tests: Added optional num attribute in CrystalExample methods; Remove…

…d ElementSymbol

CrystalStructure/atomic_constants/__init__.py

@@ -1 +1 @@
-from .atomic_constants import ElementSymbol, AtomicConstants
+from .atomic_constants import AtomicConstants

CrystalStructure/atomic_constants/atomic_constants.py

@@ -1,15 +1,13 @@
 import json
 import os.path
-from typing import Literal, Union
-from pymatgen.core import Species, Element
+from typing import Union
 
+from pymatgen.core import Species, Element
 
 SCATTERING_PARAMS_FILENAME = 'atomic_scattering_params.json'
 COVALENT_RADI_FILENAME = 'covalent_radius.json'
 VDW_FILENAME = 'vdw_radius.json'
 
-ElementSymbol = Literal['H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr', 'Rf', 'Db']
-
 def load_constants_json(fname: str) -> dict:
     dirpath = os.path.dirname(__file__)
     fpath = os.path.join(dirpath, fname)
@@ -34,11 +32,11 @@ class AtomicConstants:
     # get
 
     @classmethod
-    def get_vdw_radius(cls, element_symbol: ElementSymbol) -> float:
+    def get_vdw_radius(cls, element_symbol: str) -> float:
         return cls._vdw[element_symbol]
 
     @classmethod
-    def get_covalent(cls, element_symbol: ElementSymbol) -> float:
+    def get_covalent(cls, element_symbol: str) -> float:
         return cls._covalent[element_symbol]
 
     @classmethod

CrystalStructure/crystal/base.py

@@ -2,11 +2,11 @@
 
 import math
 import json
-from typing import Optional
+from typing import Optional, Iterable
 
 from holytools.abstract import Serializable
 
-from CrystalStructure.atomic_constants import ElementSymbol, AtomicConstants
+from CrystalStructure.atomic_constants import AtomicConstants
 from .atomic_site import AtomicSite
 
 
@@ -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 : ElementSymbol = site.get_symbol()
+            element_symbol : str = site.get_symbol()
             covalent_radius  = AtomicConstants.get_covalent(element_symbol=element_symbol)
             vdw_radius = AtomicConstants.get_vdw_radius(element_symbol=element_symbol)
 

CrystalStructure/crystal/crystal.py

@@ -68,7 +68,7 @@ def distance_from_origin(atomic_site : AtomicSite):
             cartesian_coords = new_lattice.get_fractional_coords(coords)
             return np.sum(cartesian_coords**2)
 
-        new_base = sorted(new_base, key=distance_from_origin)
+        new_base = sorted(new_base.atomic_sites, key=distance_from_origin)
         self.base = CrystalBase(new_base)
 
 

CrystalStructure/examples.py

@@ -2,57 +2,27 @@
 
 from CrystalStructure.crystal import CrystalStructure, CrystalBase
 
-cif1_fpath = os.path.join(os.path.dirname(__file__), 'cifs', "test1.cif")
-cif2_fpath = os.path.join(os.path.dirname(__file__), 'cifs', 'test2.cif')
 
 # ---------------------------------------------------------
 
 class CrystalExamples:
     @staticmethod
-    def get_crystal(secondary : bool, mute : bool = False):
-        cif_content = CrystalExamples.get_cif_content(secondary=secondary)
+    def get_crystal(num: int, mute: bool = False):
+        cif_content = CrystalExamples.get_cif_content(num=num)
         crystal_structure = CrystalStructure.from_cif(cif_content=cif_content)
         if not mute:
-            print(f'--> Cif content:\n {open(cif1_fpath).read()}')
+            print(f'--> Cif content:\n {cif_content}')
             print(f'--> Crystal structure:\n {crystal_structure}')
         return crystal_structure
 
-
     @staticmethod
-    def get_base(mute : bool = True) -> CrystalBase:
-        crystal_stucture = CrystalExamples.get_crystal(mute=mute)
+    def get_base(num : int = 1, mute : bool = True) -> CrystalBase:
+        crystal_stucture = CrystalExamples.get_crystal(num=num, mute=mute)
         return crystal_stucture.base
 
     @staticmethod
-    def get_crystal(mute : bool = False):
-        cif_content = CrystalExamples.get_cif_content()
-        crystal_structure = CrystalStructure.from_cif(cif_content=cif_content)
-        if not mute:
-            print(f'--> Cif content:\n {open(cif1_fpath).read()}')
-            print(f'--> Crystal structure:\n {crystal_structure}')
-        return crystal_structure
-
-    @staticmethod
-    def get_cif_content(secondary : bool = False) -> str:
-        cif_fpath = cif1_fpath if not secondary else cif2_fpath
+    def get_cif_content(num : int = 1) -> str:
+        cif_fpath = os.path.join(os.path.dirname(__file__), 'cifs', f"test{num}.cif")
         with open(cif_fpath, 'r') as f:
             cif_content = f.read()
         return cif_content
-
-
-
-    # @staticmethod
-    # def get_label() -> PowderExperiment:
-    #     sample = PowderSample(crystal_structure=CrystalExamples.get_crystal(mute=True), crystallite_size=500)
-    #     artifact = CrystalExamples.get_artifacts()
-    #     powder_sample = PowderExperiment(powder=sample, artifacts=artifact, is_simulated=True)
-    #     return powder_sample
-
-    # @staticmethod
-    # def get_artifacts() -> Artifacts:
-    #     artifacts = Artifacts(primary_wavelength=1.54056, secondary_wavelength=1.54439, secondary_to_primary=0.5)
-    #     return artifacts
-
-# if __name__ == "__main__":
-#     the_sample = CrystalExamples.get_label()
-#     the_sample.make_empty()

tests/t_crystal/crystal_test.py

@@ -1,17 +1,15 @@
-import math
-
 from holytools.devtools import Unittest
 from pymatgen.core import Structure
 
-from CrystalStructure.atomic_constants.atomic_constants import Void
-from CrystalStructure.crystal import CrystalStructure, AtomicSite
+from CrystalStructure.crystal import CrystalStructure
 from CrystalStructure.examples import CrystalExamples
 
+
 # ---------------------------------------------------------
 
 class CrystalTest(Unittest):
     def setUp(self):
-        self.cifs : list[str] =  [CrystalExamples.get_cif_content(), CrystalExamples.get_cif_content(secondary=True)]
+        self.cifs : list[str] = [CrystalExamples.get_cif_content(j) for j in range(1, 4)]
 
         self.pymatgen_structures : list[Structure] = [Structure.from_str(cif, fmt='cif') for cif in self.cifs]
         self.crystals : list[CrystalStructure] = [CrystalStructure.from_cif(cif_content=cif) for cif in self.cifs]