forked from lijiext/lammps
74 lines
2.8 KiB
Plaintext
74 lines
2.8 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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atom_modify command :h3
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[Syntax:]
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atom_modify keyword value ... :pre
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one or more keyword/value pairs may be appended :ulb,l
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keyword = {map} or {first} :l
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{map} value = {array} or {hash}
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{first} value = group-ID = group whose atoms will appear first in internal atom lists :pre
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:ule
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[Examples:]
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atom_modify map hash
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atom_modify first colloid :pre
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[Description:]
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Modify properties of the atom style selected within LAMMPS.
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The {map} keyword determines how atom ID lookup is done for molecular
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problems. Lookups are performed by bond (angle, etc) routines in
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LAMMPS to find the local atom index associated with a global atom ID.
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When the {array} value is used, each processor stores a lookup table
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of length N, where N is the total # of atoms in the system. This is
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the fastest method for most simulations, but a processor can run out
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of memory to store the table for very large simulations. The {hash}
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value uses a hash table to perform the lookups. This method can be
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slightly slower than the {array} method, but its memory cost is
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proportional to N/P on each processor, where P is the total number of
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processors running the simulation.
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The {first} keyword allows a "group"_group.html to be specified whose
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atoms will be maintained as the first atoms in each processor's list
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of owned atoms. This in only useful when the specified group is a
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small fraction of all the atoms, and there are other operations LAMMPS
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is performing that will be sped-up significantly by being able to loop
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over the smaller set of atoms. Otherwise the reordering required by
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this option will be a net slow-down. The "neigh_modify
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include"_neigh_modify.html and "communicate group"_communicate.html
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commands are two examples of commands that require this setting to
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work efficiently. Several "fixes"_fix.html, most notably time
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integration fixes like "fix nve"_fix_nve.html, also take advantage of
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this setting if the group they operate on is the group specified by
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this command.
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Note that because the atom_modify command must be used in an input
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script before a simulation is setup and groups are defined, this means
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the {first} keyword will specify a group that is not yet defined.
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This is OK; LAMMPS will check that the group exists before the first
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simulation is performed.
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[Restrictions:]
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This command must be used before the simulation box is defined by a
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"read_data"_read_data.html or "create_box"_create_box.html command.
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[Related commands:] none
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[Default:]
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By default, atomic (non-molecular) problems do not allocate maps. For
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molecular problems, the option default is map = array. By default, a
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"first" group is not defined.
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