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

National Laboratories, a US Department of Energy facility, with

National Laboratories, a US Department of Energy facility, with

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

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

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

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">

<ul class="simple">

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

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

<li>Stan Moore, stamoore 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>

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

</ul>

</ul>

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

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

The <strong>LAMMPS home page</strong> at <a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a>

all at Sandia. The <strong>LAMMPS home page</strong> at

has more information about the code and its uses.</p>

<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" />

<hr class="docutils" />

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

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

you find errors or omissions in this manual or have suggestions for

you find errors or omissions in this manual or have suggestions for

listed above:</p>

listed above:</p>

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

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

<colgroup>

<colgroup>

<col width="26%" />

<col width="65%" />

<col width="74%" />

<col width="35%" />

</colgroup>

</colgroup>

<tbody valign="top">

<tbody valign="top">

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

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

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

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

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

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

</tr>

</tr>

</tbody>

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

</table>

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

<div class="line-block">

</tr>

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

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

</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>

<td>make machine</td>

<td>make machine</td>

</tr>

</tr>

</tbody>

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

</table>

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

<div class="line-block">

</tr>

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

<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>

</div>

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

<blockquote>

</tr>

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

<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>

<blockquote>

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

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

</tr>

<blockquote>

<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>

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

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

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

</tr>

<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">

</tbody>

</tbody>

</table>

</table>

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

<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

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

calculations.</li>

calculations.</li>

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

<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>

</ul>

</div>

</div>

</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

<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>

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" />

<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

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

between the vectors described below. Note that by construction,

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.

<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

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

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

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

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

Aidan Thompson, athomps at sandia.gov :l

Aidan Thompson, athomps at sandia.gov :l

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

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

:ulb

:ulb

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

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

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

all at Sandia. The [LAMMPS home page] at

has more information about the code and its uses.

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

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

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

  only for GPU package |

  only for GPU package |

install the accelerator package |

install the accelerator package |

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

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

add compile/link flags to Makefile.machine |

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

  in src/MAKE, <br>

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

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

re-build LAMMPS |

re-build LAMMPS |

  make machine |

  make machine |

run a LAMMPS simulation |

prepare and test a regular LAMMPS simulation |

  lmp_machine < in.script <br> 

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

enable the accelerator package |

  only needed for KOKKOS package |

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

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

  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>

  only if defaults need to be changed |

  only if defaults need to be changed |

use accelerated styles in your input script |

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

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

:tb(c=2,s=|)

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

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

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

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

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

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

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:

The individual accelerator package doc pages explain:

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

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

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

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:]

[Differences between the two packages:]

calculations. :ulb,l

calculations. :ulb,l

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

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