Syntax:
pair_style style args
cg/cmm args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
cg/cmm/coul/cut args = cutoff (cutoff2) (kappa)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
kappa = Debye length (optional, defaults to 0.0 = disabled) (inverse distance units)
cg/cmm/coul/long args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
Examples:
pair_style cg/cmm 2.5 pair_coeff 1 1 lj12_6 1 1.1 2.8
pair_style cg/cmm/coul/cut 10.0 12.0 pair_coeff 1 1 lj9_6 100.0 3.5 9.0 pair_coeff 1 1 lj12_4 100.0 3.5 9.0 9.0
pair_style cg/cmm/coul/long 10.0 pair_style cg/cmm/coul/long 10.0 8.0 pair_coeff 1 1 lj9_6 100.0 3.5 9.0
Description:
The cg/cmm styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential, given by
as required for the CMM Coarse-grained MD parametrization discussed in (Shinoda) and (DeVane). Rc is the cutoff.
Style cg/cmm/coul/cut adds a Coulombic pairwise interaction given by
where C is an energy-conversion constant, Qi and Qj are the charges on the 2 atoms, and epsilon is the dielectric constant which can be set by the dielectric command. If one cutoff is specified in the pair_style command, it is used for both the LJ and Coulombic terms. If two cutoffs are specified, they are used as cutoffs for the LJ and Coulombic terms respectively.
This style also contains an additional exp() damping factor to the Coulombic term, given by
where kappa is the Debye length (kappa=0.0 is the unscreened coulomb). This potential is another way to mimic the screening effect of a polar solvent.
Style cg/cmm/coul/long computes the same Coulombic interactions as style cg/cmm/coul/cut except that an additional damping factor is applied to the Coulombic term so it can be used in conjunction with the kspace_style command and its ewald or pppm option. The Coulombic cutoff specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in reciprocal space.
The following coefficients must be defined for each pair of atoms types via the pair_coeff command as in the examples above, or in the data file or restart files read by the read_data or read_restart commands, or by mixing as described below:
Note that sigma is defined in the LJ formula as the zero-crossing distance for the potential, not as the energy minimum. The prefactors are chosen so that the potential minimum is at -epsilon.
The latter 2 coefficients are optional. If not specified, the global LJ and Coulombic cutoffs specified in the pair_style command are used. If only one cutoff is specified, it is used as the cutoff for both LJ and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the LJ and Coulombic cutoffs for this type pair.
For cg/cmm/coul/long only the LJ cutoff can be specified since a Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the pair_style command.
Styles with a cuda, gpu, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed in this section of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.
These accelerated styles are part of the USER-CUDA, GPU, and OPT packages respectively. They are only enabled if LAMMPS was built with those packages. See the Making LAMMPS section for more info.
You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
See this section of the manual for more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, and rRESPA info:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance for all of the cg/cmm pair styles cannot be mixed, since different pairs may have different exponents. So all parameters for all pairs have to be specified explicitly through the "pair_coeff" command. Defining then in a data file is also not supported, due to limitations of that file format.
All of the cg/cmm pair styles support the pair_modify shift option for the energy of the Lennard-Jones portion of the pair interaction.
The cg/cmm/coul/long pair styles support the pair_modify table option since they can tabulate the short-range portion of the long-range Coulombic interaction.
All of the cg/cmm pair styles write their information to binary restart files, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file.
The cg/cmm, cg/cmm/coul/cut and lj/cut/coul/long pair styles support the use of the inner, middle, and outer keywords of the run_style respa command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. See the run_style command for details.
Restrictions:
All of the cg/cmm pair styles are part of the USER-CG-CMM package. The cg/cmm/coul/long style also requires the KSPACE package to be built (which is enabled by default). They are only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.
Related commands:
pair_coeff, angle_style cg/cmm
Default: none
(Shinoda) Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
(DeVane) Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).