Coordination Analysis
Count each atom's neighbors within a cutoff and compute the radial distribution function of the frame, with partial histograms per type pair.
Coordination Analysis counts the neighbors of each atom within a cutoff radius and computes the radial distribution function g(r) of the frame up to that radius. Use it to spot under-coordinated atoms at surfaces and voids, over-coordinated atoms at interstitials, to compare the short-range order of liquid, amorphous and crystalline states, or as a feature source for MultiSOM.
| Key | Version | Builds |
|---|---|---|
coordination-analysis | 2.1.1 | Linux, macOS, Windows, browser |
How it works
The coordination number of an atom is the number of other atoms closer than the cutoff, using the minimum image across periodic boundaries. The RDF histograms all pair distances up to the cutoff into the requested number of bins and normalizes them by the ideal-gas density, so g(r) tends to 1 in a uniform liquid. When the frame has atom types, the plugin also writes a pair-distance histogram for each pair of types.
Inputs
- Atom positions and the simulation cell.
- Atom types, for the partial histograms.
Arguments
| Argument | Type | Default | Allowed values | Description |
|---|---|---|---|---|
Cutoff cutoff | number | 3.2 | ≥ 0, step 0.1 | Neighbor cutoff radius, in the frame's length units. It is also the largest r of the RDF. For coordination, put it in the first minimum of g(r). |
RDF Bins rdf_bins | number | 500 | ≥ 1, step 1 | Number of RDF bins between 0 and the cutoff. |
Outputs
| Exposure | What you get |
|---|---|
| Coordination Analysis | A listing with the cutoff, bin count, atoms, and minimum, maximum and mean coordination, and an rdf sub-listing of r and g_r. |
| Coordination Model | A listing, and a 3D model of the atoms grouped by coordination number (Coordination_12, …) and colored on a scale from the lowest to the highest value. |
| RDF Chart | A line chart of g(r) against r. |
| Partial RDF Histogram | One row per type pair and bin: pair_type, bin_center (Å) and bin_count. Stored with the analysis. No listing. Written only when the frame has types. |
The workflow declares the per-atom property coordination (Coordination number).
Reference
The coordination number and the radial distribution function are textbook quantities; see M. P. Allen, D. J. Tildesley, Computer Simulation of Liquids, 2nd ed., Oxford University Press (2017).
Chill+ Ice & Hydrate Classifier
Classify water molecules as hexagonal ice, cubic ice, interfacial ice, clathrate hydrate, interfacial hydrate or liquid with the CHILL+ algorithm.
Centrosymmetry Parameter
Measure how far each atom's neighbor shell is from centrosymmetric, to find dislocation cores, stacking faults and surfaces in centrosymmetric crystals.