forked from lijiext/lammps
126 lines
4.9 KiB
Plaintext
126 lines
4.9 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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neigh_modify command :h3
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[Syntax:]
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neigh_modify keyword values ... :pre
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one or more keyword/value pairs may be listed :ulb,l
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keyword = {delay} or {every} or {check} or {exclude} or {page} or {one}
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{delay} value = N
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N = delay building until this many steps since last build
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{every} value = M
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M = build neighbor list every this many steps
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{check} value = {yes} or {no}
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{yes} = only build if some atom has moved half the skin distance or more
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{no} = always build on 1st step that {every} and {delay} are satisfied
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{exclude} values:
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type M N
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M,N = exclude if one atom in pair is type M, other is type N
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group group1-ID group2-ID
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group1-ID,group2-ID = exclude if one atom is in 1st group, other in 2nd
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molecule group-ID
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groupname = exclude if both atoms are in the same molecule and in the same group
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none
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delete all exclude settings
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{page} value = N
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N = number of pairs stored in a single neighbor page
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{one} value = N
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N = max number of neighbors of one atom :pre
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:ule
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[Examples:]
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neigh_modify every 2 delay 10 check yes page 100000
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neigh_modify exclude type 2 3
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neigh_modify exclude group frozen frozen check no
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neigh_modify exclude group residue1 chain3
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neigh_modify exclude molecule rigid :pre
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[Description:]
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This command sets parameters that affect the pairwise neighbor list.
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The {every}, {delay}, and {check} options affect how often the list is
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built as a simulation runs. The {delay} setting means never build a
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new list until at least N steps after the previous build. The {every}
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setting means build the list every M steps (after the delay has
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passed). If the {check} setting is {no}, the list is built on the 1st
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step that satisfies the {delay} and {every} settings. If the {check}
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setting is {yes}, then the list is only built on a particular step if
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some atom has moved more than half the skin distance (specified in the
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"neighbor"_neighbor.html command) since the last build.
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When the rRESPA integrator is used (see the "run_style"_run_style.html
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command), the {every} and {delay} parameters refer to the longest
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(outermost) timestep.
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The {exclude} option turns off pairwise interactions between certain
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pairs of atoms, by not including them in the neighbor list. These are
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sample scenarios where this is useful:
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In crack simulations, pairwise interactions can be shut off between 2
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slabs of atoms to effectively create a crack. :ulb,l
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When a large collection of atoms is treated as frozen, interactions
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between those atoms can be turned off to save needless
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computation. E.g. Using the "fix setforce"_fix_setforce.html command
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to freeze a wall or portion of a bio-molecule. :l
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When one or more rigid bodies are specified, interactions within each
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body can be turned off to save needless computation. See the "fix
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rigid"_fix_rigid.html command for more details. :l,ule
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The {exclude type} option turns off the pairwise interaction if one
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atom is of type M and the other of type N. M can equal N. The
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{exclude group} option turns off the interaction if one atom is in the
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first group and the other is the second. Group1-ID can equal
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group2-ID. The {exclude molecule} option turns off the interaction if
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both atoms are in the specified group and in the same molecule, as
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determined by their molecule ID.
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Each of the exclude options can be specified multiple times. The
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{exclude type} option is the most efficient option to use; it requries
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only a single check, no matter how many times it has been specified.
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The other exclude options are more expensive if specified multiple
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times; they require one check for each time they have been specified.
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Note that the exclude options only affect pairwise interactions; see
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the "delete_bonds"_delete_bonds.html command for information on
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turning off bond interactions.
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The {page} and {one} options affect how memory is allocated for the
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neighbor lists. For most simulations the default settings for these
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options are fine, but if a very large problem is being run or a very
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long cutoff is being used, these parameters can be tuned. The indices
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of neighboring atoms are stored in "pages", which are allocated one
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after another as they fill up. The size of each page is set by the
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{page} value. A new page is allocated when the next atom's neighbors
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could potentially overflow the list. This threshhold is set by the
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{one} value which tells LAMMPS the maximum number of neighbor's one
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atom can have.
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[Restrictions:]
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If the "delay" setting is non-zero, then it must be a multiple of the
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"every" setting.
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The exclude molecule option can only be used with atom styles that
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define molecule IDs.
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[Related commands:]
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"neighbor"_neighbor.html, "delete_bonds"_delete_bonds.html
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[Default:]
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The option defaults are delay = 10, every = 1, check = yes, exclude =
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none, page = 100000, and one = 2000.
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