General: Renamed base -> basis

Author: Somerandomguy10111

tests/t_crystal/t_calculation.py

@@ -81,7 +81,7 @@ def to_clustered_pymatgen(crystal : CrystalStructure) -> Structure:
         alpha, beta, gamma = crystal.angles
         lattice = Lattice.from_parameters(a, b, c, alpha, beta, gamma)
 
-        non_void_sites = crystal.base.get_non_void_sites()
+        non_void_sites = crystal.basis.get_non_void_sites()
 
         EPSILON = 0.001
         clusters: list[list[AtomSite]] = []

tests/t_crystal/t_properties.py

@@ -25,7 +25,7 @@ def test_angles(self):
     def test_num_atoms(self):
         expected_atom_counts = [4*4, 6]
         for crystal, num_atoms_exp in zip(self.custom_structures, expected_atom_counts):
-            self.assertEqual(len(crystal.base), num_atoms_exp)
+            self.assertEqual(len(crystal.basis), num_atoms_exp)
 
 
     def test_to_cif(self):
@@ -34,10 +34,10 @@ def test_to_cif(self):
             print(f'CIF = \n{cif}')
 
     def test_standardize(self):
-        phase = CrystalStructure(lengths=(5.801, 11.272, 5.57), angles=(90, 90, 90), base=CrystalBasis.empty())
+        phase = CrystalStructure(lengths=(5.801, 11.272, 5.57), angles=(90, 90, 90), basis=CrystalBasis.empty())
         new_phase = phase.get_standardized()
 
-        self.assertTrue(len(new_phase.base) == 0)
+        self.assertTrue(len(new_phase.basis) == 0)
 
 if __name__ == "__main__":
     TestCifParsing.execute_all()

xrdpattern/crystal/components/crystal.py

@@ -22,7 +22,7 @@
 @dataclass
 class CrystalStructure(JsonDataclass):
     lattice : Lattice
-    base : CrystalBasis
+    basis : CrystalBasis
     spacegroup : Optional[int] = None
     chemical_composition : Optional[str] = None
     wyckoff_symbols : Optional[list[str]] = None
@@ -47,7 +47,7 @@ def from_pymatgen(cls, pymatgen_structure: Structure) -> CrystalStructure:
                 atomic_site = AtomSite(x, y, z, occupancy=occupancy, species_str=str(species))
                 base.append(atomic_site)
 
-        crystal_str = cls(lattice=lattice, base=base)
+        crystal_str = cls(lattice=lattice, basis=base)
 
         return crystal_str
 
@@ -59,7 +59,7 @@ def to_cif(self) -> str:
         return pymatgen_structure.to(filename='', fmt='cif')
 
     def to_pymatgen(self) -> Structure:
-        non_void_sites = self.base.atom_sites
+        non_void_sites = self.basis.atom_sites
         atoms = [site.atom.as_pymatgen for site in non_void_sites]
         positions = [(site.x, site.y, site.z) for site in non_void_sites]
 
@@ -72,14 +72,14 @@ def to_pymatgen(self) -> Structure:
     def get_view(self) -> str:
         the_dict = asdict(self)
         the_dict = {str(key) : str(value) for key, value in the_dict.items() if not isinstance(value, Structure)}
-        the_dict['base'] = f'{self.base[0]}, ...'
+        the_dict['base'] = f'{self.basis[0]}, ...'
         return json.dumps(the_dict, indent='-')
 
     # ---------------------------------------------------------
     # properties
 
     def calculate_properties(self):
-        if len(self.base) == 0:
+        if len(self.basis) == 0:
             raise ValueError('Base is empty! Cannot calculate properties of empty crystal. Aborting ...')
 
         pymatgen_structure = self.to_pymatgen()
@@ -91,11 +91,11 @@ def calculate_properties(self):
         self.chemical_composition = pymatgen_structure.composition.formula
 
     def get_standardized(self) -> CrystalStructure:
-        struct = self.to_pymatgen() if len(self.base) > 0 else Structure(self.lattice, ["H"], [[0, 0, 0]])
+        struct = self.to_pymatgen() if len(self.basis) > 0 else Structure(self.lattice, ["H"], [[0, 0, 0]])
         analzyer = SpacegroupAnalyzer(structure=struct)
         std_struct = analzyer.get_conventional_standard_structure()
-        if len(self.base) == 0:
-            return CrystalStructure(lattice=std_struct.lattice, base=CrystalBasis.empty())
+        if len(self.basis) == 0:
+            return CrystalStructure(lattice=std_struct.lattice, basis=CrystalBasis.empty())
         else:
             return CrystalStructure.from_pymatgen(pymatgen_structure=std_struct)
 
@@ -106,12 +106,12 @@ def scale(self, target_density: float):
     @cached_property
     def packing_density(self) -> float:
         volume_uc = self.volume_uc
-        atomic_volume = self.base.calculate_atomic_volume()
+        atomic_volume = self.basis.calculate_atomic_volume()
         return atomic_volume/volume_uc
 
     @cached_property
     def num_atoms(self) -> int:
-        return len(self.base)
+        return len(self.basis)
 
     @cached_property
     def volume_uc(self) -> float:

xrdpattern/crystal/examples/provider.py

@@ -17,7 +17,7 @@ def get_crystal(num: int, verbose: bool = False):
     @staticmethod
     def get_base(num : int = 1, verbose : bool = False) -> CrystalBasis:
         crystal_stucture = CrystalExamples.get_crystal(num=num, verbose=verbose)
-        return crystal_stucture.base
+        return crystal_stucture.basis
 
     @staticmethod
     def get_cif_content(num : int = 1) -> str:

xrdpattern/xrd/data.py

@@ -88,7 +88,7 @@ def has_label(self, label_type: LabelType) -> bool:
         if label_type == LabelType.lattice:
             return all(not math.isnan(x) for x in self.primary_phase.lengths) and all(not math.isnan(x) for x in self.primary_phase.angles)
         if label_type == LabelType.atom_coords:
-            return len(self.primary_phase.base) > 0
+            return len(self.primary_phase.basis) > 0
         if label_type == LabelType.spg:
             spg_explicit = self.primary_phase.spacegroup is not None
             spg_implicit = self.has_label(label_type=LabelType.lattice) and self.has_label(

xrdpattern/xrd/experiment.py

@@ -40,7 +40,7 @@ def make_empty(cls, is_simulated : bool = False, num_phases : int = 1) -> Powder
             angles = (float('nan'),float('nan'), float('nan'))
             base = CrystalBasis.empty()
 
-            p = CrystalStructure(lengths=lengths, angles=angles, base=base)
+            p = CrystalStructure(lengths=lengths, angles=angles, basis=base)
             phases.append(p)
 
         xray_info = XrayInfo.mk_empty()
@@ -90,7 +90,7 @@ def is_nonempty(self) -> bool:
         a,b,c = primary_phase.lengths
         alpha, beta, gamma = primary_phase.angles
         lattice_params_nonempty = not all(math.isnan(x) for x in [a, b, c, alpha, beta, gamma])
-        crystal_basis_nonempty = len(primary_phase.base) > 0
+        crystal_basis_nonempty = len(primary_phase.basis) > 0
         return xray_info_nonemtpy or composition_nonempty or lattice_params_nonempty or crystal_basis_nonempty
 
     @property
@@ -110,7 +110,7 @@ def get_list_repr(self) -> list:
         lattice_params = [a, b, c, alpha, beta, gamma]
         list_repr += lattice_params
 
-        base = structure.base
+        base = structure.basis
         padded_base = self.get_padded_base(base=base, nan_padding=base.is_empty())
         for atomic_site in padded_base:
             list_repr += atomic_site.as_list()