compute coord/atom command¶
Accelerator Variants: coord/atom/kk
compute ID group-ID coord/atom cstyle args ...
ID, group-ID are documented in compute command
coord/atom = style name of this compute command
cstyle = cutoff or orientorder
cutoff args = cutoff [group group2-ID] typeN cutoff = distance within which to count coordination neighbors (distance units) group group2-ID = select group-ID to restrict which atoms to consider for coordination number (optional) typeN = atom type for Nth coordination count (see asterisk form below) orientorder args = orientorderID threshold orientorderID = ID of an orientorder/atom compute threshold = minimum value of the product of two "connected" atoms
compute 1 all coord/atom cutoff 2.0 compute 1 all coord/atom cutoff 6.0 1 2 compute 1 all coord/atom cutoff 6.0 2*4 5*8 * compute 1 solute coord/atom cutoff 2.0 group solvent compute 1 all coord/atom orientorder 2 0.5
This compute performs calculations between neighboring atoms to determine a coordination value. The specific calculation and the meaning of the resulting value depend on the cstyle keyword used.
The cutoff cstyle calculates one or more traditional coordination numbers for each atom. A coordination number is defined as the number of neighbor atoms with specified atom type(s), and optionally within the specified group, that are within the specified cutoff distance from the central atom. The compute group selects only the central atoms; all neighboring atoms, unless selected by type, type range, or group option, are included in the coordination number tally.
The optional group keyword allows to specify from which group atoms contribute to the coordination number. Default setting is group ‘all’.
The typeN keywords allow specification of 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 second 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 orientorder cstyle calculates the number of “connected” neighbor atoms J around each central atom I. For this cstyle, connected is defined by the orientational order parameter calculated by the compute orientorder/atom command. This cstyle thus allows one to apply the ten Wolde’s criterion to identify crystal-like atoms in a system, as discussed in ten Wolde.
The ID of the previously specified compute orientorder/atom command is specified as orientorderID. The compute must invoke its components option to calculate components of the Ybar_lm vector for each atoms, as described in its documentation. Note that orientorder/atom compute defines its own criteria for identifying neighboring atoms. If the scalar product (Ybar_lm(i),*Ybar_lm(j)*), calculated by the orientorder/atom compute is larger than the specified threshold, then I and J are connected, and the coordination value of I is incremented by one.
For all cstyle settings, all coordination values 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.
If you have a bonded system, then the settings of special_bonds command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. 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.
Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the Accelerator packages page. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, INTEL, KOKKOS, OPENMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the Build package page for more info.
You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
See the Accelerator packages page for more instructions on how to use the accelerated styles effectively.
For cstyle cutoff, this compute can calculate a per-atom vector or array. If single type1 keyword is specified (or if none are specified), this compute calculates a per-atom vector. If multiple typeN keywords are specified, this compute calculates a per-atom array, with N columns.
For cstyle orientorder, this compute calculates a per-atom vector.
These values can be accessed by any command that uses per-atom values from a compute as input. See the Howto output doc page for an overview of LAMMPS output options.
The per-atom vector or array values will be a number >= 0.0, as explained above.
group = all
(tenWolde) P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).