jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
lammps/doc/html/pair_reax_c.html

455 lines
24 KiB
HTML
Raw Blame History

<!DOCTYPE html>
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>pair_style reax/c command &mdash; LAMMPS documentation</title>
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
</head>
<body class="wy-body-for-nav" role="document">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-nav-search">
<a href="Manual.html" class="icon icon-home"> LAMMPS
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
&nbsp;
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
<nav class="wy-nav-top" role="navigation" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="Manual.html">LAMMPS</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>pair_style reax/c command</li>
<li class="wy-breadcrumbs-aside">
<a href="http://lammps.sandia.gov">Website</a>
<a href="Section_commands.html#comm">Commands</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="pair-style-reax-c-command">
<span id="index-0"></span><h1>pair_style reax/c command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span> <span class="n">cfile</span> <span class="n">keyword</span> <span class="n">value</span>
</pre></div>
</div>
<ul class="simple">
<li>cfile = NULL or name of a control file</li>
<li>zero or more keyword/value pairs may be appended</li>
</ul>
<pre class="literal-block">
keyword = <em>checkqeq</em> or <em>lgvdw</em> or <em>safezone</em> or <em>mincap</em>
<em>checkqeq</em> value = <em>yes</em> or <em>no</em> = whether or not to require qeq/reax fix
<em>lgvdw</em> value = <em>yes</em> or <em>no</em> = whether or not to use a low gradient vdW correction
<em>safezone</em> = factor used for array allocation
<em>mincap</em> = minimum size for array allocation
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span> <span class="n">NULL</span>
<span class="n">pair_style</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span> <span class="n">controlfile</span> <span class="n">checkqeq</span> <span class="n">no</span>
<span class="n">pair_style</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span> <span class="n">NULL</span> <span class="n">lgvdw</span> <span class="n">yes</span>
<span class="n">pair_style</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span> <span class="n">NULL</span> <span class="n">safezone</span> <span class="mf">1.6</span> <span class="n">mincap</span> <span class="mi">100</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">ffield</span><span class="o">.</span><span class="n">reax</span> <span class="n">C</span> <span class="n">H</span> <span class="n">O</span> <span class="n">N</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Style <em>reax/c</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 class="reference internal" href="#chenoweth-2008"><span class="std std-ref">(Chenoweth et al., 2008)</span></a>. The version integrated into LAMMPS matches
the most up-to-date version of ReaxFF as of summer 2010. For more
technical details about the pair reax/c implementation of ReaxFF, see
the <a class="reference internal" href="#aktulga"><span class="std std-ref">(Aktulga)</span></a> paper.</p>
<p>The <em>reax/c</em> style differs from the <a class="reference internal" href="pair_reax.html"><span class="doc">pair_style reax</span></a>
command 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 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.</p>
<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/c</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>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">We do not distribute a wide variety of ReaxFF force field files
with LAMMPS. Adri van Duin&#8217;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 submit
a contact request at the Materials Computation Center (MCC) website
<a class="reference external" href="https://www.mri.psu.edu/materials-computation-center/connect-mcc">https://www.mri.psu.edu/materials-computation-center/connect-mcc</a>,
describing the 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>
</div>
<p>The <em>cfile</em> setting can be specified as NULL, in which case default
settings are used. A control file can be specified which defines
values of control variables. Some control variables are
global parameters for the ReaxFF potential. Others define certain
performance and output settings.
Each line in the control file specifies the value for
a control variable. The format of the control file is described
below.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The LAMMPS default values for the ReaxFF global parameters
correspond to those used by Adri van Duin&#8217;s stand-alone serial
code. If these are changed by setting control variables in the control
file, the results from LAMMPS and the serial code will not agree.</p>
</div>
<p>Two examples using <em>pair_style reax/c</em> are provided in the examples/reax
sub-directory, along with corresponding examples for
<a class="reference internal" href="pair_reax.html"><span class="doc">pair_style reax</span></a>.</p>
<p>Use of this pair style requires that a charge be defined for every
atom. See the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a> and
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> commands for details on how to specify
charges.</p>
<p>The ReaxFF parameter files provided were created using a charge
equilibration (QEq) model for handling the electrostatic interactions.
Therefore, by default, LAMMPS requires that the <a class="reference internal" href="fix_qeq_reax.html"><span class="doc">fix qeq/reax</span></a> command be used with <em>pair_style reax/c</em>
when simulating a ReaxFF model, to equilibrate charge each timestep.
Using the keyword <em>checkqeq</em> with the value <em>no</em>
turns off the check for <em>fix qeq/reax</em>,
allowing a simulation to be run without charge equilibration.
In this case, the static charges you
assign to each atom will be used for computing the electrostatic
interactions in the system.
See the <a class="reference internal" href="fix_qeq_reax.html"><span class="doc">fix qeq/reax</span></a> command for details.</p>
<p>Using the optional keyword <em>lgvdw</em> with the value <em>yes</em> turns on
the low-gradient correction of the ReaxFF/C for long-range
London Dispersion, as described in the <a class="reference internal" href="#liu-2011"><span class="std std-ref">(Liu)</span></a> paper. Force field
file <em>ffield.reax.lg</em> is designed for this correction, and is trained
for several energetic materials (see &#8220;Liu&#8221;). When using lg-correction,
recommended value for parameter <em>thb</em> is 0.01, which can be set in the
control file. Note: Force field files are different for the original
or lg corrected pair styles, using wrong ffield file generates an error message.</p>
<p>Optional keywords <em>safezone</em> and <em>mincap</em> are used for allocating
reax/c arrays. Increase these values can avoid memory problems, such
as segmentation faults and bondchk failed errors, that could occur under
certain conditions.</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
<em>ecoul</em>. The output of these quantities is controlled by the
<a class="reference internal" href="thermo.html"><span class="doc">thermo</span></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"><span class="doc">compute pair</span></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 original FORTRAN ReaxFF code):</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-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">reax</span> <span class="nb">all</span> <span class="n">pair</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span>
<span class="n">variable</span> <span class="n">eb</span> <span class="n">equal</span> <span class="n">c_reax</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">variable</span> <span class="n">ea</span> <span class="n">equal</span> <span class="n">c_reax</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="o">...</span>
<span class="n">variable</span> <span class="n">eqeq</span> <span class="n">equal</span> <span class="n">c_reax</span><span class="p">[</span><span class="mi">14</span><span class="p">]</span>
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">epair</span> <span class="n">v_eb</span> <span class="n">v_ea</span> <span class="o">...</span> <span class="n">v_eqeq</span>
</pre></div>
</div>
<p>Only a single pair_coeff command is used with the <em>reax/c</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 class="simple">
<li>filename</li>
<li>N indices = ReaxFF elements</li>
</ul>
<p>The filename is the ReaxFF potential file. Unlike for the <em>reax</em>
pair style, any filename can be used.</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 <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 the <em>reax/c</em> style is used as part
of the <em>hybrid</em> pair style. The NULL values are placeholders for atom
types that will be used with other potentials.</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 <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>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">ffield</span><span class="o">.</span><span class="n">reax</span> <span class="n">C</span> <span class="n">C</span> <span class="n">N</span> <span class="n">H</span>
</pre></div>
</div>
<hr class="docutils" />
<p>The format of a line in the control file is as follows:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable_name</span> <span class="n">value</span>
</pre></div>
</div>
<p>and it may be followed by an &#8221;!&#8221; character and a trailing comment.</p>
<p>If the value of a control variable is not specified, then default
values are used. What follows is the list of variables along with a
brief description of their use and default values.</p>
<p>simulation_name: Output files produced by <em>pair_style reax/c</em> carry
this name + extensions specific to their contents. Partial energies
are reported with a &#8221;.pot&#8221; extension, while the trajectory file has
&#8221;.trj&#8221; extension.</p>
<p>tabulate_long_range: To improve performance, long range interactions
can optionally be tabulated (0 means no tabulation). Value of this
variable denotes the size of the long range interaction table. The
range from 0 to long range cutoff (defined in the <em>ffield</em> file) is
divided into <em>tabulate_long_range</em> points. Then at the start of
simulation, we fill in the entries of the long range interaction table
by computing the energies and forces resulting from van der Waals and
Coulomb interactions between every possible atom type pairs present in
the input system. During the simulation we consult to the long range
interaction table to estimate the energy and forces between a pair of
atoms. Linear interpolation is used for estimation. (default value =
0)</p>
<p>energy_update_freq: Denotes the frequency (in number of steps) of
writes into the partial energies file. (default value = 0)</p>
<p>nbrhood_cutoff: Denotes the near neighbors cutoff (in Angstroms)
regarding the bonded interactions. (default value = 5.0)</p>
<p>hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen
bond interactions.(default value = 7.5. Value of 0.0 turns off hydrogen</p>
<blockquote>
<div>bonds)</div></blockquote>
<p>bond_graph_cutoff: is the threshold used in determining what is a
physical bond, what is not. Bonds and angles reported in the
trajectory file rely on this cutoff. (default value = 0.3)</p>
<p>thb_cutoff: cutoff value for the strength of bonds to be considered in
three body interactions. (default value = 0.001)</p>
<p>thb_cutoff_sq: cutoff value for the strength of bond order products
to be considered in three body interactions. (default value = 0.00001)</p>
<p>write_freq: Frequency of writes into the trajectory file. (default
value = 0)</p>
<p>traj_title: Title of the trajectory - not the name of the trajectory
file.</p>
<p>atom_info: 1 means print only atomic positions + charge (default = 0)</p>
<p>atom_forces: 1 adds net forces to atom lines in the trajectory file
(default = 0)</p>
<p>atom_velocities: 1 adds atomic velocities to atoms line (default = 0)</p>
<p>bond_info: 1 prints bonds in the trajectory file (default = 0)</p>
<p>angle_info: 1 prints angles in the trajectory file (default = 0)</p>
<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"><span class="doc">pair_modify</span></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"><span class="doc">binary restart files</span></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 <em>pair</em> keyword of the
<a class="reference internal" href="run_style.html"><span class="doc">run_style respa</span></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</h2>
<p>This pair style is part of the USER-REAXC 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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>The ReaxFF potential files provided with LAMMPS in the potentials
directory are parameterized for real <a class="reference internal" href="units.html"><span class="doc">units</span></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&#8217;t use &#8220;real&#8221; units.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a>, <a class="reference internal" href="fix_qeq_reax.html"><span class="doc">fix qeq/reax</span></a>, <a class="reference internal" href="fix_reax_bonds.html"><span class="doc">fix reax/c/bonds</span></a>, <a class="reference internal" href="fix_reaxc_species.html"><span class="doc">fix reax/c/species</span></a>, <a class="reference internal" href="pair_reax.html"><span class="doc">pair_style reax</span></a></p>
</div>
<div class="section" id="default">
<h2>Default</h2>
<p>The keyword defaults are checkqeq = yes, lgvdw = no, safezone = 1.2,
mincap = 50.</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>
<p id="aktulga">(Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
245-259 (2012).</p>
<p id="liu-2011"><strong>(Liu)</strong> L. Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal
of Physical Chemistry A, 115, 11016-11022 (2011).</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
&copy; Copyright 2013 Sandia Corporation.
</p>
</div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true
};
</script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
<script type="text/javascript" src="_static/js/theme.js"></script>
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.StickyNav.enable();
});
</script>
</body>
</html>
Reference in New Issue View Git Blame Copy Permalink