picogram:506,picosecond:[200,226,499,506],picosend:406,pictur:7,pie:[],piec:[3,11,146,200,263,488,511],pierr:9,pieter:13,pimd:[],pin:16,pink:200,pipe:[6,196,199],pipelin:[3,6],pisarev:335,pishevar:400,piston:[],pitera:6,pixel:199,pizza:[4,6,7,11,13,42,196,199,220],pjintv:13,pka:335,place:[3,6,7,9,11,12,33,42,51,73,91,166,172,176,185,192,196,199,200,202,203,204,205,222,223,226,239,240,241,243,246,247,248,249,251,253,254,263,269,270,271,282,283,286,293,296,305,307,326,327,328,335,340,343,345,364,393,412,461,468,478,479,482,489,491,496,499,507],placehold:[33,185,381,382,395,404,407,414,415,430,431,432,437,441,443,444,452,460,462,464,465,466,469],placement:[368,418],plai:[199,330],plain:[9,426,479],plan:[3,5,6,17,174,481],planar:[6,41,43,245,288,341,358,360],planck:[239,290],plane:[3,6,9,42,43,59,61,69,73,96,199,203,209,216,220,242,245,255,288,291,301,320,322,335,341,349,351,352,353,354,355,360,368,428,468,484,491],planeforc:[],plasma:[9,92,264,335,406],plastic:[],plastic_strain:[],plastic_strain_r:[],platform:[1,3,7,9,12,13,15,17,196,199,201,483,488,511],plath:[6,95,203,331,338],player:199,pleas:[0,3,7,11,12,13,209,241,250,254,289,292,303,330,346,405,407,440,448,450,451],plen:383,plimpton:[0,5,7,72,118,147,223,288,298,323,410,440],plo:29,plog:[3,12,490],ploop:[263,264,268],plot:[7,11,13,297,424,426,463,470],plu:[3,11,12,40,61,70,101,170,175,200,219,224,226,227,268,307,377,406,416],plug:9,plugin:[9,13,201,482],plum:200,pm3:171,pmb:[],pme:366,pmf:[225,312,320],png:[3,12,196,199],pni:199,poariz:6,poem:[],point1:481,point2:481,point3:481,point:[],point_data:308,pointer:[3,7,8,9,11,237,479],pois:506,poiseuil:[4,206,242],poisson:[61,226,366,410],poisson_solv:209,polak:372,polar:[6,7,112,146,154,171,209,229,395,396,418,467,502],polar_off:395,polar_on:395,polariz:[],poli:[],politano:[9,451],pollock:[7,366],polya:346,polybond:13,polychain:307,polydispers:[3,374,388,394,410,427,428,461,472],polygon:[],polyhedron:170,polym:[],polymer:7,polymorph:[],polynomi:[9,38,57,192,404,424,435,451,456,463],polytechn:292,poor:[16,17,42,220,284,285,310,380,424],poorli:[372,373],pop:[3,8],popen:12,popul:[12,302,368,403,481],popular:[12,196,405],pore:320,poros:175,porou:[250,253],port:[244,246],portabl:[7,9,12,196,198,225,443,483],portion:[1,3,11,12,15,16,42,55,73,92,95,113,114,116,119,147,148,162,196,197,200,211,212,215,216,217,218,220,224,236,250,263,265,266,267,269,270,271,299,304,305,307,308,348,364,376,380,387,389,390,391,392,396,397,399,400,406,408,409,411,412,418,422,426,429,438,445,446,466,470,480,481,486,490,491,500,507],poschel:410,posfreq:304,posit:[3,6,14,27,40,41,42,43,47,59,61,72,73,83,93,94,108,109,114,123,124,128,146,147,155,170,171,172,174,175,176,181,183,192,195,197,198,199,200,203,204,206,208,210,211,212,215,216,217,220,221,222,223,224,225,226,227,230,232,239,240,241,242,244,245,247,248,249,250,252,253,256,257,260,261,263,264,265,266,267,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,288,289,290,292,293,294,297,298,302,304,305,307,310,312,316,319,320,322,323,325,326,327,328,330,332,333,334,335,338,340,341,342,343,344,345,346,349,365,368,375,382,383,385,388,400,402,403,406,408,421,444,451,460,463,468,476,481,484,491,502,507,508],posix:244,posix_memalign:12,possibl:[1,3,6,8,9,11,12,15,38,41,42,56,61,65,72,73,91,119,121,146,147,150,151,165,195,196,197,198,200,203,205,209,210,216,220,221,222,223,227,229,234,241,248,288,293,301,302,304,307,319,323,325,335,336,354,364,366,373,376,377,380,403,412,430,444,448,450,451,463,469,479,485,494,495,496,499,502,507,508,510],post:[],post_forc:8,post_force_integr:8,post_force_respa:8,post_integrate_respa:8,postit:[216,217,277],postiv:90,postma:[294,326],postprocess:13,pot:[410,444],potentail:407,potenti:[],potentiel:426,potetni:413,potin:433,potpourri:9,pour:[],pourtoi:330,pow:226,powderblu:200,power7:17,power8:17,power:[3,9,11,110,146,200,302,365,380,386,479],pparam:[91,204,205],ppm:[12,196,199],ppn:[14,15,16,17,18,380],pppm:[],pppm_disp:3,pppmdisp:3,pproni:[3,240],pr3:171,pr4:171,practic:[3,12,224,263,264,289,296,469,478],prb:[464,466],prd:[],pre:[],pre_exchang:8,pre_forc:8,pre_force_respa:8,pre_neighbor:8,prec:451,prec_tim:14,prece:450,preced:[2,6,61,197,211,212,213,214,215,216,217,218,246,304,308,348,368,375,380,386,412,495,498,499,507],preceed:[11,12,73,160,213,340,479,507],precipit:170,precis:[1,3,9,12,13,14,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,44,46,47,48,49,50,52,54,55,57,108,115,118,149,159,172,178,179,181,182,183,184,186,187,189,190,192,196,200,206,212,218,219,224,226,233,238,242,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,298,299,300,307,309,310,326,328,339,343,349,351,352,354,355,358,360,365,366,373,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,404,405,407,408,409,410,411,412,418,419,420,421,422,423,424,425,426,427,431,433,436,437,438,440,443,445,446,451,453,462,463,464,465,466,469,471,472,473,483,484,490,491,494,499,502,506,507,508],precv:478,predefin:[190,200,346,406],predict:[1,6,10,12,277,307,380],preexponenti:495,prefactor:[24,25,28,32,35,36,166,180,191,204,205,213,340,351,355,358,373,394,408,437,445,446,453,472],prefer:[7,8,12,306,336,382],prefix:[11,12,199,225,289,475,478],preliminari:[38,57,192,235,463],prematur:373,prepar:[9,298,301,323,492,502],prepend:443,preprint:[146,452],preprocessor:244,prerecord:225,prescrib:[6,8,150,151,152,165,203,204,209,212,227,260,279,336],presenc:[196,221,222,250,253,427,428,433,472,509],present:[1,3,12,18,170,192,198,199,227,240,241,246,250,251,253,254,302,319,341,344,347,395,406,417,426,433,444,445,451,478,502],preserv:[3,61,224,226,263,310,323,345,482],press:[],pressdown:219,pressur:[],pressure_with_eviri:406,presum:[75,161,203,204,205,226,375,413,484],prevent:[2,3,6,41,126,227,238,293,323,334,358,365,371,373,375,380,400,413,439,455,456,458,460,479,483,489,491,502,507],previou:[],previouli:227,previous:[3,11,61,63,73,90,107,123,125,161,172,174,176,195,196,197,198,200,208,210,211,212,213,215,216,217,218,226,227,239,245,258,260,293,305,307,309,310,335,337,340,341,342,343,345,346,367,410,461,476,479,483,484,494,496,498,499,503,504,505,507,508],prevoiu:341,price:[6,399],primari:[0,6,9,335],primarili:[5,7,9,17,148],primaritli:[],prime:[230,248,411,433,464,466,478],primit:[3,6,343,344,368],princip:[3,244,451],principl:[6,9,11,244,264,298,406,414,433,462,478],prinicp:[43,307,374],print:[],printabl:2,printflag:414,printfluid:250,prior:[170,194,311,367,510],priori:490,prioriz:380,prism:[3,6,160,174,484],priveleg:3,privileg:[11,12,244],prob:[221,222],probab:453,probabl:[3,8,12,41,73,162,175,176,178,210,220,221,222,223,227,239,248,263,293,340,346,373,435,463,476,495,502],probe:507,problem:[],problemat:239,proc:[1,3,8,11,12,15,119,196,197,364,478],proce:[42,55,176,220,231,375,433,488,496,499],procedur:[6,12,40,42,200,210,220,239,247,248,249,263,265,266,267,268,269,270,271,282,283,284,285,286,289,326,327,328,329,332,333,373,375,382,388,482,502],proceed:[12,433],procesor:[42,478],process:[],processor:[],processsor:[42,220,478],procp1:[196,197],procsessor:500,procssor:490,produc:[1,3,4,6,7,9,12,13,14,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,43,44,46,47,48,49,50,52,54,55,57,65,67,70,71,73,81,97,114,115,116,118,119,120,121,123,125,147,149,159,170,178,179,181,182,183,184,186,187,189,190,192,196,197,200,203,206,211,212,213,215,216,217,218,219,220,223,226,233,237,238,240,241,242,247,248,249,258,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,293,297,298,299,302,307,308,309,310,324,325,326,328,335,336,337,339,340,343,348,349,351,352,354,355,358,360,366,373,375,378,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,436,437,438,440,441,444,445,446,453,462,463,464,465,466,469,471,472,473,476,478,483,484,486,487,490,495,496,507,508],product:[6,16,17,18,146,170,226,284,298,336,380,383,406,444,478,507],proessor:380,prof:292,profi:161,profil:[],program:[3,4,6,7,9,11,12,13,17,148,196,199,200,201,203,225,237,244,250,301,404,479,480,492,507],programm:[13,17],progress:[1,42,220,244,261,297,372,373,375,499,502],prohibit:491,project:[6,7,13,14,372,461],promis:7,promot:386,prompt:[8,11,12,244,492],proni:[3,240,241],proofread:8,prop:[6,296],propag:[4,9,208,263,297,313,406,413],propens:6,proper:[223,288,430,479],properati:296,properli:[206,232,307,311,319,374,375,402,479,508],properti:[],propoerti:323,proport:[6,40,42,91,108,109,168,220,247,248,249,297,331,338,339,410],proportion:247,propos:[6,146,210,224,239,263,284,302,418,432,465,467],prospect:7,protect:323,protein:[7,10,172,305,307,321,481,489],protocol:244,proton:[466,473,506],prototyp:[10,43,440],prouduc:[218,337],prove:[84,85,234,250,311],proven:284,provid:[1,3,4,6,7,8,9,11,12,13,14,15,16,17,18,29,41,43,63,69,72,124,145,148,166,170,171,172,198,199,201,211,212,218,223,224,225,226,237,239,244,246,250,254,261,263,289,297,298,301,302,307,311,312,330,332,333,336,337,348,363,365,366,371,375,380,382,386,388,393,395,396,400,405,406,410,412,415,417,426,427,430,432,433,441,442,443,444,451,452,460,461,462,464,465,466,469,478,483,489,491,494,495,499,500,507],proxim:195,psa:343,pscreen:[3,12,490],pscrozi:[0,7,13],psec:[200,226,243,247,248,263,294,307,326,327,501,506],psend:478,pseudo:[406,476,481,486],pseudodynam:330,pseudopotenti:[9,433],psf:6,psi:[407,472],psi_ij:407,pstart:[3,263,264,268,294,307],pstop:[3,263,264,268,294,307],pstyle:[91,113,204,205],psu:[443,444],psuedo:486,pt2:171,pt4:171,ptarget:224,pthread:[12,17],ptr:[6,11,237,479],ptype1:121,ptype2:121,pu3:171,pu4:171,pu6:171,publicli:5,publish:[7,250,254,298,396,430,433,464,466],pull:[312,320],puls:335,pump:[427,428],punctuat:[2,476,495],purchas:199,purdu:[9,13],pure:[11,323,413,431,432,464,466,490],purg:[3,482],purpl:[2,200],purport:11,purpos:[3,6,7,12,43,63,73,124,134,140,155,156,171,172,174,176,192,196,216,218,223,224,247,288,290,293,295,306,323,365,380,390,416,422,433,435,468,474,481,484,488,491,493,494,507,511],push:[3,8,206,219,226,245,262,288,305,312,373,410,453],pushd:245,put:[3,6,8,11,12,13,40,61,160,172,196,227,231,342,343,346,368,443,479,481,485],putenv:[492,507],px1:490,px2:490,pxx:[224,263,294,307,365,366,498,499],pxy:[3,6,499],pxz:[3,6,499],py1:490,py2:490,pydir:11,pyi:[224,263,294,307,365,366,499],pymol:[7,11,13],pymol_aspher:[],pympi:11,pypar:11,python:[],pythonpath:11,pyz:[3,6,499],pz1:490,pz2:490,pzz:[224,261,263,294,297,307,365,366,499],q_1:451,q_2:451,q_3:451,q_c:[],q_d:502,q_i:[407,426],q_j:426,qbmsst:[],qcore:298,qdamp:298,qdist:[396,418,422,426],qeq1:298,qeq2:298,qeq:[],qeqal:451,qeqallparallel:451,qfile:[298,396],qin:243,qinitmod:451,qmin:372,qmmm:[],qmol:301,qout:243,qstep:298,qtb:[],quad:[12,18,380,478],quadrat:[],quadratur:[91,209],quadrupl:381,quadruplet:[188,191,193,349,351,352,353,355,357,358,359,361],qualifi:[3,246],qualiti:[7,9,199,200],quantic:451,quantit:[76,83,108,109,110,168,410],quantiti:[],quantum:[6,9,146,237,241,290,297,301,302,386,406,433,451,461],quantum_temperatur:297,quartic:[],quartic_spher:209,quartz:[297,302],quasi:290,quat:[3,491],quaternion:[3,6,41,86,119,136,150,151,172,265,266,269,270,273,274,275,282,283,409,481,491],quati:[119,481],quatj:[119,481],quatk:[119,481],quatw:[119,481],queen:13,quench:[346,476,495],queri:[3,11,55,279,479,507],quest:[6,237],question:[8,9,12,13,288,346,440,507],queteschin:9,quick:[0,12,14,15,16,17,18,19],quickli:[3,4,8,12,13,40,96,220,226,239,244,323,372,373,375],quickmin:[371,372,373,375,495],quicktim:[4,199],quip:[],quit:[],quot:[2,3,12,198,253,295,348,430,476,477,479,489,507],quotat:451,r10:386,r12:409,r_1:146,r_2:146,r_c:[397,399,408,466],r_cut:[386,429],r_d:502,r_e:407,r_ewald:308,r_fu:[427,428],r_i:[29,146],r_ii:146,r_ij:[29,386,406,441,473],r_ik:441,r_j:29,r_jik:441,r_m:429,r_max:217,r_me:397,r_mh:408,r_min:[217,398],r_ub:20,r_x86_64_32:12,ra2:171,rad2theta:171,rad:346,radhi:484,radial:[65,73,101,102,119,122,146,156,158,163,212,217,249,264,276,285,320,329,373,406,412,435,481,484],radian:[20,21,24,28,32,35,36,38,171,179,190,192,306,349,351,355,358,481,484,491],radiat:[124,171,335],radic:[174,481],radii:[73,78,146,223,227,394,404,409,410,427,428,433,447,449,472,484],radit:406,radiu:[],radlo:484,rafferti:338,rahman:[6,7,224,261,263,264,297,440],rai:[9,17,171],ram:466,ramirez:214,ramp:[],ran:[3,4,6,10,11],random:[3,6,40,172,175,195,199,208,210,221,222,223,225,227,236,239,240,241,247,248,249,250,259,263,290,293,297,302,305,307,311,323,327,330,335,339,342,388,400,401,402,403,476,491,496,502,507,508],random_se:476,randomli:[172,175,210,227,239,247,293,323,345,495,496],rang:[1,3,6,7,8,9,10,12,14,15,16,18,38,40,57,63,73,74,79,92,112,114,115,116,118,122,123,127,146,147,158,166,171,173,176,177,184,192,196,197,199,200,209,210,222,226,227,239,241,293,308,323,324,330,331,336,338,365,366,373,376,377,380,382,384,386,387,388,389,390,391,392,394,396,397,398,399,400,403,404,406,409,411,412,413,415,418,419,420,421,422,423,424,425,426,427,428,429,430,433,434,435,436,438,441,444,445,446,451,460,461,463,466,471,472,473,475,479,490,491,499,510],rangecoulomb:[],rank:[6,11,12,244,336,363,478],rankin:268,raphson:3,rapid:[4,6,11],rapidli:[3,8,12,73,223,247,261,263,307,326,327,339,396,400],rapp:[298,299,300],rappe_and_goddard:299,rare:6,rasmol:[6,7],rasmussen:409,raster3d:[6,7],rate:[],rather:[1,2,6,9,12,41,42,64,118,155,199,220,226,240,241,307,327,335,339,341,342,343,346,406,443,463,482,486,491,493,498,507],ratio:[6,10,61,91,106,146,210,220,226,247,249,323,331,338,339,365,378,409,410,445,455,468,478,481,491,495],rational:[336,493],rattl:[],rattle_debug:310,ravelo:[268,420],rayleigh:[261,297],rb1:171,rbb:451,rbg:200,rcb:[3,42,220],rcm:[93,94],rcmx:[93,94],rcmy:[93,94],rcut:63,rcutfac:[146,452],rd1:375,rdc:17,rdf:[],rdn:375,rdt:375,rdx:4,reach:[6,12,42,125,214,220,222,224,248,268,316,323,330,348,364,379,397,502,507],react:6,reactant:406,reaction:[312,321,334,345,375,406],reactiv:[9,304,382],read:[2,3,6,7,8,9,11,12,13,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,37,38,39,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,61,121,170,172,173,175,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,195,196,197,199,200,201,202,203,209,210,223,224,226,227,235,239,241,244,260,261,263,265,266,267,268,269,270,271,282,283,284,285,286,289,290,292,293,295,296,300,307,310,312,316,319,322,325,333,334,335,341,347,349,350,351,352,353,354,355,357,358,359,360,361,362,364,370,374,375,379,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,401,402,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,436,438,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,472,473,474,476,478,481,482,483,485,486,487,488,489,491,492,493,495,507,508,509,511],read_data:[],read_dump:[],read_restart:[],read_restart_set:8,readabl:[197,199,374,488,511],reader:[3,13,482],readi:[11,12,173,175,176,244,491,502,509,510,511],readm:[1,4,6,8,9,11,12,13,170,196,197,201,301,414,433,443,444,479],real:[3,6,7,11,27,30,31,61,73,95,96,112,146,161,172,181,195,200,208,216,217,226,227,230,244,245,248,260,290,297,302,305,339,340,342,343,345,354,365,366,368,371,377,396,433,435,443,444,466,481,484,490,498,501,506,508],realist:[3,227,485],realiz:[73,203,479],realli:[1,3,8,12,118,128,147,200,245,376,413,493],realloc:3,realtim:244,reamin:[340,344],rearrang:[197,375],reason:[3,6,7,11,12,19,40,153,164,172,212,216,217,247,294,307,332,333,336,346,374,375,380,393,397,406,407,408,428,435,468,470,485,490,508],reax:[],reax_def:3,reaxc:[],reaxff:[3,4,5,7,9,13,203,298,300,303,304,413,443,444,461,493],rebal:[42,220],rebalanc:[42,220],rebo:[],rebuild:[11,12,14,15,16,239,376,400,499],rebuilt:[3,12,196,197,198,199,201,376,380],recalcul:[73,91,323],receiv:[3,219,244,246,288,478],recent:[],reciproc:[6,12,124,170,171,289,365,387,389,390,396,399,406,418,422,438,446,495],recog:12,recoginz:3,recogn:[3,12,16,75,174,221,222,263,374,404,430,443,479,481,488,489,502],recomend:6,recommend:[7,9,12,14,16,199,200,297,333,365,406,413,427,428,433,444,445,448,450,451,490,500],recompil:[1,3,9,12,201,310],recomput:[107,134,176,231,312,403,493],reconstruct:[3,225,451],record:[201,225,312],recov:[224,263],recreat:347,rectangl:[42,220,368],rectangular:[7,42,64,174,220,239,368,481,483,485],rectilinear:[124,171,197],rector:54,recurs:[42,220,386,468],recust:42,recv:478,red:[2,10,199,200,223,290],redefin:[3,483,489,507],redirect:12,redo:12,reduc:[],reduct:[18,19,123,124,171,261,297,365],redund:407,ree:456,reed:[261,297],rees:[7,9,13],ref:[332,333,372],refactor:6,refer:[],referenc:[3,6,12,65,70,73,120,196,197,203,213,218,239,296,337,366,396,412,437,445,479,499,507],reflect:[],reformat:7,refresh:209,reg:484,regard:[6,61,260,310,311,316,440,444],regardless:[15,73,172,175,195,215,216,226,247,263,265,266,267,269,270,271,294,307,317,323,380,478,484,491],regim:[6,331,338,397,490],region:[],region_spher:8,region_styl:344,regist:[8,122,148,319,443,444],regoin:6,regress:507,regspher:172,regstrip:346,regul:6,regular:[1,3,9,42,64,92,170,174,196,199,210,220,239,335,366,397,416,478,481,483,485],reigon:507,reinhardt:[332,333],reject:[172,223,443,496],rel:[1,6,14,27,36,42,61,73,96,108,128,136,146,150,154,155,157,172,181,200,203,210,216,220,226,227,230,239,245,248,259,260,284,288,293,302,304,305,312,320,323,325,330,331,335,342,346,365,366,373,406,409,410,427,428,430,445,472,482,490,495,499,502,508],relat:[],relatic:[],relationship:[6,235,298,348,365,451,472,502,507],relax:[],releas:[0,5,7,8,13,221],relect:[3,435],reles:43,relev:[2,6,12,42,80,82,117,134,172,176,200,204,205,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,226,227,228,231,233,236,238,239,240,243,244,250,251,252,254,255,256,257,259,260,262,272,273,274,275,276,277,278,279,280,281,287,291,292,293,295,296,299,301,303,304,305,308,309,310,312,317,321,323,324,325,330,331,334,335,336,337,338,339,340,341,342,343,345,346,365,373,383,384,388,394,396,397,399,400,403,406,408,409,410,411,412,417,419,420,421,423,424,425,427,428,435,436,440,445,453,460,463,471,472,473,478,494,508],reli:[3,12,299,406,444,473,481,491],reloc:12,remain:[7,12,33,37,42,51,56,61,73,91,109,152,153,154,155,159,160,161,162,164,175,185,191,192,196,204,205,210,212,213,216,217,224,226,247,248,255,263,264,269,270,271,282,283,284,286,291,292,315,323,326,327,328,334,335,346,348,356,359,374,386,406,413,426,433,435,461,476,481,482,486,491,493,495,499,502,507,508],remaina:386,remaind:[172,196,227,293,323,336,466,481],remap:[3,6,12,61,63,73,155,172,195,216,226,245,260,284,365,481,482,483],remedi:[6,502],rememb:2,remov:[2,3,6,8,9,13,55,73,74,79,96,112,120,122,146,150,151,152,153,154,155,159,160,161,162,164,165,172,175,176,197,203,212,216,221,236,247,248,253,259,261,263,269,270,271,282,283,284,286,292,298,307,308,310,323,326,327,328,330,346,365,375,399,428,433,481,484,492,493,507,508],remove_bia:8,remove_bias_al:8,remove_molecul:209,remove_sourc:209,remove_speci:209,ren:171,renam:[12,347,492],render:[12,13,196,199,200],rendon:[263,264],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:[2,3,6,11,12,42,65,93,94,123,149,150,151,152,153,154,155,158,159,160,161,162,164,165,196,197,199,200,201,212,213,215,216,217,218,220,223,227,247,268,295,302,304,396,420,463,482,483,488,489,499,507,508,509,511],replic:[],replica:[],replica_fil:12,report:[],repositori:[7,12,414,442,443,444],reprens:335,repres:[1,3,6,8,9,12,15,41,42,43,61,69,73,94,119,122,184,192,196,197,199,212,213,214,215,216,217,218,224,230,240,242,247,250,263,290,292,294,302,307,308,312,320,335,337,344,366,375,381,386,409,416,426,427,428,430,431,432,438,441,443,444,467,468,476,478,481,491,493,496,502,507,509],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:[6,7,9,36,41,46,47,114,245,298,340,341,344,382,386,394,396,400,406,410,412,426,430,434,451,460,466,469,472,473,491],reqir:[298,300],request:[3,6,8,12,42,108,175,192,196,244,250,305,311,323,325,363,365,435,443,444,476,486,491,495,507,508,509],requir:[],rerun:[],rescal:[],research:[5,7,84,85,234,250,254,311,433,476,495],resembl:302,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],resort:3,resourc:[7,381,404],respa:[3,16,231,244,263,378,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,428,429,430,431,432,433,434,436,438,440,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,468,469,471,472,473,489,490,501,507],respecifi:433,respect:[1,6,9,10,13,14,15,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,46,47,48,49,50,52,54,55,57,61,72,73,91,93,101,102,115,118,124,128,149,154,157,159,166,170,171,178,179,181,182,183,184,186,187,189,190,192,197,199,200,216,217,222,223,224,226,242,245,247,248,250,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,298,299,307,308,312,320,322,335,340,343,349,351,352,354,355,358,360,363,365,366,370,373,374,379,380,381,382,384,386,387,388,389,390,391,392,394,395,396,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,430,431,433,435,436,437,438,440,445,446,450,451,452,453,462,463,464,465,466,467,469,471,472,473,478,482,491,494,502,507,509,511],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:[1,2,3,6,7,9,11,12,13,15,16,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,46,47,48,49,50,52,54,55,57,65,66,68,69,73,77,91,94,95,98,108,109,111,115,116,118,120,121,122,123,124,125,147,149,152,155,159,166,167,169,171,172,175,178,179,181,182,183,184,186,187,189,190,192,195,196,197,199,200,203,206,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,230,233,235,238,239,240,242,247,248,250,254,261,263,265,266,267,268,269,270,271,272,273,280,282,283,284,285,286,289,290,298,299,304,305,307,309,310,323,326,328,331,332,333,335,336,337,339,340,341,343,345,348,349,351,352,354,355,358,360,365,366,375,378,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,430,431,433,435,436,437,438,440,444,445,446,453,462,463,464,465,466,467,469,471,472,473,476,478,481,483,484,485,486,490,491,492,493,495,506,507,508],resum:507,retain:[2,221,222,386,433,478],retart:[33,51,185,356],retir:[3,443],retreiv:8,retriev:[6,8,237,431,432,507],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],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:[3,6,11,12,42,148,172,190,191,195,197,220,223,245,250,260,287,348,368,396,481,484,491,507],rightmost:[42,220],rigid:[],rigidifi:307,rii:[93,94],rij:[96,112,221,222,288,400,401,402,460],rin:[412,423,424],ring:[],rino:[75,469],rinv:365,rirj:[341,410],rise:[],risi:[146,452],risk:[8,306,490],rix:[93,94],rjk:[221,222],rjone:[7,9,13],rlo:463,rmask:[3,507],rmass:3,rmax:[73,173,221],rmdir:492,rmin0:[146,452],rmin:[73,173,222,420],rmsd:334,rnemd:6,robert:9,robin:200,robust:[371,372,373],rock:430,rockett:441,rod:307,rodata:12,rodnei:302,roi:7,role:330,roll:12,ronchetti:112,room:[59,61],root:[11,91,93,94,198,330,334,380,404,488],rosati:40,rose:430,ross:430,rosski:290,rosybrown:200,rot:[6,95,290,306,330,508],rotat:[],rotation:112,rotaton:484,rough:[6,172,199,345],roughli:[7,10,12,42,155,199,214,239,247,248,262,263,277,294,307,323,326,327,330,366,375,380,447,449,483,490],round:[],rous:240,rout:[91,412,426],routin:[5,6,8,11,15,16,38,40,57,92,176,178,250,433,442,463,494],roux:[6,230,248,467,502],row:[6,67,68,70,71,77,81,94,97,98,109,111,114,120,121,122,125,152,160,167,169,170,171,212,213,215,216,217,218,253,307,335,337,345,406],royalblu:200,rozero:430,rperp:[260,316],rpi:292,rpm:12,rrespa:[1,3,5,7,8,16,204,205,260,263,376,381,382,383,384,385,387,388,389,390,391,392,394,395,396,397,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,428,429,430,431,432,434,436,438,440,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,468,469,471,472,473,490],rspace:3,rsq:[463,470],rsurfac:335,ru3:171,ru4:171,rub:20,rubia:[431,432],rudd:[435,463],rudra:[7,9],rudranarayan:[7,292],ruiz:210,rule:[],run1:[6,379,507],run2:[6,362,364,379,507],run3:[6,379,507],run4:[6,379,507],run5:[6,379,507],run6:[6,379,507],run7:[6,379,481,482,486,507],run8:[6,379,507],run:[],run_styl:[],runloop:364,runtim:[12,17,199,380],russia:9,rutherford:335,rutuparna:[464,466],ryan:9,ryckaert:[310,358],rycroft:170,rydberg:433,s00:440,s0st:6,s2050:1,s2629:404,s319:209,s_fact:313,s_i:[6,406],s_ij:6,sack:7,saddl:[262,375],saddlebrown:200,sadigh:[210,404,431,432],saed_vtk:124,safe:[12,199,230,248,380],safe_zon:3,safest:[3,323],safeti:313,safezon:444,safran:472,sagui:[366,399],sai:[1,3,12,13,200,443,444,479],said:373,sakai:465,sall:[9,451],salmon:200,salt:[397,408,430,481],salter:451,same:[1,2,3,4,6,8,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,38,40,41,42,44,45,46,47,48,49,50,51,52,54,55,57,59,61,64,65,67,71,73,74,79,81,83,86,88,89,91,92,93,94,95,96,97,99,102,108,109,110,112,114,115,116,118,119,121,122,123,146,147,148,149,150,151,152,153,154,155,158,159,160,161,162,164,165,166,168,170,172,173,174,175,176,178,179,180,181,182,183,184,185,186,187,189,190,192,194,195,196,197,198,199,200,203,204,205,206,209,210,212,215,216,217,218,219,220,221,222,223,224,226,227,231,232,233,238,239,240,241,242,243,244,245,246,247,248,249,250,253,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,285,286,288,289,290,292,293,294,297,298,299,300,302,303,304,305,306,307,309,310,312,317,320,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,341,342,343,344,346,347,348,349,350,351,352,354,355,358,360,365,366,368,369,370,374,375,376,377,378,379,380,381,382,384,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,403,404,405,406,407,408,409,410,411,412,413,414,417,418,419,420,421,422,423,424,425,426,427,428,430,431,434,435,436,437,438,440,441,445,446,451,453,460,461,462,463,464,465,466,469,471,472,473,476,478,479,481,482,483,484,486,489,490,491,492,493,494,495,499,502,506,507,508,510],sampl:[1,2,4,6,9,10,11,12,14,95,108,150,151,165,170,195,199,203,212,213,216,217,225,227,237,239,241,243,263,264,290,293,302,304,308,320,321,323,327,330,333,345,376,386,403,481,495],sample_frequ:209,san:440,sandia:[0,5,7,9,13,14,17,72,117,407,430,440],sandybrown:200,saniti:[306,376],satellit:[6,154],satifsi:507,satisfi:[3,12,75,124,146,171,224,250,268,310,343,373,376,410,495],satur:397,save:[6,8,12,19,41,61,192,197,199,214,223,240,241,247,248,249,293,302,335,347,366,376,378,386,483,486,493],sb3:171,sb5:171,sc3:171,scalabl:[],scalar:[],scale:[0,1,3,4,5,6,9,10,13,18,41,61,65,73,74,95,119,122,123,146,158,166,192,195,196,197,199,200,203,204,205,209,210,213,224,226,239,243,244,245,247,249,250,261,263,265,266,267,268,269,270,271,290,294,297,298,307,314,315,323,325,327,330,332,333,335,339,346,365,366,368,374,377,381,382,383,397,403,406,410,413,427,428,430,433,440,447,449,467,482,484,486,490,493,495,498,499,507,508],scale_factor:[447,449],scalegamma:250,scalexi:[3,224,263,268],scalexz:[224,263,268],scaleyz:[224,263,268],scan:[200,222,364,482],scatter:[11,124,171],scatter_atom:11,scatter_coord:11,scenario:[6,41,63,223,296,305,323,336,344,376,485,486,490,498],scf:502,schaik:426,schedul:476,schell:465,schemat:223,scheme:[6,9,18,240,241,263,290,302,310,335,365,467],schlitter1:334,schlitter2:334,schlitter:334,schmid:400,schneider:[247,249],schoen:365,schr:502,schroding:406,schroeder:[112,502],schulten:[248,312,366,502],schunk:323,schwen:9,sci:[75,343,395,432,441,451],scienc:[8,209,223,244,312,332,404,431,451,465],scientif:[146,404],scm:11,scratch:[12,42,220],screen:[],screenshot:11,scripe:11,script:[],scripta:69,scsl:12,sdk:[],sea:11,seagreen:200,seamlessli:296,search:[0,2,3,8,12,96,112,173,175,200,201,323,371,372,373,375,377,476,482,483,495,507],seashel:200,sec:[12,501,506],second:[1,3,6,9,10,11,12,16,55,59,61,63,73,92,95,108,110,112,118,139,140,144,147,148,160,166,170,171,173,174,175,195,196,200,203,204,212,213,215,216,217,218,223,239,240,245,260,262,290,304,306,307,310,312,320,321,323,332,333,335,346,365,368,372,373,375,376,380,385,386,387,389,390,395,396,404,406,407,410,411,413,416,417,420,430,435,437,451,462,465,466,467,469,473,476,477,478,479,481,483,488,490,494,495,499,502,506,507,508,509,511],second_mo:451,secondari:[3,184],sectinn:510,section:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,42,43,44,45,46,47,48,49,50,51,52,54,55,56,57,60,61,65,66,67,68,69,70,71,73,76,77,80,81,82,83,84,87,90,91,92,93,94,95,97,98,101,102,103,104,105,106,108,109,110,111,113,114,115,117,118,119,120,121,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,178,179,180,181,182,183,184,185,186,187,189,190,191,192,195,196,197,198,199,201,203,206,207,208,209,210,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,229,230,232,233,235,236,238,239,240,241,242,244,246,247,248,249,250,251,252,253,254,256,257,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,278,280,281,282,283,284,285,286,288,289,290,292,293,294,296,297,298,299,300,301,302,303,304,307,309,310,311,312,313,314,315,316,317,319,323,326,327,328,329,330,331,332,333,334,335,336,338,339,341,342,343,346,347,349,350,351,352,353,354,355,356,358,359,360,366,367,368,370,374,375,377,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,436,437,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,476,477,478,479,481,482,484,486,489,490,491,492,494,495,496,499,500,502,507,508],section_acceler:[9,12,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,115,118,149,159,178,179,181,182,183,184,186,187,189,190,192,206,219,226,233,238,242,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,299,307,309,310,326,328,339,343,349,351,352,354,355,358,360,366,381,382,384,387,389,390,391,392,394,395,396,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,431,436,437,438,440,445,446,453,462,463,464,465,466,469,471,472,473,484,490],section_accerl:404,section_command:[0,1,9,348],section_error:[7,12],section_exampl:[2,6],section_histori:[7,12],section_howto15:85,section_howto:[6,8,9,11,12,41,43,59,61,66,68,69,70,72,73,74,75,77,78,79,80,82,83,86,87,88,89,90,91,93,94,96,98,99,100,101,102,103,104,105,106,109,111,112,115,116,117,120,122,123,126,141,142,143,144,146,147,152,154,166,167,169,170,174,194,212,262,275,278,281,338,385,398,476,481,484,495],section_modifi:[6,7,43,196,197,199,499],section_packag:12,section_perf:7,section_python:[6,12],section_start:[3,4,6,9,11,369,375,475,476,490,496,499],section_tool:[6,7],see:[1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,59,60,61,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,232,233,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,256,257,258,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,280,281,282,283,284,285,286,288,289,290,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,309,310,311,312,313,314,315,316,317,319,320,322,323,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,362,365,366,368,369,370,372,373,374,375,376,377,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,475,476,477,478,479,481,482,483,484,486,487,488,489,490,491,493,494,495,496,497,498,499,500,501,502,507,508,509,510,511],seed1:496,seed2:496,seed:[3,172,175,195,199,208,210,221,222,223,225,227,236,239,240,241,247,248,249,250,290,293,297,302,307,323,327,330,335,342,388,400,402,403,476,491,496,502,507,508],seed_com:248,seed_drud:248,seek:[42,220],seem:[6,224,336,372,430,490],seen:[12,250,344],segement:3,segment:[3,4,6,7,12,41,43,86,119,199,203,278,293,307,323,400,416,444,460,461,481,489,491],select:[3,6,12,15,61,63,73,123,124,161,166,171,172,192,199,201,208,210,216,217,226,227,236,239,244,245,260,312,322,330,331,336,338,340,342,343,345,363,365,371,375,377,380,412,417,430,451,478,482,484,490,491,495,500,507],self:[],sellerio:13,semi:[3,201,209,210,287,289,482],semiax:150,semimet:406,send:[0,3,5,7,8,11,12,200,244,478],sender:[3,478],sens:[1,3,6,7,18,40,42,43,61,73,108,191,196,212,215,216,217,218,220,223,226,240,241,246,247,248,249,293,297,302,308,323,330,331,335,338,346,375,396,418,422,464,465,466,476,481,486,490,493,498],sensabl:244,sensibl:109,sensit:[2,6,75,224,302,508],sent:[200,244,363],sep:[6,11,507],separ:[2,3,6,7,9,12,13,41,42,78,122,128,146,172,175,197,199,200,201,209,213,220,221,222,223,224,227,230,239,247,248,263,277,290,293,294,296,298,302,307,310,323,326,327,328,331,338,346,366,380,387,389,396,397,399,401,402,418,427,428,430,437,442,452,461,462,463,466,472,479,481,482,483,490,493,498,502,508,509,510],seper:397,sequec:507,sequenc:[2,3,12,42,61,196,197,199,200,201,220,241,262,346,368,375,413,441,496,507],sequenti:[61,62,200,441,482],sequestr:7,ser:289,seri:[3,4,6,9,13,18,146,196,197,199,200,213,218,240,241,293,379,382,409,430,433,435,445,453,463,479,488,489,496,498,499,507],serial:[],serial_icc:12,serious:8,serv:[6,134,174,323,460],server:[1,246,380],set:[],set_callback:237,set_energi:237,set_vari:[6,11,479],setarea:250,sete:[212,223],setenv:[11,12,393],setfl:[13,381,404],setforc:[],setgamma:250,setmask:8,settl:224,setup:[3,4,6,7,8,11,12,13,16,37,41,56,61,73,91,95,160,173,174,175,176,191,200,209,223,226,323,336,359,376,377,380,461,478,481,489,509,511],setup_pre_exchang:8,setup_pre_forc:8,setup_pre_force_respa:8,setvel:[],seven:432,seventh:[139,144],sever:[1,4,5,6,7,8,10,11,12,13,15,18,40,41,65,73,91,166,173,176,191,196,197,198,201,203,209,221,222,224,241,247,250,254,263,292,294,296,307,312,323,330,339,363,368,373,380,383,386,390,403,404,413,422,426,430,435,441,443,444,450,451,476,479,483,487,495,499,502,507,508],sexton:433,sfactor:[3,199,200,374],sfftw:12,sgi:12,sgmc:210,sgrid:323,sgroup:170,shade:199,shake:[],shan:[17,298,299,395],shanghai:[9,13],shape:[],shapei:[119,481],shapex:[119,481],shapez:[119,481],shapshot:486,shardlow:[],share:[],shared0:[],sharon:307,sharp:[344,430,466],shawn:9,shear:[3,4,5,6,7,9,61,63,155,195,224,226,250,263,284,323,338,341,410,427,428,440,448,450],sheet:485,shell:[],shen:9,shenderova:382,sheppard:372,shflag:12,shield:[],shift:[],shiftse:323,shiga:[6,263,264],shini:[199,510],shinoda:[6,9,263,264,446],shiny:199,ship:201,shlib:[11,12],shlibflag:12,shock:[],shockvel:[261,297],shortcut:[224,263,294,307],shorter:[3,125,239,288,377,435,489],shortest:[199,377,383,490],shorthand:200,shoul:468,should:[1,2,3,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,43,44,45,46,47,48,49,50,52,54,55,57,61,63,72,73,75,83,87,91,95,101,102,103,107,108,109,115,116,118,147,149,150,151,154,155,158,159,160,162,165,168,172,174,176,178,179,180,181,182,183,184,186,187,189,190,192,194,195,196,197,199,200,204,205,206,207,210,214,219,220,221,222,223,224,226,227,229,230,232,233,235,236,237,238,239,240,241,242,243,245,247,248,249,250,252,253,254,255,260,263,265,266,267,268,269,270,271,272,273,277,280,282,283,284,286,288,289,290,291,292,293,294,295,297,298,299,300,301,302,303,304,305,306,307,309,310,317,320,323,324,326,327,328,329,330,331,334,335,336,338,339,340,341,342,343,344,345,346,348,349,350,351,352,354,355,358,360,366,368,369,371,373,374,375,376,377,378,380,381,382,384,385,387,388,389,390,391,392,393,394,395,396,398,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,430,431,433,435,436,437,438,439,440,442,443,445,446,447,449,451,453,460,462,463,464,465,466,467,469,471,472,473,476,477,478,479,481,482,483,484,485,486,488,489,490,491,493,497,498,499,502,507,508,509],shouldn:[3,8],show:[6,11,12,122,288,375,412,430,433,463],shown:[1,12,16,17,42,101,102,124,146,158,171,191,220,223,247,263,284,290,293,302,330,365,406,407,409,410,426,433,445,451,481],shrank:73,shrink:[3,6,42,59,61,73,174,195,196,199,204,205,208,220,226,227,245,250,288,323,342,346,365,366,373,396,418,422,435,481,482],shrunk:73,shut:[6,11,376,480],si4:171,siam:343,sic:[4,396,413,430,437,462,464,466,469],sic_tersoff:441,sicc:[405,462,464,466,469],sicg:[464,466],sicsi:[405,462,464,466,469],side1:484,side2:484,side3:484,side4:484,side:[3,8,42,59,63,73,162,172,210,211,220,223,227,239,245,250,260,288,293,301,320,340,344,345,346,375,396,409,410,445,468,479,481,484,491],sidewai:4,sienna:200,siepmann:338,sigam:394,sigam_ii:[],sige:[464,466],sigma0:386,sigma14:426,sigma1:386,sigma2:386,sigma:[3,6,10,46,47,51,55,91,178,196,197,200,204,205,239,250,288,311,323,339,340,344,368,377,380,382,385,386,387,391,392,394,399,400,402,403,405,406,409,411,412,416,417,418,419,420,421,422,423,424,425,426,429,434,435,445,446,456,462,468,490,506,507,508],sigma_14:391,sigma_:397,sigma_c:394,sigma_cc:[382,394],sigma_h:408,sigma_i:[407,435],sigma_ii:468,sigma_ij:[435,468],sigma_j:435,sigma_max:403,sigma_ss:394,sign:[3,6,12,183,191,287,320,343,348,433,489,498,507],signal:480,signicantli:17,signifi:[3,68,77,94,98,109,111,120,152,167,169],signific:[7,12,18,90,240,261,264,302,323,336,406,409,430,433,435,509],significantli:[1,6,40,147,170,250,263,306,406,462],sij:213,sikandar:17,silbert:410,silent:[200,479,492],silicon:[405,430,462,481],sill:440,silver:200,sim:[9,446],similar:[5,6,7,8,9,11,12,17,18,41,42,43,47,61,70,74,91,118,121,122,147,148,172,173,196,197,200,203,204,205,212,214,220,237,238,240,247,253,254,264,296,297,302,306,307,327,330,340,341,343,345,366,371,372,374,382,385,386,400,404,406,410,426,427,435,440,441,450,463,478,483,488,490,495,497,499,502,507,508,509,511],similarli:[3,6,7,8,61,118,168,174,176,195,196,199,200,211,212,215,216,217,218,222,226,232,245,263,265,266,267,269,270,271,292,294,307,308,310,323,330,331,338,344,349,366,368,375,378,390,410,422,462,478,481,484,485,490,491,495,510],simluat:[6,40,200,323,427,482,483],simlul:[307,335],simmul:338,simpl:[],simpler:[8,11,43,200,307],simplest:[3,8,41,68,77,94,98,109,111,120,122,152,167,169,298,502],simpli:[1,3,6,8,11,12,14,17,68,73,77,92,94,98,100,109,111,119,120,125,152,167,169,175,176,200,203,204,205,212,215,216,217,218,222,224,226,230,237,246,248,253,263,290,294,305,307,308,331,337,338,365,366,368,374,375,380,390,399,413,422,430,435,478,479,486,489,496,499,506,507],simplif:406,simplifi:[210,306,433],simplist:11,simualt:366,simul:[],simulatan:380,simulation_nam:444,simulationub:451,simulatoin:[12,482],simult:380,simultan:[6,7,15,16,226],sin:[226,260,340,343,345,441,481,484,491,507],sinc:[0,1,2,3,6,8,9,10,11,12,13,15,16,21,22,33,40,42,45,55,61,63,66,69,73,75,93,94,116,122,124,150,152,162,170,174,175,177,178,180,185,196,197,199,200,203,204,205,206,207,210,211,212,213,214,215,216,217,218,219,220,223,224,225,226,227,231,232,239,241,243,246,247,249,250,260,263,265,266,267,268,269,270,271,274,277,284,288,290,293,295,296,302,305,307,312,322,323,331,335,336,337,338,340,341,344,345,346,347,349,350,364,366,373,374,375,376,379,380,381,382,386,389,390,391,392,394,395,399,400,403,404,405,409,410,411,413,414,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,438,441,442,443,444,445,446,451,452,453,462,463,464,465,466,469,473,476,478,479,481,482,484,486,489,490,491,492,493,495,499,502,506,507,508,510],sinclair:[7,404,461],sine:441,singapor:146,singh:381,singl:[1,2,3,6,7,8,9,11,12,14,15,16,17,18,41,42,43,59,61,63,65,67,68,70,71,77,79,81,91,92,94,97,98,108,109,111,114,119,120,121,122,123,125,148,152,167,169,170,172,196,197,199,200,201,203,208,211,212,213,215,216,217,218,220,222,223,224,227,230,236,238,243,250,253,260,263,264,268,277,290,292,293,295,306,307,308,310,313,319,323,325,335,337,340,341,343,345,346,348,365,366,371,374,375,376,377,379,380,381,382,386,391,393,395,403,404,405,406,407,410,411,412,413,414,415,430,431,432,433,437,438,441,442,443,444,445,451,452,453,462,464,465,466,469,476,477,479,481,488,489,490,491,492,493,494,495,496,498,507,510,511],singleel:386,singular:[426,427,428],sinnott:[299,382,395],sinusoid:[172,226,340,341,343,345],sio2:469,sio:395,sirk:[147,460],sisic:[405,462,464,466,469],sisisi:[405,462,464,465,466,469],sister:393,sit:[289,481],site:[0,1,2,3,4,5,6,7,8,10,11,12,13,14,15,16,17,69,72,91,244,250,251,310,366,381,386,396,404,408,418,422,426,438,443,444,467],situat:[9,170,224,239,250,263,290,308,372,386],sival:171,six:[6,139,144,146,213,215,437,441],sixth:437,sixthpow:[392,435],size:[],size_restart:8,sizei:416,sizej:416,sizescal:3,sizex:271,sjplimp:[0,7,11,12],sjtu:9,skew:[3,6,60,61,174,199,226,263,481,484],skin:[3,12,40,63,75,121,173,175,239,277,307,311,335,376,377,380,416,439,499,506],skip:[12,16,33,185,292,293,364,374,379,417,481,486,489,498,507],skyblu:200,slab:[3,6,73,160,216,293,320,365,366,376,435],slateblu:200,slategrai:200,slater:[],sleight:55,slepoi:430,slice:[],slider:11,slight:[3,12,335],slightli:[1,6,40,41,196,197,198,199,201,302,307,366,382,396,418,422,464,466,469,476,489,509],sligthli:399,sliozberg:460,slip:[3,203,323,339,345],sllod:[],slope:[6,108,109,331,333,338,397,507],slot:1,slow:[3,6,7,12,40,240,244,247,248,261,263,323,330,365,375,380,435,451,490,500,502,508],slower:[1,10,17,40,248,366,380,386],slowest:[335,478],slowli:[12,73,220,339,373,433,453,483],slurm:12,slurm_localid:12,sm3:171,small:[],smallbig:3,smaller:[1,3,6,12,16,17,40,57,61,63,73,125,174,196,197,199,200,210,227,231,239,250,289,307,323,333,348,365,366,371,380,435,461,468,470,481,488,490,507,511],smallest:[3,43,72,73,74,170,261,304,507],smallint:3,smallq:366,smallsmal:[3,12],smart:241,smd:[],smd_contact_radiu:[],smd_lammps_userguid:9,smd_mass_dens:[],smd_user_guid:[],smi:[3,380],smirichinski:9,smit:239,smith:438,smmoth:491,smooth:[],smoother:172,smoothli:[55,146,331,338,391,411,424,426,429,466,473],smpd:12,smtb:[9,451],smtbq:[],smulat:433,sn2:171,sn4:171,sna:[],snad:[],snap:[],snapcoeff:452,snaphot:486,snapparam:452,snapshot:[],snav:[],snb:17,snow:200,soc:412,socket:[12,17,18,246,478],soderlind:433,soft:[],softer:[340,344],softwar:[1,6,9,11,12,14,15,16,17,18,19,170,244,292,308],sole:[221,222,375,441,448,450],solid:[4,6,7,9,10,40,41,42,61,72,75,95,108,147,170,209,220,224,226,231,253,263,265,266,267,269,270,271,288,289,294,307,330,333,366,368,387,420,433,440,448,450,481],solut:[3,6,13,170,224,231,261,305,310,323,344,507],solv:[3,9,12,18,250,298,310,333,335,366,372,428],solvat:[4,10,172],solvent:[4,7,13,63,73,173,175,220,236,240,241,247,263,305,307,320,323,331,338,339,391,394,396,397,408,418,427,428,445,461,481,491],solver:[],some:[1,2,3,4,6,7,8,9,10,11,12,13,16,17,18,40,41,42,56,63,65,73,107,110,113,119,123,125,150,151,152,153,164,165,166,170,172,175,180,183,191,194,196,197,199,200,203,204,205,208,210,211,212,213,215,216,217,218,220,222,223,224,225,236,239,261,263,264,293,295,296,298,300,307,312,324,330,335,336,337,339,340,346,363,364,365,366,371,372,373,374,375,376,377,380,383,385,386,393,396,404,406,413,416,433,435,443,444,461,463,474,476,478,479,480,481,483,486,487,488,489,490,491,493,495,498,499,506,507,508,511],somehow:3,someindex:347,someon:[7,373],someth:[2,3,7,8,11,12,61,224,263,340,343,345,376,413,479,488],sometim:[2,3,6,8,12,18,216,224,263,331,338,365,377],somewhat:[7,9,12,72,108,152,162,212,263,365],somewher:[17,264,406],soon:[3,43,210,223,236,239,244,443],sophist:[7,148],sorensen:495,sort:[3,13,16,40,73,196,197,200,201,244,375,376,380,403,482,483,510],sound:[134,250,261,313,458,459],soundspe:[458,459],sourc:[],source_integr:209,sourceforg:11,south:146,souza:331,space:[2,3,6,8,11,12,18,42,61,73,124,146,161,166,171,172,192,195,199,204,205,208,215,216,217,220,222,226,227,245,250,257,260,263,289,290,305,308,313,323,340,342,343,345,348,365,366,368,374,375,376,387,389,390,396,399,404,406,416,418,422,430,433,438,441,446,463,470,472,478,481,484,493,499,502,507,508],spahn:410,span:[2,12,38,73,204,205,216,245,307,365,381,382,386,395,404,407,414,415,430,431,432,437,441,452,462,464,465,466,469,475,476,484,485,507],spars:[73,192],spatial:[],spawn:244,spc:[],spcpu:499,speak:[17,323,330],spearot:[124,171,308],specfi:[12,113,245,484],speci:[],special:[],special_bond:[],specif:[1,2,3,6,7,8,9,10,12,13,15,16,17,18,22,29,33,41,42,43,51,65,73,114,119,121,122,152,154,157,170,172,180,185,196,197,199,200,201,203,204,205,208,209,212,213,215,216,217,218,220,223,225,236,237,239,240,244,250,258,293,295,296,299,307,330,335,336,340,346,350,366,373,375,380,382,385,386,398,404,409,410,413,414,415,430,433,435,443,444,445,461,462,467,468,478,481,482,486,487,488,490,491,497,498,499,506,507,508,509],specifi:[2,3,6,7,8,9,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,54,55,56,57,58,59,61,63,65,67,68,70,71,72,73,75,77,78,79,80,81,82,83,87,89,90,91,92,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,147,149,152,154,159,160,161,166,167,168,169,170,171,172,173,174,175,176,178,179,180,181,182,183,184,185,186,187,189,190,191,192,193,195,196,197,198,199,200,201,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,235,238,239,240,241,242,243,245,246,247,248,250,251,252,253,255,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,277,280,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,316,317,320,321,322,323,324,325,326,327,328,330,333,334,335,337,339,340,341,342,343,344,345,346,347,348,349,350,351,352,354,355,356,358,359,360,361,364,365,366,368,369,370,373,374,375,376,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,502,506,507,508,509,510,511],specifii:[241,250],speciti:490,spectral:452,spectrum:[9,146,297,302],sped:[40,261],speed:[1,3,6,9,12,14,15,16,17,18,19,40,42,134,196,200,220,247,250,261,297,313,323,330,336,342,365,366,375,380,386,396,433,435,458,459,464,476,490,496],speedup:[1,18,366,490],spefici:[172,199,412],speicifi:[],spell:484,spellmey:[6,178,493],spend:[12,211],spent:[1,12,13,15,476,495,500],sperhic:481,sph:[],sph_lammps_userguid:9,sph_user_guid:[],sphere1:250,sphere:[],spheric:[],spheriod:[3,6],spherioid:323,spheroid:[6,263,280,307,323],spike:122,spin:[9,41,119,197,341,383,406,481],spirit:[7,214],spit:3,spline:[],split:[1,3,6,9,11,12,18,42,212,216,220,248,263,311,343,365,380,402,468,475,478,490],splittol:[6,365],sppark:6,spread:[1,6,12,348,489],spring:[],springer:312,springgreen:200,sptial:73,sputter:227,sq2:[3,368],sqrt:[2,3,43,61,83,93,112,239,247,249,288,323,339,341,368,394,400,404,408,410,430,435,507],squar:[],squeez:[224,245,427,428],squibb:[5,7],sr2:171,src:[0,1,3,4,6,7,8,9,11,12,14,15,16,17,18,19,170,196,237,310,433],srd:[],srmax:73,srmin:73,srolovitz:404,srp:[],srtio:451,srun:12,ssa:311,ssao:[199,510],stabil:[6,9,247,263,386,443],stabl:[6,66,134,250,268,306,313,386,502],stabli:240,stack:[3,8,72],stage:[3,8,91,203,237,262,301,346,375,476,495,507],stagger:[1,2,3,200,366,488,497,507],stai:[3,14,17,204,205,261,279,297,380,481],stamp:[203,330,482],stamped:12,stan:17,stand:[0,6,7,12,13,303,443,444,479],standard:[],stanford:9,starikov:335,start:[],start_6:408,start_7:490,startstep:507,stat:[12,55,176,288,302,373,400],statcoul:506,statcoulomb:506,state:[],statement:[3,479,480],stationari:[],statist:[3,6,12,34,40,42,53,66,188,214,221,222,223,240,241,247,248,249,292,293,297,302,307,310,323,334,335,336,357,373,375,382,400,403,410,427,472,476,483,489,491,495,498,499],statu:[3,12,55,62,127,176,225,230,248,395,480,495],statvolt:506,std:12,stdin:[3,12,364],steadi:[6,261,268,297],steelblu:200,steep:463,steepest:[7,372],steer:[7,9,225,228,312],stegailov:335,steinhardt:[65,112],steinhaus:502,stencil:[3,250,365],step:[1,2,3,6,8,10,11,12,13,14,15,16,17,18,19,40,73,95,101,102,116,122,123,134,147,158,168,170,196,198,199,200,201,203,204,205,209,210,212,213,214,215,216,217,218,220,221,222,223,224,226,227,230,231,236,237,239,241,244,245,248,261,277,288,289,293,295,296,297,298,299,300,308,310,311,312,313,323,325,328,329,330,331,332,333,334,335,336,337,338,345,346,348,364,365,371,373,375,376,400,408,412,430,433,443,444,451,476,478,479,483,485,486,488,489,490,495,496,498,499,502,507,511],stepani:312,stepwis:91,stesman:330,steve:[0,5,7,13],steven:223,stiff:[6,41,52,221,222,289,290,373,440,502],stile:397,still:[1,3,6,9,11,12,13,14,17,38,39,42,58,63,73,96,114,122,170,176,192,193,194,196,197,200,204,205,220,243,247,277,298,302,323,335,348,361,365,366,371,392,404,409,410,413,417,427,439,443,445,453,461,481,483,489],stilling:[3,5,7,15,92,148,405,432,441,461,462,469,493],stipul:244,stl:[9,73,316,319],stl_surf:319,stochast:[4,7,9,203,241,311,323,330,345,402,403],stockmay:41,stoddard:399,stoichiometri:451,stoke:[250,339],stoll:[247,249],stone:[9,19,366,399],stop:[],stopstep:507,stopthresh:[42,220],storag:[3,12,15,337,380,493],store:[],store_st:324,storm:12,stouch:7,str:507,straatsma:6,straddl:[3,61,63,162,245,307,320,346,481,485,491],straight:307,straightforward:[13,406,502],strain:[],strang:[192,199,507],strategi:[],stratford:250,strcmp:348,stream:[3,6,118,147,152,155,156,199,209,226,240,241,247,248,284,293,302,323,508],streamlin:[12,489],streitz:[],streiz:396,strength:[3,9,146,166,177,199,306,340,344,413,444,445,493],stress:[],stretch:[3,55,61,123,221,312],strict:452,strictli:[6,42,192,220,261,297,330,481],stride2:507,stride:[200,241,488,497,507],strietz:396,strike:227,string:[2,3,6,11,12,42,172,196,197,198,200,212,213,214,215,216,217,218,220,239,295,308,348,367,379,430,441,442,443,452,477,479,481,491,492,498,499,507],strip:507,strong:[298,382],stronger:6,strongest:[427,428],strongli:[1,6,13,227,307,310,335,433,502],structrur:3,structur:[],structured_point:308,strucur:75,stuart:[298,299,382,395,451,461],stub:12,stuck:224,student:292,studi:[6,110,420,451],studio:[],stukowski:[210,404],style1:[33,51,185,356,413,481],style2:[33,51,185,356,413,481],style:[],style_nam:[263,264],stylecomput:451,stylist:8,sub1:492,sub:[1,3,4,6,7,8,9,11,12,13,18,33,37,40,41,42,43,51,56,60,63,65,70,91,95,113,146,166,174,185,191,198,199,200,204,205,220,224,226,263,264,268,289,297,302,307,310,311,335,336,344,346,356,359,368,370,380,385,395,403,409,410,412,413,416,435,443,444,445,451,467,468,473,478,481,484,490,498],subbox:[123,199,200],subcutoff:416,subdirectori:4,subdivis:250,subdomain:250,subequ:11,subgroup:[196,510],subinterv:198,subject:[6,42,175,220,467],submit:[],subramaniyan:13,subroutin:380,subscript:[11,335,349,407,469,507],subsequ:[3,6,11,12,42,61,108,173,200,214,220,224,239,330,335,336,337,368,379,404,461,479,481,482,488,491,492,501,507,511],subset:[6,11,12,16,42,82,146,196,197,200,220,259,263,265,266,267,268,269,270,271,293,294,298,307,375,380,382,386,413,435,475,478,481,483,486,490,507],substanti:[6,16,462,490],substep:263,substitut:[1,2,3,12,196,246,375,379,406,435,479,492,507],substract:396,substrat:[174,224,263,265,266,267,269,270,271,294,307,481],substyl:[426,490],subsystem:335,subtl:[99,101,102,241],subtleti:158,subtract:[3,6,55,65,73,95,99,102,107,108,110,118,147,149,150,151,152,153,154,155,156,158,159,160,161,162,164,165,196,197,203,212,239,240,243,247,248,249,251,255,259,284,291,307,346,376,425,481,491,499,507,508],succe:12,succeed:[213,214],succes:214,succesfulli:3,success:[2,6,11,12,14,15,122,196,200,210,213,224,227,239,277,293,307,323,330,348,373,375,479,480,488,489,496],successfulli:[3,11,196,227,479,492],successulli:11,successv:486,sucessfulli:3,sudden:36,suddenli:344,sudo:[11,12],sufac:43,suffer:[16,17,18,338,344,380],suffici:[2,3,7,17,18,42,63,73,198,216,220,261,263,289,323,330,337,340,348,417,435,481,502],suffix2:12,suffix:[],suggest:[0,6,7,12,261,297,479,502],suit:[7,9,13,205,250,406],suitabl:[4,12,13,17,55,91,196,223,296,327,386,393,410,426,430,443,444,476,495],sukumaran:214,sum:[3,6,8,9,12,41,72,73,78,82,87,92,93,94,96,99,103,108,110,112,113,115,116,118,122,123,129,145,146,147,149,152,153,154,155,158,159,160,161,162,164,166,168,169,170,212,213,215,216,217,218,227,237,240,247,248,253,288,289,293,297,302,307,308,312,322,333,335,337,340,344,346,365,366,373,385,396,400,406,407,416,418,421,430,443,444,452,468,479,499,502,507,508],summar:[6,407,451],summari:[],summat:[6,9,43,72,92,112,365,366,390,396,404,405,418,422,433,451,462,464,465,466,469],summer:[3,13,216,443,444],sumsq:123,sun:[21,44,179,349,392,435,444],sunderland:17,sup:[289,297,302,395,451,502],supercomput:[12,18,479],superpos:[413,461],superposit:7,supinski:433,supplement:[241,443,444],supplementari:[225,409,445],suppli:[12,192,239,261,335],support:[1,3,6,7,8,9,11,12,13,14,15,16,17,18,19,41,42,43,63,91,92,107,113,196,197,198,199,200,201,204,205,206,207,212,220,223,224,225,232,237,241,242,245,247,248,249,250,258,261,263,265,266,267,268,269,270,271,282,283,284,285,286,288,289,294,297,299,301,306,307,309,313,314,315,316,317,319,320,322,326,327,328,329,333,338,340,344,363,364,365,366,372,373,374,380,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,468,469,471,472,473,478,482,483,484,488,490,491,492,494,495,501,502,506,507,510,511],suppos:[3,8,407,507],suppress:[6,12,170],sure:[6,8,11,13,14,192,204,205,224,293,307,310,345,404,463],surf:[140,173],surfac:[2,3,4,6,8,9,41,43,59,72,124,140,146,170,172,175,199,203,227,236,245,250,253,288,299,306,316,319,320,323,330,335,340,344,345,375,386,413,427,428,433,449,451,468,472,478,484],surface_mov:335,surfact:[397,408],surpris:406,surrog:9,surround:[38,57,72,172,192,200,224,235,263,265,266,267,269,270,271,288,294,307,463,502],suspect:3,suspens:[427,428],sustain:[196,197,224,410],suzuki:[263,307],svg:6,svn:[7,11,12],sw_exampl:442,swamp:307,swap:[],swegat:334,swiggl:[3,260,340,343,345,484,507],swiler:[146,452],switch7_section_start:408,switchflag:[146,452],swm4:502,swol:54,swope:6,sxx:200,sy0302:9,symbol:[6,12,124,171,304,386,406,452],symmetr:[6,72,91,98,118,137,138,139,142,143,144,147,204,205,224,263,264,331,338,381,393,399,404,464,466,507],symmetri:[3,5,6,7,8,65,66,72,96,112,174,196,197,261,288,349,366,381,481,502],sync:[3,6,500],synchron:[1,241,375,500],synechococcu:7,syntax:[],sysdim:289,sysmt:17,sysstem:386,syst:451,system:[],system_:290,systemat:[6,9,214,239,247,433],systemx:3,t10:496,t11:496,t12:496,t13:496,t14:496,t15:496,t3e:12,t_chain:3,t_corr:3,t_correl:476,t_dephas:476,t_e:335,t_e_min:335,t_equil:[332,333],t_event:[3,476,495],t_hi:495,t_infil:335,t_init:[297,335],t_iter:3,t_j:29,t_lb:250,t_lo:495,t_order:3,t_oufil:335,t_out:335,t_outfil:335,t_qm:297,t_switch:[332,333],t_target:388,ta06a:452,ta4:433,ta5:171,ta6:433,tab:[2,481],tabbernor:124,tabinn:435,tabul:[3,7,13,22,37,38,45,56,57,67,73,81,97,192,235,323,365,381,386,387,389,390,391,392,393,396,404,406,418,422,429,438,441,444,446,461,463,464,470,483],tabular:441,tabulate_long_rang:444,tad:[],tadmor:9,tag:[209,502],tagint:3,tail:[3,91,116,166,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,471,472,473,499,507],tailor:[73,336],tait:[9,458,459],taitwat:[],take:[1,2,3,6,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,43,44,45,46,47,48,49,50,52,54,55,57,61,79,91,93,95,115,118,119,122,123,147,149,159,166,170,176,178,179,180,181,182,183,184,186,187,189,190,192,196,199,200,204,205,206,219,220,224,226,233,238,242,246,247,248,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,299,307,309,310,320,321,322,323,325,326,327,328,336,339,343,346,349,350,351,352,354,355,358,360,365,366,370,380,381,382,384,386,387,388,389,390,391,392,393,394,395,396,399,400,404,405,407,408,409,410,411,412,418,419,420,421,422,423,424,425,426,427,431,433,436,437,438,440,443,444,445,446,451,453,460,462,463,464,465,466,467,469,471,472,473,475,479,482,484,489,490,491,496,498,499,500,507],taken:[6,61,154,172,195,223,227,239,240,241,247,248,249,250,293,297,300,335,354,404,406,409,462,469,476,490,491],talk:[6,7],talli:[],tan:[200,507],tandem:[4,16,307],tang:433,tangent:[43,262],tangenti:[6,114,323,341,345,410],tanh:335,tantalum:[4,433,452],taper:[3,300,429],tar:12,tarbal:[0,8,11,12],target:[3,6,7,8,11,12,17,40,42,200,208,220,224,225,227,239,240,241,247,248,249,263,264,265,266,267,268,269,270,271,282,283,284,285,286,290,294,297,302,307,312,321,326,327,328,329,334,335,338,339,342,363,366,388,400,476,487,489,508],target_fil:334,task:[1,6,7,12,13,14,15,16,17,18,55,200,244,290,336,380,479,500],taskset:16,tatb:[4,303],tatom:502,tau:[3,161,214,247,248,250,263,294,307,326,327,332,333,335,501,506],tau_1:240,tau_k:240,tau_n_k:240,tb3:171,tbead:164,tbp:386,tchain:[263,264,268,284,285,307],tcl:302,tcom:248,tcsh:[11,12,393],tdamp:[247,263,264,268,307,326,327],tdephas:476,tdrude:[157,230,248,502],teal:200,tech:[7,9,13],technic:[6,7,9,250,300,323,444],techniqu:[6,7,9,91,203,224,261,297,307,339,342,366,435,463,502],technolgi:9,technolog:[9,14,19,244],tell:[2,6,11,12,37,56,191,203,289,359,376,443,444,461,479,483,502],telsa:17,temeperatur:11,temp:[],temp_drud:502,temp_eff:102,tempcom:[150,151,165],temper:[],temperar:290,temperatur:[],temperature_definit:209,tempfix:496,templ:[7,9,18],templat:[3,8,13,17,19,41,172,173,175,227,239,293,307,310,374,481],templeton2010:209,templeton2011:209,templeton:[9,209],tempor:240,temporari:[2,3,488],temporarili:[192,306,494,495],ten:14,tend:[29,263,288],tensil:[7,226],tensor:[3,6,8,65,86,87,93,94,95,98,111,118,133,136,137,138,139,142,143,144,146,147,148,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,224,250,253,263,264,268,292,294,307,338,365,366,374,406,427,428,433,448,450,499,507],tenth:[133,364],term:[0,1,3,5,6,7,8,9,12,20,21,22,27,38,41,46,47,63,91,92,93,95,116,118,147,148,150,151,160,165,166,179,180,181,192,200,204,205,211,213,215,218,226,232,240,241,242,247,248,249,250,262,263,264,265,266,267,268,269,270,271,282,283,284,286,290,294,297,306,307,321,326,327,328,335,337,339,341,349,350,360,365,373,376,381,382,386,387,388,389,390,391,392,394,395,396,397,398,399,400,401,402,404,405,406,407,409,410,411,418,422,425,426,427,428,430,431,432,433,435,438,445,451,460,462,464,465,466,469,472,490,491,493,499,502],termin:[124,263,373,375,448,450,480,489],termostat:327,terrel:372,terri:7,tersoff:[],tersoff_1:[464,465,466],tersoff_2:[464,465,466],tersoff_mod:465,tertiari:184,tessel:[9,170],test:[],test_descriptor_str:3,testf:192,testu:192,tether:[6,305,312,320,322,333,408],tetot:[9,451],tex:8,texa:440,texas_holdem:306,text:[2,3,4,6,7,8,12,13,38,42,57,192,196,197,199,200,203,209,212,213,214,215,216,217,218,220,225,235,244,295,334,335,347,366,368,375,404,407,417,430,452,463,477,481,482,498,507,509],textur:17,tfac_insert:239,tfactor:[3,200],tfinal:507,tfix:306,tflag:199,tfmc:[],th4:171,than:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,27,38,40,41,42,43,57,59,60,61,63,65,70,73,78,90,92,96,110,112,114,118,121,122,125,147,170,173,174,175,181,192,195,196,198,200,203,208,210,212,215,216,217,218,220,221,222,223,224,226,227,228,231,235,236,239,240,241,242,245,246,247,250,261,288,289,293,294,295,296,297,298,300,302,305,306,307,308,311,312,313,319,320,321,323,327,328,330,331,335,338,339,340,341,342,343,344,345,346,348,365,366,371,372,373,374,375,376,377,380,385,386,387,389,390,391,404,406,409,410,416,427,428,430,435,443,444,445,451,453,460,461,462,463,466,468,470,472,473,476,477,478,479,481,482,483,484,485,486,489,490,493,495,496,498,507,508,509],thank:[244,464,466],thb:444,thb_cutoff:444,thb_cutoff_sq:444,thei:[0,1,2,3,4,6,7,8,11,12,13,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,42,43,44,46,47,48,49,50,52,54,55,56,57,59,61,63,65,66,68,70,72,73,76,77,83,86,88,91,93,94,95,98,108,109,111,114,115,118,120,121,122,123,125,146,149,150,152,154,155,158,159,165,167,169,170,172,174,175,176,178,179,181,182,183,184,186,187,189,190,191,192,196,197,199,200,203,204,205,206,208,211,212,213,215,216,217,218,219,220,221,222,223,224,226,227,232,233,238,239,240,242,243,244,247,248,250,253,260,263,265,266,267,268,269,270,271,272,273,274,275,280,282,283,284,286,292,293,294,295,296,298,299,306,307,308,309,310,323,324,326,327,328,330,334,335,337,338,339,341,343,344,346,347,348,349,351,352,353,354,355,358,359,360,363,365,366,368,370,372,373,374,375,376,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,398,399,400,403,404,405,406,407,408,409,410,411,412,413,414,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,436,437,438,440,441,443,444,445,446,451,452,453,460,461,462,463,464,465,466,467,468,469,470,471,472,473,477,479,481,482,483,484,485,486,490,491,493,494,499,502,507,509,510],them:[1,2,3,4,6,7,8,9,11,12,13,14,17,40,41,42,55,61,73,95,108,113,120,123,125,148,174,179,196,199,200,201,211,212,213,215,216,217,218,220,223,224,226,236,244,247,248,259,263,265,266,267,268,269,270,271,282,283,286,288,294,296,304,305,306,307,310,323,326,327,328,330,334,335,337,341,342,343,345,346,349,366,368,374,375,376,380,381,386,393,404,407,409,413,416,435,445,453,468,476,479,481,488,493,496,502,507,508],themselv:[6,11,175,204,205,220,248,365,366,375,377,381,386,396,404,426,430,431,432,452,507],theor:330,theorem:[240,247,311,386,402],theoret:[110,244,297,462],theori:[3,6,9,12,41,146,209,225,241,263,289,365,366,386,433,472,495],thereaft:[73,255,291,307,331,338,479],therebi:[336,427,428],therefor:[3,6,12,66,91,157,230,239,248,250,310,330,366,398,442,444,462,467,490,502],therein:[6,430],thereof:91,thermal:[],thermo:[],thermo_modifi:[],thermo_p:[3,65,115,479,499],thermo_press:[65,118,224,230,263,265,266,267,268,269,270,271,294,498,499,502],thermo_styl:[],thermo_temp:[65,118,149,223,224,239,263,265,266,267,268,269,270,271,282,283,284,286,289,294,326,327,328,498,499,502],thermoberendsen:6,thermochem:506,thermochemistri:406,thermodyam:[499,506],thermodyanm:[65,223,323,346,490],thermodynam:[],thermophys:435,thermost:[6,154,208,225,230,248,342,502],thermostat:[],thermostatequ:6,thesi:[365,366,427,442],thess:387,theta0:[20,21,24,26,27,28,32,33,35,36,146,181,306,358],theta0max:146,theta10:386,theta1:[179,349,386],theta2:[179,349,386],theta3:[349,386],theta4:386,theta5:386,theta6:386,theta7:386,theta8:386,theta9:386,theta:[3,6,26,27,37,38,39,65,67,82,96,112,146,171,172,181,193,195,199,242,302,306,335,349,358,412,441,465,481,484,491],theta_0:437,theta_:[358,386],theta_c:412,theta_ijk:386,theta_ijl:349,theta_jik:[431,432],theta_pi:386,theta_sigma:386,thex:298,thi:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,434,435,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,502,503,504,505,506,507,508,509,510,511],thick:[73,124,199,216,484],thie:116,thijss:330,thin:[122,199],thing:[3,6,11,12,55,70,73,224,263,294,307,323,478,479,483,507],think:[3,6,7,8,11,13,200,307,346,351,355,368,373,413,443,444,463,479,483,486,507],third:[6,9,12,29,95,140,146,147,170,212,213,215,216,217,218,240,304,320,321,335,395,407,430,437,467,469,476,477,479,481,484],thirumalai:184,thistl:200,tho:405,thole:[],thompson:[0,5,7,9,13,118,146,147,298,368,452],thoroughli:9,those:[1,2,3,4,5,6,7,8,12,13,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,38,40,41,43,44,46,47,48,49,50,51,52,54,55,57,63,73,74,79,91,95,96,112,114,115,116,118,122,146,147,149,152,159,162,170,172,176,178,179,181,182,183,184,185,186,187,189,190,192,195,196,197,199,200,210,211,212,213,216,217,218,224,226,227,236,242,244,245,246,247,253,260,262,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,293,296,299,307,325,332,333,337,341,342,343,346,347,349,351,352,354,355,356,358,360,365,366,373,375,376,380,381,382,384,387,388,389,390,391,392,393,394,395,396,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,430,431,435,436,437,438,440,443,444,445,446,452,453,461,462,463,464,465,466,469,471,472,473,476,478,479,481,483,484,485,486,488,490,491,493,495,498,499,500,502,507,510,511],though:[6,8,12,39,40,41,58,65,73,95,109,172,193,196,200,210,216,221,222,224,226,231,264,305,307,309,319,331,338,348,361,365,368,375,400,403,404,406,407,409,410,426,427,435,469,476,481,483,484,489,493,500,507],thought:[155,247,284,307,339,340,372,410,417,502],thread:[1,3,9,12,16,17,18,244,336,363,380,494,500],threads_per_atom:3,three:[1,3,6,55,65,76,91,95,96,110,123,124,125,136,146,150,171,172,184,203,223,224,229,251,263,268,289,294,298,307,323,330,332,335,353,354,358,365,366,374,380,381,382,386,404,405,407,409,410,414,417,430,431,432,433,437,441,444,445,451,452,462,464,465,466,469,479,481,484,507],threebodi:462,thresh:[42,196,197,199,200,220,479],threshhold:[3,42,199,220,346,479],threshold:[3,42,90,170,200,220,288,376,444,476,495],thrid:479,through:[3,6,7,9,11,12,65,172,176,196,197,201,224,237,239,244,245,250,252,253,254,263,264,290,298,316,330,335,340,344,364,371,382,402,405,406,410,416,418,433,446,451,453,460,467,476,479,482,492,498,502],throughout:[6,16,122,124,336,380,433,481],thru:[3,6,7,11,12,68,76,77,83,93,94,98,108,109,110,111,167,195,196,200,215,260,323,343,348,364,373,379,484],thrust:1,thu:[1,2,3,6,8,9,11,12,18,33,38,40,42,43,51,61,63,65,66,68,69,72,73,74,75,77,79,83,92,94,95,96,98,108,109,111,112,114,115,119,120,121,122,123,146,147,148,152,155,160,162,167,168,169,172,174,175,176,180,185,191,192,195,196,197,199,200,201,203,204,205,206,207,211,212,213,215,216,217,218,219,220,221,222,223,224,226,227,230,232,236,240,241,242,243,244,245,247,248,253,258,263,268,279,288,294,296,298,302,305,307,308,309,310,312,316,317,320,321,322,323,324,326,327,328,330,331,334,335,337,338,339,340,343,344,345,346,348,349,356,365,366,368,371,373,374,375,379,380,381,382,385,386,387,388,389,390,391,392,393,394,395,396,400,402,403,404,405,406,407,408,409,410,413,414,415,416,418,422,426,427,428,430,431,432,433,435,436,438,440,441,442,443,444,445,451,452,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,473,476,478,479,481,482,483,484,485,486,488,489,490,491,493,495,496,497,498,499,500,502,506,507,508,509,510],thumb:[8,10,17,172,195,260,307,380,394,484,490],thz:302,ti2:171,ti3:171,ti4:171,tight:[9,386,451],tightli:296,tij:399,tildeslei:[29,91,399],tile:[3,6,42,64,172,220,416,468,478,507],tilt:[3,6,59,60,61,73,160,174,196,197,200,216,224,226,227,242,261,263,264,288,297,366,368,469,481,484,499],time:[],time_integr:209,timedelta:213,timelin:5,timer:[],timescal:[3,211,212,213,215,216,217,218,261,297,302,406,476,490],timespan:[247,248,263,294,307,326,327],timestamp:[3,486],timestep:[],timesteppnig:310,timothi:9,tin:[395,396],tine:[],tinfoil:366,tini:[74,122,172,373,386,508],tinker:7,tio2:451,tio:451,tip3p:[],tip4:6,tip4p:[],tip:[],tirrel:340,titan:15,titer:307,titl:[212,213,214,215,216,217,218,295,444],title1:[212,213,214,215,216,217,218],title2:[212,213,214,215,216,217,218],title3:[212,213,215,216,217,218],tji:399,tl1:171,tl3:171,tlbr_msw:441,tlo:495,tloop:[263,264,268],tlsph:[],tlsph_defgrad:[],tlsph_strain:[],tlsph_strain_rat:[],tlsph_stress:[],tm3:171,tmax:[3,231,495],tmd:[],tmd_dump_fil:334,tmdatom:334,tmin:231,tmp1:[215,218,492],tmp2:[215,218,492],tmp3:492,tmp:[6,12,42,68,70,71,77,94,98,109,111,120,122,152,167,169,196,197,199,200,220,296,307,331,338,379,488,492,507],tobia:[263,264,307],todd:284,toe:166,toff:[374,481],togeth:[2,3,6,11,12,17,40,42,73,121,147,152,166,173,196,197,204,205,212,215,220,224,230,241,248,263,294,307,312,317,320,323,341,345,346,408,413,479,484,489,502,510],toggl:[61,176,488],togheth:[],togther:3,tol:[310,323,365,462],toler:[3,224,298,299,300,310,323,373,375,462,476,495],toma:9,tomato:200,tong:[9,13],too:[1,3,6,7,40,42,66,69,72,74,75,79,92,96,112,146,160,173,175,199,214,220,221,222,224,227,236,239,243,263,289,294,298,302,304,310,323,330,331,335,338,366,375,376,380,400,416,476,484,495,498,502,507],took:[73,453],tool:[],toolkit:[6,7,13,14,15,197],top:[0,3,8,9,11,12,13,61,155,170,195,203,219,226,243,250,262,284,308,342,343,345,375,380,443,444,452,481,485,491],top_group:317,top_veloc:317,topic:[507,510],toplog:[3,478],topolgi:41,topolog:[2,3,6,7,8,12,13,37,40,41,56,91,114,121,175,176,191,200,221,222,244,292,359,374,413,435,478,481,482,483,485,486,493],topwal:219,torder:307,torqu:[],torsion:[6,179,180,191,382,443,444],torsion_flag:382,tosi:387,tot:[302,451],total:[3,6,11,12,14,15,16,17,18,40,42,43,65,73,83,84,85,92,93,94,95,103,107,108,109,110,113,115,116,123,128,129,130,131,133,134,135,136,137,138,139,146,147,149,152,153,154,155,158,159,160,161,162,164,166,168,169,170,196,203,206,207,210,212,214,215,216,217,219,220,222,228,230,232,237,238,239,240,245,247,248,249,250,251,253,261,263,264,268,279,289,290,292,293,297,302,304,306,307,308,309,312,314,317,320,322,331,332,333,335,338,340,344,365,373,374,375,376,377,380,381,383,385,386,395,404,406,410,430,431,432,433,441,443,444,448,451,452,468,476,478,479,481,483,489,490,495,496,499,500,507],touch:[12,245,341,483],toukmaji:[366,399],toward:[9,29,170,199,203,227,228,245,250,262,268,288,305,320,334,336,358,375],toxvaerd:423,tpa:380,tparam:307,tpartial:152,tpc:380,tpcpu:499,tperiod:307,tptask:[16,380],tqx:[119,196,197,325],tqy:[119,196,197,325],tqz:[119,196,197,325],trace:406,track:[3,7,12,222,226,250,335,345,476,481,487,495,499,507],track_displac:209,tracker:244,trade:[6,12,299,365,366,396,418,422,490,495],tradeoff:435,tradit:[6,9,366],traffic:12,trail:[2,22,45,79,91,122,166,176,180,200,204,205,307,350,370,374,375,393,407,430,444,452,475,481,489,491],train:444,traingul:319,traj:225,traj_titl:444,trajectori:[3,6,12,40,91,196,244,263,265,266,267,269,270,271,272,273,275,276,278,280,281,282,283,284,285,286,290,307,310,312,316,336,345,400,435,444,483,491,496,502,506],tran:[183,184],transfer:[1,6,16,209,230,244,246,331,335,338,365,380,386,433,502],transform:[],transit:[6,9,90,262,312,334,375,397,426,432,433,466,476,495],translat:[3,6,63,65,99,100,101,102,103,150,151,152,156,165,212,239,243,247,248,253,263,269,270,271,282,283,286,290,307,326,327,328,330,368,406,481,499],transmiss:244,transmit:[6,244],transpar:[14,17],transport:[209,335,454],transpos:12,trap:[3,6,95,168,213,245,337,507],trapezoid:[213,507],trate:[3,226,244],travel:323,treat:[2,3,6,8,17,41,43,73,86,88,89,147,150,154,165,176,194,212,213,215,218,227,238,264,289,292,293,307,323,335,337,344,348,364,365,373,374,376,385,398,406,407,409,412,416,431,432,433,445,468,481,484,486,489,491,502,507],treatment:[9,302,398],tree:[3,292,426],tref:403,tri:[],tri_surfac:[],trial:[227,239,383,490],triangl:[],triangleflag:481,triangul:[2,6,13,319,449],triangular:[4,6,43,86,119,224,281,319,449,481],tricki:[478,502],triclin:[],triflag:6,trigger:[3,11,12,64,90,220,223,239,373,439,474,499],trigon:25,trilinear:250,trilino:17,trim:[3,482],tringl:199,tripflag:443,tripl:[2,146,226,386,443,477,479],triplet:[3,34,37,39,405,437,441,462,464,465,466,469],trivial:[8,11,298],trj:444,trott:[7,9,14,17,146,452],troubl:[11,12],truli:8,truncat:[3,5,6,12,73,296,302,340,344,372,384,396,406,410,418,420,423,435,440,451,491],trung:15,tscale:[3,261,297],tschopp:69,tsige:390,tsrd:[323,345],tstart:[240,241,247,249,263,264,307,326,327,328,329,400,487],tstat:[],tstop:[240,241,247,249,263,264,307,326,327,328,329,400,487,495],tsuzuki:[75,469],tthi:133,ttm:[],ttm_mod:335,tucker:[146,452],tuckerman2006:[],tuckerman:[263,264,285,290,307,490],tune:[],tunnel:290,turkand:112,turn:[3,4,6,12,22,33,37,40,45,51,55,56,61,67,71,73,114,121,146,170,171,176,180,185,191,199,200,203,210,221,222,223,224,239,244,263,277,292,295,296,307,323,350,356,359,365,373,375,376,378,380,382,398,412,413,430,435,444,460,461,477,481,483,488,493,494,499,500,504,509],turquois:200,tutein:382,tutori:[6,9],tweak:[12,172,244,380],twice:[3,6,16,17,65,92,178,200,203,204,205,224,260,263,300,311,380,413,479,481,488],twin:69,twist:[427,428],two:[1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,22,38,40,42,43,45,55,57,59,61,63,65,67,70,71,73,78,79,81,91,92,96,97,108,113,114,119,120,121,122,123,124,146,148,150,154,155,157,158,160,166,170,171,172,173,175,180,195,196,197,198,199,200,203,204,205,210,211,212,213,215,216,217,218,220,221,222,223,224,227,230,236,239,240,241,243,245,246,247,248,250,253,262,263,264,268,288,289,290,293,294,296,297,298,302,304,307,312,320,323,330,331,333,335,338,341,344,346,348,350,360,365,366,368,370,371,373,374,375,378,380,381,382,383,385,386,387,388,389,390,393,394,395,396,398,399,400,403,404,405,406,407,409,410,413,416,417,418,422,426,427,428,430,433,435,438,441,442,443,444,445,447,451,452,453,460,461,462,464,465,466,467,468,469,472,473,475,476,478,479,481,482,483,484,485,488,491,493,494,495,496,498,499,502,506,507,508,509,510,511],two_temperatur:209,twobodi:[464,466,469],twogrid:3,twojmax:[146,452],twolevel:[3,478],txt2html:8,txt:[8,13,196,201,295,296,335,363,374,417,451,470,486,507],typcial:[42,220],type1:[79,124,171],type2:[79,124,171],type:[],typei:416,typej:416,typen:[79,124,171],typic:[1,2,3,6,7,8,10,11,12,13,14,15,16,17,18,29,40,41,42,46,47,56,59,61,63,65,72,73,90,91,107,113,125,134,166,172,173,175,196,197,198,199,200,203,204,205,206,208,209,212,214,220,221,222,223,224,226,227,232,236,237,239,242,248,263,277,289,292,293,296,298,300,306,307,310,313,315,323,330,338,339,345,365,368,372,373,374,375,376,377,380,391,393,394,396,408,409,412,413,417,418,422,427,428,430,435,445,448,450,461,463,466,476,477,479,481,482,483,484,490,493,495,496,498,506,507,509,511],typicali:12,tzou:335,u_cond:[84,85,234],u_f:250,u_i:[234,235],u_ij:441,u_mech:[84,85,234],u_prom:386,uberuaga:[262,375],ubiquit:[11,386],ucond:41,uhf:383,uiuc:[9,17],uloop:[3,290,375,379,507],ulpsh:[],ulsph:[],ulsph_num_neigh:[],ultim:495,ultra:170,umbrella:[],umech:41,umin:[26,27,49,50,181],unabl:[3,11,42,220],unaffect:[196,224,263,307,482,493,498],unalt:[204,205,277],unambigu:[73,216,469],unari:[348,507],unbalanc:3,unbias:[160,406],unbond:[222,481],unbroken:82,uncertainti:41,unchang:[61,224,227,262,263,265,266,267,269,270,271,279,294,307,481,482,485,491],uncharg:[41,366],uncom:[1,4],uncompress:[12,73,199],uncomput:[],uncorrel:[240,330,476],uncoupl:290,undefin:[3,12],under:[0,5,6,7,8,9,10,12,18,21,22,45,146,179,180,199,244,261,263,293,297,298,311,349,350,370,402,406,426,444,452,479,495,502],underestim:170,underflow:199,undergo:[6,90,91,108,160,240,247,248,263,312,323],undergon:[223,323],underli:[6,9,12,17,72,199,263,335,368],undermin:40,underpredict:6,underscor:[2,3,65,197,203,223,224,261,263,265,266,267,268,269,270,271,282,283,284,286,294,296,326,327,328,348,374,507],understand:[1,6,8,239,264,433],understood:[196,386],undesir:[61,224,226,263,307],undetermin:323,undisturb:[427,428],undo:[176,244],undump:[],unexpect:[3,487],unfix:[],unfix_flux:209,unfold:321,unfortun:[336,489,490],uniaxi:[3,150,268],uniform:[7,16,42,92,122,209,220,221,222,247,250,253,264,330,403,409,445,476,478,507,508],uniformli:[61,122,195,250,293,335,441,463,508],uninstal:12,uninterrupt:[210,227,239,260,261,263,265,266,267,268,269,270,271,282,283,284,285,286,296,297,307,312,322,325,333,335,341],union:[3,6,41,200,344,346,481,484],uniqu:[3,6,7,8,9,12,40,73,128,214,240,241,247,248,268,296,302,304,375,404,406,481,507,508],unit:[],unit_styl:3,uniti:[405,435,456],unitless:[66,69,72,73,120,177,212,216,217,226,239,261,263,297,341,373,383,410,438,440,462,464,465,466,469,506],unitlesss:[80,82,117],univ:[9,13],univers:[3,6,9,12,13,18,91,244,365,366,375,379,427,432,440,442,466,475,478,507],universit:[9,13],unix:[12,17,246,492],unknown:[3,12,66,75,481],unless:[2,3,9,11,12,15,16,56,59,69,108,124,157,171,172,196,197,200,201,208,224,227,239,247,263,265,266,267,269,270,271,293,294,307,323,334,367,373,394,435,463,479,484,488,493,507],unlik:[12,33,51,61,93,162,172,185,196,214,247,263,268,294,300,302,326,327,328,356,364,365,381,386,404,407,412,413,417,430,431,432,444,452,461,478,483,488,493,507,511],unlimit:441,unlucki:3,unmark:7,unmodifi:324,unnecessari:16,unoccupi:335,unoptim:199,unpack:[0,8,11,380],unpack_bord:8,unpack_border_bodi:8,unpack_border_hybrid:8,unpack_border_vel:8,unpack_comm:8,unpack_comm_bodi:8,unpack_comm_hybrid:8,unpack_comm_vel:8,unpack_exchang:8,unpack_restart:8,unpack_revers:8,unpack_reverse_comm:8,unpack_reverse_hybrid:8,unpad:200,unperturb:91,unphys:[3,6,248,263,307,481],unpredict:[305,491],unpublish:433,unrecogn:3,unrel:[8,9,13,178],unreli:435,unrestrain:306,unrestrict:383,unscal:[3,119,166,196,197,325,482],unset:[3,365,406],unshift:399,unsmooth:424,unsolv:[377,391],unsort:200,unspecifi:[226,481],unsplit:502,unstabl:[3,250],unstrain:226,unsuccess:[3,293],unsuffici:[],unsupport:3,untar:12,until:[2,3,6,12,14,38,40,42,57,73,125,192,199,220,224,227,235,239,244,293,316,323,325,332,348,364,365,376,379,380,386,410,463,476,481,482,486,487,489,495,506,507],untilt:484,unus:386,unusu:[3,8,376],unwant:[3,172,365],unwrap:[3,68,76,77,83,93,94,98,108,109,111,119,147,167,196,197,200,201,211,223,225,244,260,307,320,325,481,482,485,491],unwrapexpand:196,unzip:12,up_intern:199,updat:[0,3,6,8,12,13,129,130,131,141,142,143,144,195,196,197,203,210,221,222,230,237,240,247,248,250,252,253,256,257,260,261,263,264,265,266,267,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,292,294,296,297,302,307,315,316,325,326,327,328,330,335,346,347,380,386,399,433,435,443,444,450,476,481,483,491,492,495,502],upenn:[11,13],upgrad:12,upon:[6,210,244,386,467,495],upper:[2,3,42,59,61,73,92,108,110,148,161,168,195,200,213,214,216,217,220,224,230,248,250,263,297,302,340,341,346,347,373,410,451,484,508],upsid:6,upsilon:409,upto:[3,483,489],upward:227,urbana:[244,365,366,427],urey_bradlei:20,usa:9,usabl:[12,239,404],usag:[3,6,8,248,288,302,323,413,426,481],use_ldg:17,usec:501,useful:380,user:[],user_misc:[30,31,35,182,187,190,354],userguid:9,usr:[11,12,14,482],usual:[2,3,6,9,12,14,17,18,24,28,32,35,36,48,63,73,91,123,150,151,152,157,165,170,189,196,197,199,204,205,210,212,223,224,225,226,239,242,247,249,261,268,289,297,298,304,306,307,323,331,335,338,340,344,348,355,363,375,376,380,391,394,397,399,409,413,414,417,426,427,428,435,437,447,448,449,450,452,460,462,467,476,480,482,486,490,492,495,498,499,507,511],util:[8,12,17,18,380,409,500],utilizi:12,utilz:[12,500],utsa:440,utsph_strain_r:[],uttormark:13,uuml:289,uwo:9,v11:6,v22:6,v33:6,v_0:[3,335],v_2:433,v_3:433,v_4:433,v_a:[8,226],v_abc:[479,499,507],v_area:[2,507],v_atomfil:491,v_c:166,v_cluster:296,v_dc:166,v_delta:91,v_dhug:[261,297],v_diff:[168,337],v_displac:226,v_dk:166,v_dlj:166,v_drai:[261,297],v_dx:[260,484],v_dy:[260,484],v_dz:260,v_e_hbond:412,v_ea:[443,444],v_eb:[443,444],v_eqeq:[443,444],v_espac:206,v_f:479,v_fac:479,v_flux:243,v_foo:[479,507],v_ij:441,v_increas:242,v_integr:337,v_jx:95,v_jy:95,v_jz:95,v_k11:95,v_k22:95,v_k33:95,v_k:166,v_ke:[196,197,510],v_left:484,v_lgr_po:[261,297],v_lgr_vel:[261,297],v_linear:[340,343,345],v_lj:166,v_mol:200,v_mu:427,v_myi:260,v_myindex:507,v_myke:123,v_mystep:488,v_myvar:[8,200],v_myx:260,v_n:[250,433],v_name1:[166,226],v_name2:[166,226],v_name:[3,6,73,91,123,195,196,197,199,200,204,205,206,207,211,212,213,214,215,216,217,218,219,232,242,243,245,247,248,260,309,317,325,326,327,328,337,340,343,345,479,484,488,491,497,499,507,508],v_nstep:346,v_occ:408,v_omega:260,v_oscil:[206,207,219,232,309],v_phi:242,v_prefactor:[204,205,453],v_press:147,v_pressdown:[343,345],v_push:206,v_pxy:6,v_pxz:6,v_pyz:6,v_r0:245,v_r1:170,v_r2:170,v_r:[170,245],v_rad:346,v_radiu:245,v_ramp:[340,343,345],v_rate:[226,245],v_scale1:[204,205],v_scale2:[204,205],v_size:[204,205],v_t_qm:297,v_temp:331,v_theta:[242,484],v_tp:226,v_up:484,v_v0:507,v_v11:6,v_v22:6,v_v33:6,v_v:[260,507],v_valu:[199,479],v_vx:260,v_vy:260,v_vz:[260,508],v_wiggl:[340,343,345],v_x:[2,172,245,260,340,343,345,479,484,507],v_xave:6,v_xmax:6,v_xx:172,v_y:[172,245,484],v_yi:172,v_z:484,vacanc:[4,170,332,433],vacf:[],vacuum:[335,366,397,466,473],valanc:386,vale:3,valenc:[300,386,406,443,444],valent:386,valeriu:9,valid:[2,3,6,9,11,12,73,124,158,171,200,224,239,247,288,307,323,346,348,363,368,404,406,409,433,441,481,482,489,491,507],vallon:430,valon:430,valu:[],valuabl:500,value0:507,value1:[12,152,211,212,213,214,215,216,217,218,268,337,346,492],value2:[12,152,211,212,213,214,215,216,217,218,268,337,346,492],valuei:213,valuej:213,valuev:[7,9],valus:296,van:[9,54,91,113,294,298,303,326,394,395,426,430,443,444,472,508],vanadium:433,vanderwa:[435,499],vanilla:[6,8,12],vanillia:43,vanish:[230,302,310],vapor:[42,220,239,498],vapour:330,var1:492,var2:492,varaibl:[3,484],varavg:12,vare:335,vari:[1,18,42,63,64,73,91,124,160,162,171,204,205,209,212,213,216,220,224,226,261,263,294,306,307,326,327,335,340,365,391,400,401,402,411,424,427,440,453,463,478,496],variabl:[],variable_hill_factor:13,variable_nam:444,varianc:[123,400,507],variant:[1,3,6,12,87,103,263,268,307,311,365,372,380,431,432,464,466,490,494,508],variat:[12,42,220,507],varieti:[1,2,6,7,9,13,15,73,199,244,363,368,413,430,443,444,461,469,507],variou:[],varreturn:479,varshalovich:146,varshnei:13,vartiabl:3,vashishta1990:469,vashishta2007:469,vashishta:[],vbia:6,vcm:[],vdim:[161,331,338,508],vdisplac:[3,245,260,340,343,345,507],vdw:[3,395,444],vec1:[123,296],vec2:[123,296],vec:288,vector:[],vel:[3,6,63,212,216,217,226,248,293,312,342,400,402,406,410,476,483,484,486,502,507],veld:[13,323,366,390,422],veloc:[],velocit:[243,400,402,406,410],velocity_bottom:250,velocity_gradi:450,velocity_temp:508,velocity_top:250,vendor:12,verbatim:479,verbos:[12,451],veri:[1,3,6,7,8,9,10,12,13,17,42,73,74,91,122,123,196,197,199,200,211,212,213,214,215,216,217,218,220,221,222,224,239,253,263,264,277,290,305,310,326,327,337,375,376,377,380,406,410,427,428,440,452,453,463,489,499,500,502,506,509],verifi:[8,380,435,490,496],verlag:312,verlet:[1,3,7,8,12,18,209,247,263,277,284,290,310,324,335,343,346,475,478,490],versa:[3,6,13,61,166,174,223,235,245,247,248,307,481,482,502],versu:[6,14,15,16,18,40,42,82,108,109,122,168,200,220,307,310,366,390,399,410,422,435,499,507],vertex:[43,140,319],vertic:[],vfinal:507,vfrac:119,vhi:[161,508],via:[],vibrat:[6,9,227,241,288,297,302,358,406,476,490],vice:[3,6,13,61,166,174,223,235,245,247,248,307,481,482,502],video:199,view:[4,6,7,9,13,196,199,323,386,406,407,451],viewer:[196,199],viewpoint:199,vij:400,vika:13,vim:[],vincent:[9,19],violat:330,violet:200,virial:[3,65,95,118,146,147,166,204,205,224,230,263,264,265,266,267,268,269,270,271,292,294,307,310,365,380,383,400,401,402,403,406,414],virialmod:414,virtual:[6,7,8,12,462],virut:9,visa:7,viscoelast:[117,410,440],viscoelsat:440,viscos:[],viscou:[],viscous:307,vision:451,visit:[308,443,444],vista:196,visual:[],viz:[11,13],viz_tool:11,vizplotgui_tool:11,vizualiziton:308,vlo:[161,508],vmax:[224,323],vmd:[6,7,9,11,13,196,201,244,482],vmdarch:201,vmdhome:201,vname:[172,507],voigt:[6,146],vol:[],volfactor:365,volpress:433,volt:[442,506],volum:[2,3,6,41,42,60,61,65,82,91,95,105,118,122,124,132,136,145,147,170,171,172,175,210,212,216,217,220,224,226,227,234,239,250,261,263,264,268,272,273,275,276,278,280,281,282,283,284,285,286,293,294,297,307,312,335,340,344,346,365,368,374,388,427,428,433,440,458,459,473,477,478,481,484,491,499,502,506,507],volumetr:82,von:[139,144],voro:[3,9,170],vorobyov:502,voronoi:[],vorselaar:214,voter2:[476,495],voter:[431,432,476,495],voth:[41,290],vpz:342,vratio:507,vri:411,vrpn:244,vshear:341,vstream:6,vtarget:[3,338],vtk:[],vtp:197,vtr:197,vtu:197,vv0210:13,vx0:168,vxcm:307,vxhi:[227,293],vxlo:[227,293],vy0:168,vycm:307,vyhi:[227,293],vylo:[227,293],vz0:168,vzcm:307,vzhi:227,vzi:342,vzlo:227,w_1:146,w_2:146,w_i:146,w_ik:441,waal:[91,113,394,395,426,443,444,472],wadlei:[13,386],wag:[7,9,13],wagner:[7,9,209,250,430],wai:[1,2,3,6,7,8,11,12,15,18,22,34,45,53,61,65,67,68,71,73,74,77,79,81,91,94,95,96,97,98,109,111,112,114,120,121,122,146,147,149,150,151,152,153,154,155,158,159,160,161,162,164,165,166,167,169,172,175,180,188,192,195,196,197,199,200,203,204,205,212,215,216,218,219,222,223,224,226,237,240,245,247,248,250,261,263,268,277,290,293,294,296,305,307,308,312,320,323,325,326,327,328,331,334,335,337,340,343,345,346,350,351,352,353,355,357,358,366,368,370,373,375,376,380,381,382,393,396,397,400,403,404,405,407,409,412,413,415,418,430,431,432,435,437,439,441,442,445,451,452,453,460,462,464,466,469,475,476,479,481,482,483,484,485,486,489,490,491,507,508],wait:[1,12,244,289,476,478],walk:[3,240,247,248,263],wall:[],wall_surac:140,wall_surfac:[],wallhi:340,wallstyl:341,wander:320,wang:[366,430,441],want:[0,1,2,3,5,6,7,8,9,11,12,17,38,41,57,65,68,70,73,77,83,84,85,94,98,108,109,111,113,115,116,118,120,122,147,152,167,168,169,170,172,175,178,192,196,197,199,200,203,204,205,206,211,212,220,223,226,227,230,232,235,237,239,245,248,258,279,288,293,296,306,307,309,320,322,324,331,333,338,340,344,346,348,366,368,375,381,382,386,394,395,400,404,407,413,414,415,416,430,437,441,443,444,451,453,462,463,464,466,468,469,477,479,481,482,483,484,486,488,489,496,499,502,507,509,511],ward:386,warm:[16,406],warn:[],warner:381,warp:[5,430],warranti:7,warren:400,wasn:3,wast:3,watanab:[332,333],watch:375,water:[],watkin:189,wave:[7,9,41,208,261,301,342,383,406],wavefunct:[9,383,406],wavelength:[124,171],wavepacket:[41,383,406,481],wavevector:289,wbodi:87,weak:[96,298],web:[1,8,14,15,16,17,393],webb:209,weber:[3,5,7,15,92,148,405,432,441,461,462,469,493],websit:8,weckner:440,wedg:[],weight:[],welcom:479,well:[1,3,6,7,8,9,11,12,13,15,16,17,18,27,41,52,69,73,96,112,118,147,150,158,172,181,199,200,206,210,212,218,220,221,222,224,227,232,239,243,247,250,254,260,263,268,293,307,309,317,330,333,341,373,375,380,385,408,409,412,413,414,427,428,430,433,445,453,464,465,466,479,481,483,485,490,495,500,502,506,510],wennberg:365,went:[3,11],were:[3,4,5,6,7,11,12,13,15,16,19,34,42,43,53,57,62,72,73,108,112,115,118,122,149,152,172,175,176,188,196,199,200,203,206,212,215,216,217,218,220,226,232,236,243,244,277,284,308,341,342,346,357,365,377,379,406,410,413,417,440,444,463,476,478,479,481,482,483,484,486,488,496,499,507,508,510,511],weren:486,western:9,westview:472,what:[],whatev:[8,12,14,15,114,119,122,123,125,199,200,204,205,224,263,294,296,341,368,372,373,375,380,392,394,433,443,444,495,502,507],wheat:200,whelan:171,when:[0,1,2,3,4,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,40,41,42,43,44,46,47,48,49,50,51,52,54,55,56,57,61,63,64,65,73,74,83,90,92,96,108,109,110,112,113,115,118,119,122,123,125,148,149,150,155,159,160,162,168,170,172,173,174,175,176,178,179,180,181,182,183,184,185,186,187,189,190,191,192,196,197,198,199,200,201,203,204,205,206,207,208,210,211,212,213,215,216,217,218,219,220,221,222,223,224,225,226,227,231,232,233,235,236,237,238,239,241,242,244,247,250,251,253,254,258,263,264,265,266,267,268,269,270,271,272,273,277,279,280,282,283,284,286,288,292,293,294,295,296,297,299,300,301,302,306,307,308,309,310,312,320,321,323,324,325,326,328,330,331,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,351,352,354,355,356,358,359,360,362,363,364,365,366,368,371,372,373,374,375,376,377,379,380,381,382,384,387,388,389,390,391,392,393,394,395,396,398,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,435,436,437,438,440,441,443,444,445,446,452,453,460,462,463,464,465,466,468,469,471,472,473,474,476,478,479,481,482,483,484,485,486,487,488,489,490,491,492,493,495,496,498,499,500,501,506,507,508,509,511],whenev:[0,8,12,14,73,200,211,217,307,368,412,479,490,494,507,511],whenth:3,where:[1,3,6,8,9,10,11,12,14,15,18,21,23,24,25,26,27,28,29,32,35,36,37,40,41,42,44,48,49,50,52,56,63,65,67,68,70,71,72,73,75,77,81,82,84,86,87,88,89,91,92,93,94,96,97,98,99,100,101,102,103,109,111,114,118,119,120,121,122,123,124,125,147,149,150,151,152,153,154,155,158,159,160,161,162,164,165,166,167,169,171,173,175,176,179,181,191,195,196,199,200,203,204,205,206,207,212,213,216,219,220,223,224,226,227,231,232,234,236,237,239,240,241,242,243,245,247,248,249,250,253,254,256,258,260,261,263,264,268,277,280,287,288,289,290,293,295,296,297,300,302,307,308,309,310,312,316,317,320,322,325,326,327,328,331,332,333,335,338,339,340,341,343,344,345,346,349,351,352,353,354,355,358,359,360,363,366,368,372,373,374,375,376,377,380,381,382,385,386,387,389,393,394,395,396,397,398,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,418,422,427,428,429,430,431,432,433,435,437,438,440,441,442,443,444,445,451,452,455,458,459,460,461,462,463,464,465,466,469,472,473,475,476,478,479,480,481,483,484,485,486,488,490,491,493,495,496,497,498,499,502,506,507,508,509,511],wherea:[6,11,96,210,240,263,298,330,335,502],wherebi:299,wherev:243,whether:[6,8,11,12,17,40,41,55,61,63,65,72,73,107,113,115,159,160,192,199,200,202,203,204,205,212,218,221,222,223,224,225,226,230,236,239,248,260,263,268,296,310,323,331,337,338,346,348,363,365,366,374,378,380,389,391,395,411,413,417,427,428,430,435,444,451,461,476,479,481,482,484,486,493,494,495,498,507,508],which:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,28,29,32,33,37,38,40,41,42,43,45,46,47,48,51,52,54,55,56,57,60,61,63,65,66,68,69,72,73,74,75,76,77,78,79,80,82,83,84,85,86,87,89,91,92,93,94,95,98,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,116,117,118,119,120,122,123,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,178,179,180,183,184,185,186,189,191,192,195,196,197,199,200,201,203,204,205,206,207,208,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,253,254,257,258,260,261,262,263,264,265,266,267,268,269,270,271,273,275,277,278,280,281,282,283,284,285,286,288,289,290,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,312,313,314,315,317,319,320,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,340,341,342,343,344,345,346,348,349,350,352,355,356,359,360,363,364,365,366,368,370,371,372,373,374,375,376,377,379,380,381,382,383,385,386,387,389,390,391,393,394,395,396,397,398,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,422,424,426,427,428,430,431,432,433,435,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,453,456,460,461,462,463,464,465,466,467,468,469,472,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,502,507,508,509,510,511],whichev:[12,379,476,495],white:[200,240,247,248,249,307,327,335,481,507,510],whitesmok:200,whitespac:[2,3,200,374,481],who:[0,3,6,7,8,9,13,381,404],whole:[230,244,289,302,312,502],wholli:227,whose:[3,6,7,8,18,19,38,40,43,57,61,78,91,157,175,192,199,200,210,226,235,245,246,260,263,265,266,267,269,270,271,288,289,305,306,310,323,337,344,346,368,375,376,406,420,447,449,462,463,464,466,502,507,508],why:[3,6,248,331,338],wide:[1,6,7,9,63,65,203,331,338,368,377,391,394,406,443,444],wider:1,width:[199,200,383,408],wiggl:[3,226,260,316,340,341,343,345,484],wigner:146,wih:6,wiki:14,wikipedia:[6,14],wild:[3,12,22,45,79,91,122,180,204,205,307,350,370,393,412,475,483,488,509,511],wildcard:[3,12,166,176,196,197,199,200,304,393,460,488,491,510,511],wildli:263,win:380,window:[3,4,12,13,73,196,199,201,212,213,214,215,216,217,218,244,308,328,329,393,482],wipe:[203,413,461,503,505],wire:306,wirt:200,wisconsin:13,wise:[3,12,400,462,490],wish:[2,3,5,6,7,8,11,12,14,17,41,43,59,60,61,73,123,147,152,173,174,176,178,196,197,200,204,211,212,213,216,217,218,222,226,227,236,239,245,250,254,293,296,307,310,323,324,340,341,368,375,380,389,412,413,430,435,443,463,479,481,482,483,489,493,499,507,508,511],within:[1,2,3,6,8,9,11,12,13,15,16,17,29,40,41,42,43,56,61,63,65,67,71,72,73,74,75,79,81,96,97,112,114,118,121,122,123,125,128,146,163,172,175,198,199,200,204,205,210,211,212,215,216,217,218,220,221,222,223,227,229,235,236,239,245,247,288,292,293,294,296,298,307,308,310,313,315,319,320,324,335,338,340,344,346,348,364,368,373,374,375,376,377,380,385,387,389,396,401,402,403,404,405,406,408,413,414,417,418,430,433,438,439,440,445,446,461,462,464,465,466,467,469,474,476,478,479,481,489,490,493,495,502,506,507],without:[1,2,3,4,6,7,8,9,11,12,14,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,61,91,115,118,149,154,159,173,178,179,181,182,183,184,186,187,189,190,192,196,199,200,201,203,206,212,214,215,216,217,218,219,224,226,233,235,238,240,242,244,247,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,285,286,293,296,298,299,301,305,307,308,309,310,316,323,326,328,339,343,347,349,351,352,354,355,358,360,364,365,366,375,376,380,381,382,384,387,388,389,390,391,392,393,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,433,435,436,437,438,440,444,445,446,453,461,462,463,464,465,466,469,471,472,473,479,481,484,489,490,499,502,506,507],witht:[],witi:15,wolf:[],wolff:[435,463],won:[3,305,428],wong:[209,386],word:[2,3,6,8,12,29,65,200,203,210,211,212,213,216,217,218,225,245,274,279,295,300,306,337,348,364,394,435,477,479,481,507,508],work:[1,3,6,7,8,9,11,12,14,16,18,40,55,61,62,92,123,124,150,151,153,154,155,159,160,161,162,164,165,170,171,196,199,201,204,205,212,216,217,223,237,246,247,248,250,254,260,263,269,270,271,282,283,284,285,286,304,306,308,310,326,327,328,333,364,376,380,393,395,398,400,413,427,428,430,433,435,451,476,478,479,482,483,485,489,490,492,495,507],workaround:[74,122,307,435,508],worker:[12,443,444,469],workhors:8,workstat:[380,479],world:[3,12,146,364,375,379,475,478,479,496,507],worlei:400,worri:17,worsen:18,worst:344,worth:[212,213,215,216,217,218,297,308],would:[1,3,4,5,6,7,8,11,12,22,29,37,42,43,45,56,72,73,74,93,95,122,147,152,160,172,173,174,175,176,180,191,196,197,199,200,201,203,204,205,207,210,212,220,223,225,226,230,231,236,239,242,243,244,248,260,263,264,277,288,290,294,296,298,302,305,323,330,334,342,343,346,348,349,350,351,352,353,355,356,359,365,368,370,372,373,375,376,379,380,381,382,386,393,394,395,396,400,401,402,403,404,405,407,413,414,415,416,430,431,432,433,437,441,443,444,448,450,452,460,462,464,465,466,469,476,479,481,484,485,486,488,489,490,491,492,496,498,499,502,507,508,510,511],wrap:[1,3,6,11,12,59,61,172,174,195,196,197,198,200,201,211,217,225,226,227,244,250,260,307,320,323,340,342,344,365,366,375,479,481,482,484,489],wrapper:[],wrigger:312,wright:373,writabl:3,write:[],write_atom_weight:209,write_data:[],write_dump:[],write_freq:444,write_head:8,write_restart:[],writen:308,written:[3,5,6,7,8,9,12,13,14,17,67,71,121,146,170,196,197,198,199,200,201,203,204,205,206,207,208,209,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,228,230,231,232,233,236,237,238,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,259,262,272,273,274,275,276,277,278,279,280,281,287,288,289,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,320,321,323,324,326,327,328,329,330,331,332,334,335,337,338,339,340,342,343,344,345,347,363,368,376,404,413,429,433,470,472,476,477,479,482,483,487,488,495,496,497,498,507,509,510,511],wrong:[3,11,224,263,287,340,344,345,376,444,483,488],wrote:[3,483],wt1:435,wt2:435,wt3:435,wurtzit:368,www:[0,2,3,4,5,6,7,8,10,11,12,13,15,381,404,427,442,443,444,506],x86:[12,433],x_ij:441,x_ijkl:349,x_kjli:349,x_ljik:349,xave:6,xavx:16,xcm:[8,307,507],xdr:[12,196],xeon:[1,4,7,9,12,16,17,18,380,494],xflag:[159,160,251,253,259,307,330],xhe:[],xhi:[2,6,59,61,174,196,226,334,340,343,345,481,484,499,507],xhi_bound:[6,196],xhi_new:481,xhost:[9,12,16],xi_ij:441,xiaowang:[13,407,464,466],xiij:288,xlat:[172,226,245,499],xlo:[2,6,11,59,61,174,196,226,245,334,340,343,345,481,484,499,507],xlo_bound:[6,196],xlo_new:481,xmax:[6,208,231,277,507],xmgrace:[],xmin:507,xml:[197,201,442],xml_label:442,xmovi:[],xmu:[341,410],xorig:73,xplane:341,xplor:196,xpo:172,xrd:[],xsph:9,xsu:[3,196,197,325,482],xt3:196,xt4:[18,196],xt5:[18,196],xtc:[],xtcdump:200,xvf:12,xwall:[342,343,345],xxx:12,xyz:[3,6,7,13,43,68,73,111,114,160,167,172,196,198,199,200,201,216,224,253,263,264,268,294,304,305,307,320,322,341,343,345,367,374,478,482,508,510],xzhou:[13,407],xzy:478,yang:[433,441],yate:433,yb2:171,yb3:171,ybox:226,ycm:307,year:[5,7],yeh:365,yellow:[199,200],yellowgreen:200,yet:[3,7,9,17,40,43,199,204,304,340,366,372,373,380,392,394,395,406,472,479,481,482,507,509,510],yflag:[159,160,251,253,259,307,330],yhi:[6,61,174,196,226,334,340,343,345,481,484,499],yhi_bound:[6,196],yield:[6,95,116,123,147,155,160,200,213,224,230,263,284,298,331,337,338,341,346,365,385,400,410,435,440,499,507],yip:332,ylat:[172,226,245,499],ylo:[6,61,174,196,226,334,340,343,345,481,484,499],ylo_bound:[6,196],ymax:[208,507],ymin:507,yorig:73,york:[290,366],yoshida:[263,307],you:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,33,35,38,40,41,42,43,44,46,47,48,49,50,51,52,54,55,57,59,60,61,63,65,68,70,73,74,75,76,77,79,83,84,85,91,92,93,94,95,96,98,107,108,109,111,112,113,115,116,118,120,122,123,146,147,149,150,151,152,155,159,160,165,166,167,168,169,170,172,173,174,175,176,178,179,180,181,182,183,184,185,186,187,189,190,191,192,195,196,197,199,200,201,203,204,205,206,207,210,211,212,213,215,216,217,218,219,220,221,222,223,224,226,227,230,232,233,235,236,237,238,239,240,241,242,243,244,245,247,248,249,258,260,263,265,266,267,268,269,270,271,272,273,277,279,280,282,283,284,285,286,289,290,292,293,294,296,298,299,302,305,306,307,309,310,312,320,322,323,324,326,327,328,329,331,332,333,334,335,337,338,339,340,341,343,344,345,346,348,349,351,352,354,355,356,358,360,364,365,366,368,370,372,373,374,375,376,379,380,381,382,384,386,387,388,389,390,391,392,393,394,395,396,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,430,431,432,433,435,436,437,438,439,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,469,471,472,473,475,476,477,478,479,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,502,506,507,508,509,511],young:[410,447,449],your:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,44,46,47,48,49,50,52,54,55,57,61,63,113,115,118,122,149,150,151,155,159,165,170,172,173,174,175,176,178,179,181,182,183,184,186,187,189,190,192,195,196,197,198,199,206,209,213,215,218,219,221,222,223,224,226,227,233,238,239,242,244,247,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,293,296,299,305,307,309,310,312,325,326,328,331,335,337,338,339,340,341,343,344,345,346,349,351,352,354,355,358,360,366,368,374,375,376,379,380,381,382,384,386,387,388,389,390,391,392,393,394,395,396,399,400,403,404,405,407,408,409,410,411,412,413,414,415,418,419,420,421,422,423,424,425,426,427,430,431,432,433,435,436,437,438,440,441,443,444,445,446,453,460,462,463,464,465,466,469,471,472,473,475,478,479,481,483,484,485,488,489,490,491,492,493,494,498,499,506,507,509,511],yourself:[6,8,12,13,224,374],yplane:341,ypo:172,ysu:[3,196,197,325,482],yuan:9,yukawa:[],yukawa_1_1:470,yxz:478,yzx:478,z_i:[406,466,473],z_j:[466,473],z_meam:430,zachari:13,zannoni:409,zbl:[],zblcut:466,zblcutinn:452,zblcutout:452,zblexpscal:466,zblz:452,zcm:307,zcylind:341,zepeda:210,zero:[],zeta:[3,250,298,407],zfactor:199,zflag:[159,160,251,253,259,307,330],zhang:[307,331,410],zhi:[3,6,174,196,208,334,340,343,345,481,484,499],zhi_bound:[6,196],zhou:[13,386,407,441,464,466],zhu:459,ziegenhain:13,ziegler:[292,430,461,466,473],zimmerman2004:209,zimmerman2010:209,zimmerman:[9,72,209,386],zlat:[226,245,499],zlib:196,zlim:451,zlo:[3,6,174,196,208,334,340,342,343,345,481,484,499],zlo_bound:[6,196],zmax:[208,250,507],zmin:[250,507],zn2:171,zone:[124,308],zoom:[3,196,199,200],zorig:73,zplane:341,zr4:171,zrest:322,zsu:[3,196,197,325,482],zwall:340,zwall_veloc:250,zxy:478,zybin:444,zyx:478},titles:["LAMMPS Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & 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","<no title>","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","<no title>","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":[37,40,41,56,59,60,61,63,64,73,91,92,96,107,108,110,112,113,124,128,129,146,152,160,161,165,171,172,175,177,191,194,195,196,197,199,200,201,202,204,205,206,208,209,210,212,216,217,218,221,222,224,225,226,227,231,236,239,240,245,247,248,249,250,251,253,258,261,263,264,268,284,285,289,290,293,294,295,296,297,299,302,304,305,307,308,323,325,330,331,332,333,336,338,340,342,346,359,363,365,366,368,369,371,372,374,376,377,378,380,383,386,388,406,427,428,433,435,443,444,460,461,476,477,478,481,482,484,486,488,489,490,493,495,497,498,499,500,501,506,508,509,510],"function":507,"long":[214,387,389,390,391,392,396,398,399,418,422,426,438,446],"new":8,"static":12,acceler:1,ackland:66,acknowledg:7,adapt:[204,205],addforc:206,addit:[12,13],addtorqu:207,adiabat:6,adjust_dt:313,adp:381,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:[6,7,8,66,69,72,73,74,75,78,79,80,82,83,85,89,96,100,101,104,105,106,112,116,117,119,146,147,170,208,210,211,296,507],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],brownian:388,buck:[389,390,398,429],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:72,ch2lmp:13,chain:13,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:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,507],compute_modifi:107,condit:7,conduct:[6,331],conserv:401,constant:6,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:[396,418],dec:[],defgrad:133,deform:[155,156,226],delete_atom:175,delete_bond:176,delta:24,deposit:227,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],diagnost:7,diel:397,dielectr:177,diffract:9,diffus:6,dihedr:[8,81],dihedral_coeff:180,dihedral_styl:[2,178,179,181,182,183,184,185,186,187,188,189,190,191,192,193],dilat:82,dimens:194,dipol:[6,9,29,399],direct:230,discuss:6,disp:6,displac:[83,90],displace_atom:195,distanc:353,distribut:[7,12],document:0,dpd:[9,84,85,400,401,402],drag:228,dreid:[6,412],drude:[6,9,157,229,230,248],dsf:[396,418],dsmc:403,dump:[6,8,196,197,198,199,201],dump_modifi:200,dynam:298,eam:[13,404],echo:202,edip:405,eff:[9,13,101,102,156,158,163,249,264,276,285,329,406],efield:232,eim:407,elast:6,emac:13,energi:[129,402],enforce2d:233,ensembl:7,erot:[86,87,88,89],error:[3,128],evapor:236,event:90,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],exp:[27,181],expand:[47,421],extend:[8,11],extern:237,fcc:288,fdt:402,featur:[7,8,507],feb:0,fene:[46,47],fep:[9,13,91,205],field:[6,7],file:6,finit:6,fire:298,fix:[2,6,8,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,507],fix_modifi:[204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345],fld:9,flow:6,fluid:250,flux:[95,148],forc:[6,7,148,324],fourier:[30,31,182,354],freez:238,from:[6,11],futur:5,gauss:408,gaybern:409,gcmc:239,gener:[1,6,7,13],get:12,gld:240,gle:241,global:6,gpu:[9,15,384,387,389,391,392,394,396,399,400,404,408,409,411,418,419,420,421,434,436,445,446,453,462,463,464,471,472,473],gran:[341,410],granular:[6,9],graviti:242,gromac:411,group2ndx:347,group:[92,346,507],gyrat:[93,94],h5md:[9,196,198],harmon:[32,48,49,50,183,186,340,355,437],hbond:412,heat:[95,148,243],heatconduct:454,helix:184,hertz:[410,447],hexord:96,histo:215,histori:[5,410],hook:410,hourglass:128,hourglass_error:[],how:6,hybrid:[33,51,185,356,413],idealga:455,imag:[196,199],imd:244,implicit:391,improp:[8,97],improper_coeff:350,improper_styl:[2,349,351,352,353,354,355,356,357,358,359,360,361],includ:362,inclus:8,indent:245,indic:0,individu:2,induc:6,inertia:98,info:[0,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345,363],input:[2,6,8],instal:11,instruct:[],integr:[6,7],integrate_tlsph:314,integrate_ulsph:315,intel:[9,16,20,32,48,178,183,189,263,272,273,284,352,355,389,391,409,418,462,464],interfac:[6,11],intern:129,internal_energi:[],introduct:7,invers:230,ipi:246,ipp:13,jan:[],jul:[],jump:364,kate:13,keyword:435,kim:[9,414],kokko:[9,17],kspace:[2,8,9,336],kspace_modifi:365,kspace_styl:[6,366],label:367,lammp:[0,1,2,6,7,8,11,12],langevin:[247,248,249],lattic:368,lcbop:415,lennard:429,librari:[6,11,12],limit:[277,328],line:[12,278,416],linear:425,lineforc:255,list:[2,417],lj1043:340,lj126:340,lj93:340,lj96:419,lmp2arc:13,lmp2cfg:13,lmp2vmd:13,local:[6,67,70,71,81,97,114,121],log:369,lubric:427,lubricateu:428,make:12,manybodi:9,mass:370,math:507,matlab:13,mdf:429,meam:[9,430,431,432],measur:1,mesh:140,meso:[104,105,106,256,257],meso_:[],meso_rho:[],meso_t:[],messag:3,mgpt:[9,433],micelle2d:13,mie:434,min_modifi:371,min_styl:372,minim:[8,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345,373],misc:9,mod:[335,465],model:[6,7],modifi:8,molecul:[9,374],molfil:[9,196,201],moltempl:13,momentum:[251,259],morri:459,mors:[52,412,436],move:260,move_tri_surf:316,movi:[196,199],mpi:11,mpiio:9,msd:[108,109,110],msi2lmp:13,msm:[387,389,391,396,418],msst:261,multi:[6,7,186],multipl:6,nb3b:437,ndx2group:347,neb:[262,375],neigh:[135,141],neigh_modifi:376,neighbor:377,nemd:6,newton:378,next:379,nharmon:187,noforc:[274,279],non:[6,7],none:[34,53,188,357,439],nongauss:110,nonlinear:54,nph:[263,264,265,266,267,307],nphug:268,npt:[263,264,269,270,271,307],num:[135,141],nve:[272,273,274,275,276,277,278,279,280,281,307],nvt:[263,264,282,283,284,285,286,307],omega:111,omp:[9,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,44,46,47,48,49,50,52,54,55,57,178,179,181,182,183,184,186,187,189,190,192,242,263,265,267,268,269,271,272,280,282,284,286,299,349,351,352,354,355,358,360,381,382,384,387,388,389,390,391,392,394,395,396,397,399,400,404,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,432,436,437,438,440,445,446,453,462,463,464,465,466,469,471,472,473],onewai:287,open:7,oper:507,opl:189,opt:[9,19,391,404,418,422,436],optim:1,option:[6,8,12],orient:288,orientord:112,orthogon:6,other:6,output:[6,7,8,12,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345],overlai:413,overview:11,packag:[1,9,12,14,15,16,17,18,19,380],pair:[6,113,114],pair_coeff:393,pair_modifi:435,pair_styl:[2,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,474],pair_writ:470,pairwis:8,parallel:11,paramet:6,pars:2,partial:159,particl:[6,7,43],partit:475,past:5,per:6,perform:[1,10],peri:[9,440],period:25,phonon:[9,13,289],pimd:290,piston:342,planeforc:291,plastic:[117,130,131],plastic_strain:[],plastic_strain_r:[],pmb:440,poem:[9,292],point:298,polariz:6,poli:[388,427,428],polygon:[],polym:13,polymorph:441,post:7,potenti:[2,6,8],pour:293,pppm:6,prd:476,pre:7,press:294,pressur:118,previou:12,print:[295,477],problem:[3,4],process:[6,7],processor:478,profil:160,properti:[6,119,120,121,296],pymol_aspher:13,python:[9,11,13,479],qbmsst:297,qeq:[9,298,299,300],qmmm:[9,301],qtb:[9,302],quadrat:190,quantiti:6,quartic:[35,55],quip:[9,442],quit:480,radiu:126,ramp:161,rate:[131,138,143],rattl:310,rdf:122,read_data:481,read_dump:482,read_restart:483,reax:[9,13,300,303,304,443,444],reaxc:9,rebo:382,recent:305,reduc:123,refer:507,reflect:343,region:[8,123,162,163,344,484,507],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,41,42,44,45,46,47,48,49,50,51,52,54,55,56,57,58,59,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,87,88,89,90,91,93,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,196,197,198,199,200,201,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,238,239,240,241,242,243,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,302,303,304,305,307,308,309,311,312,313,314,315,316,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,362,363,364,365,366,368,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,486,487,488,489,490,491,493,494,495,496,497,498,499,500,501,503,504,505,507,508,509,510,511],relax:224,replic:485,replica:[6,7,9],report:3,requir:12,rerun:486,rescal:[328,329],reset:231,reset_timestep:487,resquar:445,restart2data:13,restart:[6,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345,488],restrain:306,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],rho:[105,132],rhosum:457,rigid:[6,9,87,103,253,307],ring:358,rotat:164,round:[],rule:2,run:[6,11,12,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345,489],run_styl:490,scalabl:10,scalar:6,screen:12,script:[2,6,8,11],sdk:[36,446],self:322,serial:11,set:[6,491],setforc:309,setvel:317,shake:310,shape:136,shardlow:311,share:[11,12],shell:[6,492],shield:298,shift:[26,27,49,50,181],shock:9,simpl:31,simul:6,size:6,slater:298,slice:125,sllod:[284,285],small:307,smd:[9,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,312,313,314,315,316,317,319,447,448,449,450],smooth:[424,425],smtbq:[9,451],sna:146,snad:146,snap:[9,452],snapshot:6,snav:146,soft:[426,453],solver:2,sourc:7,spatial:[216,217],spc:6,speci:304,special:[7,435,507],special_bond:493,sph:[9,454,455,456,457,458,459],sphere:[88,89,165,217,253,267,271,280,286],spheric:6,spline:[431,432],spring:[320,321,322,333],squar:28,srd:[9,323,345],srp:460,standard:9,start:[12,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345],state:325,stationari:257,stop:[204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345],store:[324,325],strain:[130,131,137,138,142,143],strategi:1,streitz:396,stress:[139,144,147,148],structur:2,style:[1,2,6,8],submit:8,suffix:494,summari:6,swap:[210,223],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,289,290,291,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],system:6,tabl:[0,6,38,57,192,235,463,464],tad:495,taitwat:[458,459],talli:[9,148],temp:[149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,326,327,328,329],temper:496,temperatur:6,tersoff:[464,465,466],test:11,tfmc:330,thermal:[6,331],thermo:[6,497],thermo_modifi:498,thermo_styl:499,thermodynam:[6,8],thermostat:6,thole:467,time:[6,218],timer:500,timestep:501,tip3p:6,tip4p:[6,396,418,422,426],tip:12,tlsph:[133,134,135,136,137,138,139,448],tlsph_defgrad:[],tlsph_dt:[],tlsph_num_neigh:[],tlsph_shape:[],tlsph_strain:[],tlsph_strain_rat:[],tlsph_stress:[],tmd:334,tool:[12,13],torqu:167,transform:230,tri:[281,468],tri_surfac:449,triangl:140,triangle_mesh_vertic:[],triclin:6,tstat:400,ttm:335,tune:336,type:7,ulsph:[141,142,143,144,450],ulsph_num_neigh:[],ulsph_strain:[],ulsph_strain_r:[],ulsph_stress:[],umbrella:360,uncomput:503,undump:504,unfix:505,unit:506,user:[9,12,14,16,18],vacf:168,valu:[6,507],variabl:[6,8,507],variou:1,vashishta:469,vcm:169,vector:[6,337,507],veloc:508,version:[0,5,12],vertic:140,via:12,vim:13,viscos:[6,338],viscou:[254,339],visual:6,vol:145,voronoi:[9,170],vtk:[9,196,197,308],wall:[6,340,341,342,343,344,345],wall_surfac:319,warn:3,water:6,weight:215,what:[7,12],wolf:[387,396],wrapper:11,write:6,write_data:509,write_dump:510,write_restart:511,xmgrace:13,xmovi:13,xrd:171,xtc:9,yukawa:[471,472],zbl:[466,473],zero:[39,58,193,361,474]}})
\ No newline at end of file