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pair_tersoff_mod.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>
</CENTER>
<HR>
<H3>pair_style tersoff/mod command
</H3>
<H3>pair_style tersoff/mod/kk command
</H3>
<H3>pair_style tersoff/mod/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style tersoff/mod
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style tersoff/mod
pair_coeff * * Si.tersoff.mod Si Si
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>tersoff/mod</I> style computes a bond-order type interatomic
potential <A HREF = "#Kumagai">(Kumagai)</A> based on a 3-body Tersoff potential
<A HREF = "#Tersoff_1">(Tersoff_1)</A>, <A HREF = "#Tersoff_2">(Tersoff_2)</A> with modified
cutoff function and angular-dependent term, giving the energy E of a
system of atoms as
</P>
<CENTER><IMG SRC = "Eqs/pair_tersoff_mod.jpg">
</CENTER>
<P>where f_R is a two-body term and f_A includes three-body interactions.
The summations in the formula are over all neighbors J and K of atom I
within a cutoff distance = R + D.
</P>
<P>The modified cutoff function f_C proposed by <A HREF = "#Murty">(Murty)</A> and
having a continuous second-order differential is employed. The
angular-dependent term g(theta) was modified to increase the
flexibility of the potential.
</P>
<P>The <I>tersoff/mod</I> potential is fitted to both the elastic constants
and melting point by employing the modified Tersoff potential function
form in which the angular-dependent term is improved. The model
performs extremely well in describing the crystalline, liquid, and
amorphous phases <A HREF = "#Schelling">(Schelling)</A>.
</P>
<P>Only a single pair_coeff command is used with the <I>tersoff/mod</I> style
which specifies a Tersoff/MOD 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><LI>filename
<LI>N element names = mapping of Tersoff/MOD elements to atom types
</UL>
<P>As an example, imagine the Si.tersoff_mod file has Tersoff values for Si.
If your LAMMPS simulation has 3 Si atoms types, you would use the following
pair_coeff command:
</P>
<PRE>pair_coeff * * Si.tersoff_mod Si Si Si
</PRE>
<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The three Si arguments map LAMMPS atom types 1,2,3 to the Si element
in the Tersoff/MOD file. If a mapping value is specified as NULL, the
mapping is not performed. This can be used when a <I>tersoff/mod</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>Tersoff/MOD file in the <I>potentials</I> directory of the LAMMPS
distribution have a ".tersoff.mod" suffix. Lines that are not blank
or comments (starting with #) define parameters for a triplet of
elements. The parameters in a single entry correspond to coefficients
in the formula above:
</P>
<UL><LI>element 1 (the center atom in a 3-body interaction)
<LI>element 2 (the atom bonded to the center atom)
<LI>element 3 (the atom influencing the 1-2 bond in a bond-order sense)
<LI>beta
<LI>alpha
<LI>h
<LI>eta
<LI>beta_ters = 1 (dummy parameter)
<LI>lambda2 (1/distance units)
<LI>B (energy units)
<LI>R (distance units)
<LI>D (distance units)
<LI>lambda1 (1/distance units)
<LI>A (energy units)
<LI>n
<LI>c1
<LI>c2
<LI>c3
<LI>c4
<LI>c5
</UL>
<P>The n, eta, lambda2, B, lambda1, and A parameters are only used for
two-body interactions. The beta, alpha, c1, c2, c3, c4, c5, h
parameters are only used for three-body interactions. The R and D
parameters are used for both two-body and three-body interactions. The
non-annotated parameters are unitless.
</P>
<P>The Tersoff/MOD potential file must contain entries for all the elements
listed in the pair_coeff command. It can also contain entries for
additional elements not being used in a particular simulation; LAMMPS
ignores those entries.
</P>
<P>For a single-element simulation, only a single entry is required
(e.g. SiSiSi). As annotated above, the first element in the entry is
the center atom in a three-body interaction and it is bonded to the
2nd atom and the bond is influenced by the 3rd atom. Thus an entry
for SiSiSi means Si bonded to a Si with another Si atom influencing the bond.
</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>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift, table, and tail options.
</P>
<P>This pair style does 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 and pair_coeff commands in an input
script that reads a restart file.
</P>
<P>This pair style 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>This pair style is 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>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
for pair interactions.
</P>
<P>The Tersoff/MOD potential files provided with LAMMPS (see the potentials
directory) are parameterized for metal <A HREF = "units.html">units</A>. You can
use the Tersoff/MOD potential with any LAMMPS units, but you would need to
create your own Tersoff/MOD 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_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Kumagai"></A>
<P><B>(Kumagai)</B> T. Kumagai, S. Izumi, S. Hara, S. Sakai,
Comp. Mat. Science, 39, 457 (2007).
</P>
<A NAME = "Tersoff_1"></A>
<P><B>(Tersoff_1)</B> J. Tersoff, Phys Rev B, 37, 6991 (1988).
</P>
<A NAME = "Tersoff_2"></A>
<P><B>(Tersoff_2)</B> J. Tersoff, Phys Rev B, 38, 9902 (1988).
</P>
<A NAME = "Murty"></A>
<P><B>(Murty)</B> M.V.R. Murty, H.A. Atwater, Phys Rev B, 51, 4889 (1995).
</P>
<A NAME = "Schelling"></A>
<P><B>(Schelling)</B> Patrick K. Schelling, Comp. Mat. Science, 44, 274 (2008).
</P>
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