2010-08-20 07:38:06 +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 comb command
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</H3>
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2011-10-07 01:32:51 +08:00
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<H3>pair_style comb/omp command
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</H3>
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2010-08-20 07:38:06 +08:00
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<P><B>Syntax:</B>
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</P>
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<PRE>pair_style comb
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</PRE>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style comb
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pair_coeff * * ../potentials/ffield.comb Si
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pair_coeff * * ../potentials/ffield.comb Hf Si O
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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>comb</I> computes a variable charge COMB (Charge-Optimized
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Many-Body) potential as described in <A HREF = "#COMB_1">(COMB_1)</A> and
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<A HREF = "#COMB_2">(COMB_2)</A>. The energy E of a system of atoms
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is given by
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</P>
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2010-08-31 04:17:11 +08:00
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<CENTER><IMG SRC = "Eqs/pair_comb1.jpg">
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2010-08-20 07:38:06 +08:00
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</CENTER>
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<P>where <I>E<sub>T</sub></I> is the total potential energy of the system,
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<I>E<sup>S</sup><sub>i</sub></I> is the self-energy term of atom <I>i</I>,
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<I>V<sub>ij</sub></I> is the interatomic potential between the <I>i</I>th and
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<I>j</I>th atoms, <I>r<sub>ij</sub></I> is the distance of the atoms <I>i</I> and
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<I>j</I>, and <I>q<sub>i</sub></I> and <I>q<sub>j</sub></I> are charges of the atoms,
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and <I>E<sup>BB</sup><sub>i</sub></I> is the bond-bending term of atom <I>i</I>.
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</P>
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<P>The interatomic potential energy <I>V<sub>ij</sub></I> consists of four
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components: two-body short-range repulsion,
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<I>U<sup>R</sup><sub>ij</sub></I>, many-body short-range attraction,
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<I>U<sup>A</sup><sub>ij</sub></I>, long-range Coulombic electrostatic
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interaction, <I>U<sup>I</sup><sub>ij</sub></I>, and van der Waals energy,
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<I>U<sup>V</sup><sub>ij</sub></I>, which are defined as:
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</P>
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2010-08-31 04:17:11 +08:00
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<CENTER><IMG SRC = "Eqs/pair_comb2.jpg">
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2010-08-20 07:38:06 +08:00
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</CENTER>
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<P>The short-range repulsion and attraction are based on the
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<A HREF = "#Tersoff">Tersoff</A> potential (see the <A HREF = "pair_tersoff.html">pair_style
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tersoff</A> command); thus for a zero-charge pure
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2010-09-21 00:52:24 +08:00
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element system with no van der Waals interaction, the COMB potential
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reduces to Tersoff potential, typically truncated at a short cutoff,
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e.g. 3 to 4 Angstroms. The long-range Coulombic term uses the Wolf
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summation method described in <A HREF = "#Wolf">Wolf</A>, spherically truncated at a
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longer cutoff, e.g. 12 Angstroms.
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2010-08-20 07:38:06 +08:00
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</P>
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<P>The COMB potential is a variable charge potential. The equilibrium
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charge on each atom is calculated by the electronegativity
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2010-09-21 00:52:24 +08:00
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equalization (QEq) method. See <A HREF = "#Rick">Rick</A> for further details.
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This is implemented by the <A HREF = "fix_qeq_comb.html">fix qeq/comb</A> command,
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which should normally be specified in the input script when running a
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model with the COMB potential. The <A HREF = "fix_qeq_comb.html">fix qeq/comb</A>
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command has options that determine how often charge equilibration is
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performed, its convergence criterion, and which atoms are included in
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the calculation.
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2010-08-20 07:38:06 +08:00
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</P>
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<P>Only a single pair_coeff command is used with the <I>comb</I> style which
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specifies the COMB 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 potential file in the pair_coeff
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command, where N is the number of LAMMPS atom types. The provided
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potential file <I>ffield.comb</I> contains all currently-available COMB
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parameterizations: for Si, Cu, Hf, Ti, O, their oxides and Zr, Zn and
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U metals.
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</P>
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<P>For example, if your LAMMPS simulation of a Si/SiO<sub>2</sub>/
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HfO<sub>2</sub> interface has 4 atom types, and you want the 1st and
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last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would
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use the following pair_coeff command:
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</P>
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<PRE>pair_coeff * * ../potentials/ffield.comb Si Hf O Si
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</PRE>
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<P>The first two arguments must be * * so as to span all LAMMPS atom
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types. The first and last Si arguments map LAMMPS atom types 1 and 4
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to the Si element in the <I>ffield.comb</I> file. The second Hf argument
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maps LAMMPS atom type 2 to the Hf element, and the third O argument
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maps LAMMPS atom type 3 to the O element in the potential file. If a
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mapping value is specified as NULL, the mapping is not performed.
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2010-09-02 00:40:29 +08:00
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This can be used when a <I>comb</I> potential is used as part of the
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2010-08-20 07:38:06 +08:00
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<I>hybrid</I> pair style. The NULL values are placeholders for atom types
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that will be used with other potentials.
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</P>
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<P>The <I>ffield.comb</I> potential file is in the <I>potentials</I> directory of
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the LAMMPS distribution. Lines that are not blank or comments
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(starting with #) define parameters for a triplet of elements. The 49
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parameters in a single entry correspond to coefficients in the formula
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above:
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</P>
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<UL><LI>element 1 (the center atom in a 3-body interaction)
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<LI>element 2 (the atom bonded to the center atom)
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<LI>element 3 (the atom influencing the 1-2 bond in a bond-order sense)
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<LI>m
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<LI>c
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<LI>d
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<LI>h (cos_theta0 (can be a value -1 or 1))
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<LI>n
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<LI>beta
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<LI>lambda21, lambda2 of element 1 (1/distance units)
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<LI>lambda22, lambda2 of element 2 (1/distance units)
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<LI>B of element 1 (energy units)
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<LI>B of element 2 (energy units)
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<LI>R (cutoff, distance units, 0.5*(r_outer + r_inner))
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<LI>D (cutoff, distance units, R - r_inner)
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<LI>lambda11, lambda1 of element 1 (1/distance units)
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<LI>lambda12, lambda1 of element 2 (1/distance units)
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<LI>A of element 1 (energy units)
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<LI>A of element 2 (energy units)
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<LI>K_LP_1 (energy units, 1st order Legendre polynomial coefficient)
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<LI>K_LP_3 (energy units, 3rd order Legendre polynomial coefficient)
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<LI>K_LP_6 (energy units, 6th order Legendre polynomial coefficient)
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<LI>A123 (cos_theta, theta = equilibrium MOM or OMO bond angles)
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<LI>Aconf (cos_theta, theta = equilibrium MOM or OMO bond-bending coefficient)
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<LI>addrep (energy units, additional repulsion)
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<LI>R_omiga_a (unit-less scaler for A)
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<LI>R_omiga_b (unit-less scaler for B)
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<LI>R_omiga_c (unit-less scaler for 0.5*(lambda21+lambda22))
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<LI>R_omiga_d (unit-less scaler for 0.5*(lambda11+lambda12))
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<LI>QL1 (charge units, lower charge limit for element 1)
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<LI>QU1 (charge units, upper charge limit for element 1)
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<LI>DL1 (distance units, ion radius of element 1 with charge QL1)
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<LI>DU1 (distance units, ion radius of element 1 with charge QU1)
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<LI>QL2 (charge units, lower charge limit for element 2)
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<LI>QU2 (charge units, upper charge limit for element 2)
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<LI>DL2 (distance units, ion radius of element 2 with charge QL2)
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<LI>DU2 (distance units, ion radius of element 2 with charge QU2)
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<LI>chi (energy units, self energy 1st power term)
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<LI>dJ (energy units, self energy 2nd power term)
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<LI>dK (energy units, self energy 3rd power term)
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<LI>dL (energy units, self energy 4th power term)
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<LI>dM (energy units, self energy 6th power term)
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<LI>esm (distance units, orbital exponent)
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<LI>cmn1 (self energy penalty, rho 1 of element 1)
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<LI>cml1 (self energy penalty, rho 1 of element 2)
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<LI>cmn2 (self energy penalty, rho 2 of element 1)
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<LI>cmn2 (self energy penalty, rho 2 of element 2)
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<LI>coulcut (long range Coulombic cutoff, distance units)
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<LI>hfocor (coordination term)
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</UL>
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<P>The parameterization of COMB potentials start with a pure element
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(e.g. Si, Cu) then extend to its oxide and polymorphs
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(e.g. SiO<sub>2</sub>, Cu<sub>2</sub>O). For interactions not
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involving oxygen (e.g. Si-Cu or Hf-Zr), the COMB potential uses a
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mixing rule to generate these parameters. For furthur details on the
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parameterization and parameters, see the <A HREF = "pair_tersoff.html">Tersoff</A>
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doc page and the COMB publications <A HREF = "#COMB_1">(COMB_1)</A> and
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<A HREF = "#COMB_2">(COMB_2)</A>. For more details on 3-body interaction types
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(e.g. SiSiO vs SiOSi), the mixing rule, and how to generate the
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potential file, please see the <A HREF = "pair_tersoff.html">Tersoff</A> doc page.
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</P>
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<P>In the potentials directory, the file <I>ffield.comb</I> provides the
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LAMMPS parameters for COMB's Si, Cu, Ti, Hf and their oxides, as well
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as pure U, Zn and Zr metals. This file can be used for pure elements
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(e.g. Si, Zr), binary oxides, binary alloys (e.g. SiCu, TiZr), and
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complex systems. Note that alloys and complex systems require all
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3-body entries be pre-defined in the potential file.
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</P>
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<HR>
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2011-12-14 04:35:35 +08:00
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<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> suffix are functionally
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the same as the corresponding style without the suffix. They have
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been optimized to run faster, depending on your available hardware, as
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discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A> of the
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manual. The accelerated styles take the same arguments and should
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produce the same results, except for round-off and precision issues.
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2011-10-07 01:32:51 +08:00
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</P>
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<P>These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
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packages, respectively. They are only enabled if LAMMPS was built with
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those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
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section for more info.
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</P>
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<P>You can specify the accelerated styles explicitly in your input script
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2012-01-28 07:39:14 +08:00
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by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
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2011-10-07 01:32:51 +08:00
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switch</A> when you invoke LAMMPS, or you can
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use the <A HREF = "suffix.html">suffix</A> command in your input script.
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</P>
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2011-12-14 04:35:35 +08:00
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<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
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more instructions on how to use the accelerated styles effectively.
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2011-10-07 01:32:51 +08:00
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</P>
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<HR>
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2010-08-20 07:38:06 +08:00
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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>For atom type pairs I,J and I != J, where types I and J correspond to
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two different element types, mixing is performed by LAMMPS as
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described above from values in the potential file.
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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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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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2010-08-20 08:37:54 +08:00
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need to re-specify the pair_style, pair_coeff, and <A HREF = "fix_qeq_comb.html">fix
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qeq/comb</A> commands in an input script that reads a
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restart file.
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2010-08-20 07:38:06 +08:00
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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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<HR>
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<P><B>Restrictions:</B>
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</P>
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2011-08-27 02:53:00 +08:00
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<P>This pair style is part of the MANYBODY package. It is only enabled
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2010-08-20 07:38:06 +08:00
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if LAMMPS was built with that package (which it is by default). See
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2011-08-26 00:46:23 +08:00
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the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
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2010-08-20 07:38:06 +08:00
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</P>
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<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
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for pair interactions.
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</P>
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<P>The COMB potentials in the <I>ffield.comb</I> file provided with LAMMPS
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(see the potentials directory) are parameterized for metal
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<A HREF = "units.html">units</A>. You can use the COMB potential with any LAMMPS
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units, but you would need to create your own COMB potential file with
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coefficients listed in the appropriate units if your simulation
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doesn't use "metal" 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_style.html">pair_style</A>, <A HREF = "pair_coeff.html">pair_coeff</A>,
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2010-08-20 08:37:54 +08:00
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<A HREF = "fix_qeq_comb.html">fix_qeq/comb</A>
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2010-08-20 07:38:06 +08:00
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</P>
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<P><B>Default:</B> none
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</P>
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<HR>
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<A NAME = "COMB_1"></A>
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<P><B>(COMB_1)</B> J. Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007),
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</P>
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<A NAME = "COMB_2"></A>
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<P><B>(COMB_2)</B> T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, S. R.
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Phillpot, Phys Rev B, 81, 125328 (2010).
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</P>
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<P><B>(Rick)</B> S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
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