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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14067 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp 2015-09-24 20:44:03 +00:00
parent aec30b07c2
commit 87025c6770
19 changed files with 203 additions and 85 deletions
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12
doc/Section_commands.html
View File

@ -636,7 +636,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
<td><a class="reference internal" href="fix_bond_swap.html"><em>bond/swap</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_box_relax.html"><em>box/relax</em></a></td>
<td><a class="reference internal" href="fix_deform.html"><em>deform</em></a></td>
<td><a class="reference internal" href="fix_deform.html"><em>deform (k)</em></a></td>
<td><a class="reference internal" href="fix_deposit.html"><em>deposit</em></a></td>
<td><a class="reference internal" href="fix_drag.html"><em>drag</em></a></td>
<td><a class="reference internal" href="fix_dt_reset.html"><em>dt/reset</em></a></td>
@ -658,12 +658,12 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
<td><a class="reference internal" href="fix_move.html"><em>move</em></a></td>
<td><a class="reference internal" href="fix_msst.html"><em>msst</em></a></td>
<td><a class="reference internal" href="fix_neb.html"><em>neb</em></a></td>
<td><a class="reference internal" href="fix_nh.html"><em>nph (o)</em></a></td>
<td><a class="reference internal" href="fix_nh.html"><em>nph (ko)</em></a></td>
<td><a class="reference internal" href="fix_nphug.html"><em>nphug (o)</em></a></td>
<td><a class="reference internal" href="fix_nph_asphere.html"><em>nph/asphere (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_nph_sphere.html"><em>nph/sphere (o)</em></a></td>
<td><a class="reference internal" href="fix_nh.html"><em>npt (co)</em></a></td>
<td><a class="reference internal" href="fix_nh.html"><em>npt (cko)</em></a></td>
<td><a class="reference internal" href="fix_npt_asphere.html"><em>npt/asphere (o)</em></a></td>
<td><a class="reference internal" href="fix_npt_sphere.html"><em>npt/sphere (o)</em></a></td>
<td><a class="reference internal" href="fix_nve.html"><em>nve (cko)</em></a></td>
@ -676,7 +676,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
<td><a class="reference internal" href="fix_nve_noforce.html"><em>nve/noforce</em></a></td>
<td><a class="reference internal" href="fix_nve_sphere.html"><em>nve/sphere (o)</em></a></td>
<td><a class="reference internal" href="fix_nve_tri.html"><em>nve/tri</em></a></td>
<td><a class="reference internal" href="fix_nh.html"><em>nvt (co)</em></a></td>
<td><a class="reference internal" href="fix_nh.html"><em>nvt (cko)</em></a></td>
<td><a class="reference internal" href="fix_nvt_asphere.html"><em>nvt/asphere (o)</em></a></td>
<td><a class="reference internal" href="fix_nvt_sllod.html"><em>nvt/sllod (o)</em></a></td>
</tr>
@ -740,7 +740,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
<td><a class="reference internal" href="fix_wall.html"><em>wall/lj126</em></a></td>
<td><a class="reference internal" href="fix_wall.html"><em>wall/lj93</em></a></td>
<td><a class="reference internal" href="fix_wall_piston.html"><em>wall/piston</em></a></td>
<td><a class="reference internal" href="fix_wall_reflect.html"><em>wall/reflect</em></a></td>
<td><a class="reference internal" href="fix_wall_reflect.html"><em>wall/reflect (k)</em></a></td>
<td><a class="reference internal" href="fix_wall_region.html"><em>wall/region</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_wall_srd.html"><em>wall/srd</em></a></td>
@ -903,7 +903,7 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
<tr class="row-odd"><td><a class="reference internal" href="compute_sna_atom.html"><em>snad/atom</em></a></td>
<td><a class="reference internal" href="compute_sna_atom.html"><em>snav/atom</em></a></td>
<td><a class="reference internal" href="compute_stress_atom.html"><em>stress/atom</em></a></td>
<td><a class="reference internal" href="compute_temp.html"><em>temp (c)</em></a></td>
<td><a class="reference internal" href="compute_temp.html"><em>temp (ck)</em></a></td>
<td><a class="reference internal" href="compute_temp_asphere.html"><em>temp/asphere</em></a></td>
<td><a class="reference internal" href="compute_temp_com.html"><em>temp/com</em></a></td>
</tr>

12
doc/Section_commands.txt
View File

@ -498,7 +498,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"bond/create"_fix_bond_create.html,
"bond/swap"_fix_bond_swap.html,
"box/relax"_fix_box_relax.html,
"deform"_fix_deform.html,
"deform (k)"_fix_deform.html,
"deposit"_fix_deposit.html,
"drag"_fix_drag.html,
"dt/reset"_fix_dt_reset.html,
@ -518,11 +518,11 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"move"_fix_move.html,
"msst"_fix_msst.html,
"neb"_fix_neb.html,
"nph (o)"_fix_nh.html,
"nph (ko)"_fix_nh.html,
"nphug (o)"_fix_nphug.html,
"nph/asphere (o)"_fix_nph_asphere.html,
"nph/sphere (o)"_fix_nph_sphere.html,
"npt (co)"_fix_nh.html,
"npt (cko)"_fix_nh.html,
"npt/asphere (o)"_fix_npt_asphere.html,
"npt/sphere (o)"_fix_npt_sphere.html,
"nve (cko)"_fix_nve.html,
@ -534,7 +534,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"nve/noforce"_fix_nve_noforce.html,
"nve/sphere (o)"_fix_nve_sphere.html,
"nve/tri"_fix_nve_tri.html,
"nvt (co)"_fix_nh.html,
"nvt (cko)"_fix_nh.html,
"nvt/asphere (o)"_fix_nvt_asphere.html,
"nvt/sllod (o)"_fix_nvt_sllod.html,
"nvt/sphere (o)"_fix_nvt_sphere.html,
@ -591,7 +591,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"wall/lj126"_fix_wall.html,
"wall/lj93"_fix_wall.html,
"wall/piston"_fix_wall_piston.html,
"wall/reflect"_fix_wall_reflect.html,
"wall/reflect (k)"_fix_wall_reflect.html,
"wall/region"_fix_wall_region.html,
"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
@ -709,7 +709,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"snad/atom"_compute_sna_atom.html,
"snav/atom"_compute_sna_atom.html,
"stress/atom"_compute_stress_atom.html,
"temp (c)"_compute_temp.html,
"temp (ck)"_compute_temp.html,
"temp/asphere"_compute_temp_asphere.html,
"temp/com"_compute_temp_com.html,
"temp/chunk"_compute_temp_chunk.html,

2
doc/accelerate_kokkos.html
View File

@ -207,7 +207,7 @@ you must have Kepler generation GPUs (or later). The Kokkos library
exploits texture cache options not supported by Telsa generation GPUs
(or older).</p>
</div>
<p>To build the KOKKOS package for GPUs, NVIDIA Cuda software must be
<p>To build the KOKKOS package for GPUs, NVIDIA Cuda software version 6.5 or later must be
installed on your system. See the discussion above for the USER-CUDA
and GPU packages for details of how to check and do this.</p>
<p><strong>Building LAMMPS with the KOKKOS package:</strong></p>

2
doc/accelerate_kokkos.txt
View File

@ -103,7 +103,7 @@ you must have Kepler generation GPUs (or later). The Kokkos library
exploits texture cache options not supported by Telsa generation GPUs
(or older).
To build the KOKKOS package for GPUs, NVIDIA Cuda software must be
To build the KOKKOS package for GPUs, NVIDIA Cuda software version 6.5 or later must be
installed on your system. See the discussion above for the USER-CUDA
and GPU packages for details of how to check and do this.

18
doc/compute_pe.html
View File

@ -178,14 +178,16 @@ LAMMPS starts up, as if this command were in the input script:</p>
</div>
<p>See the &#8220;thermo_style&#8221; command for more details.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</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"><em>Section_accelerate</em></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 USER-CUDA package. They are
only enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>Styles with a <em>cuda</em>, <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"><em>Section_accelerate</em></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 USER-CUDA, 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>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>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>

18
doc/compute_pe.txt
View File

@ -60,15 +60,17 @@ See the "thermo_style" command for more details.
:line
Styles with a {cuda} 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
"Section_accelerate"_Section_accelerate.html of the manual. The
accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.
Styles with a {cuda}, {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 "Section_accelerate"_Section_accelerate.html
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 USER-CUDA package. They are
only enabled if LAMMPS was built with that package. See the "Making
These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script

20
doc/compute_pressure.html
View File

@ -181,7 +181,7 @@ compute temperature or ke and/or the virial. The <em>virial</em> keyword
means include all terms except the kinetic energy <em>ke</em>.</p>
<p>Details of how LAMMPS computes the virial efficiently for the entire
system, including the effects of periodic boundary conditions is
discussed in <a class="reference internal" href="compute_stress_atom.html#thompson"><span>(Thompson)</span></a>.</p>
discussed in <a class="reference internal" href="#thompson"><span>(Thompson)</span></a>.</p>
<p>The temperature and kinetic energy tensor is not calculated by this
compute, but rather by the temperature compute specified with the
command. If the kinetic energy is not included in the pressure, than
@ -205,14 +205,16 @@ LAMMPS starts up, as if this command were in the input script:</p>
<p>where &#8220;thermo_temp&#8221; is the ID of a similarly defined compute of style
&#8220;temp&#8221;. See the &#8220;thermo_style&#8221; command for more details.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</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"><em>Section_accelerate</em></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 USER-CUDA package. They are
only enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>Styles with a <em>cuda</em>, <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"><em>Section_accelerate</em></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 USER-CUDA, 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>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>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>

18
doc/compute_pressure.txt
View File

@ -96,15 +96,17 @@ where "thermo_temp" is the ID of a similarly defined compute of style
:line
Styles with a {cuda} 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
"Section_accelerate"_Section_accelerate.html of the manual. The
accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.
Styles with a {cuda}, {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 "Section_accelerate"_Section_accelerate.html
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 USER-CUDA package. They are
only enabled if LAMMPS was built with that package. See the "Making
These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script

21
doc/compute_temp.html
View File

@ -129,6 +129,9 @@
</div>
<div class="section" id="compute-temp-cuda-command">
<h1>compute temp/cuda command<a class="headerlink" href="#compute-temp-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="compute-temp-kk-command">
<h1>compute temp/kk command<a class="headerlink" href="#compute-temp-kk-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID temp
@ -180,14 +183,16 @@ LAMMPS starts up, as if this command were in the input script:</p>
a discussion of different ways to compute temperature and perform
thermostatting.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</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"><em>Section_accelerate</em></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 USER-CUDA package. They are
only enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>Styles with a <em>cuda</em>, <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"><em>Section_accelerate</em></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 USER-CUDA, 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>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>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>

19
doc/compute_temp.txt
View File

@ -8,6 +8,7 @@
compute temp command :h3
compute temp/cuda command :h3
compute temp/kk command :h3
[Syntax:]
@ -64,15 +65,17 @@ thermostatting.
:line
Styles with a {cuda} 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
"Section_accelerate"_Section_accelerate.html of the manual. The
accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.
Styles with a {cuda}, {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 "Section_accelerate"_Section_accelerate.html
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 USER-CUDA package. They are
only enabled if LAMMPS was built with that package. See the "Making
These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script

18
doc/compute_temp_partial.html
View File

@ -185,14 +185,16 @@ needed, the subtracted degrees-of-freedom can be altered using the
a discussion of different ways to compute temperature and perform
thermostatting.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</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"><em>Section_accelerate</em></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 USER-CUDA package. They are
only enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>Styles with a <em>cuda</em>, <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"><em>Section_accelerate</em></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 USER-CUDA, 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>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>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>

18
doc/compute_temp_partial.txt
View File

@ -72,15 +72,17 @@ thermostatting.
:line
Styles with a {cuda} 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
"Section_accelerate"_Section_accelerate.html of the manual. The
accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.
Styles with a {cuda}, {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 "Section_accelerate"_Section_accelerate.html
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 USER-CUDA package. They are
only enabled if LAMMPS was built with that package. See the "Making
These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script

19
doc/fix_deform.html
View File

@ -126,6 +126,9 @@
<div class="section" id="fix-deform-command">
<span id="index-0"></span><h1>fix deform command<a class="headerlink" href="#fix-deform-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="fix-deform-kk-command">
<h1>fix deform/kk command<a class="headerlink" href="#fix-deform-kk-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID deform N parameter args ... keyword value ...
@ -614,6 +617,22 @@ defined in terms of distance/time. Also note that the units keyword
does not affect the <em>variable</em> style. You should use the <em>xlat</em>,
<em>ylat</em>, <em>zlat</em> keywords of the <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a>
command if you want to include lattice spacings in a variable formula.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <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"><em>Section_accelerate</em></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 USER-CUDA, 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>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>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline"></a></h2>

24
doc/fix_deform.txt
View File

@ -7,6 +7,7 @@
:line
fix deform command :h3
fix deform/kk command :h3
[Syntax:]
@ -539,6 +540,29 @@ does not affect the {variable} style. You should use the {xlat},
{ylat}, {zlat} keywords of the "thermo_style"_thermo_style.html
command if you want to include lattice spacings in a variable formula.
:line
Styles with a {cuda}, {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 "Section_accelerate"_Section_accelerate.html
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 USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#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 "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart

19
doc/fix_nh.html
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@ -130,6 +130,9 @@
<div class="section" id="fix-nvt-cuda-command">
<h1>fix nvt/cuda command<a class="headerlink" href="#fix-nvt-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="fix-nvt-kk-command">
<h1>fix nvt/kk command<a class="headerlink" href="#fix-nvt-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="fix-nvt-omp-command">
<h1>fix nvt/omp command<a class="headerlink" href="#fix-nvt-omp-command" title="Permalink to this headline"></a></h1>
</div>
@ -139,12 +142,18 @@
<div class="section" id="fix-npt-cuda-command">
<h1>fix npt/cuda command<a class="headerlink" href="#fix-npt-cuda-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="fix-npt-kk-command">
<h1>fix npt/kk command<a class="headerlink" href="#fix-npt-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="fix-npt-omp-command">
<h1>fix npt/omp command<a class="headerlink" href="#fix-npt-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="fix-nph-command">
<h1>fix nph command<a class="headerlink" href="#fix-nph-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="fix-nph-kk-command">
<h1>fix nph/kk command<a class="headerlink" href="#fix-nph-kk-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="fix-nph-omp-command">
<h1>fix nph/omp command<a class="headerlink" href="#fix-nph-omp-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
@ -223,12 +232,12 @@ correctly, the time-averaged temperature and stress tensor of the
particles will match the target values specified by Tstart/Tstop and
Pstart/Pstop.</p>
<p>The equations of motion used are those of Shinoda et al in
<a class="reference internal" href="pair_sdk.html#shinoda"><span>(Shinoda)</span></a>, which combine the hydrostatic equations of
Martyna, Tobias and Klein in <a class="reference internal" href="fix_rigid.html#martyna"><span>(Martyna)</span></a> with the strain
<a class="reference internal" href="#shinoda"><span>(Shinoda)</span></a>, which combine the hydrostatic equations of
Martyna, Tobias and Klein in <a class="reference internal" href="#martyna"><span>(Martyna)</span></a> with the strain
energy proposed by Parrinello and Rahman in
<a class="reference internal" href="fix_nh_eff.html#parrinello"><span>(Parrinello)</span></a>. The time integration schemes closely
<a class="reference internal" href="#parrinello"><span>(Parrinello)</span></a>. The time integration schemes closely
follow the time-reversible measure-preserving Verlet and rRESPA
integrators derived by Tuckerman et al. in <a class="reference internal" href="run_style.html#tuckerman"><span>(Tuckerman)</span></a>.</p>
integrators derived by Tuckerman et al. in <a class="reference internal" href="#tuckerman"><span>(Tuckerman)</span></a>.</p>
<hr class="docutils" />
<p>The thermostat parameters for fix styles <em>nvt</em> and <em>npt</em> is specified
using the <em>temp</em> keyword. Other thermostat-related keywords are
@ -385,7 +394,7 @@ freedom. A value of 0 corresponds to no thermostatting of the
barostat variables.</p>
<p>The <em>mtk</em> keyword controls whether or not the correction terms due to
Martyna, Tuckerman, and Klein are included in the equations of motion
<a class="reference internal" href="fix_rigid.html#martyna"><span>(Martyna)</span></a>. Specifying <em>no</em> reproduces the original
<a class="reference internal" href="#martyna"><span>(Martyna)</span></a>. Specifying <em>no</em> reproduces the original
Hoover barostat, whose volume probability distribution function
differs from the true NPT and NPH ensembles by a factor of 1/V. Hence
using <em>yes</em> is more correct, but in many cases the difference is

3
doc/fix_nh.txt
View File

@ -8,11 +8,14 @@
fix nvt command :h3
fix nvt/cuda command :h3
fix nvt/kk command :h3
fix nvt/omp command :h3
fix npt command :h3
fix npt/cuda command :h3
fix npt/kk command :h3
fix npt/omp command :h3
fix nph command :h3
fix nph/kk command :h3
fix nph/omp command :h3
[Syntax:]

19
doc/fix_wall_reflect.html
View File

@ -126,6 +126,9 @@
<div class="section" id="fix-wall-reflect-command">
<span id="index-0"></span><h1>fix wall/reflect command<a class="headerlink" href="#fix-wall-reflect-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="fix-wall-reflect-kk-command">
<h1>fix wall/reflect/kk command<a class="headerlink" href="#fix-wall-reflect-kk-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID wall/reflect face arg ... keyword value ...
@ -245,6 +248,22 @@ perturbation on the particles:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">position</span> <span class="o">=</span> <span class="n">c0</span> <span class="o">+</span> <span class="n">A</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">cos</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="n">delta</span><span class="p">))</span>
</pre></div>
</div>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <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"><em>Section_accelerate</em></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 USER-CUDA, 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>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>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">

24
doc/fix_wall_reflect.txt
View File

@ -7,6 +7,7 @@
:line
fix wall/reflect command :h3
fix wall/reflect/kk command :h3
[Syntax:]
@ -126,6 +127,29 @@ position = c0 + A (1 - cos(omega*delta)) :pre
:line
Styles with a {cuda}, {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 "Section_accelerate"_Section_accelerate.html
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 USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#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 "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart

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