def test_modes(self):
s = PymatgenTest.get_structure("CsCl")
nacl = PymatgenTest.get_structure("CsCl")
nacl.replace_species({"Cs": "Na"})
nacl.scale_lattice(184.384551033)
p = RLSVolumePredictor(radii_type="ionic", use_bv=False)
self.assertRaises(ValueError, p.predict, s, nacl)
p = RLSVolumePredictor(radii_type="ionic-atomic", use_bv=False)
self.assertAlmostEqual(p.predict(s, nacl), 391.884366481)
p = RLSVolumePredictor(radii_type="ionic-atomic", use_bv=True)
self.assertAlmostEqual(p.predict(s, nacl), 342.84905395082535)
def test_modes(self):
s = PymatgenTest.get_structure("CsCl")
nacl = PymatgenTest.get_structure("CsCl")
nacl.replace_species({"Cs": "Na"})
nacl.scale_lattice(184.384551033)
p = RLSVolumePredictor(radii_type="ionic", use_bv=False)
self.assertRaises(ValueError, p.predict, s, nacl)
p = RLSVolumePredictor(radii_type="ionic-atomic", use_bv=False)
self.assertAlmostEqual(p.predict(s, nacl), 391.884366481)
p = RLSVolumePredictor(radii_type="ionic-atomic", use_bv=True)
self.assertAlmostEqual(p.predict(s, nacl), 342.84905395082535)
def test_predict(self):
s = PymatgenTest.get_structure("CsCl")
nacl = PymatgenTest.get_structure("CsCl")
nacl.replace_species({"Cs": "Na"})
nacl.scale_lattice(184.384551033)
p = RLSVolumePredictor(radii_type="ionic")
self.assertAlmostEqual(p.predict(s, nacl), 342.84905395082535)
p = RLSVolumePredictor(radii_type="atomic")
self.assertAlmostEqual(p.predict(s, nacl), 391.884366481)
lif = PymatgenTest.get_structure("CsCl")
lif.replace_species({"Cs": "Li", "Cl": "F"})
p = RLSVolumePredictor(radii_type="ionic")
self.assertAlmostEqual(p.predict(lif, nacl), 74.268402413690467)
p = RLSVolumePredictor(radii_type="atomic")
self.assertAlmostEqual(p.predict(lif, nacl), 62.2808125839)
lfpo = PymatgenTest.get_structure("LiFePO4")
lmpo = PymatgenTest.get_structure("LiFePO4")
lmpo.replace_species({"Fe": "Mn"})
p = RLSVolumePredictor(radii_type="ionic")
self.assertAlmostEqual(p.predict(lmpo, lfpo), 310.08253254420134)
p = RLSVolumePredictor(radii_type="atomic")
self.assertAlmostEqual(p.predict(lmpo, lfpo), 299.607967711)
sto = PymatgenTest.get_structure("SrTiO3")
scoo = PymatgenTest.get_structure("SrTiO3")
scoo.replace_species({"Ti4+": "Co4+"})
p = RLSVolumePredictor(radii_type="ionic")
self.assertAlmostEqual(p.predict(scoo, sto), 56.162534974936463)
p = RLSVolumePredictor(radii_type="atomic")
self.assertAlmostEqual(p.predict(scoo, sto), 57.4777835108)
# Use Ag7P3S11 as a test case:
# (i) no oxidation states are assigned and CVP-atomic scheme is selected.
aps = Structure.from_file(os.path.join(dir_path,
"Ag7P3S11_mp-683910_primitive.cif"))
apo = Structure.from_file(os.path.join(dir_path,
"Ag7P3S11_mp-683910_primitive.cif"))
apo.replace_species({"S": "O"})
p = RLSVolumePredictor(radii_type="atomic", check_isostructural=False)
self.assertAlmostEqual(p.predict(apo, aps), 1196.31384276)
# (ii) Oxidation states are assigned.
apo.add_oxidation_state_by_element({"Ag": 1, "P": 5, "O": -2})
aps.add_oxidation_state_by_element({"Ag": 1, "P": 5, "S": -2})
p = RLSVolumePredictor(radii_type="ionic")
self.assertAlmostEqual(p.predict(apo, aps), 1165.23259079)
p = RLSVolumePredictor(radii_type="atomic")
self.assertAlmostEqual(p.predict(apo, aps), 1196.31384276)
def test_predict(self):
s = PymatgenTest.get_structure("CsCl")
nacl = PymatgenTest.get_structure("CsCl")
nacl.replace_species({"Cs": "Na"})
nacl.scale_lattice(184.384551033)
p = RLSVolumePredictor(radii_type="ionic")
self.assertAlmostEqual(p.predict(s, nacl), 342.84905395082535)
p = RLSVolumePredictor(radii_type="atomic")
self.assertAlmostEqual(p.predict(s, nacl), 391.884366481)
lif = PymatgenTest.get_structure("CsCl")
lif.replace_species({"Cs": "Li", "Cl": "F"})
p = RLSVolumePredictor(radii_type="ionic")
self.assertAlmostEqual(p.predict(lif, nacl), 74.268402413690467)
p = RLSVolumePredictor(radii_type="atomic")
self.assertAlmostEqual(p.predict(lif, nacl), 62.2808125839)
lfpo = PymatgenTest.get_structure("LiFePO4")
lmpo = PymatgenTest.get_structure("LiFePO4")
lmpo.replace_species({"Fe": "Mn"})
p = RLSVolumePredictor(radii_type="ionic")
self.assertAlmostEqual(p.predict(lmpo, lfpo), 310.08253254420134)
p = RLSVolumePredictor(radii_type="atomic")
self.assertAlmostEqual(p.predict(lmpo, lfpo), 299.607967711)
sto = PymatgenTest.get_structure("SrTiO3")
scoo = PymatgenTest.get_structure("SrTiO3")
scoo.replace_species({"Ti4+": "Co4+"})
p = RLSVolumePredictor(radii_type="ionic")
self.assertAlmostEqual(p.predict(scoo, sto), 56.162534974936463)
p = RLSVolumePredictor(radii_type="atomic")
self.assertAlmostEqual(p.predict(scoo, sto), 57.4777835108)
# Use Ag7P3S11 as a test case:
# (i) no oxidation states are assigned and CVP-atomic scheme is selected.
aps = Structure.from_file(os.path.join(dir_path,
"Ag7P3S11_mp-683910_primitive.cif"))
apo = Structure.from_file(os.path.join(dir_path,
"Ag7P3S11_mp-683910_primitive.cif"))
apo.replace_species({"S": "O"})
p = RLSVolumePredictor(radii_type="atomic", check_isostructural=False)
self.assertAlmostEqual(p.predict(apo, aps), 1196.31384276)
# (ii) Oxidation states are assigned.
apo.add_oxidation_state_by_element({"Ag": 1, "P": 5, "O": -2})
aps.add_oxidation_state_by_element({"Ag": 1, "P": 5, "S": -2})
p = RLSVolumePredictor(radii_type="ionic")
self.assertAlmostEqual(p.predict(apo, aps), 1165.23259079)
p = RLSVolumePredictor(radii_type="atomic")
self.assertAlmostEqual(p.predict(apo, aps), 1196.31384276)