Cluster Analysis
Group atoms into clusters of atoms connected by neighbor bonds within a cutoff, and measure each cluster's size, center and radius of gyration.
Cluster Analysis splits the atoms into connected clusters: two atoms belong to the same cluster when a chain of neighbor bonds, each shorter than the cutoff, links them. Use it to find precipitates, nanoparticles, voids filled by other species, fragments after fracture, or the largest connected network in a sample.
| Key | Version | Builds |
|---|---|---|
cluster-analysis | 2.1.1 | Linux, macOS, Windows, browser |
How it works
The plugin finds every pair of atoms closer than the cutoff, across periodic boundaries, and labels the connected components of that neighbor graph. Clusters are numbered from 1. Optionally it unwraps each cluster's coordinates across the periodic boundaries so it is spatially contiguous, then computes each cluster's center (equal weights per atom) and its gyration tensor and radius of gyration.
Inputs
- Atom positions and the simulation cell. Every atom in the frame takes part.
Arguments
| Argument | Type | Default | Allowed values | Description |
|---|---|---|---|---|
Cutoff cutoff | number | 3.2 | ≥ 0, step 0.1 | Largest distance at which two atoms are connected, in the frame's length units. |
Sort By Size sort_by_size | boolean | true | Number clusters by size, largest first. | |
Unwrap unwrap | boolean | false | Write each atom's unwrapped position inside its cluster. | |
Centers Of Mass centers_of_mass | boolean | false | Compute each cluster's center. | |
Radius Of Gyration radius_of_gyration | boolean | false | Compute each cluster's radius of gyration and gyration tensor. |
Turning Sort By Size off has no effect in version 2.1.1. VOLT passes a boolean argument to this plugin only when it is on, and the program sorts unless told otherwise, so clusters are always sorted by size.
Outputs
| Exposure | What you get |
|---|---|
| Cluster Analysis | A listing with the atom count, the number of clusters, the largest cluster's size and whether a zero-weight cluster exists, and a clusters sub-listing: cluster_id, size, and when computed center, radius_of_gyration and gyration_tensor (six components). |
| Cluster Model | A listing, and a 3D model of the atoms grouped by cluster (Cluster_1, Cluster_2, …). |
The per-atom table has cluster_id, and pos_unwrapped when Unwrap is on.
Reference
Distance-based cluster analysis is connected-component labeling of the cutoff neighbor graph, and has no single primary reference.
Voronoi Analysis
Build the Voronoi cell of each atom to get its volume, its topological coordination number, the shape of its cell's faces and its cavity radius.
Atomic Strain
Compute each atom's local deformation gradient and strain relative to a reference frame, with the von Mises shear strain, the volumetric strain and D²min.