Cluster Analysis

Parameters

Parameter	Type	Default	Description
`cutoff`	`float`	`3.2`	Cutoff radius used to define connectivity.
`sort_by_size`	`bool`	`true`	Sort clusters by size in descending order.
`unwrap`	`bool`	`false`	Unwrap particle coordinates inside each cluster.
`centers_of_mass`	`bool`	`false`	Compute cluster centers with uniform weights.
`radius_of_gyration`	`bool`	`false`	Compute radii and tensors of gyration with uniform weights.

Output

`{outputBase}_cluster_analysis.parquet`

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

interface Cluster {
    cluster_id: int;
    size: int;
    center?: Vec3;
    radius_of_gyration?: float;
    gyration_tensor?: GyrationTensor;
}

interface ClusterAnalysisOutput {
    main_listing: {
        total_atoms: int;
        clusters: int;
        largest_cluster_size: int;
        has_zero_weight_cluster: boolean;
    };
    sub_listings: {
        clusters: Cluster[];
    };
}

`{outputBase}_atoms.parquet`

Per-atom data in the canonical AtomisticExporter format consumed by the VOLT viewer. Atoms are grouped into named buckets: Cluster_<n> for clustered atoms, Unclustered for unassigned atoms.

type Vec3 = [float, float, float];

interface AtomEntry {
    id: int;
    pos: Vec3;
    structure_id: int;
    structure_name: string;
    cluster_id: int;
    pos_unwrapped?: Vec3;   // present only when `unwrap` is true
}

interface AtomsOutput {
    main_listing: {
        total_atoms: int;
        structure_count: int;
    };
    sub_listings: {
        structures: Array<{
            structure_id: int;
            structure_name: string;
            atom_count: int;
        }>;
    };
    export: {
        AtomisticExporter: {
            [bucketName: string]: AtomEntry[];
        };
    };
}

This file also feeds the cluster-model-export node in the workflow DAG, which produces a GLB 3D model via the AtomisticExporter.

Cluster Analysis

Parameters

Output

`{outputBase}_cluster_analysis.parquet`

`{outputBase}_atoms.parquet`

See Also

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