forked from lijiext/lammps
164 lines
5.4 KiB
Plaintext
164 lines
5.4 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
|
|
|
:link(lws,http://lammps.sandia.gov)
|
|
:link(ld,Manual.html)
|
|
:link(lc,Section_commands.html#comm)
|
|
|
|
:line
|
|
|
|
pair_style gauss command :h3
|
|
pair_style gauss/gpu command :h3
|
|
pair_style gauss/omp command :h3
|
|
pair_style gauss/cut command :h3
|
|
pair_style gauss/cut/omp command :h3
|
|
|
|
[Syntax:]
|
|
|
|
pair_style gauss cutoff
|
|
pair_style gauss/cut cutoff :pre
|
|
|
|
cutoff = global cutoff for Gauss interactions (distance units) :ul
|
|
|
|
[Examples:]
|
|
|
|
pair_style gauss 12.0
|
|
pair_coeff * * 1.0 0.9
|
|
pair_coeff 1 4 1.0 0.9 10.0 :pre
|
|
|
|
pair_style gauss/cut 3.5
|
|
pair_coeff 1 4 0.2805 1.45 0.112 :pre
|
|
|
|
|
|
[Description:]
|
|
|
|
Style {gauss} computes a tethering potential of the form
|
|
|
|
:c,image(Eqs/pair_gauss.jpg)
|
|
|
|
between an atom and its corresponding tether site which will typically
|
|
be a frozen atom in the simulation. Rc is the cutoff.
|
|
|
|
The following coefficients must be defined for each pair of atom types
|
|
via the "pair_coeff"_pair_coeff.html command as in the examples above,
|
|
or in the data file or restart files read by the
|
|
"read_data"_read_data.html or "read_restart"_read_restart.html
|
|
commands:
|
|
|
|
A (energy units)
|
|
B (1/distance^2 units)
|
|
cutoff (distance units) :ul
|
|
|
|
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:
|
|
|
|
:c,image(Eqs/pair_gauss_cut.jpg)
|
|
|
|
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)"_#Lenart and of surfactants
|
|
"(Jusufi)"_#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 hight of the potential barrier.
|
|
|
|
The following coefficients must be defined for each pair of atom types
|
|
via the "pair_coeff"_pair_coeff.html command as in the example above,
|
|
or in the data file or restart files read by the
|
|
"read_data"_read_data.html or "read_restart"_read_restart.html
|
|
commands:
|
|
|
|
H (energy * distance units)
|
|
r_mh (distance units)
|
|
sigma_h (distance units) :ul
|
|
|
|
The global cutoff (r_c) specified in the pair_style command is used.
|
|
|
|
:line
|
|
|
|
Styles with a {cuda}, {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 in "Section_accelerate"_Section_accelerate.html
|
|
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, USER-INTEL,
|
|
KOKKOS, USER-OMP and OPT packages, respectively. They are only
|
|
enabled if LAMMPS was built with those packages. See the "Making
|
|
LAMMPS"_Section_start.html#start_3 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
|
|
switch7_Section_start.html#start_6 when you invoke LAMMPS, or you can
|
|
use the "suffix"_suffix.html command in your input script.
|
|
|
|
See "Section_accelerate"_Section_accelerate.html of the manual for
|
|
more instructions on how to use the accelerated styles effectively.
|
|
|
|
:line
|
|
|
|
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
|
|
|
These pair styles do not support mixing. Thus, coefficients for all
|
|
I,J pairs must be specified explicitly.
|
|
|
|
The {gauss} style does not support the "pair_modify"_pair_modify.html
|
|
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"_pair_modify.html shift
|
|
option for the energy of the Gauss-potential portion of the pair
|
|
interaction.
|
|
|
|
The "pair_modify"_pair_modify.html table and tail options are not
|
|
relevant for these pair styles.
|
|
|
|
These pair styles write their information to "binary restart
|
|
files"_restart.html, 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"_run_style.html 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"_compute_pair.html 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 :pre
|
|
|
|
:line
|
|
|
|
[Restrictions:]
|
|
|
|
The {gauss/cut} style is part of the "user-misc" package. It is only
|
|
enabled if LAMMPS is build with that package. See the "Making of
|
|
LAMMPS"_Section_start.html#3 section for more info.
|
|
|
|
[Related commands:]
|
|
|
|
"pair_coeff"_pair_coeff.html,
|
|
"pair_style coul/diel"_pair_coul_diel.html
|
|
|
|
[Default:] none
|
|
|
|
:link(Lenart)
|
|
[(Lenart)] Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126,
|
|
044509 (2007).
|
|
|
|
:link(Jusufi)
|
|
[(Jusufi)] Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112,
|
|
13783 (2008).
|
|
|