git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14788 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_commands.html

@@ -847,95 +847,102 @@ 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="16%" />
+<col width="16%" />
+<col width="16%" />
 <col width="17%" />
-<col width="16%" />
 <col width="19%" />
 <col width="16%" />
-<col width="15%" />
-<col width="16%" />
 </colgroup>
 <tbody valign="top">
-<tr class="row-odd"><td><a class="reference internal" href="compute_angle_local.html"><em>angle/local</em></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="compute_angle.html"><em>angle</em></a></td>
+<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>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="compute_chunk_atom.html"><em>chunk/atom</em></a></td>
+<tr class="row-even"><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>
 <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>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="compute_coord_atom.html"><em>coord/atom</em></a></td>
+<tr class="row-odd"><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>
 <td><a class="reference internal" href="compute_damage_atom.html"><em>damage/atom</em></a></td>
+<td><a class="reference internal" href="compute_dihedral.html"><em>dihedral</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>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="compute_erotate_rigid.html"><em>erotate/rigid</em></a></td>
+<tr class="row-even"><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>
 <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>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="compute_gyration_chunk.html"><em>gyration/chunk</em></a></td>
+<tr class="row-odd"><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>
 <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_improper.html"><em>improper</em></a></td>
+</tr>
+<tr class="row-even"><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>
-</tr>
+<td><a class="reference internal" href="compute_ke_atom.html"><em>ke/atom</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>
+</tr>
+<tr class="row-odd"><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>
-</tr>
+<td><a class="reference internal" href="compute_orientorder_atom.html"><em>orientorder/atom</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>
+</tr>
+<tr class="row-even"><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>
-</tr>
+<td><a class="reference internal" href="compute_pressure.html"><em>pressure (c)</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>
+</tr>
+<tr class="row-odd"><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>
-</tr>
+<td><a class="reference internal" href="compute_reduce.html"><em>reduce/region</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>
+</tr>
+<tr class="row-even"><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>
-</tr>
+<td><a class="reference internal" href="compute_temp.html"><em>temp (ck)</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>
+</tr>
+<tr class="row-odd"><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>
-</tr>
+<td><a class="reference internal" href="compute_temp_partial.html"><em>temp/partial (c)</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>
+</tr>
+<tr class="row-even"><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>
-</tr>
+<td><a class="reference internal" href="compute_torque_chunk.html"><em>torque/chunk</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>
+</tr>
+<tr class="row-odd"><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>
 <td>&nbsp;</td>
 <td>&nbsp;</td>
 </tr>

doc/Section_commands.txt

@@ -669,6 +669,7 @@ package"_Section_accelerate.html.  This is indicated by additional
 letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
 KOKKOS, o = USER-OMP, t = OPT.
 
+"angle"_compute_angle.html,
 "angle/local"_compute_angle_local.html,
 "angmom/chunk"_compute_angmom_chunk.html,
 "body/local"_compute_body_local.html,
@@ -683,6 +684,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "contact/atom"_compute_contact_atom.html,
 "coord/atom"_compute_coord_atom.html,
 "damage/atom"_compute_damage_atom.html,
+"dihedral"_compute_dihedral.html,
 "dihedral/local"_compute_dihedral_local.html,
 "dilatation/atom"_compute_dilatation_atom.html,
 "displace/atom"_compute_displace_atom.html,
@@ -696,6 +698,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "gyration/chunk"_compute_gyration_chunk.html,
 "heat/flux"_compute_heat_flux.html,
 "hexorder/atom"_compute_hexorder_atom.html,
+"improper"_compute_improper.html,
 "improper/local"_compute_improper_local.html,
 "inertia/chunk"_compute_inertia_chunk.html,
 "ke"_compute_ke.html,

doc/_sources/Manual.txt

@@ -5,7 +5,7 @@
 LAMMPS Documentation
 ====================
 
-22 Mar 2016 version
+23 Mar 2016 version
 -------------------
 
 Version info:

doc/_sources/Section_commands.txt

@@ -524,31 +524,33 @@ 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 <compute_bond>`                       | :doc:`bond/local <compute_bond_local>`       | :doc:`centro/atom <compute_centro_atom>`         |
+| :doc:`angle <compute_angle>`                   | :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:`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:`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:`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:`contact/atom <compute_contact_atom>`     | :doc:`coord/atom <compute_coord_atom>`           | :doc:`damage/atom <compute_damage_atom>`         | :doc:`dihedral <compute_dihedral>`                 | :doc:`dihedral/local <compute_dihedral_local>`           | :doc:`dilatation/atom <compute_dilatation_atom>` |
-+----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
++------------------------------------------------+--------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+
-| :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:`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:`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:`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 <compute_improper>`               |
-+----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
++------------------------------------------------+--------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+
-| :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:`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:`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:`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:`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:`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:`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:`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:`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:`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/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:`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:`torque/chunk <compute_torque_chunk>`         | :doc:`vacf <compute_vacf>`                     | :doc:`vcm/chunk <compute_vcm_chunk>`                     | :doc:`voronoi/atom <compute_voronoi_atom>`       |                                              |                                                  |
+| :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>`.

doc/_sources/compute_bond.txt

@@ -8,43 +8,40 @@ Syntax
 
 .. parsed-literal::
 
-   compute ID group-ID bond bstyle
+   compute ID group-ID bond
 
 * 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 1 all bond
-   compute 2 all bond morse
 
 Description
 """""""""""
 
-Define a computation that extracts additional values calculated by a
+Define a computation that extracts the bond energy calculated by each
-bond style, sums them across processors, and makes them accessible for
+of the bond sub-styles used in the :doc:`bond_style hybrid <bond_hybrid>` command.  These values are made accessible
-output or further processing by other commands.  The group specified
+for output or further processing by other commands.  The group
-for this command is ignored.
+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.
+or more of the hybrid sub-styles.
 
 **Output info:**
 
-This compute calculates a global scalar which is the contribution of
+This compute calculates a global vector of length N where N is the
-the named bond style to the bond energy *ebond*.
+number of sub_styles defined by the :doc:`bond_style hybrid <bond_style>` command, which can be accessed by indices 1-N.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See :ref:`this section <howto_15>` for an overview of LAMMPS output
+options.
 
-The scalar value calculated by this compute is "extensive" and will be
+The vector values are "extensive" and will be in energy
-in energy :doc:`units <units>`.
+:doc:`units <units>`.
 
 Restrictions
 """"""""""""
@@ -55,10 +52,7 @@ Related commands
 
 :doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>`
 
-Default
+**Default:** none
-"""""""
-
-The default for *evalue* is *ebond*.
 
 
 .. _lws: http://lammps.sandia.gov

doc/_sources/compute_pair.txt

@@ -28,9 +28,8 @@ Description
 """""""""""
 
 Define a computation that extracts additional values calculated by a
-pair style, sums them across processors, and makes them accessible for
+pair style, and makes them accessible for output or further processing
-output or further processing by other commands.  The group specified
+by other commands.  The group specified for this command is ignored.
-for this command is ignored.
 
 The specified *pstyle* must be a pair style used in your simulation
 either by itself or as a sub-style in a :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` command.
@@ -73,8 +72,8 @@ The scalar and vector values calculated by this compute are
 "extensive".
 
 The scalar value will be in energy :doc:`units <units>`.  The vector
-values will typically also be in energy :doc:`units <units>`, but
+values will typically also be in energy :doc:`units <units>`, but see
-see the doc page for the pair style for details.
+the doc page for the pair style for details.
 
 Restrictions
 """"""""""""

doc/_sources/compute_temp.txt

@@ -106,7 +106,7 @@ vector values from a compute as input.  See :ref:`this section <howto_15>` for a
 options.
 
 The scalar value calculated by this compute is "intensive".  The
-vector are "extensive".
+vector values are "extensive".
 
 The scalar value will be in temperature :doc:`units <units>`.  The
 vector values will be in energy :doc:`units <units>`.

doc/_sources/pair_soft.txt

@@ -23,13 +23,13 @@ Examples
 
 .. parsed-literal::
 
-   pair_style soft 2.5
+   pair_style soft 1.0
    pair_coeff * * 10.0
    pair_coeff 1 1 10.0 3.0
 
 .. parsed-literal::
 
-   pair_style soft 2.5
+   pair_style soft 1.0
    pair_coeff * * 0.0
    variable prefactor equal ramp(0,30)
    fix 1 all adapt 1 pair soft a * * v_prefactor

doc/compute_bond.html

@@ -128,39 +128,37 @@
 <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
+<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID bond
 </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
+<div class="highlight-python"><div class="highlight"><pre>compute 1 all bond
-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
+<p>Define a computation that extracts the bond energy calculated by each
-bond style, sums them across processors, and makes them accessible for
+of the bond sub-styles used in the <a class="reference internal" href="bond_hybrid.html"><em>bond_style hybrid</em></a> command.  These values are made accessible
-output or further processing by other commands.  The group specified
+for output or further processing by other commands.  The group
-for this command is ignored.</p>
+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>
+or more of the hybrid sub-styles.</p>
 <p><strong>Output info:</strong></p>
-<p>This compute calculates a global scalar which is the contribution of
+<p>This compute calculates a global vector of length N where N is the
-the named bond style to the bond energy <em>ebond</em>.</p>
+number of sub_styles defined by the <a class="reference internal" href="bond_style.html"><em>bond_style hybrid</em></a> command, which can be accessed by indices 1-N.
-<p>The scalar value calculated by this compute is &#8220;extensive&#8221; and will be
+These values can be used by any command that uses global scalar or
-in energy <a class="reference internal" href="units.html"><em>units</em></a>.</p>
+vector values from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a> for an overview of LAMMPS output
+options.</p>
+<p>The vector values are &#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>
@@ -170,10 +168,7 @@ in energy <a class="reference internal" href="units.html"><em>units</em></a>.</p
 <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>
+<p><strong>Default:</strong> none</p>
-<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>
 

doc/compute_bond.txt

@@ -10,39 +10,39 @@ compute bond command :h3
 
 [Syntax:]
 
-compute ID group-ID bond bstyle :pre
+compute ID group-ID bond :pre
 
 ID, group-ID are documented in "compute"_compute.html command
-bond = style name of this compute command
+bond = style name of this compute command :ul
-bstyle = style name of a bond style that calculates additional values :ul
 
 [Examples:]
 
-compute 1 all bond harmonic
+compute 1 all bond :pre
-compute 2 all bond morse :pre
 
 [Description:]
 
-Define a computation that extracts additional values calculated by a
+Define a computation that extracts the bond energy calculated by each
-bond style, sums them across processors, and makes them accessible for
+of the bond sub-styles used in the "bond_style
-output or further processing by other commands.  The group specified
+hybrid"_bond_hybrid.html command.  These values are made accessible
-for this command is ignored.
+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 "bond_style hybrid"_bond_hybrid.html
-command.
 
 This compute is useful when using "bond_style hybrid"_bond_hybrid.html
 if you want to know the portion of the total energy contributed by one
-sub-style.
+or more of the hybrid sub-styles.
 
 [Output info:]
 
-This compute calculates a global scalar which is the contribution of
+This compute calculates a global vector of length N where N is the
-the named bond style to the bond energy {ebond}.
+number of sub_styles defined by the "bond_style
+hybrid"_bond_style.html command, which can be accessed by indices 1-N.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See "this
+section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+options.
 
-The scalar value calculated by this compute is "extensive" and will be
+The vector values are "extensive" and will be in energy
-in energy "units"_units.html.
+"units"_units.html.
 
 [Restrictions:] none
 
@@ -50,6 +50,4 @@ in energy "units"_units.html.
 
 "compute pe"_compute_pe.html, "compute pair"_compute_pair.html
 
-[Default:]
+[Default:] none
-
-The default for {evalue} is {ebond}.

doc/compute_pair.html

@@ -149,9 +149,8 @@ compute 1 all pair reax
 <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
-pair style, sums them across processors, and makes them accessible for
+pair style, and makes them accessible for output or further processing
-output or further processing by other commands.  The group specified
+by other commands.  The group specified for this command is ignored.</p>
-for this command is ignored.</p>
 <p>The specified <em>pstyle</em> must be a pair style used in your simulation
 either by itself or as a sub-style in a <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid or hybrid/overlay</em></a> command.</p>
 <p>The <em>evalue</em> setting is optional; it may be left off the command.  All
@@ -187,8 +186,8 @@ options.</p>
 <p>The scalar and vector values calculated by this compute are
 &#8220;extensive&#8221;.</p>
 <p>The scalar value will be in energy <a class="reference internal" href="units.html"><em>units</em></a>.  The vector
-values will typically also be in energy <a class="reference internal" href="units.html"><em>units</em></a>, but
+values will typically also be in energy <a class="reference internal" href="units.html"><em>units</em></a>, but see
-see the doc page for the pair style for details.</p>
+the doc page for the pair style for details.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>

doc/compute_pair.txt

@@ -26,9 +26,8 @@ compute 1 all pair reax :pre
 [Description:]
 
 Define a computation that extracts additional values calculated by a
-pair style, sums them across processors, and makes them accessible for
+pair style, and makes them accessible for output or further processing
-output or further processing by other commands.  The group specified
+by other commands.  The group specified for this command is ignored.
-for this command is ignored.
 
 The specified {pstyle} must be a pair style used in your simulation
 either by itself or as a sub-style in a "pair_style hybrid or
@@ -71,8 +70,8 @@ The scalar and vector values calculated by this compute are
 "extensive".
 
 The scalar value will be in energy "units"_units.html.  The vector
-values will typically also be in energy "units"_units.html, but
+values will typically also be in energy "units"_units.html, but see
-see the doc page for the pair style for details.
+the doc page for the pair style for details.
 
 [Restrictions:] none
 

doc/compute_temp.html

@@ -206,7 +206,7 @@ These values can be used by any command that uses global scalar or
 vector values from a compute as input.  See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a> for an overview of LAMMPS output
 options.</p>
 <p>The scalar value calculated by this compute is &#8220;intensive&#8221;.  The
-vector are &#8220;extensive&#8221;.</p>
+vector values are &#8220;extensive&#8221;.</p>
 <p>The scalar value will be in temperature <a class="reference internal" href="units.html"><em>units</em></a>.  The
 vector values will be in energy <a class="reference internal" href="units.html"><em>units</em></a>.</p>
 </div>

doc/compute_temp.txt

@@ -98,7 +98,7 @@ section"_Section_howto.html#howto_15 for an overview of LAMMPS output
 options.
 
 The scalar value calculated by this compute is "intensive".  The
-vector are "extensive".
+vector values are "extensive".
 
 The scalar value will be in temperature "units"_units.html.  The
 vector values will be in energy "units"_units.html.

doc/genindex.html

@@ -356,6 +356,10 @@
   </dt>
 
       
+  <dt><a href="compute_angle.html#index-0">compute angle</a>
+  </dt>
+
+      
   <dt><a href="compute_angle_local.html#index-0">compute angle/local</a>
   </dt>
 
@@ -416,6 +420,10 @@
   </dt>
 
       
+  <dt><a href="compute_dihedral.html#index-0">compute dihedral</a>
+  </dt>
+
+      
   <dt><a href="compute_dihedral_local.html#index-0">compute dihedral/local</a>
   </dt>
 
@@ -484,6 +492,10 @@
   </dt>
 
       
+  <dt><a href="compute_improper.html#index-0">compute improper</a>
+  </dt>
+
+      
   <dt><a href="compute_improper_local.html#index-0">compute improper/local</a>
   </dt>
 
@@ -555,12 +567,12 @@
   <dt><a href="compute_pe.html#index-0">compute pe</a>
   </dt>
 
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
       
   <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>

doc/pair_soft.html

@@ -143,12 +143,12 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
-<div class="highlight-python"><div class="highlight"><pre>pair_style soft 2.5
+<div class="highlight-python"><div class="highlight"><pre>pair_style soft 1.0
 pair_coeff * * 10.0
 pair_coeff 1 1 10.0 3.0
 </pre></div>
 </div>
-<div class="highlight-python"><div class="highlight"><pre>pair_style soft 2.5
+<div class="highlight-python"><div class="highlight"><pre>pair_style soft 1.0
 pair_coeff * * 0.0
 variable prefactor equal ramp(0,30)
 fix 1 all adapt 1 pair soft a * * v_prefactor

doc/pair_soft.txt

@@ -18,11 +18,11 @@ cutoff = global cutoff for soft interactions (distance units) :ul
 
 [Examples:]
 
-pair_style soft 2.5
+pair_style soft 1.0
 pair_coeff * * 10.0
 pair_coeff 1 1 10.0 3.0 :pre
 
-pair_style soft 2.5
+pair_style soft 1.0
 pair_coeff * * 0.0
 variable prefactor equal ramp(0,30)
 fix 1 all adapt 1 pair soft a * * v_prefactor :pre