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251 lines
9.9 KiB
Plaintext
251 lines
9.9 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/cuda command :h3
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pair_style lj/cut/experimental/cuda 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/omp command :h3
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pair_style lj/cut/coul/cut command :h3
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pair_style lj/cut/coul/cut/cuda command :h3
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pair_style lj/cut/coul/cut/gpu command :h3
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pair_style lj/cut/coul/cut/omp command :h3
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pair_style lj/cut/coul/debye command :h3
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pair_style lj/cut/coul/debye/cuda command :h3
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pair_style lj/cut/coul/debye/omp command :h3
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pair_style lj/cut/coul/long command :h3
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pair_style lj/cut/coul/long/cuda 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/opt command :h3
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pair_style lj/cut/coul/long/omp command :h3
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pair_style lj/cut/coul/long/tip4p command :h3
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pair_style lj/cut/coul/long/tip4p/omp command :h3
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pair_style lj/cut/coul/long/tip4p/opt 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/coul/cut} 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/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/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/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_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 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 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/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/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/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#howto_8 for more
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information on 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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Styles {lj/cut/coul/pppm/omp} and {lj/cut/coul/pppm/tip4p/omp}
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are variants of {lj/cut/coul/long/omp} and {lj/cut/coul/long/tip4p/omp}
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for use with k-space styles "{pppm/proxy}"_kspace_style.html and
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"{pppm/tip4p/proxy}"_kspace_style.html, respectively and OpenMP
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multi-threading and will perform the corresponding reciprocal
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space calculation concurrently with the pair calculation
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in a separate thread. For certain parallel setups, this may have
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a performance benefit over performing k-space style and pair style
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separately and one after the other.
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:line
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Styles with a {cuda}, {gpu}, {omp}, or {opt} suffix are functionally
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the same as the corresponding style without the suffix. They have
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been optimized to run faster, depending on your available hardware, as
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discussed in "Section_accelerate"_Section_accelerate.html of the
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manual. The accelerated styles take the same arguments and should
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produce the same results, except for round-off and precision issues.
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These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
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packages, respectively. They are only enabled if LAMMPS was built with
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those packages. See the "Making LAMMPS"_Section_start.html#start_3
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section for more info.
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You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the "-suffix command-line
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switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
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use the "suffix"_suffix.html command in your input script.
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See "Section_accelerate"_Section_accelerate.html of the manual for
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more instructions on how to use the accelerated styles effectively.
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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. They are only enabled if LAMMPS was built with
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those packages. See the "Making LAMMPS"_Section_start.html#start_3
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section for more info. Note that the KSPACE package is installed by
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default.
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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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