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update manual introduction to represent current status. correct some markup to better pass through sphinx

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Axel Kohlmeyer 2016-09-06 21:20:47 -04:00
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commit fc2d878305
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12
doc/html/Manual.html
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@ -168,16 +168,20 @@ run efficiently on parallel computers. It was developed at Sandia
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

54
doc/html/Section_accelerate.html
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@ -346,8 +346,8 @@ package and are explained in the individual accelerator doc pages,
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>
@ -356,40 +356,24 @@ listed above:</p>
<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
@ -528,7 +512,7 @@ full 16 lanes to each of the PCIe 2.0 16x slots.</li>
<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>

2
doc/html/Section_howto.html
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@ -933,7 +933,7 @@ vectors of a general parallelepiped, where there is no restriction on
<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.

12
doc/src/Manual.txt
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@ -62,7 +62,8 @@ 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).
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
@ -70,9 +71,12 @@ Stan Moore, stamoore 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)

31
doc/src/Section_accelerate.txt
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@ -206,24 +206,18 @@ build the accelerator library |
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
@ -303,7 +297,8 @@ overload the available bandwidth for communication. :l
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:
@ -369,7 +364,8 @@ and the GPU. Hence its performance is affected if full 16 PCIe lanes
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:]
@ -377,4 +373,5 @@ The GPU package accelerates only pair force, neighbor list, and PPPM
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

8
doc/src/Section_howto.txt
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@ -695,7 +695,8 @@ MD with quantum forces calculated by a density functional code :l
lammps_spparks: coupling of LAMMPS and "SPPARKS"_spparks, to couple
a kinetic Monte Carlo model for grain growth using MD to calculate
strain induced across grain boundaries :l,ule
strain induced across grain boundaries :l
:ule
:link(quest,http://dft.sandia.gov/Quest)
:link(spparks,http://www.sandia.gov/~sjplimp/spparks.html)
@ -829,7 +830,7 @@ rotation of [A], [B], and [C] and can be computed as follows:
:c,image(Eqs/transform.jpg)
where A = |[A]| indicates the scalar length of [A]. The ^ hat symbol
where A = |[A]| indicates the scalar length of [A]. The hat symbol
indicates the corresponding unit vector. {beta} and {gamma} are angles
between the vectors described below. Note that by construction,
[a], [b], and [c] have strictly positive x, y, and z components, respectively.
@ -1286,7 +1287,8 @@ print"_fix_print.html for single-line output of
"variables"_variable.html. Fix print can also output to the
screen. :l
"Restart files"_restart.html. :l,ule
"Restart files"_restart.html. :l
:ule
A simulation prints one set of thermodynamic output and (optionally)
restart files. It can generate any number of dump files and fix