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<li>pair_style srp command</li>
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<div itemprop="articleBody">
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<div class="section" id="pair-style-srp-command">
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<span id="index-0"></span><h1>pair_style srp command<a class="headerlink" href="#pair-style-srp-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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<p>pair_style srp cutoff bond_type dist keyword value ...</p>
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<ul class="simple">
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<li>cutoff = global cutoff for SRP interactions (distance units)</li>
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<li>bond_type = bond type to apply SRP interactions</li>
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<li>distance = <em>min</em> or <em>mid</em></li>
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<li>zero or more keyword/value pairs may be appended</li>
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<li>keyword = <em>exclude</em></li>
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</ul>
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<pre class="literal-block">
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<em>exclude</em> value = <em>yes</em> or <em>no</em>
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</pre>
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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>pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes
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pair_coeff 1 1 dpd 60.0 4.5 1.0
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pair_coeff 1 2 none
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pair_coeff 2 2 srp 100.0 0.8
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes
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pair_coeff 1 1 dpd 60.0 50 1.0
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pair_coeff 1 2 none
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pair_coeff 2 2 srp 40.0
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid srp 0.8 2 mid
|
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pair_coeff 1 1 none
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pair_coeff 1 2 none
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pair_coeff 2 2 srp 100.0 0.8
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</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>
|
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<p>Style <em>srp</em> computes a soft segmental repulsive potential (SRP) that
|
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<HR>
|
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|
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<H3>pair_style srp command
|
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</H3>
|
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<P><B>Syntax:</B>
|
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</P>
|
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<P>pair_style srp cutoff bond_type dist keyword value ...
|
||||
</P>
|
||||
<UL><LI>cutoff = global cutoff for SRP interactions (distance units)
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|
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<LI>bond_type = bond type to apply SRP interactions
|
||||
|
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<LI>distance = <I>min</I> or <I>mid</I>
|
||||
|
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<LI>zero or more keyword/value pairs may be appended
|
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|
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<LI>keyword = <I>exclude</I>
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|
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<PRE> <I>exclude</I> value = <I>yes</I> or <I>no</I>
|
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</PRE>
|
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|
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</UL>
|
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<P><B>Examples:</B>
|
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</P>
|
||||
<PRE>pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes
|
||||
pair_coeff 1 1 dpd 60.0 4.5 1.0
|
||||
pair_coeff 1 2 none
|
||||
pair_coeff 2 2 srp 100.0 0.8
|
||||
</PRE>
|
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<PRE>pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes
|
||||
pair_coeff 1 1 dpd 60.0 50 1.0
|
||||
pair_coeff 1 2 none
|
||||
pair_coeff 2 2 srp 40.0
|
||||
</PRE>
|
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<PRE>pair_style hybrid srp 0.8 2 mid
|
||||
pair_coeff 1 1 none
|
||||
pair_coeff 1 2 none
|
||||
pair_coeff 2 2 srp 100.0 0.8
|
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</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Style <I>srp</I> computes a soft segmental repulsive potential (SRP) that
|
||||
acts between pairs of bonds. This potential is useful for preventing
|
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bonds from passing through one another when a soft non-bonded
|
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potential acts between beads in, for example, DPD polymer chains. An
|
||||
example input script that uses this command is provided in
|
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examples/USER/srp.</p>
|
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<p>Bonds of type <em>btype</em> interact with one another through a
|
||||
bond-pairwise potential, such that the force on bond <em>i</em> due to bond
|
||||
<em>j</em> is as follows</p>
|
||||
<img alt="_images/pair_srp1.jpg" class="align-center" src="_images/pair_srp1.jpg" />
|
||||
<p>where <em>r</em> and <em>rij</em> are the distance and unit vector between the two
|
||||
examples/USER/srp.
|
||||
</P>
|
||||
<P>Bonds of type <I>btype</I> interact with one another through a
|
||||
bond-pairwise potential, such that the force on bond <I>i</I> due to bond
|
||||
<I>j</I> is as follows
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/pair_srp1.jpg">
|
||||
</CENTER>
|
||||
<P>where <I>r</I> and <I>rij</I> are the distance and unit vector between the two
|
||||
bonds. The bondtype can also be specified as an asterisk (*) and then
|
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this interaction applied to all bonds.
|
||||
The <em>mid</em> option computes <em>r</em> and <em>rij</em> from the midpoint
|
||||
distance between bonds. The <em>min</em> option computes <em>r</em> and <em>rij</em> from
|
||||
The <I>mid</I> option computes <I>r</I> and <I>rij</I> from the midpoint
|
||||
distance between bonds. The <I>min</I> option computes <I>r</I> and <I>rij</I> from
|
||||
the minimum distance between bonds. The force acting on a bond is
|
||||
mapped onto the two bond atoms according to the lever rule,</p>
|
||||
<img alt="_images/pair_srp2.jpg" class="align-center" src="_images/pair_srp2.jpg" />
|
||||
<p>where <em>L</em> is the normalized distance from the atom to the point of
|
||||
closest approach of bond <em>i</em> and <em>j</em>. The <em>mid</em> option takes <em>L</em> as
|
||||
0.5 for each interaction as described in <a class="reference internal" href="#sirk"><span>(Sirk)</span></a>.</p>
|
||||
<p>The following coefficients must be defined via the
|
||||
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples above, or in
|
||||
the data file or restart file read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
|
||||
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
|
||||
<ul class="simple">
|
||||
<li><em>C</em> (force units)</li>
|
||||
<li><em>rc</em> (distance units)</li>
|
||||
</ul>
|
||||
<p>The last coefficient is optional. If not specified, the global cutoff
|
||||
is used.</p>
|
||||
<div class="admonition warning">
|
||||
<p class="first admonition-title">Warning</p>
|
||||
<p class="last">Pair style srp considers each bond of type <em>btype</em> as
|
||||
a fictitious particle of type <em>bptype</em>, where <em>bptype</em> is the largest
|
||||
atom type in the system. These “bond particles” are inserted at the
|
||||
mapped onto the two bond atoms according to the lever rule,
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/pair_srp2.jpg">
|
||||
</CENTER>
|
||||
<P>where <I>L</I> is the normalized distance from the atom to the point of
|
||||
closest approach of bond <I>i</I> and <I>j</I>. The <I>mid</I> option takes <I>L</I> as
|
||||
0.5 for each interaction as described in <A HREF = "#Sirk">(Sirk)</A>.
|
||||
</P>
|
||||
<P>The following coefficients must be defined via the
|
||||
<A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above, or in
|
||||
the data file or restart file read by the <A HREF = "read_data.html">read_data</A>
|
||||
or <A HREF = "read_restart.html">read_restart</A> commands:
|
||||
</P>
|
||||
<UL><LI><I>C</I> (force units)
|
||||
<LI><I>rc</I> (distance units)
|
||||
</UL>
|
||||
<P>The last coefficient is optional. If not specified, the global cutoff
|
||||
is used.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: Pair style srp considers each bond of type <I>btype</I> as
|
||||
a fictitious particle of type <I>bptype</I>, where <I>bptype</I> is the largest
|
||||
atom type in the system. These "bond particles" are inserted at the
|
||||
beginning of the run, and serve as placeholders that define the
|
||||
position of the bonds. This allows neighbor lists to be constructed
|
||||
and pairwise interactions to be computed in almost the same way as is
|
||||
done for point particles. Because bonds interact only with other
|
||||
bonds, <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> should be used to turn off
|
||||
interactions between atom type <em>bptype</em> and all other types of atoms.
|
||||
An error will be flagged if <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> is
|
||||
bonds, <A HREF = "pair_hybrid.html">pair_style hybrid</A> should be used to turn off
|
||||
interactions between atom type <I>bptype</I> and all other types of atoms.
|
||||
An error will be flagged if <A HREF = "pair_hybrid.html">pair_style hybrid</A> is
|
||||
not used. Further, only bond particles should be given an atom type
|
||||
of <em>bptype</em>; a check is done at the beginning of the run to ensure
|
||||
there are no regular atoms of <em>bptype</em>.</p>
|
||||
</div>
|
||||
<p>The optional <em>exclude</em> keyword determines if forces are computed
|
||||
of <I>bptype</I>; a check is done at the beginning of the run to ensure
|
||||
there are no regular atoms of <I>bptype</I>.
|
||||
</P>
|
||||
<P>The optional <I>exclude</I> keyword determines if forces are computed
|
||||
between first neighbor (directly connected) bonds. For a setting of
|
||||
<em>no</em>, first neighbor forces are computed; for <em>yes</em> they are not computed. A setting of <em>no</em>
|
||||
cannot be used with the <em>min</em> option for distance calculation because the the minimum distance between
|
||||
directly connected bonds is zero.</p>
|
||||
<p>Pair style <em>srp</em> turns off normalization of thermodynamic properties
|
||||
by particle number, as if the command <a class="reference internal" href="thermo_modify.html"><em>thermo_modify norm no</em></a> had been issued.</p>
|
||||
<p>The pairwise energy associated with style <em>srp</em> is shifted to be zero
|
||||
at the cutoff distance <em>rc</em>.</p>
|
||||
<hr class="docutils" />
|
||||
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
|
||||
<p>This pair styles does not support mixing.</p>
|
||||
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
|
||||
<I>no</I>, first neighbor forces are computed; for <I>yes</I> they are not computed. A setting of <I>no</I>
|
||||
cannot be used with the <I>min</I> option for distance calculation because the the minimum distance between
|
||||
directly connected bonds is zero.
|
||||
</P>
|
||||
<P>Pair style <I>srp</I> turns off normalization of thermodynamic properties
|
||||
by particle number, as if the command <A HREF = "thermo_modify.html">thermo_modify norm
|
||||
no</A> had been issued.
|
||||
</P>
|
||||
<P>The pairwise energy associated with style <I>srp</I> is shifted to be zero
|
||||
at the cutoff distance <I>rc</I>.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
|
||||
</P>
|
||||
<P>This pair styles does not support mixing.
|
||||
</P>
|
||||
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
|
||||
shift option for the energy of the pair interaction. Note that as
|
||||
discussed above, the energy term is already shifted to be 0.0 at the
|
||||
cutoff distance <em>rc</em>.</p>
|
||||
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant for
|
||||
this pair style.</p>
|
||||
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
|
||||
cutoff distance <I>rc</I>.
|
||||
</P>
|
||||
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant for
|
||||
this pair style.
|
||||
</P>
|
||||
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
|
||||
tail option for adding long-range tail corrections to energy and
|
||||
pressure.</p>
|
||||
<p>This pair style writes global and per-atom information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. Pair srp should be used with <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a>, thus the pair_coeff commands need to be
|
||||
specified in the input script when reading a restart file.</p>
|
||||
<p>This pair style can only be used via the <em>pair</em> keyword of the
|
||||
<a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command. It does not support the
|
||||
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</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 pair style is part of the USER-MISC package. It is only enabled
|
||||
pressure.
|
||||
</P>
|
||||
<P>This pair style writes global and per-atom information to <A HREF = "restart.html">binary
|
||||
restart files</A>. Pair srp should be used with <A HREF = "pair_hybrid.html">pair_style
|
||||
hybrid</A>, thus the pair_coeff commands need to be
|
||||
specified in the input script when reading a restart file.
|
||||
</P>
|
||||
<P>This pair style can only be used via the <I>pair</I> keyword of the
|
||||
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
|
||||
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>This pair style is part of the USER-MISC package. It is only enabled
|
||||
if LAMMPS was built with that package. See the Making LAMMPS section
|
||||
for more info.</p>
|
||||
<p>This pair style must be used with <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a>.</p>
|
||||
<p>This pair style requires the <a class="reference internal" href="newton.html"><em>newton</em></a> command to be <em>on</em>
|
||||
for non-bonded interactions.</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_hybrid.html"><em>pair_style hybrid</em></a>, <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>,
|
||||
<a class="reference internal" href="pair_dpd.html"><em>pair dpd</em></a></p>
|
||||
</div>
|
||||
<div class="section" id="default">
|
||||
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The default keyword value is exclude = yes.</p>
|
||||
<hr class="docutils" />
|
||||
<p id="sirk"><strong>(Sirk)</strong> Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J
|
||||
Chem Phys, 136 (13) 134903, 2012.</p>
|
||||
</div>
|
||||
</div>
|
||||
for more info.
|
||||
</P>
|
||||
<P>This pair style must be used with <A HREF = "pair_hybrid.html">pair_style hybrid</A>.
|
||||
</P>
|
||||
<P>This pair style requires the <A HREF = "newton.html">newton</A> command to be <I>on</I>
|
||||
for non-bonded interactions.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "pair_hybrid.html">pair_style hybrid</A>, <A HREF = "pair_coeff.html">pair_coeff</A>,
|
||||
<A HREF = "pair_dpd.html">pair dpd</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>The default keyword value is exclude = yes.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "Sirk"></A>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<footer>
|
||||
|
||||
|
||||
<hr/>
|
||||
|
||||
<div role="contentinfo">
|
||||
<p>
|
||||
© Copyright .
|
||||
</p>
|
||||
</div>
|
||||
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||||
|
||||
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|
||||
|
||||
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|
||||
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|
||||
|
||||
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|
||||
|
||||
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|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<script type="text/javascript">
|
||||
var DOCUMENTATION_OPTIONS = {
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
</html>
|
||||
<P><B>(Sirk)</B> Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J
|
||||
Chem Phys, 136 (13) 134903, 2012.
|
||||
</P>
|
||||
</HTML>
|
||||
|
||||
Reference in New Issue
Block a user