def mke_pour_ion_entr(mtnme, ion_dict, stable_solids_minus_h2o, ref_state, entries_aqcorr, ref_dict):
"""
"""
#| - mke_pour_ion_entr
from pymatgen import Element # Accesses properties of element
from pymatgen.core.ion import Ion
from pymatgen.phasediagram.maker import PhaseDiagram
from pymatgen.analysis.pourbaix.entry import PourbaixEntry, IonEntry
from pd_make import ref_entry_find, ref_entry_stoich
pd = PhaseDiagram(entries_aqcorr)
ref_entry = ref_entry_find(stable_solids_minus_h2o, ref_state)
ref_stoich_fact = ref_entry_stoich(ref_entry)
## Calculate DFT reference E for ions (Persson et al, PRB (2012))
dft_for_e=pd.get_form_energy(ref_entry)/ref_stoich_fact # DFT formation E, normalized by composition "factor"
ion_correction_1 = dft_for_e-ref_dict[ref_state] # Difference of DFT form E and exp for E of reference
el = Element(mtnme)
pbx_ion_entries_1 = []
for id in ion_dict:
comp = Ion.from_formula(id['Name']) # Ion name-> Ion comp name (ex. Fe[3+] -> Ion: Fe1 +3)
# comp.composition[el] : number of Fe atoms in ion
num_el_ref = (ref_entry.composition[el]) / ref_stoich_fact # number of element atoms in reference
factor = comp.composition[el] / num_el_ref # Stoicheometric factor for ionic correction
# (i.e. Fe2O3 ref but calc E for Fe[2+] ion)
energy = id['Energy'] + ion_correction_1 * factor
#TEMP_PRINT
if id['Name']=='Pd[2+]':
energy = 123
# print id['Name']
pbx_entry_ion = PourbaixEntry(IonEntry(comp, energy))
pbx_entry_ion.name = id['Name']
pbx_ion_entries_1.append(pbx_entry_ion)
return pbx_ion_entries_1
class PhaseDiagramTest(unittest.TestCase):
def setUp(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
(self.elements, self.entries) = \
PDEntryIO.from_csv(os.path.join(module_dir, "pdentries_test.csv"))
self.pd = PhaseDiagram(self.entries)
def test_init(self):
#Ensure that a bad set of entries raises a PD error. Remove all Li
#from self.entries.
entries = filter(
lambda e: (not e.composition.is_element) or e.composition.elements[
0] != Element("Li"), self.entries)
self.assertRaises(PhaseDiagramError, PhaseDiagram, entries,
self.elements)
def test_dim1(self):
#Ensure that dim 1 PDs can eb generated.
for el in ["Li", "Fe", "O2"]:
entries = [
e for e in self.entries if e.composition.reduced_formula == el
]
pd = PhaseDiagram(entries)
self.assertEqual(len(pd.stable_entries), 1)
a = PDAnalyzer(pd)
for e in entries:
decomp, ehull = a.get_decomp_and_e_above_hull(e)
self.assertGreaterEqual(ehull, 0)
plotter = PDPlotter(pd)
lines, stable_entries, unstable_entries = plotter.pd_plot_data
self.assertEqual(lines[0][1], [0, 0])
def test_stable_entries(self):
stable_formulas = [
ent.composition.reduced_formula for ent in self.pd.stable_entries
]
expected_stable = [
"Fe2O3", "Li5FeO4", "LiFeO2", "Fe3O4", "Li", "Fe", "Li2O", "O2",
"FeO"
]
for formula in expected_stable:
self.assertTrue(formula in stable_formulas,
formula + " not in stable entries!")
def test_get_formation_energy(self):
stable_formation_energies = {
ent.composition.reduced_formula: self.pd.get_form_energy(ent)
for ent in self.pd.stable_entries
}
expected_formation_energies = {
'Li5FeO4': -164.8117344866667,
'Li2O2': -14.119232793333332,
'Fe2O3': -16.574164339999996,
'FeO': -5.7141519966666685,
'Li': 0.0,
'LiFeO2': -7.732752316666666,
'Li2O': -6.229303868333332,
'Fe': 0.0,
'Fe3O4': -22.565714456666683,
'Li2FeO3': -45.67166036000002,
'O2': 0.0
}
for formula, energy in expected_formation_energies.items():
self.assertAlmostEqual(energy, stable_formation_energies[formula],
7)
def test_all_entries_hulldata(self):
self.assertEqual(len(self.pd.all_entries_hulldata), 492)
def test_planar_inputs(self):
e1 = PDEntry('H', 0)
e2 = PDEntry('He', 0)
e3 = PDEntry('Li', 0)
e4 = PDEntry('Be', 0)
e5 = PDEntry('B', 0)
e6 = PDEntry('Rb', 0)
pd = PhaseDiagram([e1, e2, e3, e4, e5, e6],
map(Element, ['Rb', 'He', 'B', 'Be', 'Li', 'H']))
self.assertEqual(len(pd.facets), 1)
def test_str(self):
self.assertIsNotNone(str(self.pd))
class PhaseDiagramTest(unittest.TestCase):
def setUp(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
(self.elements, self.entries) = \
PDEntryIO.from_csv(os.path.join(module_dir, "pdentries_test.csv"))
self.pd = PhaseDiagram(self.entries)
def test_init(self):
#Ensure that a bad set of entries raises a PD error. Remove all Li
#from self.entries.
entries = filter(lambda e: (not e.composition.is_element) or
e.composition.elements[0] != Element("Li"),
self.entries)
self.assertRaises(PhaseDiagramError, PhaseDiagram, entries,
self.elements)
def test_dim1(self):
#Ensure that dim 1 PDs can eb generated.
for el in ["Li", "Fe", "O2"]:
entries = [e for e in self.entries
if e.composition.reduced_formula == el]
pd = PhaseDiagram(entries)
self.assertEqual(len(pd.stable_entries), 1)
a = PDAnalyzer(pd)
for e in entries:
decomp, ehull = a.get_decomp_and_e_above_hull(e)
self.assertGreaterEqual(ehull, 0)
plotter = PDPlotter(pd)
lines, stable_entries, unstable_entries = plotter.pd_plot_data
self.assertEqual(lines[0][1], [0, 0])
def test_stable_entries(self):
stable_formulas = [ent.composition.reduced_formula
for ent in self.pd.stable_entries]
expected_stable = ["Fe2O3", "Li5FeO4", "LiFeO2", "Fe3O4", "Li", "Fe",
"Li2O", "O2", "FeO"]
for formula in expected_stable:
self.assertTrue(formula in stable_formulas,
formula + " not in stable entries!")
def test_get_formation_energy(self):
stable_formation_energies = {ent.composition.reduced_formula:
self.pd.get_form_energy(ent)
for ent in self.pd.stable_entries}
expected_formation_energies = {'Li5FeO4': -164.8117344866667,
'Li2O2': -14.119232793333332,
'Fe2O3': -16.574164339999996,
'FeO': -5.7141519966666685, 'Li': 0.0,
'LiFeO2': -7.732752316666666,
'Li2O': -6.229303868333332,
'Fe': 0.0, 'Fe3O4': -22.565714456666683,
'Li2FeO3': -45.67166036000002,
'O2': 0.0}
for formula, energy in expected_formation_energies.items():
self.assertAlmostEqual(energy, stable_formation_energies[formula],
7)
def test_all_entries_hulldata(self):
self.assertEqual(len(self.pd.all_entries_hulldata), 492)
def test_planar_inputs(self):
e1 = PDEntry('H', 0)
e2 = PDEntry('He', 0)
e3 = PDEntry('Li', 0)
e4 = PDEntry('Be', 0)
e5 = PDEntry('B', 0)
e6 = PDEntry('Rb', 0)
pd = PhaseDiagram([e1, e2, e3, e4, e5, e6],
map(Element, ['Rb', 'He', 'B', 'Be', 'Li', 'H']))
self.assertEqual(len(pd.facets), 1)
def test_str(self):
self.assertIsNotNone(str(self.pd))
error = dict()
for each_formula in formula_list:
try:
stable_ent = get_most_stable_entry(each_formula)
except IndexError:
error["error"] = "No structure with that formula"
json_dir = output_path + "/" + "output.json"
with open(json_dir, "w") as outfile:
json.dump(error, outfile)
print(error)
exit()
# print stable_ent.name, phase.get_form_energy(stable_ent)
(each_comp, each_factor
) = stable_ent.composition.get_reduced_composition_and_factor()
form_energy[
stable_ent.name] = phase.get_form_energy(stable_ent) / each_factor
stable_formula.append(stable_ent)
try:
stable_result = get_most_stable_entry(result)
except IndexError:
error["error"] = "No structure with that formula"
json_dir = output_path + "/" + "output.json"
with open(json_dir, "w") as outfile:
json.dump(error, outfile)
print(error)
exit()
# print stable_result.name, phase.get_form_energy(stable_result)
(compo,
factor) = stable_result.composition.get_reduced_composition_and_factor()
