Modify FHI-aims inputs to not use species string (materialsproject#4177)

* Modify FHI-aims inputs to not use species string FHI-aims does not read spin from the species and that causes issues with magnetic calculations * Add the option for oxidation state to still be in species Issue is only with spin * Fix lint errors --------- Signed-off-by: Shyue Ping Ong <[email protected]> Co-authored-by: Shyue Ping Ong <[email protected]>
naik-aakash · Dec 11, 2024 · 653714e · 653714e
1 parent 362bf54
commit 653714e
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diff --git a/src/pymatgen/io/aims/inputs.py b/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}")

diff --git a/src/pymatgen/symmetry/groups.py b/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: