def test_get_plot_2d_concise(self):
c = TEMCalculator()
structure = self.get_structure("Si")
fig = c.get_plot_2d_concise(structure)
width = fig.layout.width
height = fig.layout.height
self.assertTrue(width == 121 and height == 121)
def test_get_first_point(self):
c = TEMCalculator()
latt = Lattice.cubic(4.209)
points = c.generate_points(-2, 2)
cubic = Structure(latt, ["Cs", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]])
first_pt = c.get_first_point(cubic, points)
self.assertTrue(4.209 in first_pt.values())
def test_generate_points(self):
# Tests that 3d points are properly generated
c = TEMCalculator()
actual = c.generate_points(-1, 1)
expected = np.array([
[-1, -1, -1],
[-1, -1, 0],
[-1, -1, 1],
[0, -1, -1],
[0, -1, 0],
[0, -1, 1],
[1, -1, -1],
[1, -1, 0],
[1, -1, 1],
[-1, 0, -1],
[-1, 0, 0],
[-1, 0, 1],
[0, 0, -1],
[0, 0, 0],
[0, 0, 1],
[1, 0, -1],
[1, 0, 0],
[1, 0, 1],
[-1, 1, -1],
[-1, 1, 0],
[-1, 1, 1],
[0, 1, -1],
[0, 1, 0],
[0, 1, 1],
[1, 1, -1],
[1, 1, 0],
[1, 1, 1],
])
self.assertArrayEqual(expected, actual)
def test_TEM_dots(self):
# All dependencies in TEM_dots method are tested. Only make sure each object created is
# the class desired.
c = TEMCalculator()
points = c.generate_points(-2, 2)
structure = self.get_structure("Si")
dots = c.tem_dots(structure, points)
self.assertTrue(all([isinstance(x, tuple) for x in dots]))
def test_zone_axis_filter(self):
# Tests that the appropriate Laue-Zoned points are returned
c = TEMCalculator()
empty_points = np.asarray([])
self.assertEqual(c.zone_axis_filter(empty_points), [])
points = np.asarray([[-1, -1, -1]])
self.assertEqual(c.zone_axis_filter(points), [])
laue_1 = np.array([[0, 0, 1], [0, 1, 0], [1, 0, 0], [0, 0, -1]])
self.assertEqual(c.zone_axis_filter(laue_1, 1), [(0, 0, 1)])
def test_get_positions(self):
c = TEMCalculator()
points = c.generate_points(-2, 2)
structure = self.get_structure("Si")
positions = c.get_positions(structure, points)
self.assertArrayEqual([0, 0], positions[(0, 0, 0)])
# Test silicon diffraction data spot rough positions:
# see https://www.doitpoms.ac.uk/tlplib/diffraction-patterns/printall.php
self.assertArrayAlmostEqual([1, 0], positions[(-1, 0, 0)], 0)
def test_normalized_cell_intensity(self):
# Test that the method correctly normalizes a value.
c = TEMCalculator()
latt = Lattice.cubic(4.209)
cubic = Structure(latt, ["Cs", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]])
point = [(2, 0, 0)]
spacings = c.get_interplanar_spacings(cubic, point)
angles = c.bragg_angles(spacings)
cellint = c.normalized_cell_intensity(cubic, angles)
self.assertAlmostEqual(cellint[(2, 0, 0)], 1)
def test_x_ray_factors(self):
c = TEMCalculator()
latt = Lattice.cubic(4.209)
cubic = Structure(latt, ["Cs", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]])
point = [(-10, 3, 0)]
spacings = c.get_interplanar_spacings(cubic, point)
angles = c.bragg_angles(spacings)
x_ray = c.x_ray_factors(cubic, angles)
self.assertAlmostEqual(x_ray["Cs"][(-10, 3, 0)], 14.42250869579648)
self.assertAlmostEqual(x_ray["Cl"][(-10, 3, 0)], 2.7804915737999103)
def test_bragg_angles(self):
# Tests that the appropriate bragg angle is returned. Testing formula with values of x-ray diffraction in
# materials project.
c = TEMCalculator()
latt = Lattice.cubic(4.209)
cubic = Structure(latt, ["Cs", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]])
point = [(1, 1, 0)]
spacings = c.get_interplanar_spacings(cubic, point)
bragg_angles_val = np.arcsin(1.5406 / (2 * spacings[point[0]]))
self.assertAlmostEqual(bragg_angles_val, 0.262, places=3)
def test_cell_scattering_factors(self):
# Test that fcc structure gives 0 intensity for mixed even, odd hkl.
c = TEMCalculator()
nacl = Structure.from_spacegroup("Fm-3m", Lattice.cubic(5.692),
["Na", "Cl"],
[[0, 0, 0], [0.5, 0.5, 0.5]])
point = [(2, 1, 0)]
spacings = c.get_interplanar_spacings(nacl, point)
angles = c.bragg_angles(spacings)
cellscatt = c.cell_scattering_factors(nacl, angles)
self.assertAlmostEqual(cellscatt[(2, 1, 0)], 0)
def test_get_s2(self):
# Tests that the appropriate s2 factor is returned.
c = TEMCalculator()
latt = Lattice.cubic(4.209)
cubic = Structure(latt, ["Cs", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]])
point = [(-10, 3, 0)]
spacings = c.get_interplanar_spacings(cubic, point)
angles = c.bragg_angles(spacings)
s2 = c.get_s2(angles)
for p in s2:
self.assertAlmostEqual(s2[p], 1.5381852947115047)
def test_interplanar_angle(self):
# test interplanar angles. Reference values from KW Andrews,
# Interpretation of Electron Diffraction pp70-90.
c = TEMCalculator()
latt = Lattice.cubic(4.209)
cubic = Structure(latt, ["Cs", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]])
phi = c.get_interplanar_angle(cubic, (0, 0, -1), (0, -1, 0))
self.assertAlmostEqual(90, phi, places=1)
tet = self.get_structure("Li10GeP2S12")
phi = c.get_interplanar_angle(tet, (0, 0, 1), (1, 0, 3))
self.assertAlmostEqual(25.796, phi, places=1)
latt = Lattice.hexagonal(2, 4)
hex = Structure(latt, ["Ab"], [[0, 0, 0]])
phi = c.get_interplanar_angle(hex, (0, 0, 1), (1, 0, 6))
self.assertAlmostEqual(21.052, phi, places=1)
def generate_diffraction_pattern(structure, *args):
structure = self.from_data(structure)
kwargs = self.reconstruct_kwargs_from_state()
calculator = TEMCalculator(**kwargs)
print("kwargs", kwargs)
return dcc.Graph(
figure=calculator.get_plot_2d(structure),
responsive=False,
config={
"displayModeBar": False,
"displaylogo": False
},
)
def test_cell_intensity(self):
# Test that bcc structure gives lower intensity for h + k + l != even.
c = TEMCalculator()
latt = Lattice.cubic(4.209)
cubic = Structure(latt, ["Cs", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]])
point = [(2, 1, 0)]
point2 = [(2, 2, 0)]
spacings = c.get_interplanar_spacings(cubic, point)
spacings2 = c.get_interplanar_spacings(cubic, point2)
angles = c.bragg_angles(spacings)
angles2 = c.bragg_angles(spacings2)
cellint = c.cell_intensity(cubic, angles)
cellint2 = c.cell_intensity(cubic, angles2)
self.assertGreater(cellint2[(2, 2, 0)], cellint[(2, 1, 0)])
def test_electron_scattering_factors(self):
# Test the electron atomic scattering factor, values approximate with
# international table of crystallography volume C. Rounding error when converting hkl to sin(theta)/lambda.
# Error increases as sin(theta)/lambda is smaller.
c = TEMCalculator()
latt = Lattice.cubic(4.209)
cubic = Structure(latt, ["Cs", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]])
nacl = Structure.from_spacegroup("Fm-3m", Lattice.cubic(5.692),
["Na", "Cl"],
[[0, 0, 0], [0.5, 0.5, 0.5]])
point = [(2, 1, 3)]
point_nacl = [(4, 2, 0)]
spacings = c.get_interplanar_spacings(cubic, point)
spacings_nacl = c.get_interplanar_spacings(nacl, point_nacl)
angles = c.bragg_angles(spacings)
angles_nacl = c.bragg_angles(spacings_nacl)
elscatt = c.electron_scattering_factors(cubic, angles)
elscatt_nacl = c.electron_scattering_factors(nacl, angles_nacl)
self.assertAlmostEqual(elscatt["Cs"][(2, 1, 3)], 2.890, places=1)
self.assertAlmostEqual(elscatt["Cl"][(2, 1, 3)], 1.138, places=1)
self.assertAlmostEqual(elscatt_nacl["Na"][(4, 2, 0)], 0.852, places=1)
self.assertAlmostEqual(elscatt_nacl["Cl"][(4, 2, 0)], 1.372, places=1)
def test_get_interplanar_spacings(self):
# Tests that the appropriate interplacing spacing is returned
c = TEMCalculator()
point = [(3, 9, 0)]
latt = Lattice.cubic(4.209)
cubic = Structure(latt, ["Cs", "Cl"], [[0, 0, 0], [0.5, 0.5, 0.5]])
tet = self.get_structure("Li10GeP2S12")
hexa = self.get_structure("Graphite")
ortho = self.get_structure("K2O2")
mono = self.get_structure("Li3V2(PO4)3")
spacings_cubic = c.get_interplanar_spacings(cubic, point)
spacings_tet = c.get_interplanar_spacings(tet, point)
spacings_hexa = c.get_interplanar_spacings(hexa, point)
spacings_ortho = c.get_interplanar_spacings(ortho, point)
spacings_mono = c.get_interplanar_spacings(mono, point)
for p in point:
self.assertAlmostEqual(spacings_cubic[p], 0.4436675557216236)
self.assertAlmostEqual(spacings_tet[p], 0.9164354445646701)
self.assertAlmostEqual(spacings_hexa[p], 0.19775826179547752)
self.assertAlmostEqual(spacings_ortho[p], 0.5072617738916)
self.assertAlmostEqual(spacings_mono[p], 0.84450786041677972)
def test_is_parallel(self):
c = TEMCalculator()
self.assertTrue(c.is_parallel((1, 0, 0), (3, 0, 0)))
self.assertFalse(c.is_parallel((1, 0, 0), (3, 0, 1)))
def test_wavelength_rel(self):
# Tests that the relativistic wavelength formula (for 200kv electron beam) is correct
c = TEMCalculator()
self.assertAlmostEqual(c.wavelength_rel(), 0.0251, places=3)
def test_get_plot_2d(self):
c = TEMCalculator()
structure = self.get_structure("Si")
self.assertTrue(isinstance(c.get_plot_2d(structure), go.Figure))
def test_get_pattern(self):
# All dependencies in get_pattern method are tested.
# Only make sure result is a pd dataframe.
c = TEMCalculator()
structure = self.get_structure("Si")
self.assertTrue(isinstance(c.get_pattern(structure), pd.DataFrame))
def test_is_parallel(self):
c = TEMCalculator()
structure = self.get_structure("Si")
self.assertTrue(c.is_parallel(structure, (1, 0, 0), (3, 0, 0)))
self.assertFalse(c.is_parallel(structure, (1, 0, 0), (3, 0, 1)))
def test_get_plot_coeffs(self):
# Test if x * p1 + y * p2 yields p3.
c = TEMCalculator()
coeffs = c.get_plot_coeffs((1, 1, 0), (1, -1, 0), (2, 0, 0), -2, False)
self.assertEqual([1, 1], coeffs)
def test_get_plot_coeffs(self):
# Test if x * p1 + y * p2 yields p3.
c = TEMCalculator()
coeffs = c.get_plot_coeffs((1, 1, 0), (1, -1, 0), (2, 0, 0))
self.assertArrayAlmostEqual(np.array([1.0, 1.0]), coeffs)