Merge branch 'master' into get_el_sp-isotope-unit-test

src/pymatgen/io/aims/inputs.py

@@ -154,16 +154,22 @@ def from_structure(cls, structure: Structure | Molecule) -> Self:
                 content_lines.append(f"lattice_vector {lv[0]: .12e} {lv[1]: .12e} {lv[2]: .12e}")
 
         for site in structure:
-            element = site.species_string
+            element = site.species_string.split(",spin=")[0]
             charge = site.properties.get("charge", 0)
             spin = site.properties.get("magmom", None)
             coord = site.coords
             v = site.properties.get("velocity", [0.0, 0.0, 0.0])
+
             if isinstance(site.specie, Species) and site.specie.spin is not None:
                 if spin is not None and spin != site.specie.spin:
                     raise ValueError("species.spin and magnetic moments don't agree. Please only define one")
                 spin = site.specie.spin
 
+            if isinstance(site.specie, Species) and site.specie.oxi_state is not None:
+                if charge is not None and charge != site.specie.oxi_state:
+                    raise ValueError("species.oxi_state and charge don't agree. Please only define one")
+                charge = site.specie.oxi_state
+
             content_lines.append(f"atom {coord[0]: .12e} {coord[1]: .12e} {coord[2]: .12e} {element}")
             if charge != 0:
                 content_lines.append(f"     initial_charge {charge:.12e}")

src/pymatgen/symmetry/groups.py

@@ -18,6 +18,7 @@
 from monty.design_patterns import cached_class
 from monty.serialization import loadfn
 
+from pymatgen.core.operations import SymmOp
 from pymatgen.util.string import Stringify
 
 if TYPE_CHECKING:

tests/io/test_phonopy.py

@@ -10,12 +10,11 @@
 from numpy.testing import assert_allclose, assert_array_equal
 from pytest import approx
 
-from pymatgen.core import Element
+from pymatgen.core import Element, Structure
 from pymatgen.io.phonopy import (
     CompletePhononDos,
     PhononBandStructure,
     PhononBandStructureSymmLine,
-    Structure,
     get_complete_ph_dos,
     get_displaced_structures,
     get_gruneisen_ph_bs_symm_line,
@@ -125,6 +124,10 @@ def test_structure_conversion(self):
         assert struct_pmg_round_trip.site_properties["magmom"] == struct_pmg.site_properties["magmom"]
 
 
+@pytest.mark.skipif(
+    platform.system() == "Windows" and int(np.__version__[0]) >= 2,
+    reason="cannot run NP2 on windows, see PR 4224",
+)
 @pytest.mark.skipif(Phonopy is None, reason="Phonopy not present")
 class TestGetDisplacedStructures(PymatgenTest):
     def test_get_displaced_structures(self):
@@ -157,11 +160,11 @@ def test_get_displaced_structures(self):
         assert os.path.isfile("test.yaml")
 
 
-@pytest.mark.skipif(Phonopy is None, reason="Phonopy not present")
 @pytest.mark.skipif(
     platform.system() == "Windows" and int(np.__version__[0]) >= 2,
-    reason="See https://github.com/conda-forge/phonopy-feedstock/pull/158#issuecomment-2227506701",
+    reason="cannot run NP2 on windows, see PR 4224",
 )
+@pytest.mark.skipif(Phonopy is None, reason="Phonopy not present")
 class TestPhonopyFromForceConstants(TestCase):
     def setUp(self) -> None:
         test_path = Path(TEST_DIR)