What this CIF checker validates
The bounded parser recognizes data blocks, scalar items, loops, quoted values, semicolon text fields, standard-uncertainty numbers, and common CIF 2.0 scalar forms. It checks positive cell lengths, valid angles, a positive Gram determinant, calculated versus declared volume, atom-site labels and fractional coordinates, nominal occupancy ranges, common atom-label references, and geometry symmetry-code references.
How symmetry expansion is diagnosed
Each supplied operation is parsed as an affine transform X′ = WX + w; JavaScript expression evaluation is never used. Rotation matrices must have integer coefficients and determinant ±1. The explicit set is checked for the identity, duplicates, and closure modulo lattice translations. Every readable atom site is transformed, wrapped into the unit cell, and deduplicated at 10⁻⁶ fractional tolerance. The resulting count is compared with a declared site multiplicity.
How occupancy findings should be read
The Core dictionary defines occupancy as the fraction of an atom type at a site and normally constrains it to 0–1, with standard uncertainty relevant near the bounds. This checker preserves that uncertainty. It also groups distinct labels that reach the same expanded coordinate and sums known nominal occupancies. A sum above 1 is a concrete conflict; a lower shared sum is only noted because disorder groups, assemblies, dummy sites, and refinement intent require expert interpretation.
Scientific and conformance boundary
This is not IUCr checkCIF, a dictionary validator, a space-group finder, or a crystal viewer. It uses the operations present in the file and does not infer missing operations from a Hermann–Mauguin symbol or number; identify Wyckoff positions; validate every Core, mmCIF, magnetic, modulated, powder, or restraint data item; assess displacement parameters, bond plausibility, diffraction data, chemistry, or refinement quality; expand CIF 2.0 compound values; or certify publication or simulation readiness. Use current dictionaries, checkCIF, and crystallographic software for authoritative validation.
Frequently asked questions
Why does a special-position atom have fewer generated positions than operations?
Several operations can map that atom onto the same unit-cell coordinate. The table retains all generating operation IDs but counts the coordinate once, which makes a wrong declared multiplicity visible.
Why is a missing operation list treated as P1 for diagnostics?
The Core dictionary gives x,y,z as the default. The checker marks that operation as inferred and does not claim that the declared space-group name is correct.
Does an occupancy sum of 1 prove a disorder model is correct?
No. It is only a nominal coordinate-level consistency check. Chemical identity, disorder assembly/group relationships, special-position constraints, and refinement evidence still need expert review.
Primary references
The IUCr publishes the formal CIF 1.1 and CIF 2.0 specifications and the active Core CIF dictionary. Its definitions describe atom-site occupancy and the affine meaning and completeness expectation of space-group operations.
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