Grain Segmentation

Split a polycrystal into grains by merging neighboring atoms with similar lattice orientations from polyhedral template matching.

Grain Segmentation divides a polycrystalline sample into grains. It identifies each atom's structure and lattice orientation with polyhedral template matching, then merges neighboring crystalline atoms into grains when their orientations are close. Use it to count and size grains, to get each grain's orientation, to follow grain growth over time, and to give ILDA the two grains of an interface.

Key	Version	Builds
`grain-segmentation`	2.1.0	Linux, macOS, Windows, browser

How it works

PTM. The plugin runs polyhedral template matching on every atom to get its structure and orientation. Atoms above the RMSD cutoff are OTHER.
Graph. Neighboring crystalline atoms are joined by bonds weighted by the disorientation angle between their lattices.
Merging. Bonds are merged in order of increasing disorientation, building a hierarchy of clusters. Merge Algorithm decides where to stop:
- Graph Clustering (Automatic) stops at a merging threshold it suggests from the data.
- Graph Clustering (Manual) and Minimum Spanning Tree stop at Merging Threshold.
Clean-up. Clusters with fewer atoms than Min Grain Atom Count, and OTHER atoms, get grain 0. Grains are renumbered from 1 by size, largest first. With Adopt Orphan Atoms, the atoms left in grain 0 join the grain of their neighbors.

Inputs

Atom positions and the simulation cell. No earlier stage is needed: the plugin runs PTM itself.

Arguments

Argument	Type	Default	Allowed values	Description
RMSD `rmsd`	number	`0.1`	≥ 0, step 0.01	RMSD cutoff for the PTM step.
Min Grain Atom Count `minGrainAtomCount`	number	`100`	≥ 1, step 1	Smallest number of atoms a grain can have; smaller clusters are dissolved.
Adopt Orphan Atoms `adoptOrphanAtoms`	select	`true`	`true` (True), `false` (False)	Assign the atoms that end up in no grain (boundaries, dissolved clusters) to a neighboring grain.
Handle Coherent Interfaces `handleCoherentInterfaces`	select	`true`	`true` (True), `false` (False)	Treat coherent interfaces between compatible structures, such as an HCP stacking fault inside an FCC grain, as part of the grain instead of a boundary.
Merge Algorithm `mergeAlgorithm`	select	`GraphClusteringAutomatic`	`GraphClusteringAutomatic` (Graph Clustering (Automatic)), `GraphClusteringManual` (Graph Clustering (Manual)), `MinimumSpanningTree` (Minimum Spanning Tree)	How clusters are merged; see above.
Merging Threshold `mergingThreshold`	number	`0`	≥ 0, step 0.01	Where merging stops, for the manual and minimum spanning tree algorithms. The automatic algorithm ignores it.
Output Bonds `outputBonds`	boolean	`false`		Passed to the grain engine, but in version 2.1.0 nothing reads it and no output contains bonds.

Outputs

Exposure	What you get
Grain Segmentation	A listing with the number of grains and the merging threshold the automatic algorithm suggested, and a `grains` sub-listing: grain `id`, `size` in atoms, `structure_type` and `structure_name`, `orientation` (quaternion `x, y, z, w`) and `pos` (the grain's center). Also shared with later stages as `grains`.
Grain Model	A listing with the atom, structure and clustered-atom counts, and a 3D model of the atoms grouped by structure. Also shared with later stages as `grain_atoms`.

The per-atom table has structure_id, structure_name, grain_id (0 for no grain), orientation, ptm_valid and, where PTM matched, rmsd.

Feeds

ILDA reads the grains and grain_atoms files it shares.

Notes

Run the automatic algorithm first and read the suggested threshold in the Grain Segmentation listing. To split or join more grains, switch to Graph Clustering (Manual) and set Merging Threshold around that value.
The 3D model groups atoms by structure. To see the grains, add a Color Coding stage after this one and color by grain_id.

Reference

Orientations come from PTM: P. M. Larsen, S. Schmidt, J. Schiøtz, "Robust structural identification via polyhedral template matching", Modelling Simul. Mater. Sci. Eng. 24, 055007 (2016).