Concepts

Asymmetric unit and P1

A Structure is a lattice, a space-group identity (the Hall symbol) and the asymmetric-unit sites. The P1 cell is derived: every atom carries its parent site, the operation that generated it and the lattice shift. An edit to a P1 atom therefore maps back to the site that owns the orbit.

Hall symbol

The Hall symbol is the identity of a space group. A number alone does not fix the setting: 227 has two origin choices, 146 has hexagonal and rhombohedral axes. A structure carries the explicit operation list read from the file or supplied by a builder; detect_symmetry supplies the operations from moyo, and set_space_group replaces them with the chosen setting.

Coordinates

• Fractional coordinates are [f64; 3].
• The lattice matrix rows are the vectors a, b, c.
• Fractional to Cartesian is frac @ M.
• The standard orientation puts a along +x and b in the xy plane.
• The reciprocal lattice uses the crystallographic convention: a . a* = 1 and d(hkl) = 1 / |hkl @ reciprocal|.

Units

Angstrom and degrees at every API boundary; radians internally. Force-field energies are in eV, forces in eV/Angstrom and stress in GPa; UFF keeps kcal/mol and Angstrom internally.

Limits

Every large allocation is estimated first (drawn atoms, supercell atoms, grid points). The soft limit warns; the hard limit refuses with a sentence that says what would fit. The profile is Standard, Generous or WarnOnly.

Bonds and rings

Bonds are perceived from covalent-radius sums on the P1 cell, then explicit additions/removals and topology edges are applied. Rings are chordless primitive cycles on the bond graph. Dummy X atoms never bond.