class WulffShapeTest(PymatgenTest):
def setUp(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
with open(os.path.join(module_dir, "surface_samples.json")) as data_file:
surface_properties = json.load(data_file)
surface_energies, miller_indices = {}, {}
for mpid in surface_properties.keys():
e_surf_list, miller_list = [], []
for surface in surface_properties[mpid]["surfaces"]:
e_surf_list.append(surface["surface_energy"])
miller_list.append(surface["miller_index"])
surface_energies[mpid] = e_surf_list
miller_indices[mpid] = miller_list
# In the case of a high anisotropy material
# Nb: mp-8636
latt_Nb = Lattice.cubic(2.992)
# In the case of an fcc material
# Ir: mp-101
latt_Ir = Lattice.cubic(3.8312)
# In the case of a hcp material
# Ti: mp-72
latt_Ti = Lattice.hexagonal(4.6000, 2.8200)
self.ucell_Nb = Structure(
latt_Nb,
["Nb", "Nb", "Nb", "Nb"],
[[0, 0, 0], [0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]],
)
self.wulff_Nb = WulffShape(latt_Nb, miller_indices["mp-8636"], surface_energies["mp-8636"])
self.ucell_Ir = Structure(
latt_Nb,
["Ir", "Ir", "Ir", "Ir"],
[[0, 0, 0], [0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]],
)
self.wulff_Ir = WulffShape(latt_Ir, miller_indices["mp-101"], surface_energies["mp-101"])
self.ucell_Ti = Structure(
latt_Ti,
["Ti", "Ti", "Ti"],
[[0, 0, 0], [0.333333, 0.666667, 0.5], [0.666667, 0.333333, 0.5]],
)
self.wulff_Ti = WulffShape(latt_Ti, miller_indices["mp-72"], surface_energies["mp-72"])
self.cube = WulffShape(Lattice.cubic(1), [(1, 0, 0)], [1])
self.hex_prism = WulffShape(Lattice.hexagonal(2.63, 5.21), [(0, 0, 1), (1, 0, 0)], [0.35, 0.53])
self.surface_properties = surface_properties
@unittest.skipIf("DISPLAY" not in os.environ, "Need display")
def test_get_plot(self):
# Basic test, not really a unittest.
self.wulff_Ti.get_plot()
self.wulff_Nb.get_plot()
self.wulff_Ir.get_plot()
@unittest.skipIf("DISPLAY" not in os.environ, "Need display")
def test_get_plotly(self):
# Basic test, not really a unittest.
self.wulff_Ti.get_plotly()
self.wulff_Nb.get_plotly()
self.wulff_Ir.get_plotly()
def symm_check(self, ucell, wulff_vertices):
"""
# Checks if the point group of the Wulff shape matches
# the point group of its conventional unit cell
Args:
ucell (string): Unit cell that the Wulff shape is based on.
wulff_vertices (list): List of all vertices on the Wulff
shape. Use wulff.wulff_pt_list to obtain the list
(see wulff_generator.py).
return (bool)
"""
space_group_analyzer = SpacegroupAnalyzer(ucell)
symm_ops = space_group_analyzer.get_point_group_operations(cartesian=True)
for point in wulff_vertices:
for op in symm_ops:
symm_point = op.operate(point)
if in_coord_list(wulff_vertices, symm_point):
continue
else:
return False
return True
def consistency_tests(self):
# For a set of given values, these tests will
# ensure that the general result given by the
# algorithm does not change as the code is editted
# For fcc Ir, make sure the (111) direction
# is the most dominant facet on the Wulff shape
fractional_areas = self.wulff_Ir.area_fraction_dict
miller_list = [hkl for hkl in fractional_areas.keys()]
area_list = [fractional_areas[hkl] for hkl in fractional_areas.keys()]
self.assertEqual(miller_list[area_list.index(max(area_list))], (1, 1, 1))
# Overall weighted surface energy of fcc Nb should be
# equal to the energy of the (310) surface, ie. fcc Nb
# is anisotropic, the (310) surface is so low in energy,
# its the only facet that exists in the Wulff shape
Nb_area_fraction_dict = self.wulff_Nb.area_fraction_dict
for hkl in Nb_area_fraction_dict.keys():
if hkl == (3, 1, 0):
self.assertEqual(Nb_area_fraction_dict[hkl], 1)
else:
self.assertEqual(Nb_area_fraction_dict[hkl], 0)
self.assertEqual(
self.wulff_Nb.miller_energy_dict[(3, 1, 0)],
self.wulff_Nb.weighted_surface_energy,
)
def symmetry_test(self):
# Maintains that all wulff shapes have the same point
# groups as the conventional unit cell they were
# derived from. This test should pass for all subsequent
# updates of the surface_properties collection
check_symmetry_Nb = self.symm_check(self.ucell_Nb, self.wulff_Nb.wulff_pt_list)
check_symmetry_Ir = self.symm_check(self.ucell_Ir, self.wulff_Ir.wulff_pt_list)
check_symmetry_Ti = self.symm_check(self.ucell_Ti, self.wulff_Ti.wulff_pt_list)
self.assertTrue(check_symmetry_Nb)
self.assertTrue(check_symmetry_Ir)
self.assertTrue(check_symmetry_Ti)
def test_get_azimuth_elev(self):
# Test out the viewing of the Wulff shape from Miller indices.
azim, elev = self.wulff_Ir._get_azimuth_elev((0, 0, 1))
self.assertEqual(azim, 0)
self.assertEqual(elev, 90)
azim, elev = self.wulff_Ir._get_azimuth_elev((1, 1, 1))
self.assertAlmostEqual(azim, 45)
def test_properties(self):
# Simple test to check if the values of some
# properties are consistent with what we already have
wulff_shapes = {
"mp-8636": self.wulff_Nb,
"mp-72": self.wulff_Ti,
"mp-101": self.wulff_Ir,
}
for mpid in wulff_shapes.keys():
properties = self.surface_properties[mpid]
wulff = wulff_shapes[mpid]
self.assertEqual(
round(wulff.weighted_surface_energy, 3),
round(properties["weighted_surface_energy"], 3),
)
self.assertEqual(round(wulff.shape_factor, 3), round(properties["shape_factor"], 3))
self.assertEqual(round(wulff.anisotropy, 3), round(properties["surface_anisotropy"], 3))
def test_corner_and_edges(self):
# Test if it is returning the correct number of corner and edges
self.assertArrayEqual(self.cube.tot_corner_sites, 8)
self.assertArrayEqual(self.cube.tot_edges, 12)
self.assertArrayEqual(self.hex_prism.tot_corner_sites, 12)
self.assertArrayEqual(self.hex_prism.tot_edges, 18)
class WulffShapeTest(PymatgenTest):
def setUp(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
with open(
os.path.join(module_dir, "surface_samples.json")) as data_file:
surface_properties = json.load(data_file)
surface_energies, miller_indices = {}, {}
for mpid in surface_properties.keys():
e_surf_list, miller_list = [], []
for surface in surface_properties[mpid]["surfaces"]:
e_surf_list.append(surface["surface_energy"])
miller_list.append(surface["miller_index"])
surface_energies[mpid] = e_surf_list
miller_indices[mpid] = miller_list
# In the case of a high anisotropy material
# Nb: mp-8636
latt_Nb = Lattice.cubic(2.992)
# In the case of an fcc material
# Ir: mp-101
latt_Ir = Lattice.cubic(3.8312)
# In the case of a hcp material
# Ti: mp-72
latt_Ti = Lattice.hexagonal(4.6000, 2.8200)
self.ucell_Nb = Structure(latt_Nb, ["Nb", "Nb", "Nb", "Nb"],
[[0, 0, 0], [0, 0.5, 0.5],
[0.5, 0, 0.5], [0.5, 0.5, 0]])
self.wulff_Nb = WulffShape(latt_Nb, miller_indices["mp-8636"],
surface_energies["mp-8636"])
self.ucell_Ir = Structure(latt_Nb, ["Ir", "Ir", "Ir", "Ir"],
[[0, 0, 0], [0, 0.5, 0.5],
[0.5, 0, 0.5], [0.5, 0.5, 0]])
self.wulff_Ir = WulffShape(latt_Ir, miller_indices["mp-101"],
surface_energies["mp-101"])
self.ucell_Ti = Structure(latt_Ti, ["Ti", "Ti", "Ti"],
[[0, 0, 0], [0.333333, 0.666667, 0.5],
[0.666667, 0.333333, 0.5]])
self.wulff_Ti = WulffShape(latt_Ti, miller_indices["mp-72"],
surface_energies["mp-72"])
self.surface_properties = surface_properties
def test_get_plot(self):
# Basic test, not really a unittest.
self.wulff_Ti.get_plot()
self.wulff_Nb.get_plot()
self.wulff_Ir.get_plot()
def symm_check(self, ucell, wulff_vertices):
"""
# Checks if the point group of the Wulff shape matches
# the point group of its conventional unit cell
Args:
ucell (string): Unit cell that the Wulff shape is based on.
wulff_vertices (list): List of all vertices on the Wulff
shape. Use wulff.wulff_pt_list to obtain the list
(see wulff_generator.py).
return (bool)
"""
space_group_analyzer = SpacegroupAnalyzer(ucell)
symm_ops = space_group_analyzer.get_point_group_operations(
cartesian=True)
for point in wulff_vertices:
for op in symm_ops:
symm_point = op.operate(point)
if in_coord_list(wulff_vertices, symm_point):
continue
else:
return False
return True
def consistency_tests(self):
# For a set of given values, these tests will
# ensure that the general result given by the
# algorithm does not change as the code is editted
# For fcc Ir, make sure the (111) direction
# is the most dominant facet on the Wulff shape
fractional_areas = self.wulff_Ir.area_fraction_dict
miller_list = [hkl for hkl in fractional_areas.keys()]
area_list = [fractional_areas[hkl] for hkl in fractional_areas.keys()]
self.assertEqual(miller_list[area_list.index(max(area_list))],
(1, 1, 1))
# Overall weighted surface energy of fcc Nb should be
# equal to the energy of the (310) surface, ie. fcc Nb
# is anisotropic, the (310) surface is so low in energy,
# its the only facet that exists in the Wulff shape
Nb_area_fraction_dict = self.wulff_Nb.area_fraction_dict
for hkl in Nb_area_fraction_dict.keys():
if hkl == (3, 1, 0):
self.assertEqual(Nb_area_fraction_dict[hkl], 1)
else:
self.assertEqual(Nb_area_fraction_dict[hkl], 0)
self.assertEqual(self.wulff_Nb.miller_energy_dict[(3, 1, 0)],
self.wulff_Nb.weighted_surface_energy)
def symmetry_test(self):
# Maintains that all wulff shapes have the same point
# groups as the conventional unit cell they were
# derived from. This test should pass for all subsequent
# updates of the surface_properties collection
check_symmetry_Nb = self.symm_check(self.ucell_Nb,
self.wulff_Nb.wulff_pt_list)
check_symmetry_Ir = self.symm_check(self.ucell_Ir,
self.wulff_Ir.wulff_pt_list)
check_symmetry_Ti = self.symm_check(self.ucell_Ti,
self.wulff_Ti.wulff_pt_list)
self.assertTrue(check_symmetry_Nb)
self.assertTrue(check_symmetry_Ir)
self.assertTrue(check_symmetry_Ti)
def test_get_azimuth_elev(self):
# Test out the viewing of the Wulff shape from Miller indices.
azim, elev = self.wulff_Ir._get_azimuth_elev((0, 0, 1))
self.assertEqual(azim, 0)
self.assertEqual(elev, 90)
azim, elev = self.wulff_Ir._get_azimuth_elev((1, 1, 1))
self.assertAlmostEqual(azim, 45)
def test_properties(self):
# Simple test to check if the values of some
# properties are consistent with what we already have
wulff_shapes = {"mp-8636": self.wulff_Nb, "mp-72": self.wulff_Ti,
"mp-101": self.wulff_Ir}
for mpid in wulff_shapes.keys():
properties = self.surface_properties[mpid]
wulff = wulff_shapes[mpid]
self.assertEqual(round(wulff.weighted_surface_energy, 3),
round(properties["weighted_surface_energy"], 3))
self.assertEqual(round(wulff.shape_factor, 3),
round(properties["shape_factor"], 3))
self.assertEqual(round(wulff.anisotropy, 3),
round(properties["surface_anisotropy"], 3))
