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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15218 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2016-06-27 22:32:39 +00:00
parent b58e008cae
commit 1c05f57bcd
10 changed files with 130 additions and 11 deletions
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2
doc/html/Section_commands.html
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@ -1230,7 +1230,7 @@ if <a class="reference internal" href="Section_start.html#start-3"><span class="
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_multi_lucy_rx.html"><span class="doc">multi/lucy/rx</span></a></td>
<td><a class="reference internal" href="pair_quip.html"><span class="doc">quip</span></a></td>
<td><a class="reference internal" href="pair_reax_c.html"><span class="doc">reax/c</span></a></td>
<td><a class="reference internal" href="pair_reax_c.html"><span class="doc">reax/c (k)</span></a></td>
<td><a class="reference internal" href="pair_smd_hertz.html"><span class="doc">smd/hertz</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_smd_tlsph.html"><span class="doc">smd/tlsph</span></a></td>

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doc/html/_sources/Section_commands.txt
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@ -665,7 +665,7 @@ if :ref:`LAMMPS is built with the appropriate package <start_3>`.
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+
| :doc:`mgpt <pair_mgpt>` | :doc:`morse/smooth/linear <pair_morse>` | :doc:`morse/soft <pair_morse>` | :doc:`multi/lucy <pair_multi_lucy>` |
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+
| :doc:`multi/lucy/rx <pair_multi_lucy_rx>` | :doc:`quip <pair_quip>` | :doc:`reax/c <pair_reax_c>` | :doc:`smd/hertz <pair_smd_hertz>` |
| :doc:`multi/lucy/rx <pair_multi_lucy_rx>` | :doc:`quip <pair_quip>` | :doc:`reax/c (k) <pair_reax_c>` | :doc:`smd/hertz <pair_smd_hertz>` |
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+
| :doc:`smd/tlsph <pair_smd_tlsph>` | :doc:`smd/triangulated/surface <pair_smd_triangulated_surface>` | :doc:`smd/ulsph <pair_smd_ulsph>` | :doc:`smtbq <pair_smtbq>` |
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+

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doc/html/_sources/fix_qeq_reax.txt
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@ -3,6 +3,9 @@
fix qeq/reax command
====================
fix qeq/reax/kk command
=======================
Syntax
""""""
@ -69,6 +72,33 @@ be used with the *start/stop* keywords of the :doc:`run <run>` command.
This fix is invoked during :doc:`energy minimization <minimize>`.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in :doc:`Section_accelerate <Section_accelerate>`
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :ref:`Making LAMMPS <start_3>` section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can
use the :doc:`suffix <suffix>` command in your input script.
See :doc:`Section_accelerate <Section_accelerate>` of the manual for
more instructions on how to use the accelerated styles effectively.
----------
Restrictions
""""""""""""

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doc/html/_sources/pair_reax_c.txt
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@ -3,6 +3,9 @@
pair_style reax/c command
=========================
pair_style reax/c/kk command
============================
Syntax
""""""
@ -46,6 +49,14 @@ the most up-to-date version of ReaxFF as of summer 2010. For more
technical details about the pair reax/c implementation of ReaxFF, see
the :ref:`(Aktulga) <Aktulga>` paper.
The *reax/c/kk* style is a Kokkos version of the ReaxFF potential that is
derived from the *reax/c* style. The Kokkos version can run on GPUs and
can also use OpenMP multithreading. For more information about the Kokkos package,
see :ref:`Section_packages <kokkos>` and :doc:`Section_accelerate <accelerate_kokkos>`.
One important consideration when using the *reax/c/kk* style is the choice of either
half or full neighbor lists. This setting can be changed using the Kokkos :doc:`package <package>`
command.
The *reax/c* style differs from the :doc:`pair_style reax <pair_reax>`
command in the lo-level implementation details. The *reax* style is a
Fortran library, linked to LAMMPS. The *reax/c* style was initially
@ -124,9 +135,11 @@ control file. Note: Force field files are different for the original
or lg corrected pair styles, using wrong ffield file generates an error message.
Optional keywords *safezone* and *mincap* are used for allocating
reax/c arrays. Increase these values can avoid memory problems, such
reax/c arrays. Increasing these values can avoid memory problems, such
as segmentation faults and bondchk failed errors, that could occur under
certain conditions.
certain conditions. These keywords aren't used by the Kokkos version, which
instead uses a more robust memory allocation scheme that checks if the sizes of
the arrays have been exceeded and automatically allocates more memory.
The thermo variable *evdwl* stores the sum of all the ReaxFF potential
energy contributions, with the exception of the Coulombic and charge
@ -287,6 +300,33 @@ This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the
*inner*\ , *middle*\ , *outer* keywords.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in :doc:`Section_accelerate <Section_accelerate>`
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :ref:`Making LAMMPS <start_3>` section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can
use the :doc:`suffix <suffix>` command in your input script.
See :doc:`Section_accelerate <Section_accelerate>` of the manual for
more instructions on how to use the accelerated styles effectively.
----------
Restrictions
""""""""""""

4
doc/html/fix_orient.html
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@ -155,7 +155,7 @@
grain boundary which can be used to induce grain boundary migration
(in the direction perpendicular to the grain boundary plane). The
motivation and explanation of this force and its application are
described in <a class="reference internal" href="fix_orient_fcc.html#janssens"><span class="std std-ref">(Janssens)</span></a>. The adaptiation to bcc crystals
described in <a class="reference internal" href="#janssens"><span class="std std-ref">(Janssens)</span></a>. The adaptiation to bcc crystals
is described in <a class="reference internal" href="#wicaksono1"><span class="std std-ref">(Wicaksono1)</span></a>. The computed force is only
applied to atoms in the fix group.</p>
<p>The basic idea is that atoms in one grain (on one side of the
@ -175,7 +175,7 @@ system can displace during the simulation, and such motion should be
accounted for in measuring the grain boundary velocity.</p>
<p>The potential energy added to atom I is given by these formulas</p>
<img alt="_images/fix_orient_fcc.jpg" class="align-center" src="_images/fix_orient_fcc.jpg" />
<p>which are fully explained in <a class="reference internal" href="fix_orient_fcc.html#janssens"><span class="std std-ref">(Janssens)</span></a>. For fcc crystals
<p>which are fully explained in <a class="reference internal" href="#janssens"><span class="std std-ref">(Janssens)</span></a>. For fcc crystals
this order parameter Xi for atom I in equation (1) is a sum over the
12 nearest neighbors of atom I. For bcc crystals it is the
corresponding sum of the 8 nearest neighbors. Rj is the vector from

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doc/html/fix_qeq_reax.html
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@ -126,6 +126,9 @@
<div class="section" id="fix-qeq-reax-command">
<span id="index-0"></span><h1>fix qeq/reax command</h1>
</div>
<div class="section" id="fix-qeq-reax-kk-command">
<h1>fix qeq/reax/kk command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">qeq</span><span class="o">/</span><span class="n">reax</span> <span class="n">Nevery</span> <span class="n">cutlo</span> <span class="n">cuthi</span> <span class="n">tolerance</span> <span class="n">params</span>
@ -184,7 +187,24 @@ of this fix are hard-coded to be A, eV, and electronic charge.</p>
quantities are stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.</p>
<p>This fix is invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
<hr class="docutils" />
<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This fix is part of the USER-REAXC package. It is only enabled if

2
doc/html/genindex.html
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@ -1296,7 +1296,7 @@
</dt>
<dt><a href="fix_orient.html#index-0">fix orient/fcc</a>, <a href="fix_orient_fcc.html#index-0">[1]</a>
<dt><a href="fix_orient.html#index-0">fix orient/fcc</a>
</dt>

33
doc/html/pair_reax_c.html
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@ -126,6 +126,9 @@
<div class="section" id="pair-style-reax-c-command">
<span id="index-0"></span><h1>pair_style reax/c command</h1>
</div>
<div class="section" id="pair-style-reax-c-kk-command">
<h1>pair_style reax/c/kk command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span> <span class="n">cfile</span> <span class="n">keyword</span> <span class="n">value</span>
@ -164,6 +167,13 @@ supplemental information of the following paper: <a class="reference internal" h
the most up-to-date version of ReaxFF as of summer 2010. For more
technical details about the pair reax/c implementation of ReaxFF, see
the <a class="reference internal" href="#aktulga"><span class="std std-ref">(Aktulga)</span></a> paper.</p>
<p>The <em>reax/c/kk</em> style is a Kokkos version of the ReaxFF potential that is
derived from the <em>reax/c</em> style. The Kokkos version can run on GPUs and
can also use OpenMP multithreading. For more information about the Kokkos package,
see <a class="reference internal" href="Section_packages.html#kokkos"><span class="std std-ref">Section_packages</span></a> and <a class="reference internal" href="accelerate_kokkos.html"><span class="doc">Section_accelerate</span></a>.
One important consideration when using the <em>reax/c/kk</em> style is the choice of either
half or full neighbor lists. This setting can be changed using the Kokkos <a class="reference internal" href="package.html"><span class="doc">package</span></a>
command.</p>
<p>The <em>reax/c</em> style differs from the <a class="reference internal" href="pair_reax.html"><span class="doc">pair_style reax</span></a>
command in the lo-level implementation details. The <em>reax</em> style is a
Fortran library, linked to LAMMPS. The <em>reax/c</em> style was initially
@ -234,9 +244,11 @@ recommended value for parameter <em>thb</em> is 0.01, which can be set in the
control file. Note: Force field files are different for the original
or lg corrected pair styles, using wrong ffield file generates an error message.</p>
<p>Optional keywords <em>safezone</em> and <em>mincap</em> are used for allocating
reax/c arrays. Increase these values can avoid memory problems, such
reax/c arrays. Increasing these values can avoid memory problems, such
as segmentation faults and bondchk failed errors, that could occur under
certain conditions.</p>
certain conditions. These keywords aren&#8217;t used by the Kokkos version, which
instead uses a more robust memory allocation scheme that checks if the sizes of
the arrays have been exceeded and automatically allocates more memory.</p>
<p>The thermo variable <em>evdwl</em> stores the sum of all the ReaxFF potential
energy contributions, with the exception of the Coulombic and charge
equilibration contributions which are stored in the thermo variable
@ -361,7 +373,24 @@ script that reads a restart file.</p>
<p>This pair style can only be used via the <em>pair</em> keyword of the
<a class="reference internal" href="run_style.html"><span class="doc">run_style respa</span></a> command. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
<hr class="docutils" />
<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This pair style is part of the USER-REAXC package. It is only enabled

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doc/src/Section_commands.txt
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@ -963,7 +963,7 @@ package"_Section_start.html#start_3.
"multi/lucy"_pair_multi_lucy.html,
"multi/lucy/rx"_pair_multi_lucy_rx.html,
"quip"_pair_quip.html,
"reax/c"_pair_reax_c.html,
"reax/c (k)"_pair_reax_c.html,
"smd/hertz"_pair_smd_hertz.html,
"smd/tlsph"_pair_smd_tlsph.html,
"smd/triangulated/surface"_pair_smd_triangulated_surface.html,