comm tiled bug fix

doc/html/Manual.html

@@ -148,7 +148,7 @@
   <H1></H1><div class="section" id="lammps-documentation">
 <h1>LAMMPS Documentation</h1>
 <div class="section" id="sep-2016-version">
-<h2>13 Sep 2016 version</h2>
+<h2>15 Sep 2016 version</h2>
 </div>
 <div class="section" id="version-info">
 <h2>Version info:</h2>

doc/html/Section_commands.html

@@ -111,7 +111,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/Section_errors.html

@@ -103,7 +103,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/Section_history.html

@@ -100,7 +100,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/Section_intro.html

@@ -116,7 +116,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/Section_modify.html

@@ -113,7 +113,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/Section_packages.html

@@ -161,7 +161,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/Section_start.html

@@ -142,7 +142,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/Section_tools.html

@@ -129,7 +129,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
@@ -217,7 +217,7 @@ own sub-directories with their own Makefiles.</p>
 <li><a class="reference internal" href="#eff"><span class="std std-ref">eff</span></a></li>
 <li><a class="reference internal" href="#emacs"><span class="std std-ref">emacs</span></a></li>
 <li><a class="reference internal" href="#fep"><span class="std std-ref">fep</span></a></li>
-<li><a class="reference internal" href="fix_ipi.html#ipi"><span class="std std-ref">i-pi</span></a></li>
+<li><a class="reference internal" href="#ipi"><span class="std std-ref">i-pi</span></a></li>
 <li><a class="reference internal" href="#ipp"><span class="std std-ref">ipp</span></a></li>
 <li><a class="reference internal" href="#kate"><span class="std std-ref">kate</span></a></li>
 <li><a class="reference internal" href="#arc"><span class="std std-ref">lmp2arc</span></a></li>

doc/html/accelerate_gpu.html

@@ -113,7 +113,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/accelerate_kokkos.html

@@ -113,7 +113,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/accelerate_omp.html

@@ -113,7 +113,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/accelerate_opt.html

@@ -113,7 +113,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/angle_table.html

@@ -97,7 +97,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="angles.html">Angle Styles</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="angle_charmm.html">angle_style charmm command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="angle_charmm.html#angle-style-charmm-intel-command">angle_style charmm/intel command</a></li>

doc/html/atom_style.html

@@ -214,7 +214,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/body.html

@@ -34,7 +34,7 @@
   
     <link rel="top" title="LAMMPS documentation" href="index.html"/>
         <link rel="up" title="Tutorials" href="tutorials.html"/>
-        <link rel="next" title="Manifolds (surfacse)" href="manifolds.html"/>
+        <link rel="next" title="Manifolds (surfaces)" href="manifolds.html"/>
         <link rel="prev" title="LAMMPS GitHub tutorial" href="tutorial_github.html"/> 
 
   
@@ -96,14 +96,14 @@
 <li class="toctree-l2"><a class="reference internal" href="tutorial_drude.html">Tutorial for Thermalized Drude oscillators in LAMMPS</a></li>
 <li class="toctree-l2"><a class="reference internal" href="tutorial_github.html">LAMMPS GitHub tutorial</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">Body particles</a></li>
-<li class="toctree-l2"><a class="reference internal" href="manifolds.html">Manifolds (surfacse)</a></li>
+<li class="toctree-l2"><a class="reference internal" href="manifolds.html">Manifolds (surfaces)</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
@@ -146,7 +146,7 @@
   
     <div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
       
-        <a href="manifolds.html" class="btn btn-neutral float-right" title="Manifolds (surfacse)" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+        <a href="manifolds.html" class="btn btn-neutral float-right" title="Manifolds (surfaces)" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
       
       
         <a href="tutorial_github.html" class="btn btn-neutral" title="LAMMPS GitHub tutorial" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
@@ -433,7 +433,7 @@ Particuology, 6, 455 (2008).</p>
   
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
       
-        <a href="manifolds.html" class="btn btn-neutral float-right" title="Manifolds (surfacse)" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+        <a href="manifolds.html" class="btn btn-neutral float-right" title="Manifolds (surfaces)" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
       
       
         <a href="tutorial_github.html" class="btn btn-neutral" title="LAMMPS GitHub tutorial" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>

doc/html/bond_table.html

@@ -33,7 +33,7 @@
 
   
     <link rel="top" title="LAMMPS documentation" href="index.html"/>
-        <link rel="up" title="Bonds" href="bonds.html"/>
+        <link rel="up" title="Bond Styles" href="bonds.html"/>
         <link rel="next" title="bond_style zero command" href="bond_zero.html"/>
         <link rel="prev" title="bond_style quartic command" href="bond_quartic.html"/> 
 
@@ -97,7 +97,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="bonds.html">Bonds</a><ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="bonds.html">Bond Styles</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="bond_class2.html">bond_style class2 command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="bond_class2.html#bond-style-class2-omp-command">bond_style class2/omp command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="bond_fene.html">bond_style fene command</a></li>
@@ -161,7 +161,7 @@
   <ul class="wy-breadcrumbs">
     <li><a href="Manual.html">Docs</a> &raquo;</li>
       
-          <li><a href="bonds.html">Bonds</a> &raquo;</li>
+          <li><a href="bonds.html">Bond Styles</a> &raquo;</li>
       
     <li>bond_style table command</li>
       <li class="wy-breadcrumbs-aside">

doc/html/boundary.html

@@ -214,7 +214,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/change_box.html

@@ -214,7 +214,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_ackland_atom.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_angmom_chunk.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_basal_atom.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_body_local.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_chunk_atom.html

@@ -226,7 +226,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_cluster_atom.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_com_chunk.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_contact_atom.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_coord_atom.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_damage_atom.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_dipole_chunk.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_displace_atom.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_dpd_atom.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_erotate_asphere.html

@@ -224,7 +224,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_erotate_rigid.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_erotate_sphere.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_erotate_sphere_atom.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_event_displace.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_inertia_chunk.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_ke.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_ke_atom.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_ke_atom_eff.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_ke_eff.html

@@ -224,7 +224,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_ke_rigid.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_meso_e_atom.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_meso_rho_atom.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_meso_t_atom.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_msd_chunk.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_msd_nongauss.html

@@ -287,19 +287,15 @@
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">msd</span><span class="o">/</span><span class="n">nongauss</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
 </pre></div>
 </div>
-<ul>
+<ul class="simple">
-<li><p class="first">ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</p>
+<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
-</li>
+<li>msd/nongauss = style name of this compute command</li>
-<li><p class="first">msd/nongauss = style name of this compute command</p>
+<li>zero or more keyword/value pairs may be appended</li>
-</li>
+<li>keyword = <em>com</em></li>
-<li><p class="first">zero or more keyword/value pairs may be appended</p>
+</ul>
-</li>
-<li><p class="first">keyword = <em>com</em></p>
 <pre class="literal-block">
 <em>com</em> value = <em>yes</em> or <em>no</em>
 </pre>
-</li>
-</ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>

doc/html/compute_omega_chunk.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_pe.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_pe_atom.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_property_chunk.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_rdf.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_reduce.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_saed.html

@@ -287,18 +287,14 @@
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">saed</span> <span class="k">lambda</span> <span class="n">type1</span> <span class="n">type2</span> <span class="o">...</span> <span class="n">typeN</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
 </pre></div>
 </div>
-<ul>
+<ul class="simple">
-<li><p class="first">ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</p>
+<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
-</li>
+<li>saed = style name of this compute command</li>
-<li><p class="first">saed = style name of this compute command</p>
+<li>lambda = wavelength of incident radiation (length units)</li>
-</li>
+<li>type1 type2 ... typeN = chemical symbol of each atom type (see valid options below)</li>
-<li><p class="first">lambda = wavelength of incident radiation (length units)</p>
+<li>zero or more keyword/value pairs may be appended</li>
-</li>
+<li>keyword = <em>Kmax</em> or <em>Zone</em> or <em>dR_Ewald</em> or <em>c</em> or <em>manual</em> or <em>echo</em></li>
-<li><p class="first">type1 type2 ... typeN = chemical symbol of each atom type (see valid options below)</p>
+</ul>
-</li>
-<li><p class="first">zero or more keyword/value pairs may be appended</p>
-</li>
-<li><p class="first">keyword = <em>Kmax</em> or <em>Zone</em> or <em>dR_Ewald</em> or <em>c</em> or <em>manual</em> or <em>echo</em></p>
 <pre class="literal-block">
 <em>Kmax</em> value = Maximum distance explored from reciprocal space origin
                (inverse length units)
@@ -314,8 +310,6 @@
            based on the values of the <em>c</em> parameters
 <em>echo</em> = flag to provide extra output for debugging purposes
 </pre>
-</li>
-</ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>

doc/html/compute_smd_contact_radius.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_smd_triangle_mesh_vertices.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_smd_ulsph_num_neighs.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_smd_ulsph_strain.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_smd_ulsph_strain_rate.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_smd_ulsph_stress.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_temp.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_temp_chunk.html

@@ -226,7 +226,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_temp_cs.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_temp_partial.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_ti.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_torque_chunk.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_vcm_chunk.html

@@ -224,7 +224,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/compute_voronoi_atom.html

@@ -225,7 +225,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/create_atoms.html

@@ -275,10 +275,10 @@
 <pre class="literal-block">
 create_atoms type style args keyword values ...
 </pre>
-<ul>
+<ul class="simple">
-<li><p class="first">type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)</p>
+<li>type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)</li>
-</li>
+<li>style = <em>box</em> or <em>region</em> or <em>single</em> or <em>random</em></li>
-<li><p class="first">style = <em>box</em> or <em>region</em> or <em>single</em> or <em>random</em></p>
+</ul>
 <pre class="literal-block">
 <em>box</em> args = none
 <em>region</em> args = region-ID
@@ -290,10 +290,10 @@ create_atoms type style args keyword values ...
   seed = random # seed (positive integer)
   region-ID = create atoms within this region, use NULL for entire simulation box
 </pre>
-</li>
+<ul class="simple">
-<li><p class="first">zero or more keyword/value pairs may be appended</p>
+<li>zero or more keyword/value pairs may be appended</li>
-</li>
+<li>keyword = <em>mol</em> or <em>basis</em> or <em>remap</em> or <em>var</em> or <em>set</em> or <em>units</em></li>
-<li><p class="first">keyword = <em>mol</em> or <em>basis</em> or <em>remap</em> or <em>var</em> or <em>set</em> or <em>units</em></p>
+</ul>
 <pre class="literal-block">
 <em>mol</em> value = template-ID seed
   template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command
@@ -313,8 +313,6 @@ create_atoms type style args keyword values ...
   <em>lattice</em> = the geometry is defined in lattice units
   <em>box</em> = the geometry is defined in simulation box units
 </pre>
-</li>
-</ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>

doc/html/create_box.html

@@ -213,7 +213,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/dihedral_coeff.html

@@ -213,7 +213,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/dihedral_table.html

@@ -97,7 +97,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="dihedral_charmm.html">dihedral_style charmm command</a></li>

doc/html/dimension.html

@@ -214,7 +214,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/dump.html

@@ -214,7 +214,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/dump_custom_vtk.html

@@ -214,7 +214,7 @@
 <li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/fix_addforce.html

@@ -311,7 +311,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/fix_ave_chunk.html

@@ -311,7 +311,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/fix_aveforce.html

@@ -310,7 +310,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/fix_box_relax.html

@@ -372,10 +372,10 @@
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">box</span><span class="o">/</span><span class="n">relax</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
 </pre></div>
 </div>
-<ul>
+<ul class="simple">
-<li><p class="first">ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</p>
+<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
-</li>
+<li>box/relax = style name of this fix command</li>
-<li><p class="first">box/relax = style name of this fix command</p>
+</ul>
 <pre class="literal-block">
 one or more keyword value pairs may be appended
 keyword = <em>iso</em> or <em>aniso</em> or <em>tri</em> or <em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>yz</em> or <em>xz</em> or <em>couple</em> or <em>nreset</em> or <em>vmax</em> or <em>dilate</em> or <em>scaleyz</em> or <em>scalexz</em> or <em>scalexy</em> or <em>fixedpoint</em>
@@ -391,8 +391,6 @@ keyword = <em>iso</em> or <em>aniso</em> or <em>tri</em> or <em>x</em> or <em>y<
   <em>fixedpoint</em> values = x y z
     x,y,z = perform relaxation dilation/contraction around this point (distance units)
 </pre>
-</li>
-</ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>

doc/html/fix_controller.html

@@ -371,22 +371,16 @@
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">controller</span> <span class="n">Nevery</span> <span class="n">alpha</span> <span class="n">Kp</span> <span class="n">Ki</span> <span class="n">Kd</span> <span class="n">pvar</span> <span class="n">setpoint</span> <span class="n">cvar</span>
 </pre></div>
 </div>
-<ul>
+<ul class="simple">
-<li><p class="first">ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</p>
+<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
-</li>
+<li>controller = style name of this fix command</li>
-<li><p class="first">controller = style name of this fix command</p>
+<li>Nevery = invoke controller every this many timesteps</li>
-</li>
+<li>alpha = coupling constant for PID equation (see units discussion below)</li>
-<li><p class="first">Nevery = invoke controller every this many timesteps</p>
+<li>Kp = proportional gain in PID equation (unitless)</li>
-</li>
+<li>Ki = integral gain in PID equation (unitless)</li>
-<li><p class="first">alpha = coupling constant for PID equation (see units discussion below)</p>
+<li>Kd = derivative gain in PID equation (unitless)</li>
-</li>
+<li>pvar = process variable of form c_ID, c_ID[I], f_ID, f_ID[I], or v_name</li>
-<li><p class="first">Kp = proportional gain in PID equation (unitless)</p>
+</ul>
-</li>
-<li><p class="first">Ki = integral gain in PID equation (unitless)</p>
-</li>
-<li><p class="first">Kd = derivative gain in PID equation (unitless)</p>
-</li>
-<li><p class="first">pvar = process variable of form c_ID, c_ID[I], f_ID, f_ID[I], or v_name</p>
 <pre class="literal-block">
 c_ID = global scalar calculated by a compute with ID
 c_ID[I] = Ith component of global vector calculated by a compute with ID
@@ -394,11 +388,9 @@ f_ID = global scalar calculated by a fix with ID
 f_ID[I] = Ith component of global vector calculated by a fix with ID
 v_name = value calculated by an equal-style variable with name
 </pre>
-</li>
+<ul class="simple">
-<li><p class="first">setpoint = desired value of process variable (same units as process variable)</p>
+<li>setpoint = desired value of process variable (same units as process variable)</li>
-</li>
+<li>cvar = name of control variable</li>
-<li><p class="first">cvar = name of control variable</p>
-</li>
 </ul>
 </div>
 <div class="section" id="examples">

doc/html/fix_deform.html

@@ -311,7 +311,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/fix_ehex.html

@@ -371,18 +371,14 @@
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">ehex</span> <span class="n">nevery</span> <span class="n">F</span> <span class="n">keyword</span> <span class="n">value</span>
 </pre></div>
 </div>
-<ul>
+<ul class="simple">
-<li><p class="first">ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</p>
+<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
-</li>
+<li>ehex  = style name of this fix command</li>
-<li><p class="first">ehex  = style name of this fix command</p>
+<li>nevery = add/subtract heat every this many timesteps</li>
-</li>
+<li>F = energy flux into the reservoir (energy/time units)</li>
-<li><p class="first">nevery = add/subtract heat every this many timesteps</p>
+<li>zero or more keyword/value pairs may be appended to args</li>
-</li>
+<li>keyword = <em>region</em> or <em>constrain</em> or <em>com</em> or <em>hex</em></li>
-<li><p class="first">F = energy flux into the reservoir (energy/time units)</p>
+</ul>
-</li>
-<li><p class="first">zero or more keyword/value pairs may be appended to args</p>
-</li>
-<li><p class="first">keyword = <em>region</em> or <em>constrain</em> or <em>com</em> or <em>hex</em></p>
 <pre class="literal-block">
 <em>region</em> value = region-ID
   region-ID = ID of region (reservoir) atoms must be in for added thermostatting force
@@ -393,8 +389,6 @@
 <em>hex</em> value = none
   omit the coordinate correction to recover the HEX algorithm
 </pre>
-</li>
-</ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>

doc/html/fix_enforce2d.html

@@ -309,7 +309,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/fix_freeze.html

@@ -310,7 +310,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/fix_gld.html

@@ -372,24 +372,17 @@
 <pre class="literal-block">
 fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ...
 </pre>
-<ul>
+<ul class="simple">
-<li><p class="first">ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</p>
+<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
-</li>
+<li>gld = style name of this fix command</li>
-<li><p class="first">gld = style name of this fix command</p>
+<li>Tstart,Tstop = desired temperature at start/end of run (temperature units)</li>
-</li>
+<li>N_k = number of terms in the Prony series representation of the memory kernel</li>
-<li><p class="first">Tstart,Tstop = desired temperature at start/end of run (temperature units)</p>
+<li>seed = random number seed to use for white noise (positive integer)</li>
-</li>
+<li>series = <em>pprony</em> is presently the only available option</li>
-<li><p class="first">N_k = number of terms in the Prony series representation of the memory kernel</p>
+<li>c_k = the weight of the kth term in the Prony series (mass per time units)</li>
-</li>
+<li>tau_k = the time constant of the kth term in the Prony series (time units)</li>
-<li><p class="first">seed = random number seed to use for white noise (positive integer)</p>
+<li>zero or more keyword/value pairs may be appended</li>
-</li>
+</ul>
-<li><p class="first">series = <em>pprony</em> is presently the only available option</p>
-</li>
-<li><p class="first">c_k = the weight of the kth term in the Prony series (mass per time units)</p>
-</li>
-<li><p class="first">tau_k = the time constant of the kth term in the Prony series (time units)</p>
-</li>
-<li><p class="first">zero or more keyword/value pairs may be appended</p>
 <pre class="literal-block">
 keyword = <em>frozen</em> or <em>zero</em>
   <em>frozen</em> value = <em>no</em> or <em>yes</em>
@@ -399,8 +392,6 @@ keyword = <em>frozen</em> or <em>zero</em>
     <em>no</em> = do not set total random force to zero
     <em>yes</em> = set total random force to zero
 </pre>
-</li>
-</ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>

doc/html/fix_gle.html

@@ -310,7 +310,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/fix_gravity.html

@@ -310,7 +310,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/fix_ipi.html

@@ -310,7 +310,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/fix_langevin.html

@@ -311,7 +311,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
@@ -424,7 +424,7 @@
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
-<p>Apply a Langevin thermostat as described in <a class="reference internal" href="fix_langevin_eff.html#schneider"><span class="std std-ref">(Schneider)</span></a>
+<p>Apply a Langevin thermostat as described in <a class="reference internal" href="#schneider"><span class="std std-ref">(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"><span class="doc">fix nve</span></a>, this command
 performs Brownian dynamics (BD), since the total force on each atom
@@ -452,7 +452,7 @@ 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="fix_langevin_eff.html#dunweg"><span class="std std-ref">(Dunweg)</span></a>, where a uniform random number is used (instead of
+<a class="reference internal" href="#dunweg"><span class="std std-ref">(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

doc/html/fix_lb_fluid.html

@@ -372,23 +372,17 @@
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">lb</span><span class="o">/</span><span class="n">fluid</span> <span class="n">nevery</span> <span class="n">LBtype</span> <span class="n">viscosity</span> <span class="n">density</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
 </pre></div>
 </div>
-<ul>
+<ul class="simple">
-<li><p class="first">ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</p>
+<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
-</li>
+<li>lb/fluid = style name of this fix command</li>
-<li><p class="first">lb/fluid = style name of this fix command</p>
+<li>nevery = update the lattice-Boltzmann fluid every this many timesteps</li>
-</li>
+<li>LBtype = 1 to use the standard finite difference LB integrator,
-<li><p class="first">nevery = update the lattice-Boltzmann fluid every this many timesteps</p>
+2 to use the LB integrator of <a class="reference internal" href="#ollila"><span class="std std-ref">Ollila et al.</span></a></li>
-</li>
+<li>viscosity = the fluid viscosity (units of mass/(time*length)).</li>
-<li><p class="first">LBtype = 1 to use the standard finite difference LB integrator,
+<li>density = the fluid density.</li>
-2 to use the LB integrator of <a class="reference internal" href="#ollila"><span class="std std-ref">Ollila et al.</span></a></p>
+<li>zero or more keyword/value pairs may be appended</li>
-</li>
+<li>keyword = <em>setArea</em> or <em>setGamma</em> or <em>scaleGamma</em> or <em>dx</em> or <em>dm</em> or <em>a0</em> or <em>noise</em> or <em>calcforce</em> or <em>trilinear</em> or <em>D3Q19</em> or <em>read_restart</em> or <em>write_restart</em> or <em>zwall_velocity</em> or <em>bodyforce</em> or <em>printfluid</em></li>
-<li><p class="first">viscosity = the fluid viscosity (units of mass/(time*length)).</p>
+</ul>
-</li>
-<li><p class="first">density = the fluid density.</p>
-</li>
-<li><p class="first">zero or more keyword/value pairs may be appended</p>
-</li>
-<li><p class="first">keyword = <em>setArea</em> or <em>setGamma</em> or <em>scaleGamma</em> or <em>dx</em> or <em>dm</em> or <em>a0</em> or <em>noise</em> or <em>calcforce</em> or <em>trilinear</em> or <em>D3Q19</em> or <em>read_restart</em> or <em>write_restart</em> or <em>zwall_velocity</em> or <em>bodyforce</em> or <em>printfluid</em></p>
 <pre class="literal-block">
 <em>setArea</em> values = type node_area
     type = atom type (1-N)
@@ -415,8 +409,6 @@
 <em>bodyforce</em> values = bodyforcex bodyforcey bodyforcez = the x,y and z components of a constant body force added to the fluid.
 <em>printfluid</em> values = N = print the fluid density and velocity at each grid point every N timesteps.
 </pre>
-</li>
-</ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>

doc/html/fix_lb_rigid_pc_sphere.html

@@ -311,7 +311,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
@@ -414,7 +414,7 @@
 created to be used in place of that fix, to integrate the equations of
 motion of spherical rigid bodies when a lattice-Boltzmann fluid is
 present with a user-specified value of the force-coupling constant.
-The fix uses the integration algorithm described in <a class="reference internal" href="fix_lb_viscous.html#mackay"><span class="std std-ref">Mackay et al.</span></a> to update the positions, velocities, and orientations of
+The fix uses the integration algorithm described in <a class="reference internal" href="#mackay"><span class="std std-ref">Mackay et al.</span></a> to update the positions, velocities, and orientations of
 a set of spherical rigid bodies experiencing velocity dependent
 hydrodynamic forces.  The spherical bodies are assumed to rotate as
 solid, uniform density spheres, with moments of inertia calculated

doc/html/fix_neb.html

@@ -310,7 +310,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/fix_nph_asphere.html

@@ -310,7 +310,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/fix_nph_body.html

@@ -310,7 +310,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/fix_nph_sphere.html

@@ -310,7 +310,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/fix_npt_asphere.html

@@ -310,7 +310,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/fix_npt_body.html

@@ -310,7 +310,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/fix_npt_sphere.html

@@ -310,7 +310,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
-<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

doc/html/fix_nve.html

@@ -310,7 +310,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
 <li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
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