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79
doc/Section_commands.html
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@ -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>
<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_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>
<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_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>
<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_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>
<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_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>
<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.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>
<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_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>
<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_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>

3
doc/Section_commands.txt
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@ -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,

2
doc/_sources/Manual.txt
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@ -5,7 +5,7 @@
LAMMPS Documentation
====================
22 Mar 2016 version
23 Mar 2016 version
-------------------
Version info:

52
doc/_sources/Section_commands.txt
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@ -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:`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 <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:`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 <compute_dihedral>` | :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 <compute_improper>` |
+------------------------------------------------+--------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+
| :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>`.

36
doc/_sources/compute_bond.txt
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@ -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 2 all bond morse
compute 1 all bond
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.
Define a computation that extracts the bond energy calculated by each
of the bond sub-styles used in the :doc:`bond_style hybrid <bond_hybrid>` command. These values are made accessible
for output or further processing by other commands. The group
specified for this command is ignored.
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
the named bond style to the bond energy *ebond*.
This compute calculates a global vector of length N where N is the
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
in energy :doc:`units <units>`.
The vector values are "extensive" and will be in energy
:doc:`units <units>`.
Restrictions
""""""""""""
@ -55,10 +52,7 @@ Related commands
:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>`
Default
"""""""
The default for *evalue* is *ebond*.
**Default:** none
.. _lws: http://lammps.sandia.gov

9
doc/_sources/compute_pair.txt
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@ -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
output or further processing by other commands. The group specified
for this command is ignored.
pair style, and makes them accessible for output or further processing
by other commands. The group specified 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
see the doc page for the pair style for details.
values will typically also be in energy :doc:`units <units>`, but see
the doc page for the pair style for details.
Restrictions
""""""""""""

2
doc/_sources/compute_temp.txt
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@ -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>`.

4
doc/_sources/pair_soft.txt
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@ -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

35
doc/compute_bond.html
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@ -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
compute 2 all bond morse
<div class="highlight-python"><div class="highlight"><pre>compute 1 all bond
</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>Define a computation that extracts the bond energy calculated by each
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
for output or further processing by other commands. The group
specified for this command is ignored.</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
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>
<p>This compute calculates a global vector of length N where N is the
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.
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 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>
<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>
<p><strong>Default:</strong> none</p>
</div>
</div>

40
doc/compute_bond.txt
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@ -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
bstyle = style name of a bond style that calculates additional values :ul
bond = style name of this compute command :ul
[Examples:]
compute 1 all bond harmonic
compute 2 all bond morse :pre
compute 1 all bond :pre
[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 "bond_style hybrid"_bond_hybrid.html
command.
Define a computation that extracts the bond energy calculated by each
of the bond sub-styles used in the "bond_style
hybrid"_bond_hybrid.html command. These values are made accessible
for output or further processing by other commands. The group
specified for this command is ignored.
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
the named bond style to the bond energy {ebond}.
This compute calculates a global vector of length N where N is the
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
in energy "units"_units.html.
The vector values are "extensive" and will be in energy
"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:]
The default for {evalue} is {ebond}.
[Default:] none

9
doc/compute_pair.html
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@ -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
output or further processing by other commands. The group specified
for this command is ignored.</p>
pair style, 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>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
see the doc page for the pair style for details.</p>
values will typically also be in energy <a class="reference internal" href="units.html"><em>units</em></a>, but see
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>

9
doc/compute_pair.txt
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@ -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
output or further processing by other commands. The group specified
for this command is ignored.
pair style, and makes them accessible for output or further processing
by other commands. The group specified 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
see the doc page for the pair style for details.
values will typically also be in energy "units"_units.html, but see
the doc page for the pair style for details.
[Restrictions:] none

2
doc/compute_temp.html
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@ -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>

2
doc/compute_temp.txt
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@ -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.

16
doc/genindex.html
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@ -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>

4
doc/pair_soft.html
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@ -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

4
doc/pair_soft.txt
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@ -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

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