Homec4science
Diffusion lammps (lammm-master) Browse

lammps/doc/pair_comb.html
a3add0b021f8lammm-master

Last Change
Raw File

pair_comb.html
View Options

<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>
<P><B>Syntax:</B>
</P>
<PRE>pair_style comb
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style comb
pair_coeff * * ../potentials/ffield.comb Si
pair_coeff * * ../potentials/ffield.comb Hf Si O
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>comb</I> computes a variable charge COMB (Charge-Optimized
Many-Body) potential as described in <A HREF = "#COMB_1">(COMB_1)</A> and
<A HREF = "#COMB_2">(COMB_2)</A>. The energy E of a system of atoms
is given by
</P>
<CENTER><IMG SRC = "Eqs/pair_comb1.jpg">
</CENTER>
<P>where <I>E<sub>T</sub></I> is the total potential energy of the system,
<I>E<sup>S</sup><sub>i</sub></I> is the self-energy term of atom <I>i</I>,
<I>V<sub>ij</sub></I> is the interatomic potential between the <I>i</I>th and
<I>j</I>th atoms, <I>r<sub>ij</sub></I> is the distance of the atoms <I>i</I> and
<I>j</I>, and <I>q<sub>i</sub></I> and <I>q<sub>j</sub></I> are charges of the atoms,
and <I>E<sup>BB</sup><sub>i</sub></I> is the bond-bending term of atom <I>i</I>.
</P>
<P>The interatomic potential energy <I>V<sub>ij</sub></I> consists of four
components: two-body short-range repulsion,
<I>U<sup>R</sup><sub>ij</sub></I>, many-body short-range attraction,
<I>U<sup>A</sup><sub>ij</sub></I>, long-range Coulombic electrostatic
interaction, <I>U<sup>I</sup><sub>ij</sub></I>, and van der Waals energy,
<I>U<sup>V</sup><sub>ij</sub></I>, which are defined as:
</P>
<CENTER><IMG SRC = "Eqs/pair_comb2.jpg">
</CENTER>
<P>The short-range repulsion and attraction are based on the
<A HREF = "#Tersoff">Tersoff</A> potential (see the <A HREF = "pair_tersoff.html">pair_style
tersoff</A> command); thus for a zero-charge pure
element system with no van der Waals interaction, the COMB potential
reduces to Tersoff potential, typically truncated at a short cutoff,
e.g. 3 to 4 Angstroms. The long-range Coulombic term uses the Wolf
summation method described in <A HREF = "#Wolf">Wolf</A>, spherically truncated at a
longer cutoff, e.g. 12 Angstroms.
</P>
<P>The COMB potential is a variable charge potential. 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> style 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. The provided
potential file <I>ffield.comb</I> contains all currently-available COMB
parameterizations: for Si, Cu, Hf, Ti, O, their oxides and Zr, Zn and
U metals.
</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>The <I>ffield.comb</I> potential file is in the <I>potentials</I> directory of
the LAMMPS distribution. Lines that are not blank or comments
(starting with #) define parameters for a triplet of elements. The 49
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>m
<LI>c
<LI>d
<LI>h (cos_theta0 (can be a value -1 or 1))
<LI>n
<LI>beta
<LI>lambda21, lambda2 of element 1 (1/distance units)
<LI>lambda22, lambda2 of element 2 (1/distance units)
<LI>B of element 1 (energy units)
<LI>B of element 2 (energy units)
<LI>R (cutoff, distance units, 0.5*(r_outer + r_inner))
<LI>D (cutoff, distance units, R - r_inner)
<LI>lambda11, lambda1 of element 1 (1/distance units)
<LI>lambda12, lambda1 of element 2 (1/distance units)
<LI>A of element 1 (energy units)
<LI>A of element 2 (energy units)
<LI>K_LP_1 (energy units, 1st order Legendre polynomial coefficient)
<LI>K_LP_3 (energy units, 3rd order Legendre polynomial coefficient)
<LI>K_LP_6 (energy units, 6th order Legendre polynomial coefficient)
<LI>A123 (cos_theta, theta = equilibrium MOM or OMO bond angles)
<LI>Aconf (cos_theta, theta = equilibrium MOM or OMO bond-bending coefficient)
<LI>addrep (energy units, additional repulsion)
<LI>R_omiga_a (unit-less scaler for A)
<LI>R_omiga_b (unit-less scaler for B)
<LI>R_omiga_c (unit-less scaler for 0.5*(lambda21+lambda22))
<LI>R_omiga_d (unit-less scaler for 0.5*(lambda11+lambda12))
<LI>QL1 (charge units, lower charge limit for element 1)
<LI>QU1 (charge units, upper charge limit for element 1)
<LI>DL1 (distance units, ion radius of element 1 with charge QL1)
<LI>DU1 (distance units, ion radius of element 1 with charge QU1)
<LI>QL2 (charge units, lower charge limit for element 2)
<LI>QU2 (charge units, upper charge limit for element 2)
<LI>DL2 (distance units, ion radius of element 2 with charge QL2)
<LI>DU2 (distance units, ion radius of element 2 with charge QU2)
<LI>chi (energy units, self energy 1st power term)
<LI>dJ (energy units, self energy 2nd power term)
<LI>dK (energy units, self energy 3rd power term)
<LI>dL (energy units, self energy 4th power term)
<LI>dM (energy units, self energy 6th power term)
<LI>esm (distance units, orbital exponent)
<LI>cmn1 (self energy penalty, rho 1 of element 1)
<LI>cml1 (self energy penalty, rho 1 of element 2)
<LI>cmn2 (self energy penalty, rho 2 of element 1)
<LI>cmn2 (self energy penalty, rho 2 of element 2)
<LI>coulcut (long range Coulombic cutoff, distance units)
<LI>hfocor (coordination term)
</UL>
<P>The parameterization of COMB potentials start with a pure element
(e.g. Si, Cu) then extend to its oxide and polymorphs
(e.g. SiO<sub>2</sub>, Cu<sub>2</sub>O). For interactions not
involving oxygen (e.g. Si-Cu or Hf-Zr), the COMB potential uses a
mixing rule to generate these parameters. For furthur details on the
parameterization and parameters, see the <A HREF = "pair_tersoff.html">Tersoff</A>
doc page and the COMB publications <A HREF = "#COMB_1">(COMB_1)</A> and
<A HREF = "#COMB_2">(COMB_2)</A>. For more details on 3-body interaction types
(e.g. SiSiO vs SiOSi), the mixing rule, and how to generate the
potential file, please see the <A HREF = "pair_tersoff.html">Tersoff</A> doc page.
</P>
<P>In the potentials directory, the file <I>ffield.comb</I> provides the
LAMMPS parameters for COMB's Si, Cu, Ti, Hf and their oxides, as well
as pure U, Zn and Zr metals. This file can be used for pure elements
(e.g. Si, Zr), binary oxides, binary alloys (e.g. SiCu, TiZr), and
complex systems. Note that alloys and complex systems require all
3-body entries be pre-defined in the potential file.
</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>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, 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>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 COMB potentials in the <I>ffield.comb</I> file 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_1"></A>
<P><B>(COMB_1)</B> J. Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007),
</P>
<A NAME = "COMB_2"></A>
<P><B>(COMB_2)</B> T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, S. R.
Phillpot, Phys Rev B, 81, 125328 (2010).
</P>
<A NAME = "Tersoff"></A>
<P><B>(Tersoff)</B> J. Tersoff, Phys Rev B, 37, 6991 (1988).
</P>
<A NAME = "Rick"></A>
<P><B>(Rick)</B> S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 16141
(1994).
</P>
<A NAME = "Wolf"></A>
<P><B>(Wolf)</B> D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem
Phys, 110, 8254 (1999).
</P>
</HTML>
c4science · Help