update manual introduction to represent current status. correct some markup to...

National Laboratories, a US Department of Energy facility, with

funding from the DOE.  It is an open-source code, distributed freely

under the terms of the GNU Public License (GPL).</p>

<p>The core group of LAMMPS developers is at Sandia National Labs and Temple University:</p>

<p>The current core group of LAMMPS developers is at Sandia National

Labs and Temple University:</p>

<ul class="simple">

<li><a class="reference external" href="http://www.sandia.gov/~sjplimp">Steve Plimpton</a>, sjplimp at sandia.gov</li>

<li>Aidan Thompson, athomps at sandia.gov</li>

<li>Stan Moore, stamoore at sandia.gov</li>

<li><a class="reference external" href="http://goo.gl/1wk0">Axel Kohlmeyer</a>, akohlmey at gmail.com</li>

</ul>

<p>Past core developers include Paul Crozier, Ray Shan and Mark Stevens, 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.</p>

<p>Past core developers include Paul Crozier, Ray Shan and Mark Stevens,

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>

<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

listed above:</p>

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

<colgroup>

<col width="26%" />

<col width="74%" />

<col width="65%" />

<col width="35%" />

</colgroup>

<tbody valign="top">

<tr class="row-odd"><td>build the accelerator library</td>

<tr class="row-even"><td>install the accelerator package</td>

<td>make yes-opt, make yes-user-intel, etc</td>

</tr>

</tbody>

</table>

<div class="line-block">

<div class="line">install the accelerator package             | make yes-opt, make yes-user-intel, etc                                                                                           |</div>

</div>

<blockquote>

<div>only for USER-INTEL, KOKKOS, USER-OMP, OPT packages                                                          |</div></blockquote>

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

<colgroup>

<col width="26%" />

<col width="74%" />

</colgroup>

<tbody valign="top">

<tr class="row-odd"><td>re-build LAMMPS</td>

<tr class="row-odd"><td>add compile/link flags to Makefile.machine in src/MAKE</td>

<td>only for USER-INTEL, KOKKOS, USER-OMP, OPT packages</td>

</tr>

<tr class="row-even"><td>re-build LAMMPS</td>

<td>make machine</td>

</tr>

</tbody>

</table>

<div class="line-block">

<div class="line">re-build LAMMPS                             | make machine                                                                                                                     |</div>

</div>

<blockquote>

<div>mpirun -np 32 lmp_machine -in in.script                                                          |</div></blockquote>

<blockquote>

<div>only for KOKKOS package                                   |</div></blockquote>

<blockquote>

<div><a class="reference internal" href="package.html"><span class="doc">package</span></a> command, &lt;br&gt;

only if defaults need to be changed |</div></blockquote>

<blockquote>

<div><a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command                                               |</div></blockquote>

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

<colgroup>

</colgroup>

<tbody valign="top">

<tr class="row-odd"><td>prepare and test a regular LAMMPS simulation</td>

<td>lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script</td>

</tr>

<tr class="row-even"><td>enable specific accelerator support via &#8216;-k on&#8217; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>,</td>

<td>only needed for KOKKOS package</td>

</tr>

<tr class="row-odd"><td>set any needed options for the package via &#8220;-pk&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> or <a class="reference internal" href="package.html"><span class="doc">package</span></a> command,</td>

<td>only if defaults need to be changed</td>

</tr>

<tr class="row-even"><td>use accelerated styles in your input via &#8220;-sf&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> or <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command</td>

<td>lmp_machine -in in.script -sf gpu</td>

</tr>

</tbody>

</table>

<p>Note that the first 4 steps can be done as a single command, using the

<li>The GPU package accelerates only pair force, neighbor list, and PPPM

calculations.</li>

<li>The GPU package requires neighbor lists to be built on the CPU when using

exclusion lists or a triclinic simulation box.</li>

exclusion lists, hybrid pair styles, or a triclinic simulation box.</li>

</ul>

</div>

</div>

<strong>A</strong> x <strong>B</strong> . <strong>C</strong> &gt; 0.  The equivalent LAMMPS <strong>a</strong>,<strong>b</strong>,<strong>c</strong> are a linear

rotation of <strong>A</strong>, <strong>B</strong>, and <strong>C</strong> and can be computed as follows:</p>

<img alt="_images/transform.jpg" class="align-center" src="_images/transform.jpg" />

<p>where A = <a href="#id3"><span class="problematic" id="id4">|</span></a><strong>A</strong>| indicates the scalar length of <strong>A</strong>. The ^ hat symbol

<p>where A = <a href="#id3"><span class="problematic" id="id4">|</span></a><strong>A</strong>| indicates the scalar length of <strong>A</strong>. The hat symbol

indicates the corresponding unit vector. <em>beta</em> and <em>gamma</em> are angles

between the vectors described below. Note that by construction,

<strong>a</strong>, <strong>b</strong>, and <strong>c</strong> have strictly positive x, y, and z components, respectively.

funding from the DOE.  It is an open-source code, distributed freely

under the terms of the GNU Public License (GPL).

The core group of LAMMPS developers is at Sandia National Labs and Temple University:

The current core group of LAMMPS developers is at Sandia National

Labs and Temple University:

"Steve Plimpton"_sjp, sjplimp at sandia.gov :ulb,l

Aidan Thompson, athomps at sandia.gov :l

"Axel Kohlmeyer"_ako, akohlmey at gmail.com :l

:ulb

Past core developers include Paul Crozier, Ray Shan and Mark Stevens, all at Sandia.

The [LAMMPS home page] at "http://lammps.sandia.gov"_http://lammps.sandia.gov

has more information about the code and its uses.

Past core developers include Paul Crozier, Ray Shan and Mark Stevens,

all at Sandia. The [LAMMPS home page] at

"http://lammps.sandia.gov"_http://lammps.sandia.gov has more information

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

bug reports and feature requests are mainly coordinated through the

"LAMMPS project on GitHub."_https://github.com/lammps/lammps

:link(bug,http://lammps.sandia.gov/bug.html)

:link(sjp,http://www.sandia.gov/~sjplimp)

  only for GPU package |

install the accelerator package |

  make yes-opt, make yes-user-intel, etc |

add compile/link flags to Makefile.machine |

  in src/MAKE, <br>

add compile/link flags to Makefile.machine in src/MAKE |

  only for USER-INTEL, KOKKOS, USER-OMP, OPT packages |

re-build LAMMPS |

  make machine |

run a LAMMPS simulation |

  lmp_machine < in.script <br> 

  mpirun -np 32 lmp_machine -in in.script |

enable the accelerator package |

  via "-c on" and "-k on" "command-line switches"_Section_start.html#start_7, <br>

  only for KOKKOS package |

set any needed options for the package |

  via "-pk" "command-line switch"_Section_start.html#start_7 or

  "package"_package.html command, <br>

prepare and test a regular LAMMPS simulation |

  lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script |

enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_7, |

  only needed for KOKKOS package |

set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_7 or "package"_package.html command, |

  only if defaults need to be changed |

use accelerated styles in your input script |

  via "-sf" "command-line switch"_Section_start.html#start_7 or

  "suffix"_suffix.html command :tb(c=2,s=|)

use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_7 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu

:tb(c=2,s=|)

Note that the first 4 steps can be done as a single command, using the

src/Make.py tool.  This tool is discussed in "Section

Styles with an "opt" suffix are part of the OPT package and typically

speed-up the pairwise calculations of your simulation by 5-25% on a

CPU. :l,ule

CPU. :l

:ule

The individual accelerator package doc pages explain:

are not available for each GPU.  In HPC environments this can be the

case if S2050/70 servers are used, where two devices generally share

one PCIe 2.0 16x slot.  Also many multi-GPU mainboards do not provide

full 16 lanes to each of the PCIe 2.0 16x slots. :l,ule

full 16 lanes to each of the PCIe 2.0 16x slots. :l

:ule

[Differences between the two packages:]

calculations. :ulb,l

The GPU package requires neighbor lists to be built on the CPU when using

exclusion lists or a triclinic simulation box. :l,ule

exclusion lists, hybrid pair styles, or a triclinic simulation box. :l

:ule