compute property/local command¶
compute ID group-ID property/local attribute1 attribute2 ... keyword args ...
ID, group-ID are documented in compute command
property/local = style name of this compute command
one or more attributes of the same type (neighbor, pair, bond, angle, dihedral, or improper) may be appended
possible attributes = natom1, natom2, ntype1, ntype2, patom1, patom2, ptype1, ptype2, batom1, batom2, btype, aatom1, aatom2, aatom3, atype, datom1, datom2, datom3, datom4, dtype, iatom1, iatom2, iatom3, iatom4, itype
natom1, natom2 = store IDs of 2 atoms in each pair (within neighbor cutoff) ntype1, ntype2 = store types of 2 atoms in each pair (within neighbor cutoff)
patom1, patom2 = store IDs of 2 atoms in each pair (within force cutoff) ptype1, ptype2 = store types of 2 atoms in each pair (within force cutoff)
batom1, batom2 = store IDs of 2 atoms in each bond btype = store bond type of each bond
aatom1, aatom2, aatom3 = store IDs of 3 atoms in each angle atype = store angle type of each angle
datom1, datom2, datom3, datom4 = store IDs of 4 atoms in each dihedral dtype = store dihedral type of each dihedral
iatom1, iatom2, iatom3, iatom4 = store IDs of 4 atoms in each improper itype = store improper type of each improper
zero or more keyword/arg pairs may be appended
keyword = cutoff
cutoff arg = type or radius
compute 1 all property/local btype batom1 batom2 compute 1 all property/local atype aatom2
Define a computation that stores the specified attributes as local data so it can be accessed by other output commands. If the input attributes refer to bond information, then the number of datums generated, aggregated across all processors, equals the number of bonds in the system. Ditto for pairs, angles, etc.
If multiple attributes are specified then they must all generate the same amount of information, so that the resulting local array has the same number of rows for each column. This means that only bond attributes can be specified together, or angle attributes, etc. Bond and angle attributes cannot be mixed in the same compute property/local command.
If the inputs are pair attributes, the local data is generated by looping over the pairwise neighbor list. Info about an individual pairwise interaction will only be included if both atoms in the pair are in the specified compute group. For natom1 and natom2, all atom pairs in the neighbor list are considered (out to the neighbor cutoff = force cutoff + neighbor skin). For patom1 and patom2, the distance between the atoms must be less than the force cutoff distance for that pair to be included, as defined by the pair_style and pair_coeff commands.
The optional cutoff keyword determines how the force cutoff distance for an interaction is determined for the patom1 and patom2 attributes. For the default setting of type, the pairwise cutoff defined by the pair_style command for the types of the two atoms is used. For the radius setting, the sum of the radii of the two particles is used as a cutoff. For example, this is appropriate for granular particles which only interact when they are overlapping, as computed by granular pair styles. Note that if a granular model defines atom types such that all particles of a specific type are monodisperse (same diameter), then the two settings are effectively identical.
If the inputs are bond, angle, etc attributes, the local data is generated by looping over all the atoms owned on a processor and extracting bond, angle, etc info. For bonds, info about an individual bond will only be included if both atoms in the bond are in the specified compute group. Likewise for angles, dihedrals, etc.
For bonds and angles, a bonds/angles that have been broken by setting their bond/angle type to 0 will not be included. Bonds/angles that have been turned off (see the fix shake or delete_bonds commands) by setting their bond/angle type negative are written into the file. This is consistent with the compute bond/local and compute angle/local commands
Note that as atoms migrate from processor to processor, there will be no consistent ordering of the entries within the local vector or array from one timestep to the next. The only consistency that is guaranteed is that the ordering on a particular timestep will be the same for local vectors or arrays generated by other compute commands. For example, output from the compute bond/local command can be combined with bond atom indices from this command and output by the dump local command in a consistent way.
The natom1 and natom2 or patom1 and patom2 attributes refer to the atom IDs of the 2 atoms in each pairwise interaction computed by the pair_style command. The ntype1 and ntype2 or ptype1 and ptype2 attributes refer to the atom types of the 2 atoms in each pairwise interaction.
For pairs, if two atoms \(I,J\) are involved in 1–2, 1–3, 1–4 interactions within the molecular topology, their pairwise interaction may be turned off, and thus they may not appear in the neighbor list, and will not be part of the local data created by this command. More specifically, this may be true of \(I,J\) pairs with a weighting factor of 0.0; pairs with a non-zero weighting factor are included. The weighting factors for 1–2, 1–3, and 1–4 pairwise interactions are set by the special_bonds command.
The batom1 and batom2 attributes refer to the atom IDs of the 2 atoms in each bond. The btype attribute refers to the type of the bond, from 1 to Nbtypes = # of bond types. The number of bond types is defined in the data file read by the read_data command.
This compute calculates a local vector or local array depending on the number of input values. The length of the vector or number of rows in the array is the number of bonds, angles, etc. If a single input is specified, a local vector is produced. If two or more inputs are specified, a local array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command that uses local values from a compute as input. See the Howto output page for an overview of LAMMPS output options.
The vector or array values will be integers that correspond to the specified attribute.
The keyword default is cutoff = type.