Commit 2fb666dc authored by Steve Plimpton's avatar Steve Plimpton
Browse files

Merge branch 'doc' into integration

parents 717e719b 2f298951

doc/html/Manual.html

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@@ -72,6 +72,7 @@ 
        

          

          

              <p class="caption"><span class="caption-text">User Documentation</span></p>

<ul>

<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>

<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
@@ -87,6 +88,18 @@ 
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>

<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>

</ul>

<p class="caption"><span class="caption-text">Index</span></p>

<ul>

<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>

<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>

<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>

<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>

<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>

<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>

<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>

<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>

<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

</ul>
@@ -181,7 +194,10 @@ all at Sandia. The <strong>LAMMPS home page</strong> at 
<a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a> has more information

about the code and its uses. Interaction with external LAMMPS developers,

bug reports and feature requests are mainly coordinated through the

<a class="reference external" href="https://github.com/lammps/lammps">LAMMPS project on GitHub.</a></p>

<a class="reference external" href="https://github.com/lammps/lammps">LAMMPS project on GitHub.</a>

The lammps.org domain, currently hosting <a class="reference external" href="https://ci.lammps.org/job/lammps/">public continuous integration testing</a> and <a class="reference external" href="http://rpm.lammps.org">precompiled Linux RPM and Windows installer packages</a> is located

at Temple University and managed by Richard Berger,

richard.berger at temple.edu.</p>

<hr class="docutils" />

<p>The LAMMPS documentation is organized into the following sections.  If

you find errors or omissions in this manual or have suggestions for
@@ -191,7 +207,8 @@ we can improve the LAMMPS documentation.</p> 
it gives quick access to documentation for all LAMMPS commands.</p>

<p><a class="reference external" href="Manual.pdf">PDF file</a> of the entire manual, generated by

<a class="reference external" href="http://freecode.com/projects/htmldoc">htmldoc</a></p>

<div class="toctree-wrapper compound">

<div class="toctree-wrapper compound" id="userdoc">

<p class="caption"><span class="caption-text">User Documentation</span></p>

<ul>

<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a><ul>

<li class="toctree-l2"><a class="reference internal" href="Section_intro.html#what-is-lammps">1.1. What is LAMMPS</a></li>
@@ -355,6 +372,8 @@ it gives quick access to documentation for all LAMMPS commands.</p> 
</li>

</ul>

</div>

<div class="toctree-wrapper compound" id="index">

</div>

</div>

</div>

<div class="section" id="indices-and-tables">

doc/html/Section_accelerate.html

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@@ -33,7 +33,7 @@ 


  

    <link rel="top" title="LAMMPS documentation" href="index.html"/>

        <link rel="next" title="6. How-to discussions" href="Section_howto.html"/>

        <link rel="next" title="5.3.1. GPU package" href="accelerate_gpu.html"/>

        <link rel="prev" title="4. Packages" href="Section_packages.html"/>
@@ -73,6 +73,7 @@ 
        

          

          

              <p class="caption"><span class="caption-text">User Documentation</span></p>

<ul class="current">

<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>

<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
@@ -81,7 +82,14 @@ 
<li class="toctree-l1 current"><a class="current reference internal" href="#">5. Accelerating LAMMPS performance</a><ul>

<li class="toctree-l2"><a class="reference internal" href="#measuring-performance">5.1. Measuring performance</a></li>

<li class="toctree-l2"><a class="reference internal" href="#general-strategies">5.2. General strategies</a></li>

<li class="toctree-l2"><a class="reference internal" href="#packages-with-optimized-styles">5.3. Packages with optimized styles</a></li>

<li class="toctree-l2"><a class="reference internal" href="#packages-with-optimized-styles">5.3. Packages with optimized styles</a><ul>

<li class="toctree-l3"><a class="reference internal" href="accelerate_gpu.html">5.3.1. GPU package</a></li>

<li class="toctree-l3"><a class="reference internal" href="accelerate_intel.html">5.3.2. USER-INTEL package</a></li>

<li class="toctree-l3"><a class="reference internal" href="accelerate_kokkos.html">5.3.3. KOKKOS package</a></li>

<li class="toctree-l3"><a class="reference internal" href="accelerate_omp.html">5.3.4. USER-OMP package</a></li>

<li class="toctree-l3"><a class="reference internal" href="accelerate_opt.html">5.3.5. OPT package</a></li>

</ul>

</li>

<li class="toctree-l2"><a class="reference internal" href="#comparison-of-various-accelerator-packages">5.4. Comparison of various accelerator packages</a></li>

</ul>

</li>
@@ -94,6 +102,18 @@ 
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>

<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>

</ul>

<p class="caption"><span class="caption-text">Index</span></p>

<ul>

<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>

<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>

<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>

<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>

<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>

<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>

<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>

<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>

<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

</ul>
@@ -130,7 +150,7 @@ 
  

    <div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">

      

        <a href="Section_howto.html" class="btn btn-neutral float-right" title="6. How-to discussions" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>

        <a href="accelerate_gpu.html" class="btn btn-neutral float-right" title="5.3.1. GPU package" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>

      

      

        <a href="Section_packages.html" class="btn btn-neutral" title="4. Packages" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
@@ -276,27 +296,29 @@ overview of packages is give in <a class="reference internal" href="Section_pack 
currently in LAMMPS, either as standard or user packages:</p>

<table border="1" class="docutils">

<colgroup>

<col width="44%" />

<col width="56%" />

<col width="46%" />

<col width="54%" />

</colgroup>

<tbody valign="top">

<tr class="row-odd"><td><a class="reference internal" href="accelerate_gpu.html"><span class="doc">GPU</span></a></td>

<tr class="row-odd"><td><a class="reference internal" href="accelerate_gpu.html"><span class="doc">GPU Package</span></a></td>

<td>for NVIDIA GPUs as well as OpenCL support</td>

</tr>

<tr class="row-even"><td><a class="reference internal" href="accelerate_intel.html"><span class="doc">USER-INTEL</span></a></td>

<tr class="row-even"><td><a class="reference internal" href="accelerate_intel.html"><span class="doc">USER-INTEL Package</span></a></td>

<td>for Intel CPUs and Intel Xeon Phi</td>

</tr>

<tr class="row-odd"><td><a class="reference internal" href="accelerate_kokkos.html"><span class="doc">KOKKOS</span></a></td>

<td>for GPUs, Intel Xeon Phi, and OpenMP threading</td>

<tr class="row-odd"><td><a class="reference internal" href="accelerate_kokkos.html"><span class="doc">KOKKOS Package</span></a></td>

<td>for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading</td>

</tr>

<tr class="row-even"><td><a class="reference internal" href="accelerate_omp.html"><span class="doc">USER-OMP</span></a></td>

<td>for OpenMP threading</td>

<tr class="row-even"><td><a class="reference internal" href="accelerate_omp.html"><span class="doc">USER-OMP Package</span></a></td>

<td>for OpenMP threading and generic CPU optimizations</td>

</tr>

<tr class="row-odd"><td><a class="reference internal" href="accelerate_opt.html"><span class="doc">OPT</span></a></td>

<tr class="row-odd"><td><a class="reference internal" href="accelerate_opt.html"><span class="doc">OPT Package</span></a></td>

<td>generic CPU optimizations</td>

</tr>

</tbody>

</table>

<div class="toctree-wrapper compound">

</div>

<p>Inverting this list, LAMMPS currently has acceleration support for

three kinds of hardware, via the listed packages:</p>

<table border="1" class="docutils">
@@ -336,7 +358,7 @@ Lennard-Jones <a class="reference internal" href="pair_lj.html"><span class="doc 
<li><a class="reference internal" href="pair_lj.html"><span class="doc">pair_style lj/cut/opt</span></a></li>

</ul>

<p>To see what accelerate styles are currently available, see

<a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section_commands 5</span></a> of the manual.  The

<a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section 3.5</span></a> of the manual.  The

doc pages for individual commands (e.g. <a class="reference internal" href="pair_lj.html"><span class="doc">pair lj/cut</span></a> or

<a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>) also list any accelerated variants available

for that style.</p>
@@ -524,7 +546,7 @@ exclusion lists, hybrid pair styles, or a triclinic simulation box.</li> 
  

    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">

      

        <a href="Section_howto.html" class="btn btn-neutral float-right" title="6. How-to discussions" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>

        <a href="accelerate_gpu.html" class="btn btn-neutral float-right" title="5.3.1. GPU package" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>

      

      

        <a href="Section_packages.html" class="btn btn-neutral" title="4. Packages" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>

doc/html/Section_commands.html

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@@ -73,6 +73,7 @@ 
        

          

          

              <p class="caption"><span class="caption-text">User Documentation</span></p>

<ul class="current">

<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>

<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
@@ -103,6 +104,18 @@ 
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>

<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>

</ul>

<p class="caption"><span class="caption-text">Index</span></p>

<ul>

<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>

<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>

<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>

<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>

<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>

<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>

<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>

<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>

<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

</ul>
@@ -318,7 +331,7 @@ allowed, but that should be sufficient for most use cases.</p> 
<p>This section describes the structure of a typical LAMMPS input script.

The &#8220;examples&#8221; directory in the LAMMPS distribution contains many

sample input scripts; the corresponding problems are discussed in

<a class="reference internal" href="Section_example.html"><span class="doc">Section_example</span></a>, and animated on the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.</p>

<a class="reference internal" href="Section_example.html"><span class="doc">Section 7</span></a>, and animated on the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.</p>

<p>A LAMMPS input script typically has 4 parts:</p>

<ol class="arabic simple">

<li>Initialization</li>
@@ -778,12 +791,12 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p> 
<a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">LAMMPS is built with the appropriate package</span></a>.</p>

<table border="1" class="docutils">

<colgroup>

<col width="14%" />

<col width="22%" />

<col width="15%" />

<col width="15%" />

<col width="15%" />

<col width="20%" />

<col width="16%" />

<col width="16%" />

<col width="16%" />

<col width="16%" />

<col width="22%" />

</colgroup>

<tbody valign="top">

<tr class="row-odd"><td><a class="reference internal" href="fix_adapt_fep.html"><span class="doc">adapt/fep</span></a></td>
@@ -843,18 +856,11 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p> 
<td><a class="reference internal" href="fix_smd_move_triangulated_surface.html"><span class="doc">smd/move/triangulated/surface</span></a></td>

</tr>

<tr class="row-odd"><td><a class="reference internal" href="fix_smd_setvel.html"><span class="doc">smd/setvel</span></a></td>

<td><a class="reference internal" href="fix_smd_tlsph_reference_configuration.html"><span class="doc">smd/tlsph/reference/configuration</span></a></td>

<td><a class="reference internal" href="fix_smd_wall_surface.html"><span class="doc">smd/wall/surface</span></a></td>

<td><a class="reference internal" href="fix_temp_rescale_eff.html"><span class="doc">temp/rescale/eff</span></a></td>

<td><a class="reference internal" href="fix_ti_rs.html"><span class="doc">ti/rs</span></a></td>

<td><a class="reference internal" href="fix_ti_spring.html"><span class="doc">ti/spring</span></a></td>

</tr>

<tr class="row-even"><td><a class="reference internal" href="fix_ttm.html"><span class="doc">ttm/mod</span></a></td>

<td>&nbsp;</td>

<td>&nbsp;</td>

<td>&nbsp;</td>

<td>&nbsp;</td>

<td>&nbsp;</td>

<td><a class="reference internal" href="fix_ttm.html"><span class="doc">ttm/mod</span></a></td>

</tr>

</tbody>

</table>

doc/html/Section_errors.html

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@@ -73,6 +73,7 @@ 
        

          

          

              <p class="caption"><span class="caption-text">User Documentation</span></p>

<ul class="current">

<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>

<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
@@ -95,6 +96,18 @@ 
</li>

<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>

</ul>

<p class="caption"><span class="caption-text">Index</span></p>

<ul>

<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>

<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>

<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>

<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>

<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>

<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>

<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>

<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>

<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

</ul>
@@ -6491,7 +6504,7 @@ per timestep.</dd> 
<dd>If there are other fixes that act immediately after the intitial stage

of time integration within a timestep (i.e. after atoms move), then

the command that sets up the dynamic group should appear after those

fixes.  This will insure that dynamic group assignements are made

fixes.  This will insure that dynamic group assignments are made

after all atoms have moved.</dd>

<dt><em>One or more respa levels compute no forces</em></dt>

<dd>This is computationally inefficient.</dd>

doc/html/Section_example.html

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@@ -73,6 +73,7 @@ 
        

          

          

              <p class="caption"><span class="caption-text">User Documentation</span></p>

<ul class="current">

<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>

<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
@@ -92,6 +93,18 @@ 
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>

<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>

</ul>

<p class="caption"><span class="caption-text">Index</span></p>

<ul>

<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>

<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>

<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>

<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>

<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>

<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>

<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>

<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>

<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>

</ul>

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