Supercells

Expand periodic structures by replicating the unit cell along lattice directions.

Source: src/lib/structure/lattice-ops.ts, src/lib/structure/ferrox-wasm.ts

Overview

Supercell generation creates an n x m x p expansion of the original unit cell, replicating all atoms and scaling the lattice accordingly. This is commonly used for:

• Creating larger simulation cells for DFT or MD
• Visualizing extended crystal structures
• Constructing defect supercells with dilute defect concentration

Key Functions

// Generate n x m x p supercell
generate_supercell_struct(structure, nx, ny, nz): Structure

// Apply arbitrary transformation matrix (3x3)
get_supercell_structure(structure, transform_matrix): Structure

Interactive UI

The CellSelect component provides a simple selector for supercell dimensions:

• Input fields for n, m, p (repeat counts along a, b, c)
• One-click supercell generation
• Camera automatically re-aligns after supercell expansion

How It Works

1. The lattice matrix is scaled: new_lattice = diag(n, m, p) * original_lattice
2. For each original atom at fractional position (fa, fb, fc):
   • Generate copies at ((fa + i)/n, (fb + j)/m, (fc + k)/p) for i=0..n-1, j=0..m-1, k=0..p-1
3. All atom properties (element, occupancy, charge) are preserved

Transformation Matrix

For non-diagonal expansions (e.g., rotating the cell), use the transformation matrix approach:

// Example: 2x2x1 supercell with 45-degree rotation
const transform = [
  [1, 1, 0],
  [-1, 1, 0],
  [0, 0, 1]
]
get_supercell_structure(structure, transform)

The new lattice is M * old_lattice, and atom positions are mapped accordingly.