Merge pull request #191 from WMD-group/oxidation_states

Oxidation states

examples/Oxidation_states/mp-540839_CsPbI3_oxi.cif

@@ -0,0 +1,52 @@
+# generated using pymatgen
+data_CsPbI3
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   4.84714164
+_cell_length_b   10.65044663
+_cell_length_c   18.03119927
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   90.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   CsPbI3
+_chemical_formula_sum   'Cs4 Pb4 I12'
+_cell_volume   930.84665829
+_cell_formula_units_Z   4
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_type_symbol
+ _atom_type_oxidation_number
+  Cs+  1.0
+  Pb2+  2.0
+  I-  -1.0
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Cs+  Cs0  1  0.75000000  0.58127558  0.17211973  1.0
+  Cs+  Cs1  1  0.25000000  0.41872442  0.82788027  1.0
+  Cs+  Cs2  1  0.75000000  0.08127558  0.32788027  1.0
+  Cs+  Cs3  1  0.25000000  0.91872442  0.67211973  1.0
+  Pb2+  Pb4  1  0.25000000  0.66184885  0.43921676  1.0
+  Pb2+  Pb5  1  0.75000000  0.33815115  0.56078324  1.0
+  Pb2+  Pb6  1  0.25000000  0.16184885  0.06078324  1.0
+  Pb2+  Pb7  1  0.75000000  0.83815115  0.93921676  1.0
+  I-  I8  1  0.75000000  0.83721116  0.50204455  1.0
+  I-  I9  1  0.25000000  0.16278884  0.49795545  1.0
+  I-  I10  1  0.75000000  0.33721116  0.99795545  1.0
+  I-  I11  1  0.25000000  0.66278884  0.00204455  1.0
+  I-  I12  1  0.25000000  0.52927197  0.61230824  1.0
+  I-  I13  1  0.75000000  0.47072803  0.38769176  1.0
+  I-  I14  1  0.25000000  0.02927197  0.88769176  1.0
+  I-  I15  1  0.75000000  0.97072803  0.11230824  1.0
+  I-  I16  1  0.25000000  0.79631664  0.28730552  1.0
+  I-  I17  1  0.75000000  0.20368336  0.71269448  1.0
+  I-  I18  1  0.25000000  0.29631664  0.21269448  1.0
+  I-  I19  1  0.75000000  0.70368336  0.78730552  1.0

smact/oxidation_states.py

@@ -12,7 +12,8 @@
 
 from numpy import mean
 from pymatgen.core import Structure
-from pymatgen.core.periodic_table import Specie as pmgSpecies
+from pymatgen.core.periodic_table import Species as pmgSpecies
+from pymatgen.core.periodic_table import get_el_sp
 
 from smact import Element, Species, data_directory
 
@@ -146,7 +147,13 @@ def compound_probability(
             if not all(isinstance(i, pmgSpecies) for i in species):
                 raise TypeError("Structure must have oxidation states.")
             else:
-                structure = [Species(i.symbol, i.oxi_state) for i in structure]
+                structure = [
+                    Species(
+                        get_el_sp(i.species_string).symbol,
+                        get_el_sp(i.species_string).oxi_state,
+                    )
+                    for i in structure
+                ]
         else:
             raise TypeError(
                 "Input requires a list of SMACT or Pymatgen Species or a Structure."

smact/properties.py

@@ -1,6 +1,6 @@
 from typing import List, Optional, Union
 
-from numpy import product, sqrt
+import numpy as np
 
 import smact
 
@@ -70,10 +70,10 @@ def band_gap_Harrison(
     V1_bar = (V1_An + V1_Cat) / 2
     V2 = 2.16 * hbarsq_over_m / (d**2)
     V3 = (Cat.eig - An.eig) / 2
-    alpha_m = (1.11 * V1_bar) / sqrt(V2**2 + V3**2)
+    alpha_m = (1.11 * V1_bar) / np.sqrt(V2**2 + V3**2)
 
     # Calculate Band gap [(3-43) Harrison 1980 ]
-    Band_gap = (3.60 / 3.0) * (sqrt(V2**2 + V3**2)) * (1 - alpha_m)
+    Band_gap = (3.60 / 3.0) * (np.sqrt(V2**2 + V3**2)) * (1 - alpha_m)
     if verbose:
         print("V1_bar = ", V1_bar)
         print("V2 = ", V2)
@@ -150,7 +150,7 @@ def compound_electroneg(
         elementlist[i] = [elementlist[i] ** stoichslist[i]]
 
     # Calculate geometric mean (n-th root of product)
-    prod = product(elementlist)
+    prod = np.prod(elementlist)
     compelectroneg = (prod) ** (1.0 / (sum(stoichslist)))
 
     if verbose:

smact/tests/files/mp-540839_CsPbI3_oxi.json

@@ -0,0 +1 @@
+{"@module": "pymatgen.core.structure", "@class": "Structure", "charge": 0, "lattice": {"matrix": [[4.84714164, -0.0, 0.0], [0.0, 10.65044663, 0.0], [0.0, 0.0, 18.03119927]], "pbc": [true, true, true], "a": 4.84714164, "b": 10.65044663, "c": 18.03119927, "alpha": 90.0, "beta": 90.0, "gamma": 90.0, "volume": 930.846658290349}, "properties": {}, "sites": [{"species": [{"element": "Cs", "oxidation_state": 1, "spin": null, "occu": 1.0}], "abc": [0.75, 0.58127558, 0.17211973], "xyz": [3.63535623, 6.190844542112295, 3.103525149928597], "properties": {"magmom": -0.0}, "label": "Cs"}, {"species": [{"element": "Cs", "oxidation_state": 1, "spin": null, "occu": 1.0}], "abc": [0.25, 0.41872442, 0.82788027], "xyz": [1.21178541, 4.4596020878877045, 14.927674120071401], "properties": {"magmom": -0.0}, "label": "Cs"}, {"species": [{"element": "Cs", "oxidation_state": 1, "spin": null, "occu": 1.0}], "abc": [0.75, 0.08127558, 0.32788027], "xyz": [3.63535623, 0.8656212271122954, 5.912074485071402], "properties": {"magmom": -0.0}, "label": "Cs"}, {"species": [{"element": "Cs", "oxidation_state": 1, "spin": null, "occu": 1.0}], "abc": [0.25, 0.91872442, 0.67211973], "xyz": [1.21178541, 9.784825402887703, 12.119124784928596], "properties": {"magmom": -0.0}, "label": "Cs"}, {"species": [{"element": "Pb", "oxidation_state": 2, "spin": null, "occu": 1.0}], "abc": [0.25, 0.66184885, 0.43921676], "xyz": [1.21178541, 7.0489858540518755, 7.919604922283765], "properties": {"magmom": 0.0}, "label": "Pb"}, {"species": [{"element": "Pb", "oxidation_state": 2, "spin": null, "occu": 1.0}], "abc": [0.75, 0.33815115, 0.56078324], "xyz": [3.63535623, 3.6014607759481243, 10.111594347716235], "properties": {"magmom": 0.0}, "label": "Pb"}, {"species": [{"element": "Pb", "oxidation_state": 2, "spin": null, "occu": 1.0}], "abc": [0.25, 0.16184885, 0.06078324], "xyz": [1.21178541, 1.7237625390518754, 1.0959947127162348], "properties": {"magmom": 0.0}, "label": "Pb"}, {"species": [{"element": "Pb", "oxidation_state": 2, "spin": null, "occu": 1.0}], "abc": [0.75, 0.83815115, 0.93921676], "xyz": [3.63535623, 8.926684090948124, 16.935204557283765], "properties": {"magmom": 0.0}, "label": "Pb"}, {"species": [{"element": "I", "oxidation_state": -1, "spin": null, "occu": 1.0}], "abc": [0.75, 0.83721116, 0.50204455], "xyz": [3.63535623, 8.91667277762039, 9.052465323467478], "properties": {"magmom": -0.0}, "label": "I"}, {"species": [{"element": "I", "oxidation_state": -1, "spin": null, "occu": 1.0}], "abc": [0.25, 0.16278884, 0.49795545], "xyz": [1.21178541, 1.733773852379609, 8.978733946532522], "properties": {"magmom": -0.0}, "label": "I"}, {"species": [{"element": "I", "oxidation_state": -1, "spin": null, "occu": 1.0}], "abc": [0.75, 0.33721116, 0.99795545], "xyz": [3.63535623, 3.5914494626203908, 17.99433358153252], "properties": {"magmom": -0.0}, "label": "I"}, {"species": [{"element": "I", "oxidation_state": -1, "spin": null, "occu": 1.0}], "abc": [0.25, 0.66278884, 0.00204455], "xyz": [1.21178541, 7.0589971673796095, 0.036865688467478494], "properties": {"magmom": -0.0}, "label": "I"}, {"species": [{"element": "I", "oxidation_state": -1, "spin": null, "occu": 1.0}], "abc": [0.25, 0.52927197, 0.61230824], "xyz": [1.21178541, 5.6369828692399615, 11.040651890102982], "properties": {"magmom": -0.0}, "label": "I"}, {"species": [{"element": "I", "oxidation_state": -1, "spin": null, "occu": 1.0}], "abc": [0.75, 0.47072803, 0.38769176], "xyz": [3.63535623, 5.013463760760039, 6.990547379897015], "properties": {"magmom": -0.0}, "label": "I"}, {"species": [{"element": "I", "oxidation_state": -1, "spin": null, "occu": 1.0}], "abc": [0.25, 0.02927197, 0.88769176], "xyz": [1.21178541, 0.3117595542399611, 16.006147014897014], "properties": {"magmom": -0.0}, "label": "I"}, {"species": [{"element": "I", "oxidation_state": -1, "spin": null, "occu": 1.0}], "abc": [0.75, 0.97072803, 0.11230824], "xyz": [3.63535623, 10.338687075760038, 2.0250522551029846], "properties": {"magmom": -0.0}, "label": "I"}, {"species": [{"element": "I", "oxidation_state": -1, "spin": null, "occu": 1.0}], "abc": [0.25, 0.79631664, 0.28730552], "xyz": [1.21178541, 8.481127874900922, 5.180463082490969], "properties": {"magmom": -0.0}, "label": "I"}, {"species": [{"element": "I", "oxidation_state": -1, "spin": null, "occu": 1.0}], "abc": [0.75, 0.20368336, 0.71269448], "xyz": [3.63535623, 2.1693187550990767, 12.850736187509028], "properties": {"magmom": -0.0}, "label": "I"}, {"species": [{"element": "I", "oxidation_state": -1, "spin": null, "occu": 1.0}], "abc": [0.25, 0.29631664, 0.21269448], "xyz": [1.21178541, 3.1559045599009234, 3.835136552509029], "properties": {"magmom": -0.0}, "label": "I"}, {"species": [{"element": "I", "oxidation_state": -1, "spin": null, "occu": 1.0}], "abc": [0.75, 0.70368336, 0.78730552], "xyz": [3.63535623, 7.494542070099076, 14.19606271749097], "properties": {"magmom": -0.0}, "label": "I"}]}

smact/tests/test_core.py

@@ -3,6 +3,7 @@
 import os
 import unittest
 
+from pymatgen.core import Structure
 from pymatgen.core.periodic_table import Specie
 
 import smact
@@ -17,6 +18,7 @@
 
 files_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), "files")
 TEST_OX_STATES = os.path.join(files_dir, "test_oxidation_states.txt")
+TEST_STRUCT = os.path.join(files_dir, "mp-540839_CsPbI3_oxi.json")
 
 
 class TestSequenceFunctions(unittest.TestCase):
@@ -417,7 +419,7 @@ def test_lattice_parameters(self):
         self.assertAlmostEqual(wurtz[0], 5.13076)
         self.assertAlmostEqual(wurtz[2], 8.3838)
 
-    # ---------- Lattice parameters -----------
+    # ---------- smact.oxidation_states module -----------
     def test_oxidation_states(self):
         ox = smact.oxidation_states.Oxidation_state_probability_finder()
         self.assertAlmostEqual(
@@ -429,3 +431,8 @@ def test_oxidation_states(self):
             0.74280230326,
         )
         self.assertEqual(len(ox.get_included_species()), 173)
+
+    def test_compound_probability_structure(self):
+        structure = Structure.from_file(TEST_STRUCT)
+        ox = smact.oxidation_states.Oxidation_state_probability_finder()
+        self.assertEqual(ox.compound_probability(structure), 1.0)