git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15372 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2016-07-27 14:13:02 +00:00
parent ee24be38cb
commit ef6ff80366
5 changed files with 69 additions and 12 deletions

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@ -76,7 +76,9 @@ Syntax
*flip* value = *yes* or *no* = allow or disallow box flips when it becomes highly skewed *flip* value = *yes* or *no* = allow or disallow box flips when it becomes highly skewed
*fixedpoint* values = x y z *fixedpoint* values = x y z
x,y,z = perform barostat dilation/contraction around this point (distance units) x,y,z = perform barostat dilation/contraction around this point (distance units)
*update* value = *dipole* update dipole orientation (only for sphere variants) *update* value = *dipole* or *dipole/dlm*
dipole = update dipole orientation (only for sphere variants)
dipole/dlm = use DLM integrator to update dipole orientation (only for sphere variants)
@ -376,6 +378,13 @@ during the time integration. This option should be used for models
where a dipole moment is assigned to finite-size particles, where a dipole moment is assigned to finite-size particles,
e.g. spheroids via use of the :doc:`atom_style hybrid sphere dipole <atom_style>` command. e.g. spheroids via use of the :doc:`atom_style hybrid sphere dipole <atom_style>` command.
The default dipole orientation integrator can be changed the
Dullweber-Leimkuhler-McLachlan integration scheme
:ref:`(Dullweber) <nh-Dullweber>` when using *update* with the value
*dipole/dlm*\ . This integrator is symplectic and time-reversible,
giving better energy conservation and allows slightly longer timesteps
at only a small additional computational cost.
---------- ----------
@ -717,6 +726,13 @@ Martyna, J Phys A: Math Gen, 39, 5629 (2006).
**(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). **(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
.. _nh-Dullweber:
**(Dullweber)** Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107,
5840 (1997).
.. _lws: http://lammps.sandia.gov .. _lws: http://lammps.sandia.gov
.. _ld: Manual.html .. _ld: Manual.html

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@ -16,11 +16,12 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command * ID, group-ID are documented in :doc:`fix <fix>` command
* nve/sphere = style name of this fix command * nve/sphere = style name of this fix command
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *update*
.. parsed-literal:: .. parsed-literal::
*update* value = *dipole* keyword = *update*
*update* value = *dipole* or *dipole/dlm*
dipole = update orientation of dipole moment during integration dipole = update orientation of dipole moment during integration
dipole/dlm = use DLM integrator to update dipole orientation
@ -31,6 +32,7 @@ Examples
fix 1 all nve/sphere fix 1 all nve/sphere
fix 1 all nve/sphere update dipole fix 1 all nve/sphere update dipole
fix 1 all nve/sphere update dipole/dlm
Description Description
""""""""""" """""""""""
@ -49,6 +51,13 @@ during the time integration. This option should be used for models
where a dipole moment is assigned to finite-size particles, where a dipole moment is assigned to finite-size particles,
e.g. spheroids via use of the :doc:`atom_style hybrid sphere dipole <atom_style>` command. e.g. spheroids via use of the :doc:`atom_style hybrid sphere dipole <atom_style>` command.
The default dipole orientation integrator can be changed the
Dullweber-Leimkuhler-McLachlan integration scheme
:ref:`(Dullweber) <nh-Dullweber>` when using *update* with the value
*dipole/dlm*\ . This integrator is symplectic and time-reversible,
giving better energy conservation and allows slightly longer timesteps
at only a small additional computational cost.
---------- ----------
@ -106,6 +115,17 @@ Related commands
**Default:** none **Default:** none
----------
.. _nve-Dullweber:
**(Dullweber)** Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107,
5840 (1997).
.. _lws: http://lammps.sandia.gov .. _lws: http://lammps.sandia.gov
.. _ld: Manual.html .. _ld: Manual.html
.. _lc: Section_commands.html#comm .. _lc: Section_commands.html#comm

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@ -198,7 +198,9 @@ keyword = <em>temp</em> or <em>iso</em> or <em>aniso</em> or <em>tri</em> or <em
<em>flip</em> value = <em>yes</em> or <em>no</em> = allow or disallow box flips when it becomes highly skewed <em>flip</em> value = <em>yes</em> or <em>no</em> = allow or disallow box flips when it becomes highly skewed
<em>fixedpoint</em> values = x y z <em>fixedpoint</em> values = x y z
x,y,z = perform barostat dilation/contraction around this point (distance units) x,y,z = perform barostat dilation/contraction around this point (distance units)
<em>update</em> value = <em>dipole</em> update dipole orientation (only for sphere variants) <em>update</em> value = <em>dipole</em> or <em>dipole/dlm</em>
dipole = update dipole orientation (only for sphere variants)
dipole/dlm = use DLM integrator to update dipole orientation (only for sphere variants)
</pre> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
@ -451,6 +453,12 @@ orientation of the dipole moment of each particle is also updated
during the time integration. This option should be used for models during the time integration. This option should be used for models
where a dipole moment is assigned to finite-size particles, where a dipole moment is assigned to finite-size particles,
e.g. spheroids via use of the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style hybrid sphere dipole</span></a> command.</p> e.g. spheroids via use of the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style hybrid sphere dipole</span></a> command.</p>
<p>The default dipole orientation integrator can be changed the
Dullweber-Leimkuhler-McLachlan integration scheme
<a class="reference internal" href="#nh-dullweber"><span class="std std-ref">(Dullweber)</span></a> when using <em>update</em> with the value
<em>dipole/dlm</em>. This integrator is symplectic and time-reversible,
giving better energy conservation and allows slightly longer timesteps
at only a small additional computational cost.</p>
<hr class="docutils" /> <hr class="docutils" />
<div class="admonition note"> <div class="admonition note">
<p class="first admonition-title">Note</p> <p class="first admonition-title">Note</p>
@ -715,6 +723,8 @@ not coupled to barostat, otherwise no.</p>
<p id="nh-tuckerman"><strong>(Tuckerman)</strong> Tuckerman, Alejandre, Lopez-Rendon, Jochim, and <p id="nh-tuckerman"><strong>(Tuckerman)</strong> Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
Martyna, J Phys A: Math Gen, 39, 5629 (2006).</p> Martyna, J Phys A: Math Gen, 39, 5629 (2006).</p>
<p id="nh-shinoda"><strong>(Shinoda)</strong> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).</p> <p id="nh-shinoda"><strong>(Shinoda)</strong> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).</p>
<p id="nh-dullweber"><strong>(Dullweber)</strong> Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107,
5840 (1997).</p>
</div> </div>
</div> </div>

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@ -138,17 +138,19 @@
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li> <li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>nve/sphere = style name of this fix command</li> <li>nve/sphere = style name of this fix command</li>
<li>zero or more keyword/value pairs may be appended</li> <li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>update</em></li>
</ul> </ul>
<pre class="literal-block"> <pre class="literal-block">
<em>update</em> value = <em>dipole</em> keyword = <em>update</em>
<em>update</em> value = <em>dipole</em> or <em>dipole/dlm</em>
dipole = update orientation of dipole moment during integration dipole = update orientation of dipole moment during integration
dipole/dlm = use DLM integrator to update dipole orientation
</pre> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">nve</span><span class="o">/</span><span class="n">sphere</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">nve</span><span class="o">/</span><span class="n">sphere</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">nve</span><span class="o">/</span><span class="n">sphere</span> <span class="n">update</span> <span class="n">dipole</span> <span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">nve</span><span class="o">/</span><span class="n">sphere</span> <span class="n">update</span> <span class="n">dipole</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">nve</span><span class="o">/</span><span class="n">sphere</span> <span class="n">update</span> <span class="n">dipole</span><span class="o">/</span><span class="n">dlm</span>
</pre></div> </pre></div>
</div> </div>
</div> </div>
@ -165,6 +167,12 @@ orientation of the dipole moment of each particle is also updated
during the time integration. This option should be used for models during the time integration. This option should be used for models
where a dipole moment is assigned to finite-size particles, where a dipole moment is assigned to finite-size particles,
e.g. spheroids via use of the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style hybrid sphere dipole</span></a> command.</p> e.g. spheroids via use of the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style hybrid sphere dipole</span></a> command.</p>
<p>The default dipole orientation integrator can be changed the
Dullweber-Leimkuhler-McLachlan integration scheme
<a class="reference internal" href="fix_nh.html#nh-dullweber"><span class="std std-ref">(Dullweber)</span></a> when using <em>update</em> with the value
<em>dipole/dlm</em>. This integrator is symplectic and time-reversible,
giving better energy conservation and allows slightly longer timesteps
at only a small additional computational cost.</p>
<hr class="docutils" /> <hr class="docutils" />
<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are <p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix. functionally the same as the corresponding style without the suffix.
@ -205,6 +213,9 @@ be point particles.</p>
<h2>Related commands</h2> <h2>Related commands</h2>
<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></p> <p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a></p>
<p><strong>Default:</strong> none</p> <p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="nve-dullweber"><strong>(Dullweber)</strong> Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107,
5840 (1997).</p>
</div> </div>
</div> </div>

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