Merge #469, bugfixing.

Ensure atom positions are expressed in the new basis when initializing Phase with structure

CHANGELOG.rst

@@ -53,6 +53,7 @@ Fixed
 -----
 - Transparency of polar stereographic grid lines can now be controlled by Matplotlib's
   ``grid.alpha``, just like the azimuth grid lines.
+- Previously ``Phase`` was failing to adjust atom position to accomodate for the change of basis. This is now fixed.
 
 2023-03-14 - version 0.11.1
 ===========================

orix/crystal_map/phase_list.py

@@ -135,7 +135,10 @@ def structure(self, value: Structure):
             old_matrix = value.lattice.base
             new_matrix = _new_structure_matrix_from_alignment(old_matrix, x="a", z="c*")
             value = copy.deepcopy(value)
+            # Ensure atom positions are expressed in the new basis
+            old_xyz_cartn = value.xyz_cartn
             value.lattice.setLatBase(new_matrix)
+            value.xyz_cartn = old_xyz_cartn
             if value.title == "" and hasattr(self, "_structure"):
                 value.title = self.name
             self._structure = value

orix/tests/test_phase_list.py

@@ -16,7 +16,7 @@
 # You should have received a copy of the GNU General Public License
 # along with orix.  If not, see <http://www.gnu.org/licenses/>.
 
-from diffpy.structure import Lattice, Structure
+from diffpy.structure import Atom, Lattice, Structure
 from diffpy.structure.spacegroups import GetSpaceGroup
 import numpy as np
 import pytest
@@ -333,6 +333,57 @@ def test_lattice_vectors(self):
         assert np.allclose(br.data, [0, 0.679, 0], atol=1e-3)
         assert np.allclose(cr.data, [0, 0, 0.714], atol=1e-3)
 
+    @pytest.mark.parametrize(
+        ["lat", "atoms"],
+        [
+            [
+                Lattice(1, 1, 1, 90, 90, 90),
+                [
+                    Atom("C", [0, 0, 0]),
+                    Atom("C", [0.5, 0.5, 0.5]),
+                    Atom("C", [0.5, 0, 0]),
+                ],
+            ],
+            [
+                Lattice(1, 1, 1, 90, 90, 120),
+                [
+                    Atom("C", [0, 0, 0]),
+                    Atom("C", [0.5, 0, 0]),
+                    Atom("C", [0.5, 0.5, 0.5]),
+                ],
+            ],
+            [
+                Lattice(1, 2, 3, 90, 90, 60),
+                [
+                    Atom("C", [0, 0, 0]),
+                    Atom("C", [0.1, 0.1, 0.6]),
+                    Atom("C", [0.5, 0, 0]),
+                ],
+            ],
+        ],
+    )
+    def test_atom_positions(self, lat, atoms):
+        structure = Structure(atoms, lat)
+        phase = Phase(structure=structure)
+        # xyz_cartn is independent of basis
+        assert np.allclose(phase.structure.xyz_cartn, structure.xyz_cartn)
+
+        # however, Phase should (in many cases) change the basis.
+        if np.allclose(structure.lattice.base, phase.structure.lattice.base):
+            # In this branch we are in the same basis & all atoms should be the same
+            for atom_from_structure, atom_from_phase in zip(structure, phase.structure):
+                assert np.allclose(atom_from_structure.xyz, atom_from_phase.xyz)
+        else:
+            # Here we have differing basis, so xyz must disagree for at least some atoms
+            disagreement_found = False
+
+            for atom_from_structure, atom_from_phase in zip(structure, phase.structure):
+                if not np.allclose(atom_from_structure.xyz, atom_from_phase.xyz):
+                    disagreement_found = True
+                    break
+
+            assert disagreement_found
+
     def test_from_cif(self, cif_file):
         """CIF files parsed correctly with space group and all."""
         phase = Phase.from_cif(cif_file)