gemmi states centred_to_primitive as an operator on COORDINATES and
CrystalLattice::Multiply combines BASIS VECTORS, so the matrix has to be
transposed on the way in - as it already is at both of the other places a gemmi
Op::Rot reaches Multiply, one of them in this same file.
A, B, C, I and F are symmetric matrices, so for them the transpose is a no-op
and the omission never showed. R and H are not. Measured on an R-centred
hexagonal lattice, ToPrimitive('R') returned 59.5 81.7 43.3 / 145.6 124.5 46.7
where the rhombohedral primitive cell is 49.3 49.3 49.3 / 60.9 60.9 60.9. What
hid it is that a determinant is unchanged by transposition, so the VOLUME came
out right - and most callers only take the volume.
It is not only cosmetic: the result feeds the re-seating path that puts a
lattice into a space group the user fixed by hand, so an R-centred lattice was
handed the classifier a "primitive" cell that is not that lattice - broken for
exactly the centring whose setting most needs re-seating.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
(cherry picked from commit 6ca00e927d664e870515c04164defa81d8a18725)
leonarski_f
e0ff51e2a0
