Deprecate Structure.ntypesp replaced by Structure.n_elems (#3562)

* deprecate Structure.ntypesp replaced by Structure.n_elems

* fix structure_to_abivars() for non-hexagonal structures

not calling structure.lattice.is_hexagonal()

Author: janosh

pymatgen/core/lattice.py

@@ -1517,7 +1517,7 @@ def is_hexagonal(self, hex_angle_tol: float = 5, hex_length_tol: float = 0.01) -
         angles = self.angles
         right_angles = [i for i in range(3) if abs(angles[i] - 90) < hex_angle_tol]
         hex_angles = [
-            i for i in range(3) if abs(angles[i] - 60) < hex_angle_tol or abs(angles[i] - 120) < hex_angle_tol
+            idx for idx in range(3) if abs(angles[idx] - 60) < hex_angle_tol or abs(angles[idx] - 120) < hex_angle_tol
         ]
 
         return (

pymatgen/core/structure.py

@@ -262,10 +262,16 @@ def species_and_occu(self) -> list[Composition]:
         return [site.species for site in self]
 
     @property
+    @deprecated(message="Use n_type_sp instead.")
     def ntypesp(self) -> int:
         """Number of types of atoms."""
         return len(self.types_of_species)
 
+    @property
+    def n_elems(self) -> int:
+        """Number of types of atoms."""
+        return len(self.types_of_species)
+
     @property
     def types_of_species(self) -> tuple[Element | Species | DummySpecies]:
         """List of types of specie."""

pymatgen/io/abinit/abiobjects.py

@@ -185,16 +185,17 @@ def species_by_znucl(structure: Structure) -> list[Species]:
     return types
 
 
-def structure_to_abivars(structure, enforce_znucl=None, enforce_typat=None, **kwargs):
+def structure_to_abivars(
+    structure: Structure, enforce_znucl: list | None = None, enforce_typat: list | None = None, **kwargs
+):
     """
     Receives a structure and returns a dictionary with ABINIT variables.
 
     Args:
-        enforce_znucl: List of ntypat entries with the value of Z for each type of atom.
-            Used to change the default ordering.
-        enforce_typat: List with natom entries with the type index.
-            Fortran conventions: start to count from 1.
-            Used to change the default ordering.
+        enforce_znucl (list): ntypat entries with the value of Z for each type of atom.
+            Used to change the default ordering. Defaults to None.
+        enforce_typat (list): natom entries with the type index.
+            Fortran conventions: start to count from 1. Used to change the default ordering.
     """
     if not structure.is_ordered:
         raise ValueError(
@@ -205,7 +206,6 @@ def structure_to_abivars(structure, enforce_znucl=None, enforce_typat=None, **kw
         )
 
     n_atoms = len(structure)
-    n_types_atom = structure.ntypesp
     enforce_order = False
 
     if enforce_znucl is not None or enforce_typat is not None:
@@ -219,19 +219,21 @@ def structure_to_abivars(structure, enforce_znucl=None, enforce_typat=None, **kw
                 f"enforce_typat contains {len(enforce_typat)} entries while it should be {len(structure)=}"
             )
 
-        if len(enforce_znucl) != n_types_atom:
-            raise ValueError(f"enforce_znucl contains {len(enforce_znucl)} entries while it should be {n_types_atom=}")
+        if len(enforce_znucl) != structure.n_elems:
+            raise ValueError(
+                f"enforce_znucl contains {len(enforce_znucl)} entries while it should be {structure.n_elems=}"
+            )
 
-    if not enforce_order:
+    if enforce_order:
+        znucl_type = enforce_znucl
+        typat = enforce_typat or []  # or [] added for mypy
+    else:
         types_of_specie = species_by_znucl(structure)
 
         znucl_type = [specie.number for specie in types_of_specie]
         typat = np.zeros(n_atoms, int)
         for atm_idx, site in enumerate(structure):
             typat[atm_idx] = types_of_specie.index(site.specie) + 1
-    else:
-        znucl_type = enforce_znucl
-        typat = enforce_typat
 
     r_prim = ArrayWithUnit(structure.lattice.matrix, "ang").to("bohr")
     ang_deg = structure.lattice.angles
@@ -245,19 +247,19 @@ def structure_to_abivars(structure, enforce_znucl=None, enforce_typat=None, **kw
     # Info on atoms.
     dct = {
         "natom": n_atoms,
-        "ntypat": n_types_atom,
+        "ntypat": structure.n_elems,
         "typat": typat,
         "znucl": znucl_type,
         "xred": x_red,
         "properties": structure.properties,
     }
 
     # Add info on the lattice.
-    # Should we use (rprim, acell) or (angdeg, acell) to specify the lattice?
+    # Should we use (rprim, acell) or (ang_deg, acell) to specify the lattice?
     geo_mode = kwargs.pop("geomode", "rprim")
     if geo_mode == "automatic":
         geo_mode = "rprim"
-        if structure.lattice.is_hexagonal:  # or structure.lattice.is_rhombohedral
+        if structure.lattice.is_hexagonal():  # or structure.lattice.is_rhombohedral
             geo_mode = "angdeg"
             ang_deg = structure.lattice.angles
             # Here one could polish a bit the numerical values if they are not exact.
@@ -281,15 +283,15 @@ def structure_to_abivars(structure, enforce_znucl=None, enforce_typat=None, **kw
     return dct
 
 
-def contract(s):
+def contract(string):
     """
     assert contract("1 1 1 2 2 3") == "3*1 2*2 1*3"
     assert contract("1 1 3 2 3") == "2*1 1*3 1*2 1*3"
     """
-    if not s:
-        return s
+    if not string:
+        return string
 
-    tokens = s.split()
+    tokens = string.split()
     old = tokens[0]
     count = [[1, old]]
 

pymatgen/io/cp2k/sets.py

@@ -1230,12 +1230,9 @@ def create_subsys(self, structure: Structure | Molecule) -> None:
         if isinstance(structure, Structure):
             subsys.insert(Cell(structure.lattice))
         else:
-            x = max(structure.cart_coords[:, 0])
-            y = max(structure.cart_coords[:, 1])
-            z = max(structure.cart_coords[:, 2])
-            x = x if x else 1
-            y = y if y else 1
-            z = z if z else 1
+            x = max(*structure.cart_coords[:, 0], 1)
+            y = max(*structure.cart_coords[:, 1], 1)
+            z = max(*structure.cart_coords[:, 2], 1)
             cell = Cell(lattice=Lattice([[10 * x, 0, 0], [0, 10 * y, 0], [0, 0, 10 * z]]))
             cell.add(Keyword("PERIODIC", "NONE"))
             subsys.insert(cell)

pymatgen/io/shengbte.py

@@ -216,7 +216,7 @@ def from_structure(cls, structure: Structure, reciprocal_density: int | None = 5
         types = [types_dict[i] + 1 for i in structure.atomic_numbers]
 
         control_dict = {
-            "nelements": structure.ntypesp,
+            "nelements": structure.n_elems,
             "natoms": len(structure),
             "norientations": 0,
             "lfactor": 0.1,

pymatgen/io/vasp/sets.py

@@ -2759,7 +2759,7 @@ def incar(self) -> Incar:
         defaults = {
             "ALGO": "Fast",
             "ISIF": 3,
-            "LANGEVIN_GAMMA": [10] * self.structure.ntypesp,
+            "LANGEVIN_GAMMA": [10] * self.structure.n_elems,
             "LANGEVIN_GAMMA_L": 1,
             "MDALGO": 3,
             "PMASS": 10,
@@ -2771,7 +2771,7 @@ def incar(self) -> Incar:
         self.user_incar_settings = defaults
 
         # Set NPT-AIMD ENCUT = 1.5 * VASP_default
-        enmax = [self.potcar[i].keywords["ENMAX"] for i in range(self.structure.ntypesp)]
+        enmax = [self.potcar[idx].keywords["ENMAX"] for idx in range(self.structure.n_elems)]
         encut = max(enmax) * 1.5
         self._config_dict["INCAR"]["ENCUT"] = encut
 

tests/core/test_structure.py

@@ -71,7 +71,7 @@ def setUp(self):
         self.struct = IStructure(self.lattice, ["Si"] * 2, coords)
         assert len(self.struct) == 2, "Wrong number of sites in structure!"
         assert self.struct.is_ordered
-        assert self.struct.ntypesp == 1
+        assert self.struct.n_elems == 1
         coords = [[0, 0, 0], [0.0, 0, 0.0000001]]
         with pytest.raises(
             StructureError, match=f"sites are less than {self.struct.DISTANCE_TOLERANCE} Angstrom apart"
@@ -967,7 +967,7 @@ def test_append_insert_remove_replace_substitute(self):
         struct = self.struct
         struct.insert(1, "O", [0.5, 0.5, 0.5])
         assert struct.formula == "Si2 O1"
-        assert struct.ntypesp == 2
+        assert struct.n_elems == 2
         assert struct.symbol_set == ("O", "Si")
         assert struct.indices_from_symbol("Si") == (0, 2)
         assert struct.indices_from_symbol("O") == (1,)
@@ -977,7 +977,7 @@ def test_append_insert_remove_replace_substitute(self):
         assert struct.indices_from_symbol("O") == (1,)
         struct.append("N", [0.25, 0.25, 0.25])
         assert struct.formula == "Si1 N1 O1"
-        assert struct.ntypesp == 3
+        assert struct.n_elems == 3
         assert struct.symbol_set == ("N", "O", "Si")
         assert struct.indices_from_symbol("Si") == (0,)
         assert struct.indices_from_symbol("O") == (1,)
@@ -987,15 +987,15 @@ def test_append_insert_remove_replace_substitute(self):
         assert struct.symbol_set == ("Ge", "N", "O")
         struct.replace_species({"Ge": "Si"})
         assert struct.formula == "Si1 N1 O1"
-        assert struct.ntypesp == 3
+        assert struct.n_elems == 3
 
         struct.replace_species({"Si": {"Ge": 0.5, "Si": 0.5}})
         assert struct.formula == "Si0.5 Ge0.5 N1 O1"
         # this should change the .5Si .5Ge sites to .75Si .25Ge
         struct.replace_species({"Ge": {"Ge": 0.5, "Si": 0.5}})
         assert struct.formula == "Si0.75 Ge0.25 N1 O1"
 
-        assert struct.ntypesp == 4
+        assert struct.n_elems == 4
 
         struct.replace_species({"Ge": "Si"})
         struct.substitute(1, "hydroxyl")

tests/io/abinit/test_inputs.py

@@ -51,8 +51,8 @@ def test_api(self):
 
         inp = BasicAbinitInput(structure=unit_cell, pseudos=abiref_file("14si.pspnc"))
 
-        shiftk = [[0.5, 0.5, 0.5], [0.5, 0.0, 0.0], [0.0, 0.5, 0.0], [0.0, 0.0, 0.5]]
-        assert_array_equal(calc_shiftk(inp.structure), shiftk)
+        shift_k = [[0.5, 0.5, 0.5], [0.5, 0.0, 0.0], [0.0, 0.5, 0.0], [0.0, 0.0, 0.5]]
+        assert_array_equal(calc_shiftk(inp.structure), shift_k)
         assert num_valence_electrons(inp.structure, inp.pseudos) == 8
 
         repr(inp), str(inp)
@@ -81,8 +81,8 @@ def test_api(self):
         inp.set_vars_ifnotin(ecut=-10)
         assert inp["ecut"] == 5
 
-        _, tmpname = tempfile.mkstemp(text=True)
-        inp.write(filepath=tmpname)
+        _, tmp_name = tempfile.mkstemp(text=True)
+        inp.write(filepath=tmp_name)
 
         # Cannot change structure variables directly.
         with pytest.raises(inp.Error):

tests/io/vasp/test_sets.py

@@ -1088,7 +1088,7 @@ def test_incar(self):
         assert incar["EDIFF"] == approx(1e-5)
         assert incar["LANGEVIN_GAMMA_L"] == 1
         assert incar["LANGEVIN_GAMMA"] == [10, 10, 10]
-        enmax = max(npt_set.potcar[i].keywords["ENMAX"] for i in range(self.struct.ntypesp))
+        enmax = max(npt_set.potcar[idx].keywords["ENMAX"] for idx in range(self.struct.n_elems))
         assert incar["ENCUT"] == approx(1.5 * enmax)
         assert incar["ALGO"] == "Fast"
         assert incar["ISIF"] == 3