Grain Segmentation

Overview

Grain Segmentation is best understood as an orientation-based grouping workflow. It uses PTM-derived orientation information to separate crystalline domains that belong to different grains, then reports grain-level properties such as size, centroid, and representative orientation.

This makes it especially useful in polycrystalline systems, coherent-interface problems, and workflows where you want to move from atom-level structure labels to grain-level organization.

Parameters

Parameter	Type	Default	Description
`rmsd`	`float`	`0.1`	RMSD threshold for PTM structure identification.
`minGrainAtomCount`	`int`	`100`	Minimum number of atoms required to keep a grain.
`adoptOrphanAtoms`	`bool`	`true`	Exposed in the interface, but the current implementation does not visibly perform a dedicated orphan-adoption phase.
`handleCoherentInterfaces`	`bool`	`true`	Handle coherent interfaces between compatible structures.
`outputBonds`	`bool`	`false`	Exposed parameter; bond output is not currently surfaced as a documented result file.

Practical notes

This plugin depends strongly on PTM-style orientation information.
It is closer to "separate differently oriented crystalline regions" than to "detect all grain boundaries geometrically."
In addition to grain listings, the implementation also exports grouped atoms data.

Output

`{outputBase}_grains.msgpack`

type Vec3 = [float, float, float];
type Quaternion = [float, float, float, float];

interface Grain {
    id: int;
    size: int;
    orientation: Quaternion;
    pos: Vec3;
}

interface GrainSegmentationOutput {
    main_listing: {
        total_grains: int;
        merging_threshold: float;
    };
    sub_listings: {
        grains: Grain[];
    };
}

`{outputBase}_atoms.msgpack`

Atoms grouped by identified structure family for downstream visualization.