Wigner-Seitz Defect Analysis
Count vacancies, interstitials and antisites by assigning every atom to the nearest site of a reference lattice.
Wigner-Seitz analysis finds point defects by comparing the current frame with a perfect reference lattice. Every atom is assigned to the reference site it is closest to, that is, to the site whose Wigner-Seitz cell contains it. A site with no atom is a vacancy, a site with more than one atom holds interstitials, and in an alloy a site occupied by an atom of the wrong type is an antisite. Use it to count Frenkel pairs after radiation damage cascades and to follow defect recombination, in crystals where the atoms stay near their sites.
| Key | Version | Builds |
|---|---|---|
wigner-seitz-defect-analysis | 1.1.1 | Linux, macOS, Windows, browser |
How it works
The plugin reads the reference frame's atoms as the lattice sites. For each atom of the current frame it finds the nearest site, optionally after mapping both configurations to a common cell, and counts the atoms on each site:
| Site occupancy | Role |
|---|---|
| 0 | Vacancy |
| 1, same type as the site | Occupied |
| 1, different type | Antisite |
| 2 or more | Interstitial (each extra atom counts as one interstitial) |
The number of atoms doesn't need to match between the two frames.
Inputs
- A reference frame that defines the lattice sites, usually the first frame of the trajectory before the defects form.
- Atom types in both frames, for antisites.
Arguments
| Argument | Type | Default | Allowed values | Description |
|---|---|---|---|---|
Reference Frame reference | frame | (none) | A timestep of the trajectory | Required. The frame whose atom positions are the lattice sites. The stage fails without it. |
Affine Mapping affineMapping | select | off | off (Off), toReference (Map to Reference Cell), toCurrent (Map to Current Cell) | Map the positions to a common cell before assigning sites, so a homogeneously deformed cell doesn't create false defects. |
Eliminate Cell Deformation eliminateCellDeformation | boolean | false | Remove the cell's deformation before assigning sites. | |
Minimum Image Convention minimumImageConvention | boolean | true | Measure atom–site distances across periodic boundaries. |
Turning off Minimum Image Convention has no effect in version 1.1.1. VOLT passes a boolean argument to this plugin only when it is on, and the program uses the minimum image convention unless told otherwise.
Outputs
| Exposure | What you get |
|---|---|
| Wigner-Seitz Sites | A listing with the vacancy, interstitial, antisite and occupied counts, the number of sites and the number of atoms in the current frame. |
| Wigner-Seitz Model | A listing, and a 3D model with one point per reference site, grouped into Vacancy, Occupied, Antisite and Interstitial, plus one Interstitial point for every extra atom on a site. Singly occupied sites are drawn at their atom's position, the others at the site. |
The workflow declares the per-atom property occupancy (Site occupancy). The table also has site_index, site_identifier (the reference atom's identifier) and site_type (the reference atom's type). Its rows are the sites and extra atoms of the model, not the atoms of the frame.
Notes
- The method assumes atoms stay close to lattice sites. In amorphous or molten regions the counts don't describe point defects.
- To count defects created during a run, pick the first frame as the reference and run the stage on the later frames.
Reference
K. Nordlund, M. Ghaly, R. S. Averback, M. Caturla, T. Diaz de la Rubia, J. Tarus, "Defect production in collision cascades in elemental semiconductors and fcc metals", Phys. Rev. B 57, 7556 (1998).
Interfacial Line Defect Analysis
Find interface dislocations and disconnections between two grains, as line segments with their Burgers vector and step height.
MultiSOM
Identify structures without labels by clustering atoms with a multilayer self-organizing map trained on per-atom features from other plugins.