diff --git a/doc/Manual.html b/doc/Manual.html
index c39f5772ae..17cb5470cd 100644
--- a/doc/Manual.html
+++ b/doc/Manual.html
@@ -135,7 +135,7 @@
   <H1></H1><div class="section" id="lammps-documentation">
 <h1>LAMMPS-ICMS Documentation<a class="headerlink" href="#lammps-documentation" title="Permalink to this headline">¶</a></h1>
 <div class="section" id="mar-2016-version">
-<h2>10 Mar 2016 version<a class="headerlink" href="#mar-2016-version" title="Permalink to this headline">¶</a></h2>
+<h2>14 Mar 2016 version<a class="headerlink" href="#mar-2016-version" title="Permalink to this headline">¶</a></h2>
 </div>
 <div class="section" id="version-info">
 <h2>Version info:<a class="headerlink" href="#version-info" title="Permalink to this headline">¶</a></h2>
diff --git a/doc/Manual.txt b/doc/Manual.txt
index 268762fa6c..ca028b4738 100644
--- a/doc/Manual.txt
+++ b/doc/Manual.txt
@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS-ICMS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="10 Mar 2016 version">
+<META NAME="docnumber" CONTENT="14 Mar 2016 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -21,7 +21,7 @@
 <H1></H1>
 
 LAMMPS-ICMS Documentation :c,h3
-10 Mar 2016 version :c,h4
+14 Mar 2016 version :c,h4
 
 Version info: :h4
 
diff --git a/doc/Section_commands.html b/doc/Section_commands.html
index 39b4b3aa79..c9cdb67684 100644
--- a/doc/Section_commands.html
+++ b/doc/Section_commands.html
@@ -847,97 +847,97 @@ letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
 KOKKOS, o = USER-OMP, t = OPT.</p>
 <table border="1" class="docutils">
 <colgroup>
+<col width="17%" />
 <col width="16%" />
 <col width="19%" />
 <col width="16%" />
 <col width="15%" />
 <col width="16%" />
-<col width="17%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td><a class="reference internal" href="compute_angle_local.html"><em>angle/local</em></a></td>
 <td><a class="reference internal" href="compute_angmom_chunk.html"><em>angmom/chunk</em></a></td>
 <td><a class="reference internal" href="compute_body_local.html"><em>body/local</em></a></td>
+<td><a class="reference internal" href="compute_bond.html"><em>bond</em></a></td>
 <td><a class="reference internal" href="compute_bond_local.html"><em>bond/local</em></a></td>
 <td><a class="reference internal" href="compute_centro_atom.html"><em>centro/atom</em></a></td>
-<td><a class="reference internal" href="compute_chunk_atom.html"><em>chunk/atom</em></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="compute_cluster_atom.html"><em>cluster/atom</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="compute_chunk_atom.html"><em>chunk/atom</em></a></td>
+<td><a class="reference internal" href="compute_cluster_atom.html"><em>cluster/atom</em></a></td>
 <td><a class="reference internal" href="compute_cna_atom.html"><em>cna/atom</em></a></td>
 <td><a class="reference internal" href="compute_com.html"><em>com</em></a></td>
 <td><a class="reference internal" href="compute_com_chunk.html"><em>com/chunk</em></a></td>
 <td><a class="reference internal" href="compute_contact_atom.html"><em>contact/atom</em></a></td>
-<td><a class="reference internal" href="compute_coord_atom.html"><em>coord/atom</em></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="compute_damage_atom.html"><em>damage/atom</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="compute_coord_atom.html"><em>coord/atom</em></a></td>
+<td><a class="reference internal" href="compute_damage_atom.html"><em>damage/atom</em></a></td>
 <td><a class="reference internal" href="compute_dihedral_local.html"><em>dihedral/local</em></a></td>
 <td><a class="reference internal" href="compute_dilatation_atom.html"><em>dilatation/atom</em></a></td>
 <td><a class="reference internal" href="compute_displace_atom.html"><em>displace/atom</em></a></td>
 <td><a class="reference internal" href="compute_erotate_asphere.html"><em>erotate/asphere</em></a></td>
-<td><a class="reference internal" href="compute_erotate_rigid.html"><em>erotate/rigid</em></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="compute_erotate_sphere.html"><em>erotate/sphere</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="compute_erotate_rigid.html"><em>erotate/rigid</em></a></td>
+<td><a class="reference internal" href="compute_erotate_sphere.html"><em>erotate/sphere</em></a></td>
 <td><a class="reference internal" href="compute_erotate_sphere_atom.html"><em>erotate/sphere/atom</em></a></td>
 <td><a class="reference internal" href="compute_event_displace.html"><em>event/displace</em></a></td>
 <td><a class="reference internal" href="compute_group_group.html"><em>group/group</em></a></td>
 <td><a class="reference internal" href="compute_gyration.html"><em>gyration</em></a></td>
-<td><a class="reference internal" href="compute_gyration_chunk.html"><em>gyration/chunk</em></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="compute_heat_flux.html"><em>heat/flux</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="compute_gyration_chunk.html"><em>gyration/chunk</em></a></td>
+<td><a class="reference internal" href="compute_heat_flux.html"><em>heat/flux</em></a></td>
 <td><a class="reference internal" href="compute_hexorder_atom.html"><em>hexorder/atom</em></a></td>
 <td><a class="reference internal" href="compute_improper_local.html"><em>improper/local</em></a></td>
 <td><a class="reference internal" href="compute_inertia_chunk.html"><em>inertia/chunk</em></a></td>
 <td><a class="reference internal" href="compute_ke.html"><em>ke</em></a></td>
-<td><a class="reference internal" href="compute_ke_atom.html"><em>ke/atom</em></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="compute_ke_rigid.html"><em>ke/rigid</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="compute_ke_atom.html"><em>ke/atom</em></a></td>
+<td><a class="reference internal" href="compute_ke_rigid.html"><em>ke/rigid</em></a></td>
 <td><a class="reference internal" href="compute_msd.html"><em>msd</em></a></td>
 <td><a class="reference internal" href="compute_msd_chunk.html"><em>msd/chunk</em></a></td>
 <td><a class="reference internal" href="compute_msd_nongauss.html"><em>msd/nongauss</em></a></td>
 <td><a class="reference internal" href="compute_omega_chunk.html"><em>omega/chunk</em></a></td>
-<td><a class="reference internal" href="compute_orientorder_atom.html"><em>orientorder/atom</em></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="compute_pair.html"><em>pair</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="compute_orientorder_atom.html"><em>orientorder/atom</em></a></td>
+<td><a class="reference internal" href="compute_pair.html"><em>pair</em></a></td>
 <td><a class="reference internal" href="compute_pair_local.html"><em>pair/local</em></a></td>
 <td><a class="reference internal" href="compute_pe.html"><em>pe (c)</em></a></td>
 <td><a class="reference internal" href="compute_pe_atom.html"><em>pe/atom</em></a></td>
 <td><a class="reference internal" href="compute_plasticity_atom.html"><em>plasticity/atom</em></a></td>
-<td><a class="reference internal" href="compute_pressure.html"><em>pressure (c)</em></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="compute_property_atom.html"><em>property/atom</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="compute_pressure.html"><em>pressure (c)</em></a></td>
+<td><a class="reference internal" href="compute_property_atom.html"><em>property/atom</em></a></td>
 <td><a class="reference internal" href="compute_property_local.html"><em>property/local</em></a></td>
 <td><a class="reference internal" href="compute_property_chunk.html"><em>property/chunk</em></a></td>
 <td><a class="reference internal" href="compute_rdf.html"><em>rdf</em></a></td>
 <td><a class="reference internal" href="compute_reduce.html"><em>reduce</em></a></td>
-<td><a class="reference internal" href="compute_reduce.html"><em>reduce/region</em></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="compute_slice.html"><em>slice</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="compute_reduce.html"><em>reduce/region</em></a></td>
+<td><a class="reference internal" href="compute_slice.html"><em>slice</em></a></td>
 <td><a class="reference internal" href="compute_sna_atom.html"><em>sna/atom</em></a></td>
 <td><a class="reference internal" href="compute_sna_atom.html"><em>snad/atom</em></a></td>
 <td><a class="reference internal" href="compute_sna_atom.html"><em>snav/atom</em></a></td>
 <td><a class="reference internal" href="compute_stress_atom.html"><em>stress/atom</em></a></td>
-<td><a class="reference internal" href="compute_temp.html"><em>temp (ck)</em></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="compute_temp_asphere.html"><em>temp/asphere</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="compute_temp.html"><em>temp (ck)</em></a></td>
+<td><a class="reference internal" href="compute_temp_asphere.html"><em>temp/asphere</em></a></td>
 <td><a class="reference internal" href="compute_temp_body.html"><em>temp/body</em></a></td>
 <td><a class="reference internal" href="compute_temp_chunk.html"><em>temp/chunk</em></a></td>
 <td><a class="reference internal" href="compute_temp_com.html"><em>temp/com</em></a></td>
 <td><a class="reference internal" href="compute_temp_deform.html"><em>temp/deform</em></a></td>
-<td><a class="reference internal" href="compute_temp_partial.html"><em>temp/partial (c)</em></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="compute_temp_profile.html"><em>temp/profile</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="compute_temp_partial.html"><em>temp/partial (c)</em></a></td>
+<td><a class="reference internal" href="compute_temp_profile.html"><em>temp/profile</em></a></td>
 <td><a class="reference internal" href="compute_temp_ramp.html"><em>temp/ramp</em></a></td>
 <td><a class="reference internal" href="compute_temp_region.html"><em>temp/region</em></a></td>
 <td><a class="reference internal" href="compute_temp_sphere.html"><em>temp/sphere</em></a></td>
 <td><a class="reference internal" href="compute_ti.html"><em>ti</em></a></td>
-<td><a class="reference internal" href="compute_torque_chunk.html"><em>torque/chunk</em></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="compute_vacf.html"><em>vacf</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="compute_torque_chunk.html"><em>torque/chunk</em></a></td>
+<td><a class="reference internal" href="compute_vacf.html"><em>vacf</em></a></td>
 <td><a class="reference internal" href="compute_vcm_chunk.html"><em>vcm/chunk</em></a></td>
 <td><a class="reference internal" href="compute_voronoi_atom.html"><em>voronoi/atom</em></a></td>
 <td>&nbsp;</td>
 <td>&nbsp;</td>
-<td>&nbsp;</td>
 </tr>
 </tbody>
 </table>
@@ -1168,10 +1168,10 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
 if <a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS is built with the appropriate package</span></a>.</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="24%" />
+<col width="23%" />
+<col width="25%" />
 <col width="30%" />
-<col width="23%" />
-<col width="23%" />
+<col width="22%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td><a class="reference internal" href="pair_awpmd.html"><em>awpmd/cut</em></a></td>
@@ -1197,42 +1197,42 @@ if <a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS
 <tr class="row-odd"><td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/coul/long/soft (o)</em></a></td>
 <td><a class="reference internal" href="pair_dipole.html"><em>lj/cut/dipole/sf (go)</em></a></td>
 <td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/soft (o)</em></a></td>
-<td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/tip4p/long/soft (o)</em></a></td>
+<td><a class="reference internal" href="pair_thole.html"><em>lj/cut/thole/long (o)</em></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="pair_mdf.html"><em>lj/mdf</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/tip4p/long/soft (o)</em></a></td>
+<td><a class="reference internal" href="pair_mdf.html"><em>lj/mdf</em></a></td>
 <td><a class="reference internal" href="pair_sdk.html"><em>lj/sdk (gko)</em></a></td>
 <td><a class="reference internal" href="pair_sdk.html"><em>lj/sdk/coul/long (go)</em></a></td>
-<td><a class="reference internal" href="pair_sdk.html"><em>lj/sdk/coul/msm (o)</em></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="pair_lj_sf.html"><em>lj/sf (o)</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="pair_sdk.html"><em>lj/sdk/coul/msm (o)</em></a></td>
+<td><a class="reference internal" href="pair_lj_sf.html"><em>lj/sf (o)</em></a></td>
 <td><a class="reference internal" href="pair_meam_spline.html"><em>meam/spline</em></a></td>
 <td><a class="reference internal" href="pair_meam_sw_spline.html"><em>meam/sw/spline</em></a></td>
-<td><a class="reference internal" href="pair_mgpt.html"><em>mgpt</em></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="pair_morse.html"><em>morse/smooth/linear</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="pair_mgpt.html"><em>mgpt</em></a></td>
+<td><a class="reference internal" href="pair_morse.html"><em>morse/smooth/linear</em></a></td>
 <td><a class="reference internal" href="pair_quip.html"><em>quip</em></a></td>
 <td><a class="reference internal" href="pair_reax_c.html"><em>reax/c</em></a></td>
-<td><a class="reference internal" href="pair_smd_hertz.html"><em>smd/hertz</em></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="pair_smd_tlsph.html"><em>smd/tlsph</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="pair_smd_hertz.html"><em>smd/hertz</em></a></td>
+<td><a class="reference internal" href="pair_smd_tlsph.html"><em>smd/tlsph</em></a></td>
 <td><a class="reference internal" href="pair_smd_triangulated_surface.html"><em>smd/triangulated/surface</em></a></td>
 <td><a class="reference internal" href="pair_smd_ulsph.html"><em>smd/ulsph</em></a></td>
-<td><a class="reference internal" href="pair_smtbq.html"><em>smtbq</em></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="pair_sph_heatconduction.html"><em>sph/heatconduction</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="pair_smtbq.html"><em>smtbq</em></a></td>
+<td><a class="reference internal" href="pair_sph_heatconduction.html"><em>sph/heatconduction</em></a></td>
 <td><a class="reference internal" href="pair_sph_idealgas.html"><em>sph/idealgas</em></a></td>
 <td><a class="reference internal" href="pair_sph_lj.html"><em>sph/lj</em></a></td>
-<td><a class="reference internal" href="pair_sph_rhosum.html"><em>sph/rhosum</em></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="pair_sph_taitwater.html"><em>sph/taitwater</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="pair_sph_rhosum.html"><em>sph/rhosum</em></a></td>
+<td><a class="reference internal" href="pair_sph_taitwater.html"><em>sph/taitwater</em></a></td>
 <td><a class="reference internal" href="pair_sph_taitwater_morris.html"><em>sph/taitwater/morris</em></a></td>
 <td><a class="reference internal" href="pair_srp.html"><em>srp</em></a></td>
-<td><a class="reference internal" href="pair_tersoff.html"><em>tersoff/table (o)</em></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="pair_thole.html"><em>thole</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="pair_tersoff.html"><em>tersoff/table (o)</em></a></td>
+<td><a class="reference internal" href="pair_thole.html"><em>thole</em></a></td>
 <td><a class="reference internal" href="pair_lj_soft.html"><em>tip4p/long/soft (o)</em></a></td>
 <td>&nbsp;</td>
-<td>&nbsp;</td>
 </tr>
 </tbody>
 </table>
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
index 3c6b9a471a..3507ae6ae7 100644
--- a/doc/Section_commands.txt
+++ b/doc/Section_commands.txt
@@ -671,6 +671,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "angle/local"_compute_angle_local.html,
 "angmom/chunk"_compute_angmom_chunk.html,
 "body/local"_compute_body_local.html,
+"bond"_compute_bond.html,
 "bond/local"_compute_bond_local.html,
 "centro/atom"_compute_centro_atom.html,
 "chunk/atom"_compute_chunk_atom.html,
@@ -930,6 +931,7 @@ package"_Section_start.html#start_3.
 "lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
 "lj/cut/dipole/sf (go)"_pair_dipole.html,
 "lj/cut/soft (o)"_pair_lj_soft.html,
+"lj/cut/thole/long (o)"_pair_thole.html,
 "lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
 "lj/mdf"_pair_mdf.html,
 "lj/sdk (gko)"_pair_sdk.html,
diff --git a/doc/Section_modify.html b/doc/Section_modify.html
index 9e71715ed7..bf1479816d 100644
--- a/doc/Section_modify.html
+++ b/doc/Section_modify.html
@@ -1060,7 +1060,7 @@ then be accessed by variables) was discussed
 <p>We encourage users to submit new features to <a class="reference external" href="http://lammps.sandia.gov/authors.html">the developers</a> that they add to
 LAMMPS, especially if you think they will be of interest to other
 users.  The preferred way to do this is via GitHub.  Once you have
-prepared the content described below, see <code class="xref doc docutils literal"><span class="pre">this</span> <span class="pre">tutorial</span></code> for instructions on how to submit
+prepared the content described below, see <a class="reference internal" href="tutorial_github.html"><em>this tutorial</em></a> for instructions on how to submit
 your changes or new files.</p>
 <p>If the new features/files are broadly useful we may add them as core
 files to LAMMPS or as part of a <a class="reference internal" href="Section_start.html#start-3"><span>standard package</span></a>.  Else we will add them as a
diff --git a/doc/Section_modify.txt b/doc/Section_modify.txt
index 023484d6fb..609bf93bf1 100644
--- a/doc/Section_modify.txt
+++ b/doc/Section_modify.txt
@@ -626,7 +626,7 @@ developers"_http://lammps.sandia.gov/authors.html that they add to
 LAMMPS, especially if you think they will be of interest to other
 users.  The preferred way to do this is via GitHub.  Once you have
 prepared the content described below, see "this
-tutorial"_doc/tutorial_github.html for instructions on how to submit
+tutorial"_tutorial_github.html for instructions on how to submit
 your changes or new files.
 
 If the new features/files are broadly useful we may add them as core
diff --git a/doc/Section_packages.html b/doc/Section_packages.html
index b689191431..b406473435 100644
--- a/doc/Section_packages.html
+++ b/doc/Section_packages.html
@@ -494,7 +494,7 @@ name links to a sub-section below with more details.</p>
 <td>python</td>
 <td>lib/python</td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="#reax"><span>REAX</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="Section_tools.html#reax"><span>REAX</span></a></td>
 <td>ReaxFF potential</td>
 <td>Aidan Thompson (Sandia)</td>
 <td><a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a></td>
diff --git a/doc/_sources/Manual.txt b/doc/_sources/Manual.txt
index 20bf18c041..905e5a5f37 100644
--- a/doc/_sources/Manual.txt
+++ b/doc/_sources/Manual.txt
@@ -5,8 +5,8 @@
 LAMMPS Documentation
 ====================
 
-1 Mar 2016 version
-------------------
+10 Mar 2016 version
+-------------------
 
 Version info:
 -------------
diff --git a/doc/_sources/Section_commands.txt b/doc/_sources/Section_commands.txt
index f65a267094..18e9b950d7 100644
--- a/doc/_sources/Section_commands.txt
+++ b/doc/_sources/Section_commands.txt
@@ -524,31 +524,31 @@ is built with the :doc:`appropriate accelerated package <Section_accelerate>`.
 letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
 KOKKOS, o = USER-OMP, t = OPT.
 
-+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
-| :doc:`angle/local <compute_angle_local>`       | :doc:`angmom/chunk <compute_angmom_chunk>`               | :doc:`body/local <compute_body_local>`           | :doc:`bond/local <compute_bond_local>`       | :doc:`centro/atom <compute_centro_atom>`         | :doc:`chunk/atom <compute_chunk_atom>`             |
-+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
-| :doc:`cluster/atom <compute_cluster_atom>`     | :doc:`cna/atom <compute_cna_atom>`                       | :doc:`com <compute_com>`                         | :doc:`com/chunk <compute_com_chunk>`         | :doc:`contact/atom <compute_contact_atom>`       | :doc:`coord/atom <compute_coord_atom>`             |
-+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
-| :doc:`damage/atom <compute_damage_atom>`       | :doc:`dihedral/local <compute_dihedral_local>`           | :doc:`dilatation/atom <compute_dilatation_atom>` | :doc:`displace/atom <compute_displace_atom>` | :doc:`erotate/asphere <compute_erotate_asphere>` | :doc:`erotate/rigid <compute_erotate_rigid>`       |
-+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
-| :doc:`erotate/sphere <compute_erotate_sphere>` | :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>` | :doc:`event/displace <compute_event_displace>`   | :doc:`group/group <compute_group_group>`     | :doc:`gyration <compute_gyration>`               | :doc:`gyration/chunk <compute_gyration_chunk>`     |
-+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
-| :doc:`heat/flux <compute_heat_flux>`           | :doc:`hexorder/atom <compute_hexorder_atom>`             | :doc:`improper/local <compute_improper_local>`   | :doc:`inertia/chunk <compute_inertia_chunk>` | :doc:`ke <compute_ke>`                           | :doc:`ke/atom <compute_ke_atom>`                   |
-+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
-| :doc:`ke/rigid <compute_ke_rigid>`             | :doc:`msd <compute_msd>`                                 | :doc:`msd/chunk <compute_msd_chunk>`             | :doc:`msd/nongauss <compute_msd_nongauss>`   | :doc:`omega/chunk <compute_omega_chunk>`         | :doc:`orientorder/atom <compute_orientorder_atom>` |
-+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
-| :doc:`pair <compute_pair>`                     | :doc:`pair/local <compute_pair_local>`                   | :doc:`pe (c) <compute_pe>`                       | :doc:`pe/atom <compute_pe_atom>`             | :doc:`plasticity/atom <compute_plasticity_atom>` | :doc:`pressure (c) <compute_pressure>`             |
-+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
-| :doc:`property/atom <compute_property_atom>`   | :doc:`property/local <compute_property_local>`           | :doc:`property/chunk <compute_property_chunk>`   | :doc:`rdf <compute_rdf>`                     | :doc:`reduce <compute_reduce>`                   | :doc:`reduce/region <compute_reduce>`              |
-+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
-| :doc:`slice <compute_slice>`                   | :doc:`sna/atom <compute_sna_atom>`                       | :doc:`snad/atom <compute_sna_atom>`              | :doc:`snav/atom <compute_sna_atom>`          | :doc:`stress/atom <compute_stress_atom>`         | :doc:`temp (ck) <compute_temp>`                    |
-+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
-| :doc:`temp/asphere <compute_temp_asphere>`     | :doc:`temp/body <compute_temp_body>`                     | :doc:`temp/chunk <compute_temp_chunk>`           | :doc:`temp/com <compute_temp_com>`           | :doc:`temp/deform <compute_temp_deform>`         | :doc:`temp/partial (c) <compute_temp_partial>`     |
-+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
-| :doc:`temp/profile <compute_temp_profile>`     | :doc:`temp/ramp <compute_temp_ramp>`                     | :doc:`temp/region <compute_temp_region>`         | :doc:`temp/sphere <compute_temp_sphere>`     | :doc:`ti <compute_ti>`                           | :doc:`torque/chunk <compute_torque_chunk>`         |
-+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
-| :doc:`vacf <compute_vacf>`                     | :doc:`vcm/chunk <compute_vcm_chunk>`                     | :doc:`voronoi/atom <compute_voronoi_atom>`       |                                              |                                                  |                                                    |
-+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
++----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
+| :doc:`angle/local <compute_angle_local>`           | :doc:`angmom/chunk <compute_angmom_chunk>`     | :doc:`body/local <compute_body_local>`                   | :doc:`bond <compute_bond>`                       | :doc:`bond/local <compute_bond_local>`       | :doc:`centro/atom <compute_centro_atom>`         |
++----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
+| :doc:`chunk/atom <compute_chunk_atom>`             | :doc:`cluster/atom <compute_cluster_atom>`     | :doc:`cna/atom <compute_cna_atom>`                       | :doc:`com <compute_com>`                         | :doc:`com/chunk <compute_com_chunk>`         | :doc:`contact/atom <compute_contact_atom>`       |
++----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
+| :doc:`coord/atom <compute_coord_atom>`             | :doc:`damage/atom <compute_damage_atom>`       | :doc:`dihedral/local <compute_dihedral_local>`           | :doc:`dilatation/atom <compute_dilatation_atom>` | :doc:`displace/atom <compute_displace_atom>` | :doc:`erotate/asphere <compute_erotate_asphere>` |
++----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
+| :doc:`erotate/rigid <compute_erotate_rigid>`       | :doc:`erotate/sphere <compute_erotate_sphere>` | :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>` | :doc:`event/displace <compute_event_displace>`   | :doc:`group/group <compute_group_group>`     | :doc:`gyration <compute_gyration>`               |
++----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
+| :doc:`gyration/chunk <compute_gyration_chunk>`     | :doc:`heat/flux <compute_heat_flux>`           | :doc:`hexorder/atom <compute_hexorder_atom>`             | :doc:`improper/local <compute_improper_local>`   | :doc:`inertia/chunk <compute_inertia_chunk>` | :doc:`ke <compute_ke>`                           |
++----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
+| :doc:`ke/atom <compute_ke_atom>`                   | :doc:`ke/rigid <compute_ke_rigid>`             | :doc:`msd <compute_msd>`                                 | :doc:`msd/chunk <compute_msd_chunk>`             | :doc:`msd/nongauss <compute_msd_nongauss>`   | :doc:`omega/chunk <compute_omega_chunk>`         |
++----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
+| :doc:`orientorder/atom <compute_orientorder_atom>` | :doc:`pair <compute_pair>`                     | :doc:`pair/local <compute_pair_local>`                   | :doc:`pe (c) <compute_pe>`                       | :doc:`pe/atom <compute_pe_atom>`             | :doc:`plasticity/atom <compute_plasticity_atom>` |
++----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
+| :doc:`pressure (c) <compute_pressure>`             | :doc:`property/atom <compute_property_atom>`   | :doc:`property/local <compute_property_local>`           | :doc:`property/chunk <compute_property_chunk>`   | :doc:`rdf <compute_rdf>`                     | :doc:`reduce <compute_reduce>`                   |
++----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
+| :doc:`reduce/region <compute_reduce>`              | :doc:`slice <compute_slice>`                   | :doc:`sna/atom <compute_sna_atom>`                       | :doc:`snad/atom <compute_sna_atom>`              | :doc:`snav/atom <compute_sna_atom>`          | :doc:`stress/atom <compute_stress_atom>`         |
++----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
+| :doc:`temp (ck) <compute_temp>`                    | :doc:`temp/asphere <compute_temp_asphere>`     | :doc:`temp/body <compute_temp_body>`                     | :doc:`temp/chunk <compute_temp_chunk>`           | :doc:`temp/com <compute_temp_com>`           | :doc:`temp/deform <compute_temp_deform>`         |
++----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
+| :doc:`temp/partial (c) <compute_temp_partial>`     | :doc:`temp/profile <compute_temp_profile>`     | :doc:`temp/ramp <compute_temp_ramp>`                     | :doc:`temp/region <compute_temp_region>`         | :doc:`temp/sphere <compute_temp_sphere>`     | :doc:`ti <compute_ti>`                           |
++----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
+| :doc:`torque/chunk <compute_torque_chunk>`         | :doc:`vacf <compute_vacf>`                     | :doc:`vcm/chunk <compute_vcm_chunk>`                     | :doc:`voronoi/atom <compute_voronoi_atom>`       |                                              |                                                  |
++----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
 
 These are additional compute styles in USER packages, which can be
 used if :ref:`LAMMPS is built with the appropriate package <start_3>`.
@@ -644,31 +644,31 @@ KOKKOS, o = USER-OMP, t = OPT.
 These are additional pair styles in USER packages, which can be used
 if :ref:`LAMMPS is built with the appropriate package <start_3>`.
 
-+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
-| :doc:`awpmd/cut <pair_awpmd>`                       | :doc:`buck/mdf <pair_mdf>`                                      | :doc:`coul/cut/soft (o) <pair_lj_soft>`           | :doc:`coul/diel (o) <pair_coul_diel>`            |
-+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
-| :doc:`coul/long/soft (o) <pair_lj_soft>`            | :doc:`dpd/conservative <pair_dpd_conservative>`                 | :doc:`dpd/fdt <pair_dpd_fdt>`                     | :doc:`dpd/fdt/energy <pair_dpd_fdt>`             |
-+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
-| :doc:`eam/cd (o) <pair_eam>`                        | :doc:`edip (o) <pair_edip>`                                     | :doc:`eff/cut <pair_eff>`                         | :doc:`gauss/cut <pair_gauss>`                    |
-+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
-| :doc:`lennard/mdf <pair_mdf>`                       | :doc:`list <pair_list>`                                         | :doc:`lj/charmm/coul/long/soft (o) <pair_charmm>` | :doc:`lj/cut/coul/cut/soft (o) <pair_lj_soft>`   |
-+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
-| :doc:`lj/cut/coul/long/soft (o) <pair_lj_soft>`     | :doc:`lj/cut/dipole/sf (go) <pair_dipole>`                      | :doc:`lj/cut/soft (o) <pair_lj_soft>`             | :doc:`lj/cut/tip4p/long/soft (o) <pair_lj_soft>` |
-+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
-| :doc:`lj/mdf <pair_mdf>`                            | :doc:`lj/sdk (gko) <pair_sdk>`                                  | :doc:`lj/sdk/coul/long (go) <pair_sdk>`           | :doc:`lj/sdk/coul/msm (o) <pair_sdk>`            |
-+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
-| :doc:`lj/sf (o) <pair_lj_sf>`                       | :doc:`meam/spline <pair_meam_spline>`                           | :doc:`meam/sw/spline <pair_meam_sw_spline>`       | :doc:`mgpt <pair_mgpt>`                          |
-+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
-| :doc:`morse/smooth/linear <pair_morse>`             | :doc:`quip <pair_quip>`                                         | :doc:`reax/c <pair_reax_c>`                       | :doc:`smd/hertz <pair_smd_hertz>`                |
-+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
-| :doc:`smd/tlsph <pair_smd_tlsph>`                   | :doc:`smd/triangulated/surface <pair_smd_triangulated_surface>` | :doc:`smd/ulsph <pair_smd_ulsph>`                 | :doc:`smtbq <pair_smtbq>`                        |
-+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
-| :doc:`sph/heatconduction <pair_sph_heatconduction>` | :doc:`sph/idealgas <pair_sph_idealgas>`                         | :doc:`sph/lj <pair_sph_lj>`                       | :doc:`sph/rhosum <pair_sph_rhosum>`              |
-+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
-| :doc:`sph/taitwater <pair_sph_taitwater>`           | :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>`         | :doc:`srp <pair_srp>`                             | :doc:`tersoff/table (o) <pair_tersoff>`          |
-+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
-| :doc:`thole <pair_thole>`                           | :doc:`tip4p/long/soft (o) <pair_lj_soft>`                       |                                                   |                                                  |
-+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
++--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
+| :doc:`awpmd/cut <pair_awpmd>`                    | :doc:`buck/mdf <pair_mdf>`                          | :doc:`coul/cut/soft (o) <pair_lj_soft>`                         | :doc:`coul/diel (o) <pair_coul_diel>`          |
++--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
+| :doc:`coul/long/soft (o) <pair_lj_soft>`         | :doc:`dpd/conservative <pair_dpd_conservative>`     | :doc:`dpd/fdt <pair_dpd_fdt>`                                   | :doc:`dpd/fdt/energy <pair_dpd_fdt>`           |
++--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
+| :doc:`eam/cd (o) <pair_eam>`                     | :doc:`edip (o) <pair_edip>`                         | :doc:`eff/cut <pair_eff>`                                       | :doc:`gauss/cut <pair_gauss>`                  |
++--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
+| :doc:`lennard/mdf <pair_mdf>`                    | :doc:`list <pair_list>`                             | :doc:`lj/charmm/coul/long/soft (o) <pair_charmm>`               | :doc:`lj/cut/coul/cut/soft (o) <pair_lj_soft>` |
++--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
+| :doc:`lj/cut/coul/long/soft (o) <pair_lj_soft>`  | :doc:`lj/cut/dipole/sf (go) <pair_dipole>`          | :doc:`lj/cut/soft (o) <pair_lj_soft>`                           | :doc:`lj/cut/thole/long (o) <pair_thole>`      |
++--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
+| :doc:`lj/cut/tip4p/long/soft (o) <pair_lj_soft>` | :doc:`lj/mdf <pair_mdf>`                            | :doc:`lj/sdk (gko) <pair_sdk>`                                  | :doc:`lj/sdk/coul/long (go) <pair_sdk>`        |
++--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
+| :doc:`lj/sdk/coul/msm (o) <pair_sdk>`            | :doc:`lj/sf (o) <pair_lj_sf>`                       | :doc:`meam/spline <pair_meam_spline>`                           | :doc:`meam/sw/spline <pair_meam_sw_spline>`    |
++--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
+| :doc:`mgpt <pair_mgpt>`                          | :doc:`morse/smooth/linear <pair_morse>`             | :doc:`quip <pair_quip>`                                         | :doc:`reax/c <pair_reax_c>`                    |
++--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
+| :doc:`smd/hertz <pair_smd_hertz>`                | :doc:`smd/tlsph <pair_smd_tlsph>`                   | :doc:`smd/triangulated/surface <pair_smd_triangulated_surface>` | :doc:`smd/ulsph <pair_smd_ulsph>`              |
++--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
+| :doc:`smtbq <pair_smtbq>`                        | :doc:`sph/heatconduction <pair_sph_heatconduction>` | :doc:`sph/idealgas <pair_sph_idealgas>`                         | :doc:`sph/lj <pair_sph_lj>`                    |
++--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
+| :doc:`sph/rhosum <pair_sph_rhosum>`              | :doc:`sph/taitwater <pair_sph_taitwater>`           | :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>`         | :doc:`srp <pair_srp>`                          |
++--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
+| :doc:`tersoff/table (o) <pair_tersoff>`          | :doc:`thole <pair_thole>`                           | :doc:`tip4p/long/soft (o) <pair_lj_soft>`                       |                                                |
++--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
 
 
 ----------
diff --git a/doc/_sources/Section_modify.txt b/doc/_sources/Section_modify.txt
index db2c86ddb2..5f129e19d9 100644
--- a/doc/_sources/Section_modify.txt
+++ b/doc/_sources/Section_modify.txt
@@ -845,7 +845,7 @@ Submitting new features for inclusion in LAMMPS
 We encourage users to submit new features to `the developers <http://lammps.sandia.gov/authors.html>`_ that they add to
 LAMMPS, especially if you think they will be of interest to other
 users.  The preferred way to do this is via GitHub.  Once you have
-prepared the content described below, see :doc:`this tutorial <doc/tutorial_github>` for instructions on how to submit
+prepared the content described below, see :doc:`this tutorial <tutorial_github>` for instructions on how to submit
 your changes or new files.
 
 If the new features/files are broadly useful we may add them as core
diff --git a/doc/_sources/compute.txt b/doc/_sources/compute.txt
index 1ae06a0f85..275d19f6ee 100644
--- a/doc/_sources/compute.txt
+++ b/doc/_sources/compute.txt
@@ -177,6 +177,7 @@ section of :ref:`this page <cmd_5>`.
 * :doc:`angle/local <compute_bond_local>` - theta and energy of each angle
 * :doc:`angmom/chunk <compute_angmom_chunk>` - angular momentum for each chunk
 * :doc:`body/local <compute_body_local>` - attributes of body sub-particles
+* :doc:`bond <compute_bond>` - values computed by a bond style
 * :doc:`bond/local <compute_bond_local>` - distance and energy of each bond
 * :doc:`centro/atom <compute_centro_atom>` - centro-symmetry parameter for each atom
 * :doc:`chunk/atom <compute_chunk_atom>` - assign chunk IDs to each atom
diff --git a/doc/_sources/compute_bond.txt b/doc/_sources/compute_bond.txt
new file mode 100644
index 0000000000..7329b51006
--- /dev/null
+++ b/doc/_sources/compute_bond.txt
@@ -0,0 +1,66 @@
+.. index:: compute bond
+
+compute bond command
+====================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   compute ID group-ID bond bstyle
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* bond = style name of this compute command
+* bstyle = style name of a bond style that calculates additional values
+
+Examples
+""""""""
+
+.. parsed-literal::
+
+   compute 1 all bond harmonic
+   compute 2 all bond morse
+
+Description
+"""""""""""
+
+Define a computation that extracts additional values calculated by a
+bond style, sums them across processors, and makes them accessible for
+output or further processing by other commands.  The group specified
+for this command is ignored.
+
+The specified *bstyle* must be a bond style used in your simulation
+either by itself or as a sub-style in a :doc:`bond_style hybrid <bond_hybrid>`
+command.
+
+This compute is useful when using :doc:`bond_style hybrid <bond_hybrid>`
+if you want to know the portion of the total energy contributed by one
+sub-style.
+
+**Output info:**
+
+This compute calculates a global scalar which is the contribution of
+the named bond style to the bond energy *ebond*.
+
+The scalar value calculated by this compute is "extensive" and will be
+in energy :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>`
+
+Default
+"""""""
+
+The default for *evalue* is *ebond*.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Section_commands.html#comm
diff --git a/doc/_sources/compute_pair.txt b/doc/_sources/compute_pair.txt
index b1ccb0435f..072134cf12 100644
--- a/doc/_sources/compute_pair.txt
+++ b/doc/_sources/compute_pair.txt
@@ -83,7 +83,7 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute pe <compute_pe>`
+:doc:`compute pe <compute_pe>`, :doc:`compute bond <compute_bond>`
 
 Default
 """""""
diff --git a/doc/_sources/pair_morse.txt b/doc/_sources/pair_morse.txt
index 60ce0b1129..09e9ccd2a9 100644
--- a/doc/_sources/pair_morse.txt
+++ b/doc/_sources/pair_morse.txt
@@ -18,6 +18,9 @@ pair_style morse/opt command
 pair_style morse/smooth/linear command
 ======================================
 
+pair_style morse/smooth/linear/omp command
+==========================================
+
 Syntax
 """"""
 
@@ -75,8 +78,6 @@ the potential energy and force go to zero at the cut-off:
 The syntax of the pair_style and pair_coeff commands are the same for
 the *morse* and *morse/smooth/linear* styles.
 
-same
-
 
 ----------
 
diff --git a/doc/_sources/pair_thole.txt b/doc/_sources/pair_thole.txt
index 91cacd93c7..6cf4f1bb58 100644
--- a/doc/_sources/pair_thole.txt
+++ b/doc/_sources/pair_thole.txt
@@ -3,16 +3,31 @@
 pair_style thole command
 ========================
 
+pair_style lj/cut/thole/long command
+====================================
+
+pair_style lj/cut/thole/long/omp command
+========================================
+
 Syntax
 """"""
 
 .. parsed-literal::
 
-   pair_style thole damp cutoff
+   pair_style style args
 
-* thole = style name
-* damp = global damping parameter
-* cutoff = global cutoff
+* style = *thole* or *lj/cut/thole/long* or *lj/cut/thole/long/omp*
+* args = list of arguments for a particular style
+
+.. parsed-literal::
+
+     *thole* args = damp cutoff
+       damp = global damping parameter
+       cutoff = global cutoff (distance units)
+     *lj/cut/thole/long* or *lj/cut/thole/long/omp* args = damp cutoff (cutoff2)
+       damp = global damping parameter
+       cutoff = global cutoff for LJ (and Thole if only 1 arg) (distance units)
+       cutoff2 = global cutoff for Thole (optional) (distance units)
 
 Examples
 """"""""
@@ -24,10 +39,14 @@ Examples
    pair_coeff 1 2 thole 1.0 2.6 10.0
    pair_coeff * 2 thole 1.0 2.6
 
+.. parsed-literal::
+
+   pair_style lj/cut/thole/long 2.6 12.0
+
 Description
 """""""""""
 
-The *thole* pair style is meant to be used with force fields that
+The *thole* pair styles are meant to be used with force fields that
 include explicit polarization through Drude dipoles.  This link
 describes how to use the :doc:`thermalized Drude oscillator model <tutorial_drude>` in LAMMPS and polarizable models in LAMMPS
 are discussed in :ref:`this Section <howto_25>`.
@@ -37,7 +56,17 @@ The *thole* pair style should be used as a sub-style within in the
 main pair style including Coulomb interactions, i.e. any pair style
 containing *coul/cut* or *coul/long* in its style name.
 
-The *thole* pair style computes the Coulomb interaction damped at
+The *lj/cut/thole/long* pair style is equivalent to, but more convenient that
+the frequent combination *hybrid/overlay lj/cut/coul/long cutoff thole damp
+cutoff2*. It is not only a shorthand for this pair_style combination, but
+it also allows for mixing pair coefficients instead of listing them all.
+The *lj/cut/thole/long* pair style is also a bit faster because it avoids an
+overlay and can benefit from OMP acceleration. Moreover, it uses a more
+precise approximation of the direct Coulomb interaction at short range similar
+to :doc:`coul/long/cs <pair_coul_long_cs>`, which stabilizes the temperature of
+Drude particles.
+
+The *thole* pair styles compute the Coulomb interaction damped at
 short distances by a function
 
 
@@ -79,9 +108,9 @@ non-polarizable atoms are also subject to these weighting factors. The
 Drude particles inherit the 1-2, 1-3 and 1-4 neighbor relations from
 their respective cores.
 
-The following coefficients must be defined for each pair of atoms
-types via the :doc:`pair_coeff <pair_coeff>` command as in the example
-above.
+For pair_style *thole*, the following coefficients must be defined for
+each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command 
+as in the example above.
 
 * alpha (distance units^3)
 * damp
@@ -92,11 +121,60 @@ Thole damping parameter or global cutoff specified in the pair_style
 command are used. In order to specify a cutoff (third argument) a damp
 parameter (second argument) must also be specified.
 
+For pair style *lj/cut/thole/long*, the following coefficients must be
+defined for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>`
+command.
+
+* epsilon (energy units)
+* sigma (length units)
+* alpha (distance units^3)
+* damps
+* LJ cutoff (distance units)
+
+The last two coefficients are optional and default to the global values from
+the *pair_style* command line.
+
+
+----------
+
+
+Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in :doc:`Section_accelerate <Section_accelerate>`
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively.  They are only
+enabled if LAMMPS was built with those packages.  See the :ref:`Making LAMMPS <start_3>` section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can
+use the :doc:`suffix <suffix>` command in your input script.
+
+See :doc:`Section_accelerate <Section_accelerate>` of the manual for
+more instructions on how to use the accelerated styles effectively.
+
 **Mixing**:
 
 The *thole* pair style does not support mixing.  Thus, coefficients
 for all I,J pairs must be specified explicitly.
 
+The *lj/cut/thole/long* pair style does support mixing. Mixed coefficients
+are defined using
+
+
+.. math::
+
+   \begin{equation} \alpha_{ij} = \sqrt{\alpha_i\alpha_j}\end{equation}
+
+
+.. math::
+
+   \begin{equation} a_{ij} = \frac 1 2 (a_i + a_j)\end{equation}
+
 Restrictions
 """"""""""""
 
@@ -108,10 +186,15 @@ This pair_style should currently not be used with the :doc:`charmm dihedral styl
 factors. This is because the *thole* pair style does not know which
 pairs are 1-4 partners of which dihedrals.
 
+The *lj/cut/thole/long* pair style should be used with a :doc:`Kspace solver <kspace_style>`
+like PPPM or Ewald, which is only enabled if LAMMPS was built with the kspace
+package.
+
 Related commands
 """"""""""""""""
 
 :doc:`fix drude <fix_drude>`, :doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`
+`pair_style lj/cut/coul/long <pair_lj_cut_coul_long>`_
 
 **Default:** none
 
diff --git a/doc/compute.html b/doc/compute.html
index a60da4aac4..94cb8389dc 100644
--- a/doc/compute.html
+++ b/doc/compute.html
@@ -278,6 +278,7 @@ section of <a class="reference internal" href="Section_commands.html#cmd-5"><spa
 <li><a class="reference internal" href="compute_bond_local.html"><em>angle/local</em></a> - theta and energy of each angle</li>
 <li><a class="reference internal" href="compute_angmom_chunk.html"><em>angmom/chunk</em></a> - angular momentum for each chunk</li>
 <li><a class="reference internal" href="compute_body_local.html"><em>body/local</em></a> - attributes of body sub-particles</li>
+<li><a class="reference internal" href="compute_bond.html"><em>bond</em></a> - values computed by a bond style</li>
 <li><a class="reference internal" href="compute_bond_local.html"><em>bond/local</em></a> - distance and energy of each bond</li>
 <li><a class="reference internal" href="compute_centro_atom.html"><em>centro/atom</em></a> - centro-symmetry parameter for each atom</li>
 <li><a class="reference internal" href="compute_chunk_atom.html"><em>chunk/atom</em></a> - assign chunk IDs to each atom</li>
diff --git a/doc/compute.txt b/doc/compute.txt
index f6f730432a..b847985bf7 100644
--- a/doc/compute.txt
+++ b/doc/compute.txt
@@ -172,6 +172,7 @@ section of "this page"_Section_commands.html#cmd_5.
 "angle/local"_compute_bond_local.html - theta and energy of each angle
 "angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk
 "body/local"_compute_body_local.html - attributes of body sub-particles
+"bond"_compute_bond.html - values computed by a bond style
 "bond/local"_compute_bond_local.html - distance and energy of each bond
 "centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
 "chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom
diff --git a/doc/compute_bond.html b/doc/compute_bond.html
new file mode 100644
index 0000000000..f5186279d7
--- /dev/null
+++ b/doc/compute_bond.html
@@ -0,0 +1,242 @@
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+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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+            <a href="Section_commands.html#comm">Commands</a>
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+            
+  <div class="section" id="compute-bond-command">
+<span id="index-0"></span><h1>compute bond command<a class="headerlink" href="#compute-bond-command" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="syntax">
+<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID bond bstyle
+</pre></div>
+</div>
+<ul class="simple">
+<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
+<li>bond = style name of this compute command</li>
+<li>bstyle = style name of a bond style that calculates additional values</li>
+</ul>
+</div>
+<div class="section" id="examples">
+<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python"><div class="highlight"><pre>compute 1 all bond harmonic
+compute 2 all bond morse
+</pre></div>
+</div>
+</div>
+<div class="section" id="description">
+<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
+<p>Define a computation that extracts additional values calculated by a
+bond style, sums them across processors, and makes them accessible for
+output or further processing by other commands.  The group specified
+for this command is ignored.</p>
+<p>The specified <em>bstyle</em> must be a bond style used in your simulation
+either by itself or as a sub-style in a <a class="reference internal" href="bond_hybrid.html"><em>bond_style hybrid</em></a>
+command.</p>
+<p>This compute is useful when using <a class="reference internal" href="bond_hybrid.html"><em>bond_style hybrid</em></a>
+if you want to know the portion of the total energy contributed by one
+sub-style.</p>
+<p><strong>Output info:</strong></p>
+<p>This compute calculates a global scalar which is the contribution of
+the named bond style to the bond energy <em>ebond</em>.</p>
+<p>The scalar value calculated by this compute is &#8220;extensive&#8221; and will be
+in energy <a class="reference internal" href="units.html"><em>units</em></a>.</p>
+</div>
+<div class="section" id="restrictions">
+<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
+<blockquote>
+<div>none</div></blockquote>
+</div>
+<div class="section" id="related-commands">
+<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
+<p><a class="reference internal" href="compute_pe.html"><em>compute pe</em></a>, <a class="reference internal" href="compute_pair.html"><em>compute pair</em></a></p>
+</div>
+<div class="section" id="default">
+<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
+<p>The default for <em>evalue</em> is <em>ebond</em>.</p>
+</div>
+</div>
+
+
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\ No newline at end of file
diff --git a/doc/compute_pair.html b/doc/compute_pair.html
index af88a7b42d..cf4b1b49a5 100644
--- a/doc/compute_pair.html
+++ b/doc/compute_pair.html
@@ -197,7 +197,7 @@ see the doc page for the pair style for details.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
-<p><a class="reference internal" href="compute_pe.html"><em>compute pe</em></a></p>
+<p><a class="reference internal" href="compute_pe.html"><em>compute pe</em></a>, <a class="reference internal" href="compute_bond.html"><em>compute bond</em></a></p>
 </div>
 <div class="section" id="default">
 <h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
diff --git a/doc/genindex.html b/doc/genindex.html
index 1a6d68f591..d5844a0055 100644
--- a/doc/genindex.html
+++ b/doc/genindex.html
@@ -372,6 +372,10 @@
   </dt>
 
       
+  <dt><a href="compute_bond.html#index-0">compute bond</a>
+  </dt>
+
+      
   <dt><a href="compute_bond_local.html#index-0">compute bond/local</a>
   </dt>
 
@@ -555,12 +559,12 @@
   <dt><a href="compute_pe_atom.html#index-0">compute pe/atom</a>
   </dt>
 
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="compute_plasticity_atom.html#index-0">compute plasticity/atom</a>
   </dt>
 
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="compute_pressure.html#index-0">compute pressure</a>
   </dt>
diff --git a/doc/pair_morse.html b/doc/pair_morse.html
index dbf62897bd..a844791475 100644
--- a/doc/pair_morse.html
+++ b/doc/pair_morse.html
@@ -141,6 +141,9 @@
 </div>
 <div class="section" id="pair-style-morse-smooth-linear-command">
 <h1>pair_style morse/smooth/linear command<a class="headerlink" href="#pair-style-morse-smooth-linear-command" title="Permalink to this headline">¶</a></h1>
+</div>
+<div class="section" id="pair-style-morse-smooth-linear-omp-command">
+<h1>pair_style morse/smooth/linear/omp command<a class="headerlink" href="#pair-style-morse-smooth-linear-omp-command" title="Permalink to this headline">¶</a></h1>
 <div class="section" id="syntax">
 <h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
 <div class="highlight-python"><div class="highlight"><pre>pair_style morse cutoff
@@ -184,7 +187,6 @@ the potential energy and force go to zero at the cut-off:</p>
 <img alt="_images/pair_morse_smooth_linear.jpg" class="align-center" src="_images/pair_morse_smooth_linear.jpg" />
 <p>The syntax of the pair_style and pair_coeff commands are the same for
 the <em>morse</em> and <em>morse/smooth/linear</em> styles.</p>
-<p>same</p>
 <hr class="docutils" />
 <p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
 functionally the same as the corresponding style without the suffix.
diff --git a/doc/pair_thole.html b/doc/pair_thole.html
index 86d87c1584..cd1cdaa93a 100644
--- a/doc/pair_thole.html
+++ b/doc/pair_thole.html
@@ -126,16 +126,30 @@
             
   <div class="section" id="pair-style-thole-command">
 <span id="index-0"></span><h1>pair_style thole command<a class="headerlink" href="#pair-style-thole-command" title="Permalink to this headline">¶</a></h1>
+</div>
+<div class="section" id="pair-style-lj-cut-thole-long-command">
+<h1>pair_style lj/cut/thole/long command<a class="headerlink" href="#pair-style-lj-cut-thole-long-command" title="Permalink to this headline">¶</a></h1>
+</div>
+<div class="section" id="pair-style-lj-cut-thole-long-omp-command">
+<h1>pair_style lj/cut/thole/long/omp command<a class="headerlink" href="#pair-style-lj-cut-thole-long-omp-command" title="Permalink to this headline">¶</a></h1>
 <div class="section" id="syntax">
 <h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
-<div class="highlight-python"><div class="highlight"><pre>pair_style thole damp cutoff
+<div class="highlight-python"><div class="highlight"><pre>pair_style style args
 </pre></div>
 </div>
 <ul class="simple">
-<li>thole = style name</li>
-<li>damp = global damping parameter</li>
-<li>cutoff = global cutoff</li>
+<li>style = <em>thole</em> or <em>lj/cut/thole/long</em> or <em>lj/cut/thole/long/omp</em></li>
+<li>args = list of arguments for a particular style</li>
 </ul>
+<pre class="literal-block">
+<em>thole</em> args = damp cutoff
+  damp = global damping parameter
+  cutoff = global cutoff (distance units)
+<em>lj/cut/thole/long</em> or <em>lj/cut/thole/long/omp</em> args = damp cutoff (cutoff2)
+  damp = global damping parameter
+  cutoff = global cutoff for LJ (and Thole if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Thole (optional) (distance units)
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
@@ -145,10 +159,13 @@ pair_coeff 1 2 thole 1.0 2.6 10.0
 pair_coeff * 2 thole 1.0 2.6
 </pre></div>
 </div>
+<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/thole/long 2.6 12.0
+</pre></div>
+</div>
 </div>
 <div class="section" id="description">
 <h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
-<p>The <em>thole</em> pair style is meant to be used with force fields that
+<p>The <em>thole</em> pair styles are meant to be used with force fields that
 include explicit polarization through Drude dipoles.  This link
 describes how to use the <a class="reference internal" href="tutorial_drude.html"><em>thermalized Drude oscillator model</em></a> in LAMMPS and polarizable models in LAMMPS
 are discussed in <a class="reference internal" href="Section_howto.html#howto-25"><span>this Section</span></a>.</p>
@@ -156,15 +173,24 @@ are discussed in <a class="reference internal" href="Section_howto.html#howto-25
 <a class="reference internal" href="pair_hybrid.html"><em>pair_hybrid/overlay</em></a> command, in conjunction with a
 main pair style including Coulomb interactions, i.e. any pair style
 containing <em>coul/cut</em> or <em>coul/long</em> in its style name.</p>
-<p>The <em>thole</em> pair style computes the Coulomb interaction damped at
+<p>The <em>lj/cut/thole/long</em> pair style is equivalent to, but more convenient that
+the frequent combination <em>hybrid/overlay lj/cut/coul/long cutoff thole damp
+cutoff2</em>. It is not only a shorthand for this pair_style combination, but
+it also allows for mixing pair coefficients instead of listing them all.
+The <em>lj/cut/thole/long</em> pair style is also a bit faster because it avoids an
+overlay and can benefit from OMP acceleration. Moreover, it uses a more
+precise approximation of the direct Coulomb interaction at short range similar
+to <code class="xref doc docutils literal"><span class="pre">coul/long/cs</span></code>, which stabilizes the temperature of
+Drude particles.</p>
+<p>The <em>thole</em> pair styles compute the Coulomb interaction damped at
 short distances by a function</p>
 <div class="math">
 \[\begin{equation} T_{ij}(r_{ij}) = 1 - \left( 1 +
 \frac{s_{ij} r_{ij} }{2} \right)
 \exp \left( - s_{ij} r_{ij} \right) \end{equation}\]</div>
 <p>This function results from an adaptation to point charges
-<a class="reference internal" href="tutorial_drude.html#noskov"><span>(Noskov)</span></a> of the dipole screening scheme originally proposed
-by <a class="reference internal" href="tutorial_drude.html#thole"><span>Thole</span></a>. The scaling coefficient <span class="math">\(s_{ij}\)</span> is determined
+<a class="reference internal" href="#noskov"><span>(Noskov)</span></a> of the dipole screening scheme originally proposed
+by <a class="reference internal" href="#thole"><span>Thole</span></a>. The scaling coefficient <span class="math">\(s_{ij}\)</span> is determined
 by the polarizability of the atoms, <span class="math">\(\alpha_i\)</span>, and by a Thole
 damping parameter <span class="math">\(a\)</span>.  This Thole damping parameter usually takes
 a value of 2.6, but in certain force fields the value can depend upon
@@ -188,9 +214,9 @@ interactions between Drude particles and core charges or
 non-polarizable atoms are also subject to these weighting factors. The
 Drude particles inherit the 1-2, 1-3 and 1-4 neighbor relations from
 their respective cores.</p>
-<p>The following coefficients must be defined for each pair of atoms
-types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the example
-above.</p>
+<p>For pair_style <em>thole</em>, the following coefficients must be defined for
+each pair of atoms types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command
+as in the example above.</p>
 <ul class="simple">
 <li>alpha (distance units^3)</li>
 <li>damp</li>
@@ -200,9 +226,43 @@ above.</p>
 Thole damping parameter or global cutoff specified in the pair_style
 command are used. In order to specify a cutoff (third argument) a damp
 parameter (second argument) must also be specified.</p>
+<p>For pair style <em>lj/cut/thole/long</em>, the following coefficients must be
+defined for each pair of atoms types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>
+command.</p>
+<ul class="simple">
+<li>epsilon (energy units)</li>
+<li>sigma (length units)</li>
+<li>alpha (distance units^3)</li>
+<li>damps</li>
+<li>LJ cutoff (distance units)</li>
+</ul>
+<p>The last two coefficients are optional and default to the global values from
+the <em>pair_style</em> command line.</p>
+<hr class="docutils" />
+<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.</p>
+<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
+KOKKOS, USER-OMP and OPT packages, respectively.  They are only
+enabled if LAMMPS was built with those packages.  See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
+<p>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
+use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
+<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
+more instructions on how to use the accelerated styles effectively.</p>
 <p><strong>Mixing</strong>:</p>
 <p>The <em>thole</em> pair style does not support mixing.  Thus, coefficients
 for all I,J pairs must be specified explicitly.</p>
+<p>The <em>lj/cut/thole/long</em> pair style does support mixing. Mixed coefficients
+are defined using</p>
+<div class="math">
+\[\begin{equation} \alpha_{ij} = \sqrt{\alpha_i\alpha_j}\end{equation}\]</div>
+<div class="math">
+\[\begin{equation} a_{ij} = \frac 1 2 (a_i + a_j)\end{equation}\]</div>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
@@ -211,10 +271,14 @@ enabled if LAMMPS was built with that package. See the <a class="reference inter
 <p>This pair_style should currently not be used with the <a class="reference internal" href="dihedral_charmm.html"><em>charmm dihedral style</em></a> if the latter has non-zero 1-4 weighting
 factors. This is because the <em>thole</em> pair style does not know which
 pairs are 1-4 partners of which dihedrals.</p>
+<p>The <em>lj/cut/thole/long</em> pair style should be used with a <a class="reference internal" href="kspace_style.html"><em>Kspace solver</em></a>
+like PPPM or Ewald, which is only enabled if LAMMPS was built with the kspace
+package.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
-<p><a class="reference internal" href="fix_drude.html"><em>fix drude</em></a>, <a class="reference internal" href="fix_langevin_drude.html"><em>fix langevin/drude</em></a>, <a class="reference internal" href="fix_drude_transform.html"><em>fix drude/transform</em></a>, <a class="reference internal" href="compute_temp_drude.html"><em>compute temp/drude</em></a></p>
+<p><a class="reference internal" href="fix_drude.html"><em>fix drude</em></a>, <a class="reference internal" href="fix_langevin_drude.html"><em>fix langevin/drude</em></a>, <a class="reference internal" href="fix_drude_transform.html"><em>fix drude/transform</em></a>, <a class="reference internal" href="compute_temp_drude.html"><em>compute temp/drude</em></a>
+<a class="reference external" href="pair_lj_cut_coul_long">pair_style lj/cut/coul/long</a></p>
 <p><strong>Default:</strong> none</p>
 <hr class="docutils" />
 <p id="noskov"><strong>(Noskov)</strong> Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005).</p>
diff --git a/doc/searchindex.js b/doc/searchindex.js
index 02abbabece..234ed7b7be 100644
--- a/doc/searchindex.js
+++ b/doc/searchindex.js
@@ -1 +1 @@
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,509],adjust_dt:[],adjust_radiu:315,adjust_radius_factor:315,admiss:268,adof:[152,212],adopt:[306,502],adp:[],adri:[9,303,443,444],adust:166,advanc:[3,244,386,476,487],advantag:[1,6,8,11,14,18,40,41,42,220,380,405,490,495],advect:[3,6,323],advertis:8,advis:[375,442],afer:3,affect:[1,6,10,14,15,16,17,41,62,63,73,92,123,147,156,170,176,199,200,205,212,213,215,216,217,218,221,222,223,224,226,227,237,243,245,247,253,260,264,265,266,267,269,270,271,277,282,283,284,286,307,308,321,335,345,358,365,371,372,373,375,376,377,380,406,427,428,435,478,479,481,483,484,486,489,491],affin:[16,17,18,226,380,395],afil:241,aforement:18,afresh:[295,489,508],afshar:400,after:[2,3,5,6,11,12,15,21,22,33,40,41,42,45,51,59,60,61,63,65,73,150,151,152,153,154,155,156,159,160,161,162,164,165,172,173,175,176,179,180,185,195,196,197,198,199,200,201,203,204,205,209,210,212,213,220,221,222,223,224,226,230,239,250,251,252,253,254,259,260,261,263,269,270,271,277,282,283,284,286,289,293,297,305,307,310,319,324,326,327,328,330,331,332,333,334,338,340,342,346,349,350,356,364,370,371,373,374,376,378,379,380,381,382,386,393,395,404,405,406,407,413,414,415,426,427,428,430,431,432,433,437,441,443,444,451,452,461,462,464,465,466,469,476,478,480,481,482,483,484,486,487,489,491,493,495,498,499,502,507,508,509,510,511,512],afterrun:489,afterward:3,afterword:42,ag1:171,ag2:171,again:[6,11,12,16,17,64,146,152,158,166,196,200,226,243,293,349,364,375,427,428,476,478,479,481,483,488,495,497,508,510],against:[11,12,13,66,227,375,443,444],aggreg:[6,12,67,70,71,81,97,114,121,243,259,305,307,321,476,509],aggress:[243,495],agilio:[9,13],agre:[3,8,192,373,382,415,444],agreement:[5,7],ahd:412,ahead:342,aidan:[0,5,7,9,13,368],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:199,akohlmei:[7,9,13,201,244],aktulga:[7,9,300,444],al2o3:451,al2o3_001:[124,308],al3:171,ala:[250,451],alain:9,alat:[288,430],alb:[441,464,466],albeit:306,albert:9,alchem:[91,166],alcohol:338,alcu:[381,386],alcu_eam:441,alderton:399,alejandr:[263,264],alessandro:13,algebra:433,algorithm:[0,1,6,7,8,9,42,63,200,209,220,223,226,250,252,253,277,290,298,307,310,311,330,331,335,338,343,371,372,373,377,380,402,406,428,433,448,450,476,478,495],alia:[9,12,16],alias:[1,366],aliceblu:200,align:[6,9,12,29,42,73,174,192,216,220,245,368,481,484,502],alkali:406,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,165,166,167,168,169,170,171,172,173,174,175,176,178,180,185,191,192,193,196,197,198,199,200,201,203,204,205,206,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,256,258,259,261,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,319,320,322,323,324,325,326,327,330,331,332,333,334,335,336,337,338,340,341,342,343,344,345,346,347,348,349,350,354,359,361,363,364,365,366,367,368,370,373,374,375,376,377,379,380,381,382,383,385,386,387,389,390,391,392,393,395,396,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,422,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,472,473,475,476,478,479,480,481,482,483,484,485,486,488,489,490,491,492,493,494,495,496,498,499,500,502,503,507,508,509,510,511,512],allen:[29,91,399,409],allentildeslei:91,allign:3,allindex:347,alloc:[3,5,6,8,9,11,12,62,237,337,374,376,380,439,444,481,489],allocat:3,alloi:[],allosw:73,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,56,59,60,61,63,64,65,79,96,112,114,148,150,151,152,165,170,171,172,174,180,191,192,196,197,199,200,201,203,204,206,208,209,210,212,213,214,215,216,217,218,220,222,223,224,225,226,227,231,232,237,239,240,241,242,244,247,250,253,254,258,260,263,264,288,292,293,294,295,296,297,301,307,308,310,312,314,315,319,323,330,331,332,333,335,336,337,338,339,340,346,348,350,359,365,366,368,373,374,375,376,379,380,383,386,387,388,389,390,391,396,404,406,410,411,412,413,418,422,427,428,433,435,441,444,445,448,450,451,460,470,472,476,479,481,483,484,485,486,487,488,491,493,494,495,498,499,503,508,509],almost:[2,3,12,62,245,297,335,366,377,380,460],alo:396,alon:[6,7,223,303,443,444,479],alond:13,along:[6,8,12,29,41,73,91,124,170,171,172,195,196,199,212,223,245,250,251,255,260,262,297,307,310,312,316,320,321,330,334,335,341,344,346,368,371,372,373,375,396,399,410,413,416,418,422,430,443,444,463,481,484,491,492,508],alonso:[431,432],alpha:[6,12,52,204,250,289,297,298,302,373,381,384,387,396,400,402,404,405,407,412,417,418,430,436,440,465,467,499,502],alpha_:[],alpha_c:426,alpha_i:452,alpha_ialpha_j:[],alpha_lj:426,alphabet:[2,3,22,37,45,56,65,180,191,203,350,359,374,393,461,481],alphanumer:[3,65,203,296,304,348,374,508],alreadi:[3,7,8,9,12,16,17,18,43,172,173,175,198,208,212,216,217,220,222,226,254,295,297,323,346,347,374,375,400,411,413,420,428,460,470,473,477,481,482,486,491,508],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,40,41,42,43,45,55,56,57,60,61,63,65,68,73,74,75,77,79,83,91,93,94,96,98,108,109,110,111,112,113,118,120,122,123,125,146,147,148,149,150,151,152,153,154,155,156,158,159,160,161,162,164,165,166,167,168,169,172,173,174,175,176,178,180,191,192,194,195,196,197,198,199,200,201,203,204,205,206,208,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,232,237,238,239,240,241,243,244,247,248,249,250,260,261,263,264,265,266,267,268,269,270,271,276,279,280,282,283,284,285,286,288,289,290,292,293,294,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,316,317,320,321,323,326,327,328,329,330,334,335,336,337,339,341,344,346,347,348,350,356,359,363,365,366,368,369,370,373,374,375,376,377,379,380,386,390,391,393,397,398,399,400,404,405,406,409,410,412,413,414,422,426,427,430,433,435,437,439,440,441,442,445,446,448,455,456,458,459,461,462,463,464,465,466,467,469,476,478,479,480,481,482,483,484,485,486,488,489,490,491,493,494,495,496,499,500,501,502,503,504,506,507,508,509,510,512],alter:[3,6,8,9,11,12,42,61,149,150,151,152,153,155,158,159,160,161,164,165,172,176,196,197,199,201,204,205,212,221,222,223,224,226,262,263,302,305,307,309,317,323,331,338,345,372,375,413,481,486,488,491,508,509,512],altern:[1,6,8,9,11,12,17,18,95,172,196,203,213,226,234,244,248,263,296,307,330,331,338,351,355,365,372,373,381,382,396,401,402,404,405,407,415,418,426,430,431,432,437,441,442,452,462,464,466,469,479,481,482,494,496,499],although:[29,43,192,253,263,294,298,307,330,364,488,502,512],aluminum:473,alwai:[0,6,11,12,17,18,55,59,65,73,170,200,212,213,214,216,217,218,222,225,239,241,245,299,302,307,323,340,344,345,349,365,366,371,373,374,376,377,380,389,392,404,421,433,443,444,451,453,463,464,466,473,476,481,482,484,486,493,495,498,502,508,509],amap:200,amatrix:241,amaz:11,amazingli:13,amber2lmp:[],amber:[],ambient:199,ambigu:[3,65,203,508],amd:[17,380,433],amend:[],amino:9,amit:9,among:[16,147,210,250],amorph:[172,465],amount:[1,3,6,12,61,92,121,170,174,195,199,210,214,224,225,239,243,247,263,288,294,307,315,323,328,331,336,338,346,365,380,400,439,481,484],amplitud:[226,260,316,341,358,484,508],amu:239,amzallag:451,analag:[6,508],analalog:6,analog:[6,112,146,174,192,410],analys:[7,486],analysi:[7,9,13,65,66,75,201,303,304,313,347,433,452,481,491],analyt:[1,3,9,13,124,166,171,310,365,386,414,415,420,433,441,463],analyz:[6,8,9,13,375,433],andersen:310,anderson:[292,400],andr:[7,9,13],andrew:13,andzelm:460,ang:288,angl:[],angle1:306,angle2:306,angle_coeff:[],angle_cosineshift:27,angle_cosineshiftexp:[26,181],angle_cutof:412,angle_cutoff:412,angle_hybrid:29,angle_info:444,angle_styl:[],angle_typ:41,angleangl:[3,349,356,481],angleangletors:[3,179,481],anglecoeff:3,angletors:[3,179,185,481],angletyp:222,angmom:[],angmomi:[119,196,197,325],angmomx:[119,196,197,325],angmomz:[119,196,197,325],angstrom:[6,10,61,73,124,161,171,172,195,196,197,199,200,208,216,217,226,227,239,244,245,260,300,305,340,342,343,345,366,368,371,377,381,382,391,404,426,430,437,442,443,444,466,473,484,490,507,509],angular:[6,29,41,63,65,68,86,87,88,89,111,119,146,150,151,164,165,172,196,197,203,247,253,259,260,265,266,267,269,270,271,273,274,275,278,280,281,282,283,286,305,307,310,316,325,381,386,395,410,427,428,430,433,441,461,464,465,481,491,508,509],angularm:274,anharmon:[27,54,181,302,495],ani:[1,3,6,7,8,9,10,11,12,13,14,15,16,17,22,29,38,40,41,42,43,45,56,57,60,61,63,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,175,176,178,180,192,195,196,197,198,199,200,203,206,207,208,210,212,213,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,232,236,239,242,243,245,247,250,253,259,260,263,268,288,290,292,293,294,296,298,299,300,302,304,305,307,309,310,312,316,317,320,322,323,324,325,334,335,340,341,342,343,344,345,346,347,348,350,364,365,366,368,370,371,373,374,375,377,378,379,380,382,386,390,391,395,396,399,400,404,405,407,409,413,414,415,422,433,435,441,443,444,445,452,460,461,462,463,464,465,466,467,468,469,474,475,476,478,479,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,499,500,502,503,504,506,507,508,509,510,511,512],anihil:426,anim:[2,4,7,11,13,199,375],anion:[407,451],aniso:[3,224,226,263,264,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304,348,374,379,406,417,441,443,444,451,463,478,479,483,488,489,508,510,511,512],character:[6,69,72,112,122,146,452,476,495],characterist:[248,323,332],charg:[1,3,4,5,6,7,9,11,15,41,91,92,119,124,171,172,196,197,201,203,204,205,210,227,232,239,296,298,299,300,304,325,338,365,366,374,387,389,395,396,398,399,404,406,407,413,418,422,426,438,443,444,451,461,466,467,469,470,472,473,481,482,486,491,493,502,507,508],charmm2lammp:13,charmm:[],chartreus:200,cheap:323,cheaper:[231,409,445],check:[3,6,8,9,11,12,15,17,40,42,73,95,192,210,216,220,221,222,227,236,239,245,246,293,306,310,323,331,333,338,346,348,364,373,374,375,376,377,380,403,414,417,435,444,476,478,479,481,489,495,498,499,508],checkf:192,checkout:503,checkqeq:444,checku:192,chem:[6,13,20,21,25,40,41,44,46,47,91,92,112,118,147,178,179,189,214,225,230,240,241,248,250,262,263,264,284,285,290,294,297,299,307,311,312,323,326,327,330,331,332,333,340,349,358,360,365,366,372,375,382,387,391,392,395,396,397,399,400,402,406,408,409,411,412,418,422,423,426,430,434,435,438,451,460,467,490,493,495,502],chemic:[9,124,166,171,196,197,209,210,239,298,303,304,330,366,443,444,456],chemistri:[297,298,300,386,406,443,444],chen:335,cheng:395,chenoweth:[443,444],chenoweth_2008:[443,444],chi:[97,161,195,288,298,300,361,407,409,509],chiefli:442,child:8,chip:[7,9,12,17,18,380,494],chipot:225,chiral:358,chmod:[11,12],cho:430,chocol:[7,200],choic:[3,6,9,12,15,16,18,41,42,55,91,147,150,151,165,176,192,212,216,217,220,223,226,227,241,247,250,261,263,290,298,307,330,359,366,371,372,375,377,380,413,426,435,439,481,490,491,494,495,501,502,507],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,91,123,162,163,199,221,222,223,224,227,236,247,250,261,263,265,266,267,268,269,270,271,293,294,311,323,327,341,365,366,372,470,476,478,490,496],chose:[464,466],chosen:[2,3,6,12,17,146,172,175,184,192,199,205,210,224,227,236,239,240,248,250,261,263,268,290,293,304,323,327,330,331,336,338,339,345,366,367,372,380,401,402,406,410,417,420,446,464,476,490,495,502],chri:170,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[68,77,94,98,109,111,120,152,167,169,212],chute:[4,9,10,242],ciccotti:310,cieplak:[6,178,493],cii:213,cij:213,ciko:2,circl:[43,73,319],circular:[3,6,150,194],circumst:18,circumv:[96,112,302],citat:[],cite:[3,7,8,12,247,451],civ:9,ckio:2,cko:2,cl1:171,clarendon:[29,399],clarifi:[7,464,466],clariti:348,clark:438,class2:[],classic:[0,3,5,6,7,8,9,237,290,297,302,335,360,406],classifi:[461,469],claus:479,clean:[6,12,14,15,17,489],cleanli:[480,511],clear:[],clearli:7,clebsch:146,clermont:[9,13],clever:485,click:[2,11,22,37,45,56,172,180,191,199,244,350,359,375,393,461,503],client:[244,246],climb:[262,375,495],clinic:[7,13],clo:[161,195,509],clock:[12,476,495],clockwis:341,clone:503,close:[3,6,11,12,13,40,42,69,73,147,175,196,222,223,224,241,248,250,263,284,307,310,341,344,364,366,369,371,372,375,380,382,386,396,397,416,430,435,447,449,463,466,485,491,502,503,505],closer:[3,10,42,122,170,195,196,220,224,228,332,375],closest:[222,288,307,338,409,445,460,470],cloud:[451,502],clovertown:18,clsuter:74,clump1:[292,307],clump2:[292,307],clump3:[292,307],clump:307,cluster:[],clutter:3,cmap:481,cmatrix:241,cmax:430,cmd:[11,12,290,492],cmdarg:11,cmin:430,cmm:[],cmoput:139,cn1:213,cn2:213,cna:[],cnn:213,cnr:[9,13],cnt:[413,485],co2:[41,171,310,374],coars:[7,9,10,29,36,41,55,184,292,307,323,411,446,490,493],coarser:[366,508],coarsest:146,code:[],coeff:[3,7,8,12,21,22,33,45,51,178,179,180,185,349,350,356,393,413,417,435,448,450,453,481],coeffcient:481,coeffici:[],coefficienct:400,coefficient0:404,coefficient1:404,coeffieci:[6,384,416],coeffincientn:404,coexist:[239,406],cohes:[6,407,430],coincid:[128,344,391,427,428,476],colberg:198,cold:[6,157,239,243,376,502],coldest:331,coleman8:9,coleman:[9,124,171,308],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,68,77,87,94,98,103,109,111,120,152,160,167,169,172,196,197,200,212,225,253,259,292,302,305,307,346,365,374,376,394,481,488,494,500,512],collid:[231,323,345],colliex:171,collinear:[3,292],collis:[3,250,323,341,345,403,410,473],colllis:323,colloid:[],colombo:40,colon:[201,346,482],color1:200,color2:200,color:[3,9,42,196,199,200,220,240,297,302],column:[3,6,9,12,13,43,65,67,68,69,70,71,73,77,79,81,83,85,94,96,97,98,109,111,112,114,116,119,120,121,122,123,125,146,147,152,160,167,169,170,171,192,196,197,200,203,211,212,213,215,216,217,218,253,260,261,297,307,324,325,335,345,408,412,443,444,482,496,498,508],columnar:170,colvar:[],colvarmodul:12,com:[],comamnd:226,comand:223,comannd:380,comb3:[],comb:[],comb_1:299,comb_2:299,combiant:397,combin:[3,6,7,9,11,13,36,41,65,67,71,81,91,97,108,114,121,150,151,165,196,199,209,215,244,253,263,290,296,311,327,336,344,347,349,365,366,368,372,380,394,396,397,402,406,407,413,425,426,452,462,464,466,469,472,484,489,494,502,508],come:[],comfort:[12,13],comit:503,comm:[0,3,11,12,63,75,198,244,246,247,366,375,380,400,435,440,463,483],comm_modifi:[],comm_modift:63,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,178,192,196,235,248,307,335,374,375,381,404,405,407,417,430,437,444,451,452,462,463,464,465,466,469,478,479,481,502,503,508],commerci:7,commit:[9,503],commmand:[3,6,12,61,113,285,416,475,476,478,495,511],common:[],commonli:[3,6,9,12,17,25,59,61,110,112,174,196,199,201,360,411,420,452,464,466,481,484,493],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,60,63,64,73,170,175,176,199,200,220,221,222,224,225,226,244,246,250,252,253,254,263,289,296,298,299,300,307,311,323,335,346,363,365,376,377,378,380,402,403,439,474,478,479,490,491,508,510,512],communc:365,comp:[7,198,246,247,310,366,375,406,435,440,445,459,463,465],compact:[65,203,393,461],compani:[5,7],compar:[1,3,4,6,8,12,17,40,90,116,124,155,171,180,191,200,230,298,346,348,365,366,373,375,430,451,476,495,496,502,507],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,9,21,22,37,44,45,56,179,180,191,349,350,359,392,461],compat:[3,5,7,8,9,11,12,13,17,18,42,73,123,125,183,196,201,205,211,212,213,215,216,217,218,220,289,301,327,330,337,340,343,365,380,414,433,435,463,478,479,508],compens:[6,221,222,305,376,406],compet:334,competit:366,compil:[3,7,8,9,12,13,14,15,16,17,18,19,170,196,198,199,201,244,334,366,380,433,481,482,486,508],compl:17,complain:[11,12,17],complement:430,complementari:[7,396,418],complet:[3,6,9,11,12,15,42,61,73,200,216,220,225,253,290,293,296,323,334,336,347,348,364,375,380,407,448,450,468,476,481,486,489,493,495,498,502,508],complex:[4,6,8,11,12,13,25,41,43,64,96,112,146,148,160,172,173,250,319,344,363,375,406,433,463,479,481,484,508],compli:[330,334],complic:[6,7,9,12,13,210,239,479],complier:12,compon:[3,6,8,12,63,65,68,69,75,83,92,93,94,95,96,98,99,102,109,110,111,112,113,114,115,116,118,119,123,133,136,137,138,139,142,143,144,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,167,168,169,195,196,197,199,200,206,207,211,212,213,214,215,216,217,218,219,223,224,226,227,232,237,242,246,247,250,253,255,259,260,262,263,264,268,269,270,271,282,283,284,286,287,289,290,291,294,305,307,309,310,312,316,317,320,323,326,327,328,330,337,338,343,344,345,365,368,372,373,374,375,380,400,406,410,427,428,448,450,451,452,481,482,491,499,508,509],componenet:6,composit:[6,210,250,404],compound:[395,406,407,469],compres:[73,120,212],compress:[],compris:[41,344,445,468],compton:[124,171],comptu:3,compuat:366,comput:[],computation:[3,6,221,222,335,386],computational:502,compute_arrai:8,compute_fep:[205,426],compute_group_group:239,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[124,308],compute_scalar:8,compute_temp:8,compute_ti:205,compute_vector:8,compute_xrd:171,concaten:[2,3,511],concav:344,concentr:[73,404],concept:[6,152,162,212,490],conceptu:[3,6,73,160,224,226,375,396,413,430,486],concern:[6,75,91,198,240],concetr:73,concis:[11,334],conclud:12,concret:8,concurr:[16,366,508],conden:[335,464,466],condens:[6,154,335,382,398,404,418,469],condit:[],conducit:6,conduct:[],cone:484,confer:433,confid:[3,495],config:[12,196,478],configfil:225,configur:[1,2,6,12,15,17,38,61,128,174,192,195,196,199,203,224,225,226,227,231,239,246,247,277,290,298,334,363,373,375,382,386,405,430,433,462,464,466,469,476,481,483,484,495,503],confin:[481,495],conflict:[3,12,41,197,435,479,503],conform:[3,6,13,61,223,224,262,306,312,334,358,375,406,493],confus:[3,469],conjuct:[9,400],conjug:[7,8,247,372,406,443,444],conjunct:[6,7,73,90,91,120,155,160,166,172,176,200,204,205,247,250,254,277,293,294,298,299,300,302,307,311,323,331,338,343,365,366,375,387,389,393,396,400,406,412,418,435,438,446,467,481,484,488,502,512],connect:[3,6,9,91,157,175,223,244,292,307,310,320,375,397,410,460,466,478,479,481,485,502],conput:3,consecut:[3,11,12,40,73,172,200,204,205,227,244,245,396,418,422,476,482,484],consequ:[1,6,210,335,417,495],conserv:[],consid:[6,72,73,80,91,121,154,157,158,175,196,197,200,204,205,211,213,216,220,222,223,227,251,264,289,307,330,331,334,335,338,366,393,406,413,444,445,451,460,476,477,479,482,483,484,486,489,491,499,502,508],consider:[6,8,247,248,326,327,328,380,490],consist:[3,6,8,9,11,12,41,43,67,71,81,97,109,114,117,118,121,152,155,157,172,184,195,201,206,207,212,226,227,230,232,237,240,247,248,249,260,263,265,266,267,268,269,270,271,272,273,275,276,277,278,280,281,282,283,284,285,286,294,297,302,304,306,307,326,327,328,329,339,365,366,368,374,375,380,382,386,388,394,396,406,409,413,416,427,428,430,433,435,445,448,450,451,463,470,479,481,482,483,484,485,486,493,502,508],consistent_fe_initi:209,consit:307,constant:[],constitu:[3,6,253,307,340,344,394,445],constitut:[448,450],constrain:[3,6,8,149,150,151,152,153,155,158,159,160,161,162,164,165,203,212,227,239,240,245,253,257,292,293,305,307,310,321,331,338,373,374,406,486,493,502],constraint:[],construct:[6,8,12,14,38,55,57,63,66,69,72,74,75,79,96,112,124,146,171,224,263,289,306,344,376,380,399,433,435,460,462,463,484,485,500,508],constructor:[8,11],consult:444,consum:[1,302,439,508],consumpt:363,contact:[],contact_stiff:[447,449],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,65,91,95,122,124,146,152,160,170,171,172,174,178,180,191,192,196,197,199,200,201,203,204,205,209,211,212,213,215,216,217,218,220,225,227,232,235,241,245,246,247,250,261,277,288,289,292,293,295,297,300,304,307,308,313,323,330,334,335,344,345,348,364,366,374,375,378,379,381,382,383,386,395,396,399,404,405,406,413,414,430,433,437,441,442,443,444,452,462,463,464,465,466,467,469,476,477,478,479,481,482,483,484,486,488,490,493,495,496,498,499,502,503,508,510,512],content:[4,8,9,12,18,444,497,499],context:[3,6,8,12,17,122,123,200,221,222,227,292,304,339,372,472,481,488,497,507,508,509],contibut:72,contigu:478,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,73,83,108,109,168,200,203,204,205,210,212,213,214,215,216,217,218,220,223,224,225,226,227,239,240,241,243,244,245,247,248,249,255,260,261,263,265,266,267,268,269,270,271,282,283,284,285,286,291,293,296,297,307,308,312,322,323,325,332,333,335,341,344,348,364,379,380,386,400,403,420,423,443,444,445,448,450,465,476,479,481,483,484,489,495,496,498,499,508,510],continuum:[6,7,9,209,335,448,450],contour_integr:209,contract:[61,224,226,263,294,307],contradictori:3,contrain:310,contraint:277,contrari:[241,248],contrast:[1,6,43,56,66,154,157,197,226,346,448,450,472,511],contrib:335,contribut:[3,4,5,6,7,8,9,12,13,17,65,68,70,72,73,76,77,79,82,88,91,92,93,94,95,98,107,109,111,113,114,115,116,118,120,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,205,210,211,212,213,215,216,217,218,224,239,247,250,253,254,258,264,284,285,292,293,301,304,307,308,310,337,365,373,375,383,400,403,404,406,413,427,428,433,435,443,444,451,493,499,502,503],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,91,95,128,146,181,196,197,199,203,209,210,220,224,225,226,243,244,247,248,263,265,266,267,268,269,270,271,294,299,307,314,315,326,327,328,335,339,363,365,377,406,409,433,443,444,447,449,462,466,476,478,490,496,497],control_typ:209,controlfil:444,convect:95,conveni:[6,12,29,196,201,218,308,368,452,503,508],convent:[3,8,29,183,190,191,197,200,306,320,347,404,406,508],converg:[3,6,42,92,196,197,199,201,206,220,223,224,232,237,268,297,299,302,306,310,371,372,373,375,395,396,418,451,476,488,495],convers:[3,8,146,199,200,210,213,294,365,396,397,398,406,418,422,426,438,479,495,507],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,61,65,73,95,172,179,196,199,200,213,218,261,293,346,349,351,355,358,368,375,381,404,433,464,466,473,479,481,482,483,488,498,502,507,508,510,512],convex:[43,344],convinc:[7,12],cook:9,cooki:7,cool:[7,162,243,305],cooordin:[196,197],cooper:[5,7],coord123:120,coord1:[3,120,212,216,217],coord2:[3,120,212,216,217],coord3:[3,120,212,216,217],coord:[],coordb:451,coordbb:451,coordiat:373,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,61,63,64,65,68,70,73,76,77,79,83,91,93,94,98,108,109,111,119,120,122,140,146,155,161,167,169,170,172,176,195,196,197,198,199,200,201,203,206,211,212,215,216,217,220,221,222,223,224,225,226,227,230,232,233,237,239,242,243,244,245,246,247,248,260,262,263,265,266,267,269,270,271,284,287,288,289,292,293,294,304,305,307,309,310,312,317,320,321,322,323,325,333,334,335,342,343,345,346,368,373,374,375,380,381,382,385,405,451,476,481,482,483,484,486,489,491,495,502,508,509],coordn:[120,212],coorind:[],copi:[0,3,4,8,9,11,12,15,17,41,125,199,335,375,393,443,479,503],copper:473,coproccesor:16,coprocessor:[1,7,9,16,17,380,494],coproprocessor:17,copy_arrai:8,copyright:[7,8,292],coral:200,core:[],core_shel:154,coreshel:[],cornel:[6,178,493],corner123i:119,corner123x:119,corner123z:119,corner1i:119,corner1x:119,corner1z:119,corner2i:119,corner2x:119,corner2z:119,corner3i:119,corner3x:119,corner3z:119,corner:[3,6,41,119,199,344,345,368,468,481,503],cornflowerblu:200,cornsilk:200,corp:9,corpor:16,corr:395,correct:[3,6,9,11,12,16,17,61,91,92,107,108,113,116,122,154,159,166,197,199,226,239,241,247,263,264,284,292,294,297,334,340,344,365,375,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,471,472,473,474,481,496,499,502,503],correction_max_iter:209,correctli:[3,8,11,17,73,83,107,108,109,149,150,151,153,155,157,158,159,160,161,164,165,168,196,200,206,227,232,237,248,257,263,264,300,307,310,320,322,341,344,375,376,380,398,428,433,478,479,481,491,503,507,509],correl:[],correpond:235,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,72,73,91,101,102,115,118,119,120,121,124,125,133,136,137,138,139,140,142,143,144,146,149,150,159,166,170,171,178,179,180,181,182,183,184,186,187,189,190,192,195,196,197,199,200,204,205,206,212,214,215,216,217,219,222,224,226,233,237,238,242,247,250,251,259,260,261,263,265,266,267,268,269,270,271,272,273,277,280,282,283,284,286,289,290,294,299,307,309,310,326,328,330,339,340,341,343,344,345,347,349,350,351,352,354,355,358,360,366,370,372,374,375,381,382,384,387,388,389,390,391,392,393,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,416,418,419,420,421,422,423,424,425,426,427,430,431,433,435,436,437,438,440,441,443,444,445,446,451,452,453,462,463,464,465,466,469,471,472,473,476,478,479,481,482,484,494,495,496,498,499,502,508],correspondingli:[427,428,490],corrupt:3,cosin:[],cosineshift:27,cosmo:[241,246],cossq:[],cost:[1,6,10,11,12,17,40,42,73,115,124,147,171,199,200,212,216,217,220,221,222,236,263,299,335,365,366,378,396,418,422,433,435,462,478,490],costheta0:[462,464,466,469],costheta:441,costli:[11,92,241,376],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,61,68,73,77,91,94,98,109,111,115,118,120,152,162,167,169,185,196,197,199,200,204,205,212,213,216,220,226,237,246,296,297,298,302,305,307,309,323,324,330,334,335,336,340,344,346,348,356,362,364,371,373,376,380,383,408,412,413,416,443,444,477,478,479,481,483,485,488,489,496,497,502,508,509],coulomb:[3,5,6,7,8,9,10,12,14,15,18,74,92,113,114,122,147,173,177,298,300,336,365,366,373,380,387,389,390,391,392,395,396,397,398,399,406,410,411,413,418,422,426,429,435,438,443,444,446,451,461,466,467,469,472,486,493,499,502,507],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,65,70,79,95,120,122,123,160,170,176,206,207,210,212,215,216,217,219,220,227,232,236,239,245,263,277,293,310,326,327,344,366,373,374,375,377,380,408,412,435,499,508],counter:[3,341,476,487,489,495],counteract:239,counterbal:243,counterbalanc:29,counterpart:[196,307,476],counterproduct:18,coupl:[],courant:313,cours:[3,8,132,134,166,196,204,205,240,306,320,334,340,342,343,345,346,366,427,453,478,481,494,502,508,510],courtesi:368,cov:451,coval:[6,9,29,406,430,451,502],covari:241,cover:[6,73,192,200,209,250,406,468],coverag:[73,216],cpc:246,cpp:[1,3,6,8,9,11,12,13,91,196,204,205,237,310],cpu:[1,3,9,10,12,14,15,16,17,18,65,73,200,214,230,248,336,363,366,380,393,461,476,494,495,498,499,500,508],cpuremain:499,cr2:171,cr3:171,crack:[4,376],crada:[5,7],crai:[5,7,13,18,196],crash:[3,12,376,502],craympi:380,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:209,create_faceset:209,create_group:198,create_nodeset:209,createatom:[],creation:[],crimson:200,critchlei:292,criteria:[3,122,173,199,200,221,222,223,258,373,440,468,483,486,508],criterion:[12,42,127,172,175,210,220,223,239,277,299,313,341,346,373,375,395,406,410,451,486,495,496],criterioni:495,critic:[6,49,50,261,330,335,373],crmax:73,crmin:73,cross:[3,12,22,73,93,150,170,180,196,197,199,211,216,222,226,260,262,284,307,316,320,322,331,338,350,368,375,391,400,403,404,411,412,413,418,420,422,441,446,448,450,464,466,473,481,485,491,510],crossov:1,crossterm:481,crozier:[0,7,13],crucial:297,crystal:[3,4,6,13,75,112,288,289,333,368,376,481,485,499,502],crystallin:[6,108,289,368,465,502],crystallis:330,crystallogr:[124,171],crystallograph:[368,499],crystallographi:[124,171,368],cs1:171,cs_chunk:6,cs_im:[41,481],cs_re:[41,481],csanyi:[146,442,452],cscl:430,csequ:6,csh:[11,12,393],cshrc:[11,12],csic:[405,462,464,466,469],csinfo:6,csisi:[405,462,464,466,469],csld:[],cst:404,cstherm:6,cstyle:478,csvr:[],ctcm:[381,404],ctemp_cor:230,cterm:312,ctr:9,ctype:11,cu1:171,cu2:171,cu3au:430,cube:[6,42,170,175,220,230,344,368,502],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_hom:[9,15],cuda_prec:[9,15],cufft:14,cuh:386,cummul:[3,6,218,221,222,223,225,236,241,247,249,323,326,327,328,329,331,338,412,499],cumul:[6,210,212,215,216,217,231,239,247,261,263,268,277,307,308,375],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,61,63,65,73,75,83,91,107,108,114,122,123,136,147,152,160,162,168,170,173,176,195,196,197,198,199,200,201,204,205,209,212,216,217,218,220,221,222,223,224,225,226,227,231,232,237,239,241,244,245,247,253,260,263,264,269,270,271,277,282,283,284,286,292,293,298,299,301,304,305,306,307,310,311,312,313,314,315,316,317,319,321,322,323,326,327,328,334,335,338,339,340,341,342,343,345,346,348,363,364,365,366,369,370,372,373,374,375,380,386,393,395,399,404,406,407,410,413,414,417,427,428,430,431,432,435,441,443,444,447,448,449,450,453,464,466,467,470,476,477,478,479,481,482,483,484,485,487,488,489,491,493,495,496,498,499,503,508,509,510,511,512],curv:[6,172,239,289],curvatur:[409,445,473],custom:[],cut0:479,cut1:490,cut2:490,cut:[],cuthi:[288,300],cutinn:[388,427,428],cutlo:[288,300],cutmax:441,cutoff1:[392,399,418,422,426,429,438,446],cutoff2:[387,389,390,392,398,399,418,422,426,429,438,446],cutoff:[3,6,8,10,16,18,40,46,47,55,56,63,72,74,75,79,91,96,112,114,121,122,146,170,173,175,176,222,223,228,235,288,297,298,300,302,304,307,311,323,336,340,344,346,363,365,366,373,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,394,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,444,445,446,451,452,453,454,455,456,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,479,483,486,490,502,508],cutoff_glob:[],cutoff_inn:[],cutoffa:405,cutoffc:405,cuu3:404,cval:171,cvd:330,cvel:312,cvff:[],cwiggl:[3,260,340,343,345,508],cyan:[2,199,200],cycl:[3,239,261,263,264,268],cyclic:[3,192],cygwin:12,cylind:[3,4,73,199,212,245,293,341,344,484],cylindr:[6,245,320,341],cypress:380,cyrot:386,cyrstal:289,d3q15:250,d3q19:250,d_double_doubl:15,d_e:335,d_flag2:296,d_flag:296,d_name:[119,196,296,325,491],d_single_doubl:15,d_single_singl:15,d_sx:296,d_sy:296,d_sz:296,daan:333,dai:12,daili:12,daivi:284,damag:[],dammak:302,damp:[3,6,203,208,247,248,249,254,263,264,268,294,297,298,302,307,326,327,339,341,342,372,373,375,387,389,391,396,399,406,410,418,426,438,446,461,467,495,502],damp_com:248,damp_drud:248,dampen:[307,502],dampflag:[341,410],dan:17,danger:[3,12,239,346,400,499],dangl:175,daniel:9,darden:[366,399],darkblu:200,darkcyan:200,darken:199,darkgoldenrod:200,darkgrai:200,darkgreen:200,darkkhaki:200,darkmagenta:200,darkolivegreen:200,darkorang:200,darkorchid:200,darkr:200,darksalmon:200,darkseagreen:200,darkslateblu:200,darkslategrai:200,darkturquois:200,darkviolet:200,dasgupta:298,dash:[410,498],dat:[6,95,192,209,477],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,308],dataset:308,datatyp:3,date:[0,4,6,12,13,195,443,444,508],datom1:121,datom2:121,datom3:121,datom4:121,datum:[3,6,43,67,70,71,81,97,114,121,196,213],davenport:429,davi:340,david:[9,19,365,366,464,466],daw:[404,441],dbg:14,dcd:[3,6,7,196,198,199,200,201,290,482,486],ddim:195,deactiv:426,dealt:246,debug:[6,7,11,12,13,14,17,124,128,171,172,290,295,363,365,380,414,435,470,479,480,488,491,498,508],deby:[],decai:[96,396,473],decid:[3,6,12,16,73,260,296,307,336,496,503],decipher:368,declar:198,declin:323,decod:199,decompos:[91,452],decomposit:[3,5,7,18,64,209,290,311],decoupl:[6,502],decreas:[3,196,197,206,207,214,223,226,232,237,239,247,334,365],decrement:312,deepli:362,deeppink:200,deepskyblu:200,def:[12,13,479],defaul:63,defect:[6,72,170,433],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,178,179,180,181,182,183,184,186,187,189,190,191,192,193,194,195,196,197,198,199,200,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,220,221,222,223,224,226,227,230,231,232,234,237,238,239,242,245,246,247,248,249,250,258,260,262,263,264,265,266,267,268,269,270,271,273,274,275,278,280,281,282,283,284,285,286,288,289,290,292,293,294,296,298,300,305,307,308,309,310,313,317,321,323,325,326,327,328,329,331,332,333,335,337,338,340,341,342,343,344,345,346,348,349,350,351,352,353,354,355,358,359,360,361,363,365,366,368,370,372,373,374,375,376,377,378,379,380,382,383,384,385,387,388,389,390,391,392,393,394,396,397,399,400,401,402,403,405,406,408,409,410,411,412,413,414,416,418,419,420,421,422,423,424,425,426,427,428,429,433,434,435,436,437,438,440,441,443,444,445,446,447,448,449,450,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,481,482,484,485,486,487,490,491,492,493,495,496,498,499,502,504,505,506,507,508,509],definit:[2,3,6,8,12,13,80,82,122,146,200,212,213,214,215,216,217,218,226,234,245,268,308,325,337,340,343,345,347,359,363,374,383,386,394,401,402,406,416,441,448,450,452,468,479,481,483,490,492,507,508],defint:499,deform:[],deg2theta:171,deg:502,degener:[3,292],degrad:[8,18,289,366,490],degre:[3,6,8,20,21,24,28,29,32,35,36,38,67,81,96,97,99,101,102,104,106,107,112,118,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,171,172,178,179,182,183,190,192,195,199,212,223,230,239,241,242,247,248,253,263,264,268,269,270,271,282,283,284,286,290,292,306,307,310,326,327,328,333,349,351,355,358,360,373,399,404,412,491,499,502,509],degress:[152,212],del:495,delai:[3,6,12,376,403,499],deleg:413,delet:[2,3,7,8,12,55,59,62,65,170,175,176,203,212,213,215,216,217,218,221,223,236,239,263,308,326,327,346,348,364,374,376,379,435,460,481,482,483,484,492,493,498,503,504,506,508,509],delete_atom:[],delete_bond:[],delete_el:209,deli:195,delimit:[479,508],deloc:[264,406,451],delr:430,delt_lo:495,delta:[],delta_1:386,delta_3:386,delta_7:386,delta_conf:3,delta_ij:[430,441],delta_mu:[],delta_pi:386,delta_r:441,delta_sigma:386,delta_ua:[],delx:195,delz:195,dem:[],demand:302,demo:11,demon:287,demonstr:[297,430],den:293,dendrim:412,denniston:[9,250,252,253,254,289],denomin:[7,177],denot:[124,230,248,289,300,302,396,411,413,444,448,450],dens:[73,223,406],densiti:[3,6,7,9,18,41,42,61,105,122,132,146,158,170,172,204,205,209,212,216,217,220,226,237,250,253,256,257,289,293,294,298,335,340,368,370,374,381,386,404,430,431,432,441,445,451,455,457,458,459,481,490,491,499,507],density_continu:450,density_summ:450,depart:[0,7],departur:[261,297],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,63,65,67,70,71,72,73,81,96,97,108,114,115,118,119,120,121,125,146,149,155,159,160,166,172,173,178,179,180,181,182,183,184,186,187,189,190,191,192,195,196,197,199,200,203,204,205,206,207,210,212,214,215,216,218,219,220,222,224,226,232,233,238,241,242,243,245,247,248,250,252,253,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,288,299,302,304,307,309,310,311,317,323,326,327,328,330,332,334,335,337,339,340,343,344,345,346,348,349,350,351,352,354,355,358,360,366,368,373,374,376,377,378,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,430,431,433,434,436,437,438,440,441,443,444,445,446,451,452,453,461,462,463,464,465,466,467,469,471,472,473,476,478,481,483,484,487,491,493,495,498,499,501,508,509],dependend:6,depflag:12,dephas:[476,495],depos:227,deposit:[],deprec:[3,298,443],depth:[52,150,199,335,409,445],dequidt:9,der:[91,113,394,395,426,443,444,472,502],deriv:[6,7,8,9,38,57,65,91,146,166,192,213,224,226,239,247,260,263,265,266,267,268,269,270,271,288,294,298,302,332,333,335,340,341,344,372,374,382,386,394,399,406,407,411,420,424,425,430,433,443,444,461,463,472,502],derjagin:472,derlet:288,descend:200,descent:[7,372],descib:[41,199,298],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,64,65,70,72,73,75,92,116,119,122,124,136,146,147,150,151,152,156,157,160,163,165,166,170,171,172,174,175,184,189,192,196,197,198,203,204,205,212,213,214,215,216,217,218,220,223,224,225,226,227,229,230,235,240,241,244,245,246,247,248,249,250,252,253,254,258,262,263,264,268,276,285,288,290,295,296,297,298,299,300,307,312,320,323,324,325,326,327,328,329,330,331,332,333,338,340,341,343,348,365,366,368,371,372,373,374,375,379,382,383,385,387,388,389,391,392,393,394,395,396,399,404,406,407,409,410,411,413,416,418,419,420,421,422,423,424,425,426,427,428,429,430,433,434,440,441,442,443,444,445,446,451,452,453,460,461,462,463,464,465,466,467,469,471,472,473,474,476,478,479,481,482,483,484,485,491,494,495,498,503,508,509,510],descript:[],descriptor:[146,196,414],deserno:366,design:[0,3,6,7,8,11,13,14,15,17,124,154,157,171,209,223,229,230,263,264,288,289,308,330,335,383,384,385,388,391,396,398,406,426,427,428,431,432,441,444,463],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,61,73,92,95,118,123,147,154,172,185,195,212,218,224,226,237,239,240,247,248,249,253,263,284,292,293,294,295,298,302,307,310,323,326,327,328,329,334,341,356,362,365,366,368,371,373,374,375,400,404,412,427,428,462,464,466,477,478,479,481,485,490,495,496,498,499,508,509,510],desk:7,desktop:[4,6,7,10,12,199],despit:502,destabil:386,destre:358,destroi:[9,11,40,221,222],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,65,68,69,70,73,77,80,94,95,98,107,109,111,113,115,117,118,120,123,125,146,147,149,150,151,152,155,165,166,167,169,172,173,176,177,180,191,195,196,197,199,200,203,204,205,209,212,213,214,215,216,218,220,222,223,224,225,226,227,237,239,240,241,242,244,245,247,249,250,254,260,261,262,263,264,265,266,267,268,269,270,271,275,277,282,283,284,285,286,289,292,293,294,296,297,299,300,301,307,310,311,323,326,327,328,329,330,331,333,334,335,336,337,338,339,346,348,350,359,365,366,369,373,374,376,377,380,381,382,383,385,386,388,390,391,392,393,394,395,396,399,400,406,407,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,429,430,434,435,440,443,444,445,451,452,453,461,468,471,472,474,479,481,482,483,484,486,487,490,491,493,496,499,500,503,508,509,512],detect:[2,3,12,43,63,65,90,96,238,293,334,375,395,412,417,476,478,481,492,495,508],determ:380,determin:[1,3,6,8,9,12,15,40,41,43,52,59,60,61,63,64,70,73,91,107,113,115,118,124,125,133,147,160,161,170,171,172,195,196,197,199,200,201,202,206,207,208,211,212,213,214,215,216,217,218,219,220,224,226,227,230,232,239,242,243,245,247,248,253,258,260,261,263,269,270,271,282,283,284,286,288,290,293,294,297,304,305,306,307,308,309,313,315,317,323,326,327,328,330,336,337,340,341,342,343,344,345,346,359,365,366,368,374,376,377,380,382,383,390,395,399,403,404,408,410,413,414,422,430,433,435,444,445,451,460,463,467,472,478,481,482,484,486,488,491,495,497,498,500,507,508,509],determinist:311,detil:114,devan:[9,446],devanathan:466,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,244,268,292,297,298,301,382,386,406,432,433,451,469,483],devemi:9,deviat:[261,268,288,408],deviator:9,devic:[1,3,12,15,17,244,380],device_typ:380,devin:[299,395],devis:432,dfactor:199,dff:502,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_sin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lon:[3,6,36,46,47,51,54,55,91,178,204,205,239,307,323,340,344,371,373,385,391,392,394,396,397,398,399,409,411,412,413,416,417,418,419,420,421,422,423,424,425,426,429,434,438,445,446,456,462,468,471,472,490,502,507],epsilon_0:473,epsilon_14:391,epsilon_:445,epsilon_d:397,epsilon_i:[409,435,445],epsilon_i_:445,epsilon_i_a:[409,445],epsilon_i_b:[409,445],epsilon_i_c:[409,445],epsilon_ij:435,epsilon_j:[409,435,445],epsilon_j_:445,epsilon_j_a:[409,445],epsilon_j_b:[409,445],epsilon_j_c:[409,445],epsilon_lj:445,epton:440,eqch:167,eqeq:[443,444],eqp:399,eqq:399,equal:[2,3,6,8,11,12,17,40,42,55,65,67,70,71,73,78,81,90,91,95,97,114,116,121,123,125,147,150,166,168,170,172,195,199,200,203,204,205,206,207,210,213,214,215,218,219,220,224,226,227,232,239,240,242,243,245,247,248,250,253,254,260,261,268,279,288,290,293,295,297,298,299,302,304,306,307,309,312,317,319,326,327,328,331,332,333,335,337,338,340,343,345,346,348,364,368,373,375,376,377,379,380,395,400,402,408,409,412,416,427,433,434,441,443,444,445,447,448,449,451,452,453,463,468,469,473,477,478,479,481,483,484,488,489,492,495,497,499,508,509],equat:[3,6,7,8,9,95,112,118,124,171,180,191,203,224,230,231,234,235,241,247,248,250,253,261,262,263,264,268,284,288,290,297,298,302,310,311,323,331,335,338,340,341,343,345,358,365,366,394,399,400,402,406,407,410,415,427,428,430,435,445,448,450,455,456,458,459,473,502],equi:264,equidist:262,equil:[3,298,369,488,512],equilater:491,equilibr:[3,4,5,6,7,9,61,95,172,203,210,213,223,224,239,261,263,264,284,285,297,298,299,300,331,332,333,338,395,396,443,444,477,491],equilibria:338,equilibribum:[221,222],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,44,48,49,50,52,54,57,61,155,156,179,181,224,226,239,240,241,248,250,263,268,284,297,298,302,306,310,312,320,323,330,331,333,338,349,351,355,358,395,430,437,451,502],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:209,equival:[6,12,13,29,61,63,130,131,139,144,170,174,200,215,218,224,226,239,247,263,284,294,306,307,343,400,406,451,464,466,481,484,489,490,499,502],equlibrium:6,equliibr:[298,300],er3:171,eradiu:[41,119,197,406,481],eras:[309,332],erat:[226,428],erc:396,erfc:[396,418,435],erforc:[119,197],erg:507,erhart:[210,404,464,466],ermscal:383,ernst:9,eror:3,eros:430,erose_form:430,erot:[],errata:[464,466],erratum:340,erron:3,error:[],erta:410,ervel:[119,197,481],escap:[227,502],especi:[8,16,160,172,203,210,220,239,297,302,305,306,380,478],espresso:[9,301],essenti:[8,11,12,27,92,134,153,154,155,158,159,160,161,162,164,181,213,268,289,339,366,382,396,418,466,486,499],essex:29,establish:[91,243],estim:[1,3,6,10,12,38,42,57,95,147,209,220,231,261,323,330,365,366,371,435,444,463,495,499],esu:507,esub:430,eta:[6,250,263,297,298,300,339,405,407,409,441,465,469,507],eta_dot:263,eta_ij:441,eta_ji:407,etag:[41,481],etail:499,etap:263,etap_dot:263,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,63,70,93,94,95,99,115,116,119,121,147,149,152,153,154,155,156,158,159,160,161,162,164,166,172,174,175,176,185,196,197,199,200,203,204,209,210,211,212,215,216,217,218,221,222,226,227,237,239,240,247,263,293,304,308,335,336,344,348,364,365,373,374,375,376,378,404,405,413,426,428,433,439,443,444,462,464,466,469,476,479,481,482,483,488,490,491,495,496,497,498,499,500,502,507,508,510,512],ethernet:18,etol:[373,375,476,495],etot0:297,etot:[6,99,101,102,116,147,158,200,230,248,261,297,498,499],eu2:171,eu3:171,euler:[373,375],eulerian:209,euqat:454,europhi:250,ev_tal:8,evalu:[2,3,9,11,12,38,57,73,91,92,95,113,123,125,146,148,152,162,170,172,195,196,197,199,200,204,205,206,207,209,211,212,213,214,215,216,217,218,219,226,232,240,242,243,245,246,247,248,289,295,298,309,313,317,326,327,328,337,340,343,345,346,348,365,366,371,373,380,433,435,441,447,449,451,463,476,477,479,483,484,486,488,489,490,491,495,497,499,508,509],evalut:[348,479],evan:[160,284],evanseck:[6,20,178,391,493],evapor:[],evaul:[8,373],evdwl:[113,443,444,499],even:[3,6,8,12,15,17,18,34,40,42,53,59,61,63,65,72,73,92,113,125,170,173,174,188,192,196,197,200,203,204,205,210,211,212,215,216,217,218,220,221,222,224,226,227,230,245,248,261,263,264,289,293,302,304,307,308,319,323,331,335,338,340,344,346,357,365,371,373,375,380,385,406,407,410,413,416,435,445,469,470,474,481,482,484,486,487,488,490,491,493,496,498,499,500,502,512],evenli:[3,42,147,192,220,250,416,470],event:[],eventu:[3,6,12,15,174,298,495],ever:[9,55,57,246,323],evera:[394,409,445,461],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,73,74,95,119,125,134,160,175,196,197,198,199,200,201,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,231,236,237,239,241,243,244,245,250,251,259,263,264,268,287,288,289,293,294,295,296,297,298,299,300,302,304,305,307,308,310,312,323,325,326,327,328,329,330,331,334,335,336,337,338,346,348,364,366,375,376,377,380,400,403,413,426,443,444,451,457,475,476,477,481,483,485,486,488,489,490,495,496,497,499,503,508,512],everyth:[8,113,503],everywher:[122,420],eviri:406,evolut:[241,250,290,476],evolv:[250,290,336],ewald:[2,3,5,6,7,8,9,12,92,116,124,147,336,365,366,373,387,389,390,396,399,406,418,422,438,446,461,463],ewald_disp:399,ewalddisp:3,exact:[22,42,45,73,128,166,175,180,220,223,240,241,247,248,249,293,302,303,323,335,350,365,393,483,488,495,508,510,512],exactli:[3,6,12,14,17,38,42,43,57,61,73,74,95,122,150,156,163,172,192,204,205,215,220,226,231,235,240,247,248,249,264,276,277,285,289,297,323,328,329,342,380,393,400,404,410,413,427,435,463,483,484,491,495,508],exager:502,examin:[6,8,17,223,289],examp:[479,508],exampl:[],exce:[3,6,16,17,18,42,60,73,174,211,212,215,216,217,218,220,224,226,231,236,263,289,304,308,314,315,323,373,380,481,508],exceed:[3,42,61,220,226,263,323,489],excel:406,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,61,62,65,73,93,94,114,115,118,123,147,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,172,176,178,179,180,181,182,183,184,186,187,189,190,191,192,195,196,197,200,203,206,212,213,215,219,220,224,226,233,238,239,242,245,247,249,263,264,265,266,267,268,269,270,271,272,273,276,277,280,282,283,284,285,286,290,299,300,307,309,310,320,323,326,328,329,335,339,343,346,347,348,349,350,351,352,354,355,358,359,360,365,366,368,370,374,375,376,378,379,380,381,382,384,387,388,389,390,391,392,393,394,395,396,398,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,431,436,437,438,440,443,444,445,446,453,461,462,463,464,465,466,469,471,472,473,476,478,479,481,483,484,486,489,490,491,492,493,495,499,502,507,508,509,511],excess:[214,406],exchang:[2,3,6,8,63,64,203,209,210,239,247,299,307,331,335,338,365,380,406,496],exchange:365,excit:406,exclud:[3,6,9,12,16,17,65,73,118,146,152,159,160,176,196,212,216,221,222,251,259,292,305,307,330,341,346,373,374,376,388,410,413,416,427,428,435,460,493],exclus:[1,3,12,16,91,380,395,433,435,490,500],excurs:[263,476],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,62,173,199,244,301,348,364,367,379,477,479,489,492,495,508],exempl:451,exemplari:240,exemplifi:406,exert:[6,245,248,302,342,343,344,366],exhaust:[209,379,508],exhibit:[96,263,372,406,490],exist:[3,6,7,8,11,12,13,16,37,56,61,70,72,128,172,173,191,198,199,200,203,208,219,222,224,227,239,292,293,295,346,347,349,351,352,353,355,359,369,374,380,401,402,413,443,460,470,477,479,481,482,483,492,493,494,503,508,509,510],exit:[2,3,11,12,42,59,196,220,235,364,379,479,480,489,498,508],exlanatori:3,exp:[],expand:[],expans:[12,146,196,492,508],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,73,107,153,164,170,192,220,232,239,241,260,288,294,296,297,302,307,346,366,376,393,430,433,435,476,479,481,483,486,490,495,508],expens:[6,73,200,288,292,307,335,346,365,366,376,380,479],experi:[6,13,15,17,219,227,244,253,262,294,306,307,371,375,400,435,490,495],experienc:[6,12,252,253],experiment:[239,365,380,495],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,61,65,67,70,71,73,74,75,78,79,81,90,97,152,160,192,196,197,199,200,203,212,213,218,220,222,224,226,263,288,296,307,320,346,348,364,365,368,374,375,379,385,404,416,451,453,468,479,482,483,486,488,491,502,503,508,512],explan:[3,6,61,119,146,196,197,212,262,288,413,475,478,479,481,490],explanatori:[3,8,123,196,197,211,212,215,216,217,307,374,478,508],explantori:[3,303],explic:434,explicit:[6,9,11,22,45,79,91,119,122,166,180,204,205,226,314,315,350,370,382,383,386,391,393,404,406,417,427,467,475,478,482,485,503],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,73,115,118,149,159,162,170,172,178,179,181,182,183,184,186,187,189,190,192,196,197,200,206,216,219,226,233,238,240,242,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,296,297,299,307,309,310,326,328,329,335,339,343,349,351,352,354,355,358,360,374,380,381,382,384,387,388,389,390,391,392,393,394,395,396,397,399,400,403,404,405,407,408,409,410,411,412,413,417,418,419,420,421,422,423,424,425,426,427,431,433,435,436,437,438,440,445,446,453,454,455,456,457,458,459,461,462,463,464,465,466,467,469,471,472,473,481,483,484,490,491,493,494,500,502,503],explictli:[16,494],exploit:[15,17,290],explor:[124,171],expon:[3,298,300,404,409,412,426,434,446],exponenti:[91,441,462,469,473,495,508],expos:11,exposit:[209,400,403],express:[6,146,158,172,204,205,224,260,288,298,335,341,348,386,404,406,420,430,451,452,461,508],expressiont:386,extend:[],extens:[3,6,9,17,45,46,47,54,56,65,86,87,88,91,92,95,99,102,103,113,115,123,125,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,197,203,206,207,210,218,219,225,228,232,237,238,239,241,242,243,245,247,249,261,263,268,277,288,289,305,306,307,309,312,317,320,322,326,327,328,329,330,332,333,335,337,340,344,345,409,430,433,444,445,452,498,499],extent:[1,3,42,43,46,59,73,170,174,196,208,216,220,245,342,345,365,368,382,447,449,463,478,481,484],exterior:[3,6,170,344],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,63,73,107,115,116,118,124,147,149,150,151,153,155,158,159,160,161,162,164,165,171,172,173,174,178,200,215,220,222,263,295,296,297,307,323,373,374,377,378,399,410,413,416,430,435,478,479,481,484,493,502,508],extract:[3,6,11,13,36,65,91,113,121,123,125,204,205,300,375,396,407,430,452,479,486,498],extract_atom:11,extract_comput:[11,479],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,60,199,214,224,226,263,333,406,465,502],extrema:426,extrins:209,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[168,337],f_a:[464,465,466],f_ave:123,f_c:465,f_f:466,f_fix_id:297,f_foo:508,f_harm:333,f_i:[29,441],f_id:[6,73,123,125,196,197,203,211,212,213,214,215,216,217,218,258,325,337,499,508],f_ij:441,f_indent:218,f_int:332,f_j:29,f_jj:95,f_k:441,f_langevin:335,f_max:[297,302],f_msst:261,f_r:[248,464,465,466],f_sigma:386,f_solid:333,f_ss:6,f_temp:[],face:[3,6,59,61,73,160,170,174,208,216,217,340,342,343,344,345,368,409,430,445,481,484],face_threshold:170,facet:170,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,241,293,323,333,410,451,493],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,59,60,61,74,91,95,107,114,121,122,124,146,166,171,174,178,189,195,196,199,200,204,205,213,220,224,226,227,239,244,247,249,250,261,263,264,268,290,294,298,306,310,313,315,323,327,331,338,339,340,344,355,366,368,374,380,382,383,386,387,389,391,396,397,398,400,401,402,406,410,413,417,418,430,433,435,437,438,444,446,453,462,467,478,481,484,485,490,493,495,496,499,502,507,508],factori:[3,479],factoriz:365,fail:[3,9,11,12,61,176,224,227,365,373,375,398,444,479],failur:[127,448,480,508],fairli:[11,435,490,495,503],faken:75,falcon:244,fall:[3,6,200,215,293,479,508],fals:[90,346,348,451,508],fame:8,famili:[469,478],familiar:[0,11,503],fan:441,far:[3,6,12,17,59,61,63,90,196,197,200,201,220,221,222,224,227,263,288,306,307,323,340,351,355,371,375,376,468,479,481,486,499],farago:247,farrel:[464,466],farther:196,fashion:[6,8,42,73,172,200,203,204,205,210,216,220,222,227,239,241,245,260,261,263,265,266,267,268,269,270,271,279,282,283,284,285,286,296,297,299,307,312,316,322,325,333,335,339,340,341,343,345,375,413,427,484,493,508,511],fasolino:415,fast:[6,7,9,12,13,17,40,196,197,274,297,336,365,366,388,427,428,433,461,463,483,488,490,499,509,512],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,63,65,110,115,118,149,159,178,179,181,182,183,184,186,187,189,190,192,196,197,200,206,219,220,226,233,238,242,246,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,294,298,299,307,309,310,323,326,328,330,332,335,339,343,349,351,352,354,355,358,360,365,366,377,378,380,381,382,384,386,387,388,389,390,391,392,393,394,395,396,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,436,437,438,440,445,446,453,461,462,463,464,465,466,469,471,472,473,476,484,490,494,502],fastest:[1,6,14,17,160,216,335,336,380,478],fatal:[3,498],fault:[72,444],faulti:12,fava:409,favor:223,favorit:7,fbmc:330,fcc:[],fcm:[279,508],fdirect:230,fdotr:414,fdt:[],fdti:91,fe2:171,fe3:171,fe_md_boundari:209,featu:8,featur:[],fecr:404,feedback:[7,244],feel:[7,244,245,253,288,344,346,375,435],felling:432,felt:344,femtosecond:507,fene:[],fennel:[396,418],fep:[],ferguson:[6,178,493],fermi:[1,9,10,12,15,158,380,466],fermion:406,fernando:429,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,65,201,211,212,213,215,216,217,218,248,263,293,296,298,310,337,365,373,374,375,382,451,478,481,486,490,492,500,510],fewer:[1,3,11,15,16,63,253,490],fewest:3,fextern:237,feynman:290,fff:479,ffield:[395,407,443,444,451],ffmpeg:[3,12,199],ffplai:199,fft:[1,3,7,9,11,12,14,15,92,115,116,147,289,365,366,490],fft_inc:[12,366],fft_lib:12,fft_path:12,fftbench:[365,500],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],ficiti:460,fictiti:[6,206,207,232,237,241,290,306,396,418,422,460],field1:[482,486],field2:482,field:[],fifth:[320,437],figur:[1,3,8,12,297,478,479,503],fij:399,file0:288,file1:[11,13,288,334,348,374,486,488,492],file2:[11,13,334,348,374,486,488,492],file:[],file_from:198,filen:374,filenam:[3,12,13,38,42,57,192,196,197,199,200,201,209,212,213,214,215,216,217,218,220,225,235,288,292,295,298,299,300,303,304,307,308,334,335,362,363,364,374,375,381,382,386,396,404,405,407,415,430,431,432,437,441,442,443,444,451,452,462,463,464,465,466,469,477,478,479,482,483,488,492,499,508,510,511,512],filennam:488,filep:[3,196,197,200,483,488,512],filepo:304,fill:[7,9,172,199,293,335,368,376,386,433,444,484,503],filter:[200,209],final_integr:8,final_integrate_respa:8,finchham:[6,154,398],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,63,73,75,91,123,175,192,201,210,223,224,235,236,239,262,288,293,294,302,306,371,373,375,376,396,413,418,422,430,451,461,463,502,503,508],find_custom:8,fine:[16,17,176,206,232,333,376,380,503,508],finer:[146,172,508],finest:365,finger:[172,195,260,484],finish:[6,11,42,220,348,362,364,365,377,379,380,468,486,508,509],finit:[],finni:[7,404,461],finvers:230,fiorin:[9,225],fire:[],firebrick:200,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,59,61,63,64,73,83,92,95,108,109,110,112,118,122,123,133,136,139,140,144,147,157,160,166,168,170,171,173,174,175,179,192,196,197,198,199,200,201,203,204,212,213,215,216,217,218,220,223,226,235,239,240,245,250,260,261,262,263,288,290,295,296,297,299,304,307,310,312,320,321,323,324,325,332,333,334,335,337,341,346,348,349,356,368,373,374,375,376,379,380,381,382,385,386,387,389,391,393,395,396,404,406,407,410,411,413,414,415,416,417,418,422,427,428,430,432,433,435,437,441,443,444,451,452,460,462,463,464,465,466,469,473,476,477,478,479,481,482,483,486,488,490,493,494,495,498,499,502,503,508,509,510,512],fischer:[6,9,19,20,178,391,493],fit:[3,6,9,12,38,57,192,235,306,323,382,386,415,430,435,456,463,465,489,503,508],five:[75,158,297,374,386,431,481,495],fix:[],fix_adapt:[166,205,426],fix_atom_swap:[],fix_bal:64,fix_deposit:[3,210,293],fix_eo:9,fix_evapor:210,fix_flux:209,fix_gcmc:[210,374],fix_gl:241,fix_gld:241,fix_grav:293,fix_id:[3,224,261,263,265,266,267,268,269,270,271,294,297],fix_manifoldforc:503,fix_modifi:[],fix_mov:[195,341],fix_nh:8,fix_npt:241,fix_nv:503,fix_nvt:[210,239],fix_poem:[3,6,9],fix_pour:[3,227],fix_qbmsst:9,fix_qeq:[3,395],fix_rattl:310,fix_reax_bond:443,fix_rigid:[253,385],fix_saed_vtk:308,fix_setforc:8,fix_shak:310,fix_shardlow:9,fix_srd:3,fix_styl:268,fix_temp_rescal:329,fixedpoint:[224,263],fixextern:237,fixid:209,fji:399,flag1:[229,378],flag2:[229,378],flag:[3,8,9,11,12,14,15,16,17,41,68,76,77,83,90,93,94,98,108,109,111,124,167,171,175,196,197,199,200,201,218,223,225,229,244,247,251,253,259,260,289,296,307,320,322,323,330,334,343,346,363,366,374,378,379,380,382,412,417,430,433,460,476,478,479,481,482,483,485,486,487,491,503,508],flag_buck:390,flag_coul:[390,399,422],flag_lj:[399,422],flagfld:[388,427,428],flaghi:[3,388,427,428],flaglog:[388,427,428],flagn:229,flagvf:[388,427,428],flat:[6,335,340,341,345],flavor:[2,7,12],fld:[],flen:383,flex_press:383,flexibl:[3,6,8,173,199,212,216,225,241,264,331,338,406,465,499],flip:[3,6,226,263,342,343],floor:508,flop:12,floralwhit:200,flow:[],fluctuat:[6,66,91,224,239,240,247,250,263,268,288,289,311,333,335,358,402],fluid:[],fluid_veloc:254,flush:[3,200,498],flux:[],flv:199,fly:[7,9,12,42,199,203,209,214,227,230,307,310,336,386,433,499,502],fmackai:9,fmag:228,fmass:290,fmax:[373,499],fmomentum:230,fmsec:[2,200,247,248,260,263,294,307,326,327,490,501,507,509],fname:364,fno:[9,12,16],fnorm:[373,499],fnpt:230,fnvt:230,foce:413,fock:383,focu:310,fogarti:[9,300,444],foil:[146,288,452],fold:[321,490],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,61,65,66,72,73,75,84,95,96,101,102,112,119,122,123,125,146,147,150,151,152,158,160,165,168,170,172,173,178,181,182,183,184,186,187,189,190,192,196,198,199,200,203,209,210,211,212,213,214,215,216,217,218,220,225,226,227,230,231,234,235,237,239,240,241,244,246,247,248,250,253,261,263,268,269,270,271,282,283,284,286,289,290,292,295,296,297,298,300,302,304,306,307,308,310,325,326,327,328,331,332,333,334,335,337,338,346,347,351,352,353,354,355,358,360,363,368,370,373,374,375,380,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,435,436,437,438,440,441,442,443,444,445,446,448,450,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,468,469,471,472,473,474,476,478,479,481,482,484,486,488,489,490,493,495,496,497,502,503,508,509,511],foo:[4,8,11,12,196,199,237,479,492,508],foot:6,footprint:[12,380],fopenmp:[9,12,16,18],forc:[],force_uvm:17,forceatom:253,forcefield:[306,412],forcegroup:250,forcezero:371,ford:399,forestgreen:200,forev:73,forget:[248,502],forgiv:263,fork:[12,196],form:[2,3,6,8,12,19,22,45,55,65,68,76,77,79,83,91,93,94,96,98,108,109,111,122,146,147,166,167,176,180,200,203,204,205,222,240,241,247,249,253,260,284,289,300,302,306,307,335,340,344,349,350,353,358,370,372,374,375,382,383,386,393,401,402,404,406,408,412,413,417,429,430,432,433,437,438,441,443,444,445,451,452,453,461,463,464,465,466,472,475,478,479,481,486,491,498,502,508],formal:[6,80,82,95,240,241,247,263,290,323,331,451],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,70,79,180,192,196,197,198,199,200,201,212,215,216,217,218,220,222,235,289,292,296,298,300,303,307,308,319,334,335,346,347,350,370,374,375,381,382,386,393,404,407,417,430,432,442,443,444,446,452,463,469,470,478,479,481,482,483,486,497,498,499,508,510],former:[6,12,16,40,42,200,220,335,339,386,388,487,493,508],formerli:[7,13],formul:[1,9,41,66,147,206,232,247,263,284,298,300,306,310,334,365,382,386,404,406,409,430,440],formula:[2,3,6,7,13,21,22,37,45,55,56,72,75,91,93,94,95,99,101,102,111,118,124,125,147,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,171,172,177,179,180,191,195,196,204,205,206,207,212,213,214,215,218,219,226,232,242,243,245,247,248,260,288,289,295,304,309,317,321,323,326,327,328,337,340,343,345,346,348,349,350,352,35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reneighbor:[3,8,12,40,59,73,216,220,239,323,336,346,400,498,499],renssela:292,renumb:73,reorder:[3,12,40,478],rep:496,repeat:[2,6,199,200,216,223,224,239,316,368,386,464,466,468,476,495],repeatedli:2,repel:245,repes:196,replac:[2,3,6,11,12,42,65,93,94,123,149,150,151,152,153,154,155,158,159,160,161,162,164,165,196,197,199,200,201,212,213,215,216,217,218,220,223,227,247,268,295,302,304,396,420,463,482,483,488,489,499,508,509,510,512],replic:[],replica:[],replica_fil:12,report:[],repositori:[7,9,12,414,442,443,444],reprens:335,repres:[1,3,6,8,9,12,15,41,42,43,61,69,73,94,119,122,184,192,196,197,199,212,213,214,215,216,217,218,224,230,240,242,247,250,263,290,292,294,302,307,308,312,320,335,337,344,366,375,381,386,409,416,426,427,428,430,431,432,438,441,443,444,467,468,476,478,481,491,493,496,502,508,510],represent:[3,6,8,9,59,61,140,174,196,240,241,290,335,386,406,409,433,445,481,484,502],reprocess:486,reproduc:[3,263,341,396,404,410],repul:430,repuls:[6,7,36,41,46,47,114,245,298,340,341,344,382,386,394,396,400,406,410,412,426,430,434,451,460,466,469,472,473,491],reqir:[298,300],request:[3,6,8,12,42,108,175,192,196,244,250,305,311,323,325,363,365,435,443,444,476,486,491,495,503,508,509,510],requir:[],rerun:[],rescal:[],research:[5,7,84,85,234,250,254,311,433,476,495],resembl:[302,503],resepct:6,reserv:[12,244,502],reservoir:[95,239,243,247,335],reset:[],reset_atomic_reference_posit:209,reset_dt:8,reset_target:8,reset_tim:209,reset_timestep:[],resid:13,residu:244,residue1:376,resist:[6,244],resolut:[214,451,463],resolv:[224,290,323,428,503],resort:3,resourc:[7,381,404],respa:[3,16,231,244,263,378,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,428,429,430,431,432,433,434,436,438,440,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,468,469,471,472,473,474,489,490,501,508],respecifi:433,respect:[1,6,9,13,14,15,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,46,47,48,49,50,52,54,55,57,61,72,73,91,93,101,102,115,118,124,128,149,154,157,159,166,170,171,178,179,181,182,183,184,186,187,189,190,192,197,199,200,215,216,217,222,223,224,226,242,245,247,248,250,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,298,299,307,308,312,320,322,335,340,343,349,351,352,354,355,358,360,363,365,366,370,373,374,379,380,381,382,384,386,387,388,389,390,391,392,394,395,396,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,430,431,433,435,436,437,438,440,445,446,450,451,452,453,462,463,464,465,466,467,469,471,472,473,478,482,491,494,502,508,510,512],respon:9,respond:[6,7,155,226,406,440],respons:[6,7,261,331,338],resquar:[],rest:[6,8,12,296,300,306,386,428,430,498,499,502],restart1:290,restart2:290,restart2data:[],restart:[],restartfil:[12,13],restor:[3,8,62,63,108,172,204,205,296,312,320,325,347,498,499],restore_bia:8,restore_bias_al:8,restrain:[],restraint:[9,225,261,306,322,417],restratin:306,restrict:[],result:[1,2,3,6,7,9,10,11,12,13,15,16,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,46,47,48,49,50,52,54,55,57,65,66,68,69,73,77,91,94,95,98,108,109,111,115,116,118,120,121,122,123,124,125,147,149,152,155,159,166,167,169,171,172,175,178,179,181,182,183,184,186,187,189,190,192,195,196,197,199,200,203,206,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,230,233,235,238,239,240,242,247,248,250,254,261,263,265,266,267,268,269,270,271,272,273,280,282,283,284,285,286,289,290,298,299,304,305,307,309,310,323,326,328,331,332,333,335,336,337,339,340,341,343,345,348,349,351,352,354,355,358,360,365,366,375,378,380,381,382,384,387,388,389,390,391,392,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,430,431,433,435,436,437,438,440,444,445,446,453,462,463,464,465,466,467,469,471,472,473,476,478,481,483,484,485,486,490,491,492,493,495,507,508,509],resum:508,retain:[2,221,222,386,433,478],retart:[33,51,185,356],retir:[3,443],retreiv:8,retriev:[6,8,237,431,432,508],reus:[3,493],rev:[6,13,66,72,96,112,116,146,147,160,210,241,247,249,261,263,264,268,284,289,299,302,307,312,323,327,330,332,333,338,372,386,394,395,396,399,404,405,406,409,410,415,420,427,428,429,430,432,441,445,452,462,464,465,466,469,476],revers:[2,6,8,91,183,223,245,263,287,288,298,316,331,332,338,375,426,490,502],review:[146,298,312,330,433,442,452,476,495,502,503],rewind:364,rewrap:196,rewrit:[5,12],rewritten:19,rezwanur:440,rfac0:[146,452],rfactor:323,rfile:307,rg0:321,rgb:200,rh3:171,rh4:171,rhaphson:3,rheolog:6,rhi:463,rho0:[430,448,450,458,459],rho0_meam:430,rho:[],rho_0:[458,459],rho_alpha_beta:404,rho_bkgd:430,rho_colloid:340,rho_e:335,rho_fin:334,rho_i:[431,432],rho_initi:334,rho_ref_meam:430,rho_wal:340,rhodo:[9,10],rhodopsin:[1,10],rhohi:293,rholo:293,rhosum:[],ribier:372,richard:9,richardson:307,richi:[9,19],rick:[298,299,395,451],rick_and_stuart:299,ridg:[9,19],right:[3,6,11,12,42,148,172,190,191,19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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying &amp; extending LAMMPS","4. Packages","8. Performance &amp; scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","&lt;no title&gt;","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","&lt;no title&gt;","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":221,"default":[37,40,41,56,59,60,61,63,64,73,91,92,96,107,108,110,112,113,124,128,129,146,152,160,161,165,171,172,175,177,191,194,195,196,197,199,200,201,202,204,205,206,208,209,210,212,216,217,218,221,222,224,225,226,227,231,236,239,240,245,247,248,249,250,251,253,258,261,263,264,268,284,285,289,290,293,294,295,296,297,299,302,304,305,307,308,323,325,330,331,332,333,336,338,340,342,346,359,363,365,366,368,369,371,372,374,376,377,378,380,383,386,388,406,427,428,433,435,443,444,460,461,476,477,478,481,482,484,486,488,489,490,493,495,497,498,499,500,501,507,509,510,511],"function":508,"long":[214,387,389,390,391,392,396,398,399,418,422,426,438,446],"new":8,"static":12,acceler:1,account:503,ackland:66,acknowledg:7,adapt:[204,205],addforc:206,addit:[12,13,503],addtorqu:207,adiabat:6,adjust_dt:313,adp:381,after:503,airebo:382,alloi:404,amber2lmp:13,amber:6,angl:[8,67],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:68,append:208,arrai:6,aspher:[6,9,86,150,265,269,273,274,282],atc:[9,209],atom:[6,7,8,66,69,72,73,74,75,78,79,80,82,83,85,89,96,100,101,104,105,106,112,116,117,119,146,147,170,208,210,211,296,508],atom_modifi:40,atom_styl:41,attract:5,aug:[],aveforc:219,awpmd:[9,383],balanc:[42,220],barostat:6,basal:69,beck:384,berendsen:[294,326],between:6,binary2txt:13,bodi:[6,8,9,43,70,151,266,270,275,283,385],bond:[8,13,71,221,222,223,303],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,58],bop:386,born:[387,398],boundari:[7,59],box:[6,60,224],branch:503,brownian:388,buck:[389,390,398,429],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:72,ch2lmp:13,chain:13,chang:503,change_box:61,charmm:[6,20,178,391,426],chunk:[6,68,73,77,94,98,109,111,120,152,167,169,212],citat:7,class2:[9,21,44,179,349,392],clear:62,cluster:74,cmm:9,cna:75,code:6,coeffici:6,colloid:[9,340,394,472],colvar:[9,13,225],com:[76,77,153],comb3:395,comb:[299,395],come:5,comm_modifi:63,comm_styl:64,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,504,505,506,507,508,509,510,511,512],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,508],compute_modifi:107,condit:7,conduct:[6,331],conserv:401,constant:[6,508],constraint:7,contact:[78,126],contact_radiu:[],coord:79,core:6,coreshel:9,correl:[213,214],cosin:[23,24,25,26,27,28,181],cossq:351,coul:[387,389,390,391,392,396,397,398,411,418,422,426,438,446],coupl:6,creat:222,create_atom:172,create_bond:173,create_box:174,createatom:13,creation:7,csld:327,csvr:327,cubic:420,cuda:[9,14,115,118,149,159,206,219,233,238,242,263,272,309,310,326,328,339,387,389,391,392,404,410,411,418,419,421,424,436,462,464],custom:[8,196,197],cut:[50,383,389,392,396,399,406,408,418,419,426,434,438],cvff:352,damag:[80,127],data2xmovi:13,data:6,databas:13,deby:[3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11,14,18,40,41,42,221,381,406,491,496],advect:[3,6,324],advertis:8,advis:[376,443],afer:3,affect:[1,6,10,14,15,16,17,41,62,63,74,93,124,148,157,171,177,200,201,206,213,214,216,217,218,219,222,223,224,225,227,228,238,244,246,248,254,261,265,266,267,268,270,271,272,278,283,284,285,287,308,309,322,336,346,359,366,372,373,374,376,377,378,381,407,428,429,436,479,480,482,484,485,487,490,492],affin:[16,17,18,227,381,396],afil:242,aforement:18,afresh:[296,490,509],afshar:401,after:[],afterrun:490,afterward:3,afterword:42,ag1:172,ag2:172,again:[6,11,12,16,17,64,147,153,159,167,197,201,227,244,294,350,365,376,428,429,477,479,480,482,484,489,496,498,509,511],against:[11,12,13,66,228,376,444,445],aggreg:[6,12,67,70,72,82,98,115,122,244,260,306,308,322,477,510],aggress:[244,496],agilio:[9,13],agre:[3,8,193,374,383,416,445],agreement:[5,7],ahd:413,ahead:343,aidan:[0,5,7,9,13,369],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:200,akohlmei:[7,9,13,202,245],aktulga:[7,9,301,445],al2o3:452,al2o3_001:[125,309],al3:172,ala:[251,452],alain:9,alat:[289,431],alb:[442,465,467],albeit:307,albert:9,alchem:[92,167],alcohol:339,alcu:[382,387],alcu_eam:442,alderton:400,alejandr:[264,265],alessandro:13,algebra:434,algorithm:[0,1,6,7,8,9,42,63,201,210,221,224,227,251,253,254,278,291,299,308,311,312,331,332,336,339,344,372,373,374,378,381,403,407,429,434,449,451,477,479,496],alia:[9,12,16],alias:[1,367],aliceblu:201,align:[6,9,12,29,42,74,175,193,217,221,246,369,482,485,503],alkali:407,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,161,166,167,168,169,170,171,172,173,174,175,176,177,179,181,186,192,193,194,197,198,199,200,201,202,204,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,234,235,236,237,238,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,257,259,260,262,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,281,282,283,284,285,286,287,288,289,290,291,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,320,321,323,324,325,326,327,328,331,332,333,334,335,336,337,338,339,341,342,343,344,345,346,347,348,349,350,351,355,360,362,364,365,366,367,368,369,371,374,375,376,377,378,380,381,382,383,384,386,387,388,390,391,392,393,394,396,397,400,401,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,427,428,429,430,431,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,479,480,481,482,483,484,485,486,487,489,490,491,492,493,494,495,496,497,499,500,501,503,504,508,509,510,511,512,513],allen:[29,92,400,410],allentildeslei:92,allign:3,allindex:348,alloc:[3,5,6,8,9,11,12,62,238,338,375,377,381,440,445,482,490],allocat:3,alloi:[],allosw:74,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,56,59,60,61,63,64,65,80,97,113,115,149,151,152,153,166,171,172,173,175,181,192,193,197,198,200,201,202,204,205,207,209,210,211,213,214,215,216,217,218,219,221,223,224,225,226,227,228,232,233,238,240,241,242,243,245,248,251,254,255,259,261,264,265,289,293,294,295,296,297,298,302,308,309,311,313,315,316,320,324,331,332,333,334,336,337,338,339,340,341,347,349,351,360,366,367,369,374,375,376,377,380,381,384,387,388,389,390,391,392,397,405,407,411,412,413,414,419,423,428,429,434,436,442,445,446,449,451,452,461,468,471,473,477,480,482,484,485,486,487,488,489,492,494,495,496,499,500,504,509,510],almost:[2,3,12,62,246,298,336,367,378,381,461],alo:397,alon:[6,7,224,304,444,445,480],alond:13,along:[6,8,12,29,41,74,92,125,171,172,173,196,197,200,213,224,246,251,252,256,261,263,298,308,311,313,317,321,322,331,335,336,342,345,347,369,372,373,374,376,397,400,411,414,417,419,423,431,444,445,464,482,485,492,493,509],alonso:[432,433],alpha:[6,12,52,205,251,290,298,299,303,374,382,385,388,397,401,403,405,406,408,413,418,419,431,437,441,466,468,500,503],alpha_:[],alpha_c:427,alpha_i:453,alpha_ialpha_j:[],alpha_lj:427,alphabet:[2,3,22,37,45,56,65,181,192,204,351,360,375,394,462,482],alphanumer:[3,65,204,297,305,349,375,509],alreadi:[3,7,8,9,12,16,17,18,43,173,174,176,199,209,213,217,218,221,223,227,255,296,298,324,347,348,375,376,401,412,414,421,429,461,471,474,478,482,483,487,492,509],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,40,41,42,43,45,55,56,57,60,61,63,65,68,74,75,76,78,80,84,92,94,95,97,99,109,110,111,112,113,114,119,121,123,124,126,147,148,149,150,151,152,153,154,155,156,157,159,160,161,162,163,165,166,167,168,169,170,173,174,175,176,177,179,181,192,193,195,196,197,198,199,200,201,202,204,205,206,207,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16,18,41,42,55,92,148,151,152,166,177,193,213,217,218,221,224,227,228,242,248,251,262,264,291,299,308,331,360,367,372,373,376,378,381,414,427,436,440,482,491,492,495,496,502,503,508],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,92,124,163,164,200,222,223,224,225,228,237,248,251,262,264,266,267,268,269,270,271,272,294,295,312,324,328,342,366,367,373,471,477,479,491,497],chose:[465,467],chosen:[2,3,6,12,17,147,173,176,185,193,200,206,211,225,228,237,240,241,249,251,262,264,269,291,294,305,324,328,331,332,337,339,340,346,367,368,373,381,402,403,407,411,418,421,447,465,477,491,496,503],chri:171,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[68,78,95,99,110,112,121,153,168,170,213],chute:[4,9,10,243],ciccotti:311,cieplak:[6,179,494],cii:214,cij:214,ciko:2,circl:[43,74,320],circular:[3,6,151,195],circumst:18,circumv:[97,113,303],citat:[],cite:[3,7,8,12,248,452],civ:9,ckio:2,cko:2,cl1:172,clarendon:[29,400],clarifi:[7,465,467],clariti:349,clark:439,class2:[],classic:[0,3,5,6,7,8,9,238,291,298,303,336,361,407],classifi:[462,470],claus:480,clean:[6,12,14,15,17,490],cleanli:[481,512],clear:[],clearli:7,clebsch:147,clermont:[9,13],clever:486,click:[2,11,22,37,45,56,173,181,192,200,245,351,360,376,394,462,504],client:[245,247],climb:[263,376,496],clinic:[7,13],clo:[162,196,510],clock:[12,477,496],clockwis:342,clone:504,close:[3,6,11,12,13,40,42,69,74,148,176,197,223,224,225,242,249,251,264,285,308,311,342,345,365,367,370,372,373,376,381,383,387,397,398,417,431,436,448,450,464,467,486,492,503,504,506],closer:[3,10,42,123,171,196,197,221,225,229,333,376],closest:[223,289,308,339,410,446,461,471],cloud:[452,503],clovertown:18,clsuter:75,clump1:[293,308],clump2:[293,308],clump3:[293,308],clump:308,cluster:[],clutter:3,cmap:482,cmatrix:242,cmax:431,cmd:[11,12,291,493],cmdarg:11,cmin:431,cmm:[],cmoput:140,cn1:214,cn2:214,cna:[],cnn:214,cnr:[9,13],cnt:[414,486],co2:[41,172,311,375],coars:[7,9,10,29,36,41,55,185,293,308,324,412,447,491,494],coarser:[367,509],coarsest:147,code:[],coeff:[3,7,8,12,21,22,33,45,51,179,180,181,186,350,351,357,394,414,418,436,449,451,454,482],coeffcient:482,coeffici:[],coefficienct:401,coefficient0:405,coefficient1:405,coeffieci:[6,385,417],coeffincientn:405,coexist:[240,407],cohes:[6,408,431],coincid:[129,345,392,428,429,477],colberg:199,cold:[6,158,240,244,377,503],coldest:332,coleman8:9,coleman:[9,125,172,309],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,68,78,88,95,99,104,110,112,121,153,161,168,170,173,197,198,201,213,226,254,260,293,303,306,308,347,366,375,377,395,482,489,495,501,513],collid:[232,324,346],colliex:172,collinear:[3,293],collis:[3,251,324,342,346,404,411,474],colllis:324,colloid:[],colombo:40,colon:[202,347,483],color1:201,color2:201,color:[3,9,42,197,200,201,221,241,298,303],column:[3,6,9,12,13,43,65,67,68,69,70,72,74,78,80,82,84,86,95,97,98,99,110,112,113,115,117,120,121,122,123,124,126,147,148,153,161,168,170,171,172,193,197,198,201,204,212,213,214,216,217,218,219,254,261,262,298,308,325,326,336,346,409,413,444,445,483,497,499,509],columnar:171,colvar:[],colvarmodul:12,com:[],comamnd:227,comand:224,comannd:381,comb3:[],comb:[],comb_1:300,comb_2:300,combiant:398,combin:[3,6,7,9,11,13,36,41,65,67,72,82,92,98,109,115,122,151,152,166,197,200,210,216,245,254,264,291,297,312,328,337,345,348,350,366,367,369,373,381,395,397,398,403,407,408,414,426,427,453,463,465,467,468,470,473,485,490,495,503,509],come:[],comfort:[12,13],comit:504,comm:[0,3,11,12,63,76,199,245,247,248,367,376,381,401,436,441,464,484],comm_modifi:[],comm_modift:63,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,179,193,197,236,249,308,336,375,376,382,405,406,408,418,431,438,445,452,453,463,464,465,466,467,470,479,480,482,503,504,509],commerci:7,commit:[9,504],commmand:[3,6,12,61,114,286,417,476,477,479,496,512],common:[],commonli:[3,6,9,12,17,25,59,61,111,113,175,197,200,202,361,412,421,453,465,467,482,485,494],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,60,63,64,74,171,176,177,200,201,221,222,223,225,226,227,245,247,251,253,254,255,264,290,297,299,300,301,308,312,324,336,347,364,366,377,378,379,381,403,404,440,475,479,480,491,492,509,511,513],communc:366,comp:[7,199,247,248,311,367,376,407,436,441,446,460,464,466],compact:[65,204,394,462],compani:[5,7],compar:[1,3,4,6,8,12,17,40,91,117,125,156,172,181,192,201,231,299,347,349,366,367,374,376,431,452,477,496,497,503,508],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,9,21,22,37,44,45,56,180,181,192,350,351,360,393,462],compat:[3,5,7,8,9,11,12,13,17,18,42,74,124,126,184,197,202,206,212,213,214,216,217,218,219,221,290,302,328,331,338,341,344,366,381,415,434,436,464,479,480,509],compens:[6,222,223,306,377,407],compet:335,competit:367,compil:[3,7,8,9,12,13,14,15,16,17,18,19,171,197,199,200,202,245,335,367,381,434,482,483,487,509],compl:17,complain:[11,12,17],complement:431,complementari:[7,397,419],complet:[3,6,9,11,12,15,42,61,74,201,217,221,226,254,291,294,297,324,335,337,348,349,365,376,381,408,449,451,469,477,482,487,490,494,496,499,503,509],complex:[4,6,8,11,12,13,25,41,43,64,97,113,147,149,161,173,174,251,320,345,364,376,407,434,464,480,482,485,509],compli:[331,335],complic:[6,7,9,12,13,211,240,480],complier:12,compon:[3,6,8,12,63,65,68,69,76,84,93,94,95,96,97,99,100,103,110,111,112,113,114,115,116,117,119,120,124,134,137,138,139,140,143,144,145,147,148,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,168,169,170,196,197,198,200,201,207,208,212,213,214,215,216,217,218,219,220,224,225,227,228,233,238,243,247,248,251,254,256,260,261,263,264,265,269,270,271,272,283,284,285,287,288,290,291,292,295,306,308,310,311,313,317,318,321,324,327,328,329,331,338,339,344,345,346,366,369,373,374,375,376,381,401,407,411,428,429,449,451,452,453,482,483,492,500,509,510],componenet:6,composit:[6,211,251,405],compound:[396,407,408,470],compres:[74,121,213],compress:[],compris:[41,345,446,469],compton:[125,172],comptu:3,compuat:367,comput:[],computation:[3,6,222,223,336,387],computational:503,compute_arrai:8,compute_fep:[206,427],compute_group_group:240,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[125,309],compute_scalar:8,compute_temp:8,compute_ti:206,compute_vector:8,compute_xrd:172,concaten:[2,3,512],concav:345,concentr:[74,405],concept:[6,153,163,213,491],conceptu:[3,6,74,161,225,227,376,397,414,431,487],concern:[6,76,92,199,241],concetr:74,concis:[11,335],conclud:12,concret:8,concurr:[16,367,509],conden:[336,465,467],condens:[6,155,336,383,399,405,419,470],condit:[],conducit:6,conduct:[],cone:485,confer:434,confid:[3,496],config:[12,197,479],configfil:226,configur:[1,2,6,12,15,17,38,61,129,175,193,196,197,200,204,225,226,227,228,232,240,247,248,278,291,299,335,364,374,376,383,387,406,431,434,463,465,467,470,477,482,484,485,496,504],confin:[482,496],conflict:[3,12,41,198,436,480,504],conform:[3,6,13,61,224,225,263,307,313,335,359,376,407,494],confus:[3,470],conjuct:[9,401],conjug:[7,8,248,373,407,444,445],conjunct:[6,7,74,91,92,121,156,161,167,173,177,201,205,206,248,251,255,278,294,295,299,300,301,303,308,312,324,332,339,344,366,367,376,388,390,394,397,401,407,413,419,436,439,447,468,482,485,489,503,513],connect:[3,6,9,92,158,176,224,245,293,308,311,321,376,398,411,461,467,479,480,482,486,503],conput:3,consecut:[3,11,12,40,74,173,201,205,206,228,245,246,397,419,423,477,483,485],consequ:[1,6,211,336,418,496],conserv:[],consid:[6,73,74,81,92,122,155,158,159,176,197,198,201,205,206,212,214,217,221,223,224,228,252,265,290,308,331,332,335,336,339,367,394,407,414,445,446,452,461,477,478,480,483,484,485,487,490,492,500,503,509],consider:[6,8,248,249,327,328,329,381,491],consist:[3,6,8,9,11,12,41,43,67,72,82,98,110,115,118,119,122,153,156,158,173,185,196,202,207,208,213,227,228,231,233,238,241,248,249,250,261,264,266,267,268,269,270,271,272,273,274,276,277,278,279,281,282,283,284,285,286,287,295,298,303,305,307,308,327,328,329,330,340,366,367,369,375,376,381,383,387,389,395,397,407,410,414,417,428,429,431,434,436,446,449,451,452,464,471,480,482,483,484,485,486,487,494,503,509],consistent_fe_initi:210,consit:308,constant:[],constitu:[3,6,254,308,341,345,395,446],constitut:[449,451],constrain:[3,6,8,150,151,152,153,154,156,159,160,161,162,163,165,166,204,213,228,240,241,246,254,258,293,294,306,308,311,322,332,339,374,375,407,487,494,503],constraint:[],construct:[6,8,12,14,38,55,57,63,66,69,73,75,76,80,97,113,125,147,172,225,264,290,307,345,377,381,400,434,436,461,463,464,485,486,501,509],constructor:[8,11],consult:445,consum:[1,303,440,509],consumpt:364,contact:[],contact_stiff:[448,450],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,65,92,96,123,125,147,153,161,171,172,173,175,179,181,192,193,197,198,200,201,202,204,205,206,210,212,213,214,216,217,218,219,221,226,228,233,236,242,246,247,248,251,262,278,289,290,293,294,296,298,301,305,308,309,314,324,331,335,336,345,346,349,365,367,375,376,379,380,382,383,384,387,396,397,400,405,406,407,414,415,431,434,438,442,443,444,445,453,463,464,465,466,467,468,470,477,478,479,480,482,483,484,485,487,489,491,494,496,497,499,500,503,504,509,511,513],content:[4,8,9,12,18,445,498,500],context:[3,6,8,12,17,123,124,201,222,223,228,293,305,340,373,473,482,489,498,508,509,510],contibut:73,contigu:479,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,74,84,109,110,169,201,204,205,206,211,213,214,215,216,217,218,219,221,224,225,226,227,228,240,241,242,244,245,246,248,249,250,256,261,262,264,266,267,268,269,270,271,272,283,284,285,286,287,292,294,297,298,308,309,313,323,324,326,333,334,336,342,345,349,365,380,381,387,401,404,421,424,444,445,446,449,451,466,477,480,482,484,485,490,496,497,499,500,509,511],continuum:[6,7,9,210,336,449,451],contour_integr:210,contract:[61,225,227,264,295,308],contradictori:3,contrain:311,contraint:278,contrari:[242,249],contrast:[1,6,43,56,66,155,158,198,227,347,449,451,473,512],contrib:336,contribut:[3,4,5,6,7,8,9,12,13,17,65,68,70,71,73,74,77,78,80,83,89,92,93,94,95,96,99,108,110,112,114,115,116,117,119,121,124,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,206,211,212,213,214,216,217,218,219,225,240,248,251,254,255,259,265,285,286,293,294,302,305,308,309,311,338,366,374,376,384,401,404,405,407,414,428,429,434,436,444,445,452,494,500,503,504],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,92,96,129,147,182,197,198,200,204,210,211,221,225,226,227,244,245,248,249,264,266,267,268,269,270,271,272,295,300,308,315,316,327,328,329,336,340,364,366,378,407,410,434,444,445,448,450,463,467,477,479,491,497,498],control_typ:210,controlfil:445,convect:96,conveni:[6,12,29,197,202,219,309,369,453,468,504,509],convent:[3,8,29,184,191,192,198,201,307,321,348,405,407,509],converg:[3,6,42,93,197,198,200,202,207,221,224,225,233,238,269,298,300,303,307,311,372,373,374,376,396,397,419,452,477,489,496],convers:[3,8,147,200,201,211,214,295,366,397,398,399,407,419,423,427,439,480,496,508],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,61,65,74,96,173,180,197,200,201,214,219,262,294,347,350,352,356,359,369,376,382,405,434,465,467,474,480,482,483,484,489,499,503,508,509,511,513],convex:[43,345],convinc:[7,12],cook:9,cooki:7,cool:[7,163,244,306],cooordin:[197,198],cooper:[5,7],coord123:121,coord1:[3,121,213,217,218],coord2:[3,121,213,217,218],coord3:[3,121,213,217,218],coord:[],coordb:452,coordbb:452,coordiat:374,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,61,63,64,65,68,70,74,77,78,80,84,92,94,95,99,109,110,112,120,121,123,141,147,156,162,168,170,171,173,177,196,197,198,199,200,201,202,204,207,212,213,216,217,218,221,222,223,224,225,226,227,228,231,233,234,238,240,243,244,245,246,247,248,249,261,263,264,266,267,268,270,271,272,285,288,289,290,293,294,295,305,306,308,310,311,313,318,321,322,323,324,326,334,335,336,343,344,346,347,369,374,375,376,381,382,383,386,406,452,477,482,483,484,485,487,490,492,496,503,509,510],coordn:[121,213],coorind:[],copi:[0,3,4,8,9,11,12,15,17,41,126,200,336,376,394,444,480,504],copper:474,coproccesor:16,coprocessor:[1,7,9,16,17,381,495],coproprocessor:17,copy_arrai:8,copyright:[7,8,293],coral:201,core:[],core_shel:155,coreshel:[],cornel:[6,179,494],corner123i:120,corner123x:120,corner123z:120,corner1i:120,corner1x:120,corner1z:120,corner2i:120,corner2x:120,corner2z:120,corner3i:120,corner3x:120,corner3z:120,corner:[3,6,41,120,200,345,346,369,469,482,504],cornflowerblu:201,cornsilk:201,corp:9,corpor:16,corr:396,correct:[3,6,9,11,12,16,17,61,92,93,108,109,114,117,123,155,160,167,198,200,227,240,242,248,264,265,285,293,295,298,335,341,345,366,376,382,383,384,385,386,387,388,389,390,391,392,393,395,396,397,398,399,400,401,404,405,406,407,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,469,470,472,473,474,475,482,497,500,503,504],correction_max_iter:210,correctli:[3,8,11,17,74,84,108,109,110,150,151,152,154,156,158,159,160,161,162,165,166,169,197,201,207,228,233,238,249,258,264,265,301,308,311,321,323,342,345,376,377,381,399,429,434,479,480,482,492,504,508,510],correl:[],correpond:236,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,73,74,92,102,103,116,119,120,121,122,125,126,134,137,138,139,140,141,143,144,145,147,150,151,160,167,171,172,179,180,181,182,183,184,185,187,188,190,191,193,196,197,198,200,201,205,206,207,213,215,216,217,218,220,223,225,227,234,238,239,243,248,251,252,260,261,262,264,266,267,268,269,270,271,272,273,274,278,281,283,284,285,287,290,291,295,300,308,310,311,327,329,331,340,341,342,344,345,346,348,350,351,352,353,355,356,359,361,367,371,373,375,376,382,383,385,388,389,390,391,392,393,394,395,396,397,400,401,405,406,407,408,409,410,411,412,413,414,417,419,420,421,422,423,424,425,426,427,428,431,432,434,436,437,438,439,441,442,444,445,446,447,452,453,454,463,464,465,466,467,468,470,472,473,474,477,479,480,482,483,485,495,496,497,499,500,503,509],correspondingli:[428,429,491],corrupt:3,cosin:[],cosineshift:27,cosmo:[242,247],cossq:[],cost:[1,6,10,11,12,17,40,42,74,116,125,148,172,200,201,213,217,218,221,222,223,237,264,300,336,366,367,379,397,419,423,434,436,463,479,491],costheta0:[463,465,467,470],costheta:442,costli:[11,93,242,377],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,61,68,74,78,92,95,99,110,112,116,119,121,153,163,168,170,186,197,198,200,201,205,206,213,214,217,221,227,238,247,297,298,299,303,306,308,310,324,325,331,335,336,337,341,345,347,349,357,363,365,372,374,377,381,384,409,413,414,417,444,445,478,479,480,482,484,486,489,490,497,498,503,509,510],coulomb:[3,5,6,7,8,9,10,12,14,15,18,75,93,114,115,123,148,174,178,299,301,337,366,367,374,381,388,390,391,392,393,396,397,398,399,400,407,411,412,414,419,423,427,430,436,439,444,445,447,452,462,467,468,470,473,487,494,500,503,508],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,65,70,80,96,121,123,124,161,171,177,207,208,211,213,216,217,218,220,221,228,233,237,240,246,264,278,294,311,327,328,345,367,374,375,376,378,381,409,413,436,500,509],counter:[3,342,477,488,490,496],counteract:240,counterbal:244,counterbalanc:29,counterpart:[197,308,477],counterproduct:18,coupl:[],courant:314,cours:[3,8,133,135,167,197,205,206,241,307,321,335,341,343,344,346,347,367,428,454,479,482,495,503,509,511],courtesi:369,cov:452,coval:[6,9,29,407,431,452,503],covari:242,cover:[6,74,193,201,210,251,407,469],coverag:[74,217],cpc:247,cpp:[1,3,6,8,9,11,12,13,92,197,205,206,238,311],cpu:[1,3,9,10,12,14,15,16,17,18,65,74,201,215,231,249,337,364,367,381,394,462,477,495,496,499,500,501,509],cpuremain:500,cr2:172,cr3:172,crack:[4,377],crada:[5,7],crai:[5,7,13,18,197],crash:[3,12,377,503],craympi:381,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:210,create_faceset:210,create_group:199,create_nodeset:210,createatom:[],creation:[],crimson:201,critchlei:293,criteria:[3,123,174,200,201,222,223,224,259,374,441,469,484,487,509],criterion:[12,42,128,173,176,211,221,224,240,278,300,314,342,347,374,376,396,407,411,452,487,496,497],criterioni:496,critic:[6,49,50,262,331,336,374],crmax:74,crmin:74,cross:[3,12,22,74,94,151,171,181,197,198,200,212,217,223,227,261,263,285,308,317,321,323,332,339,351,369,376,392,401,404,405,412,413,414,419,421,423,442,447,449,451,465,467,474,482,486,492,511],crossov:1,crossterm:482,crozier:[0,7,13],crucial:298,crystal:[3,4,6,13,76,113,289,290,334,369,377,482,486,500,503],crystallin:[6,109,290,369,466,503],crystallis:331,crystallogr:[125,172],crystallograph:[369,500],crystallographi:[125,172,369],cs1:172,cs_chunk:6,cs_im:[41,482],cs_re:[41,482],csanyi:[147,443,453],cscl:431,csequ:6,csh:[11,12,394],cshrc:[11,12],csic:[406,463,465,467,470],csinfo:6,csisi:[406,463,465,467,470],csld:[],cst:405,cstherm:6,cstyle:479,csvr:[],ctcm:[382,405],ctemp_cor:231,cterm:313,ctr:9,ctype:11,cu1:172,cu2:172,cu3au:431,cube:[6,42,171,176,221,231,345,369,503],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_hom:[9,15],cuda_prec:[9,15],cufft:14,cuh:387,cummul:[3,6,219,222,223,224,226,237,242,248,250,324,327,328,329,330,332,339,413,500],cumul:[6,211,213,216,217,218,232,240,248,262,264,269,278,308,309,376],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,61,63,65,74,76,84,92,108,109,115,123,124,137,148,153,161,163,169,171,174,177,196,197,198,199,200,201,202,205,206,210,213,217,218,219,221,222,223,224,225,226,227,228,232,233,238,240,242,245,246,248,254,261,264,265,270,271,272,278,283,284,285,287,293,294,299,300,302,305,306,307,308,311,312,313,314,315,316,317,318,320,322,323,324,327,328,329,335,336,339,340,341,342,343,344,346,347,349,364,365,366,367,370,371,373,374,375,376,381,387,394,396,400,405,407,408,411,414,415,418,428,429,431,432,433,436,442,444,445,448,449,450,451,454,465,467,468,471,477,478,479,480,482,483,484,485,486,488,489,490,492,494,496,497,499,500,504,509,510,511,512,513],curv:[6,173,240,290],curvatur:[410,446,474],custom:[],cut0:480,cut1:491,cut2:491,cut:[],cuthi:[289,301],cutinn:[389,428,429],cutlo:[289,301],cutmax:442,cutoff1:[393,400,419,423,427,430,439,447],cutoff2:[388,390,391,393,399,400,419,423,427,430,439,447,468],cutoff:[3,6,8,10,16,18,40,46,47,55,56,63,73,75,76,80,92,97,113,115,122,123,147,171,174,176,177,223,224,229,236,289,298,299,301,303,305,308,312,324,337,341,345,347,364,366,367,374,377,378,379,381,382,383,384,385,386,387,388,389,390,391,392,393,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,414,415,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,452,453,454,455,456,457,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,480,484,487,491,503,509],cutoff_glob:[],cutoff_inn:[],cutoffa:406,cutoffc:406,cuu3:405,cval:172,cvd:331,cvel:313,cvff:[],cwiggl:[3,261,341,344,346,509],cyan:[2,200,201],cycl:[3,240,262,264,265,269],cyclic:[3,193],cygwin:12,cylind:[3,4,74,200,213,246,294,342,345,485],cylindr:[6,246,321,342],cypress:381,cyrot:387,cyrstal:290,d3q15:251,d3q19:251,d_double_doubl:15,d_e:336,d_flag2:297,d_flag:297,d_name:[120,197,297,326,492],d_single_doubl:15,d_single_singl:15,d_sx:297,d_sy:297,d_sz:297,daan:334,dai:12,daili:12,daivi:285,damag:[],dammak:303,damp:[3,6,204,209,248,249,250,255,264,265,269,295,298,299,303,308,327,328,340,342,343,373,374,376,388,390,392,397,400,407,411,419,427,439,447,462,468,496,503],damp_com:249,damp_drud:249,dampen:[308,503],dampflag:[342,411],dan:17,danger:[3,12,240,347,401,500],dangl:176,daniel:9,darden:[367,400],darkblu:201,darkcyan:201,darken:200,darkgoldenrod:201,darkgrai:201,darkgreen:201,darkkhaki:201,darkmagenta:201,darkolivegreen:201,darkorang:201,darkorchid:201,darkr:201,darksalmon:201,darkseagreen:201,darkslateblu:201,darkslategrai:201,darkturquois:201,darkviolet:201,dasgupta:299,dash:[411,499],dat:[6,96,193,210,478],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,309],dataset:309,datatyp:3,date:[0,4,6,12,13,196,444,445,509],datom1:122,datom2:122,datom3:122,datom4:122,datum:[3,6,43,67,70,72,82,98,115,122,197,214],davenport:430,davi:341,david:[9,19,366,367,465,467],daw:[405,442],dbg:14,dcd:[3,6,7,197,199,200,201,202,291,483,487],ddim:196,deactiv:427,dealt:247,debug:[6,7,11,12,13,14,17,125,129,172,173,291,296,364,366,381,415,436,471,480,481,489,492,499,509],deby:[],decai:[97,397,474],decid:[3,6,12,16,74,261,297,308,337,497,504],decipher:369,declar:199,declin:324,decod:200,decompos:[92,453],decomposit:[3,5,7,18,64,210,291,312],decoupl:[6,503],decreas:[3,197,198,207,208,215,224,227,233,238,240,248,335,366],decrement:313,deepli:363,deeppink:201,deepskyblu:201,def:[12,13,480],defaul:63,defect:[6,73,171,434],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,179,180,181,182,183,184,185,187,188,190,191,192,193,194,195,196,197,198,199,200,201,204,205,206,207,208,209,210,211,212,213,214,216,217,218,219,220,221,222,223,224,225,227,228,231,232,233,235,238,239,240,243,246,247,248,249,250,251,259,261,263,264,265,266,267,268,269,270,271,272,274,275,276,279,281,282,283,284,285,286,287,289,290,291,293,294,295,297,299,301,306,308,309,310,311,314,318,322,324,326,327,328,329,330,332,333,334,336,338,339,341,342,343,344,345,346,347,349,350,351,352,353,354,355,356,359,360,361,362,364,366,367,369,371,373,374,375,376,377,378,379,380,381,383,384,385,386,388,389,390,391,392,393,394,395,397,398,400,401,402,403,404,406,407,409,410,411,412,413,414,415,417,419,420,421,422,423,424,425,426,427,428,429,430,434,435,436,437,438,439,441,442,444,445,446,447,448,449,450,451,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,479,480,482,483,485,486,487,488,491,492,493,494,496,497,499,500,503,505,506,507,508,509,510],definit:[2,3,6,8,12,13,81,83,123,147,201,213,214,215,216,217,218,219,227,235,246,269,309,326,338,341,344,346,348,360,364,375,384,387,395,402,403,407,417,442,449,451,453,469,480,482,484,491,493,508,509],defint:500,deform:[],deg2theta:172,deg:503,degener:[3,293],degrad:[8,18,290,367,491],degre:[3,6,8,20,21,24,28,29,32,35,36,38,67,82,97,98,100,102,103,105,107,108,113,119,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,172,173,179,180,183,184,191,193,196,200,213,224,231,240,242,243,248,249,254,264,265,269,270,271,272,283,284,285,287,291,293,307,308,311,327,328,329,334,350,352,356,359,361,374,400,405,413,492,500,503,510],degress:[153,213],del:496,delai:[3,6,12,377,404,500],deleg:414,delet:[2,3,7,8,12,55,59,62,65,171,176,177,204,213,214,216,217,218,219,222,224,237,240,264,309,327,328,347,349,365,375,377,380,436,461,482,483,484,485,493,494,499,504,505,507,509,510],delete_atom:[],delete_bond:[],delete_el:210,deli:196,delimit:[480,509],deloc:[265,407,452],delr:431,delt_lo:496,delta:[],delta_1:387,delta_3:387,delta_7:387,delta_conf:3,delta_ij:[431,442],delta_mu:[],delta_pi:387,delta_r:442,delta_sigma:387,delta_ua:[],delx:196,delz:196,dem:[],demand:303,demo:11,demon:288,demonstr:[298,431],den:294,dendrim:413,denniston:[9,251,253,254,255,290],denomin:[7,178],denot:[125,231,249,290,301,303,397,412,414,445,449,451],dens:[74,224,407],densiti:[3,6,7,9,18,41,42,61,106,123,133,147,159,171,173,205,206,210,213,217,218,221,227,238,251,254,257,258,290,294,295,299,336,341,369,371,375,382,387,405,431,432,433,442,446,452,456,458,459,460,482,491,492,500,508],density_continu:451,density_summ:451,depart:[0,7],departur:[262,298],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,63,65,67,70,72,73,74,82,97,98,109,115,116,119,120,121,122,126,147,150,156,160,161,167,173,174,179,180,181,182,183,184,185,187,188,190,191,192,193,196,197,198,200,201,204,205,206,207,208,211,213,215,216,217,219,220,221,223,225,227,233,234,239,242,243,244,246,248,249,251,253,254,261,264,266,267,268,269,270,271,272,273,274,281,283,284,285,287,289,300,303,305,308,310,311,312,318,324,327,328,329,331,333,335,336,338,340,341,344,345,346,347,349,350,351,352,353,355,356,359,361,367,369,374,375,377,378,379,381,382,383,385,386,387,388,389,390,391,392,393,394,395,396,397,398,400,401,405,406,407,408,409,410,411,412,413,414,419,420,421,422,423,424,425,426,427,428,431,432,434,435,437,438,439,441,442,444,445,446,447,452,453,454,462,463,464,465,466,467,468,470,472,473,474,477,479,482,484,485,488,492,494,496,499,500,502,509,510],dependend:6,depflag:12,dephas:[477,496],depos:228,deposit:[],deprec:[3,299,444],depth:[52,151,200,336,410,446],dequidt:9,der:[92,114,395,396,427,444,445,473,503],deriv:[6,7,8,9,38,57,65,92,147,167,193,214,225,227,240,248,261,264,266,267,268,269,270,271,272,289,295,299,303,333,334,336,341,342,345,373,375,383,387,395,400,407,408,412,421,425,426,431,434,444,445,462,464,473,503],derjagin:473,derlet:289,descend:201,descent:[7,373],descib:[41,200,299],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,64,65,70,73,74,76,93,117,120,123,125,137,147,148,151,152,153,157,158,161,164,166,167,171,172,173,175,176,185,190,193,197,198,199,204,205,206,213,214,215,216,217,218,219,221,224,225,226,227,228,230,231,236,241,242,245,246,247,248,249,250,251,253,254,255,259,263,264,265,269,277,286,289,291,296,297,298,299,300,301,308,313,321,324,325,326,327,328,329,330,331,332,333,334,339,341,342,344,349,366,367,369,372,373,374,375,376,380,383,384,386,388,389,390,392,393,394,395,396,397,400,405,407,408,410,411,412,414,417,419,420,421,422,423,424,425,426,427,428,429,430,431,434,435,441,442,443,444,445,446,447,452,453,454,461,462,463,464,465,466,467,468,470,472,473,474,475,477,479,480,482,483,484,485,486,492,495,496,499,504,509,510,511],descript:[],descriptor:[147,197,415],deserno:367,design:[0,3,6,7,8,11,13,14,15,17,125,155,158,172,210,224,230,231,264,265,289,290,309,331,336,384,385,386,389,392,397,399,407,427,428,429,432,433,442,445,464],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,61,74,93,96,119,124,148,155,173,186,196,213,219,225,227,238,240,241,248,249,250,254,264,285,293,294,295,296,299,303,308,311,324,327,328,329,330,335,342,357,363,366,367,369,372,374,375,376,401,405,413,428,429,463,465,467,478,479,480,482,486,491,496,497,499,500,509,510,511],desk:7,desktop:[4,6,7,10,12,200],despit:503,destabil:387,destre:359,destroi:[9,11,40,222,223],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,65,68,69,70,74,78,81,95,96,99,108,110,112,114,116,118,119,121,124,126,147,148,150,151,152,153,156,166,167,168,170,173,174,177,178,181,192,196,197,198,200,201,204,205,206,210,213,214,215,216,217,219,221,223,224,225,226,227,228,238,240,241,242,243,245,246,248,250,251,255,261,262,263,264,265,266,267,268,269,270,271,272,276,278,283,284,285,286,287,290,293,294,295,297,298,300,301,302,308,311,312,324,327,328,329,330,331,332,334,335,336,337,338,339,340,347,349,351,360,366,367,370,374,375,377,378,381,382,383,384,386,387,389,391,392,393,394,395,396,397,400,401,407,408,410,411,412,413,414,419,420,421,422,423,424,425,426,427,428,429,430,431,435,436,441,444,445,446,452,453,454,462,469,472,473,475,480,482,483,484,485,487,488,491,492,494,497,500,501,504,509,510,513],detect:[2,3,12,43,63,65,91,97,239,294,335,376,396,413,418,477,479,482,493,496,509],determ:381,determin:[1,3,6,8,9,12,15,40,41,43,52,59,60,61,63,64,70,74,92,108,114,116,119,125,126,134,148,161,162,171,172,173,196,197,198,200,201,202,203,207,208,209,212,213,214,215,216,217,218,219,220,221,225,227,228,231,233,240,243,244,246,248,249,254,259,261,262,264,270,271,272,283,284,285,287,289,291,294,295,298,305,306,307,308,309,310,314,316,318,324,327,328,329,331,337,338,341,342,343,344,345,346,347,360,366,367,369,375,377,378,381,383,384,391,396,400,404,405,409,411,414,415,423,431,434,436,445,446,452,461,464,468,473,479,482,483,485,487,489,492,496,498,499,501,508,509,510],determinist:312,detil:115,devan:[9,447],devanathan:467,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,245,269,293,298,299,302,383,387,407,433,434,452,470,484],devemi:9,deviat:[262,269,289,409],deviator:9,devic:[1,3,12,15,17,245,381],device_typ:381,devin:[300,396],devis:433,dfactor:200,dff:503,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,367],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,302,434],dhi:[61,196,227,294],dhug:[262,298],dhugoniot:[262,298],dia:431,diagnost:[],diagon:[3,6,88,147,148,149,225,264,295,308,339,449,451],diagonalstyl:453,diagram:[42,125,172,192,221,291],diallo:413,diam:[200,201,294,375],diamet:[3,6,41,43,120,173,197,198,200,201,205,206,248,294,308,324,326,340,342,375,395,410,411,421,446,469,473,482,483,492],diamond:[369,407,431],diamter:[41,294],dick:6,dicsuss:261,dictat:[211,262],did:[3,12,374,401,404,405,411,436,465,467,490],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,169,338,366],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,63,66,70,73,74,92,97,100,102,103,127,147,150,151,152,153,154,156,159,160,161,162,163,165,166,167,173,174,176,181,192,193,196,197,200,201,204,206,209,211,213,216,221,222,223,224,225,226,227,231,236,239,240,241,242,243,244,245,248,249,251,261,264,265,266,267,268,270,271,272,274,276,279,281,282,283,284,287,289,291,293,295,298,299,300,303,306,308,311,313,321,322,324,327,328,329,332,333,334,336,339,340,341,342,345,349,350,360,363,365,366,367,369,370,372,373,375,376,378,379,380,381,382,383,387,391,392,394,395,396,401,402,403,405,407,410,411,412,414,417,419,420,422,423,430,431,432,433,435,436,438,442,444,445,446,447,448,449,451,452,453,454,462,463,464,465,467,469,470,473,476,477,479,480,482,484,485,486,487,490,491,492,494,496,497,499,500,501,503,508,509,510,511],differenti:[1,3,6,29,193,366,397,442,466],difficult:[225,291,381,413,491],difficulti:[97,113,311,444],diffract:[],diffus:[],digit:[2,3,201,349,434,509],dih_table1:193,dih_table2:193,dihder:[],dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:223,dihydrid:407,dij:311,dilat:[],dim1:3,dim2:3,dim:[3,61,74,150,154,155,156,159,160,161,162,163,165,173,196,217,227,246,342,369,431,485,508,509,510],dimdim:509,dimems:290,dimens:[],dimensinon:74,dimension:[3,40,97,119,125,147,150,153,154,155,156,159,160,161,162,163,165,172,195,213,217,263,290,336,369,372,376,442,482,492],dimensionless:[111,128,129,131,134,136,138,143,147,336,367,453,473],diment:3,dimentionless:142,dimer:[6,308,431],dimgrai:201,dimstr:[42,221],dinola:[295,327],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,41,197,198,326,503],dir1:493,dir2:493,dir:[1,3,4,8,10,11,12,262,289,298,323,442,444,445,480,493,509],dirac:147,direc:442,direct:[],directli:[3,6,8,9,11,12,92,120,147,149,197,198,199,200,207,233,242,246,251,290,309,328,340,342,343,344,345,369,373,381,382,383,388,390,391,397,400,405,407,419,423,436,439,447,461,480,492,493,494,500,509],directoi:14,directori:[],disabl:[3,12,16,336,418,480,495,509],disadvantag:[6,221],disallow:[197,227,264],disappear:484,discard:[2,3,42,74,215,217,221,337,345,479,484,485],discontinu:[193,374,425],discourag:431,discov:[13,337],discret:[6,8,41,43,200,201,248,251],discuss:[],disk:[6,89,90,97,166,195,228,240,294,480],disloc:[73,434],disord:[40,73,434],disp:[],dispar:446,disperion:[400,423],dispers:[3,6,7,9,171,290,366,367,391,400,423,428,436,445,464,470],displac:[],displace_atom:[],displace_box:61,displacemet:485,displai:[11,13,22,37,45,56,181,192,197,200,351,360,394,462],dispters:3,disregard:434,dissip:[6,9,41,85,86,235,241,248,290,312,333,334,389,401,402,403,411,428,429,462],dissolut:222,dist:[6,72,96,115,124,197,291,307,404,461,477,510],distanc:[],distinct:[6,231,305,366,446],distinguish:[6,91,147,254,407,481,509],distort:[171,382],distrbut:382,distribut:[],distro:[118,394,441,442],ditto:[8,12,14,15,16,17,18,43,122,223,474,480],div:8,divd:124,diverg:[3,12,40,308,334,484,503,511],divid:[3,6,16,42,96,119,124,133,135,148,170,171,181,192,201,213,214,216,221,227,289,332,339,344,366,374,376,408,445,452,470,491,499,509],divis:[6,251,387,417,427,479,500,509],dl_poli:[6,7],dlambda:167,dlammps_async_imd:245,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,200],dlammps_gzip:[3,12,197,200,335,482,483,487],dlammps_jpeg:[3,12,200],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,200],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,197],dlen:492,dlmp_intel_offload:[9,12,16],dlo:[61,196,227,294],dlopen:6,dlvo:[7,395,473],dm_lb:251,dmax:[324,372],dmpvtk:198,dmpvtp:198,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,56,59,61,65,68,70,78,92,95,99,108,110,111,112,114,116,118,119,121,124,126,148,151,152,153,166,168,170,173,174,175,181,192,196,197,198,199,200,201,202,204,205,206,211,212,213,214,215,216,217,218,219,228,240,248,249,259,264,265,270,271,272,276,283,284,285,286,287,294,297,308,321,324,327,328,329,338,342,345,347,349,351,360,365,374,375,376,381,382,383,386,394,396,397,405,406,408,413,414,416,417,431,432,433,436,438,441,442,443,453,462,463,465,467,469,470,480,482,483,484,485,487,490,491,492,499,500,504,509,510,511,512],docuement:446,dodd:43,dodgerblu:201,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,40,42,43,51,55,57,61,64,65,69,73,74,75,92,93,96,110,114,117,123,124,125,149,151,153,155,156,161,163,167,172,173,174,175,177,179,181,186,192,193,196,197,198,199,200,201,204,210,211,213,217,220,221,223,224,225,227,231,233,236,237,240,241,244,246,248,249,251,254,260,264,265,266,267,268,270,271,272,283,284,285,286,287,295,296,297,301,303,306,308,324,327,329,331,332,336,339,340,341,344,345,346,347,352,353,354,356,357,359,365,366,367,368,369,375,376,377,382,383,384,385,386,387,389,391,392,393,395,396,397,398,400,401,404,405,406,407,409,410,411,412,414,415,416,417,418,421,422,424,425,426,428,429,431,432,433,434,436,442,443,444,445,446,448,449,450,451,452,453,454,455,456,457,458,459,460,461,463,464,465,466,467,468,469,470,472,473,474,475,477,478,479,480,482,483,484,485,486,489,490,492,493,494,495,496,499,500,503,504,509,513],doegenomestolif:7,doesn:[3,7,8,12,173,197,198,211,217,218,321,375,377,381,383,396,406,416,444,445,463,465,466,467,470,482,484],dof:[3,8,119,151,152,153,166,213,308,510],dof_per_atom:[153,213],dof_per_chunk:[153,213],doff:[375,482],doi:[6,226],domain:[3,6,7,12,13,18,40,42,43,60,63,64,74,125,162,172,175,196,199,200,201,204,211,221,225,227,228,244,247,251,264,265,291,303,308,312,336,341,342,366,367,376,381,404,436,477,479,482,486,499],domin:[1,407,496],don:[0,8,9,12,13,123,176,207,233,249,297,345,431,452,480,482,504],donadio:328,done:[1,3,6,7,8,12,14,15,16,17,18,38,40,42,57,61,64,74,167,170,173,176,193,197,200,201,210,211,213,215,216,217,218,219,221,222,223,224,225,227,228,236,238,240,245,246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ribum:[222,223],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,44,48,49,50,52,54,57,61,156,157,180,182,225,227,240,241,242,249,251,264,269,285,298,299,303,307,311,313,321,324,331,332,334,339,350,352,356,359,396,431,438,452,503],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:210,equival:[6,12,13,29,61,63,131,132,140,145,171,175,201,216,219,225,227,240,248,264,285,295,307,308,344,401,407,452,465,467,468,482,485,490,491,500,503],equlibrium:6,equliibr:[299,301],er3:172,eradiu:[41,120,198,407,482],eras:[310,333],erat:[227,429],erc:397,erfc:[397,419,436],erforc:[120,198],erg:508,erhart:[211,405,465,467],ermscal:384,ernst:9,eror:3,eros:431,erose_form:431,erot:[],errata:[465,467],erratum:341,erron:3,error:[],erta:411,ervel:[120,198,482],escap:[228,503],especi:[8,16,161,173,204,211,221,240,298,303,306,307,381,479],espresso:[9,302],essenti:[8,11,12,27,93,135,154,155,156,159,160,161,162,163,165,182,214,269,290,340,367,383,397,419,467,487,500],essex:29,establish:[92,244],estim:[1,3,6,10,12,38,42,57,96,148,210,221,232,262,324,331,366,367,372,436,445,464,496,500],esu:508,esub:431,eta:[6,251,264,298,299,301,340,406,408,410,442,466,470,508],eta_dot:264,eta_ij:442,eta_ji:408,etag:[41,482],etail:500,etap:264,etap_dot:264,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,63,70,94,95,96,100,116,117,120,122,148,150,153,154,155,156,157,159,160,161,162,163,165,167,173,175,176,177,186,197,198,200,201,204,205,210,211,212,213,216,217,218,219,222,223,227,228,238,240,241,248,264,294,305,309,336,337,345,349,365,366,374,375,376,377,379,405,406,414,427,429,434,440,444,445,463,465,467,470,477,480,482,483,484,489,491,492,496,497,498,499,500,501,503,508,509,511,513],ethernet:18,etol:[374,376,477,496],etot0:298,etot:[6,100,102,103,117,148,159,201,231,249,262,298,499,500],eu2:172,eu3:172,euler:[374,376],eulerian:210,euqat:455,europhi:251,ev_tal:8,evalu:[2,3,9,11,12,38,57,71,74,92,93,96,114,124,126,147,149,153,163,171,173,196,197,198,200,201,205,206,207,208,210,212,213,214,215,216,217,218,219,220,227,233,241,243,244,246,247,248,249,290,296,299,310,314,318,327,328,329,338,341,344,346,347,349,366,367,372,374,381,434,436,442,448,450,452,464,477,478,480,484,485,487,489,490,491,492,496,498,500,509,510],evalut:[349,480],evan:[161,285],evanseck:[6,20,179,392,494],evapor:[],evaul:[8,374],evdwl:[114,444,445,500],even:[3,6,8,12,15,17,18,34,40,42,53,59,61,63,65,73,74,93,114,126,171,174,175,189,193,197,198,201,204,205,206,211,212,213,216,217,218,219,221,222,223,225,227,228,231,246,249,262,264,265,290,294,303,305,308,309,320,324,332,336,339,341,345,347,358,366,372,374,376,381,386,407,408,411,414,417,436,446,470,471,475,482,483,485,487,488,489,491,492,494,497,499,500,501,503,513],evenli:[3,42,148,193,221,251,417,471],event:[],eventu:[3,6,12,15,175,299,496],ever:[9,55,57,247,324],evera:[395,410,446,462],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,74,75,96,120,126,135,161,176,197,198,199,200,201,202,204,205,206,207,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,227,228,232,237,238,240,242,244,245,246,251,252,260,264,265,269,288,289,290,294,295,296,297,298,299,300,301,303,305,306,308,309,311,313,324,326,327,328,329,330,331,332,335,336,337,338,339,347,349,365,367,376,377,378,381,401,404,414,427,444,445,452,458,476,477,478,482,484,486,487,489,490,491,496,497,498,500,504,509,513],everyth:[8,114,504],everywher:[123,421],eviri:407,evolut:[242,251,291,477],evolv:[251,291,337],ewald:[2,3,5,6,7,8,9,12,93,117,125,148,337,366,367,374,388,390,391,397,400,407,419,423,439,447,462,464,468],ewald_disp:400,ewalddisp:3,exact:[22,42,45,74,129,167,176,181,221,224,241,242,248,249,250,294,303,304,324,336,351,366,394,484,489,496,509,511,513],exactli:[3,6,12,14,17,38,42,43,57,61,74,75,96,123,151,157,164,173,193,205,206,216,221,227,232,236,241,248,249,250,265,277,278,286,290,298,324,329,330,343,381,394,401,405,411,414,428,436,464,484,485,492,496,509],exager:503,examin:[6,8,17,224,290],examp:[480,509],exampl:[],exce:[3,6,16,17,18,42,60,74,175,212,213,216,217,218,219,221,225,227,232,237,264,290,305,309,315,316,324,374,381,482,509],exceed:[3,42,61,221,227,264,324,490],excel:407,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,61,62,65,74,94,95,115,116,119,124,148,150,151,152,153,154,155,156,157,159,160,161,162,163,164,165,166,173,177,179,180,181,182,183,184,185,187,188,190,191,192,193,196,197,198,201,204,207,213,214,216,220,221,225,227,234,239,240,243,246,248,250,264,265,266,267,268,269,270,271,272,273,274,277,278,281,283,284,285,286,287,291,300,301,308,310,311,321,324,327,329,330,336,340,344,347,348,349,350,351,352,353,355,356,359,360,361,366,367,369,371,375,376,377,379,380,381,382,383,385,388,389,390,391,392,393,394,395,396,397,399,400,401,405,406,407,408,409,410,411,412,413,414,419,420,421,422,423,424,425,426,427,428,429,432,437,438,439,441,444,445,446,447,454,462,463,464,465,466,467,468,470,472,473,474,477,479,480,482,484,485,487,490,491,492,493,494,496,500,503,508,509,510,512],excess:[215,407],exchang:[2,3,6,8,63,64,204,210,211,240,248,300,308,332,336,339,366,381,407,497],exchange:366,excit:407,exclud:[3,6,9,12,16,17,65,74,119,147,153,160,161,177,197,213,217,222,223,252,260,293,306,308,331,342,347,374,375,377,389,411,414,417,428,429,436,461,494],exclus:[1,3,12,16,92,381,396,434,436,491,501],excurs:[264,477],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,62,174,200,245,302,349,365,368,380,478,480,490,493,496,509],exempl:452,exemplari:241,exemplifi:407,exert:[6,246,249,303,343,344,345,367],exhaust:[210,380,509],exhibit:[97,264,373,407,491],exist:[3,6,7,8,11,12,13,16,37,56,61,70,73,129,173,174,192,199,200,201,204,209,220,223,225,228,240,293,294,296,347,348,350,352,353,354,356,360,370,375,381,402,403,414,444,461,471,478,480,482,483,484,493,494,495,504,509,510,511],exit:[2,3,11,12,42,59,197,221,236,365,380,480,481,490,499,509],exlanatori:3,exp:[],expand:[],expans:[12,147,197,493,509],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,74,108,154,165,171,193,221,233,240,242,261,289,295,297,298,303,308,347,367,377,394,431,434,436,477,480,482,484,487,491,496,509],expens:[6,74,201,289,293,308,336,347,366,367,377,381,480],experi:[6,13,15,17,220,228,245,254,263,295,307,308,372,376,401,436,491,496],experienc:[6,12,253,254],experiment:[240,366,381,496],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,61,65,67,70,72,74,75,76,79,80,82,91,98,153,161,193,197,198,200,201,204,213,214,219,221,223,225,227,264,289,297,308,321,347,349,365,366,369,375,376,380,386,405,417,452,454,469,480,483,484,487,489,492,503,504,509,513],explan:[3,6,61,120,147,197,198,213,263,289,414,476,479,480,482,491],explanatori:[3,8,124,197,198,212,213,216,217,218,308,375,479,509],explantori:[3,304],explic:435,explicit:[6,9,11,22,45,80,92,120,123,167,181,205,206,227,315,316,351,371,383,384,387,392,394,405,407,418,428,468,476,479,483,486,504],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,74,116,119,150,160,163,171,173,179,180,182,183,184,185,187,188,190,191,193,197,198,201,207,217,220,227,234,239,241,243,248,264,266,267,268,269,270,271,272,273,274,281,283,284,285,287,297,298,300,308,310,311,327,329,330,336,340,344,350,352,353,355,356,359,361,375,381,382,383,385,388,389,390,391,392,393,394,395,396,397,398,400,401,404,405,406,408,409,410,411,412,413,414,418,419,420,421,422,423,424,425,426,427,428,432,434,436,437,438,439,441,446,447,454,455,456,457,458,459,460,462,463,464,465,466,467,468,470,472,473,474,482,484,485,491,492,494,495,501,503,504],explictli:[16,495],exploit:[15,17,291],explor:[125,172],expon:[3,299,301,405,410,413,427,435,447],exponenti:[92,442,463,470,474,496,509],expos:11,exposit:[210,401,404],express:[6,147,159,173,205,206,225,261,289,299,336,342,349,387,405,407,421,431,452,453,462,509],expressiont:387,extend:[],extens:[3,6,9,17,45,46,47,54,56,65,71,87,88,89,92,93,96,100,103,104,114,116,124,126,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,198,204,207,208,211,219,220,226,229,233,238,239,240,242,243,244,246,248,250,262,264,269,278,289,290,306,307,308,310,313,318,321,323,327,328,329,330,331,333,334,336,338,341,345,346,410,431,434,445,446,453,499,500],extent:[1,3,42,43,46,59,74,171,175,197,209,217,221,246,343,346,366,369,383,448,450,464,479,482,485],exterior:[3,6,171,345],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,63,74,108,116,117,119,125,148,150,151,152,154,156,159,160,161,162,163,165,166,172,173,174,175,179,201,216,221,223,264,296,297,298,308,324,374,375,378,379,400,411,414,417,431,436,479,480,482,485,494,503,509],extract:[3,6,11,13,36,65,71,92,114,122,124,126,205,206,301,376,397,408,431,453,480,487,499],extract_atom:11,extract_comput:[11,480],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,60,200,215,225,227,264,334,407,466,503],extrema:427,extrins:210,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[169,338],f_a:[465,466,467],f_ave:124,f_c:466,f_f:467,f_fix_id:298,f_foo:509,f_harm:334,f_i:[29,442],f_id:[6,74,124,126,197,198,204,212,213,214,215,216,217,218,219,259,326,338,500,509],f_ij:442,f_indent:219,f_int:333,f_j:29,f_jj:96,f_k:442,f_langevin:336,f_max:[298,303],f_msst:262,f_r:[249,465,466,467],f_sigma:387,f_solid:334,f_ss:6,f_temp:[],face:[3,6,59,61,74,161,171,175,209,217,218,341,343,344,345,346,369,410,431,446,482,485],face_threshold:171,facet:171,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,242,294,324,334,411,452,494],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,59,60,61,75,92,96,108,115,122,123,125,147,167,172,175,179,190,196,197,200,201,205,206,214,221,225,227,228,240,245,248,250,251,262,264,265,269,291,295,299,307,311,314,316,324,328,332,339,340,341,345,356,367,369,375,381,383,384,387,388,390,392,397,398,399,401,402,403,407,411,414,418,419,431,434,436,438,439,445,447,454,463,468,479,482,485,486,491,494,496,497,500,503,508,509],factori:[3,480],factoriz:366,fail:[3,9,11,12,61,177,225,228,366,374,376,399,445,480],failur:[128,449,481,509],fairli:[11,436,491,496,504],faken:76,falcon:245,fall:[3,6,201,216,294,480,509],fals:[91,347,349,452,509],fame:8,famili:[470,479],familiar:[0,11,504],fan:442,far:[3,6,12,17,59,61,63,91,197,198,201,202,221,222,223,225,228,264,289,307,308,324,341,352,356,372,376,377,469,480,482,487,500],farago:248,farrel:[465,467],farther:197,fashion:[6,8,42,74,173,201,204,205,206,211,217,221,223,228,240,242,246,261,262,264,266,267,268,269,270,271,272,280,283,284,285,286,287,297,298,300,308,313,317,323,326,334,336,340,341,342,344,346,376,414,428,485,494,509,512],fasolino:416,fast:[6,7,9,12,13,17,40,197,198,275,298,337,366,367,389,428,429,434,462,464,484,489,491,500,510,513],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,63,65,111,116,119,150,160,179,180,182,183,184,185,187,188,190,191,193,197,198,201,207,220,221,227,234,239,243,247,248,264,266,267,268,269,270,271,272,273,274,281,283,284,285,287,295,299,300,308,310,311,324,327,329,331,333,336,340,344,350,352,353,355,356,359,361,366,367,378,379,381,382,383,385,387,388,389,390,391,392,393,394,395,396,397,400,401,405,406,408,409,410,411,412,413,414,419,420,421,422,423,424,425,426,427,428,432,437,438,439,441,446,447,454,462,463,464,465,466,467,468,470,472,473,474,477,485,491,495,503],fastest:[1,6,14,17,161,217,336,337,381,479],fatal:[3,499],fault:[73,445],faulti:12,fava:410,favor:224,favorit:7,fbmc:331,fcc:[],fcm:[280,509],fdirect:231,fdotr:415,fdt:[],fdti:92,fe2:172,fe3:172,fe_md_boundari:210,featu:8,featur:[],fecr:405,feedback:[7,245],feel:[7,245,246,254,289,345,347,376,436],felling:433,felt:345,femtosecond:508,fene:[],fennel:[397,419],fep:[],ferguson:[6,179,494],fermi:[1,9,10,12,15,159,381,467],fermion:407,fernando:430,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,65,202,212,213,214,216,217,218,219,249,264,294,297,299,311,338,366,374,375,376,383,452,479,482,487,491,493,501,511],fewer:[1,3,11,15,16,63,254,491],fewest:3,fextern:238,feynman:291,fff:480,ffield:[396,408,444,445,452],ffmpeg:[3,12,200],ffplai:200,fft:[1,3,7,9,11,12,14,15,93,116,117,148,290,366,367,491],fft_inc:[12,367],fft_lib:12,fft_path:12,fftbench:[366,501],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],ficiti:461,fictiti:[6,207,208,233,238,242,291,307,397,419,423,461],field1:[483,487],field2:483,field:[],fifth:[321,438],figur:[1,3,8,12,298,479,480,504],fij:400,file0:289,file1:[11,13,289,335,349,375,487,489,493],file2:[11,13,335,349,375,487,489,493],file:[],file_from:199,filen:375,filenam:[3,12,13,38,42,57,193,197,198,200,201,202,210,213,214,215,216,217,218,219,221,226,236,289,293,296,299,300,301,304,305,308,309,335,336,363,364,365,375,376,382,383,387,397,405,406,408,416,431,432,433,438,442,443,444,445,452,453,463,464,465,466,467,470,478,479,480,483,484,489,493,500,509,511,512,513],filennam:489,filep:[3,197,198,201,484,489,513],filepo:305,fill:[7,9,173,200,294,336,369,377,387,434,445,485,504],filter:[201,210],final_integr:8,final_integrate_respa:8,finchham:[6,155,399],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,63,74,76,92,124,176,193,202,211,224,225,236,237,240,263,289,294,295,303,307,372,374,376,377,397,414,419,423,431,452,462,464,503,504,509],find_custom:8,fine:[16,17,177,207,233,334,377,381,504,509],finer:[147,173,509],finest:366,finger:[173,196,261,485],finish:[6,11,42,221,349,363,365,366,378,380,381,469,487,509,510],finit:[],finni:[7,405,462],finvers:231,fiorin:[9,226],fire:[],firebrick:201,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,59,61,63,64,74,84,93,96,109,110,111,113,119,123,124,134,137,140,141,145,148,158,161,167,169,171,172,174,175,176,180,193,197,198,199,200,201,202,204,205,213,214,216,217,218,219,221,224,227,236,240,241,246,251,261,262,263,264,289,291,296,297,298,300,305,308,311,313,321,322,324,325,326,333,334,335,336,338,342,347,349,350,357,369,374,375,376,377,380,381,382,383,386,387,388,390,392,394,396,397,405,407,408,411,412,414,415,416,417,418,419,423,428,429,431,433,434,436,438,442,444,445,452,453,461,463,464,465,466,467,470,474,477,478,479,480,482,483,484,487,489,491,494,495,496,499,500,503,504,509,510,511,513],fischer:[6,9,19,20,179,392,494],fit:[3,6,9,12,38,57,193,236,307,324,383,387,416,431,436,457,464,466,490,504,509],five:[76,159,298,375,387,432,482,496],fix:[],fix_adapt:[167,206,427],fix_atom_swap:[],fix_bal:64,fix_deposit:[3,211,294],fix_eo:9,fix_evapor:211,fix_flux:210,fix_gcmc:[211,375],fix_gl:242,fix_gld:242,fix_grav:294,fix_id:[3,225,262,264,266,267,268,269,270,271,272,295,298],fix_manifoldforc:504,fix_modifi:[],fix_mov:[196,342],fix_nh:8,fix_npt:242,fix_nv:504,fix_nvt:[211,240],fix_poem:[3,6,9],fix_pour:[3,228],fix_qbmsst:9,fix_qeq:[3,396],fix_rattl:311,fix_reax_bond:444,fix_rigid:[254,386],fix_saed_vtk:309,fix_setforc:8,fix_shak:311,fix_shardlow:9,fix_srd:3,fix_styl:269,fix_temp_rescal:330,fixedpoint:[225,264],fixextern:238,fixid:210,fji:400,flag1:[230,379],flag2:[230,379],flag:[3,8,9,11,12,14,15,16,17,41,68,77,78,84,91,94,95,99,109,110,112,125,168,172,176,197,198,200,201,202,219,224,226,230,245,248,252,254,260,261,290,297,308,321,323,324,331,335,344,347,364,367,375,379,380,381,383,413,418,431,434,461,477,479,480,482,483,484,486,487,488,492,504,509],flag_buck:391,flag_coul:[391,400,423],flag_lj:[400,423],flagfld:[389,428,429],flaghi:[3,389,428,429],flaglog:[389,428,429],flagn:230,flagvf:[389,428,429],flat:[6,336,341,342,346],flavor:[2,7,12],fld:[],flen:384,flex_press:384,flexibl:[3,6,8,174,200,213,217,226,242,265,332,339,407,466,500],flip:[3,6,227,264,343,344],floor:509,flop:12,floralwhit:201,flow:[],fluctuat:[6,66,92,225,240,241,248,251,264,269,289,290,312,334,336,359,403],fluid:[],fluid_veloc:255,flush:[3,201,499],flux:[],flv:200,fly:[7,9,12,42,200,204,210,215,228,231,308,311,337,387,434,500,503],fmackai:9,fmag:229,fmass:291,fmax:[374,500],fmomentum:231,fmsec:[2,201,248,249,261,264,295,308,327,328,491,502,508,510],fname:365,fno:[9,12,16],fnorm:[374,500],fnpt:231,fnvt:231,foce:414,fock:384,focu:311,fogarti:[9,301,445],foil:[147,289,453],fold:[322,491],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,61,65,66,73,74,76,85,96,97,102,103,113,120,123,124,126,147,148,151,152,153,159,161,166,169,171,173,174,179,182,183,184,185,187,188,190,191,193,197,199,200,201,204,210,211,212,213,214,215,216,217,218,219,221,226,227,228,231,232,235,236,238,240,241,242,245,247,248,249,251,254,262,264,269,270,271,272,283,284,285,287,290,291,293,296,297,298,299,301,303,305,307,308,309,311,326,327,328,329,332,333,334,335,336,338,339,347,348,352,353,354,355,356,359,361,364,369,371,374,375,376,381,382,383,384,385,386,387,388,389,390,391,392,393,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,436,437,438,439,441,442,443,444,445,446,447,449,451,452,453,454,455,456,457,458,459,460,461,463,464,465,466,467,468,469,470,472,473,474,475,477,479,480,482,483,485,487,489,490,491,494,496,497,498,503,504,509,510,512],foo:[4,8,11,12,197,200,238,480,493,509],foot:6,footprint:[12,381],fopenmp:[9,12,16,18],forc:[],force_uvm:17,forceatom:254,forcefield:[307,413],forcegroup:251,forcezero:372,ford:400,forestgreen:201,forev:74,forget:[249,503],forgiv:264,fork:[],form:[2,3,6,8,12,19,22,45,55,65,68,77,78,80,84,92,94,95,97,99,109,110,112,123,147,148,167,168,177,181,201,204,205,206,223,241,242,248,250,254,261,285,290,301,303,307,308,336,341,345,350,351,354,359,371,373,375,376,383,384,387,394,402,403,405,407,409,413,414,418,430,431,433,434,438,439,442,444,445,446,452,453,454,462,464,465,466,467,473,476,479,480,482,487,492,499,503,509],formal:[6,81,83,96,241,242,248,264,291,324,332,452],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,70,80,181,193,197,198,199,200,201,202,213,216,217,218,219,221,223,236,290,293,297,299,301,304,308,309,320,335,336,347,348,351,371,375,376,382,383,387,394,405,408,418,431,433,443,444,445,447,453,464,470,471,479,480,482,483,484,487,498,499,500,509,511],former:[6,12,16,40,42,201,221,336,340,387,389,488,494,509],formerli:[7,13],formul:[1,9,41,66,148,207,233,248,264,285,299,301,307,311,335,366,383,387,405,407,410,431,441],formula:[2,3,6,7,13,21,22,37,45,55,56,73,76,92,94,95,96,100,102,103,112,119,125,126,148,150,151,152,153,154,155,156,157,159,160,161,162,163,164,165,166,172,173,178,180,181,192,196,197,205,206,207,208,213,214,215,216,219,220,227,233,243,244,246,248,249,261,289,290,296,305,310,318,322,324,327,328,329,338,341,344,346,347,349,350,351,353,360,369,375,383,384,386,387,392,393,394,395,400,401,405,406,410,411,412,413,415,418,419,421,422,423,425,426,428,429,431,435,436,437,446,447,454,462,463,464,465,466,467,470,472,473,478,482,485,492,499,500,508,509,510],forth:[1,6,11,12,13,14,15,380,480,485,489],fortran:[3,6,9,11,12,13,238,405,414,431,444,445],fortun:8,forward:[3,8,92,365,376,381],foster:[387,441,442],foul:176,found:[3,6,9,12,76,167,197,224,226,240,245,251,290,331,337,349,365,377,394,397,400,477,483,484,499],four:[6,11,55,84,109,110,147,169,262,336,359,375,376,434,477],fourier:[],fourth:[6,111,307,321,331,392,438,452],fox:[6,125,179,460,494],fphi:[38,57,464],fpic:12,fplo:[38,57,464],fprime:464,fqdn:247,fqq:400,frac:[],fraction:[1,3,6,8,12,16,40,42,83,116,148,176,196,200,201,211,222,223,224,225,262,294,298,305,306,324,329,330,369,376,381,387,389,411,428,429,487,492],fragment:[43,245,305],fraig:43,frame:[88,147,201,210,262,298,343,410],framer:[200,201],framework:[5,242,382,453],franc:9,fraunhof:9,free:[5,6,7,9,13,29,62,65,73,92,167,205,206,289,324,333,334,335,336,373,376,384,407,427,434,442,473,479],freedom:[3,6,8,100,102,103,105,107,108,119,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,213,224,231,240,242,248,249,254,264,265,269,270,271,272,283,284,285,287,291,293,308,311,327,328,329,334,374,400,500,503,510],freeli:[0,6,7,12,151,152,166,171,200],freez:[],frenkel:[240,334],freq:209,frequenc:[3,6,16,40,109,201,215,278,290,291,298,303,364,401,407,445,452,477,491,496,509,512],frequent:[3,66,69,73,75,76,80,93,97,113,147,201,222,223,237,332,339,436,468,489],fri:[262,29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ryan:9,ryckaert:[311,359],rycroft:171,rydberg:434,s00:441,s0st:6,s2050:1,s2629:405,s319:210,s_fact:314,s_i:[6,407],s_ij:6,sack:7,saddl:[263,376],saddlebrown:201,sadigh:[211,405,432,433],saed_vtk:125,safe:[12,200,231,249,381,504],safe_zon:3,safest:[3,324],safeti:314,safezon:445,safran:473,sagui:[367,400],sai:[1,3,12,13,201,444,445,480,504],said:374,sakai:466,sall:[9,452],salmon:201,salt:[398,409,431,482],salter:452,same:[1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,38,40,41,42,44,45,46,47,48,49,50,51,52,54,55,57,59,61,64,65,67,72,74,75,80,82,84,87,89,90,92,93,94,95,96,97,98,100,103,109,110,111,113,115,116,117,119,120,122,123,124,147,148,149,150,151,152,153,154,155,156,159,160,161,162,163,165,166,167,169,171,173,174,175,176,177,179,180,181,182,183,184,185,186,187,188,190,191,193,195,196,197,198,199,200,201,204,205,206,207,210,211,213,216,217,218,219,220,221,222,223,224,225,227,228,232,233,234,239,240,241,242,243,244,245,246,247,248,249,250,251,254,261,264,266,267,268,269,270,271,272,273,274,281,283,284,285,286,287,289,290,291,293,294,295,298,299,300,301,303,304,305,306,307,308,310,311,313,318,321,323,324,325,326,327,328,329,330,331,332,333,334,335,336,338,339,340,342,343,344,345,347,348,349,350,351,352,353,355,356,359,361,366,367,369,370,371,375,376,377,378,379,380,381,382,383,385,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,404,405,406,407,408,409,410,411,412,413,414,415,418,419,420,421,422,423,424,425,426,427,428,429,431,432,435,436,437,438,439,441,442,446,447,452,454,461,462,463,464,465,466,467,468,470,472,473,474,477,479,480,482,483,484,485,487,490,491,492,493,494,495,496,500,503,504,508,509,510,512],sampl:[1,2,4,6,9,11,12,14,96,109,151,152,166,171,196,200,204,213,214,217,218,226,228,238,240,242,244,264,265,291,294,303,305,309,321,322,324,328,331,334,346,377,387,404,482,496],sample_frequ:210,san:441,sandia:[0,5,7,9,13,14,17,73,118,408,431,441],sandybrown:201,saniti:[307,377],satellit:[6,155],satifsi:509,satisfi:[3,12,76,125,147,172,225,251,269,311,344,374,377,411,496],satur:398,save:[6,8,12,19,41,61,193,198,200,215,224,241,242,248,249,250,294,303,336,348,367,377,379,387,484,487,494],sb3:172,sb5:172,sc3:172,scalabl:[],scalar:[],scale:[0,1,3,5,6,9,10,13,18,41,61,65,74,75,96,120,123,124,147,159,167,193,196,197,198,200,201,204,205,206,210,211,214,225,227,240,244,245,246,248,250,251,262,264,266,267,268,269,270,271,272,291,295,298,299,308,315,316,324,326,328,331,333,334,336,340,347,366,367,369,375,378,382,383,384,398,404,407,411,414,428,429,431,434,441,448,450,468,483,485,487,491,494,496,499,500,509,510],scale_factor:[448,450],scalegamma:251,scalexi:[3,225,264,269],scalexz:[225,264,269],scaleyz:[225,264,269],scan:[201,223,365,483],scatter:[11,125,172],scatter_atom:11,scatter_coord:11,scenario:[6,41,63,224,297,306,324,337,345,377,486,487,491,499],scf:503,schaik:427,schedul:477,schell:466,schemat:224,scheme:[6,9,18,241,242,264,291,303,311,336,366,468],schlitter1:335,schlitter2:335,schlitter:335,schmid:401,schneider:[248,250],schoen:366,schr:503,schroding:407,schroeder:[113,503],schulten:[249,313,367,503],schunk:324,schwen:9,sci:[76,344,396,433,442,452],scienc:[8,210,224,245,313,333,405,432,452,466],scientif:[9,147,405,509],scm:11,scratch:[12,42,221],screen:[],screenshot:11,scripe:11,script:[],scripta:69,scsl:12,sdk:[],sea:11,seagreen:201,seamlessli:297,search:[0,2,3,8,12,97,113,174,176,201,202,324,372,373,374,376,378,477,483,484,496,509],seashel:201,sec:[12,502,508],second:[1,3,6,9,11,12,16,55,59,61,63,74,93,96,109,111,113,119,140,141,145,148,149,161,167,171,172,174,175,176,196,197,201,204,205,213,214,216,217,218,219,224,240,241,246,261,263,291,305,307,308,311,313,321,322,324,333,334,336,347,366,369,373,374,376,377,381,386,387,388,390,391,396,397,405,407,408,411,412,414,417,418,421,431,436,438,452,463,466,467,468,470,474,477,478,479,480,482,484,489,491,495,496,500,503,508,509,510,511,513],second_mo:452,secondari:[3,185],sectinn:512,section:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,42,43,44,45,46,47,48,49,50,51,52,54,55,56,57,60,61,65,66,67,68,69,70,72,74,77,78,81,82,83,84,85,88,91,92,93,94,95,96,98,99,102,103,104,105,106,107,109,110,111,112,114,115,116,118,119,120,121,122,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,156,157,158,159,160,161,162,163,164,165,166,167,168,169,171,172,174,179,180,181,182,183,184,185,186,187,188,190,191,192,193,196,197,198,199,200,202,204,207,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,224,226,227,228,230,231,233,234,236,237,239,240,241,242,243,245,247,248,249,250,251,252,253,254,255,257,258,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,279,281,282,283,284,285,286,287,289,290,291,293,294,295,297,298,299,300,301,302,303,304,305,308,310,311,312,313,314,315,316,317,318,320,324,327,328,329,330,331,332,333,334,335,336,337,339,340,342,343,344,347,348,350,351,352,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,yflag:[160,161,252,254,260,308,331],yhi:[6,61,175,197,227,335,341,344,346,482,485,500],yhi_bound:[6,197],yield:[6,96,117,124,148,156,161,201,214,225,231,264,285,299,332,338,339,342,347,366,386,401,411,436,441,500,509],yip:333,ylat:[173,227,246,500],ylo:[6,61,175,197,227,335,341,344,346,482,485,500],ylo_bound:[6,197],ymax:[209,509],ymin:509,yorig:74,york:[291,367],yoshida:[264,308],you:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,33,35,38,40,41,42,43,44,46,47,48,49,50,51,52,54,55,57,59,60,61,63,65,68,70,71,74,75,76,77,78,80,84,85,86,92,93,94,95,96,97,99,108,109,110,112,113,114,116,117,119,121,123,124,147,148,150,151,152,153,156,160,161,166,167,168,169,170,171,173,174,175,176,177,179,180,181,182,183,184,185,186,187,188,190,191,192,193,196,197,198,200,201,202,204,205,206,207,208,211,212,213,214,216,217,218,219,220,221,222,223,224,225,227,228,231,233,234,236,237,238,239,240,241,242,243,244,245,246,248,249,250,259,261,264,266,267,268,269,270,271,272,273,274,278,280,281,283,284,285,286,287,290,291,293,294,295,297,299,300,303,306,307,308,310,311,313,321,323,324,325,327,328,329,330,332,333,334,335,336,338,339,340,341,342,344,345,346,347,349,350,352,353,355,356,357,359,361,365,366,367,369,371,373,374,375,376,377,380,381,382,383,385,387,388,389,390,391,392,393,394,395,396,397,400,401,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,431,432,433,434,436,437,438,439,440,441,442,443,444,445,446,447,452,453,454,455,456,457,458,459,460,461,463,464,465,466,467,468,470,472,473,474,476,477,478,479,480,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,499,500,501,503,504,508,509,510,511,513],young:[411,448,450],your:[],yourself:[6,8,12,13,225,375,504],yplane:342,ypo:173,ysu:[3,197,198,326,483],yuan:9,yukawa:[],yukawa_1_1:471,yxz:479,yzx:479,z_i:[407,467,474],z_j:[467,474],z_meam:431,zachari:13,zannoni:410,zbl:[],zblcut:467,zblcutinn:453,zblcutout:453,zblexpscal:467,zblz:453,zcm:308,zcylind:342,zepeda:211,zero:[],zeta:[3,251,299,408],zfactor:200,zflag:[160,161,252,254,260,308,331],zhang:[308,332,411],zhi:[3,6,175,197,209,335,341,344,346,482,485,500],zhi_bound:[6,197],zhou:[13,387,408,442,465,467],zhu:460,ziegenhain:13,ziegler:[293,431,462,467,474],zimmerman2004:210,zimmerman2010:210,zimmerman:[9,73,210,387],zlat:[227,246,500],zlib:[9,197],zlim:452,zlo:[3,6,175,197,209,335,341,343,344,346,482,485,500],zlo_bound:[6,197],zmax:[209,251,509],zmin:[251,509],zn2:172,zone:[125,309],zoom:[3,197,200,201],zorig:74,zplane:342,zr4:172,zrest:323,zsu:[3,197,198,326,483],zwall:341,zwall_veloc:251,zxy:479,zybin:445,zyx:479},titles:["LAMMPS Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying &amp; extending LAMMPS","4. Packages","8. Performance &amp; scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","&lt;no title&gt;","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","&lt;no title&gt;","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":222,"default":[37,40,41,56,59,60,61,63,64,71,74,92,93,97,108,109,111,113,114,125,129,130,147,153,161,162,166,172,173,176,178,192,195,196,197,198,200,201,202,203,205,206,207,209,210,211,213,217,218,219,222,223,225,226,227,228,232,237,240,241,246,248,249,250,251,252,254,259,262,264,265,269,285,286,290,291,294,295,296,297,298,300,303,305,306,308,309,324,326,331,332,333,334,337,339,341,343,347,360,364,366,367,369,370,372,373,375,377,378,379,381,384,387,389,407,428,429,434,436,444,445,461,462,477,478,479,482,483,485,487,489,490,491,494,496,498,499,500,501,502,508,510,511,512],"function":509,"long":[215,388,390,391,392,393,397,399,400,419,423,427,439,447,468],"new":8,"static":12,acceler:1,account:504,ackland:66,acknowledg:7,adapt:[205,206],addforc:207,addit:[12,13,504],addtorqu:208,adiabat:6,adjust_dt:314,adp:382,after:504,airebo:383,alloi:405,amber2lmp:13,amber:6,angl:[8,67],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:68,append:209,arrai:6,aspher:[6,9,87,151,266,270,274,275,283],atc:[9,210],atom:[6,7,8,66,69,73,74,75,76,79,80,81,83,84,86,90,97,101,102,105,106,107,113,117,118,120,147,148,171,209,211,212,297,509],atom_modifi:40,atom_styl:41,attract:5,aug:[],aveforc:220,awpmd:[9,384],balanc:[42,221],barostat:6,basal:69,beck:385,berendsen:[295,327],between:6,binary2txt:13,bodi:[6,8,9,43,70,152,267,271,276,284,386],bond:[8,13,71,72,222,223,224,304],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,58],bop:387,born:[388,399],boundari:[7,59],box:[6,60,225],branch:504,brownian:389,buck:[390,391,399,430],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:73,ch2lmp:13,chain:13,chang:504,change_box:61,charmm:[6,20,179,392,427],chunk:[6,68,74,78,95,99,110,112,121,153,168,170,213],citat:7,class2:[9,21,44,180,350,393],clear:62,cluster:75,cmm:9,cna:76,code:6,coeffici:6,colloid:[9,341,395,473],colvar:[9,13,226],com:[77,78,154],comb3:396,comb:[300,396],come:5,comm_modifi:63,comm_styl:64,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,505,506,507,508,509,510,511,512,513],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,509],compute_modifi:108,condit:7,conduct:[6,332],conserv:402,constant:[6,509],constraint:7,contact:[79,127],contact_radiu:[],coord:80,core:6,coreshel:9,correl:[214,215],cosin:[23,24,25,26,27,28,182],cossq:352,coul:[388,390,391,392,393,397,398,399,412,419,423,427,439,447],coupl:6,creat:223,create_atom:173,create_bond:174,create_box:175,createatom:13,creation:7,csld:328,csvr:328,cubic:421,cuda:[9,14,116,119,150,160,207,220,234,239,243,264,273,310,311,327,329,340,388,390,392,393,405,411,412,419,420,422,425,437,463,465],custom:[8,197,198],cut:[50,384,390,393,397,400,407,409,419,420,427,435,439,468],cvff:353,damag:[81,128],data2xmovi:13,data:6,databas:13,deby:[397,419],dec:[],defgrad:134,deform:[156,157,227],delete_atom:176,delete_bond:177,delta:24,deposit:228,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,505,506,507,508,509,510,511,512,513],diagnost:7,diel:398,dielectr:178,diffract:9,diffus:6,dihedr:[8,82],dihedral_coeff:181,dihedral_styl:[2,179,180,182,183,184,185,186,187,188,189,190,191,192,193,194],dilat:83,dimens:195,dipol:[6,9,29,400],direct:231,directori:4,discuss:6,disp:6,displac:[84,91],displace_atom:196,distanc:354,distribut:[7,12],document:0,dpd:[9,85,86,401,402,403],drag:229,dreid:[6,413],drude:[6,9,158,230,231,249],dsf:[397,419],dsmc:404,dump:[6,8,197,198,199,200,202],dump_modifi:201,dynam:299,eam:[13,405],echo:203,edip:406,eff:[9,13,102,103,157,159,164,250,265,277,286,330,407],efield:233,eim:408,elast:6,emac:13,energi:[130,403],enforce2d:234,ensembl:7,erot:[87,88,89,90],error:[3,129],evapor:237,event:91,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,329,330,331,332,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,495,496,497,498,499,500,501,502,505,506,507,508,509,510,511,512,513],exp:[27,182],expand:[47,422],extend:[8,11],extern:238,fcc:289,fdt:403,featur:[7,8,504,509],feb:[],fene:[46,47],fep:[9,13,92,206],field:[6,7],file:6,finit:6,fire:299,fix:[2,6,8,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,260,261,262,263,264,2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tord:113,orthogon:6,other:6,output:[6,7,8,12,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,231,232,233,234,237,238,239,240,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,338,339,340,341,342,343,344,345,346],overlai:414,overview:11,own:504,packag:[1,9,12,14,15,16,17,18,19,381],pair:[6,114,115],pair_coeff:394,pair_modifi:436,pair_styl:[2,382,383,384,385,386,387,388,389,390,391,392,393,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,472,473,474,475],pair_writ:471,pairwis:8,paquai:504,parallel:11,paramet:6,pars:2,partial:160,particl:[6,7,43],partit:476,past:5,per:6,perform:[1,10],peri:[9,441],period:25,phonon:[9,13,290],pimd:291,piston:343,planeforc:292,plastic:[118,131,132],plastic_strain:[],plastic_strain_r:[],pmb:441,poem:[9,293],point:299,polariz:6,poli:[389,428,429],polygon:[],polym:13,polymorph:442,post:7,potenti:[2,6,8],pour:294,pppm:6,prd:477,pre:7,press:295,pressur:119,previou:12,print:[296,478],problem:[3,4],process:[6,7],processor:479,profil:161,properti:[6,120,121,122,297],pymol_aspher:13,python:[9,11,13,480],qbmsst:298,qeq:[9,299,300,301],qmmm:[9,302],qtb:[9,303],quadrat:191,quantiti:6,quartic:[35,55],quip:[9,443],quit:481,radiu:127,ramp:162,rate:[132,139,144],rattl:311,rdf:123,read_data:482,read_dump:483,read_restart:484,reax:[9,13,301,304,305,444,445],reaxc:9,rebo:383,recent:306,reduc:124,refer:509,reflect:344,region:[8,124,163,164,345,485,509],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,41,42,44,45,46,47,48,49,50,51,52,54,55,56,57,58,59,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,88,89,90,91,92,94,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,195,196,197,198,199,200,201,202,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,235,236,237,239,240,241,242,243,244,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,301,303,304,305,306,308,309,310,312,313,314,315,316,317,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,363,364,365,366,367,369,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,487,488,489,490,491,492,494,495,496,497,498,499,500,501,502,505,506,507,509,510,511,512,513],relax:225,replic:486,replica:[6,7,9],report:3,repositori:504,requir:12,rerun:487,rescal:[329,330],reset:232,reset_timestep:488,resquar:446,restart2data:13,restart:[6,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,231,232,233,234,237,238,239,240,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,301,302,304,305,306,307,308,309,310,311,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,338,339,340,341,342,343,344,345,346,489],restrain:307,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,16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0,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,290,291,292,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,505,506,507,508,509,510,511,512,513],system:6,tabl:[0,6,38,57,193,236,464,465],tad:496,taitwat:[459,460],talli:[9,149],temp:[150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,327,328,329,330],temper:497,temperatur:6,tersoff:[465,466,467],test:11,tfmc:331,thermal:[6,332],thermo:[6,498,509],thermo_modifi:499,thermo_styl:500,thermodynam:[6,8],thermostat:6,thole:468,time:[6,219],timer:501,timestep:502,tip3p:6,tip4p:[6,397,419,423,427],tip:12,tlsph:[134,135,136,137,138,139,140,449],tlsph_defgrad:[],tlsph_dt:[],tlsph_num_neigh:[],tlsph_shape:[],tlsph_strain:[],tlsph_strain_rat:[],tlsph_stress:[],tmd:335,tool:[12,13],torqu:168,transform:231,tri:[282,469],tri_surfac:450,triangl:141,triangle_mesh_vertic:[],triclin:6,tstat:401,ttm:336,tune:337,tutori:504,type:7,ulsph:[142,143,144,145,451],ulsph_num_neigh:[],ulsph_strain:[],ulsph_strain_r:[],ulsph_stress:[],umbrella:361,uncomput:505,undump:506,unfix:507,unit:508,uppercas:4,user:[9,12,14,16,18],vacf:169,valu:[6,509],variabl:[6,8,509],variou:1,vashishta:470,vcm:170,vector:[6,338,509],veloc:510,version:[0,5,12],vertic:141,via:12,vim:13,viscos:[6,339],viscou:[255,340],visual:6,vol:146,voronoi:[9,171],vtk:[9,197,198,309],wall:[6,341,342,343,344,345,346],wall_surfac:320,warn:3,water:6,weight:216,what:[7,12],wolf:[388,397],wrapper:11,write:6,write_data:511,write_dump:512,write_restart:513,written:504,xmgrace:13,xmovi:13,xrd:172,xtc:9,your:504,yukawa:[472,473],zbl:[467,474],zero:[39,58,194,362,475]}})
\ No newline at end of file
diff --git a/src/version.h b/src/version.h
index 7e99ec97ea..34cf420cb3 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "10 Mar 2016"
+#define LAMMPS_VERSION "14 Mar 2016"
