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<div class="section" id="fix-shardlow-command">
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<span id="index-0"></span><h1>fix shardlow command<a class="headerlink" href="#fix-shardlow-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID shardlow
|
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</pre></div>
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</div>
|
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<ul class="simple">
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<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
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<li>shardlow = style name of this fix command</li>
|
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</ul>
|
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</div>
|
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
|
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<div class="highlight-python"><div class="highlight"><pre>fix 1 all shardlow
|
||||
</pre></div>
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</div>
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</div>
|
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<div class="section" id="description">
|
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Specifies that the Shardlow splitting algorithm (SSA) is to be used to
|
||||
integrate the DPD equations of motion. The SSA splits the integration
|
||||
into a stochastic and deterministic integration step. The fix
|
||||
<em>shardlow</em> performs the stochastic integration step and must be used
|
||||
in conjunction with a deterministic integrator (e.g. <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a> or <code class="xref doc docutils literal"><span class="pre">fix</span> <span class="pre">nph</span></code>). The stochastic
|
||||
integration of the dissipative and random forces is performed prior to
|
||||
the deterministic integration of the conservative force. Further
|
||||
details regarding the method are provided in <a class="reference internal" href="pair_dpd_fdt.html#lisal"><span>(Lisal)</span></a> and
|
||||
<a class="reference internal" href="fix_eos_cv.html#larentzos"><span>(Larentzos)</span></a>.</p>
|
||||
<p>The fix <em>shardlow</em> must be used with the <a class="reference internal" href="pair_style.html"><em>pair_style dpd/fdt</em></a> or <a class="reference internal" href="pair_style.html"><em>pair_style dpd/fdt/energy</em></a> command to properly initialize the
|
||||
fluctuation-dissipation theorem parameter(s) sigma (and kappa, if
|
||||
necessary).</p>
|
||||
<p>Note that numerous variants of DPD can be specified by choosing an
|
||||
appropriate combination of the integrator and <a class="reference internal" href="pair_style.html"><em>pair_style dpd/fdt</em></a> command. DPD under isothermal conditions can
|
||||
be specified by using fix <em>shardlow</em>, fix <em>nve</em> and pair_style
|
||||
<em>dpd/fdt</em>. DPD under isoenergetic conditions can be specified by
|
||||
using fix <em>shardlow</em>, fix <em>nve</em> and pair_style <em>dpd/fdt/energy</em>. DPD
|
||||
under isobaric conditions can be specified by using fix shardlow, fix
|
||||
<em>nph</em> and pair_style <em>dpd/fdt</em>. DPD under isoenthalpic conditions can
|
||||
be specified by using fix shardlow, fix <em>nph</em> and pair_style
|
||||
<em>dpd/fdt/energy</em>. Examples of each DPD variant are provided in the
|
||||
examples/USER/dpd directory.</p>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<p>This fix is only available if LAMMPS is built with the USER-DPD
|
||||
package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section
|
||||
for more info.</p>
|
||||
<p>This fix is currently limited to orthogonal simulation cell
|
||||
geometries.</p>
|
||||
<p>This fix must be used with an additional fix that specifies time
|
||||
integration, e.g. <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a> or <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a>.</p>
|
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<p>The Shardlow splitting algorithm requires the sizes of the sub-domain
|
||||
lengths to be larger than twice the cutoff+skin. Generally, the
|
||||
domain decomposition is dependant on the number of processors
|
||||
requested.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
||||
<p><a class="reference internal" href="pair_dpd_fdt.html"><em>pair_style dpd/fdt</em></a>, <a class="reference internal" href="fix_eos_cv.html"><em>fix eos/cv</em></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
<hr class="docutils" />
|
||||
<p id="lisal"><strong>(Lisal)</strong> M. Lisal, J.K. Brennan, J. Bonet Avalos, “Dissipative
|
||||
particle dynamics as isothermal, isobaric, isoenergetic, and
|
||||
isoenthalpic conditions using Shardlow-like splitting algorithms.”,
|
||||
J. Chem. Phys., 135, 204105 (2011).</p>
|
||||
<p id="larentzos"><strong>(Larentzos)</strong> J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and
|
||||
W.D. Mattson, “Parallel Implementation of Isothermal and Isoenergetic
|
||||
Dissipative Particle Dynamics Using Shardlow-Like Splitting
|
||||
Algorithms”, Comput. Phys. Commun., 185, 1987-1998 (2014).</p>
|
||||
<p id="id1"><strong>(Larentzos)</strong> J.P. Larentzos, J.K. Brennan, J.D. Moore, and
|
||||
W.D. Mattson, “LAMMPS Implementation of Constant Energy Dissipative
|
||||
Particle Dynamics (DPD-E)”, ARL-TR-6863, U.S. Army Research
|
||||
Laboratory, Aberdeen Proving Ground, MD (2014).</p>
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@ -0,0 +1,115 @@
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.. index:: fix shardlow
|
||||
|
||||
fix shardlow command
|
||||
====================
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Syntax
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""""""
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.. parsed-literal::
|
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|
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fix ID group-ID shardlow
|
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|
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* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||
* shardlow = style name of this fix command
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix 1 all shardlow
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Specifies that the Shardlow splitting algorithm (SSA) is to be used to
|
||||
integrate the DPD equations of motion. The SSA splits the integration
|
||||
into a stochastic and deterministic integration step. The fix
|
||||
*shardlow* performs the stochastic integration step and must be used
|
||||
in conjunction with a deterministic integrator (e.g. :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nph>`). The stochastic
|
||||
integration of the dissipative and random forces is performed prior to
|
||||
the deterministic integration of the conservative force. Further
|
||||
details regarding the method are provided in :ref:`(Lisal) <Lisal>` and
|
||||
:ref:`(Larentzos) <Larentzos>`.
|
||||
|
||||
The fix *shardlow* must be used with the :doc:`pair_style dpd/fdt <pair_style>` or :doc:`pair_style dpd/fdt/energy <pair_style>` command to properly initialize the
|
||||
fluctuation-dissipation theorem parameter(s) sigma (and kappa, if
|
||||
necessary).
|
||||
|
||||
Note that numerous variants of DPD can be specified by choosing an
|
||||
appropriate combination of the integrator and :doc:`pair_style dpd/fdt <pair_style>` command. DPD under isothermal conditions can
|
||||
be specified by using fix *shardlow*, fix *nve* and pair_style
|
||||
*dpd/fdt*. DPD under isoenergetic conditions can be specified by
|
||||
using fix *shardlow*, fix *nve* and pair_style *dpd/fdt/energy*. DPD
|
||||
under isobaric conditions can be specified by using fix shardlow, fix
|
||||
*nph* and pair_style *dpd/fdt*. DPD under isoenthalpic conditions can
|
||||
be specified by using fix shardlow, fix *nph* and pair_style
|
||||
*dpd/fdt/energy*. Examples of each DPD variant are provided in the
|
||||
examples/USER/dpd directory.
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
|
||||
This fix is only available if LAMMPS is built with the USER-DPD
|
||||
package. See the :ref:`Making LAMMPS <start_3>` section
|
||||
for more info.
|
||||
|
||||
This fix is currently limited to orthogonal simulation cell
|
||||
geometries.
|
||||
|
||||
This fix must be used with an additional fix that specifies time
|
||||
integration, e.g. :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nh>`.
|
||||
|
||||
The Shardlow splitting algorithm requires the sizes of the sub-domain
|
||||
lengths to be larger than twice the cutoff+skin. Generally, the
|
||||
domain decomposition is dependant on the number of processors
|
||||
requested.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_style dpd/fdt <pair_dpd_fdt>`, :doc:`fix eos/cv <fix_eos_cv>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
.. _Lisal:
|
||||
|
||||
|
||||
|
||||
**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative
|
||||
particle dynamics as isothermal, isobaric, isoenergetic, and
|
||||
isoenthalpic conditions using Shardlow-like splitting algorithms.",
|
||||
J. Chem. Phys., 135, 204105 (2011).
|
||||
|
||||
.. _Larentzos:
|
||||
|
||||
|
||||
|
||||
**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and
|
||||
W.D. Mattson, "Parallel Implementation of Isothermal and Isoenergetic
|
||||
Dissipative Particle Dynamics Using Shardlow-Like Splitting
|
||||
Algorithms", Comput. Phys. Commun., 185, 1987-1998 (2014).
|
||||
|
||||
.. _Larentzos:
|
||||
|
||||
|
||||
|
||||
**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and
|
||||
W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
|
||||
Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
|
||||
Laboratory, Aberdeen Proving Ground, MD (2014).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
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.. _ld: Manual.html
|
||||
.. _lc: Section_commands.html#comm
|
||||
|
|
@ -0,0 +1,96 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
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:link(lws,http://lammps.sandia.gov)
|
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:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix shardlow command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID shardlow :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command
|
||||
shardlow = style name of this fix command :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all shardlow :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Specifies that the Shardlow splitting algorithm (SSA) is to be used to
|
||||
integrate the DPD equations of motion. The SSA splits the integration
|
||||
into a stochastic and deterministic integration step. The fix
|
||||
{shardlow} performs the stochastic integration step and must be used
|
||||
in conjunction with a deterministic integrator (e.g. "fix
|
||||
nve"_fix_nve.html or "fix nph"_fix_nph.html). The stochastic
|
||||
integration of the dissipative and random forces is performed prior to
|
||||
the deterministic integration of the conservative force. Further
|
||||
details regarding the method are provided in "(Lisal)"_#Lisal and
|
||||
"(Larentzos)"_#Larentzos.
|
||||
|
||||
The fix {shardlow} must be used with the "pair_style
|
||||
dpd/fdt"_pair_style.html or "pair_style
|
||||
dpd/fdt/energy"_pair_style.html command to properly initialize the
|
||||
fluctuation-dissipation theorem parameter(s) sigma (and kappa, if
|
||||
necessary).
|
||||
|
||||
Note that numerous variants of DPD can be specified by choosing an
|
||||
appropriate combination of the integrator and "pair_style
|
||||
dpd/fdt"_pair_style.html command. DPD under isothermal conditions can
|
||||
be specified by using fix {shardlow}, fix {nve} and pair_style
|
||||
{dpd/fdt}. DPD under isoenergetic conditions can be specified by
|
||||
using fix {shardlow}, fix {nve} and pair_style {dpd/fdt/energy}. DPD
|
||||
under isobaric conditions can be specified by using fix shardlow, fix
|
||||
{nph} and pair_style {dpd/fdt}. DPD under isoenthalpic conditions can
|
||||
be specified by using fix shardlow, fix {nph} and pair_style
|
||||
{dpd/fdt/energy}. Examples of each DPD variant are provided in the
|
||||
examples/USER/dpd directory.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is only available if LAMMPS is built with the USER-DPD
|
||||
package. See the "Making LAMMPS"_Section_start.html#start_3 section
|
||||
for more info.
|
||||
|
||||
This fix is currently limited to orthogonal simulation cell
|
||||
geometries.
|
||||
|
||||
This fix must be used with an additional fix that specifies time
|
||||
integration, e.g. "fix nve"_fix_nve.html or "fix nph"_fix_nh.html.
|
||||
|
||||
The Shardlow splitting algorithm requires the sizes of the sub-domain
|
||||
lengths to be larger than twice the cutoff+skin. Generally, the
|
||||
domain decomposition is dependant on the number of processors
|
||||
requested.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style dpd/fdt"_pair_dpd_fdt.html, "fix eos/cv"_fix_eos_cv.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Lisal)
|
||||
[(Lisal)] M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative
|
||||
particle dynamics as isothermal, isobaric, isoenergetic, and
|
||||
isoenthalpic conditions using Shardlow-like splitting algorithms.",
|
||||
J. Chem. Phys., 135, 204105 (2011).
|
||||
|
||||
:link(Larentzos)
|
||||
[(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and
|
||||
W.D. Mattson, "Parallel Implementation of Isothermal and Isoenergetic
|
||||
Dissipative Particle Dynamics Using Shardlow-Like Splitting
|
||||
Algorithms", Comput. Phys. Commun., 185, 1987-1998 (2014).
|
||||
|
||||
:link(Larentzos)
|
||||
[(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and
|
||||
W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
|
||||
Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
|
||||
Laboratory, Aberdeen Proving Ground, MD (2014).
|
||||
Loading…
Reference in New Issue