pair_style gauss command¶
Accelerator Variants: gauss/gpu, gauss/omp
pair_style gauss/cut command¶
Accelerator Variants: gauss/cut/omp
Syntax¶
pair_style gauss cutoff
pair_style gauss/cut cutoff
cutoff = global cutoff for Gauss interactions (distance units)
Examples¶
pair_style gauss 12.0
pair_coeff * * 1.0 0.9
pair_coeff 1 4 1.0 0.9 10.0
pair_style gauss/cut 3.5
pair_coeff 1 4 0.2805 1.45 0.112
Description¶
Style gauss computes a tethering potential of the form
between an atom and its corresponding tether site which will typically be a frozen atom in the simulation. \(r_c\) is the cutoff.
The following coefficients must be defined for each pair of atom 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:
A (energy units)
B (1/distance^2 units)
cutoff (distance units)
The last coefficient is optional. If not specified, the global cutoff is used.
Style gauss/cut computes a generalized Gaussian interaction potential between pairs of particles:
where H determines together with the standard deviation \(\sigma_h\) the peak height of the Gaussian function, and \(r_{mh}\) the peak position. Examples of the use of the Gaussian potentials include implicit solvent simulations of salt ions (Lenart) and of surfactants (Jusufi). In these instances the Gaussian potential mimics the hydration barrier between a pair of particles. The hydration barrier is located at \(r_{mh}\) and has a width of \(\sigma_h\). The prefactor determines the height of the potential barrier.
The following coefficients must be defined for each pair of atom types via the pair_coeff command as in the example above, or in the data file or restart files read by the read_data or read_restart commands:
H (energy * distance units)
\(r_{mh}\) (distance units)
\(\sigma_h\) (distance units)
cutoff (distance units)
The last coefficient is optional. If not specified, the global cutoff is used.
Styles with a gpu, intel, kk, omp, 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 on the Speed packages doc page. 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 GPU, INTEL, KOKKOS, OPENMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the Build package page 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 the Speed packages page for more instructions on how to use the accelerated styles effectively.
Mixing, shift, table, tail correction, restart, rRESPA info¶
For atom type pairs I,J and I != J, the A, B, H, sigma_h, r_mh parameters, and the cutoff distance for these pair styles can be mixed: A (energy units) sqrt(1/B) (distance units, see below) H (energy units) sigma_h (distance units) r_mh (distance units) cutoff (distance units):ul
The default mix value is geometric. Only arithmetic and geometric mix values are supported. See the “pair_modify” command for details.
The A and H parameters are mixed using the same rules normally used to mix the “epsilon” parameter in a Lennard Jones interaction. The sigma_h, r_mh, and the cutoff distance are mixed using the same rules used to mix the “sigma” parameter in a Lennard Jones interaction. The B parameter is converted to a distance (sigma), before mixing (using sigma=B^-0.5), and converted back to a coefficient afterwards (using B=sigma^2). Negative A values are converted to positive A values (using abs(A)) before mixing, and converted back after mixing (by multiplying by min(sign(Ai),sign(Aj))). This way, if either particle is repulsive (if Ai<0 or Aj<0), then the default interaction between both particles will be repulsive.
The gauss style does not support the pair_modify shift option. There is no effect due to the Gaussian well beyond the cutoff; hence reasonable cutoffs need to be specified.
The gauss/cut style supports the pair_modify shift option for the energy of the Gauss-potential portion of the pair interaction.
The pair_modify table and tail options are not relevant for these pair styles.
These 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.
These pair styles can only be used via the pair keyword of the run_style respa command. They do not support the inner, middle, outer keywords.
The gauss pair style tallies an “occupancy” count of how many Gaussian-well sites have an atom within the distance at which the force is a maximum = sqrt(0.5/b). This quantity can be accessed via the compute pair command as a vector of values of length 1.
To print this quantity to the log file (with a descriptive column heading) the following commands could be included in an input script:
compute gauss all pair gauss
variable occ equal c_gauss[1]
thermo_style custom step temp epair v_occ
Restrictions¶
The gauss and gauss/cut styles are part of the EXTRA-PAIR package. They are only enabled if LAMMPS is build with that package. See the Build package page for more info.
The gauss style does not apply special_bonds factors. When using this pair style on a system that has bonds, the special_bonds factors, if using the default setting of 0.0, may need to be adjusted to some very small number (e.g. 1.0e-100), so that those special pairs are not completely excluded from the neighbor lists, but won’t contribute forces or energies from styles (e.g. when used in combination with a hybrid pair style) that do apply those factors.
Default¶
none
(Lenart) Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126, 044509 (2007).
(Jusufi) Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112, 13783 (2008).