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< title > pair_style tersoff/mod command — LAMMPS documentation< / title >
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< li > pair_style tersoff/mod command< / li >
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< span id = "index-0" > < / span > < h1 > pair_style tersoff/mod command< a class = "headerlink" href = "#pair-style-tersoff-mod-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< / div >
< div class = "section" id = "pair-style-tersoff-mod-kk-command" >
< h1 > pair_style tersoff/mod/kk command< a class = "headerlink" href = "#pair-style-tersoff-mod-kk-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< / div >
< div class = "section" id = "pair-style-tersoff-mod-omp-command" >
< h1 > pair_style tersoff/mod/omp command< a class = "headerlink" href = "#pair-style-tersoff-mod-omp-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > pair_style tersoff/mod
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > pair_style tersoff/mod
pair_coeff * * Si.tersoff.mod Si Si
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > The < em > tersoff/mod< / em > style computes a bond-order type interatomic
potential < a class = "reference internal" href = "#kumagai" > < span > (Kumagai)< / span > < / a > based on a 3-body Tersoff potential
< a class = "reference internal" href = "pair_tersoff_zbl.html#tersoff-1" > < span > (Tersoff_1)< / span > < / a > , < a class = "reference internal" href = "pair_tersoff_zbl.html#tersoff-2" > < span > (Tersoff_2)< / span > < / a > 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< / p >
< img alt = "_images/pair_tersoff_mod.jpg" class = "align-center" src = "_images/pair_tersoff_mod.jpg" / >
< p > 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.< / p >
< p > The modified cutoff function f_C proposed by < a class = "reference internal" href = "#murty" > < span > (Murty)< / span > < / a > and
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having a continuous second-order differential is employed. The
angular-dependent term g(theta) was modified to increase the
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flexibility of the potential.< / p >
< p > The < em > tersoff/mod< / em > potential is fitted to both the elastic constants
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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
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amorphous phases < a class = "reference internal" href = "#schelling" > < span > (Schelling)< / span > < / a > .< / p >
< p > Only a single pair_coeff command is used with the < em > tersoff/mod< / em > style
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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,
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where N is the number of LAMMPS atom types:< / p >
< ul class = "simple" >
< li > filename< / li >
< li > N element names = mapping of Tersoff/MOD elements to atom types< / li >
< / ul >
< p > 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:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > pair_coeff * * Si.tersoff_mod Si Si Si
< / pre > < / div >
< / div >
< p > 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
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 < em > tersoff/mod< / em >
potential is used as part of the < em > hybrid< / em > 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.< / p >
< p > Tersoff/MOD file in the < em > potentials< / em > directory of the LAMMPS
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
elements. The parameters in a single entry correspond to coefficients
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in the formula above:< / p >
< ul class = "simple" >
< li > element 1 (the center atom in a 3-body interaction)< / li >
< li > element 2 (the atom bonded to the center atom)< / li >
< li > element 3 (the atom influencing the 1-2 bond in a bond-order sense)< / li >
< li > beta< / li >
< li > alpha< / li >
< li > h< / li >
< li > eta< / li >
< li > beta_ters = 1 (dummy parameter)< / li >
< li > lambda2 (1/distance units)< / li >
< li > B (energy units)< / li >
< li > R (distance units)< / li >
< li > D (distance units)< / li >
< li > lambda1 (1/distance units)< / li >
< li > A (energy units)< / li >
< li > n< / li >
< li > c1< / li >
< li > c2< / li >
< li > c3< / li >
< li > c4< / li >
< li > c5< / li >
< / ul >
< p > 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
parameters are only used for three-body interactions. The R and D
parameters are used for both two-body and three-body interactions. The
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non-annotated parameters are unitless.< / p >
< p > 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
additional elements not being used in a particular simulation; LAMMPS
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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 class = "docutils" / >
< p > Styles with a < em > cuda< / em > , < em > gpu< / em > , < em > intel< / em > , < em > kk< / em > , < em > omp< / em > , or < em > opt< / em > suffix are
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functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
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hardware, as discussed in < a class = "reference internal" href = "Section_accelerate.html" > < em > Section_accelerate< / em > < / a >
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of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
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issues.< / p >
< p > These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
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KOKKOS, USER-OMP and OPT packages, respectively. They are only
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enabled if LAMMPS was built with those packages. See the < a class = "reference internal" href = "Section_start.html#start-3" > < span > Making LAMMPS< / span > < / 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 class = "reference internal" href = "Section_start.html#start-7" > < span > -suffix command-line switch< / span > < / a > when you invoke LAMMPS, or you can
use the < a class = "reference internal" href = "suffix.html" > < em > suffix< / em > < / a > command in your input script.< / p >
< p > See < a class = "reference internal" href = "Section_accelerate.html" > < em > Section_accelerate< / em > < / a > of the manual for
more instructions on how to use the accelerated styles effectively.< / p >
< hr class = "docutils" / >
< p > < strong > Mixing, shift, table, tail correction, restart, rRESPA info< / strong > :< / p >
< p > This pair style does not support the < a class = "reference internal" href = "pair_modify.html" > < em > pair_modify< / em > < / a >
shift, table, and tail options.< / p >
< p > This pair style does not write its information to < a class = "reference internal" href = "restart.html" > < em > binary restart files< / em > < / 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.< / p >
< p > This pair style can only be used via the < em > pair< / em > keyword of the
< a class = "reference internal" href = "run_style.html" > < em > run_style respa< / em > < / a > command. It does not support the
< em > inner< / em > , < em > middle< / em > , < em > outer< / em > keywords.< / p >
< / div >
< hr class = "docutils" / >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > 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 < a class = "reference internal" href = "Section_start.html#start-3" > < span > Making LAMMPS< / span > < / a > section for more info.< / p >
< p > This pair style requires the < a class = "reference internal" href = "newton.html" > < em > newton< / em > < / 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 class = "reference internal" href = "units.html" > < em > units< / em > < / a > . You can
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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
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appropriate units if your simulation doesn’ t use “ metal” units.< / p >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< a class = "headerlink" href = "#related-commands" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > < a class = "reference internal" href = "pair_coeff.html" > < em > pair_coeff< / em > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
< hr class = "docutils" / >
< p id = "kumagai" > < strong > (Kumagai)< / strong > T. Kumagai, S. Izumi, S. Hara, S. Sakai,
Comp. Mat. Science, 39, 457 (2007).< / p >
< p id = "tersoff-1" > < strong > (Tersoff_1)< / strong > J. Tersoff, Phys Rev B, 37, 6991 (1988).< / p >
< p id = "tersoff-2" > < strong > (Tersoff_2)< / strong > J. Tersoff, Phys Rev B, 38, 9902 (1988).< / p >
< p id = "murty" > < strong > (Murty)< / strong > M.V.R. Murty, H.A. Atwater, Phys Rev B, 51, 4889 (1995).< / p >
< p id = "schelling" > < strong > (Schelling)< / strong > Patrick K. Schelling, Comp. Mat. Science, 44, 274 (2008).< / p >
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2015-12-11 01:23:56 +08:00
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