forked from lijiext/lammps
193 lines
7.6 KiB
Plaintext
193 lines
7.6 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 comb command :h3
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pair_style comb/omp command :h3
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pair_style comb3 command :h3
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[Syntax:]
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pair_style comb
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pair_style comb3 keyword :pre
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keyword = {polar}
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{polar} value = {polar_on} or {polar_off} = whether or not to include atomic polarization :pre
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:ule
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[Examples:]
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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 :pre
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pair_style comb3 polar_off
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pair_coeff * * ../potentials/ffield.comb3 O Cu N C O :pre
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[Description:]
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Style {comb} computes the second-generation variable charge COMB
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(Charge-Optimized Many-Body) potential. Style {comb3} computes the
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third-generation COMB potential. These COMB potentials are described
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in "(COMB)"_#COMB and "(COMB3)"_#COMB3. Briefly, the total energy
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{E<sub>T</sub>} of a system of atoms is given by
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:c,image(Eqs/pair_comb1.jpg)
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where {E<sub>i</sub><sup>self</sup>} is the self-energy of atom {i}
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(including atomic ionization energies and electron affinities),
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{E<sub>ij</sub><sup>short</sup>} is the bond-order potential between
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atoms {i} and {j},
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{E<sub>ij</sub><sup>Coul</sup>} is the Coulomb interactions,
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{E<sup>polar</sup>} is the polarization term for organic systems
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(style {comb3} only),
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{E<sup>vdW</sup>} is the van der Waals energy (style {comb3} only),
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{E<sup>barr</sup>} is a charge barrier function, and
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{E<sup>corr</sup>} are angular correction terms.
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The COMB potentials (styles {comb} and {comb3}) are variable charge
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potentials. The equilibrium charge on each atom is calculated by the
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electronegativity equalization (QEq) method. See "Rick"_#Rick for
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further details. This is implemented by the "fix
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qeq/comb"_fix_qeq_comb.html command, which should normally be
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specified in the input script when running a model with the COMB
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potential. The "fix qeq/comb"_fix_qeq_comb.html command has options
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that determine how often charge equilibration is performed, its
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convergence criterion, and which atoms are included in the
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calculation.
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Only a single pair_coeff command is used with the {comb} and {comb3}
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styles which specifies the COMB 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 potential file in the pair_coeff
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command, where N is the number of LAMMPS atom types.
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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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pair_coeff * * ../potentials/ffield.comb Si Hf O Si :pre
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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 {ffield.comb} 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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This can be used when a {comb} potential is used as part of the
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{hybrid} 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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For style {comb}, the provided potential file {ffield.comb} contains
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all currently-available 2nd generation COMB parameterizations: for Si,
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Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals. For style
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{comb3}, the potential file {ffield.comb3} contains all
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currently-available 3rd generation COMB paramterizations: O, Cu, N, C,
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H, Ti, Zn and Zr. The status of the optimization of the compounds, for
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example Cu<sub>2</sub>O, TiN and hydrocarbons, are given in the
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following table:
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:c,image(Eqs/pair_comb2.jpg)
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For style {comb3}, in addition to ffield.comb3, a special parameter
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file, {lib.comb3}, that is exclusively used for C/O/H systems, will be
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automatically loaded if carbon atom is detected in LAMMPS input
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structure. This file must be in your working directory or in the
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directory pointed to by the environment variable LAMMPS_POTENTIALS, as
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described on the "pair_coeff"_pair_coeff.html command doc page.
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Keyword {polar} indicates whether the force field includes
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the atomic polarization. Since the equilibration of the polarization
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has not yet been implemented, it can only set polar_off at present.
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NOTE: You can not use potential file {ffield.comb} with style {comb3},
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nor file {ffield.comb3} with style {comb}.
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:line
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Styles with a {cuda}, {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in "Section_accelerate"_Section_accelerate.html
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.
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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 "Making
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LAMMPS"_Section_start.html#start_3 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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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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These pair styles does not support the "pair_modify"_pair_modify.html
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shift, table, and tail options.
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These pair styles do 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, pair_coeff, and "fix
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qeq/comb"_fix_qeq_comb.html commands in an input script that reads a
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restart file.
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These pair styles 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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These pair styles are 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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These pair styles requires the "newton"_newton.html setting to be "on"
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for pair interactions.
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The COMB potentials in the {ffield.comb} and {ffield.comb3} files provided
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with LAMMPS (see the potentials directory) are parameterized for metal
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"units"_units.html. 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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[Related commands:]
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"pair_style"_pair_style.html, "pair_coeff"_pair_coeff.html,
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"fix qeq/comb"_fix_qeq_comb.html
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[Default:] none
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:line
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:link(COMB)
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[(COMB)] T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and
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S. R. Phillpot, Phys. Rev. B 81, 125328 (2010)
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:link(COMB3)
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[(COMB3)] T. Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek,
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Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74,
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255-279 (2013).
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:link(Rick)
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[(Rick)] S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
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(1994).
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