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"""Test Pourbaix diagram."""
import numpy as np
import pytest
from ase.phasediagram import Pourbaix as Pourbaix_old
from ase.phasediagram import solvated
from ase.pourbaix import (
PREDEF_ENERGIES,
U_STD_AGCL,
U_STD_SCE,
Pourbaix,
RedOx,
Species,
get_main_products,
)
@pytest.fixture
def refs():
return {
'Zn': 0.0,
'ZnO': -3.336021896,
'Zn++(aq)': -1.525613424,
'ZnOH+(aq)': -3.4125107,
'HZnO2-(aq)': -4.8087349,
'ZnO2--(aq)': -4.03387383
}
@pytest.fixture
def pbx(refs):
return Pourbaix('Zn', refs)
def test_old_pourbaix():
"""Test ZnO system from docs."""
refs_old = solvated('Zn')
refs_old += [('Zn', 0.0), ('ZnO', -3.323), ('ZnO2(aq)', -2.921)]
with pytest.warns(FutureWarning):
pb = Pourbaix_old(refs_old, 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, _ = pb.diagram(U, pH, plot=False)
assert d.shape == (3, 11)
assert np.ptp(d) == 6
assert names == ['Zn', 'ZnO2(aq)', 'Zn++(aq)', 'HZnO2-(aq)',
'ZnOH+(aq)', 'ZnO', 'ZnO2--(aq)']
def test_Zn_diagram(pbx):
"""Test module against Zn Pourbaix diagram from the Atlas"""
U = np.linspace(-2, 2, 5)
pH = np.linspace(0, 14, 8)
diagram = pbx.diagram(U, pH)
# Verify that the stability domains are the expected ones
names = [get_main_products(txt[2])[0] for txt in diagram.text]
for name in ['Zn', 'ZnO', 'Zn++(aq)', 'HZnO2-(aq)', 'ZnO2--(aq)']:
assert name in names
assert 'ZnOH+(aq)' not in names
# Verify that Zn is stable at U=-2, pH=0
assert diagram.meta[0, 0] <= 0
# Verify that Zn++ is the stable phase at U=0, pH=6
i0 = int(diagram.pour[2, 3])
phase0 = pbx.phases[i0]
assert 'Zn++(aq)' in phase0.count
# Verify that the pourbaix energy at U=1, pH=7 is the expected one
# and similarly for U=-2, pH=0
Epbx1 = pbx.get_pourbaix_energy(1.0, 7.0, verbose=True)[0]
assert Epbx1 == pytest.approx(3.880, abs=0.001)
Epbx2 = pbx.get_pourbaix_energy(-2.0, 0.0, verbose=True)[0]
assert Epbx2 == pytest.approx(-2.119, abs=0.001)
def test_plotting(pbx, figure):
"""Test all the plotting functionalities and options"""
diagram = pbx.diagram(U=np.linspace(-2, 2, 10), pH=np.linspace(0, 14, 10))
ax = figure.gca()
args = {'include_text': True,
'include_water': True,
'labeltype': 'phases',
'cap': 1.0,
# 'figsize': [12, 6],
'cmap': "RdYlGn_r",
'normalize': True,
'show': False,
'filename': None,
'ax': ax}
diagram.plot(**args)
args.update({'include_text': False,
'include_water': False,
'labeltype': 'numbers',
'normalize': False,
'cap': [0, 1]})
diagram.plot(**args)
args.update({'labeltype': 'askjglkjh'})
with pytest.raises(ValueError):
diagram.plot(**args)
def test_redox():
"""Test different reference electrode corrections
Plus other unused RedOx methods
Reaction:
Zn + H2O + e- ➜ H+ + HZnO--(aq)
"""
reactant = Species.from_string('Zn', 0.0)
products = [Species.from_string('HZnO--(aq)', 0.0)]
products_noredox = [Species.from_string('Pt', 0.0)]
reaction = RedOx.from_species(reactant, products)
noreaction = RedOx.from_species(reactant, products_noredox)
assert reaction is not None
assert noreaction is None
corr = []
for reference in ['SHE', 'RHE', 'Pt', 'AgCl', 'SCE']:
corr.append(reaction.get_ref_correction(reference, alpha=1.0))
assert corr[0][0] == pytest.approx(corr[0][1]) == pytest.approx(0.0)
assert corr[1][1] == pytest.approx(-1.0)
assert corr[2][0] == pytest.approx(-0.5 * PREDEF_ENERGIES['H2O'])
assert corr[3][0] == pytest.approx(U_STD_AGCL)
assert corr[4][0] == pytest.approx(U_STD_SCE)
assert reaction.equation()
G = reaction.get_free_energy(1.0, 1.0)
assert G == pytest.approx(3.044, abs=0.001)
def test_species_extras():
"""Test some methods of Species not used by Pourbaix"""
s = Species.from_string('H2O', 0.0)
chemsys = s.get_chemsys()
assert len(chemsys) == 3
frac = s.get_fractional_composition('H')
assert frac == pytest.approx(2 / 3)
def test_trigger_phases_error():
"""Produce an error when provided refs don't produce valid reactions"""
refs = {
'Zn': 0.0,
'Mn': 0.0
}
with pytest.raises(ValueError):
Pourbaix('Zn', refs)
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