regenerate html pages with the updated content from the corrections

<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

<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="#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>

</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>

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>

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

<colgroup>

<col width="44%" />

<col width="56%" />

</colgroup>

<tbody valign="top">

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

<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>

<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>

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

<td>generic CPU optimizations</td>

</tr>

</tbody>

</table>

<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>

</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">

<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>

</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">

<p>This section describes the structure of a typical LAMMPS input script.

The “examples” 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>

<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>

</div>

<div class="section" id="coming-attractions">

<span id="hist-1"></span><h2>13.1. Coming attractions</h2>

<p>The <a class="reference external" href="http://lammps.sandia.gov/future.html">Wish list link</a> on the

LAMMPS WWW page gives a list of features we are hoping to add to

LAMMPS in the future, including contact names of individuals you can

email if you are interested in contributing to the developement or

would be a future user of that feature.</p>

<p>You can also send <a class="reference external" href="http://lammps.sandia.gov/authors.html">email to the developers</a> if you want to add

your wish to the list.</p>

<p>As of summer 2016 we are using the <a class="reference external" href="https://github.com/lammps/lammps/issues">LAMMPS project issue tracker on GitHub</a> for keeping

track of suggested, planned or pending new features. This includes

discussions of how to best implement them, or why they would be

useful. Especially if a planned or proposed feature is non-trivial

to add, e.g. because it requires changes to some of the core

classes of LAMMPS, people planning to contribute a new feature to

LAMMS are encouraged to submit an issue about their planned

implementation this way in order to receive feedback from the

LAMMPS core developers. They will provide suggestions about

the validity of the proposed approach and possible improvements,

pitfalls or alternatives.</p>

<p>Please see some of the closed issues for examples of how to

suggest code enhancements, submit proposed changes, or report

elated issues and how they are resoved.</p>

<p>As an alternative to using GitHub, you may e-mail the

<a class="reference external" href="http://lammps.sandia.gov/authors.html">core developers</a> or send

an e-mail to the <a class="reference external" href="http://lammps.sandia.gov/mail.html">LAMMPS Mail list</a>

if you want to have your suggestion added to the list.</p>

<hr class="docutils" />

</div>

<div class="section" id="past-versions">