forked from lijiext/lammps
312 lines
13 KiB
Plaintext
312 lines
13 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 lj/cut command :h3
|
|
pair_style lj/cut/cuda command :h3
|
|
pair_style lj/cut/experimental/cuda command :h3
|
|
pair_style lj/cut/gpu command :h3
|
|
pair_style lj/cut/opt command :h3
|
|
pair_style lj/cut/omp command :h3
|
|
pair_style lj/cut/coul/cut command :h3
|
|
pair_style lj/cut/coul/cut/cuda command :h3
|
|
pair_style lj/cut/coul/cut/gpu command :h3
|
|
pair_style lj/cut/coul/cut/omp command :h3
|
|
pair_style lj/cut/coul/debye command :h3
|
|
pair_style lj/cut/coul/debye/cuda command :h3
|
|
pair_style lj/cut/coul/debye/gpu command :h3
|
|
pair_style lj/cut/coul/debye/omp command :h3
|
|
pair_style lj/cut/coul/dsf command :h3
|
|
pair_style lj/cut/coul/dsf/gpu command :h3
|
|
pair_style lj/cut/coul/dsf/omp command :h3
|
|
pair_style lj/cut/coul/long command :h3
|
|
pair_style lj/cut/coul/long/cuda command :h3
|
|
pair_style lj/cut/coul/long/gpu command :h3
|
|
pair_style lj/cut/coul/long/opt command :h3
|
|
pair_style lj/cut/coul/long/omp command :h3
|
|
pair_style lj/cut/coul/msm command :h3
|
|
pair_style lj/cut/coul/msm/gpu command :h3
|
|
pair_style lj/cut/coul/msm/omp command :h3
|
|
pair_style lj/cut/tip4p/cut command :h3
|
|
pair_style lj/cut/tip4p/cut/omp command :h3
|
|
pair_style lj/cut/tip4p/long command :h3
|
|
pair_style lj/cut/tip4p/long/omp command :h3
|
|
pair_style lj/cut/tip4p/long/opt command :h3
|
|
|
|
[Syntax:]
|
|
|
|
pair_style style args :pre
|
|
|
|
style = {lj/cut} or {lj/cut/coul/cut} or {lj/cut/coul/debye} or {lj/cut/coul/dsf} or {lj/cut/coul/long} or {lj/cut/coul/msm} or {lj/cut/tip4p/long}
|
|
args = list of arguments for a particular style :ul
|
|
{lj/cut} args = cutoff
|
|
cutoff = global cutoff for Lennard Jones interactions (distance units)
|
|
{lj/cut/coul/cut} args = cutoff (cutoff2)
|
|
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
|
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
|
{lj/cut/coul/debye} args = kappa cutoff (cutoff2)
|
|
kappa = inverse of the Debye length (inverse distance units)
|
|
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
|
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
|
{lj/cut/coul/dsf} args = alpha cutoff (cutoff2)
|
|
alpha = damping parameter (inverse distance units)
|
|
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
|
cutoff2 = global cutoff for Coulombic (distance units)
|
|
{lj/cut/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)
|
|
{lj/cut/coul/msm} args = cutoff (cutoff2)
|
|
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
|
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
|
{lj/cut/tip4p/cut} args = otype htype btype atype qdist cutoff (cutoff2)
|
|
otype,htype = atom types for TIP4P O and H
|
|
btype,atype = bond and angle types for TIP4P waters
|
|
qdist = distance from O atom to massless charge (distance units)
|
|
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
|
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
|
{lj/cut/tip4p/long} args = otype htype btype atype qdist cutoff (cutoff2)
|
|
otype,htype = atom types for TIP4P O and H
|
|
btype,atype = bond and angle types for TIP4P waters
|
|
qdist = distance from O atom to massless charge (distance units)
|
|
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
|
|
cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
|
|
|
|
[Examples:]
|
|
|
|
pair_style lj/cut 2.5
|
|
pair_coeff * * 1 1
|
|
pair_coeff 1 1 1 1.1 2.8 :pre
|
|
|
|
pair_style lj/cut/coul/cut 10.0
|
|
pair_style lj/cut/coul/cut 10.0 8.0
|
|
pair_coeff * * 100.0 3.0
|
|
pair_coeff 1 1 100.0 3.5 9.0
|
|
pair_coeff 1 1 100.0 3.5 9.0 9.0 :pre
|
|
|
|
pair_style lj/cut/coul/debye 1.5 3.0
|
|
pair_style lj/cut/coul/debye 1.5 2.5 5.0
|
|
pair_coeff * * 1.0 1.0
|
|
pair_coeff 1 1 1.0 1.5 2.5
|
|
pair_coeff 1 1 1.0 1.5 2.5 5.0 :pre
|
|
|
|
pair_style lj/cut/coul/dsf 0.05 2.5 10.0
|
|
pair_coeff * * 1.0 1.0
|
|
pair_coeff 1 1 1.0 1.0 2.5 :pre
|
|
|
|
pair_style lj/cut/coul/long 10.0
|
|
pair_style lj/cut/coul/long 10.0 8.0
|
|
pair_coeff * * 100.0 3.0
|
|
pair_coeff 1 1 100.0 3.5 9.0 :pre
|
|
|
|
pair_style lj/cut/coul/msm 10.0
|
|
pair_style lj/cut/coul/msm 10.0 8.0
|
|
pair_coeff * * 100.0 3.0
|
|
pair_coeff 1 1 100.0 3.5 9.0 :pre
|
|
|
|
pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0
|
|
pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0
|
|
pair_coeff * * 100.0 3.0
|
|
pair_coeff 1 1 100.0 3.5 9.0 :pre
|
|
|
|
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0
|
|
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0
|
|
pair_coeff * * 100.0 3.0
|
|
pair_coeff 1 1 100.0 3.5 9.0 :pre
|
|
|
|
[Description:]
|
|
|
|
The {lj/cut} styles compute the standard 12/6 Lennard-Jones potential,
|
|
given by
|
|
|
|
:c,image(Eqs/pair_lj.jpg)
|
|
|
|
Rc is the cutoff.
|
|
|
|
Style {lj/cut/coul/cut} adds a Coulombic pairwise interaction given by
|
|
|
|
:c,image(Eqs/pair_coulomb.jpg)
|
|
|
|
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"_dielectric.html 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.
|
|
|
|
Style {lj/cut/coul/debye} adds an additional exp() damping factor
|
|
to the Coulombic term, given by
|
|
|
|
:c,image(Eqs/pair_debye.jpg)
|
|
|
|
where kappa is the inverse of the Debye length. This potential is
|
|
another way to mimic the screening effect of a polar solvent.
|
|
|
|
Style {lj/cut/coul/dsf} computes the Coulombic term via the damped
|
|
shifted force model described in "Fennell"_#Fennell, given by:
|
|
|
|
:c,image(Eqs/pair_coul_dsf.jpg)
|
|
|
|
where {alpha} is the damping parameter and erfc() is the complementary
|
|
error-function. This potential is essentially a short-range,
|
|
spherically-truncated, charge-neutralized, shifted, pairwise {1/r}
|
|
summation. The potential is based on Wolf summation, proposed as an
|
|
alternative to Ewald summation for condensed phase systems where
|
|
charge screening causes electrostatic interactions to become
|
|
effectively short-ranged. In order for the electrostatic sum to be
|
|
absolutely convergent, charge neutralization within the cutoff radius
|
|
is enforced by shifting the potential through placement of image
|
|
charges on the cutoff sphere. Convergence can often be improved by
|
|
setting {alpha} to a small non-zero value.
|
|
|
|
Styles {lj/cut/coul/long} and {lj/cut/coul/msm} compute the same
|
|
Coulombic interactions as style {lj/cut/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"_kspace_style.html
|
|
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.
|
|
|
|
Styles {lj/cut/tip4p/cut} and {lj/cut/tip4p/long} implement the TIP4P
|
|
water model of "(Jorgensen)"_#Jorgensen, which introduces a massless
|
|
site located a short distance away from the oxygen atom along the
|
|
bisector of the HOH angle. The atomic types of the oxygen and
|
|
hydrogen atoms, the bond and angle types for OH and HOH interactions,
|
|
and the distance to the massless charge site are specified as
|
|
pair_style arguments. Style {lj/cut/tip4p/cut} uses a cutoff for
|
|
Coulomb interactions; style {lj/cut/tip4p/long} is for use with a
|
|
long-range Coulombic solver (Ewald or PPPM).
|
|
|
|
IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom
|
|
IDs for the O and 2 H atoms must be consecutive, with the O atom
|
|
first. This is to enable LAMMPS to "find" the 2 H atoms associated
|
|
with each O atom. For example, if the atom ID of an O atom in a TIP4P
|
|
water molecule is 500, then its 2 H atoms must have IDs 501 and 502.
|
|
|
|
See the "howto section"_Section_howto.html#howto_8 for more
|
|
information on how to use the TIP4P pair styles and lists of
|
|
parameters to set. Note that the neighobr list cutoff for Coulomb
|
|
interactions is effectively extended by a distance 2*qdist when using
|
|
the TIP4P pair style, to account for the offset distance of the
|
|
fictitious charges on O atoms in water molecules. Thus it is
|
|
typically best in an efficiency sense to use a LJ cutoff >= Coulomb
|
|
cutoff + 2*qdist, to shrink the size of the neighbor list. This leads
|
|
to slightly larger cost for the long-range calculation, so you can
|
|
test the trade-off for your model.
|
|
|
|
For all of the {lj/cut} pair styles, the following coefficients must
|
|
be defined for each pair of atoms 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, or by mixing as
|
|
described below:
|
|
|
|
epsilon (energy units)
|
|
sigma (distance units)
|
|
cutoff1 (distance units)
|
|
cutoff2 (distance units) :ul
|
|
|
|
Note that sigma is defined in the LJ formula as the zero-crossing
|
|
distance for the potential, not as the energy minimum at 2^(1/6)
|
|
sigma.
|
|
|
|
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. You cannot specify 2 cutoffs for style {lj/cut}, since it
|
|
has no Coulombic terms.
|
|
|
|
For {lj/cut/coul/long} and {lj/cut/coul/msm} and {lj/cut/tip4p/cut}
|
|
and {lj/cut/tip4p/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.
|
|
|
|
:line
|
|
|
|
Styles with a {cuda}, {gpu}, {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-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
|
|
switch"_Section_start.html#start_7 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]:
|
|
|
|
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
|
and cutoff distance for all of the lj/cut pair styles can be mixed.
|
|
The default mix value is {geometric}. See the "pair_modify" command
|
|
for details.
|
|
|
|
All of the {lj/cut} pair styles support the
|
|
"pair_modify"_pair_modify.html shift option for the energy of the
|
|
Lennard-Jones portion of the pair interaction.
|
|
|
|
The {lj/cut/coul/long} and {lj/cut/tip4p/long} pair styles support the
|
|
"pair_modify"_pair_modify.html table option since they can tabulate
|
|
the short-range portion of the long-range Coulombic interaction.
|
|
|
|
All of the {lj/cut} pair styles support the
|
|
"pair_modify"_pair_modify.html tail option for adding a long-range
|
|
tail correction to the energy and pressure for the Lennard-Jones
|
|
portion of the pair interaction.
|
|
|
|
All of the {lj/cut} 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.
|
|
|
|
The {lj/cut} and {lj/cut/coul/long} pair styles support the use of the
|
|
{inner}, {middle}, and {outer} keywords of the "run_style
|
|
respa"_run_style.html command, meaning the pairwise forces can be
|
|
partitioned by distance at different levels of the rRESPA hierarchy.
|
|
The other styles only support the {pair} keyword of run_style respa.
|
|
See the "run_style"_run_style.html command for details.
|
|
|
|
:line
|
|
|
|
[Restrictions:]
|
|
|
|
The {lj/cut/coul/long} and {lj/cut/tip4p/long} styles are part of the
|
|
KSPACE package. The {lj/cut/tip4p/cut} style is part of the MOLECULE
|
|
package. These styles are only enabled if LAMMPS was built with those
|
|
packages. See the "Making LAMMPS"_Section_start.html#start_3 section
|
|
for more info. Note that the KSPACE and MOLECULE packages are
|
|
installed by default.
|
|
|
|
[Related commands:]
|
|
|
|
"pair_coeff"_pair_coeff.html
|
|
|
|
[Default:] none
|
|
|
|
:line
|
|
|
|
:link(Jorgensen)
|
|
[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
|
|
Phys, 79, 926 (1983).
|
|
|
|
:link(Fennell)
|
|
[(Fennell)] C. J. Fennell, J. D. Gezelter, J Chem Phys, 124,
|
|
234104 (2006).
|