forked from lijiext/lammps
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This commit is contained in:
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@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands.
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.. toctree::
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:maxdepth: 2
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:numbered: // comment
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:numbered:
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Section_intro
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Section_start
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@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands.
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Indices and tables
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==================
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* :ref:`genindex` // comment
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* :ref:`search` // comment
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* :ref:`genindex`
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* :ref:`search`
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END_RST -->
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@ -1,17 +1,143 @@
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<HTML>
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<CENTER><A HREF = "Section_howto.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_perf.html">Next Section</A>
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<title>7. Example problems — LAMMPS 15 May 2015 version documentation</title>
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<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
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</a>
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<ul class="current">
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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_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</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_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="">7. Example problems</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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<HR>
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<H3>7. Example problems
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</H3>
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<P>The LAMMPS distribution includes an examples sub-directory with
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<div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
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<a href="Section_perf.html" class="btn btn-neutral float-right" title="8. Performance & scalability" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
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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="example-problems">
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<h1>7. Example problems<a class="headerlink" href="#example-problems" title="Permalink to this headline">¶</a></h1>
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<p>The LAMMPS distribution includes an examples sub-directory with
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several sample problems. Each problem is in a sub-directory of its
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own. Most are 2d models so that they run quickly, requiring at most a
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couple of minutes to run on a desktop machine. Each problem has an
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@ -20,111 +146,256 @@ input script (in.*) and produces a log file (log.*) and dump file
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coordinates as additional input. A few sample log file outputs on
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different machines and different numbers of processors are included in
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the directories to compare your answers to. E.g. a log file like
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log.crack.foo.P means it ran on P processors of machine "foo".
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</P>
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<P>For examples that use input data files, many of them were produced by
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<A HREF = "http://pizza.sandia.gov">Pizza.py</A> or setup tools described in the
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<A HREF = "Section_tools.html">Additional Tools</A> section of the LAMMPS
|
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documentation and provided with the LAMMPS distribution.
|
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</P>
|
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<P>If you uncomment the <A HREF = "dump.html">dump</A> command in the input script, a
|
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log.crack.foo.P means it ran on P processors of machine “foo”.</p>
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<p>For examples that use input data files, many of them were produced by
|
||||
<a class="reference external" href="http://pizza.sandia.gov">Pizza.py</a> or setup tools described in the
|
||||
<a class="reference internal" href="Section_tools.html"><em>Additional Tools</em></a> section of the LAMMPS
|
||||
documentation and provided with the LAMMPS distribution.</p>
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<p>If you uncomment the <a class="reference internal" href="dump.html"><em>dump</em></a> command in the input script, a
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text dump file will be produced, which can be animated by various
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<A HREF = "http://lammps.sandia.gov/viz.html">visualization programs</A>. It can
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also be animated using the xmovie tool described in the <A HREF = "Section_tools.html">Additional
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Tools</A> section of the LAMMPS documentation.
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</P>
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<P>If you uncomment the <A HREF = "dump.html">dump image</A> command in the input
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<a class="reference external" href="http://lammps.sandia.gov/viz.html">visualization programs</a>. It can
|
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also be animated using the xmovie tool described in the <a class="reference internal" href="Section_tools.html"><em>Additional Tools</em></a> section of the LAMMPS documentation.</p>
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<p>If you uncomment the <a class="reference internal" href="dump.html"><em>dump image</em></a> command in the input
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script, and assuming you have built LAMMPS with a JPG library, JPG
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snapshot images will be produced when the simulation runs. They can
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be quickly post-processed into a movie using commands described on the
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<A HREF = "dump_image.html">dump image</A> doc page.
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</P>
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<P>Animations of many of these examples can be viewed on the Movies
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section of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
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</P>
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<P>These are the sample problems in the examples sub-directories:
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</P>
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<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
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<TR><TD >balance</TD><TD > dynamic load balancing, 2d system</TD></TR>
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<TR><TD >body</TD><TD > body particles, 2d system</TD></TR>
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<TR><TD >colloid</TD><TD > big colloid particles in a small particle solvent, 2d system</TD></TR>
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<TR><TD >comb</TD><TD > models using the COMB potential</TD></TR>
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<TR><TD >crack</TD><TD > crack propagation in a 2d solid</TD></TR>
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<TR><TD >cuda</TD><TD > use of the USER-CUDA package for GPU acceleration</TD></TR>
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<TR><TD >dipole</TD><TD > point dipolar particles, 2d system</TD></TR>
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<TR><TD >dreiding</TD><TD > methanol via Dreiding FF</TD></TR>
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<TR><TD >eim</TD><TD > NaCl using the EIM potential</TD></TR>
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<TR><TD >ellipse</TD><TD > ellipsoidal particles in spherical solvent, 2d system</TD></TR>
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<TR><TD >flow</TD><TD > Couette and Poiseuille flow in a 2d channel</TD></TR>
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<TR><TD >friction</TD><TD > frictional contact of spherical asperities between 2d surfaces</TD></TR>
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<TR><TD >gpu</TD><TD > use of the GPU package for GPU acceleration</TD></TR>
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<TR><TD >hugoniostat</TD><TD > Hugoniostat shock dynamics</TD></TR>
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<TR><TD >indent</TD><TD > spherical indenter into a 2d solid</TD></TR>
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<TR><TD >intel</TD><TD > use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor</TD></TR>
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<TR><TD >kim</TD><TD > use of potentials in Knowledge Base for Interatomic Models (KIM)</TD></TR>
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<TR><TD >line</TD><TD > line segment particles in 2d rigid bodies</TD></TR>
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<TR><TD >meam</TD><TD > MEAM test for SiC and shear (same as shear examples)</TD></TR>
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<TR><TD >melt</TD><TD > rapid melt of 3d LJ system</TD></TR>
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<TR><TD >micelle</TD><TD > self-assembly of small lipid-like molecules into 2d bilayers</TD></TR>
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<TR><TD >min</TD><TD > energy minimization of 2d LJ melt</TD></TR>
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<TR><TD >msst</TD><TD > MSST shock dynamics</TD></TR>
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<TR><TD >nb3b</TD><TD > use of nonbonded 3-body harmonic pair style</TD></TR>
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<TR><TD >neb</TD><TD > nudged elastic band (NEB) calculation for barrier finding</TD></TR>
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<TR><TD >nemd</TD><TD > non-equilibrium MD of 2d sheared system</TD></TR>
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<TR><TD >obstacle</TD><TD > flow around two voids in a 2d channel</TD></TR>
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<TR><TD >peptide</TD><TD > dynamics of a small solvated peptide chain (5-mer)</TD></TR>
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<TR><TD >peri</TD><TD > Peridynamic model of cylinder impacted by indenter</TD></TR>
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<TR><TD >pour</TD><TD > pouring of granular particles into a 3d box, then chute flow</TD></TR>
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<TR><TD >prd</TD><TD > parallel replica dynamics of vacancy diffusion in bulk Si</TD></TR>
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<TR><TD >qeq</TD><TD > use of the QEQ pacakge for charge equilibration</TD></TR>
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<TR><TD >reax</TD><TD > RDX and TATB models using the ReaxFF</TD></TR>
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<TR><TD >rigid</TD><TD > rigid bodies modeled as independent or coupled</TD></TR>
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<TR><TD >shear</TD><TD > sideways shear applied to 2d solid, with and without a void</TD></TR>
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<TR><TD >snap</TD><TD > NVE dynamics for BCC tantalum crystal using SNAP potential</TD></TR>
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<TR><TD >srd</TD><TD > stochastic rotation dynamics (SRD) particles as solvent</TD></TR>
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<TR><TD >tad</TD><TD > temperature-accelerated dynamics of vacancy diffusion in bulk Si</TD></TR>
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<TR><TD >tri</TD><TD > triangular particles in rigid bodies
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</TD></TR></TABLE></DIV>
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<P>Here is how you might run and visualize one of the sample problems:
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</P>
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<PRE>cd indent
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<a class="reference internal" href="dump_image.html"><em>dump image</em></a> doc page.</p>
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<p>Animations of many of these examples can be viewed on the Movies
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||||
section of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.</p>
|
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<p>These are the sample problems in the examples sub-directories:</p>
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<table border="1" class="docutils">
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<colgroup>
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<col width="15%" />
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<col width="85%" />
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</colgroup>
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<tbody valign="top">
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<tr class="row-odd"><td>balance</td>
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<td>dynamic load balancing, 2d system</td>
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</tr>
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<tr class="row-even"><td>body</td>
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<td>body particles, 2d system</td>
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</tr>
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<tr class="row-odd"><td>colloid</td>
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<td>big colloid particles in a small particle solvent, 2d system</td>
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</tr>
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<tr class="row-even"><td>comb</td>
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<td>models using the COMB potential</td>
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</tr>
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<tr class="row-odd"><td>crack</td>
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<td>crack propagation in a 2d solid</td>
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</tr>
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<tr class="row-even"><td>cuda</td>
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<td>use of the USER-CUDA package for GPU acceleration</td>
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</tr>
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<tr class="row-odd"><td>dipole</td>
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<td>point dipolar particles, 2d system</td>
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</tr>
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<tr class="row-even"><td>dreiding</td>
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<td>methanol via Dreiding FF</td>
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</tr>
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<tr class="row-odd"><td>eim</td>
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<td>NaCl using the EIM potential</td>
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</tr>
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<tr class="row-even"><td>ellipse</td>
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<td>ellipsoidal particles in spherical solvent, 2d system</td>
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</tr>
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<tr class="row-odd"><td>flow</td>
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<td>Couette and Poiseuille flow in a 2d channel</td>
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</tr>
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<tr class="row-even"><td>friction</td>
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<td>frictional contact of spherical asperities between 2d surfaces</td>
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</tr>
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<tr class="row-odd"><td>gpu</td>
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<td>use of the GPU package for GPU acceleration</td>
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</tr>
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<tr class="row-even"><td>hugoniostat</td>
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<td>Hugoniostat shock dynamics</td>
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</tr>
|
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<tr class="row-odd"><td>indent</td>
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<td>spherical indenter into a 2d solid</td>
|
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</tr>
|
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<tr class="row-even"><td>intel</td>
|
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<td>use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor</td>
|
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</tr>
|
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<tr class="row-odd"><td>kim</td>
|
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<td>use of potentials in Knowledge Base for Interatomic Models (KIM)</td>
|
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</tr>
|
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<tr class="row-even"><td>line</td>
|
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<td>line segment particles in 2d rigid bodies</td>
|
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</tr>
|
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<tr class="row-odd"><td>meam</td>
|
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<td>MEAM test for SiC and shear (same as shear examples)</td>
|
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</tr>
|
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<tr class="row-even"><td>melt</td>
|
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<td>rapid melt of 3d LJ system</td>
|
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</tr>
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<tr class="row-odd"><td>micelle</td>
|
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<td>self-assembly of small lipid-like molecules into 2d bilayers</td>
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</tr>
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<tr class="row-even"><td>min</td>
|
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<td>energy minimization of 2d LJ melt</td>
|
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</tr>
|
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<tr class="row-odd"><td>msst</td>
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<td>MSST shock dynamics</td>
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</tr>
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<tr class="row-even"><td>nb3b</td>
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<td>use of nonbonded 3-body harmonic pair style</td>
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</tr>
|
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<tr class="row-odd"><td>neb</td>
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<td>nudged elastic band (NEB) calculation for barrier finding</td>
|
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</tr>
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<tr class="row-even"><td>nemd</td>
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<td>non-equilibrium MD of 2d sheared system</td>
|
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</tr>
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<tr class="row-odd"><td>obstacle</td>
|
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<td>flow around two voids in a 2d channel</td>
|
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</tr>
|
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<tr class="row-even"><td>peptide</td>
|
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<td>dynamics of a small solvated peptide chain (5-mer)</td>
|
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</tr>
|
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<tr class="row-odd"><td>peri</td>
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<td>Peridynamic model of cylinder impacted by indenter</td>
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</tr>
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<tr class="row-even"><td>pour</td>
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<td>pouring of granular particles into a 3d box, then chute flow</td>
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</tr>
|
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<tr class="row-odd"><td>prd</td>
|
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<td>parallel replica dynamics of vacancy diffusion in bulk Si</td>
|
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</tr>
|
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<tr class="row-even"><td>qeq</td>
|
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<td>use of the QEQ pacakge for charge equilibration</td>
|
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</tr>
|
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<tr class="row-odd"><td>reax</td>
|
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<td>RDX and TATB models using the ReaxFF</td>
|
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</tr>
|
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<tr class="row-even"><td>rigid</td>
|
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<td>rigid bodies modeled as independent or coupled</td>
|
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</tr>
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<tr class="row-odd"><td>shear</td>
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<td>sideways shear applied to 2d solid, with and without a void</td>
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</tr>
|
||||
<tr class="row-even"><td>snap</td>
|
||||
<td>NVE dynamics for BCC tantalum crystal using SNAP potential</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>srd</td>
|
||||
<td>stochastic rotation dynamics (SRD) particles as solvent</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>tad</td>
|
||||
<td>temperature-accelerated dynamics of vacancy diffusion in bulk Si</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>tri</td>
|
||||
<td>triangular particles in rigid bodies</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>vashishta: models using the Vashishta potential</p>
|
||||
<p>Here is how you might run and visualize one of the sample problems:</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre>cd indent
|
||||
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
|
||||
lmp_linux -in in.indent # run the problem
|
||||
</PRE>
|
||||
<P>Running the simulation produces the files <I>dump.indent</I> and
|
||||
<I>log.lammps</I>. You can visualize the dump file as follows:
|
||||
</P>
|
||||
<PRE>../../tools/xmovie/xmovie -scale dump.indent
|
||||
</PRE>
|
||||
<P>If you uncomment the <A HREF = "dump_image.html">dump image</A> line(s) in the input
|
||||
lmp_linux -in in.indent # run the problem
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Running the simulation produces the files <em>dump.indent</em> and
|
||||
<em>log.lammps</em>. You can visualize the dump file as follows:</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre>../../tools/xmovie/xmovie -scale dump.indent
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>If you uncomment the <a class="reference internal" href="dump_image.html"><em>dump image</em></a> line(s) in the input
|
||||
script a series of JPG images will be produced by the run. These can
|
||||
be viewed individually or turned into a movie or animated by tools
|
||||
like ImageMagick or QuickTime or various Windows-based tools. See the
|
||||
<A HREF = "dump_image.html">dump image</A> doc page for more details. E.g. this
|
||||
<a class="reference internal" href="dump_image.html"><em>dump image</em></a> doc page for more details. E.g. this
|
||||
Imagemagick command would create a GIF file suitable for viewing in a
|
||||
browser.
|
||||
</P>
|
||||
<PRE>% convert -loop 1 *.jpg foo.gif
|
||||
</PRE>
|
||||
<HR>
|
||||
|
||||
<P>There is also a COUPLE directory with examples of how to use LAMMPS as
|
||||
browser.</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre>% convert -loop 1 *.jpg foo.gif
|
||||
</pre></div>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<p>There is also a COUPLE directory with examples of how to use LAMMPS as
|
||||
a library, either by itself or in tandem with another code or library.
|
||||
See the COUPLE/README file to get started.
|
||||
</P>
|
||||
<P>There is also an ELASTIC directory with an example script for
|
||||
See the COUPLE/README file to get started.</p>
|
||||
<p>There is also an ELASTIC directory with an example script for
|
||||
computing elastic constants at zero temperature, using an Si example. See
|
||||
the ELASTIC/in.elastic file for more info.
|
||||
</P>
|
||||
<P>There is also an ELASTIC_T directory with an example script for
|
||||
the ELASTIC/in.elastic file for more info.</p>
|
||||
<p>There is also an ELASTIC_T directory with an example script for
|
||||
computing elastic constants at finite temperature, using an Si example. See
|
||||
the ELASTIC_T/in.elastic file for more info.
|
||||
</P>
|
||||
<P>There is also a USER directory which contains subdirectories of
|
||||
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|
||||
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|
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|
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<H3>fix gcmc command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>fix ID group-ID gcmc N X M type seed T mu displace keyword values ...
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
||||
|
||||
<LI>gcmc = style name of this fix command
|
||||
|
||||
<LI>N = invoke this fix every N steps
|
||||
|
||||
<LI>X = average number of GCMC exchanges to attempt every N steps
|
||||
|
||||
<LI>M = average number of MC moves to attempt every N steps
|
||||
|
||||
<LI>type = atom type for inserted atoms (must be 0 if mol keyword used)
|
||||
|
||||
<LI>seed = random # seed (positive integer)
|
||||
|
||||
<LI>T = temperature of the ideal gas reservoir (temperature units)
|
||||
|
||||
<LI>mu = chemical potential of the ideal gas reservoir (energy units)
|
||||
|
||||
<LI>translate = maximum Monte Carlo translation distance (length units)
|
||||
|
||||
<LI>zero or more keyword/value pairs may be appended to args
|
||||
|
||||
<PRE>keyword = <I>mol</I>, <I>region</I>, <I>maxangle</I>, <I>pressure</I>, <I>fugacity_coeff</I>, <I>full_energy</I>, <I>charge</I>, <I>group</I>, <I>grouptype</I>, <I>intra_energy</I>, or <I>tfac_insert</I>
|
||||
<I>mol</I> value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
|
||||
<I>shake</I> value = fix-ID
|
||||
fix-ID = ID of <A HREF = "fix_shake.html">fix shake</A> command
|
||||
<I>region</I> value = region-ID
|
||||
region-ID = ID of region where MC moves are allowed
|
||||
<I>maxangle</I> value = maximum molecular rotation angle (degrees)
|
||||
<I>pressure</I> value = pressure of the gas reservoir (pressure units)
|
||||
<I>fugacity_coeff</I> value = fugacity coefficient of the gas reservoir (unitless)
|
||||
<I>full_energy</I> = compute the entire system energy when performing MC moves
|
||||
<I>charge</I> value = charge of inserted atoms (charge units)
|
||||
<I>group</I> value = group-ID
|
||||
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||||
<div class="section" id="fix-gcmc-command">
|
||||
<span id="index-0"></span><h1>fix gcmc command<a class="headerlink" href="#fix-gcmc-command" title="Permalink to this headline">¶</a></h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
|
||||
<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID gcmc N X M type seed T mu displace keyword values ...
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
|
||||
<li>gcmc = style name of this fix command</li>
|
||||
<li>N = invoke this fix every N steps</li>
|
||||
<li>X = average number of GCMC exchanges to attempt every N steps</li>
|
||||
<li>M = average number of MC moves to attempt every N steps</li>
|
||||
<li>type = atom type for inserted atoms (must be 0 if mol keyword used)</li>
|
||||
<li>seed = random # seed (positive integer)</li>
|
||||
<li>T = temperature of the ideal gas reservoir (temperature units)</li>
|
||||
<li>mu = chemical potential of the ideal gas reservoir (energy units)</li>
|
||||
<li>translate = maximum Monte Carlo translation distance (length units)</li>
|
||||
<li>zero or more keyword/value pairs may be appended to args</li>
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
keyword = <em>mol</em>, <em>region</em>, <em>maxangle</em>, <em>pressure</em>, <em>fugacity_coeff</em>, <em>full_energy</em>, <em>charge</em>, <em>group</em>, <em>grouptype</em>, <em>intra_energy</em>, or <em>tfac_insert</em>
|
||||
<em>mol</em> value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><em>molecule</em></a> command
|
||||
<em>shake</em> value = fix-ID
|
||||
fix-ID = ID of <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command
|
||||
<em>region</em> value = region-ID
|
||||
region-ID = ID of region where MC moves are allowed
|
||||
<em>maxangle</em> value = maximum molecular rotation angle (degrees)
|
||||
<em>pressure</em> value = pressure of the gas reservoir (pressure units)
|
||||
<em>fugacity_coeff</em> value = fugacity coefficient of the gas reservoir (unitless)
|
||||
<em>full_energy</em> = compute the entire system energy when performing MC moves
|
||||
<em>charge</em> value = charge of inserted atoms (charge units)
|
||||
<em>group</em> value = group-ID
|
||||
group-ID = group-ID for inserted atoms (string)
|
||||
<I>grouptype</I> values = type group-ID
|
||||
<em>grouptype</em> values = type group-ID
|
||||
type = atom type (int)
|
||||
group-ID = group-ID for inserted atoms (string)
|
||||
<I>intra_energy</I> value = intramolecular energy (energy units)
|
||||
<I>tfac_insert</I> value = scale up/down temperature of inserted atoms (unitless)
|
||||
</PRE>
|
||||
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
|
||||
<em>intra_energy</em> value = intramolecular energy (energy units)
|
||||
<em>tfac_insert</em> value = scale up/down temperature of inserted atoms (unitless)
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
|
||||
<div class="highlight-python"><div class="highlight"><pre>fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
|
||||
fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
|
||||
fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>This fix performs grand canonical Monte Carlo (GCMC) exchanges of
|
||||
fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>This fix performs grand canonical Monte Carlo (GCMC) exchanges of
|
||||
atoms or molecules of the given type with an imaginary ideal gas reservoir at
|
||||
the specified T and chemical potential (mu) as discussed in
|
||||
<A HREF = "#Frenkel">(Frenkel)</A>. If used with the <A HREF = "fix_nh.html">fix nvt</A> command,
|
||||
<a class="reference internal" href="#frenkel"><span>(Frenkel)</span></a>. If used with the <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a> command,
|
||||
simulations in the grand canonical ensemble (muVT, constant chemical
|
||||
potential, constant volume, and constant temperature) can be
|
||||
performed. Specific uses include computing isotherms in microporous
|
||||
materials, or computing vapor-liquid coexistence curves.
|
||||
</P>
|
||||
<P>Every N timesteps the fix attempts a number of GCMC exchanges (insertions
|
||||
materials, or computing vapor-liquid coexistence curves.</p>
|
||||
<p>Every N timesteps the fix attempts a number of GCMC exchanges (insertions
|
||||
or deletions) of gas atoms or molecules of
|
||||
the given type between the simulation cell and the imaginary
|
||||
reservoir. It also attempts a number of Monte Carlo
|
||||
moves (translations and molecule rotations) of gas of the given type
|
||||
within the simulation cell or region. The average number of
|
||||
within the simulation cell or region. The average number of
|
||||
attempted GCMC exchanges is X. The average number of attempted MC moves is M.
|
||||
M should typically be chosen to be
|
||||
approximately equal to the expected number of gas atoms or molecules
|
||||
of the given type within the simulation cell or region,
|
||||
of the given type within the simulation cell or region,
|
||||
which will result in roughly one
|
||||
MC translation per atom or molecule per MC cycle.
|
||||
</P>
|
||||
<P>For MC moves of molecular gasses, rotations and translations are each
|
||||
MC translation per atom or molecule per MC cycle.</p>
|
||||
<p>For MC moves of molecular gasses, rotations and translations are each
|
||||
attempted with 50% probability. For MC moves of atomic gasses,
|
||||
translations are attempted 100% of the time. For MC exchanges of
|
||||
either molecular or atomic gasses, deletions and insertions are each
|
||||
attempted with 50% probability.
|
||||
</P>
|
||||
<P>All inserted particles are always assigned to two groups: the default group
|
||||
"all" and the group specified in the fix gcmc command (which can also
|
||||
be "all"). In addition, particles are also added to any groups specified
|
||||
by the <I>group</I> and <I>grouptype</I> keywords.
|
||||
attempted with 50% probability.</p>
|
||||
<p>All inserted particles are always assigned to two groups: the default group
|
||||
“all” and the group specified in the fix gcmc command (which can also
|
||||
be “all”). In addition, particles are also added to any groups specified
|
||||
by the <em>group</em> and <em>grouptype</em> keywords.
|
||||
If inserted particles are individual atoms, they are
|
||||
assigned the atom type given by the type argument. If they are molecules,
|
||||
the type argument has no effect and must be set to zero. Instead,
|
||||
the type of each atom in the inserted molecule is specified
|
||||
in the file read by the <A HREF = "molecule.html">molecule</A> command.
|
||||
</P>
|
||||
<P>This fix cannot be used to perform MC insertions of gas atoms or
|
||||
assigned the atom type given by the type argument. If they are molecules,
|
||||
the type argument has no effect and must be set to zero. Instead,
|
||||
the type of each atom in the inserted molecule is specified
|
||||
in the file read by the <a class="reference internal" href="molecule.html"><em>molecule</em></a> command.</p>
|
||||
<p>This fix cannot be used to perform MC insertions of gas atoms or
|
||||
molecules other than the exchanged type, but MC deletions,
|
||||
translations, and rotations can be performed on any atom/molecule in
|
||||
the fix group. All atoms in the simulation cell can be moved using
|
||||
regular time integration translations, e.g. via
|
||||
<A HREF = "fix_nvt.html">fix_nvt</A>, resulting in a hybrid GCMC+MD simulation. A
|
||||
<code class="xref doc docutils literal"><span class="pre">fix_nvt</span></code>, resulting in a hybrid GCMC+MD simulation. A
|
||||
smaller-than-usual timestep size may be needed when running such a
|
||||
hybrid simulation, especially if the inserted molecules are not well
|
||||
equilibrated.
|
||||
</P>
|
||||
<P>This command may optionally use the <I>region</I> keyword to define an
|
||||
exchange and move volume. The specified region must have been
|
||||
previously defined with a <A HREF = "region.html">region</A> command. It must be
|
||||
defined with side = <I>in</I>. Insertion attempts occur only within the
|
||||
specified region. For non-rectangular regions, random trial
|
||||
equilibrated.</p>
|
||||
<p>This command may optionally use the <em>region</em> keyword to define an
|
||||
exchange and move volume. The specified region must have been
|
||||
previously defined with a <a class="reference internal" href="region.html"><em>region</em></a> command. It must be
|
||||
defined with side = <em>in</em>. Insertion attempts occur only within the
|
||||
specified region. For non-rectangular regions, random trial
|
||||
points are generated within the rectangular bounding box until a point is found
|
||||
that lies inside the region. If no valid point is generated after 1000 trials,
|
||||
no insertion is performed, but it is counted as an attempted insertion.
|
||||
Move and deletion attempt candidates are selected
|
||||
Move and deletion attempt candidates are selected
|
||||
from gas atoms or molecules within the region. If there are no candidates,
|
||||
no move or deletion is performed, but it is counted as an attempt move
|
||||
or deletion. If an attempted move places the atom or molecule center-of-mass outside
|
||||
the specified region, a new attempted move is generated. This process is repeated
|
||||
until the atom or molecule center-of-mass is inside the specified region.
|
||||
</P>
|
||||
<P>If used with <A HREF = "fix_nvt.html">fix_nvt</A>, the temperature of the imaginary
|
||||
or deletion. If an attempted move places the atom or molecule center-of-mass outside
|
||||
the specified region, a new attempted move is generated. This process is repeated
|
||||
until the atom or molecule center-of-mass is inside the specified region.</p>
|
||||
<p>If used with <code class="xref doc docutils literal"><span class="pre">fix_nvt</span></code>, the temperature of the imaginary
|
||||
reservoir, T, should be set to be equivalent to the target temperature
|
||||
used in <A HREF = "fix_nvt.html">fix_nvt</A>. Otherwise, the imaginary reservoir
|
||||
used in <code class="xref doc docutils literal"><span class="pre">fix_nvt</span></code>. Otherwise, the imaginary reservoir
|
||||
will not be in thermal equilibrium with the simulation cell. Also,
|
||||
it is important that the temperature used by fix nvt be dynamic,
|
||||
which can be achieved as follows:
|
||||
</P>
|
||||
<PRE>compute mdtemp mdatoms temp
|
||||
which can be achieved as follows:</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre>compute mdtemp mdatoms temp
|
||||
compute_modify mdtemp dynamic yes
|
||||
fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
|
||||
fix_modify mdnvt temp mdtemp
|
||||
</PRE>
|
||||
<P>Note that neighbor lists are re-built every timestep that this fix is
|
||||
fix_modify mdnvt temp mdtemp
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Note that neighbor lists are re-built every timestep that this fix is
|
||||
invoked, so you should not set N to be too small. However, periodic
|
||||
rebuilds are necessary in order to avoid dangerous rebuilds and missed
|
||||
interactions. Specifically, avoid performing so many MC translations
|
||||
per timestep that atoms can move beyond the neighbor list skin
|
||||
distance. See the <A HREF = "neighbor.html">neighbor</A> command for details.
|
||||
</P>
|
||||
<P>When an atom or molecule is to be inserted, its
|
||||
distance. See the <a class="reference internal" href="neighbor.html"><em>neighbor</em></a> command for details.</p>
|
||||
<p>When an atom or molecule is to be inserted, its
|
||||
coordinates are chosen at a random position within the current
|
||||
simulation cell or region, and new atom velocities are randomly chosen from
|
||||
the specified temperature distribution given by T. The effective
|
||||
temperature for new atom velocities can be increased or decreased
|
||||
using the optional keyword <I>tfac_insert</I> (see below). Relative
|
||||
using the optional keyword <em>tfac_insert</em> (see below). Relative
|
||||
coordinates for atoms in a molecule are taken from the template
|
||||
molecule provided by the user. The center of mass of the molecule
|
||||
is placed at the insertion point. The orientation of the molecule
|
||||
is chosen at random by rotating about this point.
|
||||
</P>
|
||||
<P>Individual atoms are inserted, unless the <I>mol</I> keyword is used. It
|
||||
specifies a <I>template-ID</I> previously defined using the
|
||||
<A HREF = "molecule.html">molecule</A> command, which reads a file that defines the
|
||||
is chosen at random by rotating about this point.</p>
|
||||
<p>Individual atoms are inserted, unless the <em>mol</em> keyword is used. It
|
||||
specifies a <em>template-ID</em> previously defined using the
|
||||
<a class="reference internal" href="molecule.html"><em>molecule</em></a> command, which reads a file that defines the
|
||||
molecule. The coordinates, atom types, charges, etc, as well as any
|
||||
bond/angle/etc and special neighbor information for the molecule can
|
||||
be specified in the molecule file. See the <A HREF = "molecule.html">molecule</A>
|
||||
be specified in the molecule file. See the <a class="reference internal" href="molecule.html"><em>molecule</em></a>
|
||||
command for details. The only settings required to be in this file
|
||||
are the coordinates and types of atoms in the molecule.
|
||||
</P>
|
||||
<P>When not using the <I>mol</I> keyword, you should ensure you do not delete
|
||||
are the coordinates and types of atoms in the molecule.</p>
|
||||
<p>When not using the <em>mol</em> keyword, you should ensure you do not delete
|
||||
atoms that are bonded to other atoms, or LAMMPS will
|
||||
soon generate an error when it tries to find bonded neighbors. LAMMPS will
|
||||
warn you if any of the atoms eligible for deletion have a non-zero
|
||||
molecule ID, but does not check for this at the time of deletion.
|
||||
</P>
|
||||
<P>If you wish to insert molecules via the <I>mol</I> keyword, that will have
|
||||
their bonds or angles constrained via SHAKE, use the <I>shake</I> keyword,
|
||||
specifying as its value the ID of a separate <A HREF = "fix_shake.html">fix
|
||||
shake</A> command which also appears in your input script.
|
||||
</P>
|
||||
<P>Optionally, users may specify the maximum rotation angle for
|
||||
molecular rotations using the <I>maxangle</I> keyword and specifying
|
||||
molecule ID, but does not check for this at the time of deletion.</p>
|
||||
<p>If you wish to insert molecules via the <em>mol</em> keyword, that will have
|
||||
their bonds or angles constrained via SHAKE, use the <em>shake</em> keyword,
|
||||
specifying as its value the ID of a separate <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command which also appears in your input script.</p>
|
||||
<p>Optionally, users may specify the maximum rotation angle for
|
||||
molecular rotations using the <em>maxangle</em> keyword and specifying
|
||||
the angle in degrees. Rotations are performed by generating a random
|
||||
point on the unit sphere and a random rotation angle on the
|
||||
range [0,maxangle). The molecule is then rotated by that angle about an
|
||||
axis passing through the molecule center of mass. The axis is parallel
|
||||
to the unit vector defined by the point on the unit sphere.
|
||||
axis passing through the molecule center of mass. The axis is parallel
|
||||
to the unit vector defined by the point on the unit sphere.
|
||||
The same procedure is used for randomly rotating molecules when they
|
||||
are inserted, except that the maximum angle is 360 degrees.
|
||||
</P>
|
||||
<P>Note that fix GCMC does not use configurational bias
|
||||
MC or any other kind of sampling of intramolecular degrees of freedom.
|
||||
Inserted molecules can have different orientations, but they will all
|
||||
have the same intramolecular configuration,
|
||||
which was specified in the molecule command input.
|
||||
</P>
|
||||
<P>For atomic gasses, inserted atoms have the specified atom type, but
|
||||
deleted atoms are any atoms that have been inserted or that belong
|
||||
to the user-specified fix group. For molecular gasses, exchanged
|
||||
molecules use the same atom types as in the template molecule
|
||||
are inserted, except that the maximum angle is 360 degrees.</p>
|
||||
<p>Note that fix GCMC does not use configurational bias
|
||||
MC or any other kind of sampling of intramolecular degrees of freedom.
|
||||
Inserted molecules can have different orientations, but they will all
|
||||
have the same intramolecular configuration,
|
||||
which was specified in the molecule command input.</p>
|
||||
<p>For atomic gasses, inserted atoms have the specified atom type, but
|
||||
deleted atoms are any atoms that have been inserted or that belong
|
||||
to the user-specified fix group. For molecular gasses, exchanged
|
||||
molecules use the same atom types as in the template molecule
|
||||
supplied by the user. In both cases, exchanged
|
||||
atoms/molecules are assigned to two groups: the default group "all"
|
||||
and the group specified in the fix gcmc command (which can also be
|
||||
"all").
|
||||
</P>
|
||||
<P>The gas reservoir pressure can be specified using the <I>pressure</I>
|
||||
keyword, in which case the user-specified chemical potential is
|
||||
ignored. For non-ideal gas reservoirs, the user may also specify the
|
||||
fugacity coefficient using the <I>fugacity_coeff</I> keyword.
|
||||
</P>
|
||||
<P>The <I>full_energy</I> option means that fix GCMC will compute the total
|
||||
atoms/molecules are assigned to two groups: the default group “all”
|
||||
and the group specified in the fix gcmc command (which can also be
|
||||
“all”).</p>
|
||||
<p>The gas reservoir pressure can be specified using the <em>pressure</em>
|
||||
keyword, in which case the user-specified chemical potential is
|
||||
ignored. For non-ideal gas reservoirs, the user may also specify the
|
||||
fugacity coefficient using the <em>fugacity_coeff</em> keyword.</p>
|
||||
<p>The <em>full_energy</em> option means that fix GCMC will compute the total
|
||||
potential energy of the entire simulated system. The total system
|
||||
energy before and after the proposed GCMC move is then used in the
|
||||
Metropolis criterion to determine whether or not to accept the
|
||||
Metropolis criterion to determine whether or not to accept the
|
||||
proposed GCMC move. By default, this option is off, in which case
|
||||
only partial energies are computed to determine the difference in
|
||||
energy that would be caused by the proposed GCMC move.
|
||||
</P>
|
||||
<P>The <I>full_energy</I> option is needed for systems with complicated
|
||||
potential energy calculations, including the following:
|
||||
</P>
|
||||
<UL><LI> long-range electrostatics (kspace)
|
||||
<LI> many-body pair styles
|
||||
<LI> hybrid pair styles
|
||||
<LI> eam pair styles
|
||||
<LI> triclinic systems
|
||||
<LI> need to include potential energy contributions from other fixes
|
||||
</UL>
|
||||
<P>In these cases, LAMMPS will automatically apply the <I>full_energy</I>
|
||||
keyword and issue a warning message.
|
||||
</P>
|
||||
<P>When the <I>mol</I> keyword is used, the <I>full_energy</I> option also includes
|
||||
the intramolecular energy of inserted and deleted molecules. If this
|
||||
is not desired, the <I>intra_energy</I> keyword can be used to define an
|
||||
energy that would be caused by the proposed GCMC move.</p>
|
||||
<p>The <em>full_energy</em> option is needed for systems with complicated
|
||||
potential energy calculations, including the following:</p>
|
||||
<ul class="simple">
|
||||
<li>long-range electrostatics (kspace)</li>
|
||||
<li>many-body pair styles</li>
|
||||
<li>hybrid pair styles</li>
|
||||
<li>eam pair styles</li>
|
||||
<li>triclinic systems</li>
|
||||
<li>need to include potential energy contributions from other fixes</li>
|
||||
</ul>
|
||||
<p>In these cases, LAMMPS will automatically apply the <em>full_energy</em>
|
||||
keyword and issue a warning message.</p>
|
||||
<p>When the <em>mol</em> keyword is used, the <em>full_energy</em> option also includes
|
||||
the intramolecular energy of inserted and deleted molecules. If this
|
||||
is not desired, the <em>intra_energy</em> keyword can be used to define an
|
||||
amount of energy that is subtracted from the final energy when a molecule
|
||||
is inserted, and added to the initial energy when a molecule is
|
||||
deleted. For molecules that have a non-zero intramolecular energy, this
|
||||
will ensure roughly the same behavior whether or not the <I>full_energy</I>
|
||||
option is used.
|
||||
</P>
|
||||
<P>Inserted atoms and molecules are assigned random velocities based on the
|
||||
will ensure roughly the same behavior whether or not the <em>full_energy</em>
|
||||
option is used.</p>
|
||||
<p>Inserted atoms and molecules are assigned random velocities based on the
|
||||
specified temperature T. Because the relative velocity of
|
||||
all atoms in the molecule is zero, this may result in inserted molecules
|
||||
that are systematically too cold. In addition, the intramolecular potential
|
||||
energy of the inserted molecule may cause the kinetic energy
|
||||
of the molecule to quickly increase or decrease after insertion.
|
||||
The <I>tfac_insert</I> keyword allows the user to counteract these effects
|
||||
by changing the temperature used to assign velocities to
|
||||
of the molecule to quickly increase or decrease after insertion.
|
||||
The <em>tfac_insert</em> keyword allows the user to counteract these effects
|
||||
by changing the temperature used to assign velocities to
|
||||
inserted atoms and molecules by a constant factor. For a
|
||||
particular application, some experimentation may be required
|
||||
to find a value of <I>tfac_insert</I> that results in inserted molecules that
|
||||
equilibrate quickly to the correct temperature.
|
||||
</P>
|
||||
<P>Some fixes have an associated potential energy. Examples of such fixes
|
||||
include: <A HREF = "fix_efield.html">efield</A>, <A HREF = "fix_gravity.html">gravity</A>,
|
||||
<A HREF = "fix_addforce.html">addforce</A>, <A HREF = "fix_langevin.html">langevin</A>,
|
||||
<A HREF = "fix_restrain.html">restrain</A>, <A HREF = "fix_temp_berendsen.html">temp/berendsen</A>,
|
||||
<A HREF = "fix_temp_rescale.html">temp/rescale</A>, and <A HREF = "fix_wall.html">wall fixes</A>.
|
||||
For that energy to be included in the total potential energy of the
|
||||
to find a value of <em>tfac_insert</em> that results in inserted molecules that
|
||||
equilibrate quickly to the correct temperature.</p>
|
||||
<p>Some fixes have an associated potential energy. Examples of such fixes
|
||||
include: <a class="reference internal" href="fix_efield.html"><em>efield</em></a>, <a class="reference internal" href="fix_gravity.html"><em>gravity</em></a>,
|
||||
<a class="reference internal" href="fix_addforce.html"><em>addforce</em></a>, <a class="reference internal" href="fix_langevin.html"><em>langevin</em></a>,
|
||||
<a class="reference internal" href="fix_restrain.html"><em>restrain</em></a>, <a class="reference internal" href="fix_temp_berendsen.html"><em>temp/berendsen</em></a>,
|
||||
<a class="reference internal" href="fix_temp_rescale.html"><em>temp/rescale</em></a>, and <a class="reference internal" href="fix_wall.html"><em>wall fixes</em></a>.
|
||||
For that energy to be included in the total potential energy of the
|
||||
system (the quantity used when performing GCMC moves),
|
||||
you MUST enable the <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for
|
||||
that fix. The doc pages for individual <A HREF = "fix.html">fix</A> commands
|
||||
specify if this should be done.
|
||||
</P>
|
||||
<P>Use the <I>charge</I> option to insert atoms with a user-specified point
|
||||
charge. Note that doing so will cause the system to become non-neutral.
|
||||
LAMMPS issues a warning when using long-range electrostatics (kspace)
|
||||
with non-neutral systems. See the
|
||||
<A HREF = "compute_group_group.html">compute_group_group</A> documentation for more
|
||||
details about simulating non-neutral systems with kspace on.
|
||||
</P>
|
||||
<P>Use of this fix typically will cause the number of atoms to fluctuate,
|
||||
you MUST enable the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>energy</em> option for
|
||||
that fix. The doc pages for individual <a class="reference internal" href="fix.html"><em>fix</em></a> commands
|
||||
specify if this should be done.</p>
|
||||
<p>Use the <em>charge</em> option to insert atoms with a user-specified point
|
||||
charge. Note that doing so will cause the system to become non-neutral.
|
||||
LAMMPS issues a warning when using long-range electrostatics (kspace)
|
||||
with non-neutral systems. See the
|
||||
<a class="reference internal" href="compute_group_group.html"><em>compute_group_group</em></a> documentation for more
|
||||
details about simulating non-neutral systems with kspace on.</p>
|
||||
<p>Use of this fix typically will cause the number of atoms to fluctuate,
|
||||
therefore, you will want to use the
|
||||
<A HREF = "compute_modify.html">compute_modify</A> command to insure that the
|
||||
<a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command to insure that the
|
||||
current number of atoms is used as a normalizing factor each time
|
||||
temperature is computed. Here is the necessary command:
|
||||
</P>
|
||||
<PRE>compute_modify thermo_temp dynamic yes
|
||||
</PRE>
|
||||
<P>If LJ units are used, note that a value of 0.18292026 is used by this
|
||||
fix as the reduced value for Planck's constant. This value was
|
||||
temperature is computed. Here is the necessary command:</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre>compute_modify thermo_temp dynamic yes
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>If LJ units are used, note that a value of 0.18292026 is used by this
|
||||
fix as the reduced value for Planck’s constant. This value was
|
||||
derived from LJ parameters for argon, where h* = h/sqrt(sigma^2 *
|
||||
epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and
|
||||
mass = 39.948 amu.
|
||||
</P>
|
||||
<P>The <I>group</I> keyword assigns all inserted atoms to the <A HREF = "group.html">group</A>
|
||||
of the group-ID value. The <I>grouptype</I> keyword assigns all
|
||||
inserted atoms of the specified type to the <A HREF = "group.html">group</A>
|
||||
of the group-ID value.
|
||||
</P>
|
||||
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
||||
</P>
|
||||
<P>This fix writes the state of the fix to <A HREF = "restart.html">binary restart
|
||||
files</A>. This includes information about the random
|
||||
mass = 39.948 amu.</p>
|
||||
<p>The <em>group</em> keyword assigns all inserted atoms to the <a class="reference internal" href="group.html"><em>group</em></a>
|
||||
of the group-ID value. The <em>grouptype</em> keyword assigns all
|
||||
inserted atoms of the specified type to the <a class="reference internal" href="group.html"><em>group</em></a>
|
||||
of the group-ID value.</p>
|
||||
</div>
|
||||
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
||||
<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
|
||||
<p>This fix writes the state of the fix to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. This includes information about the random
|
||||
number generator seed, the next timestep for MC exchanges, etc. See
|
||||
the <A HREF = "read_restart.html">read_restart</A> command for info on how to
|
||||
the <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command for info on how to
|
||||
re-specify a fix in an input script that reads a restart file, so that
|
||||
the operation of the fix continues in an uninterrupted fashion.
|
||||
</P>
|
||||
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
|
||||
fix.
|
||||
</P>
|
||||
<P>This fix computes a global vector of length 8, which can be accessed
|
||||
by various <A HREF = "Section_howto.html#howto_15">output commands</A>. The vector
|
||||
values are the following global cumulative quantities:
|
||||
</P>
|
||||
<UL><LI>1 = translation attempts
|
||||
<LI>2 = translation successes
|
||||
<LI>3 = insertion attempts
|
||||
<LI>4 = insertion successes
|
||||
<LI>5 = deletion attempts
|
||||
<LI>6 = deletion successes
|
||||
<LI>7 = rotation attempts
|
||||
<LI>8 = rotation successes
|
||||
</UL>
|
||||
<P>The vector values calculated by this fix are "extensive".
|
||||
</P>
|
||||
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
|
||||
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
|
||||
minimization</A>.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>This fix is part of the MC package. It is only enabled if LAMMPS was
|
||||
built with that package. See the <A HREF = "Section_start.html#start_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P>Do not set "neigh_modify once yes" or else this fix will never be
|
||||
called. Reneighboring is required.
|
||||
</P>
|
||||
<P>Can be run in parallel, but aspects of the GCMC part will not scale
|
||||
well in parallel. Only usable for 3D simulations.
|
||||
</P>
|
||||
<P>Note that very lengthy simulations involving insertions/deletions of
|
||||
the operation of the fix continues in an uninterrupted fashion.</p>
|
||||
<p>None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options are relevant to this
|
||||
fix.</p>
|
||||
<p>This fix computes a global vector of length 8, which can be accessed
|
||||
by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The vector
|
||||
values are the following global cumulative quantities:</p>
|
||||
<ul class="simple">
|
||||
<li>1 = translation attempts</li>
|
||||
<li>2 = translation successes</li>
|
||||
<li>3 = insertion attempts</li>
|
||||
<li>4 = insertion successes</li>
|
||||
<li>5 = deletion attempts</li>
|
||||
<li>6 = deletion successes</li>
|
||||
<li>7 = rotation attempts</li>
|
||||
<li>8 = rotation successes</li>
|
||||
</ul>
|
||||
<p>The vector values calculated by this fix are “extensive”.</p>
|
||||
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
|
||||
the <a class="reference internal" href="run.html"><em>run</em></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<p>This fix is part of the MC package. It is only enabled if LAMMPS was
|
||||
built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
|
||||
<p>Do not set “neigh_modify once yes” or else this fix will never be
|
||||
called. Reneighboring is required.</p>
|
||||
<p>Can be run in parallel, but aspects of the GCMC part will not scale
|
||||
well in parallel. Only usable for 3D simulations.</p>
|
||||
<p>Note that very lengthy simulations involving insertions/deletions of
|
||||
billions of gas molecules may run out of atom or molecule IDs and
|
||||
trigger an error, so it is better to run multiple shorter-duration
|
||||
trigger an error, so it is better to run multiple shorter-duration
|
||||
simulations. Likewise, very large molecules have not been tested
|
||||
and may turn out to be problematic.
|
||||
</P>
|
||||
<P>Use of multiple fix gcmc commands in the same input script can be
|
||||
problematic if using a template molecule. The issue is that the
|
||||
and may turn out to be problematic.</p>
|
||||
<p>Use of multiple fix gcmc commands in the same input script can be
|
||||
problematic if using a template molecule. The issue is that the
|
||||
user-referenced template molecule in the second fix gcmc command
|
||||
may no longer exist since it might have been deleted by the first
|
||||
fix gcmc command. An existing template molecule will need to be
|
||||
referenced by the user for each subsequent fix gcmc command.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "fix_atom_swap.html">fix atom/swap</A>,
|
||||
<A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "neighbor.html">neighbor</A>,
|
||||
<A HREF = "fix_deposit.html">fix deposit</A>, <A HREF = "fix_evaporate.html">fix evaporate</A>,
|
||||
<A HREF = "delete_atoms.html">delete_atoms</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>The option defaults are mol = no, maxangle = 10, full_energy = no,
|
||||
referenced by the user for each subsequent fix gcmc command.</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="fix_atom_swap.html"><em>fix atom/swap</em></a>,
|
||||
<code class="xref doc docutils literal"><span class="pre">fix</span> <span class="pre">nvt</span></code>, <a class="reference internal" href="neighbor.html"><em>neighbor</em></a>,
|
||||
<a class="reference internal" href="fix_deposit.html"><em>fix deposit</em></a>, <a class="reference internal" href="fix_evaporate.html"><em>fix evaporate</em></a>,
|
||||
<a class="reference internal" href="delete_atoms.html"><em>delete_atoms</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 option defaults are mol = no, maxangle = 10, full_energy = no,
|
||||
except for the situations where full_energy is required, as
|
||||
listed above.
|
||||
</P>
|
||||
<HR>
|
||||
listed above.</p>
|
||||
<hr class="docutils" />
|
||||
<p id="frenkel"><strong>(Frenkel)</strong> Frenkel and Smit, Understanding Molecular Simulation,
|
||||
Academic Press, London, 2002.</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<A NAME = "Frenkel"></A>
|
||||
|
||||
<P><B>(Frenkel)</B> Frenkel and Smit, Understanding Molecular Simulation,
|
||||
Academic Press, London, 2002.
|
||||
</P>
|
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</HTML>
|
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|
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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|
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</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_howto.html">6. How-to discussions</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</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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<HR>
|
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|
||||
<H3>pair_style reax command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>pair_style reax hbcut hbnewflag tripflag precision
|
||||
</PRE>
|
||||
<UL><LI>hbcut = hydrogen-bond cutoff (optional) (distance units)
|
||||
<LI>hbnewflag = use old or new hbond function style (0 or 1) (optional)
|
||||
<LI>tripflag = apply stabilization to all triple bonds (0 or 1) (optional)
|
||||
<LI>precision = precision for charge equilibration (optional)
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>pair_style reax
|
||||
|
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<li>pair_style reax command</li>
|
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<li class="wy-breadcrumbs-aside">
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<a href="http://lammps.sandia.gov">Website</a>
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<a href="Section_commands.html#comm">Commands</a>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div itemprop="articleBody">
|
||||
|
||||
<div class="section" id="pair-style-reax-command">
|
||||
<span id="index-0"></span><h1>pair_style reax command<a class="headerlink" href="#pair-style-reax-command" title="Permalink to this headline">¶</a></h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
|
||||
<div class="highlight-python"><div class="highlight"><pre>pair_style reax hbcut hbnewflag tripflag precision
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>hbcut = hydrogen-bond cutoff (optional) (distance units)</li>
|
||||
<li>hbnewflag = use old or new hbond function style (0 or 1) (optional)</li>
|
||||
<li>tripflag = apply stabilization to all triple bonds (0 or 1) (optional)</li>
|
||||
<li>precision = precision for charge equilibration (optional)</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
|
||||
<div class="highlight-python"><div class="highlight"><pre>pair_style reax
|
||||
pair_style reax 10.0 0 1 1.0e-5
|
||||
pair_coeff * * ffield.reax 3 1 2 2
|
||||
pair_coeff * * ffield.reax 3 NULL NULL 3
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Style <I>reax</I> computes the ReaxFF potential of van Duin, Goddard and
|
||||
pair_coeff * * ffield.reax 3 NULL NULL 3
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Style <em>reax</em> computes the ReaxFF potential of van Duin, Goddard and
|
||||
co-workers. ReaxFF uses distance-dependent bond-order functions to
|
||||
represent the contributions of chemical bonding to the potential
|
||||
energy. There is more than one version of ReaxFF. The version
|
||||
implemented in LAMMPS uses the functional forms documented in the
|
||||
supplemental information of the following paper:
|
||||
<A HREF = "#Chenoweth_2008">(Chenoweth)</A>. The version integrated into LAMMPS matches
|
||||
the most up-to-date version of ReaxFF as of summer 2010.
|
||||
</P>
|
||||
<P>WARNING: pair style reax is now deprecated and will soon be retired. Users
|
||||
should switch to <A HREF = "pair_reax_c.html">pair_style reax/c</A>. The <I>reax</I> style
|
||||
differs from the <I>reax/c</I> style in the lo-level implementation details.
|
||||
The <I>reax</I> style is a
|
||||
Fortran library, linked to LAMMPS. The <I>reax/c</I> style was initially
|
||||
<a class="reference internal" href="#chenoweth-2008"><span>(Chenoweth)</span></a>. The version integrated into LAMMPS matches
|
||||
the most up-to-date version of ReaxFF as of summer 2010.</p>
|
||||
<p>WARNING: pair style reax is now deprecated and will soon be retired. Users
|
||||
should switch to <a class="reference internal" href="pair_reax_c.html"><em>pair_style reax/c</em></a>. The <em>reax</em> style
|
||||
differs from the <em>reax/c</em> style in the lo-level implementation details.
|
||||
The <em>reax</em> style is a
|
||||
Fortran library, linked to LAMMPS. The <em>reax/c</em> style was initially
|
||||
implemented as stand-alone C code and is now integrated into LAMMPS as
|
||||
a package.
|
||||
</P>
|
||||
<P>LAMMPS requires that a file called ffield.reax be provided, containing
|
||||
a package.</p>
|
||||
<p>LAMMPS requires that a file called ffield.reax be provided, containing
|
||||
the ReaxFF parameters for each atom type, bond type, etc. The format
|
||||
is identical to the ffield file used by van Duin and co-workers. The
|
||||
filename is required as an argument in the pair_coeff command. Any
|
||||
value other than "ffield.reax" will be rejected (see below).
|
||||
</P>
|
||||
<P>LAMMPS provides several different versions of ffield.reax in its
|
||||
value other than “ffield.reax” will be rejected (see below).</p>
|
||||
<p>LAMMPS provides several different versions of ffield.reax in its
|
||||
potentials dir, each called potentials/ffield.reax.label. These are
|
||||
documented in potentials/README.reax. The default ffield.reax
|
||||
contains parameterizations for the following elements: C, H, O, N, S.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: We do not distribute a wide variety of ReaxFF force
|
||||
field files with LAMMPS. Adri van Duin's group at PSU is the central
|
||||
contains parameterizations for the following elements: C, H, O, N, S.</p>
|
||||
<div class="admonition warning">
|
||||
<p class="first admonition-title">Warning</p>
|
||||
<p class="last">We do not distribute a wide variety of ReaxFF force
|
||||
field files with LAMMPS. Adri van Duin’s group at PSU is the central
|
||||
repository for this kind of data as they are continuously deriving and
|
||||
updating parameterizations for different classes of materials. You
|
||||
can visit their WWW site at
|
||||
<A HREF = "http://www.engr.psu.edu/adri">http://www.engr.psu.edu/adri</A>, register
|
||||
as a "new user", and then submit a request to their group describing
|
||||
<a class="reference external" href="http://www.engr.psu.edu/adri">http://www.engr.psu.edu/adri</a>, register
|
||||
as a “new user”, and then submit a request to their group describing
|
||||
material(s) you are interested in modeling with ReaxFF. They can tell
|
||||
you what is currently available or what it would take to create a
|
||||
suitable ReaxFF parameterization.
|
||||
</P>
|
||||
<P>The format of these files is identical to that used originally by van
|
||||
Duin. We have tested the accuracy of <I>pair_style reax</I> potential
|
||||
suitable ReaxFF parameterization.</p>
|
||||
</div>
|
||||
<p>The format of these files is identical to that used originally by van
|
||||
Duin. We have tested the accuracy of <em>pair_style reax</em> potential
|
||||
against the original ReaxFF code for the systems mentioned above. You
|
||||
can use other ffield files for specific chemical systems that may be
|
||||
available elsewhere (but note that their accuracy may not have been
|
||||
tested).
|
||||
</P>
|
||||
<P>The <I>hbcut</I>, <I>hbnewflag</I>, <I>tripflag</I>, and <I>precision</I> settings are
|
||||
tested).</p>
|
||||
<p>The <em>hbcut</em>, <em>hbnewflag</em>, <em>tripflag</em>, and <em>precision</em> settings are
|
||||
optional arguments. If none are provided, default settings are used:
|
||||
<I>hbcut</I> = 6 (which is Angstroms in real units), <I>hbnewflag</I> = 1 (use
|
||||
new hbond function style), <I>tripflag</I> = 1 (apply stabilization to all
|
||||
triple bonds), and <I>precision</I> = 1.0e-6 (one part in 10^6). If you
|
||||
<em>hbcut</em> = 6 (which is Angstroms in real units), <em>hbnewflag</em> = 1 (use
|
||||
new hbond function style), <em>tripflag</em> = 1 (apply stabilization to all
|
||||
triple bonds), and <em>precision</em> = 1.0e-6 (one part in 10^6). If you
|
||||
wish to override any of these defaults, then all of the settings must
|
||||
be specified.
|
||||
</P>
|
||||
<P>Two examples using <I>pair_style reax</I> are provided in the examples/reax
|
||||
sub-directory, along with corresponding examples for
|
||||
<A HREF = "pair_reax_c.html">pair_style reax/c</A>.
|
||||
</P>
|
||||
<P>Use of this pair style requires that a charge be defined for every
|
||||
atom since the <I>reax</I> pair style performs a charge equilibration (QEq)
|
||||
calculation. See the <A HREF = "atom_style.html">atom_style</A> and
|
||||
<A HREF = "read_data.html">read_data</A> commands for details on how to specify
|
||||
charges.
|
||||
</P>
|
||||
<P>The thermo variable <I>evdwl</I> stores the sum of all the ReaxFF potential
|
||||
be specified.</p>
|
||||
<p>Two examples using <em>pair_style reax</em> are provided in the examples/reax
|
||||
sub-directory, along with corresponding examples for
|
||||
<a class="reference internal" href="pair_reax_c.html"><em>pair_style reax/c</em></a>.</p>
|
||||
<p>Use of this pair style requires that a charge be defined for every
|
||||
atom since the <em>reax</em> pair style performs a charge equilibration (QEq)
|
||||
calculation. See the <a class="reference internal" href="atom_style.html"><em>atom_style</em></a> and
|
||||
<a class="reference internal" href="read_data.html"><em>read_data</em></a> commands for details on how to specify
|
||||
charges.</p>
|
||||
<p>The thermo variable <em>evdwl</em> stores the sum of all the ReaxFF potential
|
||||
energy contributions, with the exception of the Coulombic and charge
|
||||
equilibration contributions which are stored in the thermo variable
|
||||
<I>ecoul</I>. The output of these quantities is controlled by the
|
||||
<A HREF = "thermo.html">thermo</A> command.
|
||||
</P>
|
||||
<P>This pair style tallies a breakdown of the total ReaxFF potential
|
||||
energy into sub-categories, which can be accessed via the <A HREF = "compute_pair.html">compute
|
||||
pair</A> command as a vector of values of length 14.
|
||||
<em>ecoul</em>. The output of these quantities is controlled by the
|
||||
<a class="reference internal" href="thermo.html"><em>thermo</em></a> command.</p>
|
||||
<p>This pair style tallies a breakdown of the total ReaxFF potential
|
||||
energy into sub-categories, which can be accessed via the <a class="reference internal" href="compute_pair.html"><em>compute pair</em></a> command as a vector of values of length 14.
|
||||
The 14 values correspond to the following sub-categories (the variable
|
||||
names in italics match those used in the ReaxFF FORTRAN library):
|
||||
</P>
|
||||
<OL><LI><I>eb</I> = bond energy
|
||||
<LI><I>ea</I> = atom energy
|
||||
<LI><I>elp</I> = lone-pair energy
|
||||
<LI><I>emol</I> = molecule energy (always 0.0)
|
||||
<LI><I>ev</I> = valence angle energy
|
||||
<LI><I>epen</I> = double-bond valence angle penalty
|
||||
<LI><I>ecoa</I> = valence angle conjugation energy
|
||||
<LI><I>ehb</I> = hydrogen bond energy
|
||||
<LI><I>et</I> = torsion energy
|
||||
<LI><I>eco</I> = conjugation energy
|
||||
<LI><I>ew</I> = van der Waals energy
|
||||
<LI><I>ep</I> = Coulomb energy
|
||||
<LI><I>efi</I> = electric field energy (always 0.0)
|
||||
<LI><I>eqeq</I> = charge equilibration energy
|
||||
</OL>
|
||||
<P>To print these quantities to the log file (with descriptive column
|
||||
headings) the following commands could be included in an input script:
|
||||
</P>
|
||||
<PRE>compute reax all pair reax
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
names in italics match those used in the ReaxFF FORTRAN library):</p>
|
||||
<ol class="arabic simple">
|
||||
<li><em>eb</em> = bond energy</li>
|
||||
<li><em>ea</em> = atom energy</li>
|
||||
<li><em>elp</em> = lone-pair energy</li>
|
||||
<li><em>emol</em> = molecule energy (always 0.0)</li>
|
||||
<li><em>ev</em> = valence angle energy</li>
|
||||
<li><em>epen</em> = double-bond valence angle penalty</li>
|
||||
<li><em>ecoa</em> = valence angle conjugation energy</li>
|
||||
<li><em>ehb</em> = hydrogen bond energy</li>
|
||||
<li><em>et</em> = torsion energy</li>
|
||||
<li><em>eco</em> = conjugation energy</li>
|
||||
<li><em>ew</em> = van der Waals energy</li>
|
||||
<li><em>ep</em> = Coulomb energy</li>
|
||||
<li><em>efi</em> = electric field energy (always 0.0)</li>
|
||||
<li><em>eqeq</em> = charge equilibration energy</li>
|
||||
</ol>
|
||||
<p>To print these quantities to the log file (with descriptive column
|
||||
headings) the following commands could be included in an input script:</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre>compute reax all pair reax
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
...
|
||||
variable eqeq equal c_reax[14]
|
||||
thermo_style custom step temp epair v_eb v_ea ... v_eqeq
|
||||
</PRE>
|
||||
<P>Only a single pair_coeff command is used with the <I>reax</I> style which
|
||||
variable eqeq equal c_reax[14]
|
||||
thermo_style custom step temp epair v_eb v_ea ... v_eqeq
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Only a single pair_coeff command is used with the <em>reax</em> style which
|
||||
specifies a ReaxFF potential file with parameters for all needed
|
||||
elements. These are mapped to LAMMPS atom types by specifying N
|
||||
additional arguments after the filename in the pair_coeff command,
|
||||
where N is the number of LAMMPS atom types:
|
||||
</P>
|
||||
<UL><LI>filename
|
||||
<LI>N indices = mapping of ReaxFF elements to atom types
|
||||
</UL>
|
||||
<P>The specification of the filename and the mapping of LAMMPS atom types
|
||||
where N is the number of LAMMPS atom types:</p>
|
||||
<ul class="simple">
|
||||
<li>filename</li>
|
||||
<li>N indices = mapping of ReaxFF elements to atom types</li>
|
||||
</ul>
|
||||
<p>The specification of the filename and the mapping of LAMMPS atom types
|
||||
recognized by the ReaxFF is done differently than for other LAMMPS
|
||||
potentials, due to the non-portable difficulty of passing character
|
||||
strings (e.g. filename, element names) between C++ and Fortran.
|
||||
</P>
|
||||
<P>The filename has to be "ffield.reax" and it has to exist in the
|
||||
strings (e.g. filename, element names) between C++ and Fortran.</p>
|
||||
<p>The filename has to be “ffield.reax” and it has to exist in the
|
||||
directory you are running LAMMPS in. This means you cannot prepend a
|
||||
path to the file in the potentials dir. Rather, you should copy that
|
||||
file into the directory you are running from. If you wish to use
|
||||
another ReaxFF potential file, then name it "ffield.reax" and put it
|
||||
in the directory you run from.
|
||||
</P>
|
||||
<P>In the ReaxFF potential file, near the top, after the general
|
||||
another ReaxFF potential file, then name it “ffield.reax” and put it
|
||||
in the directory you run from.</p>
|
||||
<p>In the ReaxFF potential file, near the top, after the general
|
||||
parameters, is the atomic parameters section that contains element
|
||||
names, each with a couple dozen numeric parameters. If there are M
|
||||
elements specified in the <I>ffield</I> file, think of these as numbered 1
|
||||
elements specified in the <em>ffield</em> file, think of these as numbered 1
|
||||
to M. Each of the N indices you specify for the N atom types of LAMMPS
|
||||
atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will
|
||||
be mapped to whatever element you specify as the first index value,
|
||||
etc. If a mapping value is specified as NULL, the mapping is not
|
||||
performed. This can be used when a ReaxFF potential is used as part
|
||||
of the <I>hybrid</I> pair style. The NULL values are placeholders for atom
|
||||
types that will be used with other potentials.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: Currently the reax pair style cannot be used as part
|
||||
of the <I>hybrid</I> pair style. Some additional changes still need to be
|
||||
made to enable this.
|
||||
</P>
|
||||
<P>As an example, say your LAMMPS simulation has 4 atom types and the
|
||||
elements are ordered as C, H, O, N in the <I>ffield</I> file. If you want
|
||||
of the <em>hybrid</em> pair style. The NULL values are placeholders for atom
|
||||
types that will be used with other potentials.</p>
|
||||
<div class="admonition warning">
|
||||
<p class="first admonition-title">Warning</p>
|
||||
<p class="last">Currently the reax pair style cannot be used as part
|
||||
of the <em>hybrid</em> pair style. Some additional changes still need to be
|
||||
made to enable this.</p>
|
||||
</div>
|
||||
<p>As an example, say your LAMMPS simulation has 4 atom types and the
|
||||
elements are ordered as C, H, O, N in the <em>ffield</em> file. If you want
|
||||
the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
|
||||
H, you would use the following pair_coeff command:
|
||||
</P>
|
||||
<PRE>pair_coeff * * ffield.reax 1 1 4 2
|
||||
</PRE>
|
||||
<HR>
|
||||
|
||||
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
|
||||
</P>
|
||||
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
|
||||
mix, shift, table, and tail options.
|
||||
</P>
|
||||
<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
|
||||
files</A>, since it is stored in potential files. Thus, you
|
||||
H, you would use the following pair_coeff command:</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * ffield.reax 1 1 4 2
|
||||
</pre></div>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
|
||||
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
|
||||
mix, shift, table, and tail options.</p>
|
||||
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, since it is stored in potential files. Thus, you
|
||||
need to re-specify the pair_style and pair_coeff commands 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>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>The ReaxFF potential files provided with LAMMPS in the potentials
|
||||
directory are parameterized for real <A HREF = "units.html">units</A>. You can use
|
||||
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>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The ReaxFF potential files provided with LAMMPS in the potentials
|
||||
directory are parameterized for real <a class="reference internal" href="units.html"><em>units</em></a>. You can use
|
||||
the ReaxFF potential with any LAMMPS units, but you would need to
|
||||
create your own potential file with coefficients listed in the
|
||||
appropriate units if your simulation doesn't use "real" units.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_reax_c.html">pair_style reax/c</A>,
|
||||
<A HREF = "fix_reax_bonds.html">fix_reax_bonds</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>The keyword defaults are <I>hbcut</I> = 6, <I>hbnewflag</I> = 1, <I>tripflag</I> = 1,
|
||||
<I>precision</I> = 1.0e-6.
|
||||
</P>
|
||||
<HR>
|
||||
appropriate units if your simulation doesn’t use “real” units.</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_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="pair_reax_c.html"><em>pair_style reax/c</em></a>,
|
||||
<a class="reference internal" href="fix_reax_bonds.html"><em>fix_reax_bonds</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 keyword defaults are <em>hbcut</em> = 6, <em>hbnewflag</em> = 1, <em>tripflag</em> = 1,
|
||||
<em>precision</em> = 1.0e-6.</p>
|
||||
<hr class="docutils" />
|
||||
<p id="chenoweth-2008"><strong>(Chenoweth_2008)</strong> Chenoweth, van Duin and Goddard,
|
||||
Journal of Physical Chemistry A, 112, 1040-1053 (2008).</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<A NAME = "Chenoweth_2008"></A>
|
||||
|
||||
<P><B>(Chenoweth_2008)</B> Chenoweth, van Duin and Goddard,
|
||||
Journal of Physical Chemistry A, 112, 1040-1053 (2008).
|
||||
</P>
|
||||
</HTML>
|
||||
</div>
|
||||
</div>
|
||||
<footer>
|
||||
|
||||
|
||||
<hr/>
|
||||
|
||||
<div role="contentinfo">
|
||||
<p>
|
||||
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|
||||
</p>
|
||||
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