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<title>pair_style reax/c command — LAMMPS 15 May 2015 version documentation</title>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li>pair_style reax/c command</li>
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<div class="section" id="pair-style-reax-c-command">
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<span id="index-0"></span><h1>pair_style reax/c command<a class="headerlink" href="#pair-style-reax-c-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>pair_style reax/c cfile keyword value
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</pre></div>
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</div>
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<ul class="simple">
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<li>cfile = NULL or name of a control file</li>
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<li>zero or more keyword/value pairs may be appended</li>
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</ul>
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<pre class="literal-block">
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keyword = <em>checkqeq</em> or <em>lgvdw</em> or <em>safezone</em> or <em>mincap</em>
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<em>checkqeq</em> value = <em>yes</em> or <em>no</em> = whether or not to require qeq/reax fix
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<em>lgvdw</em> value = <em>yes</em> or <em>no</em> = whether or not to use a low gradient vdW correction
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<em>safezone</em> = factor used for array allocation
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<em>mincap</em> = minimum size for array allocation
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>pair_style reax/c NULL
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pair_style reax/c controlfile checkqeq no
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pair_style reax/c NULL lgvdw yes
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pair_style reax/c NULL safezone 1.6 mincap 100
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pair_coeff * * ffield.reax C H O N
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Style <em>reax/c</em> computes the ReaxFF potential of van Duin, Goddard and
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co-workers. ReaxFF uses distance-dependent bond-order functions to
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represent the contributions of chemical bonding to the potential
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energy. There is more than one version of ReaxFF. The version
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implemented in LAMMPS uses the functional forms documented in the
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supplemental information of the following paper: <a class="reference internal" href="#chenoweth-2008"><span>(Chenoweth et al., 2008)</span></a>. The version integrated into LAMMPS matches
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the most up-to-date version of ReaxFF as of summer 2010. For more
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technical details about the pair reax/c implementation of ReaxFF, see
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the <a class="reference internal" href="#aktulga"><span>(Aktulga)</span></a> paper.</p>
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<p>The <em>reax/c</em> style differs from the <a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a>
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command in the lo-level implementation details. The <em>reax</em> style is a
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Fortran library, linked to LAMMPS. The <em>reax/c</em> style was initially
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implemented as stand-alone C code and is now integrated into LAMMPS as
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a package.</p>
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<p>LAMMPS provides several different versions of ffield.reax in its
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potentials dir, each called potentials/ffield.reax.label. These are
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documented in potentials/README.reax. The default ffield.reax
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contains parameterizations for the following elements: C, H, O, N, S.</p>
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<p>The format of these files is identical to that used originally by van
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Duin. We have tested the accuracy of <em>pair_style reax/c</em> potential
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against the original ReaxFF code for the systems mentioned above. You
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can use other ffield files for specific chemical systems that may be
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available elsewhere (but note that their accuracy may not have been
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tested).</p>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">We do not distribute a wide variety of ReaxFF force
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field files with LAMMPS. Adri van Duin’s group at PSU is the central
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repository for this kind of data as they are continuously deriving and
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updating parameterizations for different classes of materials. You
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can visit their WWW site at
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<a class="reference external" href="http://www.engr.psu.edu/adri">http://www.engr.psu.edu/adri</a>, register
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as a “new user”, and then submit a request to their group describing
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material(s) you are interested in modeling with ReaxFF. They can tell
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you what is currently available or what it would take to create a
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suitable ReaxFF parameterization.</p>
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</div>
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<p>The <em>cfile</em> setting can be specified as NULL, in which case default
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settings are used. A control file can be specified which defines
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values of control variables. Some control variables are
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global parameters for the ReaxFF potential. Others define certain
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performance and output settings.
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Each line in the control file specifies the value for
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a control variable. The format of the control file is described
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below.</p>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">The LAMMPS default values for the ReaxFF global parameters
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correspond to those used by
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Adri van Duin’s stand-alone serial code. If these are changed by
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setting control variables in the control file, the results from
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LAMMPS and the serial code will not agree.</p>
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</div>
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<p>Two examples using <em>pair_style reax/c</em> are provided in the examples/reax
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sub-directory, along with corresponding examples for
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<a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a>.</p>
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<p>Use of this pair style requires that a charge be defined for every
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atom. See the <a class="reference internal" href="atom_style.html"><em>atom_style</em></a> and
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<a class="reference internal" href="read_data.html"><em>read_data</em></a> commands for details on how to specify
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charges.</p>
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<p>The ReaxFF parameter files provided were created using a charge
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equilibration (QEq) model for handling the electrostatic interactions.
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Therefore, by default, LAMMPS requires that the <a class="reference internal" href="fix_qeq_reax.html"><em>fix qeq/reax</em></a> command be used with <em>pair_style reax/c</em>
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when simulating a ReaxFF model, to equilibrate charge each timestep.
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Using the keyword <em>checkqeq</em> with the value <em>no</em>
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turns off the check for <em>fix qeq/reax</em>,
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allowing a simulation to be run without charge equilibration.
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In this case, the static charges you
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assign to each atom will be used for computing the electrostatic
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interactions in the system.
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See the <a class="reference internal" href="fix_qeq_reax.html"><em>fix qeq/reax</em></a> command for details.</p>
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<p>Using the optional keyword <em>lgvdw</em> with the value <em>yes</em> turns on
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the low-gradient correction of the ReaxFF/C for long-range
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London Dispersion, as described in the <a class="reference internal" href="#liu-2011"><span>(Liu)</span></a> paper. Force field
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file <em>ffield.reax.lg</em> is designed for this correction, and is trained
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for several energetic materials (see “Liu”). When using lg-correction,
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recommended value for parameter <em>thb</em> is 0.01, which can be set in the
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control file. Note: Force field files are different for the original
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or lg corrected pair styles, using wrong ffield file generates an error message.</p>
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<p>Optional keywords <em>safezone</em> and <em>mincap</em> are used for allocating
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reax/c arrays. Increase these values can avoid memory problems, such
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as segmentation faults and bondchk failed errors, that could occur under
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certain conditions.</p>
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<p>The thermo variable <em>evdwl</em> stores the sum of all the ReaxFF potential
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energy contributions, with the exception of the Coulombic and charge
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equilibration contributions which are stored in the thermo variable
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<em>ecoul</em>. The output of these quantities is controlled by the
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<a class="reference internal" href="thermo.html"><em>thermo</em></a> command.</p>
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<p>This pair style tallies a breakdown of the total ReaxFF potential
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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.
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The 14 values correspond to the following sub-categories (the variable
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names in italics match those used in the original FORTRAN ReaxFF code):</p>
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<ol class="arabic simple">
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<li><em>eb</em> = bond energy</li>
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<li><em>ea</em> = atom energy</li>
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<li><em>elp</em> = lone-pair energy</li>
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<li><em>emol</em> = molecule energy (always 0.0)</li>
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<li><em>ev</em> = valence angle energy</li>
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<li><em>epen</em> = double-bond valence angle penalty</li>
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<li><em>ecoa</em> = valence angle conjugation energy</li>
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<li><em>ehb</em> = hydrogen bond energy</li>
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<li><em>et</em> = torsion energy</li>
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<li><em>eco</em> = conjugation energy</li>
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<li><em>ew</em> = van der Waals energy</li>
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<li><em>ep</em> = Coulomb energy</li>
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<li><em>efi</em> = electric field energy (always 0.0)</li>
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<li><em>eqeq</em> = charge equilibration energy</li>
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</ol>
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<p>To print these quantities to the log file (with descriptive column
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headings) the following commands could be included in an input script:</p>
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<div class="highlight-python"><div class="highlight"><pre>compute reax all pair reax/c
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variable eb equal c_reax[1]
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variable ea equal c_reax[2]
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...
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variable eqeq equal c_reax[14]
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thermo_style custom step temp epair v_eb v_ea ... v_eqeq
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</pre></div>
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</div>
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<p>Only a single pair_coeff command is used with the <em>reax/c</em> style which
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specifies a ReaxFF potential file with parameters for all needed
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elements. These are mapped to LAMMPS atom types by specifying N
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additional arguments after the filename in the pair_coeff command,
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where N is the number of LAMMPS atom types:</p>
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<ul class="simple">
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<li>filename</li>
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<li>N indices = ReaxFF elements</li>
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</ul>
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<p>The filename is the ReaxFF potential file. Unlike for the <em>reax</em>
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pair style, any filename can be used.</p>
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<p>In the ReaxFF potential file, near the top, after the general
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parameters, is the atomic parameters section that contains element
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names, each with a couple dozen numeric parameters. If there are M
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elements specified in the <em>ffield</em> file, think of these as numbered 1
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to M. Each of the N indices you specify for the N atom types of LAMMPS
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atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will
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be mapped to whatever element you specify as the first index value,
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etc. If a mapping value is specified as NULL, the mapping is not
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performed. This can be used when the <em>reax/c</em> style is used as part
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of the <em>hybrid</em> pair style. The NULL values are placeholders for atom
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types that will be used with other potentials.</p>
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<p>As an example, say your LAMMPS simulation has 4 atom types and the
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elements are ordered as C, H, O, N in the <em>ffield</em> file. If you want
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the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
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H, you would use the following pair_coeff command:</p>
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<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * ffield.reax C C N H
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</pre></div>
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</div>
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<hr class="docutils" />
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<p>The format of a line in the control file is as follows:</p>
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<div class="highlight-python"><div class="highlight"><pre>variable_name value
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</pre></div>
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</div>
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<p>and it may be followed by an ”!” character and a trailing comment.</p>
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<p>If the value of a control variable is not specified, then default
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values are used. What follows is the list of variables along with a
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brief description of their use and default values.</p>
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<p>simulation_name: Output files produced by <em>pair_style reax/c</em> carry
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this name + extensions specific to their contents. Partial energies
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are reported with a ”.pot” extension, while the trajectory file has
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”.trj” extension.</p>
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<p>tabulate_long_range: To improve performance, long range interactions
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can optionally be tabulated (0 means no tabulation). Value of this
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variable denotes the size of the long range interaction table. The
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range from 0 to long range cutoff (defined in the <em>ffield</em> file) is
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divided into <em>tabulate_long_range</em> points. Then at the start of
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simulation, we fill in the entries of the long range interaction table
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by computing the energies and forces resulting from van der Waals and
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Coulomb interactions between every possible atom type pairs present in
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the input system. During the simulation we consult to the long range
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interaction table to estimate the energy and forces between a pair of
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atoms. Linear interpolation is used for estimation. (default value =
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0)</p>
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<p>energy_update_freq: Denotes the frequency (in number of steps) of
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writes into the partial energies file. (default value = 0)</p>
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<p>nbrhood_cutoff: Denotes the near neighbors cutoff (in Angstroms)
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regarding the bonded interactions. (default value = 5.0)</p>
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<p>hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen
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bond interactions.(default value = 7.5. Value of 0.0 turns off hydrogen</p>
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<blockquote>
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<div>bonds)</div></blockquote>
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<p>bond_graph_cutoff: is the threshold used in determining what is a
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physical bond, what is not. Bonds and angles reported in the
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trajectory file rely on this cutoff. (default value = 0.3)</p>
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<p>thb_cutoff: cutoff value for the strength of bonds to be considered in
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three body interactions. (default value = 0.001)</p>
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<p>thb_cutoff_sq: cutoff value for the strength of bond order products
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to be considered in three body interactions. (default value = 0.00001)</p>
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<p>write_freq: Frequency of writes into the trajectory file. (default
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value = 0)</p>
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<p>traj_title: Title of the trajectory - not the name of the trajectory
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file.</p>
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<p>atom_info: 1 means print only atomic positions + charge (default = 0)</p>
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<p>atom_forces: 1 adds net forces to atom lines in the trajectory file
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(default = 0)</p>
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<p>atom_velocities: 1 adds atomic velocities to atoms line (default = 0)</p>
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<p>bond_info: 1 prints bonds in the trajectory file (default = 0)</p>
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<p>angle_info: 1 prints angles in the trajectory file (default = 0)</p>
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<hr class="docutils" />
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<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
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<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
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mix, shift, table, and tail options.</p>
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<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
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need to re-specify the pair_style and pair_coeff commands in an input
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script that reads a restart file.</p>
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<p>This pair style can only be used via the <em>pair</em> keyword of the
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<a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command. It does not support the
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<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<p>This pair style is part of the USER-REAXC package. It is only enabled
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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>
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<p>The ReaxFF potential files provided with LAMMPS in the potentials
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directory are parameterized for real <a class="reference internal" href="units.html"><em>units</em></a>. You can use
|
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the ReaxFF potential with any LAMMPS units, but you would need to
|
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create your own potential file with coefficients listed in the
|
|
appropriate units if your simulation doesn’t use “real” units.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="fix_qeq_reax.html"><em>fix qeq/reax</em></a>, <a class="reference internal" href="fix_reax_bonds.html"><em>fix reax/c/bonds</em></a>, <a class="reference internal" href="fix_reaxc_species.html"><em>fix reax/c/species</em></a>, <a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a></p>
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</div>
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<div class="section" id="default">
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<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
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<p>The keyword defaults are checkqeq = yes, lgvdw = no, safezone = 1.2,
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|
mincap = 50.</p>
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<hr class="docutils" />
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|
<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>
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