2010-10-27 00:18:21 +08:00
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<HTML>
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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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<HR>
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<H3>pair_style reax/c command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>pair_style reax/c cfile keyword value
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</PRE>
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<UL><LI>cfile = NULL or name of a control file
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<LI>zero or more keyword/value pairs may be appended
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<PRE>keyword = <I>checkqeq</I> or <I>lgvdw</I>
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<I>checkqeq</I> value = <I>yes</I> or <I>no</I> = whether or not to require qeq/reax fix
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<I>lgvdw</I> value = <I>yes</I> or <I>no</I> = whether or not to use a low gradient vdW correction
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</PRE>
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2010-10-27 00:18:21 +08:00
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style 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_coeff * * ffield.reax 1 2 2 3
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Style <I>reax/c</I> 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 HREF = "#Chenoweth_2008">(Chenoweth et al.,
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2008)</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 "(Aktulga)" paper.
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</P>
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<P>The <I>reax/c</I> style differs from the <A HREF = "pair_reax.html">pair_style reax</A>
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command in the lo-level implementation details. The <I>reax</I> style is a
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Fortran library, linked to LAMMPS. The <I>reax/c</I> 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.
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</P>
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2010-10-27 04:54:38 +08:00
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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.
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</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 <I>pair_style reax/c</I> 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).
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</P>
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<P>The <I>cfile</I> setting can be specified as NULL, in which case default
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settings are used. Or a control file can be specified which contains
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cutoff values for the ReaxFF potential in addition to some performance
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and output controls. Each line in the control specifies the value for
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a control variable. The format of the control file is described
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below.
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</P>
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<P>Two examples using <I>pair_style reax/c</I> are provided in the examples/reax
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sub-directory, along with corresponding examples for
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<A HREF = "pair_reax.html">pair_style reax</A>.
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</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 HREF = "atom_style.html">atom_style</A> and
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<A HREF = "read_data.html">read_data</A> commands for details on how to specify
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charges.
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</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 HREF = "fix_qeq_reax.html">fix
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qeq/reax</A> command be used with <I>pair_style reax/c</I>
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when simulating a ReaxFF model, to equilibrate charge each timestep.
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Using the keyword <I>checkqeq</I> with the value <I>no</I>
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turns off the check for <I>fix qeq/reax</I>,
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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 HREF = "fix_qeq_reax.html">fix qeq/reax</A> command for details.
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</P>
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<P>Using the optional keyword <I>lgvdw</I> with the value <I>yes</I> 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 "(Liu)" paper. Force field
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file <I>ffield.reax.lg</I> 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 <I>thb</I> is 0.01, which can be set in
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the control file. Note: Force field files
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are different for the original or lg corrected pair styles, using
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wrong ffield file generates an error message.
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</P>
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<P>The thermo variable <I>evdwl</I> 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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<I>ecoul</I>. The output of these quantities is controlled by the
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<A HREF = "thermo.html">thermo</A> command.
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</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 HREF = "compute_pair.html">compute
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pair</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):
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</P>
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<OL><LI><I>eb</I> = bond energy
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<LI><I>ea</I> = atom energy
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<LI><I>elp</I> = lone-pair energy
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<LI><I>emol</I> = molecule energy (always 0.0)
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<LI><I>ev</I> = valence angle energy
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<LI><I>epen</I> = double-bond valence angle penalty
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<LI><I>ecoa</I> = valence angle conjugation energy
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<LI><I>ehb</I> = hydrogen bond energy
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<LI><I>et</I> = torsion energy
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<LI><I>eco</I> = conjugation energy
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<LI><I>ew</I> = van der Waals energy
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<LI><I>ep</I> = Coulomb energy
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<LI><I>efi</I> = electric field energy (always 0.0)
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<LI><I>eqeq</I> = charge equilibration energy
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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:
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</P>
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<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>
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<P>Only a single pair_coeff command is used with the <I>reax/c</I> 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:
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</P>
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<UL><LI>filename
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<LI>N indices = mapping of ReaxFF elements to atom types
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</UL>
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<P>The filename is the ReaxFF potential file. Unlike for the <I>reax</I>
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pair style, any filename can be used.
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</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 <I>ffield</I> 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 <I>reax/c</I> style is used as part
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of the <I>hybrid</I> pair style. The NULL values are placeholders for atom
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types that will be used with other potentials.
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</P>
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2011-02-16 02:42:22 +08:00
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<P>IMPORTANT NOTE: Currently the reax/c pair style cannot be used as part
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of the <I>hybrid</I> pair style. Some additional work still need to be
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done to enable this.
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</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 <I>ffield</I> 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:
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</P>
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<PRE>pair_coeff * * ffield.reax 1 1 4 2
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</PRE>
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<HR>
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<P>The format of a line in the control file is as follows:
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</P>
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<PRE>variable_name value
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</PRE>
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<P>and it may be followed by an "!" character and a trailing comment.
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</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.
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</P>
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<P>simulation_name: Output files produced by <I>pair_style reax/c</I> 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.
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</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 <I>ffield</I> file) is
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divided into <I>tabulate_long_range</I> 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)
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</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)
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</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 = 4)
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</P>
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<P>hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen
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bond interactions.(default value = 0 - means no hydrogen bonds are
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present)
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</P>
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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)
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</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)
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</P>
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<P>write_freq: Frequency of writes into the trajectory file. (default
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value = 0)
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</P>
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<P>traj_title: Title of the trajectory - not the name of the trajectory
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file.
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</P>
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<P>atom_info: 1 means print only atomic positions + charge (default = 0)
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</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)
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</P>
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<P>atom_velocities: 1 adds atomic velocities to atoms line (default = 0)
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</P>
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<P>bond_info: 1 prints bonds in the trajectory file (default = 0)
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</P>
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<P>angle_info: 1 prints angles in the trajectory file (default = 0)
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</P>
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<HR>
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<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
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</P>
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<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
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mix, shift, table, and tail options.
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</P>
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<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
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files</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.
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</P>
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<P>This pair style can only be used via the <I>pair</I> keyword of the
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<A HREF = "run_style.html">run_style respa</A> command. It does not support the
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<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
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</P>
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<P><B>Restrictions:</B>
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</P>
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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 HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info.
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</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 HREF = "units.html">units</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
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appropriate units if your simulation doesn't use "real" units.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_qeq_reax.html">fix_qeq_reax</A>,
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<A HREF = "pair_reax.html">pair_style reax</A>
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</P>
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2011-01-04 01:10:54 +08:00
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<P><B>Default:</B>
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</P>
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2012-01-07 04:39:16 +08:00
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<P>The keyword defaults are checkqeq = yes, lgvdw = no.
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2010-10-27 00:18:21 +08:00
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</P>
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<HR>
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2010-10-27 04:54:38 +08:00
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<A NAME = "Chenoweth_2008"></A>
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2010-10-27 00:18:21 +08:00
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2010-10-27 04:54:38 +08:00
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<P><B>(Chenoweth_2008)</B> Chenoweth, van Duin and Goddard,
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2010-10-27 00:18:21 +08:00
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Journal of Physical Chemistry A, 112, 1040-1053 (2008).
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</P>
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2011-09-13 08:28:42 +08:00
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<A NAME = "Aktulga"></A>
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2011-10-06 22:15:34 +08:00
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<P><B>(Aktulga)</B> Aktulga, Fogarty, Pandit, Grama, Parallel Computing, to
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appear (2011).
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2011-08-25 22:13:49 +08:00
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</P>
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2012-01-07 04:39:16 +08:00
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<A NAME = "Liu"></A>
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<P><B>(Liu)</B> L. Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal
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of Physical Chemistry A, 115, 11016-11022 (2011).
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</P>
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2010-10-27 00:18:21 +08:00
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</HTML>
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