def test_primitive_cell_for_rhombohedral_lattice(self):
with self.assertRaises(ValueError):
PrimitiveCell.for_rhombohedral_lattice(-1, np.pi / 4)
with self.assertRaises(ValueError):
PrimitiveCell.for_rhombohedral_lattice(1, np.pi)
with self.assertRaises(ValueError):
# angle too big
PrimitiveCell.for_rhombohedral_lattice(1, np.pi * 2. / 3. + 0.1)
cosa = np.cos(self.alpha)
sina = np.sin(self.alpha)
p1 = (self.a, 0, 0)
p2 = (self.a * cosa, self.a * sina, 0)
p3 = (self.a * cosa, self.a * (cosa - cosa**2) / sina,
self.a * np.sqrt(sina**2 - ((cosa - cosa**2) / sina)**2))
pc = PrimitiveCell.for_rhombohedral_lattice(self.a, self.alpha)
self.assertIsInstance(pc, PrimitiveCell)
self.assertEqual(pc.bravais_lattice, BravaisLattice.RHOMBOHEDRAL)
assert_array_equal(pc.p1, p1)
assert_array_equal(pc.p2, p2)
assert_array_equal(pc.p3, p3)
def test_primitive_cell_for_rhombohedral_lattice(self):
with self.assertRaises(ValueError):
PrimitiveCell.for_rhombohedral_lattice(-1, np.pi/4)
with self.assertRaises(ValueError):
PrimitiveCell.for_rhombohedral_lattice(1, np.pi)
with self.assertRaises(ValueError):
# angle too big
PrimitiveCell.for_rhombohedral_lattice(1, np.pi*2./3.+0.1)
cosa = np.cos(self.alpha)
sina = np.sin(self.alpha)
p1 = (self.a, 0, 0)
p2 = (self.a*cosa, self.a*sina, 0)
p3 = (self.a*cosa, self.a*(cosa-cosa**2) / sina,
self.a*np.sqrt(sina**2 - ((cosa-cosa**2) / sina)**2))
pc = PrimitiveCell.for_rhombohedral_lattice(self.a, self.alpha)
self.assertIsInstance(pc, PrimitiveCell)
self.assertEqual(pc.bravais_lattice,
BravaisLattice.RHOMBOHEDRAL)
assert_array_equal(pc.p1, p1)
assert_array_equal(pc.p2, p2)
assert_array_equal(pc.p3, p3)
def test_exception_guess_vectors_with_unsorted_points(self):
# given
primitive_cell = PrimitiveCell.for_rhombohedral_lattice(0.1, 0.7)
# when
p1, p2, p3 = self._get_primitive_vectors(primitive_cell)
points = create_points_from_pc(p1, p2, p3, (4, 5, 3))
numpy.random.shuffle(points)
# then
with self.assertRaises(ValueError):
lattice_tools.guess_primitive_vectors(points)
def test_exception_guess_vectors_with_unsorted_points(self):
# given
primitive_cell = PrimitiveCell.for_rhombohedral_lattice(0.1, 0.7)
# when
p1, p2, p3 = self._get_primitive_vectors(primitive_cell)
points = create_points_from_pc(p1, p2, p3, (4, 5, 3))
numpy.random.shuffle(points)
# then
with self.assertRaises(ValueError):
lattice_tools.guess_primitive_vectors(points)
def make_rhombohedral_lattice(name, h, angle, size, origin=(0, 0, 0)):
"""Create and return a 3D rhombohedral lattice.
Parameters
----------
name : str
h : float
lattice spacing
angle : float
angle between the (conventional) unit cell edges (in radians)
size : int[3]
Number of lattice nodes in each axis direction.
origin : float[3], default value = (0, 0, 0)
lattice origin
Returns
-------
lattice : Lattice
A reference to a Lattice object.
"""
pc = PrimitiveCell.for_rhombohedral_lattice(h, angle)
return Lattice(name, pc, size, origin)
# a cubic lattice on a rotated coordinates represented using PolyData pcs = rotate_primitive_cell(PrimitiveCell.for_cubic_lattice(1.)) datasets.append(create_polydata_from_pc(*pcs)) # BCC lattice in a rotated coor. sys. pcs = rotate_primitive_cell(PrimitiveCell.for_body_centered_cubic_lattice(1.)) datasets.append(create_polydata_from_pc(*pcs)) # FCC lattice in a rotated coor. sys. pcs = rotate_primitive_cell(PrimitiveCell.for_face_centered_cubic_lattice(1.)) datasets.append(create_polydata_from_pc(*pcs)) # rhombohedral lattice in a rotated coor. sys. pcs = rotate_primitive_cell(PrimitiveCell.for_rhombohedral_lattice(1., 1.)) datasets.append(create_polydata_from_pc(*pcs)) # tetragonal lattice in a rotated coor. sys. pcs = rotate_primitive_cell(PrimitiveCell.for_tetragonal_lattice(0.5, 1.)) datasets.append(create_polydata_from_pc(*pcs)) # body_centered_tetragonal lattice in a rotated coor. sys. factory = PrimitiveCell.for_body_centered_tetragonal_lattice pcs = rotate_primitive_cell(factory(1., 0.5)) datasets.append(create_polydata_from_pc(*pcs)) # hexagonal lattice in a rotated coor. sys. pcs = rotate_primitive_cell(PrimitiveCell.for_hexagonal_lattice(1., 0.5)) datasets.append(create_polydata_from_pc(*pcs))
