Merge pull request #491 from dasilvaale/fix-from-cif-xyz

Discrepancy between Phase.from_cif and Phase(structure)

.zenodo.json

@@ -46,6 +46,10 @@
       "name": "Viljar Johan Femoen",
       "affiliation": "Norwegian University of Science and Technology"
     },
+    {
+      "name": "Alessandra da Silva",
+      "orcid": "0000-0003-0465-504X"
+    },
     {
       "name": "Alexander Clausen",
       "orcid": "0000-0002-9555-7455",

CHANGELOG.rst

@@ -6,26 +6,16 @@ All user facing changes to this project are documented in this file. The format
 on `Keep a Changelog <https://keepachangelog.com/en/1.0.0/>`__, and this project tries
 its best to adhere to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`__.
 
-Unreleased
-==========
-
-Added
------
-
-Changed
--------
-
-Removed
--------
-
-Deprecated
-----------
+2024-04-21 - version 0.12.1
+===========================
 
 Fixed
 -----
 - ``ax2qu`` and ``Quaternion.from_axes_angles()`` would raise if the input arrays were
   broadcastable but the final dimension was ``1``. This has been fixed.
-
+- ``Phase.from_cif()`` now correctly adjusts atom positions when forcing
+  ``Phase.structure.lattice.base`` to use the crystal axes alignment ``e1 || a``,
+  ``e3 || c*``. This bug was introduced in 0.12.0.
 
 2024-04-13 - version 0.12.0
 ===========================

orix/__init__.py

@@ -1,5 +1,5 @@
 __name__ = "orix"
-__version__ = "0.13.dev0"
+__version__ = "0.12.1"
 __author__ = "orix developers"
 __author_email__ = "[email protected]"
 __description__ = "orix is an open-source Python library for handling crystal orientation mapping data."
@@ -16,5 +16,6 @@
     "Carter Francis",
     "Simon Høgås",
     "Viljar Johan Femoen",
+    "Alessandra da Silva",
     "Alexander Clausen",
 ]

orix/crystal_map/phase_list.py

@@ -339,9 +339,6 @@ def from_cif(cls, filename: str) -> Phase:
         parser = p_cif.P_cif()
         name = os.path.splitext(os.path.split(filename)[1])[0]
         structure = parser.parseFile(filename)
-        lattice = structure.lattice
-        new_base = _new_structure_matrix_from_alignment(lattice.base, x="a", z="c*")
-        lattice.setLatBase(new_base)
         space_group = parser.spacegroup.number
         return cls(name, space_group, structure=structure)
 

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 Atom, Lattice, Structure
+from diffpy.structure import Atom, Lattice, Structure, loadStructure
 from diffpy.structure.spacegroups import GetSpaceGroup
 import numpy as np
 import pytest
@@ -396,6 +396,13 @@ def test_from_cif(self, cif_file):
             lattice.base, [[15.5, 0, 0], [0, 4.05, 0], [-1.779, 0, 6.501]], atol=1e-3
         )
 
+    def test_from_cif_same_structure(self, cif_file):
+        phase1 = Phase.from_cif(cif_file)
+        structure = loadStructure(cif_file)
+        phase2 = Phase(structure=structure)
+        assert np.allclose(phase1.structure.lattice.base, phase2.structure.lattice.base)
+        assert np.allclose(phase1.structure.xyz, phase2.structure.xyz)
+
 
 class TestPhaseList:
     @pytest.mark.parametrize("empty_input", [(), [], {}])