forked from lijiext/lammps
200 lines
8.3 KiB
Plaintext
200 lines
8.3 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/charmm/coul/charmm command :h3
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pair_style lj/charmm/coul/charmm/cuda command :h3
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pair_style lj/charmm/coul/charmm/omp command :h3
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pair_style lj/charmm/coul/charmm/implicit command :h3
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pair_style lj/charmm/coul/charmm/implicit/cuda command :h3
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pair_style lj/charmm/coul/charmm/implicit/omp command :h3
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pair_style lj/charmm/coul/long command :h3
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pair_style lj/charmm/coul/long/cuda command :h3
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pair_style lj/charmm/coul/long/gpu command :h3
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pair_style lj/charmm/coul/long/intel command :h3
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pair_style lj/charmm/coul/long/opt command :h3
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pair_style lj/charmm/coul/long/omp command :h3
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pair_style lj/charmm/coul/msm command :h3
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pair_style lj/charmm/coul/msm/omp command :h3
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[Syntax:]
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pair_style style args :pre
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style = {lj/charmm/coul/charmm} or {lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long} or {lj/charmm/coul/msm}
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args = list of arguments for a particular style :ul
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{lj/charmm/coul/charmm} args = inner outer (inner2) (outer2)
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inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
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inner2, outer2 = global switching cutoffs for Coulombic (optional)
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{lj/charmm/coul/charmm/implicit} args = inner outer (inner2) (outer2)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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inner2, outer2 = global switching cutoffs for Coulombic (optional)
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{lj/charmm/coul/long} args = inner outer (cutoff)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
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{lj/charmm/coul/msm} args = inner outer (cutoff)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) :pre
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[Examples:]
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pair_style lj/charmm/coul/charmm 8.0 10.0
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pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
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pair_style lj/charmm/coul/charmm/implicit 8.0 10.0
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pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
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pair_style lj/charmm/coul/long 8.0 10.0
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pair_style lj/charmm/coul/long 8.0 10.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
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pair_style lj/charmm/coul/msm 8.0 10.0
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pair_style lj/charmm/coul/msm 8.0 10.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
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[Description:]
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The {lj/charmm} styles compute LJ and Coulombic interactions with an
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additional switching function S(r) that ramps the energy and force
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smoothly to zero between an inner and outer cutoff. It is a widely
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used potential in the "CHARMM"_http://www.scripps.edu/brooks MD code.
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See "(MacKerell)"_#MacKerell for a description of the CHARMM force
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field.
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:c,image(Eqs/pair_charmm.jpg)
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Both the LJ and Coulombic terms require an inner and outer cutoff.
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They can be the same for both formulas or different depending on
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whether 2 or 4 arguments are used in the pair_style command. In each
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case, the inner cutoff distance must be less than the outer cutoff.
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It it typical to make the difference between the 2 cutoffs about 1.0
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Angstrom.
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Style {lj/charmm/coul/charmm/implicit} computes the same formulas as
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style {lj/charmm/coul/charmm} except that an additional 1/r term is
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included in the Coulombic formula. The Coulombic energy thus varies
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as 1/r^2. This is effectively a distance-dependent dielectric term
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which is a simple model for an implicit solvent with additional
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screening. It is designed for use in a simulation of an unsolvated
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biomolecule (no explicit water molecules).
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Styles {lj/charmm/coul/long} and {lj/charmm/coul/msm} compute the same
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formulas as style {lj/charmm/coul/charmm} except that an additional
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damping factor is applied to the Coulombic term, as described for the
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"lj/cut"_pair_lj.html pair styles. Only one Coulombic cutoff is
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specified for {lj/charmm/coul/long} and {lj/charmm/coul/msm}; if only
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2 arguments are used in the pair_style command, then the outer LJ
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cutoff is used as the single Coulombic cutoff.
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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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epsilon_14 (energy units)
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sigma_14 (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 they are specified, they
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are used in the LJ formula between 2 atoms of these types which are
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also first and fourth atoms in any dihedral. No cutoffs are specified
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because this CHARMM force field does not allow varying cutoffs for
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individual atom pairs; all pairs use the global cutoff(s) specified in
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the pair_style command.
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:line
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Styles with a {cuda}, {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 in "Section_accelerate"_Section_accelerate.html
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.
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These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
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KOKKOS, USER-OMP and OPT packages, respectively. They are only
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enabled if LAMMPS was built with those packages. See the "Making
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LAMMPS"_Section_start.html#start_3 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_7 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, sigma, epsilon_14,
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and sigma_14 coefficients for all of the lj/charmm pair styles can be
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mixed. The default mix value is {arithmetic} to coincide with the
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usual settings for the CHARMM force field. See the "pair_modify"
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command for details.
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None of the lj/charmm pair styles support the
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"pair_modify"_pair_modify.html shift option, since the Lennard-Jones
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portion of the pair interaction is smoothed to 0.0 at the cutoff.
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The {lj/charmm/coul/long} style supports the
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"pair_modify"_pair_modify.html table option since it can tabulate the
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short-range portion of the long-range Coulombic interaction.
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None of the lj/charmm pair styles support the
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"pair_modify"_pair_modify.html tail option for adding long-range tail
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corrections to energy and pressure, since the Lennard-Jones portion of
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the pair interaction is smoothed to 0.0 at the cutoff.
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All of the lj/charmm 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/charmm/coul/long pair style supports the use of the {inner},
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{middle}, and {outer} keywords of the "run_style respa"_run_style.html
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command, meaning the pairwise forces can be partitioned by distance at
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different levels of the rRESPA hierarchy. The other styles only
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support the {pair} keyword of run_style respa. See the
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"run_style"_run_style.html command for details.
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:line
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[Restrictions:]
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The {lj/charmm/coul/charmm} and {lj/charmm/coul/charmm/implicit}
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styles are part of the MOLECULE package. The {lj/charmm/coul/long}
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style is part of the KSPACE package. They are only enabled if LAMMPS
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was built with those packages. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info. Note that
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the MOLECULE and KSPACE packages are installed by 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(MacKerell)
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[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
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Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
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