crystal: Added typecasting pymatgen elements to species in .from_pyma…

…tgen

.gitignore

@@ -42,7 +42,6 @@ pip-delete-this-directory.txt
 htmlcov/
 .tox/
 .nox/
-.coverage
 .coverage.*
 .cache
 nosetests.xml

CrystalStructure/atomic_constants/atomic_constants.py

@@ -1,8 +1,5 @@
 import json
 import os.path
-from typing import Union
-
-from pymatgen.core import Species, Element
 
 SCATTERING_PARAMS_FILENAME = 'atomic_scattering_params.json'
 COVALENT_RADI_FILENAME = 'covalent_radius.json'

CrystalStructure/crystal/atomic_site.py

@@ -2,10 +2,10 @@
 
 import json
 from dataclasses import dataclass
-from typing import Union, Optional
-from pymatgen.core import Species, Element, DummySpecies
+from typing import Optional
 
 from holytools.abstract import Serializable
+from pymatgen.core import Species, DummySpecies
 from pymatgen.util.typing import SpeciesLike
 
 from CrystalStructure.atomic_constants.atomic_constants import AtomicConstants
@@ -30,7 +30,7 @@ class AtomicSite(Serializable):
     wyckoff_letter : Optional[str] = None
 
     def __post_init__(self):
-        self.atom_type = AtomType(symbol=self.species_symbol)
+        self.atom_type : AtomType = AtomType(symbol=self.species_symbol)
 
     @classmethod
     def make_void(cls) -> AtomicSite:
@@ -48,9 +48,6 @@ def is_nonstandard(self) -> bool:
     # ---------------------------------------------------------
     # properties
 
-    def get_symbol(self) -> str:
-        return self.atom_type.get_symbol()
-
     def as_list(self) -> list[float]:
         site_arr = [*self.get_scattering_params(), self.x, self.y, self.z, self.occupancy]
         return site_arr
@@ -87,14 +84,14 @@ class AtomType:
 
     def __init__(self, symbol : str):
         if symbol == self.void_symbol:
-            self.species_like : SpeciesLike = DummySpecies(symbol=self.void_symbol)
+            self.specifier : SpeciesLike = DummySpecies(symbol=self.void_symbol)
         if symbol == self.placeholder_symbol:
-            self.species_like : SpeciesLike = DummySpecies(symbol=self.placeholder_symbol)
+            self.specifier : SpeciesLike = DummySpecies(symbol=self.placeholder_symbol)
         else:
-            self.species_like : SpeciesLike = Species.from_str(species_string=symbol)
+            self.specifier : SpeciesLike = Species.from_str(species_string=symbol)
 
     def get_symbol(self):
-        return str(self.species_like)
+        return str(self.specifier)
 
     @property
     def scattering_params(self) -> ScatteringParams:
@@ -106,7 +103,7 @@ def scattering_params(self) -> ScatteringParams:
         else:
             # TODO: This casting only currently exists beacuse the scattering param table only has values for (unoxidized) elements, not ions
             # TODO: Normally would simply be species_symbol=str(self.species_like)
-            species_symbol = self.species_like.element.symbol
+            species_symbol = self.specifier.element.symbol
             values = AtomicConstants.get_scattering_params(species_symbol=species_symbol)
 
         (a1, b1), (a2, b2), (a3, b3), (a4, b4) = values

CrystalStructure/crystal/base.py

@@ -23,7 +23,7 @@ def __init__(self, atomic_sites : Optional[list[AtomicSite]] = None):
     def calculate_atomic_volume(self) -> float:
         total_atomic_volume = 0
         for site in self.get_non_void_sites():
-            element_symbol : str = site.get_symbol()
+            element_symbol : str = site.species_symbol
             covalent_radius  = AtomicConstants.get_covalent(element_symbol=element_symbol)
             vdw_radius = AtomicConstants.get_vdw_radius(element_symbol=element_symbol)
 

CrystalStructure/crystal/crystal.py

@@ -6,7 +6,7 @@
 
 import numpy as np
 from holytools.abstract import JsonDataclass
-from pymatgen.core import Structure, Lattice
+from pymatgen.core import Structure, Lattice, Species, Element
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.symmetry.groups import SpaceGroup
 
@@ -59,7 +59,7 @@ def standardize(self):
         new_base = CrystalBase()
         for site in self.base:
             x,y,z = apply_permutation([site.x, site.y, site.z], sort_permutation)
-            new_site = AtomicSite(x=x, y=y, z=z, occupancy=site.occupancy, atom_type=site.atom_type)
+            new_site = AtomicSite(x=x, y=y, z=z, occupancy=site.occupancy, species_symbol=site.species_symbol)
             new_base.append(new_site)
 
 
@@ -101,8 +101,10 @@ def from_pymatgen(cls, pymatgen_structure: Structure) -> CrystalStructure:
         for index, site in enumerate(pymatgen_structure.sites):
             site_composition = site.species
             for species, occupancy in site_composition.items():
+                if isinstance(species, Element):
+                    species = Species(symbol=species.symbol, oxidation_state=0)
                 x,y,z = lattice.get_fractional_coords(site.coords)
-                atomic_site = AtomicSite(x, y, z, occupancy=occupancy, atom_type=species)
+                atomic_site = AtomicSite(x, y, z, occupancy=occupancy, species_symbol=str(species))
                 base.append(atomic_site)
 
         crystal_str = cls(lengths=Lengths(a=lattice.a, b=lattice.b, c=lattice.c),
@@ -120,7 +122,7 @@ def to_pymatgen(self) -> Structure:
         lattice = Lattice.from_parameters(a, b, c, alpha, beta, gamma)
 
         non_void_sites = self.base.get_non_void_sites()
-        atoms = [site.atom_type for site in non_void_sites]
+        atoms = [site.atom_type.specifier for site in non_void_sites]
         positions = [(site.x, site.y, site.z) for site in non_void_sites]
         return Structure(lattice, atoms, positions)
 

tests/t_crystal/t_standard.py

@@ -1,8 +1,7 @@
 from holytools.devtools import Unittest
-from pymatgen.core import Species
 
-from CrystalStructure.atomic_constants.atomic_constants import Void
 from CrystalStructure.crystal import CrystalStructure, AtomicSite, Lengths, Angles, CrystalBase
+from CrystalStructure.crystal.atomic_site import AtomType
 
 
 # ---------------------------------------------------------
@@ -12,9 +11,9 @@ def setUp(self):
         primitives = Lengths(5, 3, 4)
         mock_angles = Angles(90, 90, 90)
         mock_base = CrystalBase([
-            AtomicSite(x=0.5, y=0.5, z=0.5, occupancy=1.0, atom_type=Species("Si")),
-            AtomicSite(x=0.1, y=0.1, z=0.1, occupancy=1.0, atom_type=Species("O")),
-            AtomicSite(x=0.9, y=0.9, z=0.9, occupancy=1.0, atom_type=Void())
+            AtomicSite(x=0.5, y=0.5, z=0.5, occupancy=1.0, species_symbol="Si"),
+            AtomicSite(x=0.1, y=0.1, z=0.1, occupancy=1.0, species_symbol="O"),
+            AtomicSite(x=0.9, y=0.9, z=0.9, occupancy=1.0, species_symbol=AtomType.void_symbol)
         ])
         crystal = CrystalStructure(lengths=primitives, angles=mock_angles, base=mock_base)
         crystal.calculate_properties()
@@ -35,8 +34,8 @@ def test_scaling(self):
 
     def test_standardization(self):
         self.mock_crystal.standardize()
-        expected_species_list = ['O', 'Si', Void.symbol]
-        acrual_species_list = [self.get_site_symbol(site) for site in self.mock_crystal.base]
+        expected_species_list = ['O', 'Si', AtomType.void_symbol]
+        acrual_species_list = [site.species_symbol for site in self.mock_crystal.base]
         self.assertEqual(acrual_species_list, expected_species_list)
 
         actual_primitives = self.mock_crystal.lengths.as_tuple()
@@ -45,14 +44,5 @@ def test_standardization(self):
 
 
 
-    @staticmethod
-    def get_site_symbol(site : AtomicSite):
-        if isinstance(site.atom_type, Void):
-            symbol = Void.symbol
-        else:
-            symbol = site.atom_type.element.symbol
-        return symbol
-
-
 if __name__ == "__main__":
     TestCrystalStandardization.execute_all()