2008-10-01 23:02:48 +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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</CENTER>
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<HR>
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<H3>pair_style tersoff/zbl 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 tersoff/zbl/omp command
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</H3>
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2008-10-01 23:02:48 +08:00
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<P><B>Syntax:</B>
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</P>
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<PRE>pair_style tersoff/zbl
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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 tersoff/zbl
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pair_coeff * * SiC.tersoff.zbl Si C Si
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>The <I>tersoff/zbl</I> style computes a 3-body Tersoff potential
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<A HREF = "#Tersoff_1">(Tersoff_1)</A> with a close-separation pairwise modification
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based on a Coulomb potential and the Ziegler-Biersack-Littmark
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universal screening function <A HREF = "#ZBL">(ZBL)</A>, giving the energy E of a
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system of atoms as
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</P>
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<CENTER><IMG SRC = "Eqs/pair_tersoff_zbl.jpg">
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</CENTER>
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<P>The f_F term is a fermi-like function used to smoothly connect the ZBL
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repulsive potential with the Tersoff potential. There are 2
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parameters used to adjust it: A_F and r_C. A_F controls how "sharp"
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the transition is between the two, and r_C is essentially the cutoff
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for the ZBL potential.
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</P>
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<P>For the ZBL portion, there are two terms. The first is the Coulomb
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repulsive term, with Z1, Z2 as the number of protons in each nucleus,
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e as the electron charge (1 for metal and real units) and epsilon0 as
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the permittivity of vacuum. The second part is the ZBL universal
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screening function, with a0 being the Bohr radius (typically 0.529
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Angstroms), and the remainder of the coefficients provided by the
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original paper. This screening function should be applicable to most
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systems. However, it is only accurate for small separations
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(i.e. less than 1 Angstrom).
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</P>
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<P>For the Tersoff portion, f_R is a two-body term and f_A includes
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three-body interactions. The summations in the formula are over all
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neighbors J and K of atom I within a cutoff distance = R + D.
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</P>
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<P>Only a single pair_coeff command is used with the <I>tersoff/zbl</I> style
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which specifies a Tersoff/ZBL potential file with parameters for all
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needed elements. These are mapped to LAMMPS atom types by specifying
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N 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 element names = mapping of Tersoff/ZBL elements to atom types
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</UL>
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<P>As an example, imagine the SiC.tersoff.zbl file has Tersoff/ZBL values
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for Si and C. If your LAMMPS simulation has 4 atoms types and you
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want the 1st 3 to be Si, and the 4th to be C, you would use the
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following pair_coeff command:
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</P>
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<PRE>pair_coeff * * SiC.tersoff Si Si Si C
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</PRE>
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<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
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The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
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element in the Tersoff/ZBL file. The final C argument maps LAMMPS
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atom type 4 to the C element in the Tersoff/ZBL file. If a mapping
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value is specified as NULL, the mapping is not performed. This can be
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used when a <I>tersoff/zbl</I> potential is used as part of the <I>hybrid</I>
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pair style. The NULL values are placeholders for atom types that will
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be used with other potentials.
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</P>
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<P>Tersoff/ZBL files in the <I>potentials</I> directory of the LAMMPS
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distribution have a ".tersoff.zbl" suffix. Lines that are not blank
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or comments (starting with #) define parameters for a triplet of
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elements. The parameters in a single entry correspond to coefficients
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in the formula 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>gamma
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<LI>lambda3 (1/distance units)
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<LI>c
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<LI>d
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<LI>costheta0 (can be a value < -1 or > 1)
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<LI>n
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<LI>beta
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<LI>lambda2 (1/distance units)
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<LI>B (energy units)
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<LI>R (distance units)
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<LI>D (distance units)
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<LI>lambda1 (1/distance units)
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<LI>A (energy units)
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<LI>Z_i
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<LI>Z_j
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<LI>ZBLcut (distance units)
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<LI>ZBLexpscale (1/distance units)
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</UL>
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<P>The n, beta, lambda2, B, lambda1, and A parameters are only used for
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two-body interactions. The m, gamma, lambda3, c, d, and costheta0
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parameters are only used for three-body interactions. The R and D
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parameters are used for both two-body and three-body interactions. The
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Z_i,Z_j, ZBLcut, ZBLexpscale parameters are used in the ZBL repulsive
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portion of the potential and in the Fermi-like function. The
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non-annotated parameters are unitless. The value of m must be 3 or 1.
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</P>
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<P>The Tersoff/ZBL potential file must contain entries for all the
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elements listed in the pair_coeff command. It can also contain
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entries for additional elements not being used in a particular
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simulation; LAMMPS ignores those entries.
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</P>
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<P>For a single-element simulation, only a single entry is required
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(e.g. SiSiSi). For a two-element simulation, the file must contain 8
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entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
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specify Tersoff parameters for all permutations of the two elements
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interacting in three-body configurations. Thus for 3 elements, 27
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entries would be required, etc.
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</P>
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<P>As annotated above, the first element in the entry is the center atom
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in a three-body interaction and it is bonded to the 2nd atom and the
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bond is influenced by the 3rd atom. Thus an entry for SiCC means Si
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bonded to a C with another C atom influencing the bond. Thus
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three-body parameters for SiCSi and SiSiC entries will not, in
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general, be the same. The parameters used for the two-body
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interaction come from the entry where the 2nd element is repeated.
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Thus the two-body parameters for Si interacting with C, comes from the
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SiCC entry. By symmetry, the twobody parameters in the SiCC and CSiSi
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entries should thus be the same. The parameters used for a particular
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three-body interaction come from the entry with the corresponding
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three elements. The parameters used only for two-body interactions
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(n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd
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element are different (e.g. SiCSi) are not used for anything and can
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be set to 0.0 if desired.
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</P>
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<P>We chose the above form so as to enable users to define all commonly
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used variants of the Tersoff portion of the potential. In particular,
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our form reduces to the original Tersoff form when m = 3 and gamma =
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1, while it reduces to the form of <A HREF = "#Albe">Albe et al.</A> when beta = 1
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and m = 1. Note that in the current Tersoff implementation in LAMMPS,
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m must be specified as either 3 or 1. Tersoff used a slightly
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different but equivalent form for alloys, which we will refer to as
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Tersoff_2 potential <A HREF = "#Tersoff_2">(Tersoff_2)</A>.
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</P>
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<P>LAMMPS parameter values for Tersoff_2 can be obtained as follows:
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gamma = 1, just as for Tersoff_1, but now lambda3 = 0 and the value of
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m has no effect. The parameters for species i and j can be calculated
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using the Tersoff_2 mixing rules:
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</P>
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<CENTER><IMG SRC = "Eqs/pair_tersoff_2.jpg">
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</CENTER>
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2009-01-23 02:05:05 +08:00
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<P>Values not shown are determined by the first<73>atom type. Finally, the
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2008-10-01 23:02:48 +08:00
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Tersoff_2 parameters R and S must be converted to the LAMMPS
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parameters R and D (R is different in both forms), using the following
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relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the
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Tersoff_2 parameters.
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</P>
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<P>In the potentials directory, the file SiCGe.tersoff provides the
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LAMMPS parameters for Tersoff's various versions of Si, as well as his
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alloy parameters for Si, C, and Ge. This file can be used for pure Si,
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(three different versions), pure C, pure Ge, binary SiC, and binary
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SiGe. LAMMPS will generate an error if this file is used with any
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combination involving C and Ge, since there are no entries for the GeC
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interactions (Tersoff did not publish parameters for this
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cross-interaction.) Tersoff files are also provided for the SiC alloy
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(SiC.tersoff) and the GaN (GaN.tersoff) alloys.
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</P>
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<P>Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou
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for helping clarify how Tersoff parameters for alloys have been
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defined in various papers. Also thanks to Ram Devanathan for
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providing the base ZBL implementation.
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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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by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
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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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2008-10-01 23:02:48 +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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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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<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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2008-10-01 23:02:48 +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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2008-10-01 23:02:48 +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 Tersoff/ZBL potential files provided with LAMMPS (see the
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potentials directory) are parameterized for metal <A HREF = "units.html">units</A>.
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You can use the Tersoff potential with any LAMMPS units, but you would
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need to create your own Tersoff potential file with coefficients
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listed in the appropriate units if your simulation doesn't use "metal"
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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_coeff.html">pair_coeff</A>
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</P>
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<P><B>Default:</B> none
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<HR>
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<A NAME = "Tersoff_1"></A>
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<P><B>(Tersoff_1)</B> J. Tersoff, Phys Rev B, 37, 6991 (1988).
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</P>
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<A NAME = "ZBL"></A>
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<P><B>(ZBL)</B> J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges
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of Ions in Matter' Vol 1, 1985, Pergamon Press.
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<A NAME = "Albe"></A>
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<P><B>(Albe)</B> J. Nord, K. Albe, P. Erhartand K. Nordlund, J. Phys.:
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Condens. Matter, 15, 5649(2003).
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<A NAME = "Tersoff_2"></A>
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<P><B>(Tersoff_2)</B> J. Tersoff, Phys Rev B, 39, 5566 (1989)
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