\(\renewcommand{\AA}{\text{Å}}\)

compute composition/atom command

Accelerator Variants: composition/atom/kk

Syntax

compute ID group-ID composition/atom keyword values ...

  • ID, group-ID are documented in compute command

  • composition/atom = style name of this compute command

  • one or more keyword/value pairs may be appended

    keyword = cutoff
  cutoff value = distance cutoff

Examples

compute 1 all composition/atom

compute 1 all composition/atom cutoff 9.0
comm_modify cutoff 9.0

Description

New in version TBD.

Define a computation that calculates a local composition vector for each atom. For a central atom with \(M\) neighbors within the neighbor cutoff sphere, composition is defined as the number of atoms of a given type (including the central atom) divided by (\(M+1\)). For a given central atom, the sum of all compositions equals one.

Note

This compute uses the number of atom types, not chemical species, assigned in pair_coeff command. If an interatomic potential has two species (i.e., Cu and Ni) assigned to four different atom types in pair_coeff (i.e., ‘Cu Cu Ni Ni’), the compute will output four fractional values. In those cases, the user may desire an extra calculation step to consolidate per-type fractions into per-species fractions. This calculation can be conducted within LAMMPS using another compute such as compute reduce, an atom-style variable command, or as a post-processing step.

The optional keyword cutoff defines the distance cutoff used when searching for neighbors. The default value is the cutoff specified by the pair style. If no pair style is defined, then a cutoff must be defined using this keyword. If the specified cutoff is larger than that of the pair_style plus neighbor skin (or no pair style is defined), the comm_modify cutoff option must also be set to match that of the cutoff keyword.

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.

Note

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 compute uses the neighbor list, it also means those pairs will not be included in the order parameter. This difficulty can be circumvented by writing a dump file, and using the rerun command to compute the order parameter 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

This compute calculates a per-atom array with \(1 + N\) columns, where \(N\) is the number of atom types. The first column is a count of the number of atoms used to calculate composition (including the central atom), and each subsequent column indicates the fraction of that atom type within the cutoff sphere.

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.

Restrictions

This compute is part of the EXTRA-COMPUTE package. It is only enabled if LAMMPS was built with that package. See the Build package page for more info.

Default

The option defaults are cutoff = pair style cutoff.