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_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 setUpClass(cls):
cls.test_data = loadfn(
os.path.join(PymatgenTest.TEST_FILES_DIR,
"pourbaix_test_data.json"))
cls.pbx = PourbaixDiagram(cls.test_data["Zn"], filter_solids=True)
cls.pbx_nofilter = PourbaixDiagram(cls.test_data["Zn"],
filter_solids=False)
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_pourbaix_heavy(self):
entries = self.rester.get_pourbaix_entries(["Li", "Mg", "Sn", "Pd"])
pbx = PourbaixDiagram(entries, nproc=4, filter_solids=False)
entries = self.rester.get_pourbaix_entries(["Ba", "Ca", "V", "Cu", "F"])
pbx = PourbaixDiagram(entries, nproc=4, filter_solids=False)
entries = self.rester.get_pourbaix_entries(["Ba", "Ca", "V", "Cu", "F", "Fe"])
pbx = PourbaixDiagram(entries, nproc=4, filter_solids=False)
entries = self.rester.get_pourbaix_entries(["Na", "Ca", "Nd", "Y", "Ho", "F"])
pbx = PourbaixDiagram(entries, nproc=4, filter_solids=False)
def test_get_pourbaix_entries(self):
pbx_entries = self.rester.get_pourbaix_entries(["Fe"])
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
# Ensure entries are pourbaix compatible
pbx = PourbaixDiagram(pbx_entries)
# Try binary system
pbx_entries = self.rester.get_pourbaix_entries(["Fe", "Cr"])
pbx = PourbaixDiagram(pbx_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_heavy(self):
from pymatgen import MPRester
mpr = MPRester()
entries = mpr.get_pourbaix_entries(["Li", "Mg", "Sn", "Pd"])
pbx = PourbaixDiagram(entries, nproc=4, filter_solids=False)
entries = mpr.get_pourbaix_entries(["Ba", "Ca", "V", "Cu", "F"])
pbx = PourbaixDiagram(entries, nproc=4, filter_solids=False)
entries = mpr.get_pourbaix_entries(["Ba", "Ca", "V", "Cu", "F", "Fe"])
pbx = PourbaixDiagram(entries, nproc=4, filter_solids=False)
entries = mpr.get_pourbaix_entries(["Na", "Ca", "Nd", "Y", "Ho", "F"])
pbx = PourbaixDiagram(entries, nproc=4, filter_solids=False)
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_get_pourbaix_entries(self):
pbx_entries = self.rester.get_pourbaix_entries(["Fe"])
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
# Ensure entries are pourbaix compatible
pbx = PourbaixDiagram(pbx_entries)
# Try binary system
pbx_entries = self.rester.get_pourbaix_entries(["Fe", "Cr"])
pbx = PourbaixDiagram(pbx_entries)
# Test Zn-S, which has Na in reference solids
pbx_entries = self.rester.get_pourbaix_entries(["Zn", "S"])
def test_pourbaix_diagram(self):
self.assertEqual(
{e.name
for e in self.pbx.stable_entries},
{"ZnO(s)", "Zn[2+]", "ZnHO2[-]", "ZnO2[2-]", "Zn(s)"},
"List of stable entries does not match",
)
self.assertEqual(
{e.name
for e in self.pbx_nofilter.stable_entries},
{
"ZnO(s)", "Zn[2+]", "ZnHO2[-]", "ZnO2[2-]", "Zn(s)", "ZnO2(s)",
"ZnH(s)"
},
"List of stable entries for unfiltered pbx does not match",
)
pbx_lowconc = PourbaixDiagram(self.test_data["Zn"],
conc_dict={"Zn": 1e-8},
filter_solids=True)
self.assertEqual(
{e.name
for e in pbx_lowconc.stable_entries},
{"Zn(HO)2(aq)", "Zn[2+]", "ZnHO2[-]", "ZnO2[2-]", "Zn(s)"},
)
def test_get_pourbaix_entries(self, mpr):
# test input chemsys as a list of elements
pbx_entries = mpr.get_pourbaix_entries(["Fe", "Cr"])
for pbx_entry in pbx_entries:
assert isinstance(pbx_entry, PourbaixEntry)
# test input chemsys as a string
pbx_entries = mpr.get_pourbaix_entries("Fe-Cr")
for pbx_entry in pbx_entries:
assert isinstance(pbx_entry, PourbaixEntry)
# test use_gibbs kwarg
pbx_entries = mpr.get_pourbaix_entries("Li-O", use_gibbs=300)
for pbx_entry in pbx_entries:
assert isinstance(pbx_entry, PourbaixEntry)
# test solid_compat kwarg
with pytest.raises(ValueError,
match="Solid compatibility can only be"):
mpr.get_pourbaix_entries("Ti-O", solid_compat=None)
# test removal of extra elements from reference solids
# Li-Zn-S has Na in reference solids
pbx_entries = mpr.get_pourbaix_entries("Li-Zn-S")
assert not any([e for e in pbx_entries if 'Na' in e.composition])
# Ensure entries are pourbaix compatible
PourbaixDiagram(pbx_entries)
def get_electrochemical_stability(mpid, pH, potential):
'''
A wrapper for pymatgen to construct Pourbaix amd calculate electrochemical
stability under reaction condition (i.e. at a given pH and applied potential).
Arg:
mpid Materials project ID of a bulk composition. e.g. Pt: 'mp-126'.
pH: pH at reaction condition. Commonly ones are: acidic: pH=0,
neutral: pH=7, and basic pH=14.
potential: Applied potential at reaction condition.
Returns:
stability Electrochemical stability of a composition under reaction condition,
unit is eV/atom.
'''
mpr = MPRester(read_rc('matproj_api_key'))
try:
entry = mpr.get_entries(mpid)[0]
composition = entry.composition
comp_dict = {str(key): value for key, value in composition.items()
if key not in ELEMENTS_HO}
entries = mpr.get_pourbaix_entries(list(comp_dict.keys()))
entry = [entry for entry in entries if entry.entry_id == mpid][0]
pbx = PourbaixDiagram(entries, comp_dict=comp_dict, filter_solids=False)
stability = pbx.get_decomposition_energy(entry, pH=pH, V=potential)
stability = round(stability, 3)
# Some mpid's stability are not available
except IndexError:
stability = np.nan
return stability
def setUp(self):
warnings.simplefilter("ignore")
self.test_data = loadfn(
os.path.join(PymatgenTest.TEST_FILES_DIR,
"pourbaix_test_data.json"))
self.pd = PourbaixDiagram(self.test_data["Zn"])
self.plotter = PourbaixPlotter(self.pd)
def test_get_pourbaix_entries(self):
# test input chemsys as a list of elements
pbx_entries = self.rester.get_pourbaix_entries(["Fe", "Cr"])
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
# test input chemsys as a string
pbx_entries = self.rester.get_pourbaix_entries("Fe-Cr")
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
fe_two_plus = [e for e in pbx_entries if e.entry_id == "ion-0"][0]
self.assertAlmostEqual(fe_two_plus.energy,
-1.6228450214319294,
places=2)
feo2 = [e for e in pbx_entries if e.entry_id == "mp-25332"][0]
self.assertAlmostEqual(feo2.energy, 2.5523680849999995, places=2)
# Test S, which has Na in reference solids
pbx_entries = self.rester.get_pourbaix_entries(["S"])
so4_two_minus = pbx_entries[9]
self.assertAlmostEqual(so4_two_minus.energy,
0.0644980568750011,
places=2)
# Ensure entries are pourbaix compatible
PourbaixDiagram(pbx_entries)
def test_serialization(self):
d = self.pbx.as_dict()
new = PourbaixDiagram.from_dict(d)
self.assertEqual(set([e.name for e in new.stable_entries]),
{"ZnO(s)", "Zn[2+]", "ZnHO2[-]", "ZnO2[2-]", "Zn(s)"},
"List of stable entries does not match")
# Test with unprocessed entries included, this should result in the
# previously filtered entries being included
d = self.pbx.as_dict(include_unprocessed_entries=True)
new = PourbaixDiagram.from_dict(d)
self.assertEqual(
set([e.name for e in new.stable_entries]), {
"ZnO(s)", "Zn[2+]", "ZnHO2[-]", "ZnO2[2-]", "Zn(s)", "ZnO2(s)",
"ZnH(s)"
}, "List of stable entries for unfiltered pbx does not match")
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
})
new_binary = PourbaixDiagram.from_dict(pd_binary.as_dict())
self.assertEqual(len(pd_binary.stable_entries),
len(new_binary.stable_entries))
def test_plot_entry_stability(self):
entry = self.pd.all_entries[0]
self.plotter.plot_entry_stability(entry, limits=[[-2, 14], [-3, 3]])
# binary system
pd_binary = PourbaixDiagram(self.test_data["Ag-Te"], comp_dict={"Ag": 0.5, "Te": 0.5})
binary_plotter = PourbaixPlotter(pd_binary)
plt = binary_plotter.plot_entry_stability(self.test_data["Ag-Te"][53])
plt.close()
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)
def test_get_decomposition(self):
# Test a stable entry to ensure that it's zero in the stable region
entry = self.test_data["Zn"][12] # Should correspond to mp-2133
self.assertAlmostEqual(
self.pbx.get_decomposition_energy(entry, 10, 1),
0.0,
5,
"Decomposition energy of ZnO is not 0.",
)
# Test an unstable entry to ensure that it's never zero
entry = self.test_data["Zn"][11]
ph, v = np.meshgrid(np.linspace(0, 14), np.linspace(-2, 4))
result = self.pbx_nofilter.get_decomposition_energy(entry, ph, v)
self.assertTrue((result >= 0).all(),
"Unstable energy has hull energy of 0 or less")
# Test an unstable hydride to ensure HER correction works
self.assertAlmostEqual(
self.pbx.get_decomposition_energy(entry, -3, -2), 3.6979147983333)
# Test a list of pHs
self.pbx.get_decomposition_energy(entry, np.linspace(0, 2, 5), 2)
# Test a list of Vs
self.pbx.get_decomposition_energy(entry, 4, np.linspace(-3, 3, 10))
# Test a set of matching arrays
ph, v = np.meshgrid(np.linspace(0, 14), np.linspace(-3, 3))
self.pbx.get_decomposition_energy(entry, ph, v)
# Test custom ions
entries = self.test_data["C-Na-Sn"]
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)
def test_get_pourbaix_entries(self):
pbx_entries = self.rester.get_pourbaix_entries(["Fe", "Cr"])
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
fe_two_plus = [e for e in pbx_entries if e.entry_id == "ion-0"][0]
self.assertAlmostEqual(fe_two_plus.energy, -1.580096075)
feo2 = [e for e in pbx_entries if e.entry_id == "mp-25332"][0]
self.assertAlmostEqual(feo2.energy, 2.51083231)
# Test S, which has Na in reference solids
pbx_entries = self.rester.get_pourbaix_entries(["S"])
so4_two_minus = pbx_entries[9]
self.assertAlmostEqual(so4_two_minus.energy, 0.047817821)
# Ensure entries are pourbaix compatible
pbx = PourbaixDiagram(pbx_entries)
def test_get_pourbaix_entries(self):
pbx_entries = self.rester.get_pourbaix_entries(["Fe", "Cr"])
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
fe_two_plus = [e for e in pbx_entries if e.entry_id == "ion-0"][0]
self.assertAlmostEqual(fe_two_plus.energy, -1.6228450214319294)
feo2 = [e for e in pbx_entries if e.entry_id == "mp-25332"][0]
self.assertAlmostEqual(feo2.energy, 4.424365035000003)
# Test S, which has Na in reference solids
pbx_entries = self.rester.get_pourbaix_entries(["S"])
so4_two_minus = pbx_entries[9]
self.assertAlmostEqual(so4_two_minus.energy, 0.0644980568750011)
# Ensure entries are pourbaix compatible
pbx = PourbaixDiagram(pbx_entries)
def test_serialization(self):
d = self.pbx.as_dict()
new = PourbaixDiagram.from_dict(d)
self.assertEqual(
{e.name
for e in new.stable_entries},
{"ZnO(s)", "Zn[2+]", "ZnHO2[-]", "ZnO2[2-]", "Zn(s)"},
"List of stable entries does not match",
)
# Test with unstable solid entries included (filter_solids=False), this should result in the
# previously filtered entries being included
with pytest.warns(
DeprecationWarning,
match="The include_unprocessed_entries kwarg is deprecated!"):
d = self.pbx_nofilter.as_dict(include_unprocessed_entries=True)
new = PourbaixDiagram.from_dict(d)
self.assertEqual(
{e.name
for e in new.stable_entries},
{
"ZnO(s)", "Zn[2+]", "ZnHO2[-]", "ZnO2[2-]", "Zn(s)", "ZnO2(s)",
"ZnH(s)"
},
"List of stable entries for unfiltered pbx does not match",
)
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
},
)
new_binary = PourbaixDiagram.from_dict(pd_binary.as_dict())
self.assertEqual(len(pd_binary.stable_entries),
len(new_binary.stable_entries))
def create_pbx_object(
pourbaix_entries, pourbaix_diagram_options, conc_dict, struct
):
# Pass along element restriction
if pourbaix_entries == "too_many_elements":
return "too_many_elements"
self.logger.debug("Updating entries")
if pourbaix_entries is None or not pourbaix_entries:
self.logger.debug("Preventing updating entries")
raise PreventUpdate
pourbaix_entries = self.from_data(pourbaix_entries)
# filter_solids = True
if pourbaix_diagram_options is not None:
filter_solids = "filter_solids" in pourbaix_diagram_options
else:
filter_solids = True
# Get composition from structure
struct = self.from_data(struct)
comp_dict = {
str(elt): coeff
for elt, coeff in struct.composition.items()
if elt not in ELEMENTS_HO
}
if conc_dict is not None:
conc_dict = self.from_data(conc_dict)
pourbaix_diagram = PourbaixDiagram(
pourbaix_entries,
comp_dict=comp_dict,
conc_dict=conc_dict,
filter_solids=filter_solids,
)
self.logger.debug("Generated pourbaix diagram")
return self.to_data(pourbaix_diagram)
def getentrystability(entry,
stabilitydata,
ehullmax,
newcomp,
plotterobj=None,
compdict=None,
all_entries=None):
if newcomp == True:
if compdict == None or all_entries == None:
raise Exception(
'Need to provide all_entries and compdict when using new composition!'
)
pbx = PourbaixDiagram(all_entries, comp_dict=compdict)
plotterobj = PourbaixPlotter(pbx)
elif plotterobj == None:
raise Exception(
'Need to provide plotter object if using previous composition!')
stability, (pH, V) = plotterobj.get_entry_stability(entry,
e_hull_max=ehullmax)
stability_metrics = stabilitymetrics(stability, pH, V)
return (stability_metrics, plotterobj)
def test_get_pourbaix_entries(self):
# test input chemsys as a list of elements
pbx_entries = self.rester.get_pourbaix_entries(["Fe", "Cr"])
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
# test input chemsys as a string
pbx_entries = self.rester.get_pourbaix_entries("Fe-Cr")
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
# fe_two_plus = [e for e in pbx_entries if e.entry_id == "ion-0"][0]
# self.assertAlmostEqual(fe_two_plus.energy, -1.12369, places=3)
#
# feo2 = [e for e in pbx_entries if e.entry_id == "mp-25332"][0]
# self.assertAlmostEqual(feo2.energy, 3.56356, places=3)
#
# # Test S, which has Na in reference solids
# pbx_entries = self.rester.get_pourbaix_entries(["S"])
# so4_two_minus = pbx_entries[9]
# self.assertAlmostEqual(so4_two_minus.energy, 0.301511, places=3)
# Ensure entries are Pourbaix compatible
PourbaixDiagram(pbx_entries)
def test_multielement_parallel(self):
# Simple test to ensure that multiprocessing is working
test_entries = self.test_data["Ag-Te-N"]
nproc = multiprocessing.cpu_count()
pbx = PourbaixDiagram(test_entries, filter_solids=True, nproc=nproc)
self.assertEqual(len(pbx.stable_entries), 49)
def setUpClass(cls):
cls.test_data = loadfn(os.path.join(test_dir, 'pourbaix_test_data.json'))
cls.pbx = PourbaixDiagram(cls.test_data['Zn'], filter_solids=True)
cls.pbx_nofilter = PourbaixDiagram(cls.test_data['Zn'],
filter_solids=False)
def setUp(self):
warnings.simplefilter("ignore")
self.test_data = loadfn(os.path.join(test_dir, "pourbaix_test_data.json"))
self.pd = PourbaixDiagram(self.test_data["Zn"])
self.plotter = PourbaixPlotter(self.pd)
def test_solid_filter(self):
entries = self.test_data['Ag-Te-N']
pbx = PourbaixDiagram(entries, filter_solids=True)
pbx.get_decomposition_energy(entries[0], 0, 0)