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

This commit is contained in:
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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@ -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_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_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_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_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>
<tr class="row-even"><td><a class="reference internal" href="fix_nvt_sphere.html"><em>nvt/sphere (o)</em></a></td> <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> <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"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="21%" /> <col width="21%" />
<col width="25%" /> <col width="24%" />
<col width="28%" /> <col width="28%" />
<col width="27%" /> <col width="27%" />
</colgroup> </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_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> <td><a class="reference internal" href="angle_cosine_squared.html"><em>cosine/squared (o)</em></a></td>
</tr> </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><a class="reference internal" href="angle_table.html"><em>table (o)</em></a></td>
<td>&nbsp;</td> <td>&nbsp;</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_charmm.html"><em>charmm (ko)</em></a></td>
<td><a class="reference internal" href="dihedral_class2.html"><em>class2 (o)</em></a></td> <td><a class="reference internal" href="dihedral_class2.html"><em>class2 (o)</em></a></td>
</tr> </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_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_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> </tr>
</tbody> </tbody>
</table> </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> <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_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_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>
<tr class="row-even"><td><a class="reference internal" href="improper_harmonic.html"><em>harmonic (ko)</em></a></td> <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> <td><a class="reference internal" href="improper_umbrella.html"><em>umbrella (o)</em></a></td>

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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/noforce"_fix_nve_noforce.html,
"nve/sphere (o)"_fix_nve_sphere.html, "nve/sphere (o)"_fix_nve_sphere.html,
"nve/tri"_fix_nve_tri.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/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, "nvt/sphere (o)"_fix_nvt_sphere.html,
"oneway"_fix_oneway.html, "oneway"_fix_oneway.html,
"orient/fcc"_fix_orient_fcc.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/delta (o)"_angle_cosine_delta.html,
"cosine/periodic (o)"_angle_cosine_periodic.html, "cosine/periodic (o)"_angle_cosine_periodic.html,
"cosine/squared (o)"_angle_cosine_squared.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) "table (o)"_angle_table.html :tb(c=4,ea=c)
These are additional angle styles in USER packages, which can be used 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, "hybrid"_dihedral_hybrid.html,
"charmm (ko)"_dihedral_charmm.html, "charmm (ko)"_dihedral_charmm.html,
"class2 (o)"_dihedral_class2.html, "class2 (o)"_dihedral_class2.html,
"harmonic (o)"_dihedral_harmonic.html, "harmonic (io)"_dihedral_harmonic.html,
"helix (o)"_dihedral_helix.html, "helix (o)"_dihedral_helix.html,
"multi/harmonic (o)"_dihedral_multi_harmonic.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 These are additional dihedral styles in USER packages, which can be
used if "LAMMPS is built with the appropriate used if "LAMMPS is built with the appropriate
@ -1063,7 +1063,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"none"_improper_none.html, "none"_improper_none.html,
"hybrid"_improper_hybrid.html, "hybrid"_improper_hybrid.html,
"class2 (o)"_improper_class2.html, "class2 (o)"_improper_class2.html,
"cvff (o)"_improper_cvff.html, "cvff (io)"_improper_cvff.html,
"harmonic (ko)"_improper_harmonic.html, "harmonic (ko)"_improper_harmonic.html,
"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c) "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

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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:`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>` | | :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 = letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT. 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:`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:`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 These are additional angle styles in USER packages, which can be used
if :ref:`LAMMPS is built with the appropriate package <start_3>`. 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 = letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT. 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:`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 These are additional dihedral styles in USER packages, which can be
used if :ref:`LAMMPS is built with the appropriate package <start_3>`. 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 = letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT. 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>` | | | | :doc:`harmonic (ko) <improper_harmonic>` | :doc:`umbrella (o) <improper_umbrella>` | | |
+------------------------------------------+-----------------------------------------+-------------------------------------+---------------------------------+ +------------------------------------------+-----------------------------------------+-------------------------------------+----------------------------------+
These are additional improper styles in USER packages, which can be These are additional improper styles in USER packages, which can be
used if :ref:`LAMMPS is built with the appropriate package <start_3>`. used if :ref:`LAMMPS is built with the appropriate package <start_3>`.

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@ -3,6 +3,9 @@
angle_style harmonic command angle_style harmonic command
============================ ============================
angle_style harmonic/intel command
==================================
angle_style harmonic/kk command angle_style harmonic/kk command
=============================== ===============================

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@ -3,6 +3,9 @@
dihedral_style harmonic command dihedral_style harmonic command
=============================== ===============================
dihedral_style harmonic/intel command
=====================================
dihedral_style harmonic/omp command dihedral_style harmonic/omp command
=================================== ===================================

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@ -3,6 +3,9 @@
dihedral_style opls command dihedral_style opls command
=========================== ===========================
dihedral_style opls/intel command
=================================
dihedral_style opls/kk command dihedral_style opls/kk command
============================== ==============================

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@ -6,6 +6,9 @@ fix nvt command
fix nvt/cuda command fix nvt/cuda command
==================== ====================
fix nvt/intel command
=====================
fix nvt/kk command fix nvt/kk command
================== ==================

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@ -3,6 +3,9 @@
fix nvt/sllod command fix nvt/sllod command
===================== =====================
fix nvt/sllod/intel command
===========================
fix nvt/sllod/omp command fix nvt/sllod/omp command
========================= =========================

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@ -3,6 +3,9 @@
improper_style cvff command improper_style cvff command
=========================== ===========================
improper_style cvff/intel command
=================================
improper_style cvff/omp command improper_style cvff/omp command
=============================== ===============================

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@ -127,6 +127,9 @@
<div class="section" id="angle-style-harmonic-command"> <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> <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>
<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"> <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> <h1>angle_style harmonic/kk command<a class="headerlink" href="#angle-style-harmonic-kk-command" title="Permalink to this headline"></a></h1>
</div> </div>

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@ -7,6 +7,7 @@
:line :line
angle_style harmonic command :h3 angle_style harmonic command :h3
angle_style harmonic/intel command :h3
angle_style harmonic/kk command :h3 angle_style harmonic/kk command :h3
angle_style harmonic/omp command :h3 angle_style harmonic/omp command :h3

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@ -127,6 +127,9 @@
<div class="section" id="dihedral-style-harmonic-command"> <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> <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>
<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"> <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> <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"> <div class="section" id="syntax">

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@ -7,6 +7,7 @@
:line :line
dihedral_style harmonic command :h3 dihedral_style harmonic command :h3
dihedral_style harmonic/intel command :h3
dihedral_style harmonic/omp command :h3 dihedral_style harmonic/omp command :h3
[Syntax:] [Syntax:]

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@ -127,6 +127,9 @@
<div class="section" id="dihedral-style-opls-command"> <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> <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>
<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"> <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> <h1>dihedral_style opls/kk command<a class="headerlink" href="#dihedral-style-opls-kk-command" title="Permalink to this headline"></a></h1>
</div> </div>

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@ -7,6 +7,7 @@
:line :line
dihedral_style opls command :h3 dihedral_style opls command :h3
dihedral_style opls/intel command :h3
dihedral_style opls/kk command :h3 dihedral_style opls/kk command :h3
dihedral_style opls/omp command :h3 dihedral_style opls/omp command :h3

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@ -130,6 +130,9 @@
<div class="section" id="fix-nvt-cuda-command"> <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> <h1>fix nvt/cuda command<a class="headerlink" href="#fix-nvt-cuda-command" title="Permalink to this headline"></a></h1>
</div> </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"> <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> <h1>fix nvt/kk command<a class="headerlink" href="#fix-nvt-kk-command" title="Permalink to this headline"></a></h1>
</div> </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 particles will match the target values specified by Tstart/Tstop and
Pstart/Pstop.</p> Pstart/Pstop.</p>
<p>The equations of motion used are those of Shinoda et al in <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 <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="fix_rigid.html#martyna"><span>(Martyna)</span></a> with the strain 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 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 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" /> <hr class="docutils" />
<p>The thermostat parameters for fix styles <em>nvt</em> and <em>npt</em> is specified <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 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> barostat variables.</p>
<p>The <em>mtk</em> keyword controls whether or not the correction terms due to <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 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 Hoover barostat, whose volume probability distribution function
differs from the true NPT and NPH ensembles by a factor of 1/V. Hence 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 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 scheme at little extra cost. The initial and final updates of the
thermostat variables are broken up into <em>tloop</em> substeps, each of 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 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> does the same thing for the barostat thermostat.</p>
<p>The keyword <em>nreset</em> controls how often the reference dimensions used <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, to define the strain energy are reset. If this keyword is not used,

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@ -8,6 +8,7 @@
fix nvt command :h3 fix nvt command :h3
fix nvt/cuda command :h3 fix nvt/cuda command :h3
fix nvt/intel command :h3
fix nvt/kk command :h3 fix nvt/kk command :h3
fix nvt/omp command :h3 fix nvt/omp command :h3
fix npt command :h3 fix npt command :h3

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@ -127,6 +127,9 @@
<div class="section" id="fix-nvt-sllod-command"> <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> <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>
<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"> <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> <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"> <div class="section" id="syntax">

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@ -7,6 +7,7 @@
:line :line
fix nvt/sllod command :h3 fix nvt/sllod command :h3
fix nvt/sllod/intel command :h3
fix nvt/sllod/omp command :h3 fix nvt/sllod/omp command :h3
[Syntax:] [Syntax:]

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@ -127,6 +127,9 @@
<div class="section" id="improper-style-cvff-command"> <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> <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>
<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"> <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> <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"> <div class="section" id="syntax">

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@ -7,6 +7,7 @@
:line :line
improper_style cvff command :h3 improper_style cvff command :h3
improper_style cvff/intel command :h3
improper_style cvff/omp command :h3 improper_style cvff/omp command :h3
[Syntax:] [Syntax:]

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