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_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 setUp(self):
# comp = Composition("Mn2O3")
self.solentry = ComputedEntry("Mn2O3", 49)
ion = Ion.from_formula("MnO4-")
self.ionentry = IonEntry(ion, 25)
self.PxIon = PourbaixEntry(self.ionentry)
self.PxSol = PourbaixEntry(self.solentry)
self.PxIon.concentration = 1e-4
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)
# -
pbx_entry_ion.energy
assert False
# + jupyter={}
# | - Ion Entries
# Calculate DFT reference energy for ions (See Persson et al, PRB (2012))
pbx_ion_entries = []
for id in ion_dict:
# Ion name-> Ion comp name (ex. Fe[3+] -> Ion: Fe1 +3)
comp = Ion.from_formula(id['Name'])
energy = id['Energy'] # + ion_correction * factor
print(id['Name'], comp, energy)
pbx_entry_ion = PourbaixEntry(IonEntry(comp, energy))
# AP pbx_entry_ion.name = id['Name']
pbx_entry_ion.conc = 1.0e-6
if pbx_entry_ion.name not in ['jfdksl']: # ['H2RuO2[2+]']: #["RuO4(aq)"]:
pbx_ion_entries.append(pbx_entry_ion)
#__|
all_entries = pbx_solid_entries + pbx_ion_entries
#__|
# | - Save all_entries
# Pickling data ######################################################
# import os; import pickle
# directory = "out_data"
# if not os.path.exists(directory): os.makedirs(directory)
def get_ion_entries(self,
pd: PhaseDiagram,
ion_ref_data: List[dict] = None) -> List[IonEntry]:
"""
Retrieve IonEntry objects that can be used in the construction of
Pourbaix Diagrams. The energies of the IonEntry are calculaterd from
the solid energies in the provided Phase Diagram to be
consistent with experimental free energies.
NOTE! This is an advanced method that assumes detailed understanding
of how to construct computational Pourbaix Diagrams. If you just want
to build a Pourbaix Diagram using default settings, use get_pourbaix_entries.
Args:
pd: Solid phase diagram on which to construct IonEntry. Note that this
Phase Diagram MUST include O and H in its chemical system. For example,
to retrieve IonEntry for Ti, the phase diagram passed here should contain
materials in the H-O-Ti chemical system. It is also assumed that solid
energies have already been corrected with MaterialsProjectAqueousCompatibility,
which is necessary for proper construction of Pourbaix diagrams.
ion_ref_data: Aqueous ion reference data. If None (default), the data
are downloaded from the Aqueous Ion Reference Data project hosted
on MPContribs. To add a custom ionic species, first download
data using get_ion_reference_data, then add or customize it with
your additional data, and pass the customized list here.
Returns:
[IonEntry]: IonEntry are similar to PDEntry objects. Their energies
are free energies in eV.
"""
# determine the chemsys from the phase diagram
chemsys = "-".join([el.symbol for el in pd.elements])
# raise ValueError if O and H not in chemsys
if "O" not in chemsys or "H" not in chemsys:
raise ValueError(
"The phase diagram chemical system must contain O and H! Your"
f" diagram chemical system is {chemsys}.")
if not ion_ref_data:
ion_data = self.get_ion_reference_data_for_chemsys(chemsys)
else:
ion_data = ion_ref_data
# position the ion energies relative to most stable reference state
ion_entries = []
for n, i_d in enumerate(ion_data):
ion = Ion.from_formula(i_d["formula"])
refs = [
e for e in pd.all_entries
if e.composition.reduced_formula == i_d["data"]["RefSolid"]
]
if not refs:
raise ValueError("Reference solid not contained in entry list")
stable_ref = sorted(refs, key=lambda x: x.energy_per_atom)[0]
rf = stable_ref.composition.get_reduced_composition_and_factor()[1]
# TODO - need a more robust way to convert units
# use pint here?
if i_d["data"]["ΔGᶠRefSolid"]["unit"] == "kJ/mol":
# convert to eV/formula unit
ref_solid_energy = i_d["data"]["ΔGᶠRefSolid"]["value"] / 96.485
elif i_d["data"]["ΔGᶠRefSolid"]["unit"] == "MJ/mol":
# convert to eV/formula unit
ref_solid_energy = i_d["data"]["ΔGᶠRefSolid"]["value"] / 96485
else:
raise ValueError(
f"Ion reference solid energy has incorrect unit {i_d['data']['ΔGᶠRefSolid']['unit']}"
)
solid_diff = pd.get_form_energy(stable_ref) - ref_solid_energy * rf
elt = i_d["data"]["MajElements"]
correction_factor = ion.composition[elt] / stable_ref.composition[
elt]
# TODO - need a more robust way to convert units
# use pint here?
if i_d["data"]["ΔGᶠ"]["unit"] == "kJ/mol":
# convert to eV/formula unit
ion_free_energy = i_d["data"]["ΔGᶠ"]["value"] / 96.485
elif i_d["data"]["ΔGᶠ"]["unit"] == "MJ/mol":
# convert to eV/formula unit
ion_free_energy = i_d["data"]["ΔGᶠ"]["value"] / 96485
else:
raise ValueError(
f"Ion free energy has incorrect unit {i_d['data']['ΔGᶠ']['unit']}"
)
energy = ion_free_energy + solid_diff * correction_factor
ion_entries.append(IonEntry(ion, energy))
return ion_entries
def get_pourbaix_entries(self, chemsys):
"""
A helper function to get all entries necessary to generate
a pourbaix diagram from the rest interface.
Args:
chemsys ([str]): A list of elements comprising the chemical
system, e.g. ['Li', 'Fe']
"""
from pymatgen.analysis.pourbaix_diagram import PourbaixEntry, IonEntry
from pymatgen.analysis.phase_diagram import PhaseDiagram
from pymatgen.core.ion import Ion
from pymatgen.entries.compatibility import\
MaterialsProjectAqueousCompatibility
pbx_entries = []
# Get ion entries first, because certain ions have reference
# solids that aren't necessarily in the chemsys (Na2SO4)
url = '/pourbaix_diagram/reference_data/' + '-'.join(chemsys)
ion_data = self._make_request(url)
ion_ref_comps = [Composition(d['Reference Solid']) for d in ion_data]
ion_ref_elts = list(itertools.chain.from_iterable(
i.elements for i in ion_ref_comps))
ion_ref_entries = self.get_entries_in_chemsys(
list(set([str(e) for e in ion_ref_elts] + ['O', 'H'])),
property_data=['e_above_hull'], compatible_only=False)
compat = MaterialsProjectAqueousCompatibility("Advanced")
ion_ref_entries = compat.process_entries(ion_ref_entries)
ion_ref_pd = PhaseDiagram(ion_ref_entries)
# position the ion energies relative to most stable reference state
for n, i_d in enumerate(ion_data):
ion_entry = IonEntry(Ion.from_formula(i_d['Name']), i_d['Energy'])
refs = [e for e in ion_ref_entries
if e.composition.reduced_formula == i_d['Reference Solid']]
if not refs:
raise ValueError("Reference solid not contained in entry list")
stable_ref = sorted(refs, key=lambda x: x.data['e_above_hull'])[0]
rf = stable_ref.composition.get_reduced_composition_and_factor()[1]
solid_diff = ion_ref_pd.get_form_energy(stable_ref)\
- i_d['Reference solid energy'] * rf
elt = i_d['Major_Elements'][0]
correction_factor = ion_entry.ion.composition[elt]\
/ stable_ref.composition[elt]
ion_entry.energy += solid_diff * correction_factor
pbx_entries.append(PourbaixEntry(ion_entry, 'ion-{}'.format(n)))
# import nose; nose.tools.set_trace()
# Construct the solid pourbaix entries from filtered ion_ref entries
extra_elts = set(ion_ref_elts) - {Element(s) for s in chemsys}\
- {Element('H'), Element('O')}
for entry in ion_ref_entries:
entry_elts = set(entry.composition.elements)
# Ensure no OH chemsys or extraneous elements from ion references
if not (entry_elts <= {Element('H'), Element('O')} or \
extra_elts.intersection(entry_elts)):
# replace energy with formation energy, use dict to
# avoid messing with the ion_ref_pd and to keep all old params
form_e = ion_ref_pd.get_form_energy(entry)
new_entry = deepcopy(entry)
new_entry.uncorrected_energy = form_e
new_entry.correction = 0.0
pbx_entry = PourbaixEntry(new_entry)
if entry.entry_id == "mp-697146":
pass
# import nose; nose.tools.set_trace()
# pbx_entry.reduced_entry()
pbx_entries.append(pbx_entry)
return pbx_entries
