def test_pourbaix():
"""Test ZnO system from docs."""
refs = solvated('Zn')
print(refs)
refs += [('Zn', 0.0), ('ZnO', -3.323), ('ZnO2(aq)', -2.921)]
pb = Pourbaix(refs, formula='ZnO')
_, e = pb.decompose(-1.0, 7.0)
assert e == pytest.approx(-3.625, abs=0.001)
U = np.linspace(-2, 2, 3)
pH = np.linspace(6, 16, 11)
d, names, text = pb.diagram(U, pH, plot=False)
print(d, names, text)
assert d.shape == (3, 11)
assert d.ptp() == 6
assert names == ['Zn', 'ZnO2(aq)', 'Zn++(aq)', 'HZnO2-(aq)',
'ZnOH+(aq)', 'ZnO', 'ZnO2--(aq)']
# creates: zno.png
import numpy as np
import matplotlib.pyplot as plt
from ase.phasediagram import Pourbaix, solvated
refs = solvated('Zn')
print(refs)
refs += [('Zn', 0.0), ('ZnO', -3.323), ('ZnO2(aq)', -2.921)]
pb = Pourbaix(refs, Zn=1, O=1)
print(pb.decompose(1.0, 9.0))
U = np.linspace(-2, 2, 200)
pH = np.linspace(-2, 16, 300)
d, names, text = pb.diagram(U, pH, plot=True, show=False)
print(names, text)
assert len(names) == 7
plt.savefig('zno.png')
energy = 0.0
refs.append((refcount, energy))
if 1:
refs = [#({'O': 1}, 0.0),
('O4Ti2', -17.511826939900217),
('Sr4O4', -20.474907588620653),
('Sr4', 0.0),
('Ti2', 0.0)]
else:
refs = [({'O': 1}, 0.0),
({'Zn': 1}, 0.0),
({'Zn': 2, 'O': 2}, -5.33991412178575),
({'Zn': 4, 'O': 8}, -7.594)]
pb = Pourbaix(refs + solvated('SrTi'), Sr=1, Ti=1, O=3)
#pb = Pourbaix(refs, Zn=1, O=1)
print(pb.decompose(0, 9))
pH = np.linspace(-1, 15, 17)
if 0:
d, names = pb.diagram([0], pH)
print(d)
print('\n'.join(names))
U = np.linspace(-2, 2, 5)
if 0:
d, names = pb.diagram(U, [0])
for i, u in zip(d, U):
print(u, names[i])
if 1:
U = np.linspace(-3, 3, 200)
# creates: SrTiO3_pourbaix.png
import numpy as np
import ase.db
from ase.phasediagram import Pourbaix, solvated
con = ase.db.connect('cubic_perovskites.db')
refs = []
for row in con.select('reference'):
refs.append((row.formula, row.standard_energy))
# Add other solid/dissolved phases not included before:
refs += [('Ti6O', -5.443), ('Ti2O3', -13.907), ('Ti2O', -5.164),
('TiO', -4.838), ('SrO2', -5.356), ('Ti3O', -5.346),
('Ti3O5', -22.917), ('Sr4Ti3O10', -50.756), ('SrTi11O20', -93.313)]
# Extract the dissolved phases:
refs += solvated('SrTi')
pb = Pourbaix(refs, Sr=1, Ti=1, O=3)
U = np.linspace(-2, 2, 200)
pH = np.linspace(-2, 15, 300)
d, names, text = pb.diagram(U, pH, plot=True, show=False)
import matplotlib.pyplot as plt
plt.savefig('SrTiO3_pourbaix.png')
# creates: zno.png
from ase.phasediagram import Pourbaix, solvated
refs = solvated('Zn')
print(refs)
refs += [('Zn', 0.0), ('ZnO', -3.323), ('ZnO2(aq)', -2.921)]
pb = Pourbaix(refs, Zn=1, O=1)
print(pb.decompose(1.0, 9.0))
import numpy as np
U = np.linspace(-2, 2, 200)
pH = np.linspace(-2, 16, 300)
d, names, text = pb.diagram(U, pH, plot=True)
import matplotlib.pyplot as plt
plt.savefig('zno.png')
('Sr4', 0.0), ('Ti2', 0.0)
]
else:
refs = [({
'O': 1
}, 0.0), ({
'Zn': 1
}, 0.0), ({
'Zn': 2,
'O': 2
}, -5.33991412178575), ({
'Zn': 4,
'O': 8
}, -7.594)]
pb = Pourbaix(refs + solvated('SrTi'), Sr=1, Ti=1, O=3)
#pb = Pourbaix(refs, Zn=1, O=1)
print(pb.decompose(0, 9))
pH = np.linspace(-1, 15, 17)
if 0:
d, names = pb.diagram([0], pH)
print(d)
print('\n'.join(names))
U = np.linspace(-2, 2, 5)
if 0:
d, names = pb.diagram(U, [0])
for i, u in zip(d, U):
print(u, names[i])
if 1:
U = np.linspace(-3, 3, 200)
row.CB_ind <= 0 - E0 and row.VB_ind >= 1.23 - E0) or \
(row.gllbsc_dir_gap >= 1.4 and row.gllbsc_dir_gap <= 3.1 and
row.CB_dir <= 0 - E0 and row.VB_dir >= 1.23 - E0):
name = row.A_ion + row.B_ion + row.anion
energy = row.standard_energy
info.append([name, row.gllbsc_ind_gap + E0, row.gllbsc_dir_gap + E0,
row.VB_ind + E0, row.CB_ind + E0,
row.VB_dir + E0, row.CB_dir + E0])
refs = []
for row_ref in con.select('reference'):
refs.append((row_ref.formula, row_ref.standard_energy))
# Extract the dissolved phases:
refs += solvated(row.A_ion + row.B_ion)
for U in Us:
pb = Pourbaix(refs, name)
results, refs_energy = pb.decompose(U, pH, verbose=False)
Ediff = (energy - refs_energy) / 5
Ediff = min(Ediff, ub)
Ediff = max(Ediff, lb)
xs.append(len(info) - 1)
ys.append(U)
heats.append(Ediff)
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from matplotlib.collections import PatchCollection
import matplotlib.patches as patches