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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14597 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2016-02-15 15:36:35 +00:00
parent d615b660c1
commit e98647efb2
22 changed files with 80 additions and 38 deletions
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14
doc/Section_commands.html
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@ -676,9 +676,9 @@ 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 (cko)</em></a></td>
<td><a class="reference internal" href="fix_nh.html"><em>nvt (ciko)</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>
<td><a class="reference internal" href="fix_nvt_sllod.html"><em>nvt/sllod (io)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_nvt_sphere.html"><em>nvt/sphere (o)</em></a></td>
<td><a class="reference internal" href="fix_oneway.html"><em>oneway</em></a></td>
@ -1293,7 +1293,7 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
<table border="1" class="docutils">
<colgroup>
<col width="21%" />
<col width="25%" />
<col width="24%" />
<col width="28%" />
<col width="27%" />
</colgroup>
@ -1308,7 +1308,7 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
<td><a class="reference internal" href="angle_cosine_periodic.html"><em>cosine/periodic (o)</em></a></td>
<td><a class="reference internal" href="angle_cosine_squared.html"><em>cosine/squared (o)</em></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="angle_harmonic.html"><em>harmonic (ko)</em></a></td>
<tr class="row-odd"><td><a class="reference internal" href="angle_harmonic.html"><em>harmonic (iko)</em></a></td>
<td><a class="reference internal" href="angle_table.html"><em>table (o)</em></a></td>
<td>&nbsp;</td>
<td>&nbsp;</td>
@ -1360,10 +1360,10 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
<td><a class="reference internal" href="dihedral_charmm.html"><em>charmm (ko)</em></a></td>
<td><a class="reference internal" href="dihedral_class2.html"><em>class2 (o)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="dihedral_harmonic.html"><em>harmonic (o)</em></a></td>
<tr class="row-even"><td><a class="reference internal" href="dihedral_harmonic.html"><em>harmonic (io)</em></a></td>
<td><a class="reference internal" href="dihedral_helix.html"><em>helix (o)</em></a></td>
<td><a class="reference internal" href="dihedral_multi_harmonic.html"><em>multi/harmonic (o)</em></a></td>
<td><a class="reference internal" href="dihedral_opls.html"><em>opls (ko)</em></a></td>
<td><a class="reference internal" href="dihedral_opls.html"><em>opls (iko)</em></a></td>
</tr>
</tbody>
</table>
@ -1410,7 +1410,7 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
<tr class="row-odd"><td><a class="reference internal" href="improper_none.html"><em>none</em></a></td>
<td><a class="reference internal" href="improper_hybrid.html"><em>hybrid</em></a></td>
<td><a class="reference internal" href="improper_class2.html"><em>class2 (o)</em></a></td>
<td><a class="reference internal" href="improper_cvff.html"><em>cvff (o)</em></a></td>
<td><a class="reference internal" href="improper_cvff.html"><em>cvff (io)</em></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="improper_harmonic.html"><em>harmonic (ko)</em></a></td>
<td><a class="reference internal" href="improper_umbrella.html"><em>umbrella (o)</em></a></td>

12
doc/Section_commands.txt
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@ -534,9 +534,9 @@ 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 (cko)"_fix_nh.html,
"nvt (ciko)"_fix_nh.html,
"nvt/asphere (o)"_fix_nvt_asphere.html,
"nvt/sllod (o)"_fix_nvt_sllod.html,
"nvt/sllod (io)"_fix_nvt_sllod.html,
"nvt/sphere (o)"_fix_nvt_sphere.html,
"oneway"_fix_oneway.html,
"orient/fcc"_fix_orient_fcc.html,
@ -1002,7 +1002,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"cosine/delta (o)"_angle_cosine_delta.html,
"cosine/periodic (o)"_angle_cosine_periodic.html,
"cosine/squared (o)"_angle_cosine_squared.html,
"harmonic (ko)"_angle_harmonic.html,
"harmonic (iko)"_angle_harmonic.html,
"table (o)"_angle_table.html :tb(c=4,ea=c)
These are additional angle styles in USER packages, which can be used
@ -1033,10 +1033,10 @@ KOKKOS, o = USER-OMP, t = OPT.
"hybrid"_dihedral_hybrid.html,
"charmm (ko)"_dihedral_charmm.html,
"class2 (o)"_dihedral_class2.html,
"harmonic (o)"_dihedral_harmonic.html,
"harmonic (io)"_dihedral_harmonic.html,
"helix (o)"_dihedral_helix.html,
"multi/harmonic (o)"_dihedral_multi_harmonic.html,
"opls (ko)"_dihedral_opls.html :tb(c=4,ea=c)
"opls (iko)"_dihedral_opls.html :tb(c=4,ea=c)
These are additional dihedral styles in USER packages, which can be
used if "LAMMPS is built with the appropriate
@ -1063,7 +1063,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"none"_improper_none.html,
"hybrid"_improper_hybrid.html,
"class2 (o)"_improper_class2.html,
"cvff (o)"_improper_cvff.html,
"cvff (io)"_improper_cvff.html,
"harmonic (ko)"_improper_harmonic.html,
"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

28
doc/_sources/Section_commands.txt
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@ -468,7 +468,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
| :doc:`nph/sphere (o) <fix_nph_sphere>` | :doc:`npt (ckio) <fix_nh>` | :doc:`npt/asphere (o) <fix_npt_asphere>` | :doc:`npt/sphere (o) <fix_npt_sphere>` | :doc:`nve (ckio) <fix_nve>` | :doc:`nve/asphere (i) <fix_nve_asphere>` | :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>` | :doc:`nve/body <fix_nve_body>` |
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
| :doc:`nve/limit <fix_nve_limit>` | :doc:`nve/line <fix_nve_line>` | :doc:`nve/noforce <fix_nve_noforce>` | :doc:`nve/sphere (o) <fix_nve_sphere>` | :doc:`nve/tri <fix_nve_tri>` | :doc:`nvt (cko) <fix_nh>` | :doc:`nvt/asphere (o) <fix_nvt_asphere>` | :doc:`nvt/sllod (o) <fix_nvt_sllod>` |
| :doc:`nve/limit <fix_nve_limit>` | :doc:`nve/line <fix_nve_line>` | :doc:`nve/noforce <fix_nve_noforce>` | :doc:`nve/sphere (o) <fix_nve_sphere>` | :doc:`nve/tri <fix_nve_tri>` | :doc:`nvt (ciko) <fix_nh>` | :doc:`nvt/asphere (o) <fix_nvt_asphere>` | :doc:`nvt/sllod (io) <fix_nvt_sllod>` |
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
| :doc:`nvt/sphere (o) <fix_nvt_sphere>` | :doc:`oneway <fix_oneway>` | :doc:`orient/fcc <fix_orient_fcc>` | :doc:`planeforce <fix_planeforce>` | :doc:`poems <fix_poems>` | :doc:`pour <fix_pour>` | :doc:`press/berendsen <fix_press_berendsen>` | :doc:`print <fix_print>` |
+--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
@ -713,13 +713,13 @@ LAMMPS is built with the :doc:`appropriate accelerated package <Section_accelera
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
+---------------------------------------+----------------------------------------------+----------------------------------------------------+--------------------------------------------------+
+----------------------------------------+----------------------------------------------+----------------------------------------------------+--------------------------------------------------+
| :doc:`none <angle_none>` | :doc:`hybrid <angle_hybrid>` | :doc:`charmm (ko) <angle_charmm>` | :doc:`class2 (o) <angle_class2>` |
+---------------------------------------+----------------------------------------------+----------------------------------------------------+--------------------------------------------------+
+----------------------------------------+----------------------------------------------+----------------------------------------------------+--------------------------------------------------+
| :doc:`cosine (o) <angle_cosine>` | :doc:`cosine/delta (o) <angle_cosine_delta>` | :doc:`cosine/periodic (o) <angle_cosine_periodic>` | :doc:`cosine/squared (o) <angle_cosine_squared>` |
+---------------------------------------+----------------------------------------------+----------------------------------------------------+--------------------------------------------------+
| :doc:`harmonic (ko) <angle_harmonic>` | :doc:`table (o) <angle_table>` | | |
+---------------------------------------+----------------------------------------------+----------------------------------------------------+--------------------------------------------------+
+----------------------------------------+----------------------------------------------+----------------------------------------------------+--------------------------------------------------+
| :doc:`harmonic (iko) <angle_harmonic>` | :doc:`table (o) <angle_table>` | | |
+----------------------------------------+----------------------------------------------+----------------------------------------------------+--------------------------------------------------+
These are additional angle styles in USER packages, which can be used
if :ref:`LAMMPS is built with the appropriate package <start_3>`.
@ -744,11 +744,11 @@ be used if LAMMPS is built with the :doc:`appropriate accelerated package <Secti
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
+-----------------------------------------+-----------------------------------+-----------------------------------------------------+-------------------------------------+
+------------------------------------------+-----------------------------------+-----------------------------------------------------+-------------------------------------+
| :doc:`none <dihedral_none>` | :doc:`hybrid <dihedral_hybrid>` | :doc:`charmm (ko) <dihedral_charmm>` | :doc:`class2 (o) <dihedral_class2>` |
+-----------------------------------------+-----------------------------------+-----------------------------------------------------+-------------------------------------+
| :doc:`harmonic (o) <dihedral_harmonic>` | :doc:`helix (o) <dihedral_helix>` | :doc:`multi/harmonic (o) <dihedral_multi_harmonic>` | :doc:`opls (ko) <dihedral_opls>` |
+-----------------------------------------+-----------------------------------+-----------------------------------------------------+-------------------------------------+
+------------------------------------------+-----------------------------------+-----------------------------------------------------+-------------------------------------+
| :doc:`harmonic (io) <dihedral_harmonic>` | :doc:`helix (o) <dihedral_helix>` | :doc:`multi/harmonic (o) <dihedral_multi_harmonic>` | :doc:`opls (iko) <dihedral_opls>` |
+------------------------------------------+-----------------------------------+-----------------------------------------------------+-------------------------------------+
These are additional dihedral styles in USER packages, which can be
used if :ref:`LAMMPS is built with the appropriate package <start_3>`.
@ -773,11 +773,11 @@ be used if LAMMPS is built with the :doc:`appropriate accelerated package <Secti
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
+------------------------------------------+-----------------------------------------+-------------------------------------+---------------------------------+
| :doc:`none <improper_none>` | :doc:`hybrid <improper_hybrid>` | :doc:`class2 (o) <improper_class2>` | :doc:`cvff (o) <improper_cvff>` |
+------------------------------------------+-----------------------------------------+-------------------------------------+---------------------------------+
+------------------------------------------+-----------------------------------------+-------------------------------------+----------------------------------+
| :doc:`none <improper_none>` | :doc:`hybrid <improper_hybrid>` | :doc:`class2 (o) <improper_class2>` | :doc:`cvff (io) <improper_cvff>` |
+------------------------------------------+-----------------------------------------+-------------------------------------+----------------------------------+
| :doc:`harmonic (ko) <improper_harmonic>` | :doc:`umbrella (o) <improper_umbrella>` | | |
+------------------------------------------+-----------------------------------------+-------------------------------------+---------------------------------+
+------------------------------------------+-----------------------------------------+-------------------------------------+----------------------------------+
These are additional improper styles in USER packages, which can be
used if :ref:`LAMMPS is built with the appropriate package <start_3>`.

3
doc/_sources/angle_harmonic.txt
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@ -3,6 +3,9 @@
angle_style harmonic command
============================
angle_style harmonic/intel command
==================================
angle_style harmonic/kk command
===============================

3
doc/_sources/dihedral_harmonic.txt
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@ -3,6 +3,9 @@
dihedral_style harmonic command
===============================
dihedral_style harmonic/intel command
=====================================
dihedral_style harmonic/omp command
===================================

3
doc/_sources/dihedral_opls.txt
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@ -3,6 +3,9 @@
dihedral_style opls command
===========================
dihedral_style opls/intel command
=================================
dihedral_style opls/kk command
==============================

3
doc/_sources/fix_nh.txt
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@ -6,6 +6,9 @@ fix nvt command
fix nvt/cuda command
====================
fix nvt/intel command
=====================
fix nvt/kk command
==================

3
doc/_sources/fix_nvt_sllod.txt
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@ -3,6 +3,9 @@
fix nvt/sllod command
=====================
fix nvt/sllod/intel command
===========================
fix nvt/sllod/omp command
=========================

3
doc/_sources/improper_cvff.txt
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@ -3,6 +3,9 @@
improper_style cvff command
===========================
improper_style cvff/intel command
=================================
improper_style cvff/omp command
===============================

3
doc/angle_harmonic.html
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@ -127,6 +127,9 @@
<div class="section" id="angle-style-harmonic-command">
<span id="index-0"></span><h1>angle_style harmonic command<a class="headerlink" href="#angle-style-harmonic-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-harmonic-intel-command">
<h1>angle_style harmonic/intel command<a class="headerlink" href="#angle-style-harmonic-intel-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-harmonic-kk-command">
<h1>angle_style harmonic/kk command<a class="headerlink" href="#angle-style-harmonic-kk-command" title="Permalink to this headline"></a></h1>
</div>

1
doc/angle_harmonic.txt
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@ -7,6 +7,7 @@
:line
angle_style harmonic command :h3
angle_style harmonic/intel command :h3
angle_style harmonic/kk command :h3
angle_style harmonic/omp command :h3

3
doc/dihedral_harmonic.html
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@ -127,6 +127,9 @@
<div class="section" id="dihedral-style-harmonic-command">
<span id="index-0"></span><h1>dihedral_style harmonic command<a class="headerlink" href="#dihedral-style-harmonic-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="dihedral-style-harmonic-intel-command">
<h1>dihedral_style harmonic/intel command<a class="headerlink" href="#dihedral-style-harmonic-intel-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="dihedral-style-harmonic-omp-command">
<h1>dihedral_style harmonic/omp command<a class="headerlink" href="#dihedral-style-harmonic-omp-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">

1
doc/dihedral_harmonic.txt
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@ -7,6 +7,7 @@
:line
dihedral_style harmonic command :h3
dihedral_style harmonic/intel command :h3
dihedral_style harmonic/omp command :h3
[Syntax:]

3
doc/dihedral_opls.html
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@ -127,6 +127,9 @@
<div class="section" id="dihedral-style-opls-command">
<span id="index-0"></span><h1>dihedral_style opls command<a class="headerlink" href="#dihedral-style-opls-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="dihedral-style-opls-intel-command">
<h1>dihedral_style opls/intel command<a class="headerlink" href="#dihedral-style-opls-intel-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="dihedral-style-opls-kk-command">
<h1>dihedral_style opls/kk command<a class="headerlink" href="#dihedral-style-opls-kk-command" title="Permalink to this headline"></a></h1>
</div>

1
doc/dihedral_opls.txt
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@ -7,6 +7,7 @@
:line
dihedral_style opls command :h3
dihedral_style opls/intel command :h3
dihedral_style opls/kk command :h3
dihedral_style opls/omp command :h3

15
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-intel-command">
<h1>fix nvt/intel command<a class="headerlink" href="#fix-nvt-intel-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>
@ -236,12 +239,12 @@ 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
@ -398,7 +401,7 @@ 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
@ -407,7 +410,7 @@ negligible.</p>
scheme at little extra cost. The initial and final updates of the
thermostat variables are broken up into <em>tloop</em> substeps, each of
length <em>dt</em>/<em>tloop</em>. This corresponds to using a first-order
Suzuki-Yoshida scheme <a class="reference internal" href="run_style.html#tuckerman"><span>(Tuckerman)</span></a>. The keyword <em>ploop</em>
Suzuki-Yoshida scheme <a class="reference internal" href="#tuckerman"><span>(Tuckerman)</span></a>. The keyword <em>ploop</em>
does the same thing for the barostat thermostat.</p>
<p>The keyword <em>nreset</em> controls how often the reference dimensions used
to define the strain energy are reset. If this keyword is not used,

1
doc/fix_nh.txt
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@ -8,6 +8,7 @@
fix nvt command :h3
fix nvt/cuda command :h3
fix nvt/intel command :h3
fix nvt/kk command :h3
fix nvt/omp command :h3
fix npt command :h3

3
doc/fix_nvt_sllod.html
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@ -127,6 +127,9 @@
<div class="section" id="fix-nvt-sllod-command">
<span id="index-0"></span><h1>fix nvt/sllod command<a class="headerlink" href="#fix-nvt-sllod-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="fix-nvt-sllod-intel-command">
<h1>fix nvt/sllod/intel command<a class="headerlink" href="#fix-nvt-sllod-intel-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="fix-nvt-sllod-omp-command">
<h1>fix nvt/sllod/omp command<a class="headerlink" href="#fix-nvt-sllod-omp-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">

1
doc/fix_nvt_sllod.txt
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@ -7,6 +7,7 @@
:line
fix nvt/sllod command :h3
fix nvt/sllod/intel command :h3
fix nvt/sllod/omp command :h3
[Syntax:]

3
doc/improper_cvff.html
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@ -127,6 +127,9 @@
<div class="section" id="improper-style-cvff-command">
<span id="index-0"></span><h1>improper_style cvff command<a class="headerlink" href="#improper-style-cvff-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="improper-style-cvff-intel-command">
<h1>improper_style cvff/intel command<a class="headerlink" href="#improper-style-cvff-intel-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="improper-style-cvff-omp-command">
<h1>improper_style cvff/omp command<a class="headerlink" href="#improper-style-cvff-omp-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">

1
doc/improper_cvff.txt
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@ -7,6 +7,7 @@
:line
improper_style cvff command :h3
improper_style cvff/intel command :h3
improper_style cvff/omp command :h3
[Syntax:]

2
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