2007-05-15 00:14:29 +08:00
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"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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compute coord/atom command :h3
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[Syntax:]
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2012-08-08 23:17:00 +08:00
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compute ID group-ID coord/atom cutoff type1 type2 ... :pre
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2007-05-15 00:14:29 +08:00
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ID, group-ID are documented in "compute"_compute.html command
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2007-05-15 00:21:52 +08:00
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coord/atom = style name of this compute command
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2012-08-08 23:17:00 +08:00
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cutoff = distance within which to count coordination neighbors (distance units)
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typeN = atom type for Nth coordination count (see asterisk form below) :ul
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2007-05-15 00:14:29 +08:00
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[Examples:]
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2012-08-08 23:17:00 +08:00
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compute 1 all coord/atom 2.0
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compute 1 all coord/atom 6.0 1 2
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compute 1 all coord/atom 6.0 2*4 5*8 * :pre
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2007-05-15 00:14:29 +08:00
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[Description:]
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2012-08-08 23:17:00 +08:00
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Define a computation that calculates one or more coordination numbers
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for each atom in a group.
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A coordination number is defined as the number of neighbor atoms with
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specified atom type(s) that are within the specified cutoff distance
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from the central atom. Atoms not in the group are included in a
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coordination number of atoms in the group.
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The {typeN} keywords allow you to specify which atom types contribute
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to each coordination number. One coordination number is computed for
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each of the {typeN} keywords listed. If no {typeN} keywords are
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listed, a single coordination number is calculated, which includes
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atoms of all types (same as the "*" format, see below).
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The {typeN} keywords can be specified in one of two ways. An explicit
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numeric value can be used, as in the 2nd example above. Or a
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wild-card asterisk can be used to specify a range of atom types. This
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takes the form "*" or "*n" or "n*" or "m*n". If N = the number of
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atom types, then an asterisk with no numeric values means all types
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from 1 to N. A leading asterisk means all types from 1 to n
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(inclusive). A trailing asterisk means all types from n to N
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(inclusive). A middle asterisk means all types from m to n
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(inclusive).
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The value of all coordination numbers will be 0.0 for atoms not in the
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2007-11-20 23:37:16 +08:00
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specified compute group.
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2007-05-15 00:14:29 +08:00
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The neighbor list needed to compute this quantity is constructed each
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time the calculation is performed (i.e. each time a snapshot of atoms
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is dumped). Thus it can be inefficient to compute/dump this quantity
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2012-08-08 23:17:00 +08:00
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too frequently.
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2007-05-15 00:14:29 +08:00
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2013-10-30 22:40:51 +08:00
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IMPORTANT NOTE: If you have a bonded system, then the settings of
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"special_bonds"_special_bonds.html command can remove pairwise
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interactions between atoms in the same bond, angle, or dihedral. This
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is the default setting for the "special_bonds"_special_bonds.html
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command, and means those pairwise interactions do not appear in the
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neighbor list. Because this fix uses the neighbor list, it also means
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those pairs will not be included in the coordination count. One way
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to get around this, is to write a dump file, and use the
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"rerun"_rerun.html command to compute the coordination for snapshots
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in the dump file. The rerun script can use a
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"special_bonds"_special_bonds.html command that includes all pairs in
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the neighbor list.
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2008-01-04 08:56:10 +08:00
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[Output info:]
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2012-08-08 23:17:00 +08:00
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If single {type1} keyword is specified (or if none are specified),
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this compute calculates a per-atom vector. If multiple {typeN}
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keywords are specified, this compute calculates a per-atom array, with
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N columns. These values can be accessed by any command that uses
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per-atom values from a compute as input. See "Section_howto
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15"_Section_howto.html#howto_15 for an overview of LAMMPS output
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options.
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2008-01-04 08:56:10 +08:00
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2012-08-08 23:17:00 +08:00
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The per-atom vector or array values will be a number >= 0.0, as
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explained above.
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2010-01-24 07:20:05 +08:00
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2007-05-15 00:14:29 +08:00
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[Restrictions:] none
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2011-03-09 06:23:59 +08:00
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[Related commands:]
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"compute cluster/atom"_compute_cluster_atom.html
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2007-05-15 00:14:29 +08:00
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[Default:] none
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