Atomic Strain

Measure local deformation by comparing atomic neighborhoods against a reference configuration.

Parameters

Parameter	Type	Default	Description
`cutoff`	`float`	`3.0`	Cutoff radius for neighbor search.
`reference`	`frame`	—	Reference frame to compare against. If omitted, the current frame is used, which usually produces near-zero strain.
`eliminate_cell_deformation`	`bool`	`false`	Eliminate cell deformation before the local fit.
`assume_unwrapped`	`bool`	`false`	Assume coordinates are already unwrapped.
`calc_deformation_gradient`	`bool`	`true`	Compute deformation gradient `F`.
`calc_strain_tensors`	`bool`	`true`	Compute strain tensors.
`calc_d2min`	`bool`	`true`	Compute `D2min`, the non-affine residual.

Output

`{outputBase}_atomic_strain.parquet`

Summary statistics for the analysis run.

interface AtomicStrainOutput {
    main_listing: {
        cutoff: float;
        num_invalid_particles: int;
        average_shear_strain: float;
        average_volumetric_strain: float;
        max_shear_strain: float;
    };
    is_failed: boolean;
}

`{outputBase}_atoms.parquet`

Per-atom data in the canonical AtomisticExporter format consumed by the VOLT viewer. Atoms are partitioned into VALID and INVALID buckets.

type StrainTensor = [float, float, float, float, float, float];
type DeformationGradient = [float, float, float, float, float, float, float, float, float];

interface AtomRecord {
    // Base fields (always present)
    id: int;
    pos: [float, float, float];
    structure_id: int;
    structure_name: string;
    cluster_id: int;
    // Plugin-specific fields
    shear_strain: float;
    volumetric_strain: float;
    invalid: boolean;
    strain_tensor?: StrainTensor;       // present when calc_strain_tensors is true
    deformation_gradient?: DeformationGradient; // present when calc_deformation_gradient is true
    D2min?: float;                      // present when calc_d2min is true (key absent when disabled)
}

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: {
            VALID: AtomRecord[];
            INVALID: AtomRecord[];
        };
    };
}

The atoms.parquet result is also exported to a renderable GLB model via AtomisticExporter for 3D viewing in the VOLT client.

Atomic Strain

Parameters

Output

`{outputBase}_atomic_strain.parquet`

`{outputBase}_atoms.parquet`

See Also

On this page