def setUp(self):
entrylist = list()
weights = list()
comp = Composition("Mn2O3")
entry = PDEntry(comp, 49)
entrylist.append(PourbaixEntry(entry))
weights.append(1.0)
comp = Ion.from_formula("MnO4[-]")
entry = IonEntry(comp, 25)
entrylist.append(PourbaixEntry(entry))
weights.append(0.25)
comp = Composition("Fe2O3")
entry = PDEntry(comp, 50)
entrylist.append(PourbaixEntry(entry))
weights.append(0.5)
comp = Ion.from_formula("Fe[2+]")
entry = IonEntry(comp, 15)
entrylist.append(PourbaixEntry(entry))
weights.append(2.5)
comp = Ion.from_formula("Fe[3+]")
entry = IonEntry(comp, 20)
entrylist.append(PourbaixEntry(entry))
weights.append(1.5)
self.weights = weights
self.entrylist = entrylist
self.multientry = MultiEntry(entrylist, weights)
def setUp(self):
entrylist = list()
weights = list()
comp = Composition("Mn2O3")
entry = PDEntry(comp, 49)
entrylist.append(PourbaixEntry(entry))
weights.append(1.0)
comp = Ion.from_formula("MnO4[-]")
entry = IonEntry(comp, 25)
entrylist.append(PourbaixEntry(entry))
weights.append(0.25)
comp = Composition("Fe2O3")
entry = PDEntry(comp, 50)
entrylist.append(PourbaixEntry(entry))
weights.append(0.5)
comp = Ion.from_formula("Fe[2+]")
entry = IonEntry(comp, 15)
entrylist.append(PourbaixEntry(entry))
weights.append(2.5)
comp = Ion.from_formula("Fe[3+]")
entry = IonEntry(comp, 20)
entrylist.append(PourbaixEntry(entry))
weights.append(1.5)
self.weights = weights
self.entrylist = entrylist
self.multientry = MultiEntry(entrylist, weights)
def setUp(self):
self.comp = list()
self.comp.append(Ion.from_formula("Li+"))
self.comp.append(Ion.from_formula("MnO4-"))
self.comp.append(Ion.from_formula("Mn++"))
self.comp.append(Ion.from_formula("PO3-2"))
self.comp.append(Ion.from_formula("Fe(CN)6-3"))
self.comp.append(Ion.from_formula("Fe(CN)6----"))
self.comp.append(Ion.from_formula("Fe2((PO4)3(CO3)5)2-3"))
self.comp.append(Ion.from_formula("Ca[2+]"))
self.comp.append(Ion.from_formula("NaOH(aq)"))
def setUp(self):
self.comp = list()
self.comp.append(Ion.from_formula("Li+"))
self.comp.append(Ion.from_formula("MnO4-"))
self.comp.append(Ion.from_formula("Mn++"))
self.comp.append(Ion.from_formula("PO3-2"))
self.comp.append(Ion.from_formula("Fe(CN)6-3"))
self.comp.append(Ion.from_formula("Fe(CN)6----"))
self.comp.append(Ion.from_formula("Fe2((PO4)3(CO3)5)2-3"))
self.comp.append(Ion.from_formula("Ca[2+]"))
self.comp.append(Ion.from_formula("NaOH(aq)"))
def len_elts(entry):
if "(s)" in entry:
comp = Composition(entry[:-3])
else:
comp = Ion.from_formula(entry)
return len([el for el in comp.elements if el not in
[Element("H"), Element("O")]])
def len_elts(entry):
if "(s)" in entry:
comp = Composition(entry[:-3])
else:
comp = Ion.from_formula(entry)
return len([el for el in comp.elements if el not in
[Element("H"), Element("O")]])
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_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_read_write_csv(self):
Zn_solids = ["Zn", "ZnO", "ZnO2"]
sol_g = [0.0, -3.338, -1.315]
Zn_ions = ["Zn[2+]", "ZnOH[+]", "HZnO2[-]", "ZnO2[2-]", "ZnO"]
liq_g = [-1.527, -3.415, -4.812, -4.036, -2.921]
liq_conc = [1e-6, 1e-6, 1e-6, 1e-6, 1e-6]
solid_entry = list()
for sol in Zn_solids:
comp = Composition(sol)
delg = sol_g[Zn_solids.index(sol)]
solid_entry.append(PourbaixEntry(PDEntry(comp, delg)))
ion_entry = list()
for ion in Zn_ions:
comp_ion = Ion.from_formula(ion)
delg = liq_g[Zn_ions.index(ion)]
conc = liq_conc[Zn_ions.index(ion)]
PoE = PourbaixEntry(IonEntry(comp_ion, delg))
PoE.conc = conc
ion_entry.append(PoE)
entries = solid_entry + ion_entry
PourbaixEntryIO.to_csv("pourbaix_test_entries.csv", entries)
(elements,
entries) = PourbaixEntryIO.from_csv("pourbaix_test_entries.csv")
self.assertEqual(
elements, [Element('Zn'),
Element('H'), Element('O')], "Wrong elements!")
self.assertEqual(len(entries), 8, "Wrong number of entries!")
os.remove("pourbaix_test_entries.csv")
def test_read_write_csv(self):
Zn_solids = ["Zn", "ZnO", "ZnO2"]
sol_g = [0.0, -3.338, -1.315]
Zn_ions = ["Zn[2+]", "ZnOH[+]", "HZnO2[-]", "ZnO2[2-]", "ZnO"]
liq_g = [-1.527, -3.415, -4.812, -4.036, -2.921]
liq_conc = [1e-6, 1e-6, 1e-6, 1e-6, 1e-6]
solid_entry = list()
for sol in Zn_solids:
comp = Composition(sol)
delg = sol_g[Zn_solids.index(sol)]
solid_entry.append(PourbaixEntry(PDEntry(comp, delg)))
ion_entry = list()
for ion in Zn_ions:
comp_ion = Ion.from_formula(ion)
delg = liq_g[Zn_ions.index(ion)]
conc = liq_conc[Zn_ions.index(ion)]
PoE = PourbaixEntry(IonEntry(comp_ion, delg))
PoE.set_conc(conc)
ion_entry.append(PoE)
entries = solid_entry + ion_entry
PourbaixEntryIO.to_csv("pourbaix_test_entries.csv", entries)
(elements, entries) = PourbaixEntryIO.from_csv(
"pourbaix_test_entries.csv")
self.assertEqual(elements,
[Element('Zn'), Element('H'), Element('O')],
"Wrong elements!")
self.assertEqual(len(entries), 8, "Wrong number of entries!")
os.remove("pourbaix_test_entries.csv")
def setUp(self):
comp = Composition("Mn2O3")
self.solentry = PDEntry(comp, 49)
ion = Ion.from_formula("MnO4-")
self.ionentry = IonEntry(ion, 25)
self.PxIon = PourbaixEntry(self.ionentry)
self.PxSol = PourbaixEntry(self.solentry)
self.PxIon.set_conc(1e-4)
def setUp(self):
comp = Composition("Mn2O3")
self.solentry = PDEntry(comp, 49)
ion = Ion.from_formula("MnO4-")
self.ionentry = IonEntry(ion, 25)
self.PxIon = PourbaixEntry(self.ionentry)
self.PxSol = PourbaixEntry(self.solentry)
self.PxIon.conc = 1e-4
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 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 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.entry import PourbaixEntry, IonEntry
from pymatgen.analysis.phase_diagram import PhaseDiagram
from pymatgen.core.ion import Ion
from pymatgen.entries.compatibility import\
MaterialsProjectAqueousCompatibility
chemsys = list(set(chemsys + ['O', 'H']))
entries = self.get_entries_in_chemsys(chemsys,
property_data=['e_above_hull'],
compatible_only=False)
compat = MaterialsProjectAqueousCompatibility("Advanced")
entries = compat.process_entries(entries)
solid_pd = PhaseDiagram(
entries) # Need this to get ion formation energy
url = '/pourbaix_diagram/reference_data/' + '-'.join(chemsys)
ion_data = self._make_request(url)
pbx_entries = []
for entry in entries:
if not set(entry.composition.elements)\
<= {Element('H'), Element('O')}:
pbx_entry = PourbaixEntry(entry)
pbx_entry.g0_replace(solid_pd.get_form_energy(entry))
pbx_entry.reduced_entry()
pbx_entries.append(pbx_entry)
# 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 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 = solid_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]
correction = solid_diff * correction_factor
pbx_entries.append(
PourbaixEntry(ion_entry, correction, 'ion-{}'.format(n)))
return pbx_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.entry import PourbaixEntry, IonEntry
from pymatgen.analysis.phase_diagram import PhaseDiagram
from pymatgen.core.ion import Ion
from pymatgen.entries.compatibility import\
MaterialsProjectAqueousCompatibility
chemsys = list(set(chemsys + ['O', 'H']))
entries = self.get_entries_in_chemsys(
chemsys, property_data=['e_above_hull'], compatible_only=False)
compat = MaterialsProjectAqueousCompatibility("Advanced")
entries = compat.process_entries(entries)
solid_pd = PhaseDiagram(entries) # Need this to get ion formation energy
url = '/pourbaix_diagram/reference_data/' + '-'.join(chemsys)
ion_data = self._make_request(url)
pbx_entries = []
for entry in entries:
if not set(entry.composition.elements)\
<= {Element('H'), Element('O')}:
pbx_entry = PourbaixEntry(entry)
pbx_entry.g0_replace(solid_pd.get_form_energy(entry))
pbx_entry.reduced_entry()
pbx_entries.append(pbx_entry)
# 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 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 = solid_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]
correction = solid_diff * correction_factor
pbx_entries.append(PourbaixEntry(ion_entry, correction,
'ion-{}'.format(n)))
return pbx_entries
def test_get_ion_entries(self, mpr):
entries = mpr.get_entries_in_chemsys("Ti-O-H")
pd = PhaseDiagram(entries)
ion_entry_data = mpr.get_ion_reference_data_for_chemsys("Ti-O-H")
ion_entries = mpr.get_ion_entries(pd, ion_entry_data)
assert len(ion_entries) == 5
assert all([isinstance(i, IonEntry) for i in ion_entries])
# test an incomplete phase diagram
entries = mpr.get_entries_in_chemsys("Ti-O")
pd = PhaseDiagram(entries)
with pytest.raises(ValueError,
match="The phase diagram chemical system"):
mpr.get_ion_entries(pd)
# test ion energy calculation
ion_data = mpr.get_ion_reference_data_for_chemsys('S')
ion_ref_comps = [
Ion.from_formula(d["data"]["RefSolid"]).composition
for d in ion_data
]
ion_ref_elts = set(
itertools.chain.from_iterable(i.elements for i in ion_ref_comps))
ion_ref_entries = mpr.get_entries_in_chemsys(
list([str(e) for e in ion_ref_elts] + ["O", "H"]))
mpc = MaterialsProjectAqueousCompatibility()
ion_ref_entries = mpc.process_entries(ion_ref_entries)
ion_ref_pd = PhaseDiagram(ion_ref_entries)
ion_entries = mpr.get_ion_entries(ion_ref_pd, ion_ref_data=ion_data)
# In ion ref data, SO4-2 is -744.27 kJ/mol; ref solid is -1,279.0 kJ/mol
# so the ion entry should have an energy (-744.27 +1279) = 534.73 kJ/mol
# or 5.542 eV/f.u. above the energy of Na2SO4
so4_two_minus = [
e for e in ion_entries if e.ion.reduced_formula == "SO4[-2]"
][0]
# the ref solid is Na2SO4, ground state mp-4770
# the rf factor correction is necessary to make sure the composition
# of the reference solid is normalized to a single formula unit
ref_solid_entry = [
e for e in ion_ref_entries if e.entry_id == 'mp-4770'
][0]
rf = ref_solid_entry.composition.get_reduced_composition_and_factor(
)[1]
solid_energy = ion_ref_pd.get_form_energy(ref_solid_entry) / rf
assert np.allclose(so4_two_minus.energy,
solid_energy + 5.542,
atol=1e-3)
def test_special_formulas(self):
special_formulas = [
("Cl-", "Cl[-1]"),
("H+", "H[+1]"),
("F-", "F[-1]"),
("H4O4", "H2O2(aq)"),
("OH-", "OH[-1]"),
("CH3COO-", "CH3COO[-1]"),
("CH3COOH", "CH3COOH(aq)"),
("CH3OH", "CH3OH(aq)"),
("H4CO", "CH3OH(aq)"),
("C2H6O", "C2H5OH(aq)"),
("C3H8O", "C3H7OH(aq)"),
("C4H10O", "C4H9OH(aq)"),
("Fe(OH)4+", "FeO2.2H2O[+1]"),
("Zr(OH)4", "ZrO2.2H2O(aq)"),
]
for tup in special_formulas:
self.assertEqual(Ion.from_formula(tup[0]).reduced_formula, tup[1])
self.assertEqual(Ion.from_formula("Fe(OH)4+").get_reduced_formula_and_factor(hydrates=False), ("Fe(OH)4", 1))
self.assertEqual(Ion.from_formula("Zr(OH)4").get_reduced_formula_and_factor(hydrates=False), ("Zr(OH)4", 1))
def __init__(self, entries, comp_dict=None):
"""
Args:
entries:
Entries list containing both Solids and Ions
comp_dict:
Dictionary of compositions
"""
self._solid_entries = list()
self._ion_entries = list()
for entry in entries:
if entry.phase_type == "Solid":
self._solid_entries.append(entry)
elif entry.phase_type == "Ion":
self._ion_entries.append(entry)
else:
raise StandardError("Incorrect Phase type - needs to be \
Pourbaix entry of phase type Ion/Solid")
self._unprocessed_entries = self._solid_entries + self._ion_entries
self._elt_comp = comp_dict
if comp_dict:
self._multielement = True
self.pourbaix_elements = [key for key in comp_dict]
w = [comp_dict[key] for key in comp_dict]
A = []
for comp in comp_dict:
m = re.search(r"\[([^\[\]]+)\]|\(aq\)", comp)
if m:
comp_obj = Ion.from_formula(comp)
else:
comp_obj = Composition.from_formula(comp)
Ai = []
for elt in self.pourbaix_elements:
Ai.append(comp_obj[Element(elt)])
A.append(Ai)
A = np.array(A).T.astype(float)
w = np.array(w)
A /= np.dot([A[i].sum() for i in xrange(len(A))], w)
x = np.linalg.solve(A, w)
self._elt_comp = dict(zip(self.pourbaix_elements, x))
else:
self._multielement = False
self.pourbaix_elements = [
el.symbol for el in entries[0].composition.elements
if el.symbol not in ["H", "O"]
]
self._make_pourbaixdiagram()
def __init__(self, entries, comp_dict=None):
"""
Args:
entries:
Entries list containing both Solids and Ions
comp_dict:
Dictionary of compositions
"""
self._solid_entries = list()
self._ion_entries = list()
for entry in entries:
if entry.phase_type == "Solid":
self._solid_entries.append(entry)
elif entry.phase_type == "Ion":
self._ion_entries.append(entry)
else:
raise StandardError("Incorrect Phase type - needs to be \
Pourbaix entry of phase type Ion/Solid")
self._unprocessed_entries = self._solid_entries + self._ion_entries
self._elt_comp = comp_dict
if comp_dict:
self._multielement = True
self.pourbaix_elements = [key for key in comp_dict]
w = [comp_dict[key] for key in comp_dict]
A = []
for comp in comp_dict:
m = re.search(r"\[([^\[\]]+)\]|\(aq\)", comp)
if m:
comp_obj = Ion.from_formula(comp)
else:
comp_obj = Composition.from_formula(comp)
Ai = []
for elt in self.pourbaix_elements:
Ai.append(comp_obj[Element(elt)])
A.append(Ai)
A = np.array(A).T.astype(float)
w = np.array(w)
A /= np.dot([A[i].sum() for i in xrange(len(A))], w)
x = np.linalg.solve(A, w)
self._elt_comp = dict(zip(self.pourbaix_elements, x))
else:
self._multielement = False
self.pourbaix_elements = [el.symbol
for el in entries[0].composition.elements
if el.symbol not in ["H", "O"]]
self._make_pourbaixdiagram()
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 ion_or_solid_comp_object(formula):
"""
Returns either an ion object or composition object given
a formula.
Args:
formula: String formula. Eg. of ion: NaOH(aq), Na[+];
Eg. of solid: Fe2O3(s), Fe(s), Na2O
Returns:
Composition/Ion object
"""
m = re.search(r"\[([^\[\]]+)\]|\(aq\)", formula)
if m:
comp_obj = Ion.from_formula(formula)
elif re.search(r"\(s\)", formula):
comp_obj = Composition(formula[:-3])
else:
comp_obj = Composition(formula)
return comp_obj
def ion_or_solid_comp_object(formula):
"""
Returns either an ion object or composition object given
a formula.
Args:
formula: String formula. Eg. of ion: NaOH(aq), Na[+];
Eg. of solid: Fe2O3(s), Fe(s), Na2O
Returns:
Composition/Ion object
"""
m = re.search(r"\[([^\[\]]+)\]|\(aq\)", formula)
if m:
comp_obj = Ion.from_formula(formula)
elif re.search(r"\(s\)", formula):
comp_obj = Composition(formula[:-3])
else:
comp_obj = Composition(formula)
return comp_obj
def from_csv(filename):
"""
Imports PourbaixEntries from a csv.
Args:
filename - Filename to import from.
Returns:
List of Entries
"""
import csv
reader = csv.reader(open(filename, "rb"),
delimiter=",",
quotechar="\"",
quoting=csv.QUOTE_MINIMAL)
entries = list()
header_read = False
for row in reader:
if not header_read:
elements = row[1:(len(row) - 4)]
header_read = True
else:
name = row[0]
energy = float(row[-4])
conc = float(row[-1])
comp = dict()
for ind in range(1, len(row) - 4):
if float(row[ind]) > 0:
comp[Element(elements[ind - 1])] = float(row[ind])
phase_type = row[-3]
if phase_type == "Ion":
PoE = PourbaixEntry(
IonEntry(Ion.from_formula(name), energy))
PoE.set_conc(conc)
PoE.set_name(name)
entries.append(PoE)
else:
entries.append(
PourbaixEntry(PDEntry(Composition(comp), energy)))
elements = [Element(el) for el in elements]
return elements, entries
def from_csv(filename):
"""
Imports PourbaixEntries from a csv.
Args:
filename: Filename to import from.
Returns:
List of Entries
"""
with open(filename, "r") as f:
reader = csv.reader(f, delimiter=unicode2str(","),
quotechar=unicode2str("\""),
quoting=csv.QUOTE_MINIMAL)
entries = list()
header_read = False
for row in reader:
if not header_read:
elements = row[1:(len(row) - 4)]
header_read = True
else:
name = row[0]
energy = float(row[-4])
conc = float(row[-1])
comp = dict()
for ind in range(1, len(row) - 4):
if float(row[ind]) > 0:
comp[Element(elements[ind - 1])] = float(row[ind])
phase_type = row[-3]
if phase_type == "Ion":
PoE = PourbaixEntry(IonEntry(Ion.from_formula(name),
energy))
PoE.conc = conc
PoE.name = name
entries.append(PoE)
else:
entries.append(PourbaixEntry(PDEntry(Composition(comp),
energy)))
elements = [Element(el) for el in elements]
return elements, entries
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 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
Created on Wed Feb 28 15:40:02 2018
@author: jherfson
"""
from pymatgen.analysis.pourbaix.entry import PourbaixEntry, IonEntry #, MultiEntry
from pymatgen.analysis.pourbaix.entry import PourbaixEntryIO
from pymatgen.analysis.phase_diagram import PDEntry
from pymatgen.core.ion import Ion
from pymatgen.core.structure import Composition
Zn_solids = ["Zn", "ZnO", "ZnO2"]
sol_g = [0.0, -3.338, -1.315]
Zn_ions = ["Zn[2+]", "ZnOH[+]", "HZnO2[-]", "ZnO2[2-]", "ZnO"]
liq_g = [-1.527, -3.415, -4.812, -4.036, -2.921]
liq_conc = [1e-6, 1e-6, 1e-6, 1e-6, 1e-6]
solid_entry = list()
for sol in Zn_solids:
comp = Composition(sol)
delg = sol_g[Zn_solids.index(sol)]
solid_entry.append(PourbaixEntry(PDEntry(comp, delg)))
ion_entry = list()
for ion in Zn_ions:
comp_ion = Ion.from_formula(ion)
delg = liq_g[Zn_ions.index(ion)]
conc = liq_conc[Zn_ions.index(ion)]
PoE = PourbaixEntry(IonEntry(comp_ion, delg))
PoE.conc = conc
ion_entry.append(PoE)
entries = solid_entry + ion_entry
PourbaixEntryIO.to_csv("pourbaix_test_entries.csv", 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
def get_pourbaix_plot_colorfill_by_element(self, limits=None, title="",
label_domains=True, element=None):
"""
Color domains by element
"""
from matplotlib.patches import Polygon
entry_dict_of_multientries = collections.defaultdict(list)
plt = pretty_plot(16)
optim_colors = ['#0000FF', '#FF0000', '#00FF00', '#FFFF00', '#FF00FF',
'#FF8080', '#DCDCDC', '#800000', '#FF8000']
optim_font_color = ['#FFFFA0', '#00FFFF', '#FF00FF', '#0000FF', '#00FF00',
'#007F7F', '#232323', '#7FFFFF', '#007FFF']
hatch = ['/', '\\', '|', '-', '+', 'o', '*']
(stable, unstable) = self.pourbaix_plot_data(limits)
num_of_overlaps = {key: 0 for key in stable.keys()}
for entry in stable:
if isinstance(entry, MultiEntry):
for e in entry.entrylist:
if element in e.composition.elements:
entry_dict_of_multientries[e.name].append(entry)
num_of_overlaps[entry] += 1
else:
entry_dict_of_multientries[entry.name].append(entry)
if limits:
xlim = limits[0]
ylim = limits[1]
else:
xlim = self._analyzer.chempot_limits[0]
ylim = self._analyzer.chempot_limits[1]
h_line = np.transpose([[xlim[0], -xlim[0] * PREFAC],
[xlim[1], -xlim[1] * PREFAC]])
o_line = np.transpose([[xlim[0], -xlim[0] * PREFAC + 1.23],
[xlim[1], -xlim[1] * PREFAC + 1.23]])
neutral_line = np.transpose([[7, ylim[0]], [7, ylim[1]]])
V0_line = np.transpose([[xlim[0], 0], [xlim[1], 0]])
ax = plt.gca()
ax.set_xlim(xlim)
ax.set_ylim(ylim)
from pymatgen import Composition, Element
from pymatgen.core.ion import Ion
def len_elts(entry):
if "(s)" in entry:
comp = Composition(entry[:-3])
else:
comp = Ion.from_formula(entry)
return len([el for el in comp.elements if el not in
[Element("H"), Element("O")]])
sorted_entry = entry_dict_of_multientries.keys()
sorted_entry.sort(key=len_elts)
i = -1
label_chr = map(chr, list(range(65, 91)))
for entry in sorted_entry:
color_indx = 0
x_coord = 0.0
y_coord = 0.0
npts = 0
i += 1
for e in entry_dict_of_multientries[entry]:
hc = 0
fc = 0
bc = 0
xy = self.domain_vertices(e)
c = self.get_center(stable[e])
x_coord += c[0]
y_coord += c[1]
npts += 1
color_indx = i
if "(s)" in entry:
comp = Composition(entry[:-3])
else:
comp = Ion.from_formula(entry)
if len([el for el in comp.elements if el not in
[Element("H"), Element("O")]]) == 1:
if color_indx >= len(optim_colors):
color_indx = color_indx -\
int(color_indx / len(optim_colors)) * len(optim_colors)
patch = Polygon(xy, facecolor=optim_colors[color_indx],
closed=True, lw=3.0, fill=True)
bc = optim_colors[color_indx]
else:
if color_indx >= len(hatch):
color_indx = color_indx - int(color_indx / len(hatch)) * len(hatch)
patch = Polygon(xy, hatch=hatch[color_indx], closed=True, lw=3.0, fill=False)
hc = hatch[color_indx]
ax.add_patch(patch)
xy_center = (x_coord / npts, y_coord / npts)
if label_domains:
if color_indx >= len(optim_colors):
color_indx = color_indx -\
int(color_indx / len(optim_colors)) * len(optim_colors)
fc = optim_font_color[color_indx]
if bc and not hc:
bbox = dict(boxstyle="round", fc=fc)
if hc and not bc:
bc = 'k'
fc = 'w'
bbox = dict(boxstyle="round", hatch=hc, fill=False)
if bc and hc:
bbox = dict(boxstyle="round", hatch=hc, fc=fc)
# bbox.set_path_effects([PathEffects.withSimplePatchShadow()])
plt.annotate(latexify_ion(latexify(entry)), xy_center,
color=bc, fontsize=30, bbox=bbox)
# plt.annotate(label_chr[i], xy_center,
# color=bc, fontsize=30, bbox=bbox)
lw = 3
plt.plot(h_line[0], h_line[1], "r--", linewidth=lw)
plt.plot(o_line[0], o_line[1], "r--", linewidth=lw)
plt.plot(neutral_line[0], neutral_line[1], "k-.", linewidth=lw)
plt.plot(V0_line[0], V0_line[1], "k-.", linewidth=lw)
plt.xlabel("pH")
plt.ylabel("E (V)")
plt.title(title, fontsize=20, fontweight='bold')
return plt
def test_charge_from_formula(self):
self.assertEqual(Ion.from_formula("Li+").charge, 1)
self.assertEqual(Ion.from_formula("Li[+]").charge, 1)
self.assertEqual(Ion.from_formula("Ca[2+]").charge, 2)
self.assertEqual(Ion.from_formula("Ca[+2]").charge, 2)
self.assertEqual(Ion.from_formula("Ca++").charge, 2)
self.assertEqual(Ion.from_formula("Ca[++]").charge, 2)
self.assertEqual(Ion.from_formula("Ca2+").charge, 1)
self.assertEqual(Ion.from_formula("Cl-").charge, -1)
self.assertEqual(Ion.from_formula("Cl[-]").charge, -1)
self.assertEqual(Ion.from_formula("SO4[-2]").charge, -2)
self.assertEqual(Ion.from_formula("SO4-2").charge, -2)
self.assertEqual(Ion.from_formula("SO42-").charge, -1)
self.assertEqual(Ion.from_formula("SO4--").charge, -2)
self.assertEqual(Ion.from_formula("SO4[--]").charge, -2)
self.assertEqual(Ion.from_formula("Na[+-+]").charge, 1)
def get_pourbaix_plot_colorfill_by_element(self, limits=None, title="",
label_domains=True, element=None):
"""
Color domains by element
"""
from matplotlib.patches import Polygon
import matplotlib.patheffects as PathEffects
entry_dict_of_multientries = collections.defaultdict(list)
plt = get_publication_quality_plot(16)
optim_colors = ['#0000FF', '#FF0000', '#00FF00', '#FFFF00', '#FF00FF',
'#FF8080', '#DCDCDC', '#800000', '#FF8000']
optim_font_color = ['#FFFFA0', '#00FFFF', '#FF00FF', '#0000FF', '#00FF00',
'#007F7F', '#232323', '#7FFFFF', '#007FFF']
hatch = ['/', '\\', '|', '-', '+', 'o', '*']
(stable, unstable) = self.pourbaix_plot_data(limits)
num_of_overlaps = {key: 0 for key in stable.keys()}
for entry in stable:
if isinstance(entry, MultiEntry):
for e in entry.entrylist:
if element in e.composition.elements:
entry_dict_of_multientries[e.name].append(entry)
num_of_overlaps[entry] += 1
else:
entry_dict_of_multientries[entry.name].append(entry)
if limits:
xlim = limits[0]
ylim = limits[1]
else:
xlim = self._analyzer.chempot_limits[0]
ylim = self._analyzer.chempot_limits[1]
h_line = np.transpose([[xlim[0], -xlim[0] * PREFAC],
[xlim[1], -xlim[1] * PREFAC]])
o_line = np.transpose([[xlim[0], -xlim[0] * PREFAC + 1.23],
[xlim[1], -xlim[1] * PREFAC + 1.23]])
neutral_line = np.transpose([[7, ylim[0]], [7, ylim[1]]])
V0_line = np.transpose([[xlim[0], 0], [xlim[1], 0]])
ax = plt.gca()
ax.set_xlim(xlim)
ax.set_ylim(ylim)
from pymatgen import Composition, Element
from pymatgen.core.ion import Ion
def len_elts(entry):
if "(s)" in entry:
comp = Composition(entry[:-3])
else:
comp = Ion.from_formula(entry)
return len([el for el in comp.elements if el not in
[Element("H"), Element("O")]])
sorted_entry = entry_dict_of_multientries.keys()
sorted_entry.sort(key=len_elts)
i = -1
label_chr = map(chr, range(65, 91))
for entry in sorted_entry:
color_indx = 0
x_coord = 0.0
y_coord = 0.0
npts = 0
i += 1
for e in entry_dict_of_multientries[entry]:
hc = 0
fc = 0
bc = 0
xy = self.domain_vertices(e)
c = self.get_center(stable[e])
x_coord += c[0]
y_coord += c[1]
npts += 1
color_indx = i
if "(s)" in entry:
comp = Composition(entry[:-3])
else:
comp = Ion.from_formula(entry)
if len([el for el in comp.elements if el not in
[Element("H"), Element("O")]]) == 1:
if color_indx >= len(optim_colors):
color_indx = color_indx -\
int(color_indx / len(optim_colors)) * len(optim_colors)
patch = Polygon(xy, facecolor=optim_colors[color_indx],
closed=True, lw=3.0, fill=True)
bc = optim_colors[color_indx]
else:
if color_indx >= len(hatch):
color_indx = color_indx - int(color_indx / len(hatch)) * len(hatch)
patch = Polygon(xy, hatch=hatch[color_indx], closed=True, lw=3.0, fill=False)
hc = hatch[color_indx]
ax.add_patch(patch)
xy_center = (x_coord / npts, y_coord / npts)
if label_domains:
if color_indx >= len(optim_colors):
color_indx = color_indx -\
int(color_indx / len(optim_colors)) * len(optim_colors)
fc = optim_font_color[color_indx]
if bc and not hc:
bbox = dict(boxstyle="round", fc=fc)
if hc and not bc:
bc = 'k'
fc = 'w'
bbox = dict(boxstyle="round", hatch=hc, fill=False)
if bc and hc:
bbox = dict(boxstyle="round", hatch=hc, fc=fc)
# bbox.set_path_effects([PathEffects.withSimplePatchShadow()])
# plt.annotate(latexify_ion(latexify(entry)), xy_center,
# color=fc, fontsize=30, bbox=bbox)
plt.annotate(label_chr[i], xy_center,
color=bc, fontsize=30, bbox=bbox)
lw = 3
plt.plot(h_line[0], h_line[1], "r--", linewidth=lw)
plt.plot(o_line[0], o_line[1], "r--", linewidth=lw)
plt.plot(neutral_line[0], neutral_line[1], "k-.", linewidth=lw)
plt.plot(V0_line[0], V0_line[1], "k-.", linewidth=lw)
plt.xlabel("pH")
plt.ylabel("E (V)")
plt.title(title, fontsize=20, fontweight='bold')
return plt
def get_ion(
ion: Union[Ion, str],
parameter_set: str = "auto",
water_model: str = "auto",
mixing_rule: Optional[str] = None,
) -> LammpsData:
"""
Retrieve force field parameters for an ion in water.
Args:
ion: Formula of the ion (e.g., "Li+"). Not case sensitive. May be
passed as either a string or an Ion object.
parameter_set: Force field parameters to use for ions.
Valid choices are:
1. "jj" for the Jensen and Jorgensen parameters (2006)"
2. "jc" for Joung-Cheatham parameters (2008)
3. "lm" for the Li and Merz group parameters (2020-2021)"
The default parameter set is "auto", which assigns a recommended
parameter set that is compatible with the chosen water model.
water_model: Water model to use. Models must be given as a string
(not case sensitive). "-" and "/" are ignored. Hence "tip3pfb"
and "TIP3P-FB" are both valid inputs for the TIP3P-FB water model.
Available water models are:
1. SPC
2. SPC/E
3. TIP3P-EW
4. TIP3P-FB
5. OPC3
6. TIP4P-EW
7. TIP4P-2005
8. TIP4P-FB
9. OPC
The default water model is "auto", which assigns a recommended
water model that is compatible with the chosen ion parameters. Other
combinations are possible at your own risk. See documentation.
When both the parameter_set and water_model are set to "auto", the function returns the
Joung-Cheatham parameters for the SPC/E water model.
For a systematic comparison of the performance of different water models, refer to
Sachini et al., Systematic Comparison of the Structural and Dynamic Properties of
Commonly Used Water Models for Molecular Dynamics Simulations. J. Chem. Inf. Model.
2021, 61, 9, 4521–4536. https://doi.org/10.1021/acs.jcim.1c00794
mixing_rule: The mixing rule to use for the ion parameter. Default to None, which does not
change the original mixing rule of the parameter set. Available choices are 'LB'
(Lorentz-Berthelot or arithmetic) and 'geometric'. If the specified mixing rule does not
match the default mixing rule of the parameter set, the output parameter will be converted
accordingly.
Returns:
Force field parameters for the chosen water model.
"""
alias = {
"aq": "aqvist",
"jj": "jensen_jorgensen",
"jc": "joung_cheatham",
"lm": "li_merz"
}
default_sets = {
"spc": "N/A",
"spce": "jc",
"tip3p": "jc",
"tip3pew": "N/A",
"tip3pfb": "lm",
"opc3": "lm",
"tip4p2005": "N/A",
"tip4p": "jj",
"tip4pew": "jc",
"tip4pfb": "lm",
"opc": "lm",
"jj": "tip4p",
"jc": "spce",
"lm": "tip4pfb",
}
water_model = water_model.replace("-", "").replace("/", "").lower()
parameter_set = parameter_set.lower()
if water_model == "auto" and parameter_set == "auto":
water_model = "spce"
parameter_set = "jc"
elif parameter_set == "auto":
parameter_set = default_sets.get(water_model, parameter_set)
if parameter_set == "N/A":
raise ValueError(
f"The {water_model} water model has no specifically parameterized ion parameter sets"
"Please try a different water model.")
elif water_model == "auto":
water_model = default_sets.get(parameter_set, water_model)
parameter_set = alias.get(parameter_set, parameter_set)
# Make the Ion object to get mass and charge
if isinstance(ion, Ion):
ion_obj = ion
else:
ion_obj = Ion.from_formula(ion.capitalize())
# load ion data as a list of IonLJData objects
ion_data = loadfn(os.path.join(DATA_DIR, "ion_lj_params.json"))
# make sure the ion is in the DataFrame
key = ion_obj.reduced_formula
filtered_data = [d for d in ion_data if d.formula == key]
if len(filtered_data) == 0:
raise ValueError(
f"Ion {key} not found in database. Please try a different ion."
)
# make sure the parameter set is in the DataFrame
filtered_data = [
d for d in filtered_data
if d.name == parameter_set and d.water_model == water_model
]
if len(filtered_data) == 0:
raise ValueError(
f"No {parameter_set} parameters for water model {water_model} for ion {key}. "
"See documentation and try a different combination.")
if len(filtered_data) != 1:
raise ValueError(
f"Something is wrong: multiple ion data entries for {key}, {parameter_set}, and {water_model}"
)
# we only consider monatomic ions at present
# construct a cubic LammpsBox from a lattice
lat = Lattice([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
box = lattice_2_lmpbox(lat)[0]
# put it in the center of a cubic Structure
struct = Structure(lat, ion_obj, [[0.5, 0.5, 0.5]])
# construct Topology with the ion centered in the box
topo = Topology(struct, charges=[ion_obj.charge])
# retrieve Lennard-Jones parameters
# construct ForceField object
sigma = filtered_data[0].sigma
epsilon = filtered_data[0].epsilon
if mixing_rule is None:
pass
else:
default_mixing = filtered_data[0].combining_rule
water_sigma = WATER_SIGMA.get(filtered_data[0].water_model)
if mixing_rule.lower() in [
"lb", "arithmetic", "lorentz-berthelot",
"lorentz berthelot"
]:
mixing_rule = "LB"
elif mixing_rule.lower() == "geometric":
mixing_rule = "geometric"
else:
raise ValueError(
"Invalid mixing rule. Supported mixing rules are 'LB'(arithmetic) and 'geometric'. "
)
if default_mixing == mixing_rule:
pass
elif default_mixing == "LB" and mixing_rule == "geometric":
sigma = ((water_sigma + sigma) / 2)**2 / water_sigma
print(
"The parameter mixing rule has been converted from the original 'LB' to 'geometric'.\n"
"Please use the parameter set with caution!")
else:
sigma = 2 * ((water_sigma * sigma)**(1 / 2)) - water_sigma
print(
"The parameter mixing rule has been converted from the original 'geometric' to 'LB'.\n"
"Please use the parameter set with caution!")
ff = ForceField([(str(e), e) for e in ion_obj.elements],
nonbond_coeffs=[[epsilon, sigma]])
return LammpsData.from_ff_and_topologies(box,
ff, [topo],
atom_style="full")
def setUp(self):
ion = Ion.from_formula("MnO4[-]")
self.entry = IonEntry(ion, 49)
def plot_pourbaix_diagram(metastability=0.0, ion_concentration=1e-6, fmt='pdf'):
"""
Creates a Pourbaix diagram for the material in the cwd.
Args:
metastability (float): desired metastable tolerance energy
(meV/atom). <~50 is generally a sensible range to use.
ion_concentration (float): in mol/kg. Sensible values are
generally between 1e-8 and 1.
fmt (str): matplotlib format style. Check the matplotlib
docs for options.
"""
# Create a ComputedEntry object for the 2D material.
composition = Structure.from_file('POSCAR').composition
energy = Vasprun('vasprun.xml').final_energy
cmpd = ComputedEntry(composition, energy)
# Define the chemsys that describes the 2D compound.
chemsys = ['O', 'H'] + [elt.symbol for elt in composition.elements
if elt.symbol not in ['O', 'H']]
# Pick out the ions pertaining to the 2D compound.
ion_dict = dict()
for elt in chemsys:
if elt not in ['O', 'H'] and ION_FORMATION_ENERGIES[elt]:
ion_dict.update(ION_FORMATION_ENERGIES[elt])
elements = [Element(elt) for elt in chemsys if elt not in ['O', 'H']]
# Add "correction" for metastability
cmpd.correction -= float(cmpd.composition.num_atoms)\
* float(metastability) / 1000.0
# Calculate formation energy of the compound from its end
# members
form_energy = cmpd.energy
for elt in composition.as_dict():
form_energy -= CHEMICAL_POTENTIALS[elt] * cmpd.composition[elt]
# Convert the compound entry to a pourbaix entry.
# Default concentration for solid entries = 1
pbx_cmpd = PourbaixEntry(cmpd)
pbx_cmpd.g0_replace(form_energy)
pbx_cmpd.reduced_entry()
# Add corrected ionic entries to the pourbaix diagram
# dft corrections for experimental ionic energies:
# Persson et.al PHYSICAL REVIEW B 85, 235438 (2012)
pbx_ion_entries = list()
# Get PourbaixEntry corresponding to each ion.
# Default concentration for ionic entries = 1e-6
# ion_energy = ion_exp_energy + ion_correction * factor
# where factor = fraction of element el in the ionic entry
# compared to the reference entry
for elt in elements:
for key in ion_dict:
comp = Ion.from_formula(key)
if comp.composition[elt] != 0:
factor = comp.composition[elt]
energy = ion_dict[key]
pbx_entry_ion = PourbaixEntry(IonEntry(comp, energy))
pbx_entry_ion.correction = (
ION_CORRECTIONS[elt.symbol] * factor
)
pbx_entry_ion.conc = ion_concentration
pbx_entry_ion.name = key
pbx_ion_entries.append(pbx_entry_ion)
# Generate and plot Pourbaix diagram
# Each bulk solid/ion has a free energy g of the form:
# g = g0_ref + 0.0591 * log10(conc) - nO * mu_H2O +
# (nH - 2nO) * pH + phi * (-nH + 2nO + q)
all_entries = [pbx_cmpd] + pbx_ion_entries
total = sum([composition[el] for el in elements])
comp_dict = {el.symbol: composition[el]/total for el in elements}
pourbaix_diagram = PourbaixDiagram(all_entries, comp_dict=comp_dict)
plotter = PourbaixPlotter(pourbaix_diagram)
# Plotting details...
font = "serif"
fig = plt.figure(figsize=(14, 9))
ax1 = fig.gca()
ax1.set_xlim([0, 14])
ax1.set_xticklabels([int(t) for t in ax1.get_xticks()], fontname=font,
fontsize=18)
ax1.set_ylim(-2, 2)
ax1.set_yticklabels(ax1.get_yticks(), fontname=font, fontsize=18)
ax1.set_xlabel("pH", fontname=font, fontsize=18)
ax1.set_ylabel("Potential vs. SHE (V)", fontname=font, fontsize=18)
# Outline water's stability range.
ax1.plot([0, 14], [0, -0.829], color="gray", linestyle="--", alpha=0.7,
linewidth=2)
ax1.plot([0, 14], [1.229, 0.401], color="gray", linestyle="--", alpha=0.7,
linewidth=2)
stable_entries = plotter.pourbaix_plot_data(
limits=[[0, 14], [-2, 2]])[0]
# Add coloring.
colors = sb.color_palette("Set2", len(stable_entries))
i = 0
for entry in stable_entries:
col = colors[i]
i += 1
vertices = plotter.domain_vertices(entry)
center_x = sum([v[0] for v in vertices])/len(vertices)
center_y = sum([v[1] for v in vertices])/len(vertices)
patch = Polygon(vertices, closed=True, fill=True, facecolor=col,
linewidth=2, edgecolor="w")
ax1.text(center_x, center_y, plotter.print_name(entry),
verticalalignment="center", horizontalalignment="center",
fontname=font, fontsize=18)
ax1.add_patch(patch)
plt.savefig("pourbaix.{}".format(fmt))
plt.close()
def setUp(self):
ion = Ion.from_formula("MnO4[-]")
self.entry = IonEntry(ion, 49)
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 plot_pourbaix_diagram(metastability=0.0,
ion_concentration=1e-6,
fmt='pdf'):
"""
Creates a Pourbaix diagram for the material in the cwd.
Args:
metastability (float): desired metastable tolerance energy
(meV/atom). <~50 is generally a sensible range to use.
ion_concentration (float): in mol/kg. Sensible values are
generally between 1e-8 and 1.
fmt (str): matplotlib format style. Check the matplotlib
docs for options.
"""
# Create a ComputedEntry object for the 2D material.
composition = Structure.from_file('POSCAR').composition
energy = Vasprun('vasprun.xml').final_energy
cmpd = ComputedEntry(composition, energy)
# Define the chemsys that describes the 2D compound.
chemsys = ['O', 'H'] + [
elt.symbol
for elt in composition.elements if elt.symbol not in ['O', 'H']
]
# Pick out the ions pertaining to the 2D compound.
ion_dict = dict()
for elt in chemsys:
if elt not in ['O', 'H'] and ION_FORMATION_ENERGIES[elt]:
ion_dict.update(ION_FORMATION_ENERGIES[elt])
elements = [Element(elt) for elt in chemsys if elt not in ['O', 'H']]
# Add "correction" for metastability
cmpd.correction -= float(cmpd.composition.num_atoms)\
* float(metastability) / 1000.0
# Calculate formation energy of the compound from its end
# members
form_energy = cmpd.energy
for elt in composition.as_dict():
form_energy -= CHEMICAL_POTENTIALS[elt] * cmpd.composition[elt]
# Convert the compound entry to a pourbaix entry.
# Default concentration for solid entries = 1
pbx_cmpd = PourbaixEntry(cmpd)
pbx_cmpd.g0_replace(form_energy)
pbx_cmpd.reduced_entry()
# Add corrected ionic entries to the pourbaix diagram
# dft corrections for experimental ionic energies:
# Persson et.al PHYSICAL REVIEW B 85, 235438 (2012)
pbx_ion_entries = list()
# Get PourbaixEntry corresponding to each ion.
# Default concentration for ionic entries = 1e-6
# ion_energy = ion_exp_energy + ion_correction * factor
# where factor = fraction of element el in the ionic entry
# compared to the reference entry
for elt in elements:
for key in ion_dict:
comp = Ion.from_formula(key)
if comp.composition[elt] != 0:
factor = comp.composition[elt]
energy = ion_dict[key]
pbx_entry_ion = PourbaixEntry(IonEntry(comp, energy))
pbx_entry_ion.correction = (ION_CORRECTIONS[elt.symbol] *
factor)
pbx_entry_ion.conc = ion_concentration
pbx_entry_ion.name = key
pbx_ion_entries.append(pbx_entry_ion)
# Generate and plot Pourbaix diagram
# Each bulk solid/ion has a free energy g of the form:
# g = g0_ref + 0.0591 * log10(conc) - nO * mu_H2O +
# (nH - 2nO) * pH + phi * (-nH + 2nO + q)
all_entries = [pbx_cmpd] + pbx_ion_entries
pourbaix = PourbaixDiagram(all_entries)
# Analysis features
# panalyzer = PourbaixAnalyzer(pourbaix)
# instability = panalyzer.get_e_above_hull(pbx_cmpd)
plotter = PourbaixPlotter(pourbaix)
plot = plotter.get_pourbaix_plot(limits=[[0, 14], [-2, 2]],
label_domains=True)
fig = plot.gcf()
ax1 = fig.gca()
# Add coloring to highlight the stability region for the 2D
# material, if one exists.
stable_entries = plotter.pourbaix_plot_data(limits=[[0, 14], [-2, 2]])[0]
for entry in stable_entries:
if entry == pbx_cmpd:
col = plt.cm.Blues(0)
else:
col = plt.cm.rainbow(
float(ION_COLORS[entry.composition.reduced_formula]))
vertices = plotter.domain_vertices(entry)
patch = Polygon(vertices, closed=True, fill=True, color=col)
ax1.add_patch(patch)
fig.set_size_inches((11.5, 9))
plot.tight_layout(pad=1.09)
# Save plot
if metastability:
plot.suptitle('Metastable Tolerance ='
' {} meV/atom'.format(metastability),
fontsize=20)
plot.savefig('{}_{}.{}'.format(composition.reduced_formula,
ion_concentration, fmt),
transparent=True)
else:
plot.savefig('{}_{}.{}'.format(composition.reduced_formula,
ion_concentration, fmt),
transparent=True)
plot.close()
def len_elts(entry):
comp = Composition(entry[:-3]) if "(s)" in entry else Ion.from_formula(entry)
return len(set(comp.elements) - {Element("H"), Element("O")})
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
pbx_solid_entries = []
for entry in stable_solids_minus_h2o:
pbx_entry = PourbaixEntry(entry)
# Replace E with newly corrected E
pbx_entry.g0_replace(pd.get_form_energy(entry))
pbx_entry.reduced_entry() # Applies reduction factor?????
pbx_solid_entries.append(pbx_entry)
# | - Processing My Solid Entries
for key, value in ion_dict_solids_expt.items():
print("IDJFIJDS")
split_key = key.split("_")
formula_i = split_key[0]
comp = Ion.from_formula(formula_i)
energy = value
pbx_entry_ion = PourbaixEntry(
ComputedEntry(comp, energy, attribute={"full_name": key}))
# AP pbx_entry_ion.name = key
pbx_entry_ion.conc = 1
pbx_solid_entries.append(pbx_entry_ion)
for a in pbx_solid_entries:
print(a, a.conc)
print('hkjo')
#__|
# +
def get_pourbaix_entries(
self,
chemsys: Union[str, List],
solid_compat="MaterialsProject2020Compatibility",
use_gibbs: Optional[Literal[300]] = None,
):
"""
A helper function to get all entries necessary to generate
a Pourbaix diagram from the rest interface.
Args:
chemsys (str or [str]): Chemical system string comprising element
symbols separated by dashes, e.g., "Li-Fe-O" or List of element
symbols, e.g., ["Li", "Fe", "O"].
solid_compat: Compatiblity scheme used to pre-process solid DFT energies prior
to applying aqueous energy adjustments. May be passed as a class (e.g.
MaterialsProject2020Compatibility) or an instance
(e.g., MaterialsProject2020Compatibility()). If None, solid DFT energies
are used as-is. Default: MaterialsProject2020Compatibility
use_gibbs: Set to 300 (for 300 Kelvin) to use a machine learning model to
estimate solid free energy from DFT energy (see GibbsComputedStructureEntry).
This can slightly improve the accuracy of the Pourbaix diagram in some
cases. Default: None. Note that temperatures other than 300K are not
permitted here, because MaterialsProjectAqueousCompatibility corrections,
used in Pourbaix diagram construction, are calculated based on 300 K data.
"""
# imports are not top-level due to expense
from pymatgen.analysis.pourbaix_diagram import PourbaixEntry
from pymatgen.entries.compatibility import (
Compatibility,
MaterialsProject2020Compatibility,
MaterialsProjectAqueousCompatibility,
MaterialsProjectCompatibility,
)
from pymatgen.entries.computed_entries import ComputedEntry
if solid_compat == "MaterialsProjectCompatibility":
solid_compat = MaterialsProjectCompatibility()
elif solid_compat == "MaterialsProject2020Compatibility":
solid_compat = MaterialsProject2020Compatibility()
elif isinstance(solid_compat, Compatibility):
solid_compat = solid_compat
else:
raise ValueError(
"Solid compatibility can only be 'MaterialsProjectCompatibility', "
"'MaterialsProject2020Compatibility', or an instance of a Compatability class"
)
pbx_entries = []
if isinstance(chemsys, str):
chemsys = chemsys.split("-")
# capitalize and sort the elements
chemsys = sorted(e.capitalize() for e in chemsys)
# Get ion entries first, because certain ions have reference
# solids that aren't necessarily in the chemsys (Na2SO4)
# download the ion reference data from MPContribs
ion_data = self.get_ion_reference_data_for_chemsys(chemsys)
# build the PhaseDiagram for get_ion_entries
ion_ref_comps = [
Ion.from_formula(d["data"]["RefSolid"]).composition
for d in ion_data
]
ion_ref_elts = set(
itertools.chain.from_iterable(i.elements for i in ion_ref_comps))
# TODO - would be great if the commented line below would work
# However for some reason you cannot process GibbsComputedStructureEntry with
# MaterialsProjectAqueousCompatibility
ion_ref_entries = self.get_entries_in_chemsys(
list([str(e) for e in ion_ref_elts] + ["O", "H"]),
# use_gibbs=use_gibbs
)
# suppress the warning about supplying the required energies; they will be calculated from the
# entries we get from MPRester
with warnings.catch_warnings():
warnings.filterwarnings(
"ignore",
message="You did not provide the required O2 and H2O energies.",
)
compat = MaterialsProjectAqueousCompatibility(
solid_compat=solid_compat)
# suppress the warning about missing oxidation states
with warnings.catch_warnings():
warnings.filterwarnings(
"ignore", message="Failed to guess oxidation states.*")
ion_ref_entries = compat.process_entries(ion_ref_entries)
# TODO - if the commented line above would work, this conditional block
# could be removed
if use_gibbs:
# replace the entries with GibbsComputedStructureEntry
from pymatgen.entries.computed_entries import GibbsComputedStructureEntry
ion_ref_entries = GibbsComputedStructureEntry.from_entries(
ion_ref_entries, temp=use_gibbs)
ion_ref_pd = PhaseDiagram(ion_ref_entries)
ion_entries = self.get_ion_entries(ion_ref_pd, ion_ref_data=ion_data)
pbx_entries = [
PourbaixEntry(e, f"ion-{n}") for n, e in enumerate(ion_entries)
]
# 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)):
# Create new computed entry
form_e = ion_ref_pd.get_form_energy(entry)
new_entry = ComputedEntry(entry.composition,
form_e,
entry_id=entry.entry_id)
pbx_entry = PourbaixEntry(new_entry)
pbx_entries.append(pbx_entry)
return pbx_entries
def len_elts(entry):
comp = Composition(
entry[:-3]) if "(s)" in entry else Ion.from_formula(entry)
return len(set(comp.elements) - {Element("H"), Element("O")})
def test_get_composition(self):
comp = self.entry.composition
expected_comp = Ion.from_formula('MnO4[-]')
self.assertEqual(comp, expected_comp, "Wrong composition!")
def plot_pourbaix_diagram(metastability=0.0, ion_concentration=1e-6, fmt='pdf'):
"""
Creates a Pourbaix diagram for the material in the cwd.
Args:
metastability (float): desired metastable tolerance energy
(meV/atom). <~50 is generally a sensible range to use.
ion_concentration (float): in mol/kg. Sensible values are
generally between 1e-8 and 1.
fmt (str): matplotlib format style. Check the matplotlib
docs for options.
"""
# Create a ComputedEntry object for the 2D material.
composition = Structure.from_file('POSCAR').composition
energy = Vasprun('vasprun.xml').final_energy
cmpd = ComputedEntry(composition, energy)
# Define the chemsys that describes the 2D compound.
chemsys = ['O', 'H'] + [elt.symbol for elt in composition.elements
if elt.symbol not in ['O', 'H']]
# Experimental ionic energies
# See ions.yaml for ion formation energies and references.
exp_dict = ION_DATA['ExpFormEnergy']
ion_correction = ION_DATA['IonCorrection']
# Pick out the ions pertaining to the 2D compound.
ion_dict = dict()
for elt in chemsys:
if elt not in ['O', 'H'] and exp_dict[elt]:
ion_dict.update(exp_dict[elt])
elements = [Element(elt) for elt in chemsys if elt not in ['O', 'H']]
# Add "correction" for metastability
cmpd.correction -= float(cmpd.composition.num_atoms)\
* float(metastability) / 1000.0
# Calculate formation energy of the compound from its end
# members
form_energy = cmpd.energy
for elt in composition.as_dict():
form_energy -= END_MEMBERS[elt] * cmpd.composition[elt]
# Convert the compound entry to a pourbaix entry.
# Default concentration for solid entries = 1
pbx_cmpd = PourbaixEntry(cmpd)
pbx_cmpd.g0_replace(form_energy)
pbx_cmpd.reduced_entry()
# Add corrected ionic entries to the pourbaix diagram
# dft corrections for experimental ionic energies:
# Persson et.al PHYSICAL REVIEW B 85, 235438 (2012)
pbx_ion_entries = list()
# Get PourbaixEntry corresponding to each ion.
# Default concentration for ionic entries = 1e-6
# ion_energy = ion_exp_energy + ion_correction * factor
# where factor = fraction of element el in the ionic entry
# compared to the reference entry
for elt in elements:
for key in ion_dict:
comp = Ion.from_formula(key)
if comp.composition[elt] != 0:
factor = comp.composition[elt]
energy = ion_dict[key]
pbx_entry_ion = PourbaixEntry(IonEntry(comp, energy))
pbx_entry_ion.correction = ion_correction[elt.symbol]\
* factor
pbx_entry_ion.conc = ion_concentration
pbx_entry_ion.name = key
pbx_ion_entries.append(pbx_entry_ion)
# Generate and plot Pourbaix diagram
# Each bulk solid/ion has a free energy g of the form:
# g = g0_ref + 0.0591 * log10(conc) - nO * mu_H2O +
# (nH - 2nO) * pH + phi * (-nH + 2nO + q)
all_entries = [pbx_cmpd] + pbx_ion_entries
pourbaix = PourbaixDiagram(all_entries)
# Analysis features
panalyzer = PourbaixAnalyzer(pourbaix)
# instability = panalyzer.get_e_above_hull(pbx_cmpd)
plotter = PourbaixPlotter(pourbaix)
plot = plotter.get_pourbaix_plot(limits=[[0, 14], [-2, 2]],
label_domains=True)
fig = plot.gcf()
ax1 = fig.gca()
# Add coloring to highlight the stability region for the 2D
# material, if one exists.
stable_entries = plotter.pourbaix_plot_data(
limits=[[0, 14], [-2, 2]])[0]
for entry in stable_entries:
if entry == pbx_cmpd:
col = plt.cm.Blues(0)
else:
col = plt.cm.rainbow(float(
ION_COLORS[entry.composition.reduced_formula]))
vertices = plotter.domain_vertices(entry)
patch = Polygon(vertices, closed=True, fill=True, color=col)
ax1.add_patch(patch)
fig.set_size_inches((11.5, 9))
plot.tight_layout(pad=1.09)
# Save plot
if metastability:
plot.suptitle('Metastable Tolerance ='
' {} meV/atom'.format(metastability),
fontsize=20)
plot.savefig('{}_{}.{}'.format(
composition.reduced_formula, ion_concentration, fmt),
transparent=True)
else:
plot.savefig('{}_{}.{}'.format(composition.reduced_formula,
ion_concentration, fmt),
transparent=True)
plot.close()
def test_get_composition(self):
comp = self.entry.composition
expected_comp = Ion.from_formula('MnO4[-]')
self.assertEquals(comp, expected_comp, "Wrong composition!")