forked from lijiext/lammps
Modifed ZBL to accomodate mixing
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14048 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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athomps
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<title>pair_style zbl command — LAMMPS 15 May 2015 version documentation</title>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<li>pair_style zbl command</li>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div itemprop="articleBody">
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<div class="section" id="pair-style-zbl-command">
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<span id="index-0"></span><h1>pair_style zbl command<a class="headerlink" href="#pair-style-zbl-command" title="Permalink to this headline">¶</a></h1>
|
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</div>
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<div class="section" id="pair-style-zbl-gpu-command">
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<h1>pair_style zbl/gpu command<a class="headerlink" href="#pair-style-zbl-gpu-command" title="Permalink to this headline">¶</a></h1>
|
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</div>
|
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<div class="section" id="pair-style-zbl-omp-command">
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<h1>pair_style zbl/omp command<a class="headerlink" href="#pair-style-zbl-omp-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>pair_style zbl inner outer
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</pre></div>
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</div>
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<ul class="simple">
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<li>inner = distance where switching function begins</li>
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<li>outer = global cutoff for ZBL interaction</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>pair_style zbl 3.0 4.0
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pair_coeff * * 73.0
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pair_coeff 1 1 14.0
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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>zbl</em> computes the Ziegler-Biersack-Littmark (ZBL) screened nuclear
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<HR>
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|
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<H3>pair_style zbl command
|
||||
</H3>
|
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<H3>pair_style zbl/gpu command
|
||||
</H3>
|
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<H3>pair_style zbl/omp command
|
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</H3>
|
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<P><B>Syntax:</B>
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</P>
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<PRE>pair_style zbl inner outer
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</PRE>
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<UL><LI>inner = distance where switching function begins
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<LI>outer = global cutoff for ZBL interaction
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style zbl 3.0 4.0
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pair_coeff * * 73.0 73.0
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pair_coeff 1 1 14.0 14.0
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</PRE>
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<P><B>Description:</B>
|
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</P>
|
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<P>Style <I>zbl</I> computes the Ziegler-Biersack-Littmark (ZBL) screened nuclear
|
||||
repulsion for describing high-energy collisions between atoms.
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<a class="reference internal" href="#ziegler"><span>(Ziegler)</span></a>. It includes an additional switching function
|
||||
that ramps the energy, force, and curvature smoothly to zero
|
||||
<A HREF = "#Ziegler">(Ziegler)</A>. It includes an additional switching function
|
||||
that ramps the energy, force, and curvature smoothly to zero
|
||||
between an inner and outer cutoff. The potential
|
||||
energy due to a pair of atoms at a distance r_ij is given by:</p>
|
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<img alt="_images/pair_zbl.jpg" class="align-center" src="_images/pair_zbl.jpg" />
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<p>where e is the electron charge, epsilon_0 is the electrical
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energy due to a pair of atoms at a distance r_ij is given by:
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</P>
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<CENTER><IMG SRC = "Eqs/pair_zbl.jpg">
|
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</CENTER>
|
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<P>where e is the electron charge, epsilon_0 is the electrical
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permittivity of vacuum, and Z_i and Z_j are the nuclear charges of the
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two atoms. The switching function S(r) is identical to that used by
|
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<a class="reference internal" href="pair_gromacs.html"><em>pair_style lj/gromacs</em></a>. Here, the inner and outer
|
||||
cutoff are the same for all pairs of atom types.</p>
|
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<p>The following coefficient must be defined for each pair of atom types
|
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via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples above,
|
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or in the LAMMPS data file. Z can not be specified for two different
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atoms types. Therefore the lists of atom types I and atom types J
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must match.</p>
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<ul class="simple">
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<li>Z (multiples of proton charge, e.g. 13.0 for aluminum)</li>
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</ul>
|
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<p>Although Z must be defined for all atom type pairs I,J, it is only
|
||||
stored for individual atom types, i.e. when I = J. Z is normally equal
|
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to the atomic number of the atom type.</p>
|
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<div class="admonition warning">
|
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<p class="first admonition-title">Warning</p>
|
||||
<p class="last">The numerical values of the exponential decay
|
||||
<A HREF = "pair_gromacs.html">pair_style lj/gromacs</A>. Here, the inner and outer
|
||||
cutoff are the same for all pairs of atom types.
|
||||
</P>
|
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<P>The following coefficients must be defined for each pair of atom types
|
||||
via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above,
|
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or in the LAMMPS data file.
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||||
</P>
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||||
<UL><LI>Z_i (atomic number for first atom type, e.g. 13.0 for aluminum)
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</UL>
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<UL><LI>Z_j (ditto for second atom type)
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</UL>
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<P>The values of Z_i and Z_j are normally equal to the atomic
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numbers of the two atom types. Thus, the user may optionally
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specify only the coefficients for each I==I pair, and rely
|
||||
on the obvious mixing rule for cross interactions (see below).
|
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Note that when I==I it is required that Z_i == Z_j. When used
|
||||
with <A HREF = "pair_hybrid.html">hybrid/overlay</A> and pairs are assigned
|
||||
to more than one sub-style, the mixing rule is not used and
|
||||
each pair of types interacting with the ZBL sub-style must
|
||||
be included in a pair_coeff command.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: The numerical values of the exponential decay
|
||||
constants in the screening function depend on the unit of distance. In
|
||||
the above equation they are given for units of angstroms. LAMMPS will
|
||||
automatically convert these values to the distance unit of the
|
||||
specified LAMMPS <a class="reference internal" href="units.html"><em>units</em></a> setting. The values of Z should
|
||||
always be given as multiples of a proton’s charge, e.g. 29.0 for
|
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copper.</p>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
|
||||
specified LAMMPS <A HREF = "units.html">units</A> setting. The values of Z should
|
||||
always be given as multiples of a proton's charge, e.g. 29.0 for
|
||||
copper.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
|
||||
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
|
||||
of the manual. The accelerated styles take the same arguments and
|
||||
should produce the same results, except for round-off and precision
|
||||
issues.</p>
|
||||
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
|
||||
issues.
|
||||
</P>
|
||||
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
|
||||
KOKKOS, USER-OMP and OPT packages, respectively. They are only
|
||||
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
|
||||
<p>You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.</p>
|
||||
<hr class="docutils" />
|
||||
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
|
||||
<p>Mixing is not relevant for this pair style, since as explained above,
|
||||
Z values are stored on a per-type basis, and both Zi and Zj are used
|
||||
explicitly in the ZBL formula.</p>
|
||||
<p>The ZBL pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
|
||||
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P>You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
|
||||
switch</A> when you invoke LAMMPS, or you can
|
||||
use the <A HREF = "suffix.html">suffix</A> command in your input script.
|
||||
</P>
|
||||
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
|
||||
</P>
|
||||
<P>For atom type pairs I,J and I != J, the Z_i and Z_j coefficients
|
||||
can be mixed by taking Z_i and Z_j from the values specified for
|
||||
I == I and J == J cases. When used
|
||||
with <A HREF = "pair_hybrid.html">hybrid/overlay</A> and pairs are assigned
|
||||
to more than one sub-style, the mixing rule is not used and
|
||||
each pair of types interacting with the ZBL sub-style
|
||||
must be included in a pair_coeff command.
|
||||
The <A HREF = "pair_modify.html">pair_modify</A> mix option has no effect on
|
||||
the mixing behavior
|
||||
</P>
|
||||
<P>The ZBL pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
|
||||
shift option, since the ZBL interaction is already smoothed to 0.0 at
|
||||
the cutoff.</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>
|
||||
the cutoff.
|
||||
</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, since there are no corrections for a potential that goes to
|
||||
0.0 at the cutoff.</p>
|
||||
<p>This pair style does not write information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands must be
|
||||
specified in an input script that reads 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>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</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_coeff.html"><em>pair_coeff</em></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
<hr class="docutils" />
|
||||
<p id="ziegler"><strong>(Ziegler)</strong> J.F. Ziegler, J. P. Biersack and U. Littmark, “The
|
||||
Stopping and Range of Ions in Matter,” Volume 1, Pergamon, 1985.</p>
|
||||
</div>
|
||||
</div>
|
||||
0.0 at the cutoff.
|
||||
</P>
|
||||
<P>This pair style does not write information to <A HREF = "restart.html">binary restart
|
||||
files</A>, so pair_style and pair_coeff commands must be
|
||||
specified in an input script that reads 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> none
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "pair_coeff.html">pair_coeff</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<footer>
|
||||
|
||||
<A NAME = "Ziegler"></A>
|
||||
|
||||
<hr/>
|
||||
|
||||
<div role="contentinfo">
|
||||
<p>
|
||||
© Copyright .
|
||||
</p>
|
||||
</div>
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|
||||
<P><B>(Ziegler)</B> J.F. Ziegler, J. P. Biersack and U. Littmark, "The
|
||||
Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985.
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
|
|||
|
|
@ -20,8 +20,8 @@ outer = global cutoff for ZBL interaction :ul
|
|||
[Examples:]
|
||||
|
||||
pair_style zbl 3.0 4.0
|
||||
pair_coeff * * 73.0
|
||||
pair_coeff 1 1 14.0 :pre
|
||||
pair_coeff * * 73.0 73.0
|
||||
pair_coeff 1 1 14.0 14.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
@ -40,17 +40,22 @@ two atoms. The switching function S(r) is identical to that used by
|
|||
"pair_style lj/gromacs"_pair_gromacs.html. Here, the inner and outer
|
||||
cutoff are the same for all pairs of atom types.
|
||||
|
||||
The following coefficient must be defined for each pair of atom types
|
||||
The following coefficients must be defined for each pair of atom types
|
||||
via the "pair_coeff"_pair_coeff.html command as in the examples above,
|
||||
or in the LAMMPS data file. Z can not be specified for two different
|
||||
atoms types. Therefore the lists of atom types I and atom types J
|
||||
must match.
|
||||
or in the LAMMPS data file.
|
||||
|
||||
Z (multiples of proton charge, e.g. 13.0 for aluminum) :ul
|
||||
Z_i (atomic number for first atom type, e.g. 13.0 for aluminum) :ul
|
||||
Z_j (ditto for second atom type) :ul
|
||||
|
||||
Although Z must be defined for all atom type pairs I,J, it is only
|
||||
stored for individual atom types, i.e. when I = J. Z is normally equal
|
||||
to the atomic number of the atom type.
|
||||
The values of Z_i and Z_j are normally equal to the atomic
|
||||
numbers of the two atom types. Thus, the user may optionally
|
||||
specify only the coefficients for each I==I pair, and rely
|
||||
on the obvious mixing rule for cross interactions (see below).
|
||||
Note that when I==I it is required that Z_i == Z_j. When used
|
||||
with "hybrid/overlay"_pair_hybrid.html and pairs are assigned
|
||||
to more than one sub-style, the mixing rule is not used and
|
||||
each pair of types interacting with the ZBL sub-style must
|
||||
be included in a pair_coeff command.
|
||||
|
||||
IMPORTANT NOTE: The numerical values of the exponential decay
|
||||
constants in the screening function depend on the unit of distance. In
|
||||
|
|
@ -87,9 +92,15 @@ more instructions on how to use the accelerated styles effectively.
|
|||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
Mixing is not relevant for this pair style, since as explained above,
|
||||
Z values are stored on a per-type basis, and both Zi and Zj are used
|
||||
explicitly in the ZBL formula.
|
||||
For atom type pairs I,J and I != J, the Z_i and Z_j coefficients
|
||||
can be mixed by taking Z_i and Z_j from the values specified for
|
||||
I == I and J == J cases. When used
|
||||
with "hybrid/overlay"_pair_hybrid.html and pairs are assigned
|
||||
to more than one sub-style, the mixing rule is not used and
|
||||
each pair of types interacting with the ZBL sub-style
|
||||
must be included in a pair_coeff command.
|
||||
The "pair_modify"_pair_modify.html mix option has no effect on
|
||||
the mixing behavior
|
||||
|
||||
The ZBL pair style does not support the "pair_modify"_pair_modify.html
|
||||
shift option, since the ZBL interaction is already smoothed to 0.0 at
|
||||
|
|
|
|||
Loading…
Reference in New Issue