Support Pymatgen Species object in aims (#4118)

* Support pymatgen Species in FHI-aims control.in

* Simplify building geometry.in file

* A bug fixed

src/pymatgen/io/aims/inputs.py

@@ -148,28 +148,23 @@ def from_structure(cls, structure: Structure | Molecule) -> Self:
             for lv in structure.lattice.matrix:
                 content_lines.append(f"lattice_vector {lv[0]: .12e} {lv[1]: .12e} {lv[2]: .12e}")
 
-        charges = structure.site_properties.get("charge", np.zeros(structure.num_sites))
-        magmoms = structure.site_properties.get("magmom", [None] * structure.num_sites)
-        velocities = structure.site_properties.get("velocity", [None for _ in structure.species])
-
-        for species, coord, charge, magmom, v in zip(
-            structure.species, structure.cart_coords, charges, magmoms, velocities, strict=True
-        ):
-            if isinstance(species, Element):
-                spin = magmom
-                element = species
-            else:
-                spin = species.spin
-                element = species.element
-                if magmom is not None and magmom != spin:
+        for site in structure:
+            element = site.species_string
+            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
 
             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}")
             if (spin is not None) and (spin != 0):
                 content_lines.append(f"     initial_moment {spin:.12e}")
-            if v is not None and any(v_i != 0.0 for v_i in v):
+            if (v is not None) and any(v_i != 0.0 for v_i in v):
                 content_lines.append(f"     velocity   {'  '.join([f'{v_i:.12e}' for v_i in v])}")
 
         return cls(_content="\n".join(content_lines), _structure=structure)
@@ -865,15 +860,12 @@ def from_structure(
         """Initialize species defaults from a structure."""
         labels = []
         elements = {}
-        for label, el in sorted(zip(struct.labels, struct.species, strict=True)):
-            if isinstance(el, Species):
-                el = el.element
-            if (label is None) or (el is None):
-                raise ValueError("Something is terribly wrong with the structure")
-            if label not in labels:
-                labels.append(label)
-                elements[label] = el.name
-        return SpeciesDefaults(labels, basis_set, species_dir=species_dir, elements=elements)
+        for site in struct:
+            el = site.specie
+            if site.species_string not in labels:
+                labels.append(site.species_string)
+                elements[site.species_string] = el.name
+        return SpeciesDefaults(sorted(labels), basis_set, species_dir=species_dir, elements=elements)
 
     def to_dict(self):
         """Dictionary representation of the species' defaults"""

tests/io/aims/test_inputs.py

@@ -9,7 +9,7 @@
 from monty.json import MontyDecoder, MontyEncoder
 from numpy.testing import assert_allclose
 
-from pymatgen.core import SETTINGS, Lattice, Species, Structure
+from pymatgen.core import SETTINGS, Composition, Lattice, Species, Structure
 from pymatgen.io.aims.inputs import (
     ALLOWED_AIMS_CUBE_TYPES,
     ALLOWED_AIMS_CUBE_TYPES_STATE,
@@ -297,9 +297,9 @@ def test_species_defaults(monkeypatch: pytest.MonkeyPatch):
     ]
     assert species_defaults.elements == {"Si": "Si"}
 
-    si.relabel_sites()
+    si[0].species = Composition({"Si0+": 1}, strict=True)
     species_defaults = SpeciesDefaults.from_structure(si, "light")
-    assert species_defaults.labels == ["Si_1", "Si_2"]
-    assert species_defaults.elements == {"Si_1": "Si", "Si_2": "Si"}
-    assert "Si_1" in str(species_defaults)
-    assert "Si_2" in str(species_defaults)
+    assert species_defaults.labels == ["Si", "Si0+"]
+    assert species_defaults.elements == {"Si": "Si", "Si0+": "Si"}
+    assert "Si0+" in str(species_defaults)
+    assert "Si" in str(species_defaults)