forked from lijiext/lammps
84 lines
3.2 KiB
Plaintext
84 lines
3.2 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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neighbor command :h3
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[Syntax:]
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neighbor skin style :pre
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skin = extra distance beyond force cutoff (distance units)
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style = {bin} or {nsq} or {multi} :ul
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[Examples:]
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neighbor 0.3 bin
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neighbor 2.0 nsq :pre
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[Description:]
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This command sets parameters that affect the building of pairwise
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neighbor lists. All atom pairs within a neighbor cutoff distance
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equal to the their force cutoff plus the {skin} distance are stored in
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the list. Typically, the larger the skin distance, the less often
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neighbor lists need to be built, but more pairs must be checked for
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possible force interactions every timestep. The default value for
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{skin} depends on the choice of units for the simulation; see the
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default values below.
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The {skin} distance is also used to determine how often atoms migrate
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to new processors if the {check} option of the
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"neigh_modify"_neigh_modify.html command is set to {yes}. Atoms are
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migrated (communicated) to new processors on the same timestep that
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neighbor lists are re-built.
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The {style} value selects what algorithm is used to build the list.
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The {bin} style creates the list by binning which is an operation that
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scales linearly with N/P, the number of atoms per processor where N =
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total number of atoms and P = number of processors. It is almost
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always faster than the {nsq} style which scales as (N/P)^2. For
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unsolvated small molecules in a non-periodic box, the {nsq} choice can
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sometimes be faster. Either style should give the same answers.
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The {multi} style is a modified binning algorithm that is useful for
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systems with a wide range of cutoff distances, e.g. due to different
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size particles. For the {bin} style, the bin size is set to 1/2 of
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the largest cutoff distance between any pair of atom types and a
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single set of bins is defined to search over for all atom types. This
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can be inefficient if one pair of types has a very long cutoff, but
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other type pairs have a much shorter cutoff. For style {multi} the
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bin size is set to 1/2 of the shortest cutoff distance and multiple
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sets of bins are defined to search over for different atom types.
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This imposes some extra setup overhead, but the searches themselves
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may be much faster for the short-cutoff cases. See the "communicate
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multi"_communicate.html command for a communication option option that
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may also be beneficial for simulations of this kind.
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The "neigh_modify"_neigh_modify.html command has additional options
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that control how often neighbor lists are built and which pairs are
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stored in the list.
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When a run is finished, counts of the number of neighbors stored in
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the pairwise list and the number of times neighbor lists were built
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are printed to the screen and log file. See "this
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section"_Section_start.html#2_7 for details.
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[Restrictions:] none
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[Related commands:]
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"neigh_modify"_neigh_modify.html, "units"_units.html,
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"communicate"_communicate.html
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[Default:]
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0.3 bin for units = lj, skin = 0.3 sigma
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2.0 bin for units = real or metal, skin = 2.0 Angstroms
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0.001 bin for units = si, skin = 0.001 meters = 1.0 mm
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0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm :all(b)
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