Displacements Analysis

Compute each atom's displacement from a reference frame across periodic boundaries, and the slip vector that shows where crystal planes have slipped.

Displacements Analysis gives the vector each atom has moved since a reference frame, corrected for periodic boundaries, and its length. It also computes the slip vector, which picks out atoms on either side of a slipped plane and points along the slip. Use it to follow diffusion, to see where a sample deformed, or to locate slip planes and dislocation paths after loading.

Key	Version	Builds
`displacements-analysis`	2.1.1	Linux, macOS, Windows, browser

How it works

Atoms are matched between the two frames by identifier. The displacement is u = x − X, the current position minus the reference one. With the minimum image convention, a component that crosses a periodic boundary is wrapped back, so an atom that leaves through one face and comes back through the opposite one isn't counted as moving a whole cell length.

The slip vector of atom i averages, over the neighbors j it had within Slip Neighbor Cutoff in the reference frame, the relative displacements uⱼ − uᵢ that are longer than Slip Threshold, with a minus sign: sᵢ = −(1/nₛ) Σ (uⱼ − uᵢ). Atoms whose neighbors all moved with them have no slip vector. Atoms next to a slipped plane get a slip vector close to the Burgers vector of the dislocation that crossed it.

Inputs

A reference frame of the same trajectory, with the same atoms.
Atom positions and the simulation cell of both frames.
Optionally a structure column (structure_id or structure_type) from an earlier structure identification stage, used to group the 3D model.

Arguments

Argument	Type	Default	Allowed values	Description
Reference Frame `reference`	frame	(none)	A timestep of the trajectory	The frame displacements are measured from. If you leave it empty, each frame is its own reference and every displacement is zero.
Minimum Image Convention `mic`	boolean	`true`		Wrap displacement components that cross a periodic boundary.
Affine Mapping `affine_mapping`	select	`none`	`none` (None), `toReference` (To Reference), `toCurrent` (To Current)	Remove the homogeneous deformation of the cell by mapping both configurations to the reference cell or to the current cell before taking differences.
Compute Slip Vector `compute_slip_vector`	boolean	`true`		Compute the slip vector.
Slip Neighbor Cutoff (Å) `slip_cutoff`	number	`3.5`	≥ 0, step 0.1	Neighbor cutoff in the reference frame for the slip vector. Include the first neighbor shell. `0` skips the slip vector.
Slip Threshold (Å) `slip_threshold`	number	`0.5`	≥ 0, step 0.05	A neighbor counts as slipped when its displacement relative to the atom is longer than this.

In version 2.1.1, two of these arguments don't reach the program as set:

To Reference and To Current are applied as None: the program expects the values toReferenceCell and toCurrentCell, logs Unknown affine_mapping and maps nothing.
Turning off Minimum Image Convention or Compute Slip Vector has no effect. VOLT passes a boolean argument to this plugin only when it is on, and the program enables both unless told otherwise. Set Slip Neighbor Cutoff to 0 to skip the slip vector.

Outputs

Exposure	What you get
Displacements	A listing with the mean, maximum and minimum displacement length and, when computed, the mean and maximum slip vector length.
Displacements Model	A listing, and a 3D model of the atoms, grouped by structure when the frame has a structure column and as `All` otherwise.

The per-atom table has displacement (three components), magnitude, and when computed slip_vector (three components) and slip_vector_magnitude.

Reference

Slip vector: J. A. Zimmerman, C. L. Kelchner, P. A. Klein, J. C. Hamilton, S. M. Foiles, "Surface step effects on nanoindentation", Phys. Rev. Lett. 87, 165507 (2001).