From 847090cd89e2ae814b44348a94fb06cc583471c7 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Mon, 21 Mar 2016 16:14:31 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14759
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/Section_commands.html         | 20 ++++++++++----------
 doc/Section_commands.txt          |  1 +
 doc/_sources/Section_commands.txt | 30 +++++++++++++++---------------
 3 files changed, 26 insertions(+), 25 deletions(-)

diff --git a/doc/Section_commands.html b/doc/Section_commands.html
index 88dfc9f353..5c17d595da 100644
--- a/doc/Section_commands.html
+++ b/doc/Section_commands.html
@@ -945,12 +945,12 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
 used 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="16%" />
 <col width="15%" />
 <col width="18%" />
 <col width="17%" />
 <col width="15%" />
 <col width="19%" />
-<col width="16%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td><a class="reference internal" href="compute_ackland_atom.html"><em>ackland/atom</em></a></td>
@@ -968,39 +968,39 @@ used if <a class="reference internal" href="Section_start.html#start-3"><span>LA
 <td><a class="reference internal" href="compute_meso_t_atom.html"><em>meso/t/atom</em></a></td>
 </tr>
 <tr class="row-odd"><td><a class="reference internal" href="compute_tally.html"><em>pe/tally</em></a></td>
+<td><a class="reference internal" href="compute_tally.html"><em>pe/mol/tally</em></a></td>
 <td><a class="reference internal" href="compute_saed.html"><em>saed</em></a></td>
 <td><a class="reference internal" href="compute_smd_contact_radius.html"><em>smd/contact/radius</em></a></td>
 <td><a class="reference internal" href="compute_smd_damage.html"><em>smd/damage</em></a></td>
 <td><a class="reference internal" href="compute_smd_hourglass_error.html"><em>smd/hourglass/error</em></a></td>
-<td><a class="reference internal" href="compute_smd_internal_energy.html"><em>smd/internal/energy</em></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="compute_smd_plastic_strain.html"><em>smd/plastic/strain</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="compute_smd_internal_energy.html"><em>smd/internal/energy</em></a></td>
+<td><a class="reference internal" href="compute_smd_plastic_strain.html"><em>smd/plastic/strain</em></a></td>
 <td><a class="reference internal" href="compute_smd_plastic_strain_rate.html"><em>smd/plastic/strain/rate</em></a></td>
 <td><a class="reference internal" href="compute_smd_rho.html"><em>smd/rho</em></a></td>
 <td><a class="reference internal" href="compute_smd_tlsph_defgrad.html"><em>smd/tlsph/defgrad</em></a></td>
 <td><a class="reference internal" href="compute_smd_tlsph_dt.html"><em>smd/tlsph/dt</em></a></td>
-<td><a class="reference internal" href="compute_smd_tlsph_num_neighs.html"><em>smd/tlsph/num/neighs</em></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="compute_smd_tlsph_shape.html"><em>smd/tlsph/shape</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="compute_smd_tlsph_num_neighs.html"><em>smd/tlsph/num/neighs</em></a></td>
+<td><a class="reference internal" href="compute_smd_tlsph_shape.html"><em>smd/tlsph/shape</em></a></td>
 <td><a class="reference internal" href="compute_smd_tlsph_strain.html"><em>smd/tlsph/strain</em></a></td>
 <td><a class="reference internal" href="compute_smd_tlsph_strain_rate.html"><em>smd/tlsph/strain/rate</em></a></td>
 <td><a class="reference internal" href="compute_smd_tlsph_stress.html"><em>smd/tlsph/stress</em></a></td>
 <td><a class="reference internal" href="compute_smd_triangle_mesh_vertices.html"><em>smd/triangle/mesh/vertices</em></a></td>
-<td><a class="reference internal" href="compute_smd_ulsph_num_neighs.html"><em>smd/ulsph/num/neighs</em></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="compute_smd_ulsph_strain.html"><em>smd/ulsph/strain</em></a></td>
+<tr class="row-even"><td><a class="reference internal" href="compute_smd_ulsph_num_neighs.html"><em>smd/ulsph/num/neighs</em></a></td>
+<td><a class="reference internal" href="compute_smd_ulsph_strain.html"><em>smd/ulsph/strain</em></a></td>
 <td><a class="reference internal" href="compute_smd_ulsph_strain_rate.html"><em>smd/ulsph/strain/rate</em></a></td>
 <td><a class="reference internal" href="compute_smd_ulsph_stress.html"><em>smd/ulsph/stress</em></a></td>
 <td><a class="reference internal" href="compute_smd_vol.html"><em>smd/vol</em></a></td>
 <td><a class="reference internal" href="compute_tally.html"><em>stress/tally</em></a></td>
-<td><a class="reference internal" href="compute_temp_drude.html"><em>temp/drude</em></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="compute_temp_eff.html"><em>temp/eff</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="compute_temp_drude.html"><em>temp/drude</em></a></td>
+<td><a class="reference internal" href="compute_temp_eff.html"><em>temp/eff</em></a></td>
 <td><a class="reference internal" href="compute_temp_deform_eff.html"><em>temp/deform/eff</em></a></td>
 <td><a class="reference internal" href="compute_temp_region_eff.html"><em>temp/region/eff</em></a></td>
 <td><a class="reference internal" href="compute_temp_rotate.html"><em>temp/rotate</em></a></td>
 <td><a class="reference internal" href="compute_xrd.html"><em>xrd</em></a></td>
-<td>&nbsp;</td>
 </tr>
 </tbody>
 </table>
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
index 79db9331bd..7952c3153a 100644
--- a/doc/Section_commands.txt
+++ b/doc/Section_commands.txt
@@ -757,6 +757,7 @@ package"_Section_start.html#start_3.
 "meso/rho/atom"_compute_meso_rho_atom.html,
 "meso/t/atom"_compute_meso_t_atom.html,
 "pe/tally"_compute_tally.html,
+"pe/mol/tally"_compute_tally.html,
 "saed"_compute_saed.html,
 "smd/contact/radius"_compute_smd_contact_radius.html,
 "smd/damage"_compute_smd_damage.html,
diff --git a/doc/_sources/Section_commands.txt b/doc/_sources/Section_commands.txt
index 2ecc580fae..73e4941691 100644
--- a/doc/_sources/Section_commands.txt
+++ b/doc/_sources/Section_commands.txt
@@ -553,21 +553,21 @@ KOKKOS, o = USER-OMP, t = OPT.
 These are additional compute styles in USER packages, which can be
 used if :ref:`LAMMPS is built with the appropriate package <start_3>`.
 
-+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------------------------+------------------------------------------------------------+
-| :doc:`ackland/atom <compute_ackland_atom>`             | :doc:`basal/atom <compute_basal_atom>`                           | :doc:`dpd <compute_dpd>`                                     | :doc:`dpd/atom <compute_dpd_atom>`                   | :doc:`fep <compute_fep>`                                               | :doc:`force/tally <compute_tally>`                         |
-+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------------------------+------------------------------------------------------------+
-| :doc:`heat/flux/tally <compute_tally>`                 | :doc:`ke/eff <compute_ke_eff>`                                   | :doc:`ke/atom/eff <compute_ke_atom_eff>`                     | :doc:`meso/e/atom <compute_meso_e_atom>`             | :doc:`meso/rho/atom <compute_meso_rho_atom>`                           | :doc:`meso/t/atom <compute_meso_t_atom>`                   |
-+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------------------------+------------------------------------------------------------+
-| :doc:`pe/tally <compute_tally>`                        | :doc:`saed <compute_saed>`                                       | :doc:`smd/contact/radius <compute_smd_contact_radius>`       | :doc:`smd/damage <compute_smd_damage>`               | :doc:`smd/hourglass/error <compute_smd_hourglass_error>`               | :doc:`smd/internal/energy <compute_smd_internal_energy>`   |
-+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------------------------+------------------------------------------------------------+
-| :doc:`smd/plastic/strain <compute_smd_plastic_strain>` | :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>` | :doc:`smd/rho <compute_smd_rho>`                             | :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>` | :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>`                             | :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>` |
-+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------------------------+------------------------------------------------------------+
-| :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>`       | :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>`               | :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>` | :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`   | :doc:`smd/triangle/mesh/vertices <compute_smd_triangle_mesh_vertices>` | :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` |
-+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------------------------+------------------------------------------------------------+
-| :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`     | :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`     | :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>`           | :doc:`smd/vol <compute_smd_vol>`                     | :doc:`stress/tally <compute_tally>`                                    | :doc:`temp/drude <compute_temp_drude>`                     |
-+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------------------------+------------------------------------------------------------+
-| :doc:`temp/eff <compute_temp_eff>`                     | :doc:`temp/deform/eff <compute_temp_deform_eff>`                 | :doc:`temp/region/eff <compute_temp_region_eff>`             | :doc:`temp/rotate <compute_temp_rotate>`             | :doc:`xrd <compute_xrd>`                                               |                                                            |
-+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------------------------+------------------------------------------------------------+
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------------------------+
+| :doc:`ackland/atom <compute_ackland_atom>`                 | :doc:`basal/atom <compute_basal_atom>`                 | :doc:`dpd <compute_dpd>`                                         | :doc:`dpd/atom <compute_dpd_atom>`                           | :doc:`fep <compute_fep>`                             | :doc:`force/tally <compute_tally>`                                     |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------------------------+
+| :doc:`heat/flux/tally <compute_tally>`                     | :doc:`ke/eff <compute_ke_eff>`                         | :doc:`ke/atom/eff <compute_ke_atom_eff>`                         | :doc:`meso/e/atom <compute_meso_e_atom>`                     | :doc:`meso/rho/atom <compute_meso_rho_atom>`         | :doc:`meso/t/atom <compute_meso_t_atom>`                               |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------------------------+
+| :doc:`pe/tally <compute_tally>`                            | :doc:`pe/mol/tally <compute_tally>`                    | :doc:`saed <compute_saed>`                                       | :doc:`smd/contact/radius <compute_smd_contact_radius>`       | :doc:`smd/damage <compute_smd_damage>`               | :doc:`smd/hourglass/error <compute_smd_hourglass_error>`               |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------------------------+
+| :doc:`smd/internal/energy <compute_smd_internal_energy>`   | :doc:`smd/plastic/strain <compute_smd_plastic_strain>` | :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>` | :doc:`smd/rho <compute_smd_rho>`                             | :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>` | :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>`                             |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------------------------+
+| :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>` | :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>`       | :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>`               | :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>` | :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`   | :doc:`smd/triangle/mesh/vertices <compute_smd_triangle_mesh_vertices>` |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------------------------+
+| :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` | :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`     | :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`     | :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>`           | :doc:`smd/vol <compute_smd_vol>`                     | :doc:`stress/tally <compute_tally>`                                    |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------------------------+
+| :doc:`temp/drude <compute_temp_drude>`                     | :doc:`temp/eff <compute_temp_eff>`                     | :doc:`temp/deform/eff <compute_temp_deform_eff>`                 | :doc:`temp/region/eff <compute_temp_region_eff>`             | :doc:`temp/rotate <compute_temp_rotate>`             | :doc:`xrd <compute_xrd>`                                               |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------------------------+
 
 
 ----------