forked from lijiext/lammps
276 lines
12 KiB
Plaintext
276 lines
12 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,Commands_all.html)
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:line
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pair_style lj/cut/dipole/cut command :h3
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pair_style lj/cut/dipole/cut/gpu command :h3
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pair_style lj/cut/dipole/cut/omp command :h3
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pair_style lj/sf/dipole/sf command :h3
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pair_style lj/sf/dipole/sf/gpu command :h3
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pair_style lj/sf/dipole/sf/omp command :h3
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pair_style lj/cut/dipole/long command :h3
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pair_style lj/cut/dipole/long/gpu command :h3
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pair_style lj/long/dipole/long command :h3
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[Syntax:]
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pair_style lj/cut/dipole/cut cutoff (cutoff2)
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pair_style lj/sf/dipole/sf cutoff (cutoff2)
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pair_style lj/cut/dipole/long cutoff (cutoff2)
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pair_style lj/long/dipole/long flag_lj flag_coul cutoff (cutoff2) :pre
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cutoff = global cutoff LJ (and Coulombic if only 1 arg) (distance units) :ulb,l
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cutoff2 = global cutoff for Coulombic and dipole (optional) (distance units) :l
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flag_lj = {long} or {cut} or {off} :l
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{long} = use long-range damping on dispersion 1/r^6 term
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{cut} = use a cutoff on dispersion 1/r^6 term
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{off} = omit disperion 1/r^6 term entirely :pre
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flag_coul = {long} or {off} :l
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{long} = use long-range damping on Coulombic 1/r and point-dipole terms
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{off} = omit Coulombic and point-dipole terms entirely :pre
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:ule
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[Examples:]
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pair_style lj/cut/dipole/cut 10.0
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pair_coeff * * 1.0 1.0
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pair_coeff 2 3 1.0 1.0 2.5 4.0 :pre
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pair_style lj/sf/dipole/sf 9.0
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pair_coeff * * 1.0 1.0
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pair_coeff 2 3 1.0 1.0 2.5 4.0 scale 0.5
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pair_coeff 2 3 1.0 1.0 2.5 4.0 :pre
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pair_style lj/cut/dipole/long 10.0
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pair_coeff * * 1.0 1.0
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pair_coeff 2 3 1.0 1.0 2.5 4.0 :pre
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pair_style lj/long/dipole/long long long 3.5 10.0
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pair_coeff * * 1.0 1.0
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pair_coeff 2 3 1.0 1.0 2.5 4.0 :pre
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[Description:]
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Style {lj/cut/dipole/cut} computes interactions between pairs of particles
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that each have a charge and/or a point dipole moment. In addition to
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the usual Lennard-Jones interaction between the particles (Elj) the
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charge-charge (Eqq), charge-dipole (Eqp), and dipole-dipole (Epp)
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interactions are computed by these formulas for the energy (E), force
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(F), and torque (T) between particles I and J.
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:c,image(Eqs/pair_dipole.jpg)
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where qi and qj are the charges on the two particles, pi and pj are
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the dipole moment vectors of the two particles, r is their separation
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distance, and the vector r = Ri - Rj is the separation vector between
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the two particles. Note that Eqq and Fqq are simply Coulombic energy
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and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
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torques do not act symmetrically. These formulas are discussed in
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"(Allen)"_#Allen2 and in "(Toukmaji)"_#Toukmaji2.
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Also note, that in the code, all of these terms (except Elj) have a
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C/epsilon prefactor, the same as the Coulombic term in the LJ +
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Coulombic pair styles discussed "here"_pair_lj.html. C is an
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energy-conversion constant and epsilon is the dielectric constant
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which can be set by the "dielectric"_dielectric.html command. The
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same is true of the equations that follow for other dipole pair
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styles.
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Style {lj/sf/dipole/sf} computes "shifted-force" interactions between
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pairs of particles that each have a charge and/or a point dipole
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moment. In general, a shifted-force potential is a (slightly) modified
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potential containing extra terms that make both the energy and its
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derivative go to zero at the cutoff distance; this removes
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(cutoff-related) problems in energy conservation and any numerical
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instability in the equations of motion "(Allen)"_#Allen2. Shifted-force
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interactions for the Lennard-Jones (E_LJ), charge-charge (Eqq),
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charge-dipole (Eqp), dipole-charge (Epq) and dipole-dipole (Epp)
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potentials are computed by these formulas for the energy (E), force
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(F), and torque (T) between particles I and J:
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:c,image(Eqs/pair_dipole_sf.jpg)
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:c,image(Eqs/pair_dipole_sf2.jpg)
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where epsilon and sigma are the standard LJ parameters, r_c is the
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cutoff, qi and qj are the charges on the two particles, pi and pj are
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the dipole moment vectors of the two particles, r is their separation
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distance, and the vector r = Ri - Rj is the separation vector between
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the two particles. Note that Eqq and Fqq are simply Coulombic energy
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and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
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torques do not act symmetrically. The shifted-force formula for the
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Lennard-Jones potential is reported in "(Stoddard)"_#Stoddard. The
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original (non-shifted) formulas for the electrostatic potentials,
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forces and torques can be found in "(Price)"_#Price2. The shifted-force
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electrostatic potentials have been obtained by applying equation 5.13
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of "(Allen)"_#Allen2. The formulas for the corresponding forces and
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torques have been obtained by applying the 'chain rule' as in appendix
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C.3 of "(Allen)"_#Allen2.
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If one cutoff is specified in the pair_style command, it is used for
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both the LJ and Coulombic (q,p) terms. If two cutoffs are specified,
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they are used as cutoffs for the LJ and Coulombic (q,p) terms
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respectively. This pair style also supports an optional {scale} keyword
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as part of a pair_coeff statement, where the interactions can be
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scaled according to this factor. This scale factor is also made available
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for use with fix adapt.
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Style {lj/cut/dipole/long} computes long-range point-dipole
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interactions as discussed in "(Toukmaji)"_#Toukmaji2. Dipole-dipole,
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dipole-charge, and charge-charge interactions are all supported, along
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with the standard 12/6 Lennard-Jones interactions, which are computed
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with a cutoff. A "kspace_style"_kspace_style.html must be defined to
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use this pair style. Currently, only "kspace_style
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ewald/disp"_kspace_style.html support long-range point-dipole
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interactions.
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Style {lj/long/dipole/long} also computes point-dipole interactions as
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discussed in "(Toukmaji)"_#Toukmaji2. Long-range dipole-dipole,
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dipole-charge, and charge-charge interactions are all supported, along
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with the standard 12/6 Lennard-Jones interactions. LJ interactions
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can be cutoff or long-ranged.
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For style {lj/long/dipole/long}, if {flag_lj} is set to {long}, no
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cutoff is used on the LJ 1/r^6 dispersion term. The long-range
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portion is calculated by using the "kspace_style
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ewald_disp"_kspace_style.html command. The specified LJ cutoff then
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determines which portion of the LJ interactions are computed directly
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by the pair potential versus which part is computed in reciprocal
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space via the Kspace style. If {flag_lj} is set to {cut}, the LJ
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interactions are simply cutoff, as with "pair_style
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lj/cut"_pair_lj.html. If {flag_lj} is set to {off}, LJ interactions
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are not computed at all.
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If {flag_coul} is set to {long}, no cutoff is used on the Coulombic or
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dipole interactions. The long-range portion is calculated by using
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{ewald_disp} of the "kspace_style"_kspace_style.html command. If
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{flag_coul} is set to {off}, Coulombic and dipole interactions are not
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computed at all.
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Atoms with dipole moments should be integrated using the "fix
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nve/sphere update dipole"_fix_nve_sphere.html or the "fix
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nvt/sphere update dipole"_fix_nvt_sphere.html command to rotate the
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dipole moments. The {omega} option on the "fix
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langevin"_fix_langevin.html command can be used to thermostat the
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rotational motion. The "compute temp/sphere"_compute_temp_sphere.html
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command can be used to monitor the temperature, since it includes
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rotational degrees of freedom. The "atom_style
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hybrid dipole sphere"_atom_style.html command should be used since
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it defines the point dipoles and their rotational state.
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The magnitude and orientation of the dipole moment for each particle
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can be defined by the "set"_set.html command or in the "Atoms" section
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of the data file read in by the "read_data"_read_data.html command.
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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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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.
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:line
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Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed on the "Speed packages"_Speed_packages.html doc
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page. 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 GPU, USER-INTEL, KOKKOS,
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USER-OMP and OPT packages, respectively. They are only enabled if
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LAMMPS was built with those packages. See the "Build
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package"_Build_package.html doc page 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"_Run_options.html when you invoke LAMMPS, or you can use the
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"suffix"_suffix.html command in your input script.
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See the "Speed packages"_Speed_packages.html doc page for more
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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 distances for this pair style can be mixed. The default
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mix value is {geometric}. See the "pair_modify" command for details.
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For atom type pairs I,J and I != J, the A, sigma, d1, and d2
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coefficients and cutoff distance for this pair style can be mixed. A
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is an energy value mixed like a LJ epsilon. D1 and d2 are distance
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values and are mixed like sigma. The default mix value is
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{geometric}. See the "pair_modify" command for details.
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This pair style does not support the "pair_modify"_pair_modify.html
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shift option for the energy of the Lennard-Jones portion of the pair
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interaction; such energy goes to zero at the cutoff by construction.
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The "pair_modify"_pair_modify.html table option is not relevant
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for this pair style.
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This pair style does not support the "pair_modify"_pair_modify.html
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tail option for adding long-range tail corrections to energy and
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pressure.
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This pair style writes its information to "binary restart
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files"_restart.html, so pair_style and pair_coeff commands do not need
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to be specified in an input script that reads a restart file.
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This pair style can only be used via the {pair} keyword of the
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"run_style respa"_run_style.html command. It does not support the
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{inner}, {middle}, {outer} keywords.
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[Restrictions:]
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The {lj/cut/dipole/cut}, {lj/cut/dipole/long}, and
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{lj/long/dipole/long} styles are part of the DIPOLE package. They are
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only enabled if LAMMPS was built with that package. See the "Build
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package"_Build_package.html doc page for more info.
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The {lj/sf/dipole/sf} style is part of the USER-MISC package. It is
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only enabled if LAMMPS was built with that package. See the "Build
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package"_Build_package.html doc page for more info.
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Using dipole pair styles with {electron} "units"_units.html is not
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currently supported.
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[Related commands:]
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"pair_coeff"_pair_coeff.html, "set"_set.html, "read_data"_read_data.html,
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"fix nve/sphere"_fix_nve_sphere.html, "fix nvt/sphere"_fix_nvt_sphere.html
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[Default:] none
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:line
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:link(Allen2)
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[(Allen)] Allen and Tildesley, Computer Simulation of Liquids,
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Clarendon Press, Oxford, 1987.
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:link(Toukmaji2)
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[(Toukmaji)] Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113,
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10913 (2000).
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:link(Stoddard)
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[(Stoddard)] Stoddard and Ford, Phys Rev A, 8, 1504 (1973).
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:link(Price2)
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[(Price)] Price, Stone and Alderton, Mol Phys, 52, 987 (1984).
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