compute coord/atom command¶

Syntax¶

compute ID group-ID coord/atom general_keyword general_values cutoff keyword value

ID, group-ID are documented in compute command
coord/atom = style name of this compute command
general_keywords general_values are documented in compute
cutoff = distance within which to count coordination neighbors (distance units)
zero or more keyword/value pairs may be appended to args
keyword = mix or type1, type2, ...

mix value = yes or no
  no = count all neighbors
  yes = count only neighbors that have different atom types

typeN = atom type for Nth coordination count (see asterisk form below)

Examples¶

compute 1 all coord/atom 0.003 mix yes
compute 1 all coord/atom 2.0
compute 1 all coord/atom 6.0 1 2
compute 1 all coord/atom 6.0 2*4 5*8 *

Description¶

Define a computation that calculates one or more coordination numbers for each atom in a group.

A coordination number is defined as the number of neighbor atoms with specified atom type(s) that are within the specified cutoff distance from the central atom. Atoms not in the group are included in a coordination number of atoms in the group.

This compute is one of the three different ways to compute a coordination number. The following table gives an overview over the different options:

style	contact counted condition	formula
compute contact/atom	particles touch each other	r < r_i + r_j
compute contact/atom/gran	particles interact with each other	f_ij > 0
compute coord/atom	particles are in the vicinity of each other	r < cutoff

The typeN keywords allow you to specify which atom types contribute to each coordination number. One coordination number is computed for each of the typeN keywords listed. If no typeN keywords are listed, a single coordination number is calculated, which includes atoms of all types (same as the “*” format, see below).

The typeN keywords can be specified in one of two ways. An explicit numeric value can be used, as in the 2nd example above. Or a wild-card asterisk can be used to specify a range of atom types. This takes the form “*” or “n” or “n” or “m*n”. If N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive).

The value of all coordination numbers will be 0.0 for atoms not in the specified compute group.

The neighbor list needed to compute this quantity is constructed each time the calculation is performed (i.e. each time a snapshot of atoms is dumped). Thus it can be inefficient to compute/dump this quantity too frequently.

Keyword mix controls if all neighbors are counted or if only neighbors with different atom types are counted. The latter can be useful to quantify mixture of different species.

Warning

If you have a bonded system, then the settings of special_bonds command can remove pairwise interactions between atoms in the same bond. This is the default setting for the special_bonds command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses the neighbor list, it also means those pairs will not be included in the coordination count. One way to get around this, is to write a dump file, and use the rerun command to compute the coordination for snapshots in the dump file. The rerun script can use a special_bonds command that includes all pairs in the neighbor list.

Output info¶

If single type1 keyword is specified (or if none are specified), or the mix keyword is used, this compute calculates a per-atom vector. If multiple typeN keywords are specified, this compute calculates a per-atom array, with N columns. These values can be accessed by any command that uses per-atom values from a compute as input. See Section_howto 15 for an overview of LIGGGHTS(R)-PUBLIC output options.

The per-atom vector or array values will be a number >= 0.0, as explained above.

Restrictions¶

none