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doc/Section_commands.txt
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@ -671,6 +671,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"angle/local"_compute_angle_local.html, "angle/local"_compute_angle_local.html,
"angmom/chunk"_compute_angmom_chunk.html, "angmom/chunk"_compute_angmom_chunk.html,
"bond"_compute_bond.html,
"body/local"_compute_body_local.html, "body/local"_compute_body_local.html,
"bond/local"_compute_bond_local.html, "bond/local"_compute_bond_local.html,
"centro/atom"_compute_centro_atom.html, "centro/atom"_compute_centro_atom.html,

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doc/Section_modify.html
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@ -1060,7 +1060,7 @@ then be accessed by variables) was discussed
<p>We encourage users to submit new features to <a class="reference external" href="http://lammps.sandia.gov/authors.html">the developers</a> that they add to <p>We encourage users to submit new features to <a class="reference external" href="http://lammps.sandia.gov/authors.html">the developers</a> that they add to
LAMMPS, especially if you think they will be of interest to other LAMMPS, especially if you think they will be of interest to other
users. The preferred way to do this is via GitHub. Once you have users. The preferred way to do this is via GitHub. Once you have
prepared the content described below, see <code class="xref doc docutils literal"><span class="pre">this</span> <span class="pre">tutorial</span></code> for instructions on how to submit prepared the content described below, see <a class="reference internal" href="tutorial_github.html"><em>this tutorial</em></a> for instructions on how to submit
your changes or new files.</p> your changes or new files.</p>
<p>If the new features/files are broadly useful we may add them as core <p>If the new features/files are broadly useful we may add them as core
files to LAMMPS or as part of a <a class="reference internal" href="Section_start.html#start-3"><span>standard package</span></a>. Else we will add them as a files to LAMMPS or as part of a <a class="reference internal" href="Section_start.html#start-3"><span>standard package</span></a>. Else we will add them as a

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doc/Section_modify.txt
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@ -626,7 +626,7 @@ developers"_http://lammps.sandia.gov/authors.html that they add to
LAMMPS, especially if you think they will be of interest to other LAMMPS, especially if you think they will be of interest to other
users. The preferred way to do this is via GitHub. Once you have users. The preferred way to do this is via GitHub. Once you have
prepared the content described below, see "this prepared the content described below, see "this
tutorial"_doc/tutorial_github.html for instructions on how to submit tutorial"_tutorial_github.html for instructions on how to submit
your changes or new files. your changes or new files.
If the new features/files are broadly useful we may add them as core If the new features/files are broadly useful we may add them as core

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doc/Section_packages.html
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@ -494,7 +494,7 @@ name links to a sub-section below with more details.</p>
<td>python</td> <td>python</td>
<td>lib/python</td> <td>lib/python</td>
</tr> </tr>
<tr class="row-even"><td><a class="reference internal" href="#reax"><span>REAX</span></a></td> <tr class="row-even"><td><a class="reference internal" href="Section_tools.html#reax"><span>REAX</span></a></td>
<td>ReaxFF potential</td> <td>ReaxFF potential</td>
<td>Aidan Thompson (Sandia)</td> <td>Aidan Thompson (Sandia)</td>
<td><a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a></td> <td><a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a></td>

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doc/_sources/Manual.txt
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@ -5,8 +5,8 @@
LAMMPS Documentation LAMMPS Documentation
==================== ====================
1 Mar 2016 version 10 Mar 2016 version
------------------ -------------------
Version info: Version info:
------------- -------------

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doc/_sources/Section_modify.txt
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@ -845,7 +845,7 @@ Submitting new features for inclusion in LAMMPS
We encourage users to submit new features to `the developers <http://lammps.sandia.gov/authors.html>`_ that they add to We encourage users to submit new features to `the developers <http://lammps.sandia.gov/authors.html>`_ that they add to
LAMMPS, especially if you think they will be of interest to other LAMMPS, especially if you think they will be of interest to other
users. The preferred way to do this is via GitHub. Once you have users. The preferred way to do this is via GitHub. Once you have
prepared the content described below, see :doc:`this tutorial <doc/tutorial_github>` for instructions on how to submit prepared the content described below, see :doc:`this tutorial <tutorial_github>` for instructions on how to submit
your changes or new files. your changes or new files.
If the new features/files are broadly useful we may add them as core If the new features/files are broadly useful we may add them as core

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doc/_sources/compute_pair.txt
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@ -83,7 +83,7 @@ Restrictions
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`compute pe <compute_pe>` :doc:`compute pe <compute_pe>`, :doc:`compute bond <compute_bond>`
Default Default
""""""" """""""

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<li>compute bond command</li>
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<div class="section" id="compute-bond-command">
<span id="index-0"></span><h1>compute bond command<a class="headerlink" href="#compute-bond-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID bond bstyle
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>bond = style name of this compute command</li>
<li>bstyle = style name of a bond style that calculates additional values</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 all bond harmonic
compute 2 all bond morse
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that extracts additional values calculated by a
bond style, sums them across processors, and makes them accessible for
output or further processing by other commands. The group specified
for this command is ignored.</p>
<p>The specified <em>bstyle</em> must be a bond style used in your simulation
either by itself or as a sub-style in a <a class="reference internal" href="bond_hybrid.html"><em>bond_style hybrid</em></a>
command.</p>
<p>This compute is useful when using <a class="reference internal" href="bond_hybrid.html"><em>bond_style hybrid</em></a>
if you want to know the portion of the total energy contributed by one
sub-style.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global scalar which is the contribution of
the named bond style to the bond energy <em>ebond</em>.</p>
<p>The scalar value calculated by this compute is &#8220;extensive&#8221; and will be
in energy <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_pe.html"><em>compute pe</em></a>, <a class="reference internal" href="compute_pair.html"><em>compute pair</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The default for <em>evalue</em> is <em>ebond</em>.</p>
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55
doc/compute_bond.txt Normal file
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@ -0,0 +1,55 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute bond command :h3
[Syntax:]
compute ID group-ID bond bstyle :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
[Examples:]
compute 1 all bond harmonic
compute 2 all bond morse :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.
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.
[Output info:]
This compute calculates a global scalar which is the contribution of
the named bond style to the bond energy {ebond}.
The scalar value calculated by this compute is "extensive" and will be
in energy "units"_units.html.
[Restrictions:] none
[Related commands:]
"compute pe"_compute_pe.html, "compute pair"_compute_pair.html
[Default:]
The default for {evalue} is {ebond}.

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doc/compute_pair.html
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@ -197,7 +197,7 @@ see the doc page for the pair style for details.</p>
</div> </div>
<div class="section" id="related-commands"> <div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2> <h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="compute_pe.html"><em>compute pe</em></a></p> <p><a class="reference internal" href="compute_pe.html"><em>compute pe</em></a>, <a class="reference internal" href="compute_bond.html"><em>compute bond</em></a></p>
</div> </div>
<div class="section" id="default"> <div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2> <h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>

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doc/compute_pair.txt
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@ -78,7 +78,7 @@ see the doc page for the pair style for details.
[Related commands:] [Related commands:]
"compute pe"_compute_pe.html "compute pe"_compute_pe.html, "compute bond"_compute_bond.html
[Default:] [Default:]

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doc/genindex.html
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@ -372,6 +372,10 @@
</dt> </dt>
<dt><a href="compute_bond.html#index-0">compute bond</a>
</dt>
<dt><a href="compute_bond_local.html#index-0">compute bond/local</a> <dt><a href="compute_bond_local.html#index-0">compute bond/local</a>
</dt> </dt>
@ -555,12 +559,12 @@
<dt><a href="compute_pe_atom.html#index-0">compute pe/atom</a> <dt><a href="compute_pe_atom.html#index-0">compute pe/atom</a>
</dt> </dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="compute_plasticity_atom.html#index-0">compute plasticity/atom</a> <dt><a href="compute_plasticity_atom.html#index-0">compute plasticity/atom</a>
</dt> </dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="compute_pressure.html#index-0">compute pressure</a> <dt><a href="compute_pressure.html#index-0">compute pressure</a>
</dt> </dt>

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