Commit 7025a3f5 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer Committed by GitHub
Browse files

Merge pull request #32 from rbberger/doc-cleanups-and-updates 

Various updates to tools and some minor documentation fixes
parents b76a42d3 df304f8c

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">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>
@@ -194,7 +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>
@@ -358,6 +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>
@@ -82,11 +83,11 @@ 
<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><ul>

<li class="toctree-l3"><a class="reference internal" href="#gpu-package-with-cuda-and-opencl-support-for-nvidia-gpus-and-others">5.3.1. <code class="docutils literal"><span class="pre">GPU</span> <span class="pre">Package</span></code> with CUDA and OpenCL support for Nvidia GPUs and others</a></li>

<li class="toctree-l3"><a class="reference internal" href="#user-intel-package-for-intel-cpus-and-intel-xeon-phi">5.3.2. <code class="docutils literal"><span class="pre">USER-INTEL</span> <span class="pre">Package</span></code> for Intel CPUs and Intel Xeon Phi</a></li>

<li class="toctree-l3"><a class="reference internal" href="#kokkos-package-for-nvidia-gpus-intel-xeon-phi-and-openmp-threading">5.3.3. <code class="docutils literal"><span class="pre">KOKKOS</span> <span class="pre">Package</span></code> for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading</a></li>

<li class="toctree-l3"><a class="reference internal" href="#user-omp-package-for-openmp-threading-and-generic-cpu-optimizations">5.3.4. <code class="docutils literal"><span class="pre">USER-OMP</span> <span class="pre">Package</span></code> for OpenMP threading and generic CPU optimizations</a></li>

<li class="toctree-l3"><a class="reference internal" href="#opt-package-generic-cpu-optimizations">5.3.5. <code class="docutils literal"><span class="pre">OPT</span> <span class="pre">Package</span></code> generic CPU optimizations</a></li>

<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>
@@ -101,6 +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">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>
@@ -137,7 +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>
@@ -281,20 +294,31 @@ coprocessors.</p> 
overview of packages is give in <a class="reference internal" href="Section_packages.html"><span class="doc">Section packages</span></a>.</p>

<p>These are the accelerator packages

currently in LAMMPS, either as standard or user packages:</p>

<div class="section" id="gpu-package-with-cuda-and-opencl-support-for-nvidia-gpus-and-others">

<h3>5.3.1. <a class="reference internal" href="accelerate_gpu.html"><span class="doc">GPU Package</span></a> with CUDA and OpenCL support for Nvidia GPUs and others</h3>

</div>

<div class="section" id="user-intel-package-for-intel-cpus-and-intel-xeon-phi">

<h3>5.3.2. <a class="reference internal" href="accelerate_intel.html"><span class="doc">USER-INTEL Package</span></a> for Intel CPUs and Intel Xeon Phi</h3>

</div>

<div class="section" id="kokkos-package-for-nvidia-gpus-intel-xeon-phi-and-openmp-threading">

<h3>5.3.3. <a class="reference internal" href="accelerate_kokkos.html"><span class="doc">KOKKOS Package</span></a> for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading</h3>

</div>

<div class="section" id="user-omp-package-for-openmp-threading-and-generic-cpu-optimizations">

<h3>5.3.4. <a class="reference internal" href="accelerate_omp.html"><span class="doc">USER-OMP Package</span></a> for OpenMP threading and generic CPU optimizations</h3>

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

<colgroup>

<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 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 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 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 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 Package</span></a></td>

<td>generic CPU optimizations</td>

</tr>

</tbody>

</table>

<div class="toctree-wrapper compound">

</div>

<div class="section" id="opt-package-generic-cpu-optimizations">

<h3>5.3.5. <a class="reference internal" href="accelerate_opt.html"><span class="doc">OPT Package</span></a> generic CPU optimizations</h3>

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

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

<table border="1" class="docutils">
@@ -455,7 +479,6 @@ CPU.</li> 
</ul>

<hr class="docutils" />

</div>

</div>

<div class="section" id="comparison-of-various-accelerator-packages">

<span id="acc-4"></span><h2>5.4. Comparison of various accelerator packages</h2>

<div class="admonition note">
@@ -523,7 +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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              <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>
@@ -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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              <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>

doc/html/Section_example.html

+14 −1
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              <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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