forked from lijiext/lammps
166 lines
6.1 KiB
Plaintext
166 lines
6.1 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 cg/cmm command :h3
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pair_style cg/cmm/coul/cut command :h3
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pair_style cg/cmm/coul/long command :h3
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[Syntax:]
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pair_style style args :pre
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style = {cg/cmm} or {cg/cmm/coul/cut} or {cg/cmm/coul/long}
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args = list of arguments for a particular style :ul
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{cg/cmm} args = cutoff
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cutoff = global cutoff for Lennard Jones interactions (distance units)
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{cg/cmm/coul/cut} args = cutoff (cutoff2) (kappa)
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units)
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kappa = Debye length (optional, defaults to 0.0 = disabled) (inverse distance units)
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{cg/cmm/coul/long} args = cutoff (cutoff2)
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
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[Examples:]
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pair_style cg/cmm 2.5
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pair_coeff 1 1 lj12_6 1 1.1 2.8 :pre
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pair_style cg/cmm/coul/cut 10.0 12.0
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pair_coeff 1 1 lj9_6 100.0 3.5 9.0
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pair_coeff 1 1 lj12_4 100.0 3.5 9.0 9.0 :pre
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pair_style cg/cmm/coul/long 10.0
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pair_style cg/cmm/coul/long 10.0 8.0
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pair_coeff 1 1 lj9_6 100.0 3.5 9.0 :pre
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[Description:]
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The {cg/cmm} styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
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given by
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:c,image(Eqs/pair_cmm.jpg)
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as required for the CMM Coarse-grained MD parametrization discussed in
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"(Shinoda)"_#Shinoda and "(DeVane)"_#DeVane. Rc is the cutoff.
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Style {cg/cmm/coul/cut} adds a Coulombic pairwise interaction given by
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:c,image(Eqs/pair_coulomb.jpg)
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where C is an energy-conversion constant, Qi and Qj are the charges on
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the 2 atoms, and epsilon is the dielectric constant which can be set
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by the "dielectric"_dielectric.html command. If one cutoff is
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specified in the pair_style command, it is used for both the LJ and
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Coulombic terms. If two cutoffs are specified, they are used as
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cutoffs for the LJ and Coulombic terms respectively.
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This style also contains an additional exp() damping factor
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to the Coulombic term, given by
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:c,image(Eqs/pair_debye.jpg)
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where kappa is the Debye length (kappa=0.0 is the unscreened coulomb).
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This potential is another way to mimic the screening effect of a polar
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solvent.
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Style {cg/cmm/coul/long} computes the same Coulombic interactions as
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style {cg/cmm/coul/cut} except that an additional damping factor is
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applied to the Coulombic term so it can be used in conjunction with
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the "kspace_style"_kspace_style.html command and its {ewald} or {pppm}
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option. The Coulombic cutoff specified for this style means that
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pairwise interactions within this distance are computed directly;
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interactions outside that distance are computed in reciprocal space.
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The following coefficients must be defined for each pair of atoms
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types via the "pair_coeff"_pair_coeff.html command as in the examples
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above, or in the data file or restart files read by the
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"read_data"_read_data.html or "read_restart"_read_restart.html
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commands, or by mixing as described below:
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cg_type (lj9_6, lj12_4, or lj12_6)
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epsilon (energy units)
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sigma (distance units)
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cutoff1 (distance units)
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cutoff2 (distance units) :ul
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Note that sigma is defined in the LJ formula as the zero-crossing
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distance for the potential, not as the energy minimum. The prefactors
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are chosen so that the potential minimum is at -epsilon.
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The latter 2 coefficients are optional. If not specified, the global
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LJ and Coulombic cutoffs specified in the pair_style command are used.
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If only one cutoff is specified, it is used as the cutoff for both LJ
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and Coulombic interactions for this type pair. If both coefficients
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are specified, they are used as the LJ and Coulombic cutoffs for this
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type pair.
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For {cg/cmm/coul/long} only the LJ cutoff can be specified since a
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Coulombic cutoff cannot be specified for an individual I,J type pair.
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All type pairs use the same global Coulombic cutoff specified in the
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pair_style command.
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:line
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[Mixing, shift, table, tail correction, restart, and rRESPA info]:
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For atom type pairs I,J and I != J, the epsilon and sigma coefficients
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and cutoff distance for all of the cg/cmm pair styles {cannot} be mixed,
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since different pairs may have different exponents. So all parameters
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for all pairs have to be specified explicitly through the "pair_coeff"
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command. Defining then in a data file is also not supported, due to
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limitations of that file format.
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All of the cg/cmm pair styles support the
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"pair_modify"_pair_modify.html shift option for the energy of the
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Lennard-Jones portion of the pair interaction.
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The {cg/cmm/coul/long} pair styles support the
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"pair_modify"_pair_modify.html table option since they can tabulate
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the short-range portion of the long-range Coulombic interaction.
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All of the cg/cmm pair styles write their information to "binary
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restart files"_restart.html, so pair_style and pair_coeff commands do
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not need to be specified in an input script that reads a restart file.
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The cg/cmm, cg/cmm/coul/cut and lj/cut/coul/long pair styles support
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the use of the {inner}, {middle}, and {outer} keywords of the "run_style
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respa"_run_style.html command, meaning the pairwise forces can be
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partitioned by distance at different levels of the rRESPA hierarchy.
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See the "run_style"_run_style.html command for details.
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:line
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[Restrictions:]
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All of the cg/cmm pair styles are part of the "user-cg-cmm"
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package. They are only enabled if LAMMPS was built with that
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package. The {cg/cmm/coul/long} style also requires the "kspace"
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package to be built (which is enabled by default). See the "Making
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LAMMPS"_Section_start.html#2_3 section for more info.
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On some 64-bit machines, compiling with -O3 appears to break the
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Coulombic tabling option used by the {cg/cmm/coul/long} style. See
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the "Additional build tips" section of the Making LAMMPS documentation
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pages for workarounds on this issue.
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[Related commands:]
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"pair_coeff"_pair_coeff.html, "angle_style cg/cmm"_angle_cmm.html
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[Default:] none
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:line
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:link(Shinoda)
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[(Shinoda)] Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
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:link(DeVane)
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[(DeVane)] Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
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