Plugins
Structure Identification
Classify local atomic environments and provide the structural labels many other plugins build on.
Parameters
| Parameter | Type | Default | Description |
|---|---|---|---|
mode | string | CNA | Identification algorithm. Options exposed in the product are CNA, PTM, and DIAMOND. |
rmsd | float | 0.1 | RMSD threshold for PTM classification. Only applies in PTM mode. |
Output
{outputBase}_structure_identification.msgpack
type Vec3 = [float, float, float];
type Quaternion = [float, float, float, float];
interface PerAtomProperties {
id: int;
structure_type: int;
structure_name: string;
pos: Vec3;
}
interface PTMPerAtomProperties {
id: int;
structure_type: int;
pos: Vec3;
correspondence: int;
orientation: Quaternion;
}
interface StructureIdentificationOutput {
main_listing: {
total_atoms: int;
analysis_method: string;
[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[];
}{outputBase}_atoms.msgpack
Atoms grouped by structure name for visualization and downstream use.
See Also
- OpenDXA — dislocation analysis built on local structure work
- Grain Segmentation — grain grouping driven by PTM-related orientation data
- Centrosymmetry Parameter — complementary scalar defect highlighting