def test_mpr_pipeline(self):
from pymatgen import MPRester
mpr = MPRester()
data = mpr.get_pourbaix_entries(["Zn"])
pbx = PourbaixDiagram(data, filter_solids=True, conc_dict={"Zn": 1e-8})
pbx.find_stable_entry(10, 0)
data = mpr.get_pourbaix_entries(["Ag", "Te"])
pbx = PourbaixDiagram(data,
filter_solids=True,
conc_dict={
"Ag": 1e-8,
"Te": 1e-8
})
self.assertEqual(len(pbx.stable_entries), 30)
test_entry = pbx.find_stable_entry(8, 2)
self.assertAlmostEqual(test_entry.energy, 2.3936747835000016, 3)
# Test custom ions
entries = mpr.get_pourbaix_entries(["Sn", "C", "Na"])
ion = IonEntry(Ion.from_formula("NaO28H80Sn12C24+"), -161.676)
custom_ion_entry = PourbaixEntry(ion, entry_id='my_ion')
pbx = PourbaixDiagram(entries + [custom_ion_entry],
filter_solids=True,
comp_dict={
"Na": 1,
"Sn": 12,
"C": 24
})
self.assertAlmostEqual(
pbx.get_decomposition_energy(custom_ion_entry, 5, 2),
8.31202738629504, 2)
def test_pourbaix_mpr_pipeline(self):
data = self.rester.get_pourbaix_entries(["Zn"])
pbx = PourbaixDiagram(data, filter_solids=True, conc_dict={"Zn": 1e-8})
pbx.find_stable_entry(10, 0)
data = self.rester.get_pourbaix_entries(["Ag", "Te"])
pbx = PourbaixDiagram(data,
filter_solids=True,
conc_dict={
"Ag": 1e-8,
"Te": 1e-8
})
self.assertEqual(len(pbx.stable_entries), 29)
test_entry = pbx.find_stable_entry(8, 2)
self.assertEqual(sorted(test_entry.entry_id), ["ion-10", "mp-499"])
# Test against ion sets with multiple equivalent ions (Bi-V regression)
entries = self.rester.get_pourbaix_entries(["Bi", "V"])
pbx = PourbaixDiagram(entries,
filter_solids=True,
conc_dict={
"Bi": 1e-8,
"V": 1e-8
})
self.assertTrue(
all([
"Bi" in entry.composition and "V" in entry.composition
for entry in pbx.all_entries
]))
def test_mpr_pipeline(self):
from pymatgen.ext.matproj import MPRester
mpr = MPRester()
data = mpr.get_pourbaix_entries(["Zn"])
pbx = PourbaixDiagram(data, filter_solids=True, conc_dict={"Zn": 1e-8})
pbx.find_stable_entry(10, 0)
data = mpr.get_pourbaix_entries(["Ag", "Te"])
pbx = PourbaixDiagram(data, filter_solids=True, conc_dict={"Ag": 1e-8, "Te": 1e-8})
self.assertEqual(len(pbx.stable_entries), 30)
test_entry = pbx.find_stable_entry(8, 2)
self.assertAlmostEqual(test_entry.energy, 2.3894017960000009, 1)
# Test custom ions
entries = mpr.get_pourbaix_entries(["Sn", "C", "Na"])
ion = IonEntry(Ion.from_formula("NaO28H80Sn12C24+"), -161.676)
custom_ion_entry = PourbaixEntry(ion, entry_id="my_ion")
pbx = PourbaixDiagram(
entries + [custom_ion_entry],
filter_solids=True,
comp_dict={"Na": 1, "Sn": 12, "C": 24},
)
self.assertAlmostEqual(pbx.get_decomposition_energy(custom_ion_entry, 5, 2), 2.1209002582, 1)
# Test against ion sets with multiple equivalent ions (Bi-V regression)
entries = mpr.get_pourbaix_entries(["Bi", "V"])
pbx = PourbaixDiagram(entries, filter_solids=True, conc_dict={"Bi": 1e-8, "V": 1e-8})
self.assertTrue(all(["Bi" in entry.composition and "V" in entry.composition for entry in pbx.all_entries]))
def test_solid_filter(self):
entries = self.test_data["Zn"]
pbx = PourbaixDiagram(entries, filter_solids=False)
oxidized_phase = pbx.find_stable_entry(10, 2)
self.assertEqual(oxidized_phase.name, "ZnO2(s)")
entries = self.test_data["Zn"]
pbx = PourbaixDiagram(entries, filter_solids=True)
oxidized_phase = pbx.find_stable_entry(10, 2)
self.assertEqual(oxidized_phase.name, "ZnO(s)")
def test_multicomponent(self):
# Assure no ions get filtered at high concentration
ag_n = [e for e in self.test_data['Ag-Te-N']
if not "Te" in e.composition]
highconc = PourbaixDiagram(ag_n, filter_solids=True,
conc_dict={"Ag": 1e-5, "N": 1})
entry_sets = [set(e.entry_id) for e in highconc.stable_entries]
self.assertIn({"mp-124", "ion-17"}, entry_sets)
# Binary system
pd_binary = PourbaixDiagram(self.test_data['Ag-Te'], filter_solids=True,
comp_dict={"Ag": 0.5, "Te": 0.5},
conc_dict={"Ag": 1e-8, "Te": 1e-8})
self.assertEqual(len(pd_binary.stable_entries), 30)
test_entry = pd_binary.find_stable_entry(8, 2)
self.assertTrue("mp-499" in test_entry.entry_id)
# Find a specific multientry to test
self.assertEqual(pd_binary.get_decomposition_energy(test_entry, 8, 2), 0)
self.assertEqual(pd_binary.get_decomposition_energy(
test_entry.entry_list[0], 8, 2), 0)
pd_ternary = PourbaixDiagram(self.test_data['Ag-Te-N'], filter_solids=True)
self.assertEqual(len(pd_ternary.stable_entries), 49)
ag = self.test_data['Ag-Te-N'][30]
self.assertAlmostEqual(pd_ternary.get_decomposition_energy(ag, 2, -1), 0)
self.assertAlmostEqual(pd_ternary.get_decomposition_energy(ag, 10, -2), 0)
# Test invocation of pourbaix diagram from ternary data
new_ternary = PourbaixDiagram(pd_ternary.all_entries)
self.assertEqual(len(new_ternary.stable_entries), 49)
self.assertAlmostEqual(new_ternary.get_decomposition_energy(ag, 2, -1), 0)
self.assertAlmostEqual(new_ternary.get_decomposition_energy(ag, 10, -2), 0)
def test_multicomponent(self):
# Assure no ions get filtered at high concentration
ag_n = [e for e in self.test_data['Ag-Te-N']
if not "Te" in e.composition]
highconc = PourbaixDiagram(ag_n, filter_solids=True,
conc_dict={"Ag": 1e-5, "N": 1})
entry_sets = [set(e.entry_id) for e in highconc.stable_entries]
self.assertIn({"mp-124", "ion-17"}, entry_sets)
# Binary system
pd_binary = PourbaixDiagram(self.test_data['Ag-Te'], filter_solids=True,
comp_dict={"Ag": 0.5, "Te": 0.5},
conc_dict={"Ag": 1e-8, "Te": 1e-8})
self.assertEqual(len(pd_binary.stable_entries), 30)
test_entry = pd_binary.find_stable_entry(8, 2)
self.assertTrue("mp-499" in test_entry.entry_id)
# Find a specific multientry to test
self.assertEqual(pd_binary.get_decomposition_energy(test_entry, 8, 2), 0)
self.assertEqual(pd_binary.get_decomposition_energy(
test_entry.entry_list[0], 8, 2), 0)
pd_ternary = PourbaixDiagram(self.test_data['Ag-Te-N'], filter_solids=True)
self.assertEqual(len(pd_ternary.stable_entries), 49)
ag = self.test_data['Ag-Te-N'][30]
self.assertAlmostEqual(pd_ternary.get_decomposition_energy(ag, 2, -1), 0)
self.assertAlmostEqual(pd_ternary.get_decomposition_energy(ag, 10, -2), 0)
# Test invocation of pourbaix diagram from ternary data
new_ternary = PourbaixDiagram(pd_ternary.all_entries)
self.assertEqual(len(new_ternary.stable_entries), 49)
self.assertAlmostEqual(new_ternary.get_decomposition_energy(ag, 2, -1), 0)
self.assertAlmostEqual(new_ternary.get_decomposition_energy(ag, 10, -2), 0)
def test_multicomponent(self):
# Assure no ions get filtered at high concentration
ag_n = [e for e in self.test_data["Ag-Te-N"] if "Te" not in e.composition]
highconc = PourbaixDiagram(
ag_n, filter_solids=True, conc_dict={"Ag": 1e-5, "N": 1}
)
entry_sets = [set(e.entry_id) for e in highconc.stable_entries]
self.assertIn({"mp-124", "ion-17"}, entry_sets)
# Binary system
pd_binary = PourbaixDiagram(
self.test_data["Ag-Te"],
filter_solids=True,
comp_dict={"Ag": 0.5, "Te": 0.5},
conc_dict={"Ag": 1e-8, "Te": 1e-8},
)
self.assertEqual(len(pd_binary.stable_entries), 30)
test_entry = pd_binary.find_stable_entry(8, 2)
self.assertTrue("mp-499" in test_entry.entry_id)
# Find a specific multientry to test
self.assertEqual(pd_binary.get_decomposition_energy(test_entry, 8, 2), 0)
pd_ternary = PourbaixDiagram(self.test_data["Ag-Te-N"], filter_solids=True)
self.assertEqual(len(pd_ternary.stable_entries), 49)
# Fetch a solid entry and a ground state entry mixture
ag_te_n = self.test_data["Ag-Te-N"][-1]
ground_state_ag_with_ions = MultiEntry(
[self.test_data["Ag-Te-N"][i] for i in [4, 18, 30]],
weights=[1 / 3, 1 / 3, 1 / 3],
)
self.assertAlmostEqual(
pd_ternary.get_decomposition_energy(ag_te_n, 2, -1), 2.767822855765
)
self.assertAlmostEqual(
pd_ternary.get_decomposition_energy(ag_te_n, 10, -2), 3.756840056890625
)
self.assertAlmostEqual(
pd_ternary.get_decomposition_energy(ground_state_ag_with_ions, 2, -1), 0
)
# Test invocation of pourbaix diagram from ternary data
new_ternary = PourbaixDiagram(pd_ternary.all_entries)
self.assertEqual(len(new_ternary.stable_entries), 49)
self.assertAlmostEqual(
new_ternary.get_decomposition_energy(ag_te_n, 2, -1), 2.767822855765
)
self.assertAlmostEqual(
new_ternary.get_decomposition_energy(ag_te_n, 10, -2), 3.756840056890625
)
self.assertAlmostEqual(
new_ternary.get_decomposition_energy(ground_state_ag_with_ions, 2, -1), 0
)
def test_mpr_pipeline(self):
from pymatgen import MPRester
mpr = MPRester()
data = mpr.get_pourbaix_entries(["Zn"])
pbx = PourbaixDiagram(data, filter_solids=True, conc_dict={"Zn": 1e-8})
pbx.find_stable_entry(10, 0)
data = mpr.get_pourbaix_entries(["Ag", "Te"])
pbx = PourbaixDiagram(data, filter_solids=True,
conc_dict={"Ag": 1e-8, "Te": 1e-8})
self.assertEqual(len(pbx.stable_entries), 30)
test_entry = pbx.find_stable_entry(8, 2)
self.assertAlmostEqual(test_entry.energy, 2.393900378500001)
# Test custom ions
entries = mpr.get_pourbaix_entries(["Sn", "C", "Na"])
ion = IonEntry(Ion.from_formula("NaO28H80Sn12C24+"), -161.676)
custom_ion_entry = PourbaixEntry(ion, entry_id='my_ion')
pbx = PourbaixDiagram(entries + [custom_ion_entry], filter_solids=True,
comp_dict={"Na": 1, "Sn": 12, "C": 24})
self.assertAlmostEqual(pbx.get_decomposition_energy(custom_ion_entry, 5, 2),
8.31082110278154)
def test_multicomponent(self):
# Binary system
pd_binary = PourbaixDiagram(self.test_data['Ag-Te'], filter_solids=True,
comp_dict={"Ag": 0.5, "Te": 0.5},
conc_dict={"Ag": 1e-8, "Te": 1e-8})
self.assertEqual(len(pd_binary.stable_entries), 30)
test_entry = pd_binary.find_stable_entry(8, 2)
self.assertTrue("mp-499" in test_entry.entry_id)
# Find a specific multientry to test
self.assertEqual(pd_binary.get_decomposition_energy(test_entry, 8, 2), 0)
self.assertEqual(pd_binary.get_decomposition_energy(
test_entry.entry_list[0], 8, 2), 0)
pd_ternary = PourbaixDiagram(self.test_data['Ag-Te-N'], filter_solids=True)
self.assertEqual(len(pd_ternary.stable_entries), 49)
ag = self.test_data['Ag-Te-N'][30]
self.assertAlmostEqual(pd_ternary.get_decomposition_energy(ag, 2, -1), 0)
self.assertAlmostEqual(pd_ternary.get_decomposition_energy(ag, 10, -2), 0)