Identify Diamond Structure
Find cubic and hexagonal diamond atoms with a second-neighbor common neighbor analysis, and label the atoms next to them.
Identify Diamond Structure finds atoms in cubic diamond and hexagonal diamond (lonsdaleite) environments, the structures of Si, Ge and C. It also labels the first and second neighbors of those atoms, so atoms at surfaces, stacking faults and dislocation cores show up as next to diamond instead of plain OTHER. Methods built for close-packed metals, such as Ackland-Jones, see a diamond crystal as OTHER.
| Key | Version | Builds |
|---|---|---|
identify-diamond | 1.1.1 | Linux, macOS, Windows, browser |
How it works
For each atom, the plugin takes its 4 nearest neighbors and, through them, the 12 second neighbors. In a perfect diamond lattice those 12 atoms form an FCC (cubic diamond) or HCP (hexagonal diamond) shell, so the plugin runs common neighbor analysis on them: 12 × (4,2,1) is cubic diamond, 6 × (4,2,1) + 6 × (4,2,2) is hexagonal diamond. It then marks the unclassified nearest neighbors of diamond atoms as first-neighbor atoms, and the unclassified neighbors of those as second-neighbor atoms.
Inputs
- Atom positions and the simulation cell.
Arguments
This plugin has no arguments.
Outputs
| Exposure | What you get |
|---|---|
| Diamond Structure | A listing, and a 3D model of the atoms colored by structure. |
| Diamond Summary | The frame's totals: atoms, and atoms per structure. Stored with the analysis. No listing. |
The workflow declares one per-atom property, structure_type (Structure Type):
| Value | Structure |
|---|---|
0 | OTHER |
5 | CUBIC_DIAMOND |
6 | HEX_DIAMOND |
9 | CUBIC_DIAMOND_FIRST_NEIGH |
10 | CUBIC_DIAMOND_SECOND_NEIGH |
11 | HEX_DIAMOND_FIRST_NEIGH |
12 | HEX_DIAMOND_SECOND_NEIGH |
Notes
- For dislocation analysis in a diamond crystal, run Polyhedral Template Matching or Adaptive Common Neighbor Analysis with Crystal Structure set to cubic diamond: they share the cluster tables OpenDXA needs, this plugin doesn't.
Reference
E. Maras, O. Trushin, A. Stukowski, T. Ala-Nissila, H. Jónsson, "Global transition path search for dislocation formation in Ge on Si(001)", Comput. Phys. Commun. 205, 13 (2016).
Ackland-Jones Analysis
Classify FCC, HCP, BCC and icosahedral atoms from the distribution of bond angles to their nearest neighbors, with no cutoff to set.
Chill+ Ice & Hydrate Classifier
Classify water molecules as hexagonal ice, cubic ice, interfacial ice, clathrate hydrate, interfacial hydrate or liquid with the CHILL+ algorithm.