def test_get_entry_energy(self):
# Test warning message.
comp = Composition('MnO3')
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
energy = InterfacialReactivity._get_entry_energy(self.pd, comp)
self.assertTrue(len(w) == 1)
self.assertTrue(
"The reactant MnO3 has no matching entry with"
" negative formation energy, instead convex "
"hull energy for this composition will be used"
" for reaction energy calculation." in str(w[-1].message))
test1 = np.isclose(energy, -30, atol=1e-03)
self.assertTrue(
test1, '_get_entry_energy: energy for {} is wrong!'.format(
comp.reduced_formula))
# Test normal functionality
comp = Composition('MnO2')
test2 = np.isclose(InterfacialReactivity._get_entry_energy(
self.pd, comp),
-30,
atol=1e-03)
self.assertTrue(
test2, '_get_entry_energy: energy for {} is wrong!'.format(
comp.reduced_formula))
def test_get_chempot_correction(self):
# test data from fig. 6 in ref:
# Prediction of A2BX4 metal-chalcogenide compounds via
# first-principles thermodynamics, PHYSICAL REVIEW B 86, 014109 (2012)
# test pressure effect.
actual = InterfacialReactivity.get_chempot_correction("O", 298.15, 100e5)
expect = 0.05916
self.assertTrue(
np.isclose(actual, expect, atol=1e-2),
"get_chempot_correction gets error, {0} expected but gets {1}".format(expect, actual),
)
# test temperature effect.
actual_2 = InterfacialReactivity.get_chempot_correction("O", 1000, 1e5)
expect_2 = -0.82352
self.assertTrue(
np.isclose(actual_2, expect_2, atol=1e-2),
"get_chempot_correction gets error, {0} expected but gets {1}".format(expect_2, actual_2),
)
actual_3 = InterfacialReactivity.get_chempot_correction("O", 500, 1e5)
expect_3 = -0.223
self.assertTrue(
np.isclose(actual_3, expect_3, atol=1e-2),
"get_chempot_correction gets error, {0} expected but gets {1}".format(expect_3, actual_3),
)
# test mixed effect.
actual_4 = InterfacialReactivity.get_chempot_correction("O", 1000, 1e-25)
expect_4 = -3.800
self.assertTrue(
np.isclose(actual_4, expect_4, atol=1e-2),
"get_chempot_correction gets error, {0} expected but gets {1}".format(expect_4, actual_4),
)
actual_5 = InterfacialReactivity.get_chempot_correction("O", 1250, 1e-25)
expect_5 = -4.86
self.assertTrue(
np.isclose(actual_5, expect_5, atol=1e-2),
"get_chempot_correction gets error, {0} expected but gets {1}".format(expect_5, actual_5),
)
actual_6 = InterfacialReactivity.get_chempot_correction("O", 1500, 1e-25)
expect_6 = -5.928
self.assertTrue(
np.isclose(actual_6, expect_6, atol=1e-2),
"get_chempot_correction gets error, {0} expected but gets {1}".format(expect_6, actual_6),
)
actual_7 = InterfacialReactivity.get_chempot_correction("O", 1000, 1e-15)
expect_7 = -2.808
self.assertTrue(
np.isclose(actual_7, expect_7, atol=1e-2),
"get_chempot_correction gets error, {0} expected but gets {1}".format(expect_7, actual_7),
)
# test non-gas phase.
actual_8 = InterfacialReactivity.get_chempot_correction("Li", 1000, 1e15)
expect_8 = 0
self.assertTrue(
np.isclose(actual_8, expect_8, atol=1e-5),
"get_chempot_correction gets error, {0} expected but gets {1}".format(expect_8, actual_8),
)
def test_convert(self):
test_array = [(0.5, 1, 3), (0.4, 2, 3), (0, 1, 9), (1, 2, 7)]
result = [InterfacialReactivity._convert(x, f1, f2) for x, f1, f2 in test_array]
answer = [0.75, 0.5, 0, 1]
self.assertTrue(np.allclose(result, answer),
'_convert: conversion gets error! {0} expected,'
' but gets {1}'.format(answer, result))
def test_reverse_convert(self):
test_array = [(0.5, 1, 3), (0.4, 2, 3), (0, 1, 9), (1, 2, 7)]
result = [InterfacialReactivity._reverse_convert(x, f1, f2)
for x, f1, f2 in test_array]
answer = [0.25, 0.3076923, 0, 1]
self.assertTrue(np.allclose(result, answer),
'_convert: conversion gets error! {0} expected,'
' but gets {1}'.format(answer, result))
def react_interface(r1, r2, pd, num_entries, grand_pd=None):
"""
Calculate thermodynamically predicted reactions at the interface between two
materials.
Args:
r1 (Composition): first reactant
r2 (Composition): second reactant
pd (PhaseDiagram): pymatgen phase diagram object
num_entries (int): total number of entries in system, used in building reaction
vector
grand_pd (GrandPotentialPhaseDiagram): pymatgen grand pot. phase diagram object
Returns:
[ComputedReaction]: List of computed reacitons
"""
if grand_pd:
interface = InterfacialReactivity(
r1,
r2,
grand_pd,
norm=True,
include_no_mixing_energy=False,
pd_non_grand=pd,
use_hull_energy=True,
)
else:
interface = InterfacialReactivity(
r1,
r2,
pd,
norm=False,
include_no_mixing_energy=False,
pd_non_grand=None,
use_hull_energy=True,
)
entries = pd.all_entries
rxns = {
get_computed_rxn(rxn, entries, num_entries)
for _, _, _, rxn, _ in interface.get_kinks()
}
return rxns
def test_convert(self):
test_array = [(0.5, 1, 3), (0.4, 2, 3), (0, 1, 9), (1, 2, 7)]
result = [
InterfacialReactivity._convert(x, f1, f2)
for x, f1, f2 in test_array
]
answer = [0.75, 0.5, 0, 1]
self.assertTrue(
np.allclose(result, answer),
f"_convert: conversion gets error! {answer} expected, but gets {result}",
)
def test_get_entry_energy(self):
# Test warning message.
comp = Composition('MnO3')
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
energy = InterfacialReactivity._get_entry_energy(self.pd, comp)
self.assertTrue(len(w) == 1)
self.assertTrue("The reactant MnO3 has no matching entry with"
" negative formation energy, instead convex "
"hull energy for this composition will be used"
" for reaction energy calculation."
in str(w[-1].message))
test1 = np.isclose(energy, -30, atol=1e-03)
self.assertTrue(test1,
'_get_entry_energy: energy for {} is wrong!'.format(
comp.reduced_formula))
# Test normal functionality
comp = Composition('MnO2')
test2 = np.isclose(InterfacialReactivity._get_entry_energy(self.pd, comp), -30,
atol=1e-03)
self.assertTrue(test2,
'_get_entry_energy: energy for {} is wrong!'.format(
comp.reduced_formula))
def setUp(self):
self.entries = [ComputedEntry(Composition('Li'), 0),
ComputedEntry(Composition('Mn'), 0),
ComputedEntry(Composition('O2'), 0),
ComputedEntry(Composition('MnO2'), -10),
ComputedEntry(Composition('Mn2O4'), -60),
ComputedEntry(Composition('MnO3'), 20),
ComputedEntry(Composition('Li2O'), -10),
ComputedEntry(Composition('Li2O2'), -8),
ComputedEntry(Composition('LiMnO2'), -30)
]
self.pd = PhaseDiagram(self.entries)
chempots = {'Li': -3}
self.gpd = GrandPotentialPhaseDiagram(self.entries, chempots)
self.ir = []
self.ir.append(
InterfacialReactivity(Composition('O2'), Composition('Mn'),
self.pd, norm=0, include_no_mixing_energy=0,
pd_non_grand=None, use_hull_energy=False))
self.ir.append(
InterfacialReactivity(Composition('MnO2'), Composition('Mn'),
self.gpd, norm=0, include_no_mixing_energy=1,
pd_non_grand=self.pd, use_hull_energy=False))
self.ir.append(
InterfacialReactivity(Composition('Mn'), Composition('O2'),
self.gpd, norm=1, include_no_mixing_energy=1,
pd_non_grand=self.pd, use_hull_energy=False))
self.ir.append(
InterfacialReactivity(Composition('Li2O'), Composition('Mn'),
self.gpd, norm=0, include_no_mixing_energy=1,
pd_non_grand=self.pd, use_hull_energy=False))
self.ir.append(
InterfacialReactivity(Composition('Mn'), Composition('O2'),
self.gpd, norm=1, include_no_mixing_energy=0,
pd_non_grand=self.pd, use_hull_energy=False))
self.ir.append(
InterfacialReactivity(Composition('Mn'), Composition('Li2O'),
self.gpd, norm=1, include_no_mixing_energy=1,
pd_non_grand=self.pd, use_hull_energy=False))
self.ir.append(
InterfacialReactivity(Composition('Li2O2'), Composition('Li'),
self.pd, norm=0, include_no_mixing_energy=0,
pd_non_grand=None, use_hull_energy=True))
self.ir.append(
InterfacialReactivity(Composition('Li2O2'), Composition('Li'),
self.pd, norm=0, include_no_mixing_energy=0,
pd_non_grand=None, use_hull_energy=False))
self.ir.append(
InterfacialReactivity(Composition('Li2O2'), Composition('MnO2'),
self.gpd, norm=0, include_no_mixing_energy=0,
pd_non_grand=self.pd, use_hull_energy=True))
self.ir.append(
InterfacialReactivity(Composition('Li2O2'), Composition('MnO2'),
self.gpd, norm=0, include_no_mixing_energy=0,
pd_non_grand=self.pd, use_hull_energy=False))
self.ir.append(
InterfacialReactivity(Composition('O2'), Composition('Mn'),
self.pd, norm=1, include_no_mixing_energy=0,
pd_non_grand=None, use_hull_energy=False))
self.ir.append(
InterfacialReactivity(Composition('Li2O2'), Composition('Li2O2'),
self.gpd, norm=1, include_no_mixing_energy=1,
pd_non_grand=self.pd, use_hull_energy=False))
self.ir.append(
InterfacialReactivity(Composition('Li2O2'), Composition('Li2O2'),
self.pd, norm=1, include_no_mixing_energy=0,
pd_non_grand=None, use_hull_energy=False))
with self.assertRaises(Exception) as context1:
self.ir.append(
InterfacialReactivity(Composition('Li2O2'), Composition('Li'),
self.pd, norm=1,
include_no_mixing_energy=1,
pd_non_grand=None))
self.assertTrue(
'Please provide grand phase diagram '
'to compute no_mixing_energy!' == str(context1.exception))
with self.assertRaises(Exception) as context2:
self.ir.append(
InterfacialReactivity(Composition('O2'), Composition('Mn'),
self.gpd, norm=0,
include_no_mixing_energy=1,
pd_non_grand=None))
self.assertTrue(
'Please provide non-grand phase diagram '
'to compute no_mixing_energy!' == str(context2.exception))
def setUp(self):
self.entries = [
ComputedEntry(Composition("Li"), 0),
ComputedEntry(Composition("Mn"), 0),
ComputedEntry(Composition("O2"), 0),
ComputedEntry(Composition("MnO2"), -10),
ComputedEntry(Composition("Mn2O4"), -60),
ComputedEntry(Composition("MnO3"), 20),
ComputedEntry(Composition("Li2O"), -10),
ComputedEntry(Composition("Li2O2"), -8),
ComputedEntry(Composition("LiMnO2"), -30),
]
self.pd = PhaseDiagram(self.entries)
chempots = {"Li": -3}
self.gpd = GrandPotentialPhaseDiagram(self.entries, chempots)
self.ir = []
# ir[0]
self.ir.append(
InterfacialReactivity(
Composition("O2"),
Composition("Mn"),
self.pd,
norm=0,
include_no_mixing_energy=0,
pd_non_grand=None,
use_hull_energy=False,
)
)
# ir[1]
self.ir.append(
InterfacialReactivity(
Composition("MnO2"),
Composition("Mn"),
self.gpd,
norm=0,
include_no_mixing_energy=1,
pd_non_grand=self.pd,
use_hull_energy=False,
)
)
# ir[2]
self.ir.append(
InterfacialReactivity(
Composition("Mn"),
Composition("O2"),
self.gpd,
norm=1,
include_no_mixing_energy=1,
pd_non_grand=self.pd,
use_hull_energy=False,
)
)
# ir[3]
self.ir.append(
InterfacialReactivity(
Composition("Li2O"),
Composition("Mn"),
self.gpd,
norm=0,
include_no_mixing_energy=1,
pd_non_grand=self.pd,
use_hull_energy=False,
)
)
# ir[4]
self.ir.append(
InterfacialReactivity(
Composition("Mn"),
Composition("O2"),
self.gpd,
norm=1,
include_no_mixing_energy=0,
pd_non_grand=self.pd,
use_hull_energy=False,
)
)
# ir[5]
self.ir.append(
InterfacialReactivity(
Composition("Mn"),
Composition("Li2O"),
self.gpd,
norm=1,
include_no_mixing_energy=1,
pd_non_grand=self.pd,
use_hull_energy=False,
)
)
# ir[6]
self.ir.append(
InterfacialReactivity(
Composition("Li2O2"),
Composition("Li"),
self.pd,
norm=0,
include_no_mixing_energy=0,
pd_non_grand=None,
use_hull_energy=True,
)
)
# ir[7]
self.ir.append(
InterfacialReactivity(
Composition("Li2O2"),
Composition("Li"),
self.pd,
norm=0,
include_no_mixing_energy=0,
pd_non_grand=None,
use_hull_energy=False,
)
)
# ir[8]
self.ir.append(
InterfacialReactivity(
Composition("Li2O2"),
Composition("MnO2"),
self.gpd,
norm=0,
include_no_mixing_energy=0,
pd_non_grand=self.pd,
use_hull_energy=True,
)
)
# ir[9]
self.ir.append(
InterfacialReactivity(
Composition("Li2O2"),
Composition("MnO2"),
self.gpd,
norm=0,
include_no_mixing_energy=0,
pd_non_grand=self.pd,
use_hull_energy=False,
)
)
# ir[10]
self.ir.append(
InterfacialReactivity(
Composition("O2"),
Composition("Mn"),
self.pd,
norm=1,
include_no_mixing_energy=0,
pd_non_grand=None,
use_hull_energy=False,
)
)
# ir[11]
self.ir.append(
InterfacialReactivity(
Composition("Li2O2"),
Composition("Li2O2"),
self.gpd,
norm=1,
include_no_mixing_energy=1,
pd_non_grand=self.pd,
use_hull_energy=False,
)
)
# ir[12]
self.ir.append(
InterfacialReactivity(
Composition("Li2O2"),
Composition("Li2O2"),
self.pd,
norm=1,
include_no_mixing_energy=0,
pd_non_grand=None,
use_hull_energy=False,
)
)
with self.assertRaises(Exception) as context1:
self.ir.append(
InterfacialReactivity(
Composition("Li2O2"),
Composition("Li"),
self.pd,
norm=1,
include_no_mixing_energy=1,
pd_non_grand=None,
)
)
self.assertTrue("Please provide grand phase diagram to compute no_mixing_energy!" == str(context1.exception))
with self.assertRaises(Exception) as context2:
self.ir.append(
InterfacialReactivity(
Composition("O2"),
Composition("Mn"),
self.gpd,
norm=0,
include_no_mixing_energy=1,
pd_non_grand=None,
)
)
self.assertTrue(
"Please provide non-grand phase diagram to compute no_mixing_energy!" == str(context2.exception)
)
def setUp(self):
self.entries = [
ComputedEntry(Composition("Li"), 0),
ComputedEntry(Composition("Mn"), 0),
ComputedEntry(Composition("O2"), 0),
ComputedEntry(Composition("MnO2"), -10),
ComputedEntry(Composition("Mn2O4"), -60),
ComputedEntry(Composition("MnO3"), 20),
ComputedEntry(Composition("Li2O"), -10),
ComputedEntry(Composition("Li2O2"), -8),
ComputedEntry(Composition("LiMnO2"), -30),
]
self.pd = PhaseDiagram(self.entries)
chempots = {Element("Li"): -3}
self.gpd = GrandPotentialPhaseDiagram(self.entries, chempots)
ir_0 = InterfacialReactivity(
c1=Composition("O2"),
c2=Composition("Mn"),
pd=self.pd,
norm=False,
use_hull_energy=False,
)
ir_1 = GrandPotentialInterfacialReactivity(
c1=Composition("MnO2"),
c2=Composition("Mn"),
grand_pd=self.gpd,
pd_non_grand=self.pd,
norm=False,
include_no_mixing_energy=True,
use_hull_energy=False,
)
ir_2 = GrandPotentialInterfacialReactivity(
c1=Composition("Mn"),
c2=Composition("O2"),
grand_pd=self.gpd,
pd_non_grand=self.pd,
norm=True,
include_no_mixing_energy=True,
use_hull_energy=False,
)
ir_3 = GrandPotentialInterfacialReactivity(
c1=Composition("Li2O"),
c2=Composition("Mn"),
grand_pd=self.gpd,
norm=False,
include_no_mixing_energy=True,
pd_non_grand=self.pd,
use_hull_energy=False,
)
ir_4 = GrandPotentialInterfacialReactivity(
c1=Composition("Mn"),
c2=Composition("O2"),
grand_pd=self.gpd,
norm=True,
include_no_mixing_energy=False,
pd_non_grand=self.pd,
use_hull_energy=False,
)
ir_5 = GrandPotentialInterfacialReactivity(
c1=Composition("Mn"),
c2=Composition("Li2O"),
grand_pd=self.gpd,
pd_non_grand=self.pd,
norm=True,
include_no_mixing_energy=True,
use_hull_energy=False,
)
ir_6 = InterfacialReactivity(
c1=Composition("Li2O2"),
c2=Composition("Li"),
pd=self.pd,
norm=False,
use_hull_energy=True,
)
ir_7 = InterfacialReactivity(
c1=Composition("Li2O2"),
c2=Composition("Li"),
pd=self.pd,
norm=False,
use_hull_energy=False,
)
ir_8 = GrandPotentialInterfacialReactivity(
c1=Composition("Li2O2"),
c2=Composition("MnO2"),
grand_pd=self.gpd,
pd_non_grand=self.pd,
norm=False,
include_no_mixing_energy=False,
use_hull_energy=True,
)
ir_9 = GrandPotentialInterfacialReactivity(
c1=Composition("Li2O2"),
c2=Composition("MnO2"),
grand_pd=self.gpd,
pd_non_grand=self.pd,
norm=False,
include_no_mixing_energy=False,
use_hull_energy=False,
)
ir_10 = InterfacialReactivity(
Composition("O2"),
Composition("Mn"),
pd=self.pd,
norm=True,
use_hull_energy=False,
)
ir_11 = GrandPotentialInterfacialReactivity(
Composition("Li2O2"),
Composition("Li2O2"),
grand_pd=self.gpd,
norm=True,
include_no_mixing_energy=True,
pd_non_grand=self.pd,
use_hull_energy=False,
)
ir_12 = InterfacialReactivity(
Composition("Li2O2"),
Composition("Li2O2"),
pd=self.pd,
norm=True,
use_hull_energy=False,
)
with self.assertRaises(Exception) as context1:
ir_13 = InterfacialReactivity(Composition("Li2O2"),
Composition("Li"),
pd=self.gpd,
norm=True)
self.assertTrue(
"Please use the GrandPotentialInterfacialReactivity "
"class for interfacial reactions with open elements!" == str(
context1.exception))
with self.assertRaises(Exception) as context2:
ir_14 = GrandPotentialInterfacialReactivity(
Composition("O2"),
Composition("Mn"),
grand_pd=self.gpd,
pd_non_grand=None,
norm=False,
include_no_mixing_energy=True,
)
self.assertTrue(
"Please provide non-grand phase diagram to compute no_mixing_energy!"
== str(context2.exception))
self.ir = [
ir_0, ir_1, ir_2, ir_3, ir_4, ir_5, ir_6, ir_7, ir_8, ir_9, ir_10,
ir_11, ir_12
]
def test_get_chempot_correction(self):
# test data from fig. 6 in ref:
# Prediction of A2BX4 metal-chalcogenide compounds via
# first-principles thermodynamics, PHYSICAL REVIEW B 86, 014109 (2012)
# test pressure effect.
actual = InterfacialReactivity.get_chempot_correction("O", 298.15,
100E5)
expect = 0.05916
self.assertTrue(np.isclose(actual, expect, atol=1E-2),
"get_chempot_correction gets "
"error, {0} expected but gets {1}".format(expect,
actual))
# test temperature effect.
actual_2 = InterfacialReactivity.get_chempot_correction("O", 1000,
1E5)
expect_2 = -0.82352
self.assertTrue(np.isclose(actual_2, expect_2, atol=1E-2),
"get_chempot_correction gets "
"error, {0} expected but gets {1}".format(expect_2,
actual_2))
actual_3 = InterfacialReactivity.get_chempot_correction("O", 500,
1E5)
expect_3 = -0.223
self.assertTrue(np.isclose(actual_3, expect_3, atol=1E-2),
"get_chempot_correction gets "
"error, {0} expected but gets {1}".format(expect_3,
actual_3))
# test mixed effect.
actual_4 = InterfacialReactivity.get_chempot_correction("O", 1000,
1E-25)
expect_4 = -3.800
self.assertTrue(np.isclose(actual_4, expect_4, atol=1E-2),
"get_chempot_correction gets "
"error, {0} expected but gets {1}".format(expect_4,
actual_4))
actual_5 = InterfacialReactivity.get_chempot_correction("O", 1250,
1E-25)
expect_5 = -4.86
self.assertTrue(np.isclose(actual_5, expect_5, atol=1E-2),
"get_chempot_correction gets "
"error, {0} expected but gets {1}".format(expect_5,
actual_5))
actual_6 = InterfacialReactivity.get_chempot_correction("O", 1500,
1E-25)
expect_6 = -5.928
self.assertTrue(np.isclose(actual_6, expect_6, atol=1E-2),
"get_chempot_correction gets "
"error, {0} expected but gets {1}".format(expect_6,
actual_6))
actual_7 = InterfacialReactivity.get_chempot_correction("O", 1000,
1E-15)
expect_7 = -2.808
self.assertTrue(np.isclose(actual_7, expect_7, atol=1E-2),
"get_chempot_correction gets "
"error, {0} expected but gets {1}".format(expect_7,
actual_7))
# test non-gas phase.
actual_8 = InterfacialReactivity.get_chempot_correction("Li", 1000,
1E15)
expect_8 = 0
self.assertTrue(np.isclose(actual_8, expect_8, atol=1E-5),
"get_chempot_correction gets "
"error, {0} expected but gets {1}".format(expect_8,
actual_8))
entries = mpr.get_entries_in_chemsys(elements)
# Build a phase diagram using these entries.
pd = PhaseDiagram(entries)
# For an open system, include the grand potential phase diagram.
if grand:
# Get the chemical potential of the pure subtance.
mu = pd.get_transition_chempots(Element(open_el))[0]
# Set the chemical potential in the elemental reservoir.
chempots = {open_el: relative_mu + mu}
# Build the grand potential phase diagram
gpd = GrandPotentialPhaseDiagram(entries, chempots)
# Create InterfacialReactivity object.
interface = InterfacialReactivity(comp1,
comp2,
gpd,
norm=True,
include_no_mixing_energy=True,
pd_non_grand=pd,
use_hull_energy=False)
else:
interface = InterfacialReactivity(comp1,
comp2,
pd,
norm=True,
include_no_mixing_energy=False,
pd_non_grand=None,
use_hull_energy=False)
plt = interface.plot()