Plugins
Structure Identification
Crystal structure identification algorithms for atomistic simulations.
Overview
Structure Identification classifies atoms by their local structural environment to detect BCC, FCC, HCP, diamond cubic, and other crystal structures. It helps identify phase boundaries, defects, and amorphous regions in simulation data.
Parameters
| Parameter | Type | Default | Description |
|---|---|---|---|
mode | string | CNA | Identification algorithm to use. Options: CNA, PTM, DIAMOND. |
rmsd | float | 0.1 | RMSD threshold for PTM classification (only applies when using PTM). |
Output
{outputBase}_structure_identification.msgpack
type Vec3 = [float, float, float];
// [x, y, z, w]
type Quaternion = [float, float, float, float];
// CNA / DIAMOND mode
interface PerAtomProperties {
id: int;
structure_type: int;
structure_name: string;
pos: Vec3;
}
// PTM mode
interface PTMPerAtomProperties {
id: int;
structure_type: int;
pos: Vec3;
correspondence: int;
orientation: Quaternion;
}
interface StructureIdentificationOutput {
main_listing: {
total_atoms: int;
analysis_method: string;
// For each detected structure type, a pair of keys is added dynamically:
// `{type}_count`: int
// `{type}_percentage`: float
[key: `${string}_count`]: int;
[key: `${string}_percentage`]: float;
total_identified: int;
total_unidentified: int;
identification_rate: float;
unique_structure_types: int;
};
"per-atom-properties": PerAtomProperties[] | PTMPerAtomProperties[];
}