2009-02-07 00:12:07 +08:00
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<HTML>
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2010-09-21 22:58:42 +08:00
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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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2009-02-07 00:12:07 +08:00
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</CENTER>
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<HR>
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<H3>pair_style reax 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 hbcut hbnewflag tripflag precision
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</PRE>
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<UL><LI>hbcut = hydrogen-bond cutoff (optional) (distance units)
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<LI>hbnewflag = use old or new hbond function style (0 or 1) (optional)
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<LI>tripflag = apply stabilization to all triple bonds (0 or 1) (optional)
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<LI>precision = precision for charge equilibration (optional)
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2009-02-07 00:12:07 +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
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pair_style reax 10.0 0 1 1.0e-5
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pair_coeff * * ffield.reax 3 1 2 2
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pair_coeff * * ffield.reax 3 NULL NULL 3
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2009-02-07 00:12:07 +08:00
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</PRE>
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<P><B>Description:</B>
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</P>
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2010-09-04 08:17:54 +08:00
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<P>Style <I>reax</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:
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2010-10-27 04:54:38 +08:00
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<A HREF = "#Chenoweth_2008">(Chenoweth)</A>. The version integrated into LAMMPS matches
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the most up-to-date version of ReaxFF as of summer 2010.
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</P>
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<P>The <I>reax</I> style differs from the <A HREF = "pair_reax_c.html">pair_style reax/c</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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<P>LAMMPS requires that a file called ffield.reax be provided, containing
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the ReaxFF parameters for each atom type, bond type, etc. The format
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is identical to the ffield file used by van Duin and co-workers. The
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filename is required as an argument in the pair_coeff command. Any
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value other than "ffield.reax" will be rejected (see below).
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</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.
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</P>
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2012-02-28 02:49:13 +08:00
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<P>IMPORTANT NOTE: 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 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.
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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</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>hbcut</I>, <I>hbnewflag</I>, <I>tripflag</I>, and <I>precision</I> settings are
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optional arguments. If none are provided, default settings are used:
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<I>hbcut</I> = 6 (which is Angstroms in real units), <I>hbnewflag</I> = 1 (use
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new hbond function style), <I>tripflag</I> = 1 (apply stabilization to all
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triple bonds), and <I>precision</I> = 1.0e-6 (one part in 10^6). If you
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wish to override any of these defaults, then all of the settings must
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be specified.
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</P>
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2010-10-27 04:54:38 +08:00
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<P>Two examples using <I>pair_style reax</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_c.html">pair_style reax/c</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 since the <I>reax</I> pair style performs a charge equilibration (QEq)
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calculation. 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 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 ReaxFF FORTRAN library):
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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
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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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2009-02-07 00:40:44 +08:00
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<P>Only a single pair_coeff command is used with the <I>reax</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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2009-02-13 04:45:46 +08:00
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<P>The specification of the filename and the mapping of LAMMPS atom types
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recognized by the ReaxFF is done differently than for other LAMMPS
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potentials, due to the non-portable difficulty of passing character
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strings (e.g. filename, element names) between C++ and Fortran.
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</P>
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<P>The filename has to be "ffield.reax" and it has to exist in the
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directory you are running LAMMPS in. This means you cannot prepend a
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path to the file in the potentials dir. Rather, you should copy that
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file into the directory you are running from. If you wish to use
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another ReaxFF potential file, then name it "ffield.reax" and put it
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in the directory you run from.
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2009-02-13 04:45:46 +08:00
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</P>
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2010-09-04 08:17:54 +08:00
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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 a ReaxFF potential 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 pair style cannot be used as part
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of the <I>hybrid</I> pair style. Some additional changes still need to be
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made to enable this.
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</P>
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2010-09-04 08:17:54 +08:00
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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><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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2010-10-22 01:31:01 +08:00
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<P><B>Restrictions:</B>
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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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2010-10-27 04:54:38 +08:00
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<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_reax_c.html">pair_style reax/c</A>,
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<A HREF = "fix_reax_bonds.html">fix_reax_bonds</A>
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</P>
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<P><B>Default:</B>
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</P>
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2011-02-16 02:42:22 +08:00
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<P>The keyword defaults are <I>hbcut</I> = 6, <I>hbnewflag</I> = 1, <I>tripflag</I> = 1,
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<I>precision</I> = 1.0e-6.
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</P>
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<HR>
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2009-06-04 03:59:51 +08:00
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<A NAME = "Chenoweth_2008"></A>
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2009-02-07 00:12:07 +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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Journal of Physical Chemistry A, 112, 1040-1053 (2008).
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</P>
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</HTML>
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