class NanoscaleStabilityTest(PymatgenTest):
def setUp(self):
# Load all entries
La_hcp_entry_dict = get_entry_dict(
os.path.join(get_path(""), "La_hcp_entries.txt"))
La_fcc_entry_dict = get_entry_dict(
os.path.join(get_path(""), "La_fcc_entries.txt"))
with open(os.path.join(get_path(""),
'ucell_entries.txt')) as ucell_entries:
ucell_entries = json.loads(ucell_entries.read())
La_hcp_ucell_entry = ComputedStructureEntry.from_dict(
ucell_entries["La_hcp"])
La_fcc_ucell_entry = ComputedStructureEntry.from_dict(
ucell_entries["La_fcc"])
# Set up the NanoscaleStabilityClass
self.La_hcp_analyzer = SurfaceEnergyPlotter(La_hcp_entry_dict,
La_hcp_ucell_entry)
self.La_fcc_analyzer = SurfaceEnergyPlotter(La_fcc_entry_dict,
La_fcc_ucell_entry)
self.nanoscale_stability = NanoscaleStability(
[self.La_fcc_analyzer, self.La_hcp_analyzer])
def test_stability_at_r(self):
# Check that we have a different polymorph that is
# stable below or above the equilibrium particle size
r = self.nanoscale_stability.solve_equilibrium_point(
self.La_hcp_analyzer, self.La_fcc_analyzer) * 10
# hcp phase of La particle should be the stable
# polymorph above the equilibrium radius
hcp_wulff = self.La_hcp_analyzer.wulff_from_chempot()
bulk = self.La_hcp_analyzer.ucell_entry
ghcp, rhcp = self.nanoscale_stability.wulff_gform_and_r(
hcp_wulff, bulk, r + 10, from_sphere_area=True)
fcc_wulff = self.La_fcc_analyzer.wulff_from_chempot()
bulk = self.La_fcc_analyzer.ucell_entry
gfcc, rfcc = self.nanoscale_stability.wulff_gform_and_r(
fcc_wulff, bulk, r + 10, from_sphere_area=True)
self.assertGreater(gfcc, ghcp)
# fcc phase of La particle should be the stable
# polymorph below the equilibrium radius
hcp_wulff = self.La_hcp_analyzer.wulff_from_chempot()
bulk = self.La_hcp_analyzer.ucell_entry
ghcp, rhcp = self.nanoscale_stability.wulff_gform_and_r(
hcp_wulff, bulk, r - 10, from_sphere_area=True)
fcc_wulff = self.La_fcc_analyzer.wulff_from_chempot()
bulk = self.La_fcc_analyzer.ucell_entry
gfcc, rfcc = self.nanoscale_stability.wulff_gform_and_r(
fcc_wulff, bulk, r - 10, from_sphere_area=True)
self.assertLess(gfcc, ghcp)
class NanoscaleStabilityTest(PymatgenTest):
def setUp(self):
# Load all entries
La_hcp_entry_dict = get_entry_dict(os.path.join(get_path(""),
"La_hcp_entries.txt"))
La_fcc_entry_dict = get_entry_dict(os.path.join(get_path(""),
"La_fcc_entries.txt"))
with open(os.path.join(get_path(""), 'ucell_entries.txt')) as ucell_entries:
ucell_entries = json.loads(ucell_entries.read())
La_hcp_ucell_entry = ComputedStructureEntry.from_dict(ucell_entries["La_hcp"])
La_fcc_ucell_entry = ComputedStructureEntry.from_dict(ucell_entries["La_fcc"])
# Set up the NanoscaleStabilityClass
self.La_hcp_analyzer = SurfaceEnergyPlotter(La_hcp_entry_dict,
La_hcp_ucell_entry)
self.La_fcc_analyzer = SurfaceEnergyPlotter(La_fcc_entry_dict,
La_fcc_ucell_entry)
self.nanoscale_stability = NanoscaleStability([self.La_fcc_analyzer,
self.La_hcp_analyzer])
def test_stability_at_r(self):
# Check that we have a different polymorph that is
# stable below or above the equilibrium particle size
r = self.nanoscale_stability.solve_equilibrium_point(self.La_hcp_analyzer,
self.La_fcc_analyzer)*10
# hcp phase of La particle should be the stable
# polymorph above the equilibrium radius
hcp_wulff = self.La_hcp_analyzer.wulff_from_chempot()
bulk = self.La_hcp_analyzer.ucell_entry
ghcp, rhcp = self.nanoscale_stability.wulff_gform_and_r(hcp_wulff, bulk, r+10,
from_sphere_area=True)
fcc_wulff = self.La_fcc_analyzer.wulff_from_chempot()
bulk = self.La_fcc_analyzer.ucell_entry
gfcc, rfcc = self.nanoscale_stability.wulff_gform_and_r(fcc_wulff, bulk, r+10,
from_sphere_area=True)
self.assertGreater(gfcc, ghcp)
# fcc phase of La particle should be the stable
# polymorph below the equilibrium radius
hcp_wulff = self.La_hcp_analyzer.wulff_from_chempot()
bulk = self.La_hcp_analyzer.ucell_entry
ghcp, rhcp = self.nanoscale_stability.wulff_gform_and_r(hcp_wulff, bulk, r-10,
from_sphere_area=True)
fcc_wulff = self.La_fcc_analyzer.wulff_from_chempot()
bulk = self.La_fcc_analyzer.ucell_entry
gfcc, rfcc = self.nanoscale_stability.wulff_gform_and_r(fcc_wulff, bulk, r-10,
from_sphere_area=True)
self.assertLess(gfcc, ghcp)
class SurfaceEnergyPlotterTest(PymatgenTest):
def setUp(self):
entry_dict = get_entry_dict(os.path.join(get_path(""),
"Cu_entries.txt"))
self.Cu_entry_dict = entry_dict
with open(os.path.join(get_path(""), 'ucell_entries.txt')) as ucell_entries:
ucell_entries = json.loads(ucell_entries.read())
self.Cu_ucell_entry = ComputedStructureEntry.from_dict(ucell_entries["Cu"])
self.Cu_analyzer = SurfaceEnergyPlotter(entry_dict, self.Cu_ucell_entry)
self.metals_O_entry_dict = load_O_adsorption()
ucell_entry = ComputedStructureEntry.from_dict(ucell_entries["Pt"])
self.Pt_analyzer = SurfaceEnergyPlotter(self.metals_O_entry_dict["Pt"],
ucell_entry)
ucell_entry = ComputedStructureEntry.from_dict(ucell_entries["Ni"])
self.Ni_analyzer = SurfaceEnergyPlotter(self.metals_O_entry_dict["Ni"],
ucell_entry)
ucell_entry = ComputedStructureEntry.from_dict(ucell_entries["Rh"])
self.Rh_analyzer = SurfaceEnergyPlotter(self.metals_O_entry_dict["Rh"],
ucell_entry)
self.Oads_analyzer_dict = {"Pt": self.Pt_analyzer,
"Ni": self.Ni_analyzer,
"Rh": self.Rh_analyzer}
def test_get_stable_entry_at_u(self):
for el in self.Oads_analyzer_dict.keys():
plotter = self.Oads_analyzer_dict[el]
for hkl in plotter.all_slab_entries.keys():
# Test that the surface energy is clean for specific range of chempot
entry1, gamma1 = \
plotter.get_stable_entry_at_u(hkl, delu_dict={Symbol("delu_O"): -7})
entry2, gamma2 = \
plotter.get_stable_entry_at_u(hkl, delu_dict={Symbol("delu_O"): -6})
self.assertEqual(gamma1, gamma2)
self.assertEqual(entry1.label, entry2.label)
# Now test that for a high chempot, adsorption
# occurs and gamma is not equal to clean gamma
entry3, gamma3 = \
plotter.get_stable_entry_at_u(hkl, delu_dict={Symbol("delu_O"): -1})
self.assertNotEqual(entry3.label, entry2.label)
self.assertNotEqual(gamma3, gamma2)
# For any chempot greater than -6, surface energy should vary
# but the configuration should remain the same
entry4, gamma4 = \
plotter.get_stable_entry_at_u(hkl, delu_dict={Symbol("delu_O"): 0})
self.assertEqual(entry3.label, entry4.label)
self.assertNotEqual(gamma3, gamma4)
def test_wulff_from_chempot(self):
# Test if it generates a Wulff shape, test if
# all the facets for Cu wulff shape are inside.
Cu_wulff = self.Cu_analyzer.wulff_from_chempot()
area_frac_dict = Cu_wulff.area_fraction_dict
facets_hkl = [(1, 1, 1), (3, 3, 1), (3, 1, 0), (1, 0, 0),
(3, 1, 1), (2, 1, 0), (2, 2, 1)]
for hkl in area_frac_dict.keys():
if hkl in facets_hkl:
self.assertNotEqual(area_frac_dict[hkl], 0)
else:
self.assertEqual(area_frac_dict[hkl], 0)
for el in self.Oads_analyzer_dict.keys():
# Test WulffShape for adsorbed surfaces
analyzer = self.Oads_analyzer_dict[el]
# chempot = analyzer.max_adsorption_chempot_range(0)
wulff = analyzer.wulff_from_chempot(delu_default=-6)
se = wulff.weighted_surface_energy
# Test if a different Wulff shape is generated
# for Ni when adsorption comes into play
wulff_neg7 = self.Oads_analyzer_dict["Ni"].wulff_from_chempot(delu_default=-7)
wulff_neg6 = self.Oads_analyzer_dict["Ni"].wulff_from_chempot(delu_default=-6)
self.assertEqual(wulff_neg7.weighted_surface_energy,
wulff_neg6.weighted_surface_energy)
wulff_neg55 = self.Oads_analyzer_dict["Ni"].wulff_from_chempot(delu_default=-5.5)
self.assertNotEqual(wulff_neg55.weighted_surface_energy,
wulff_neg6.weighted_surface_energy)
wulff_neg525 = self.Oads_analyzer_dict["Ni"].wulff_from_chempot(delu_default=-5.25)
self.assertNotEqual(wulff_neg55.weighted_surface_energy,
wulff_neg525.weighted_surface_energy)
def test_color_palette_dict(self):
for el in self.metals_O_entry_dict.keys():
analyzer = self.Oads_analyzer_dict[el]
color_dict = analyzer.color_palette_dict()
for hkl in self.metals_O_entry_dict[el].keys():
for clean in self.metals_O_entry_dict[el][hkl].keys():
color = color_dict[clean]
for ads in self.metals_O_entry_dict[el][hkl][clean]:
color = color_dict[ads]
def test_get_surface_equilibrium(self):
# For clean stoichiometric system, the two equations should
# be parallel because the surface energy is a constant. Then
# get_surface_equilibrium should return None
clean111_entry = list(self.Cu_entry_dict[(1, 1, 1)].keys())[0]
clean100_entry = list(self.Cu_entry_dict[(1, 0, 0)].keys())[0]
soln = self.Cu_analyzer.get_surface_equilibrium([clean111_entry,
clean100_entry])
self.assertFalse(soln)
# For adsorbed system, we should find one intercept
Pt_entries = self.metals_O_entry_dict["Pt"]
clean = list(Pt_entries[(1, 1, 1)].keys())[0]
ads = Pt_entries[(1, 1, 1)][clean][0]
Pt_analyzer = self.Oads_analyzer_dict["Pt"]
soln = Pt_analyzer.get_surface_equilibrium([clean, ads])
self.assertNotEqual(list(soln.values())[0], list(soln.values())[1])
# Check if the number of parameters for adsorption are correct
self.assertEqual((Symbol("delu_O"), Symbol("gamma")), tuple(soln.keys()))
# Adsorbed systems have a b2=(-1*Nads) / (Nsurfs * Aads)
se = ads.surface_energy(Pt_analyzer.ucell_entry, Pt_analyzer.ref_entries)
self.assertAlmostEqual(se.as_coefficients_dict()[Symbol("delu_O")],
-1 / (2 * ads.surface_area))
def test_stable_u_range_dict(self):
for el in self.Oads_analyzer_dict.keys():
analyzer = self.Oads_analyzer_dict[el]
stable_u_range = analyzer.stable_u_range_dict([-1, 0], Symbol("delu_O"),
no_doped=False)
all_u = []
for entry in stable_u_range.keys():
all_u.extend(stable_u_range[entry])
self.assertGreater(len(all_u), 1)
def test_entry_dict_from_list(self):
# Plug in a list of entries to see if it works
all_Pt_slab_entries = []
Pt_entries = self.Pt_analyzer.all_slab_entries
for hkl in Pt_entries.keys():
for clean in Pt_entries[hkl].keys():
all_Pt_slab_entries.append(clean)
all_Pt_slab_entries.extend(Pt_entries[hkl][clean])
a = SurfaceEnergyPlotter(all_Pt_slab_entries,
self.Pt_analyzer.ucell_entry)
self.assertEqual(type(a).__name__, "SurfaceEnergyPlotter")
class SurfaceEnergyPlotterTest(PymatgenTest):
def setUp(self):
entry_dict = get_entry_dict(os.path.join(get_path(""),
"Cu_entries.txt"))
self.Cu_entry_dict = entry_dict
with open(os.path.join(get_path(""), 'ucell_entries.txt')) as ucell_entries:
ucell_entries = json.loads(ucell_entries.read())
self.Cu_ucell_entry = ComputedStructureEntry.from_dict(ucell_entries["Cu"])
self.Cu_analyzer = SurfaceEnergyPlotter(entry_dict, self.Cu_ucell_entry)
self.metals_O_entry_dict = load_O_adsorption()
ucell_entry = ComputedStructureEntry.from_dict(ucell_entries["Pt"])
self.Pt_analyzer = SurfaceEnergyPlotter(self.metals_O_entry_dict["Pt"],
ucell_entry)
ucell_entry = ComputedStructureEntry.from_dict(ucell_entries["Ni"])
self.Ni_analyzer = SurfaceEnergyPlotter(self.metals_O_entry_dict["Ni"],
ucell_entry)
ucell_entry = ComputedStructureEntry.from_dict(ucell_entries["Rh"])
self.Rh_analyzer = SurfaceEnergyPlotter(self.metals_O_entry_dict["Rh"],
ucell_entry)
self.Oads_analyzer_dict = {"Pt": self.Pt_analyzer,
"Ni": self.Ni_analyzer,
"Rh": self.Rh_analyzer}
def test_get_stable_entry_at_u(self):
for el in self.Oads_analyzer_dict.keys():
plotter = self.Oads_analyzer_dict[el]
for hkl in plotter.all_slab_entries.keys():
# Test that the surface energy is clean for specific range of chempot
entry1, gamma1 = \
plotter.get_stable_entry_at_u(hkl, delu_dict={Symbol("delu_O"): -7})
entry2, gamma2 = \
plotter.get_stable_entry_at_u(hkl, delu_dict={Symbol("delu_O"): -6})
self.assertEqual(gamma1, gamma2)
self.assertEqual(entry1.label, entry2.label)
# Now test that for a high chempot, adsorption
# occurs and gamma is not equal to clean gamma
entry3, gamma3 = \
plotter.get_stable_entry_at_u(hkl, delu_dict={Symbol("delu_O"): -1})
self.assertNotEqual(entry3.label, entry2.label)
self.assertNotEqual(gamma3, gamma2)
# For any chempot greater than -6, surface energy should vary
# but the configuration should remain the same
entry4, gamma4 = \
plotter.get_stable_entry_at_u(hkl, delu_dict={Symbol("delu_O"): 0})
self.assertEqual(entry3.label, entry4.label)
self.assertNotEqual(gamma3, gamma4)
def test_wulff_from_chempot(self):
# Test if it generates a Wulff shape, test if
# all the facets for Cu wulff shape are inside.
Cu_wulff = self.Cu_analyzer.wulff_from_chempot()
area_frac_dict = Cu_wulff.area_fraction_dict
facets_hkl = [(1,1,1), (3,3,1), (3,1,0), (1,0,0),
(3,1,1), (2,1,0), (2,2,1)]
for hkl in area_frac_dict.keys():
if hkl in facets_hkl:
self.assertNotEqual(area_frac_dict[hkl], 0)
else:
self.assertEqual(area_frac_dict[hkl], 0)
for el in self.Oads_analyzer_dict.keys():
# Test WulffShape for adsorbed surfaces
analyzer = self.Oads_analyzer_dict[el]
# chempot = analyzer.max_adsorption_chempot_range(0)
wulff = analyzer.wulff_from_chempot(delu_default=-6)
se = wulff.weighted_surface_energy
# Test if a different Wulff shape is generated
# for Ni when adsorption comes into play
wulff_neg7 = self.Oads_analyzer_dict["Ni"].wulff_from_chempot(delu_default=-7)
wulff_neg6 = self.Oads_analyzer_dict["Ni"].wulff_from_chempot(delu_default=-6)
self.assertEqual(wulff_neg7.weighted_surface_energy,
wulff_neg6.weighted_surface_energy)
wulff_neg55 = self.Oads_analyzer_dict["Ni"].wulff_from_chempot(delu_default=-5.5)
self.assertNotEqual(wulff_neg55.weighted_surface_energy,
wulff_neg6.weighted_surface_energy)
wulff_neg525 = self.Oads_analyzer_dict["Ni"].wulff_from_chempot(delu_default=-5.25)
self.assertNotEqual(wulff_neg55.weighted_surface_energy,
wulff_neg525.weighted_surface_energy)
def test_color_palette_dict(self):
for el in self.metals_O_entry_dict.keys():
analyzer = self.Oads_analyzer_dict[el]
color_dict = analyzer.color_palette_dict()
for hkl in self.metals_O_entry_dict[el].keys():
for clean in self.metals_O_entry_dict[el][hkl].keys():
color = color_dict[clean]
for ads in self.metals_O_entry_dict[el][hkl][clean]:
color = color_dict[ads]
def test_get_surface_equilibrium(self):
# For clean stoichiometric system, the two equations should
# be parallel because the surface energy is a constant. Then
# get_surface_equilibrium should return None
clean111_entry = list(self.Cu_entry_dict[(1, 1, 1)].keys())[0]
clean100_entry = list(self.Cu_entry_dict[(1, 0, 0)].keys())[0]
soln = self.Cu_analyzer.get_surface_equilibrium([clean111_entry,
clean100_entry])
self.assertFalse(soln)
# For adsorbed system, we should find one intercept
Pt_entries = self.metals_O_entry_dict["Pt"]
clean = list(Pt_entries[(1, 1, 1)].keys())[0]
ads = Pt_entries[(1, 1, 1)][clean][0]
Pt_analyzer = self.Oads_analyzer_dict["Pt"]
soln = Pt_analyzer.get_surface_equilibrium([clean, ads])
self.assertNotEqual(list(soln.values())[0], list(soln.values())[1])
# Check if the number of parameters for adsorption are correct
self.assertEqual((Symbol("delu_O"), Symbol("gamma")), tuple(soln.keys()))
# Adsorbed systems have a b2=(-1*Nads) / (Nsurfs * Aads)
se = ads.surface_energy(Pt_analyzer.ucell_entry, Pt_analyzer.ref_entries)
self.assertAlmostEqual(se.as_coefficients_dict()[Symbol("delu_O")],
-1 / (2 * ads.surface_area))
def test_stable_u_range_dict(self):
for el in self.Oads_analyzer_dict.keys():
analyzer = self.Oads_analyzer_dict[el]
stable_u_range = analyzer.stable_u_range_dict([-1,0], Symbol("delu_O"),
no_doped=False)
all_u = []
for entry in stable_u_range.keys():
all_u.extend(stable_u_range[entry])
self.assertGreater(len(all_u), 1)
def test_entry_dict_from_list(self):
# Plug in a list of entries to see if it works
all_Pt_slab_entries = []
Pt_entries = self.Pt_analyzer.all_slab_entries
for hkl in Pt_entries.keys():
for clean in Pt_entries[hkl].keys():
all_Pt_slab_entries.append(clean)
all_Pt_slab_entries.extend(Pt_entries[hkl][clean])
a = SurfaceEnergyPlotter(all_Pt_slab_entries,
self.Pt_analyzer.ucell_entry)
self.assertEqual(type(a).__name__, "SurfaceEnergyPlotter")