forked from lijiext/lammps
264 lines
10 KiB
Plaintext
264 lines
10 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 lj/cut command :h3
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pair_style lj/cut/gpu command :h3
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pair_style lj/cut/opt command :h3
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pair_style lj/cut/coul/cut command :h3
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pair_style lj/cut/coul/cut/gpu command :h3
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pair_style lj/cut/coul/debye command :h3
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pair_style lj/cut/coul/long command :h3
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pair_style lj/cut/coul/long/gpu command :h3
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pair_style lj/cut/coul/long/tip4p command :h3
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[Syntax:]
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pair_style style args :pre
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style = {lj/cut} or {lj/cut/gpu} or {lj/cut/opt} or {lj/cut/coul/cut} \
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or {lj/cut/coul/debye} or {lj/cut/coul/long} or {lj/cut/coul/long/tip4p}
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args = list of arguments for a particular style :ul
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{lj/cut} args = cutoff
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cutoff = global cutoff for Lennard Jones interactions (distance units)
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{lj/cut/gpu} args = cutoff
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cutoff = global cutoff for Lennard Jones interactions (distance units)
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{lj/cut/opt} args = cutoff
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cutoff = global cutoff for Lennard Jones interactions (distance units)
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{lj/cut/coul/cut} 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)
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{lj/cut/coul/cut/gpu} 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)
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{lj/cut/coul/debye} args = kappa cutoff (cutoff2)
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kappa = Debye length (inverse distance units)
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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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{lj/cut/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)
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{lj/cut/coul/long/gpu} 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)
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{lj/cut/coul/long/tip4p} args = otype htype btype atype qdist cutoff (cutoff2)
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otype,htype = atom types for TIP4P O and H
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btype,atype = bond and angle types for TIP4P waters
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qdist = distance from O atom to massless charge (distance units)
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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 lj/cut 2.5
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pair_style lj/cut/gpu 2.5
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pair_style lj/cut/opt 2.5
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pair_coeff * * 1 1
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pair_coeff 1 1 1 1.1 2.8 :pre
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pair_style lj/cut/coul/cut 10.0
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pair_style lj/cut/coul/cut/gpu 10.0
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pair_style lj/cut/coul/cut 10.0 8.0
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pair_coeff * * 100.0 3.0
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pair_coeff 1 1 100.0 3.5 9.0
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pair_coeff 1 1 100.0 3.5 9.0 9.0 :pre
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pair_style lj/cut/coul/debye 1.5 3.0
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pair_style lj/cut/coul/debye 1.5 2.5 5.0
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pair_coeff * * 1.0 1.0
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pair_coeff 1 1 1.0 1.5 2.5
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pair_coeff 1 1 1.0 1.5 2.5 5.0 :pre
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pair_style lj/cut/coul/long 10.0
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pair_style lj/cut/coul/long/gpu 10.0
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pair_style lj/cut/coul/long 10.0 8.0
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pair_coeff * * 100.0 3.0
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pair_coeff 1 1 100.0 3.5 9.0 :pre
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pair_style lj/cut/coul/long/tip4p 1 2 7 8 0.3 12.0
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pair_style lj/cut/coul/long/tip4p 1 2 7 8 0.3 12.0 10.0
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pair_coeff * * 100.0 3.0
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pair_coeff 1 1 100.0 3.5 9.0 :pre
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[Description:]
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The {lj/cut} styles compute the standard 12/6 Lennard-Jones potential,
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given by
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:c,image(Eqs/pair_lj.jpg)
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Rc is the cutoff.
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Style {lj/cut/gpu} is a GPU-enabled version of style {lj/cut}.
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See more details below.
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Style {lj/cut/opt} is an optimized version of style {lj/cut} that
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should give identical answers. Depending on system size and the
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processor you are running on, it may be 5-25% faster (for the pairwise
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portion of the run time).
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Style {lj/cut/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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Style {lj/cut/coul/cut/gpu} is a GPU-enabled version of style {lj/cut/coul/cut}.
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See more details below.
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Style {lj/cut/coul/debye} adds 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. This potential is another way to
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mimic the screening effect of a polar solvent.
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Style {lj/cut/coul/long} computes the same Coulombic interactions as
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style {lj/cut/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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Style {lj/cut/coul/long/gpu} is a GPU-enabled version of style {lj/cut/coul/long}.
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See more details below.
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Style {lj/cut/coul/long/tip4p} implements the TIP4P water model of
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"(Jorgensen)"_#Jorgensen, which introduces a massless site located a
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short distance away from the oxygen atom along the bisector of the HOH
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angle. The atomic types of the oxygen and hydrogen atoms, the bond
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and angle types for OH and HOH interactions, and the distance to the
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massless charge site are specified as pair_style arguments.
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IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom
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IDs for the O and 2 H atoms must be consecutive, with the O atom
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first. This is to enable LAMMPS to "find" the 2 H atoms associated
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with each O atom. For example, if the atom ID of an O atom in a TIP4P
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water molecule is 500, then its 2 H atoms must have IDs 501 and 502.
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See the "howto section"_Section_howto.html#4_8 for more information on
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how to use the TIP4P pair style.
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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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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 at 2^(1/6)
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sigma.
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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. You cannot specify 2 cutoffs for style {lj/cut}, since it
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has no Coulombic terms.
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For {lj/cut/coul/long} and {lj/cut/coul/long/tip4p} only the LJ cutoff
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can be specified since a Coulombic cutoff cannot be specified for an
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individual I,J type pair. All type pairs use the same global
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Coulombic cutoff specified in the pair_style command.
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:line
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The {lj/cut/gpu}, {lj/cut/coul/cut/gpu}, and {lj/cut/coul/long/gpu} styles
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are identical to the {lj/cut}, {lj/cut/coul/cut}, and {lj/cut/coul/long}
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styles, except that each processor off-loads its pairwise calculations to a
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GPU chip. Depending on the hardware available on your system this can provide a
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speed-up. See the "Running on GPUs"_Section_start.html#2_8 section of
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the manual for more details about hardware and software requirements
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for using GPUs.
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More details about these settings and various possible hardware
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configuration are in "this section"_Section_start.html#2_8 of the
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manual.
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Additional requirements in your input script to run with GPU-enabled styles
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are as follows:
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The "newton pair"_newton.html setting must be {off} and
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"fix gpu"_fix_gpu.html must be used. The fix controls
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the essential GPU selection and initialization steps.
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:line
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[Mixing, shift, table, tail correction, restart, 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 lj/cut pair styles can be mixed.
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The default mix value is {geometric}. See the "pair_modify" command
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for details.
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All of the lj/cut 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 {lj/cut/coul/long} and {lj/cut/coul/long/tip4p} pair styles
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support the "pair_modify"_pair_modify.html table option since they can
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tabulate the short-range portion of the long-range Coulombic
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interaction.
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All of the lj/cut pair styles support the
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"pair_modify"_pair_modify.html tail option for adding a long-range
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tail correction to the energy and pressure for the Lennard-Jones
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portion of the pair interaction.
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All of the lj/cut 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 lj/cut and lj/cut/coul/long pair styles support the use of the
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{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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The other styles only support the {pair} keyword of run_style respa.
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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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The {lj/cut/coul/long} and {lj/cut/coul/long/tip4p} styles are part of
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the "kspace" package. The {lj/cut/gpu}, {lj/cut/coul/cut/gpu}, and
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{lj/cut/coul/long/gpu} styles are part of the "gpu"
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package. The {lj/cut/opt} style is part of the "opt" package. They
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are only enabled if LAMMPS was built with those packages. See the
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"Making LAMMPS"_Section_start.html#2_3 section for more info. Note
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that the "kspace" package is installed by default.
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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 {lj/cut/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
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[Default:] none
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:line
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:link(Jorgensen)
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[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
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Phys, 79, 926 (1983).
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