forked from lijiext/lammps
191 lines
6.7 KiB
Plaintext
191 lines
6.7 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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pair_style tersoff/mod command :h3
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pair_style tersoff/mod/omp command :h3
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[Syntax:]
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pair_style tersoff/mod :pre
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[Examples:]
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pair_style tersoff/mod
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pair_coeff * * Si.tersoff.mod Si Si :pre
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[Description:]
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The {tersoff/mod} style computes a bond-order type interatomic
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potential "(Kumagai)"_#Kumagai based on a 3-body Tersoff potential
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"(Tersoff_1)"_#Tersoff_1, "(Tersoff_2)"_#Tersoff_2 with modified
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cutoff function and angular-dependent term, giving the energy E of a
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system of atoms as
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:c,image(Eqs/pair_tersoff_mod.jpg)
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where f_R is a two-body term and f_A includes three-body interactions.
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The summations in the formula are over all neighbors J and K of atom I
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within a cutoff distance = R + D.
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The modified cutoff function f_C proposed by "(Murty)"_#Murty and
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having a continuous second-order differential is employed. The
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angular-dependent term g(theta) was modified to increase the
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flexibility of the potential.
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The {tersoff/mod} potential is fitted to both the elastic constants
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and melting point by employing the modified Tersoff potential function
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form in which the angular-dependent term is improved. The model
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performs extremely well in describing the crystalline, liquid, and
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amorphous phases "(Schelling)"_#Schelling.
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Only a single pair_coeff command is used with the {tersoff/mod} style
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which specifies a Tersoff/MOD 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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filename
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N element names = mapping of Tersoff/MOD elements to atom types :ul
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As an example, imagine the Si.tersoff_mod file has Tersoff values for Si.
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If your LAMMPS simulation has 3 Si atoms types, you would use the following
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pair_coeff command:
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pair_coeff * * Si.tersoff_mod Si Si Si :pre
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The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
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The three Si arguments map LAMMPS atom types 1,2,3 to the Si element
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in the Tersoff/MOD file. If a mapping value is specified as NULL, the
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mapping is not performed. This can be used when a {tersoff/mod}
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potential is used as part of the {hybrid} pair style. The NULL values
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are placeholders for atom types that will be used with other
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potentials.
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Tersoff/MOD file in the {potentials} directory of the LAMMPS
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distribution have a ".tersoff.mod" 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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element 1 (the center atom in a 3-body interaction)
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element 2 (the atom bonded to the center atom)
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element 3 (the atom influencing the 1-2 bond in a bond-order sense)
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beta
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alpha
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h
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eta
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beta_ters = 1 (dummy parameter)
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lambda2 (1/distance units)
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B (energy units)
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R (distance units)
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D (distance units)
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lambda1 (1/distance units)
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A (energy units)
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n
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c1
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c2
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c3
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c4
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c5 :ul
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The n, eta, lambda2, B, lambda1, and A parameters are only used for
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two-body interactions. The beta, alpha, c1, c2, c3, c4, c5, h
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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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non-annotated parameters are unitless.
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The Tersoff/MOD potential file must contain entries for all the elements
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listed in the pair_coeff command. It can also contain entries for
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additional elements not being used in a particular simulation; LAMMPS
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ignores those entries.
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For a single-element simulation, only a single entry is required
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(e.g. SiSiSi). As annotated above, the first element in the entry is
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the center atom in a three-body interaction and it is bonded to the
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2nd atom and the bond is influenced by the 3rd atom. Thus an entry
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for SiSiSi means Si bonded to a Si with another Si atom influencing the bond.
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:line
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Styles with a {cuda}, {gpu}, {omp}, or {opt} 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 "Section_accelerate"_Section_accelerate.html 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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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 "Making LAMMPS"_Section_start.html#start_3
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section for more info.
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You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the "-suffix command-line
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switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
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use the "suffix"_suffix.html command in your input script.
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See "Section_accelerate"_Section_accelerate.html of the manual for
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more instructions on how to use the accelerated styles effectively.
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:line
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[Mixing, shift, table, tail correction, restart, rRESPA info]:
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This pair style does not support the "pair_modify"_pair_modify.html
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shift, table, and tail options.
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This pair style does not write its information to "binary restart
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files"_restart.html, 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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This pair style can only be used via the {pair} keyword of the
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"run_style respa"_run_style.html command. It does not support the
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{inner}, {middle}, {outer} keywords.
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:line
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[Restrictions:]
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This pair style is part of the MANYBODY package. It is only enabled
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if LAMMPS was built with that package (which it is by default). See
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the "Making LAMMPS"_Section_start.html#start_3 section for more info.
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This pair style requires the "newton"_newton.html setting to be "on"
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for pair interactions.
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The Tersoff/MOD potential files provided with LAMMPS (see the potentials
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directory) are parameterized for metal "units"_units.html. You can
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use the Tersoff/MOD potential with any LAMMPS units, but you would need to
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create your own Tersoff/MOD potential file with coefficients listed in the
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appropriate units if your simulation doesn't use "metal" units.
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[Related commands:]
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"pair_coeff"_pair_coeff.html
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[Default:] none
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:line
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:link(Kumagai)
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[(Kumagai)] T. Kumagai, S. Izumi, S. Hara, S. Sakai,
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Comp. Mat. Science, 39, 457 (2007).
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:link(Tersoff_1)
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[(Tersoff_1)] J. Tersoff, Phys Rev B, 37, 6991 (1988).
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:link(Tersoff_2)
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[(Tersoff_2)] J. Tersoff, Phys Rev B, 38, 9902 (1988).
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:link(Murty)
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[(Murty)] M.V.R. Murty, H.A. Atwater, Phys Rev B, 51, 4889 (1995).
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:link(Schelling)
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[(Schelling)] Patrick K. Schelling, Comp. Mat. Science, 44, 274 (2008).
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