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 = CompoundPhaseDiagram(
self.entries,
[Composition("Li2O"), Composition("Fe2O3")])
class CompoundPhaseDiagramTest(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 = CompoundPhaseDiagram(
self.entries,
[Composition("Li2O"), Composition("Fe2O3")])
def test_stable_entries(self):
stable_formulas = [ent.name for ent in self.pd.stable_entries]
expected_stable = ["Fe2O3", "Li5FeO4", "LiFeO2", "Li2O"]
for formula in expected_stable:
self.assertTrue(formula in stable_formulas)
def test_get_formation_energy(self):
stable_formation_energies = {
ent.name: self.pd.get_form_energy(ent)
for ent in self.pd.stable_entries
}
expected_formation_energies = {
'Li5FeO4': -7.0773284399999739,
'Fe2O3': 0,
'LiFeO2': -0.47455929750000081,
'Li2O': 0
}
for formula, energy in expected_formation_energies.items():
self.assertAlmostEqual(energy, stable_formation_energies[formula],
7)
def test_str(self):
self.assertIsNotNone(str(self.pd))
class CompoundPhaseDiagramTest(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 = CompoundPhaseDiagram(self.entries, [Composition("Li2O"),
Composition("Fe2O3")])
def test_stable_entries(self):
stable_formulas = [ent.name for ent in self.pd.stable_entries]
expected_stable = ["Fe2O3", "Li5FeO4", "LiFeO2", "Li2O"]
for formula in expected_stable:
self.assertTrue(formula in stable_formulas)
def test_get_formation_energy(self):
stable_formation_energies = {ent.name:
self.pd.get_form_energy(ent)
for ent in self.pd.stable_entries}
expected_formation_energies = {'Li5FeO4': -7.0773284399999739,
'Fe2O3': 0,
'LiFeO2': -0.47455929750000081,
'Li2O': 0}
for formula, energy in expected_formation_energies.items():
self.assertAlmostEqual(energy, stable_formation_energies[formula],
7)
def test_str(self):
self.assertIsNotNone(str(self.pd))
def get_phase_diagram_plot(self):
"""
Returns a phase diagram plot, as a matplotlib plot object.
"""
# set the font to Times, rendered with Latex
plt.rc('font', **{'family': 'serif', 'serif': ['Times']})
plt.rc('text', usetex=True)
# parse the composition space endpoints
endpoints_line = self.lines[0].split()
endpoints = []
for word in endpoints_line[::-1]:
if word == 'endpoints:':
break
else:
endpoints.append(Composition(word))
if len(endpoints) < 2:
print('There must be at least 2 endpoint compositions to make a '
'phase diagram.')
quit()
# parse the compositions and total energies of all the structures
compositions = []
total_energies = []
for i in range(4, len(self.lines)):
line = self.lines[i].split()
compositions.append(Composition(line[1]))
total_energies.append(float(line[2]))
# make a list of PDEntries
pdentries = []
for i in range(len(compositions)):
pdentries.append(PDEntry(compositions[i], total_energies[i]))
# make a CompoundPhaseDiagram
compound_pd = CompoundPhaseDiagram(pdentries, endpoints)
# make a PhaseDiagramPlotter
pd_plotter = PDPlotter(compound_pd, show_unstable=100)
return pd_plotter.get_plot(label_unstable=False)
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 = CompoundPhaseDiagram(self.entries, [Composition("Li2O"),
Composition("Fe2O3")])
term_comp = [
Composition(names[7]),
Composition(names[11]),
Composition(names[32])
]
# creating entries from for the LDA phase diagram
entries_lda = []
for i in range(len(names)):
# entries_lda.append(PDEntry(names[i],enlda[i], names[i], "LDA"))
entries_lda.append(PDEntry(names[i], enlda[i], " ", "LDA"))
# creating the phase diagram for LDA
pd_lda = PhaseDiagram(entries_lda)
cpd_lda = CompoundPhaseDiagram(entries_lda,
term_comp,
normalize_terminal_compositions=True)
a_lda = PDAnalyzer(pd_lda)
# creating entries from for the PBE phase diagram
entries_pbe = []
for i in range(len(names)):
# entries_pbe.append(PDEntry(names[i],enpbe[i], names[i], "PBE"))
entries_pbe.append(PDEntry(names[i], enpbe[i], " ", "PBE"))
# creating the phase diagram for PBE
pd_pbe = PhaseDiagram(entries_pbe)
cpd_pbe = CompoundPhaseDiagram(entries_pbe,
term_comp,
normalize_terminal_compositions=True)
a_pbe = PDAnalyzer(pd_pbe)
