forked from lijiext/lammps
205 lines
8.5 KiB
HTML
205 lines
8.5 KiB
HTML
<HTML>
|
|
<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>
|
|
</CENTER>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<HR>
|
|
|
|
<H3>pair_style comb command
|
|
</H3>
|
|
<H3>pair_style comb/omp command
|
|
</H3>
|
|
<H3>pair_style comb3 command
|
|
</H3>
|
|
<P><B>Syntax:</B>
|
|
</P>
|
|
<PRE>pair_style comb
|
|
pair_style comb3 keyword
|
|
</PRE>
|
|
<PRE>keyword = <I>polar</I>
|
|
<I>polar</I> value = <I>polar_on</I> or <I>polar_off</I> = whether or not to include atomic polarization
|
|
</PRE>
|
|
|
|
</UL>
|
|
<P><B>Examples:</B>
|
|
</P>
|
|
<PRE>pair_style comb
|
|
pair_coeff * * ../potentials/ffield.comb Si
|
|
pair_coeff * * ../potentials/ffield.comb Hf Si O
|
|
</PRE>
|
|
<PRE>pair_style comb3 polar_off
|
|
pair_coeff * * ../potentials/ffield.comb3 O Cu N C O
|
|
</PRE>
|
|
<P><B>Description:</B>
|
|
</P>
|
|
<P>Style <I>comb</I> computes the second-generation variable charge COMB
|
|
(Charge-Optimized Many-Body) potential. Style <I>comb3</I> computes the
|
|
third-generation COMB potential. These COMB potentials are described
|
|
in <A HREF = "#COMB">(COMB)</A> and <A HREF = "#COMB3">(COMB3)</A>. Briefly, the total energy
|
|
<I>E<sub>T</sub></I> of a system of atoms is given by
|
|
</P>
|
|
<CENTER><IMG SRC = "Eqs/pair_comb1.jpg">
|
|
</CENTER>
|
|
<P>where <I>E<sub>i</sub><sup>self</sup></I> is the self-energy of atom <I>i</I>
|
|
(including atomic ionization energies and electron affinities),
|
|
<I>E<sub>ij</sub><sup>short</sup></I> is the bond-order potential between
|
|
atoms <I>i</I> and <I>j</I>,
|
|
<I>E<sub>ij</sub><sup>Coul</sup></I> is the Coulomb interactions,
|
|
<I>E<sup>polar</sup></I> is the polarization term for organic systems
|
|
(style <I>comb3</I> only),
|
|
<I>E<sup>vdW</sup></I> is the van der Waals energy (style <I>comb3</I> only),
|
|
<I>E<sup>barr</sup></I> is a charge barrier function, and
|
|
<I>E<sup>corr</sup></I> are angular correction terms.
|
|
</P>
|
|
<P>The COMB potentials (styles <I>comb</I> and <I>comb3</I>) are variable charge
|
|
potentials. The equilibrium charge on each atom is calculated by the
|
|
electronegativity equalization (QEq) method. See <A HREF = "#Rick">Rick</A> for
|
|
further details. This is implemented by the <A HREF = "fix_qeq_comb.html">fix
|
|
qeq/comb</A> command, which should normally be
|
|
specified in the input script when running a model with the COMB
|
|
potential. The <A HREF = "fix_qeq_comb.html">fix qeq/comb</A> command has options
|
|
that determine how often charge equilibration is performed, its
|
|
convergence criterion, and which atoms are included in the
|
|
calculation.
|
|
</P>
|
|
<P>Only a single pair_coeff command is used with the <I>comb</I> and <I>comb3</I>
|
|
styles which specifies the COMB potential file with parameters for all
|
|
needed elements. These are mapped to LAMMPS atom types by specifying
|
|
N additional arguments after the potential file in the pair_coeff
|
|
command, where N is the number of LAMMPS atom types.
|
|
</P>
|
|
<P>For example, if your LAMMPS simulation of a Si/SiO<sub>2</sub>/
|
|
HfO<sub>2</sub> interface has 4 atom types, and you want the 1st and
|
|
last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would
|
|
use the following pair_coeff command:
|
|
</P>
|
|
<PRE>pair_coeff * * ../potentials/ffield.comb Si Hf O Si
|
|
</PRE>
|
|
<P>The first two arguments must be * * so as to span all LAMMPS atom
|
|
types. The first and last Si arguments map LAMMPS atom types 1 and 4
|
|
to the Si element in the <I>ffield.comb</I> file. The second Hf argument
|
|
maps LAMMPS atom type 2 to the Hf element, and the third O argument
|
|
maps LAMMPS atom type 3 to the O element in the potential file. If a
|
|
mapping value is specified as NULL, the mapping is not performed.
|
|
This can be used when a <I>comb</I> potential is used as part of the
|
|
<I>hybrid</I> pair style. The NULL values are placeholders for atom types
|
|
that will be used with other potentials.
|
|
</P>
|
|
<P>For style <I>comb</I>, the provided potential file <I>ffield.comb</I> contains
|
|
all currently-available 2nd generation COMB parameterizations: for Si,
|
|
Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals. For style
|
|
<I>comb3</I>, the potential file <I>ffield.comb3</I> contains all
|
|
currently-available 3rd generation COMB paramterizations: O, Cu, N, C,
|
|
H, Ti, Zn and Zr. The status of the optimization of the compounds, for
|
|
example Cu<sub>2</sub>O, TiN and hydrocarbons, are given in the
|
|
following table:
|
|
</P>
|
|
<CENTER><IMG SRC = "Eqs/pair_comb2.jpg">
|
|
</CENTER>
|
|
<P>For style <I>comb3</I>, in addition to ffield.comb3, a special parameter
|
|
file, <I>lib.comb3</I>, that is exclusively used for C/O/H systems, will be
|
|
automatically loaded if carbon atom is detected in LAMMPS input
|
|
structure. This file must be in your working directory or in the
|
|
directory pointed to by the environment variable LAMMPS_POTENTIALS, as
|
|
described on the <A HREF = "pair_coeff.html">pair_coeff</A> command doc page.
|
|
</P>
|
|
<P>Keyword <I>polar</I> indicates whether the force field includes
|
|
the atomic polarization. Since the equilibration of the polarization
|
|
has not yet been implemented, it can only set polar_off at present.
|
|
</P>
|
|
<P>IMPORTANT NOTE: You can not use potential file <I>ffield.comb</I> with
|
|
style <I>comb3</I>, nor file <I>ffield.comb3</I> with style <I>comb</I>.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
|
|
functionally the same as the corresponding style without the suffix.
|
|
They have been optimized to run faster, depending on your available
|
|
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
|
|
of the manual. The accelerated styles take the same arguments and
|
|
should produce the same results, except for round-off and precision
|
|
issues.
|
|
</P>
|
|
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
|
|
KOKKOS, USER-OMP and OPT packages, respectively. They are only
|
|
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
|
|
LAMMPS</A> section for more info.
|
|
</P>
|
|
<P>You can specify the accelerated styles explicitly in your input script
|
|
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
|
|
switch</A> when you invoke LAMMPS, or you can
|
|
use the <A HREF = "suffix.html">suffix</A> command in your input script.
|
|
</P>
|
|
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
|
|
more instructions on how to use the accelerated styles effectively.
|
|
</P>
|
|
<HR>
|
|
|
|
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
|
|
</P>
|
|
<P>For atom type pairs I,J and I != J, where types I and J correspond to
|
|
two different element types, mixing is performed by LAMMPS as
|
|
described above from values in the potential file.
|
|
</P>
|
|
<P>These pair styles does not support the <A HREF = "pair_modify.html">pair_modify</A>
|
|
shift, table, and tail options.
|
|
</P>
|
|
<P>These pair styles do not write its information to <A HREF = "restart.html">binary restart
|
|
files</A>, since it is stored in potential files. Thus, you
|
|
need to re-specify the pair_style, pair_coeff, and <A HREF = "fix_qeq_comb.html">fix
|
|
qeq/comb</A> commands in an input script that reads a
|
|
restart file.
|
|
</P>
|
|
<P>These pair styles can only be used via the <I>pair</I> keyword of the
|
|
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
|
|
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
|
|
</P>
|
|
<HR>
|
|
|
|
<P><B>Restrictions:</B>
|
|
</P>
|
|
<P>These pair styles are part of the MANYBODY package. It is only enabled
|
|
if LAMMPS was built with that package (which it is by default). See
|
|
the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
|
|
</P>
|
|
<P>These pair styles requires the <A HREF = "newton.html">newton</A> setting to be "on"
|
|
for pair interactions.
|
|
</P>
|
|
<P>The COMB potentials in the <I>ffield.comb</I> and <I>ffield.comb3</I> files provided
|
|
with LAMMPS (see the potentials directory) are parameterized for metal
|
|
<A HREF = "units.html">units</A>. You can use the COMB potential with any LAMMPS
|
|
units, but you would need to create your own COMB potential file with
|
|
coefficients listed in the appropriate units if your simulation
|
|
doesn't use "metal" units.
|
|
</P>
|
|
<P><B>Related commands:</B>
|
|
</P>
|
|
<P><A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_coeff.html">pair_coeff</A>,
|
|
<A HREF = "fix_qeq_comb.html">fix_qeq/comb</A>
|
|
</P>
|
|
<P><B>Default:</B> none
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "COMB"></A>
|
|
|
|
<P><B>(COMB)</B> T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and
|
|
S. R. Phillpot, Phys. Rev. B 81, 125328 (2010)
|
|
</P>
|
|
<A NAME = "COMB3"></A>
|
|
|
|
<P><B>(COMB3)</B> T. Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek,
|
|
Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74,
|
|
255-279 (2013).
|
|
</P>
|
|
<A NAME = "Rick"></A>
|
|
|
|
<P><B>(Rick)</B> S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
|
|
(1994).
|
|
</P>
|
|
</HTML>
|