Atomic Strain

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

Overview

Atomic Strain compares each atom's neighborhood in the current frame against a reference frame and estimates the best local affine deformation that connects the two. From that fit, it reports strain-related measures such as shear strain, volumetric strain, deformation gradient, and optionally D2min.

This makes it especially useful when you want to study local deformation relative to a known reference state rather than relative to an ideal crystal lattice.

Parameters

Parameter	Type	Default	Description
`cutoff`	`float`	`3.0`	Cutoff radius for neighbor search.
`reference`	`file`	—	Reference LAMMPS dump file. If omitted, the current frame is used, which usually produces near-zero strain.
`eliminateCellDeformation`	`bool`	`false`	Eliminate cell deformation before the local fit.
`assumeUnwrapped`	`bool`	`false`	Assume coordinates are already unwrapped.
`calcDeformationGradient`	`bool`	`true`	Compute deformation gradient `F`.
`calcStrainTensors`	`bool`	`true`	Compute strain tensors.
`calcD2min`	`bool`	`true`	Compute `D2min`, the non-affine residual.

Practical notes

This plugin does not currently emit principal strains, even though that is a common expectation from the name.
invalid is an important field. It marks atoms for which the local fit could not be computed reliably, and those atoms are emitted with zeroed deformation outputs.
Atomic Strain is often easiest to interpret when paired with a carefully chosen reference frame.

Output

`{outputBase}_atomic_strain.msgpack`

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

interface PerAtomProperties {
    id: int;
    shear_strain: float;
    volumetric_strain: float;
    strain_tensor?: StrainTensor;
    deformation_gradient?: DeformationGradient;
    D2min: float | null;
    invalid: boolean;
}

interface AtomicStrainOutput {
    main_listing: {
        cutoff: float;
        num_invalid_particles: int;
        average_shear_strain: float;
        average_volumetric_strain: float;
        max_shear_strain: float;
    };
    "per-atom-properties": PerAtomProperties[];
}