Merge remote-tracking branch 'akohlmey/integration' into library_interface_abort

.gitignore

@@ -9,6 +9,8 @@
 *.x
 *.exe
 *.dll
+*.pyc
+__pycache__
 
 Obj_*
 log.lammps
@@ -20,6 +22,8 @@ log.cite
 *.orig
 *.rej
 .vagrant
+\#*#
+.#*
 
 .DS_Store
 .DS_Store?

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>15 Sep 2016 version</h2>
+<h2>20 Sep 2016 version</h2>
 </div>
 <div class="section" id="version-info">
 <h2>Version info:</h2>

doc/html/Section_commands.html

@@ -858,9 +858,9 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
 <tr class="row-odd"><td><a class="reference internal" href="fix_smd_setvel.html"><span class="doc">smd/setvel</span></a></td>
 <td><a class="reference internal" href="fix_smd_wall_surface.html"><span class="doc">smd/wall/surface</span></a></td>
 <td><a class="reference internal" href="fix_temp_rescale_eff.html"><span class="doc">temp/rescale/eff</span></a></td>
-<td><a class="reference internal" href="fix_ti_rs.html"><span class="doc">ti/rs</span></a></td>
 <td><a class="reference internal" href="fix_ti_spring.html"><span class="doc">ti/spring</span></a></td>
 <td><a class="reference internal" href="fix_ttm.html"><span class="doc">ttm/mod</span></a></td>
+<td>&nbsp;</td>
 </tr>
 </tbody>
 </table>

doc/html/Section_example.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_perf.html

@@ -96,7 +96,7 @@
 <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_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/angle_hybrid.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/angle_none.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/angle_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/angle_zero.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_modify.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/bond_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/bond_hybrid.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 morse command" href="bond_morse.html"/>
         <link rel="prev" title="bond_style harmonic/shift/cut command" href="bond_harmonic_shift_cut.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 hybrid command</li>
       <li class="wy-breadcrumbs-aside">

doc/html/bond_none.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 nonlinear command" href="bond_nonlinear.html"/>
         <link rel="prev" title="bond_style morse command" href="bond_morse.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>
@@ -160,7 +160,7 @@
   <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 none command</li>
       <li class="wy-breadcrumbs-aside">

doc/html/bond_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/bond_write.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/bond_zero.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="Angle Styles" href="angles.html"/>
         <link rel="prev" title="bond_style table command" href="bond_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 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 zero command</li>
       <li class="wy-breadcrumbs-aside">

doc/html/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/clear.html

@@ -212,7 +212,7 @@
 <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/comm_modify.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/comm_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/compute.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/compute_angle.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_angle_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_bond.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_bond_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_com.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_dihedral.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_dihedral_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_dilatation_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_group_group.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_improper.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_improper_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_modify.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_msd.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_msd_nongauss.html

@@ -287,15 +287,19 @@
 <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 class="simple">
-<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
-<li>msd/nongauss = style name of this compute command</li>
-<li>zero or more keyword/value pairs may be appended</li>
-<li>keyword = <em>com</em></li>
-</ul>
+<ul>
+<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>
+<li><p class="first">msd/nongauss = style name of this compute command</p>
+</li>
+<li><p class="first">zero or more keyword/value pairs may be appended</p>
+</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_pair.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_pair_local.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_plasticity_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_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_local.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_rigid_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_saed.html

@@ -287,14 +287,18 @@
 <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 class="simple">
-<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
-<li>saed = style name of this compute command</li>
-<li>lambda = wavelength of incident radiation (length units)</li>
-<li>type1 type2 ... typeN = chemical symbol of each atom type (see valid options below)</li>
-<li>zero or more keyword/value pairs may be appended</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>
-</ul>
+<ul>
+<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>
+<li><p class="first">saed = style name of this compute command</p>
+</li>
+<li><p class="first">lambda = wavelength of incident radiation (length units)</p>
+</li>
+<li><p class="first">type1 type2 ... typeN = chemical symbol of each atom type (see valid options below)</p>
+</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)
@@ -310,6 +314,8 @@
            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_slice.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_damage.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_hourglass_error.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_internal_energy.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_plastic_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_plastic_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_rho.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_tlsph_defgrad.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_tlsph_dt.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_tlsph_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_tlsph_shape.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_tlsph_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_tlsph_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_tlsph_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_smd_vol.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_tally.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_asphere.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_body.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_com.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_deform.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_deform_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_temp_drude.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_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_temp_profile.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_ramp.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_region.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_region_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_temp_rotate.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_sphere.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_vacf.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 class="simple">
-<li>type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)</li>
-<li>style = <em>box</em> or <em>region</em> or <em>single</em> or <em>random</em></li>
-</ul>
+<ul>
+<li><p class="first">type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)</p>
+</li>
+<li><p class="first">style = <em>box</em> or <em>region</em> or <em>single</em> or <em>random</em></p>
 <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>
-<ul class="simple">
-<li>zero or more keyword/value pairs may be appended</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>
-</ul>
+</li>
+<li><p class="first">zero or more keyword/value pairs may be appended</p>
+</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>
 <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
@@ -313,6 +313,8 @@ 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_bonds.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/delete_atoms.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/delete_bonds.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/dielectric.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/dihedral_hybrid.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/dihedral_none.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/dihedral_zero.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/displace_atoms.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_h5md.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/dump_modify.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_molfile.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/echo.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/fix.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/fix_adapt.html

@@ -287,7 +287,6 @@
 <li class="toctree-l2"><a class="reference internal" href="fix_temp_rescale_eff.html">fix temp/rescale/eff command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_tfmc.html">fix tfmc command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_thermal_conductivity.html">fix thermal/conductivity command</a></li>
-<li class="toctree-l2"><a class="reference internal" href="fix_ti_rs.html">fix ti/rs command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_ti_spring.html">fix ti/spring command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_tmd.html">fix tmd command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_ttm.html">fix ttm command</a></li>
@@ -311,7 +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>
@@ -470,8 +469,8 @@ pages for individual pair styles and their energy formulas for the
 meaning of these parameters:</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="49%" />
-<col width="36%" />
+<col width="51%" />
+<col width="34%" />
 <col width="15%" />
 </colgroup>
 <tbody valign="top">
@@ -495,35 +494,39 @@ meaning of these parameters:</p>
 <td>scale</td>
 <td>type pairs</td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="pair_lj.html"><span class="doc">lj/cut</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="pair_eam.html"><span class="doc">eam, eam/alloy, eam/fs</span></a></td>
+<td>scale</td>
+<td>type pairs</td>
+</tr>
+<tr class="row-odd"><td><a class="reference internal" href="pair_lj.html"><span class="doc">lj/cut</span></a></td>
 <td>epsilon,sigma</td>
 <td>type pairs</td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="pair_lj_expand.html"><span class="doc">lj/expand</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="pair_lj_expand.html"><span class="doc">lj/expand</span></a></td>
 <td>epsilon,sigma,delta</td>
 <td>type pairs</td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="pair_dipole.html"><span class="doc">lj/sf/dipole/sf</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="pair_dipole.html"><span class="doc">lj/sf/dipole/sf</span></a></td>
 <td>epsilon,sigma,scale</td>
 <td>type pairs</td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="pair_lubricate.html"><span class="doc">lubricate</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="pair_lubricate.html"><span class="doc">lubricate</span></a></td>
 <td>mu</td>
 <td>global</td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="pair_gauss.html"><span class="doc">gauss</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="pair_gauss.html"><span class="doc">gauss</span></a></td>
 <td>a</td>
 <td>type pairs</td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="pair_morse.html"><span class="doc">morse</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="pair_morse.html"><span class="doc">morse</span></a></td>
 <td>d0,r0,alpha</td>
 <td>type pairs</td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="pair_soft.html"><span class="doc">soft</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="pair_soft.html"><span class="doc">soft</span></a></td>
 <td>a</td>
 <td>type pairs</td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="pair_kim.html"><span class="doc">kim</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="pair_kim.html"><span class="doc">kim</span></a></td>
 <td>PARAM_FREE_*&amp;#58i,j,...</td>
 <td>global</td>
 </tr>
@@ -531,9 +534,9 @@ meaning of these parameters:</p>
 </table>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">It is easy to add new potentials and their parameters to this
-list.  All it typically takes is adding an extract() method to the
-pair_*.cpp file associated with the potential.</p>
+<p class="last">It is easy to add new pairwise potentials and their parameters
+to this list.  All it typically takes is adding an extract() method to
+the pair_*.cpp file associated with the potential.</p>
 </div>
 <p>Some parameters are global settings for the pair style, e.g. the
 viscosity setting &#8220;mu&#8221; for <a class="reference internal" href="pair_lubricate.html"><span class="doc">pair_style lubricate</span></a>.

doc/html/fix_adapt_fep.html

@@ -287,7 +287,6 @@
 <li class="toctree-l2"><a class="reference internal" href="fix_temp_rescale_eff.html">fix temp/rescale/eff command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_tfmc.html">fix tfmc command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_thermal_conductivity.html">fix thermal/conductivity command</a></li>
-<li class="toctree-l2"><a class="reference internal" href="fix_ti_rs.html">fix ti/rs command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_ti_spring.html">fix ti/spring command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_tmd.html">fix tmd command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_ttm.html">fix ttm command</a></li>
@@ -311,7 +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_addforce.html

@@ -287,7 +287,6 @@
 <li class="toctree-l2"><a class="reference internal" href="fix_temp_rescale_eff.html">fix temp/rescale/eff command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_tfmc.html">fix tfmc command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_thermal_conductivity.html">fix thermal/conductivity command</a></li>
-<li class="toctree-l2"><a class="reference internal" href="fix_ti_rs.html">fix ti/rs command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_ti_spring.html">fix ti/spring command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_tmd.html">fix tmd command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_ttm.html">fix ttm command</a></li>

doc/html/fix_addtorque.html

@@ -286,7 +286,6 @@
 <li class="toctree-l2"><a class="reference internal" href="fix_temp_rescale_eff.html">fix temp/rescale/eff command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_tfmc.html">fix tfmc command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_thermal_conductivity.html">fix thermal/conductivity command</a></li>
-<li class="toctree-l2"><a class="reference internal" href="fix_ti_rs.html">fix ti/rs command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_ti_spring.html">fix ti/spring command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_tmd.html">fix tmd command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_ttm.html">fix ttm command</a></li>
@@ -310,7 +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_append_atoms.html

@@ -287,7 +287,6 @@
 <li class="toctree-l2"><a class="reference internal" href="fix_temp_rescale_eff.html">fix temp/rescale/eff command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_tfmc.html">fix tfmc command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_thermal_conductivity.html">fix thermal/conductivity command</a></li>
-<li class="toctree-l2"><a class="reference internal" href="fix_ti_rs.html">fix ti/rs command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_ti_spring.html">fix ti/spring command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_tmd.html">fix tmd command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_ttm.html">fix ttm command</a></li>
@@ -311,7 +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_atc.html

@@ -287,7 +287,6 @@
 <li class="toctree-l2"><a class="reference internal" href="fix_temp_rescale_eff.html">fix temp/rescale/eff command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_tfmc.html">fix tfmc command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_thermal_conductivity.html">fix thermal/conductivity command</a></li>
-<li class="toctree-l2"><a class="reference internal" href="fix_ti_rs.html">fix ti/rs command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_ti_spring.html">fix ti/spring command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_tmd.html">fix tmd command</a></li>
 <li class="toctree-l2"><a class="reference internal" href="fix_ttm.html">fix ttm command</a></li>