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Add transformation matrix to the case of aP lattice #111

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Add transformation matrix to the case of aP lattice #111

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Add transformation matrix to the case of aP lattice
adrybakov Aug 6, 2025
2366610
Merge branch 'main' into patch-1
adrybakov Feb 3, 2026
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13 changes: 5 additions & 8 deletions seekpath/hpkot/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -116,6 +116,8 @@ def get_path(
- ``inverse_primitive_transformation_matrix``: the inverse of the matrix :math:`P`
(the determinant is integer and gives the ratio in volume between
the conventional and primitive cells)
- ``transformation_matrix``: the transformation matrix between the original and the
conventional cell
- ``rotation_matrix``: rotation matrix in Cartesian space from the input
cell to the standardized cell
- ``volume_original_wrt_conv``: volume ratio of the user-provided cell
Expand Down Expand Up @@ -318,7 +320,7 @@ def get_path(
## This is Niggli-reduced
reciprocal_cell2 = spglib.niggli_reduce(reciprocal_cell_orig)
real_cell2 = get_real_cell_from_reciprocal_rows(reciprocal_cell2)
# TODO: get transformation matrix?
M1 = np.dot(np.linalg.inv(conv_lattice.T), real_cell2)

ka2, kb2, kc2, coskalpha2, coskbeta2, coskgamma2 = get_cell_params(
reciprocal_cell2
Expand Down Expand Up @@ -413,11 +415,8 @@ def get_path(
# Store the relative coords with respect to the new vectors
# TODO: decide if we want to do %1. for the fractional coordinates
conv_positions = np.dot(conv_pos_abs, np.linalg.inv(conv_lattice))
# TODO: implement the correct one (probably we need the matrix
# out from niggli, and then we can combine it with M2 and M3??)
# We set it to None for the time being to avoid confusion

# transformation_matrix = None
transf_matrix = M1 @ M2 @ M3

else:
raise ValueError(
Expand Down Expand Up @@ -498,9 +497,7 @@ def get_path(
# spg_mapping.get_P_matrix
'inverse_primitive_transformation_matrix': invP,
'primitive_transformation_matrix': P,
# For the time being disabled, not valid for aP lattices
# (for which we would need the transformation matrix from niggli)
#'transformation_matrix': transf_matrix,
'transformation_matrix': transf_matrix,
'volume_original_wrt_conv': volume_conv_wrt_original,
'volume_original_wrt_prim': volume_conv_wrt_original * np.linalg.det(invP),
'spacegroup_number': dataset.number,
Expand Down