compute rattlers/atom command — LAMMPS documentation

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# compute rattlers/atom command

## Syntax

    compute ID group-ID rattlers/atom cutoff zmin ntries

- ID, group-ID are documented in compute command

- rattlers/atom = style name of this compute command

- cutoff = type or radius

      type = cutoffs determined based on atom types
      radius = cutoffs determined based on atom diameters (atom style sphere)

- zmin = minimum coordination for a non-rattler atom

- ntries = maximum number of iterations to remove rattlers

## Examples

    compute 1 all rattlers/atom type 4 10

## Description

Added in version 7Feb2024.

Define a compute that identifies rattlers in a system. Rattlers are often identified in granular or glassy packings as under-coordinated atoms that do not have the required number of contacts to constrain their translational degrees of freedom. Such atoms are not considered rigid and can often freely rattle around in the system. This compute identifies rattlers which can be helpful for excluding them from analysis or providing extra damping forces to accelerate relaxation processes.

Rattlers are identified using an interactive approach. The coordination number of all atoms is first calculated. The type and radius settings are used to select whether interaction cutoffs are determined by atom types or by the sum of atomic radii (atom style sphere), respectively. Rattlers are then identified as atoms with a coordination number less than zmin and are removed from consideration. Atomic coordination numbers are then recalculated, excluding previously identified rattlers, to identify a new set of rattlers. This process is iterated up to a maximum of ntries or until no new rattlers are identified and the remaining atoms form a stable network of contacts.

In dense homogeneous systems where the average atom coordination number is expected to be larger than zmin, this process usually only takes a few iterations and a value of ntries around ten may be sufficient. In systems with significant heterogeneity or average coordination numbers less than zmin, an appropriate value of ntries depends heavily on the specific system. For instance, a linear chain of N rattler atoms with a zmin of 2 would take N/2 iterations to identify that all the atoms are rattlers.

## Output info

This compute calculates a per-atom vector and a global scalar. The vector designates which atoms are rattlers, indicated by a value 1. Non-rattlers have a value of 0. The global scalar returns the total number of rattlers in the system. See the Howto output 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.

The radius cutoff option requires that atoms store a radius as defined by the atom_style sphere or similar commands.

## Related commands

compute coord/atom compute contact/atom

## Default

none