def test_axis_angle_from_rotation_matrix():
for angle in np.linspace(0.0, 2 * np.pi, np.pi / 4):
for rmatrix in (Rx, Ry, Rz):
rot_axis, rot_angle = \
axis_angle_from_rotation_matrix(rmatrix(angle))
assert_true(
np.allclose(rotation_matrix(angle=rot_angle, axis=rot_axis),
rmatrix(angle)))
def test_axis_angle_from_rotation_matrix():
for angle in np.linspace(0.0, 2 * np.pi, np.pi / 4):
for rmatrix in (Rx, Ry, Rz):
rot_axis, rot_angle = \
axis_angle_from_rotation_matrix(rmatrix(angle))
assert_true(np.allclose(rotation_matrix(angle=rot_angle,
axis=rot_axis),
rmatrix(angle)))
def rotate(self,
angle=None,
axis=None,
anchor_point=None,
rot_point=None,
from_vector=None,
to_vector=None,
degrees=False,
transform_matrix=None,
verbose=False,
**kwargs):
"""Rotate unit cell.
Parameters
----------
angle : float
axis : :class:`~sknano.core.math.Vector`, optional
anchor_point : :class:`~sknano.core.math.Point`, optional
rot_point : :class:`~sknano.core.math.Point`, optional
from_vector, to_vector : :class:`~sknano.core.math.Vector`, optional
degrees : bool, optional
transform_matrix : :class:`~numpy:numpy.ndarray`
See Also
--------
core.math.rotate
"""
if self.nd == 2:
axis = 'z'
if transform_matrix is None:
transform_matrix = \
np.asmatrix(
rotation_matrix(angle=angle, axis=axis,
anchor_point=anchor_point,
rot_point=rot_point,
from_vector=from_vector,
to_vector=to_vector, degrees=degrees,
verbose=verbose, **kwargs))
# print('transform_matrix: {}'.format(transform_matrix))
# transform_matrix = \
# transformation_matrix(angle=angle, axis=axis,
# anchor_point=anchor_point,
# rot_point=rot_point,
# from_vector=from_vector,
# to_vector=to_vector, degrees=degrees,
# verbose=verbose, **kwargs)
self.orientation_matrix = \
transform_matrix * self.orientation_matrix
def test20():
a = np.sqrt(3) * aCC
orientation_matrix = rotation_matrix(angle=-np.pi / 6, axis=zhat)
dlattice = Crystal3DLattice(a=a,
b=a,
c=2 * r_CC_vdw,
alpha=90,
beta=90,
gamma=120,
orientation_matrix=orientation_matrix)
rlattice = \
Reciprocal3DLattice(a_star=dlattice.reciprocal_lattice.a_star,
b_star=dlattice.reciprocal_lattice.b_star,
c_star=dlattice.reciprocal_lattice.c_star,
alpha_star=dlattice.reciprocal_lattice.alpha_star,
beta_star=dlattice.reciprocal_lattice.beta_star,
gamma_star=dlattice.reciprocal_lattice.gamma_star)
print('\ndlattice.reciprocal_lattice.matrix:\n{}'.format(
dlattice.reciprocal_lattice.matrix))
print('\nrlattice.matrix:\n{}'.format(rlattice.matrix))
print('\ndlattice.matrix:\n{}'.format(dlattice.matrix))
print('\nrlattice.reciprocal_lattice.matrix:\n{}'.format(
rlattice.reciprocal_lattice.matrix))
print('\ndlattice.reciprocal_lattice.matrix:\n{}'.format(
dlattice.reciprocal_lattice.matrix))
pmg_rlattice = \
pmg.Lattice.from_parameters(dlattice.reciprocal_lattice.a_star,
dlattice.reciprocal_lattice.b_star,
dlattice.reciprocal_lattice.c_star,
dlattice.reciprocal_lattice.alpha_star,
dlattice.reciprocal_lattice.beta_star,
dlattice.reciprocal_lattice.gamma_star)
print('\npmg_rlattice.matrix:\n{}'.format(pmg_rlattice.matrix))
print('\nrlattice.matrix:\n{}'.format(rlattice.matrix))
print('\npmg_rlattice.reciprocal_lattice.matrix:\n{}'.format(
pmg_rlattice.reciprocal_lattice.matrix))
print('\nrlattice.reciprocal_lattice.matrix:\n{}'.format(
rlattice.reciprocal_lattice.matrix))
assert_true(np.allclose(rlattice.matrix, pmg_rlattice.matrix))
assert_true(
np.allclose(dlattice.reciprocal_lattice.matrix, pmg_rlattice.matrix))
assert_true(np.allclose(rlattice.matrix, pmg_rlattice.matrix))
def rotate(self, **kwargs):
"""Rotate `Atom` vectors.
Parameters
----------
angle : float
axis : :class:`~sknano.core.math.Vector`, optional
anchor_point : :class:`~sknano.core.math.Point`, optional
rot_point : :class:`~sknano.core.math.Point`, optional
from_vector, to_vector : :class:`~sknano.core.math.Vector`, optional
degrees : bool, optional
transform_matrix : :class:`~numpy:numpy.ndarray`
"""
if kwargs.get('transform_matrix', None) is None:
kwargs['transform_matrix'] = rotation_matrix(**kwargs)
[atom.rotate(**kwargs) for atom in self]
def test20():
a = np.sqrt(3) * aCC
orientation_matrix = rotation_matrix(angle=-np.pi / 6, axis=zhat)
dlattice = Crystal3DLattice(a=a, b=a, c=2 * r_CC_vdw,
alpha=90, beta=90, gamma=120,
orientation_matrix=orientation_matrix)
rlattice = \
Reciprocal3DLattice(a_star=dlattice.reciprocal_lattice.a_star,
b_star=dlattice.reciprocal_lattice.b_star,
c_star=dlattice.reciprocal_lattice.c_star,
alpha_star=dlattice.reciprocal_lattice.alpha_star,
beta_star=dlattice.reciprocal_lattice.beta_star,
gamma_star=dlattice.reciprocal_lattice.gamma_star)
print('\ndlattice.reciprocal_lattice.matrix:\n{}'.format(
dlattice.reciprocal_lattice.matrix))
print('\nrlattice.matrix:\n{}'.format(rlattice.matrix))
print('\ndlattice.matrix:\n{}'.format(dlattice.matrix))
print('\nrlattice.reciprocal_lattice.matrix:\n{}'.format(
rlattice.reciprocal_lattice.matrix))
print('\ndlattice.reciprocal_lattice.matrix:\n{}'.format(
dlattice.reciprocal_lattice.matrix))
pmg_rlattice = \
pmg.Lattice.from_parameters(dlattice.reciprocal_lattice.a_star,
dlattice.reciprocal_lattice.b_star,
dlattice.reciprocal_lattice.c_star,
dlattice.reciprocal_lattice.alpha_star,
dlattice.reciprocal_lattice.beta_star,
dlattice.reciprocal_lattice.gamma_star)
print('\npmg_rlattice.matrix:\n{}'.format(pmg_rlattice.matrix))
print('\nrlattice.matrix:\n{}'.format(rlattice.matrix))
print('\npmg_rlattice.reciprocal_lattice.matrix:\n{}'.format(
pmg_rlattice.reciprocal_lattice.matrix))
print('\nrlattice.reciprocal_lattice.matrix:\n{}'.format(
rlattice.reciprocal_lattice.matrix))
assert_true(np.allclose(rlattice.matrix,
pmg_rlattice.matrix))
assert_true(np.allclose(dlattice.reciprocal_lattice.matrix,
pmg_rlattice.matrix))
assert_true(np.allclose(rlattice.matrix,
pmg_rlattice.matrix))
def rotate(self, angle=None, axis=None, anchor_point=None,
rot_point=None, from_vector=None, to_vector=None, degrees=False,
transform_matrix=None, verbose=False, **kwargs):
"""Rotate unit cell.
Parameters
----------
angle : float
axis : :class:`~sknano.core.math.Vector`, optional
anchor_point : :class:`~sknano.core.math.Point`, optional
rot_point : :class:`~sknano.core.math.Point`, optional
from_vector, to_vector : :class:`~sknano.core.math.Vector`, optional
degrees : bool, optional
transform_matrix : :class:`~numpy:numpy.ndarray`
See Also
--------
core.math.rotate
"""
if self.nd == 2:
axis = 'z'
if transform_matrix is None:
transform_matrix = \
np.asmatrix(
rotation_matrix(angle=angle, axis=axis,
anchor_point=anchor_point,
rot_point=rot_point,
from_vector=from_vector,
to_vector=to_vector, degrees=degrees,
verbose=verbose, **kwargs))
# print('transform_matrix: {}'.format(transform_matrix))
# transform_matrix = \
# transformation_matrix(angle=angle, axis=axis,
# anchor_point=anchor_point,
# rot_point=rot_point,
# from_vector=from_vector,
# to_vector=to_vector, degrees=degrees,
# verbose=verbose, **kwargs)
self.orientation_matrix = \
transform_matrix * self.orientation_matrix
def test1():
dlattice = Crystal2DLattice(a=4.0, b=8.0, gamma=120)
orientation_matrix = rotation_matrix(angle=np.pi/6, axis=zhat)
rlattice = \
Reciprocal2DLattice(a_star=dlattice.reciprocal_lattice.a_star,
b_star=dlattice.reciprocal_lattice.b_star,
gamma_star=dlattice.reciprocal_lattice.gamma_star,
orientation_matrix=orientation_matrix)
print('\ndlattice.matrix:\n{}'.format(dlattice.matrix))
print('\nrlattice.matrix:\n{}'.format(rlattice.matrix))
print('\ndlattice.reciprocal_lattice.matrix:\n{}'.format(
dlattice.reciprocal_lattice.matrix))
print('\nrlattice.reciprocal_lattice.matrix:\n{}'.format(
rlattice.reciprocal_lattice.matrix))
assert_true(np.allclose(dlattice.matrix,
rlattice.reciprocal_lattice.matrix))
assert_true(np.allclose(dlattice.reciprocal_lattice.matrix,
rlattice.matrix))
def test1():
dlattice = Crystal2DLattice(a=4.0, b=8.0, gamma=120)
orientation_matrix = rotation_matrix(angle=np.pi / 6, axis=zhat)
rlattice = \
Reciprocal2DLattice(a_star=dlattice.reciprocal_lattice.a_star,
b_star=dlattice.reciprocal_lattice.b_star,
gamma_star=dlattice.reciprocal_lattice.gamma_star,
orientation_matrix=orientation_matrix)
print('\ndlattice.matrix:\n{}'.format(dlattice.matrix))
print('\nrlattice.matrix:\n{}'.format(rlattice.matrix))
print('\ndlattice.reciprocal_lattice.matrix:\n{}'.format(
dlattice.reciprocal_lattice.matrix))
print('\nrlattice.reciprocal_lattice.matrix:\n{}'.format(
rlattice.reciprocal_lattice.matrix))
assert_true(
np.allclose(dlattice.matrix, rlattice.reciprocal_lattice.matrix))
assert_true(
np.allclose(dlattice.reciprocal_lattice.matrix, rlattice.matrix))
def test_rotation_matrix():
assert_true(np.allclose(rotation_matrix(angle=np.pi/2),
np.array([[0.0, -1.0], [1.0, 0.0]])))
sqrt2 = np.sqrt(2)
assert_true(np.allclose(rotation_matrix(angle=np.pi/4),
np.array([[1 / sqrt2, -1 / sqrt2],
[1 / sqrt2, 1 / sqrt2]])))
sqrt3 = np.sqrt(3)
assert_true(np.allclose(
rotation_matrix(angle=np.pi/2, axis=Vector(np.ones(3))),
np.array([[1 / 3, 1 / 3 - 1 / sqrt3, 1 / 3 + 1 / sqrt3],
[1 / 3 + 1 / sqrt3, 1 / 3, 1 / 3 - 1 / sqrt3],
[1 / 3 - 1 / sqrt3, 1 / 3 + 1 / sqrt3, 1 / 3]])))
[[assert_true(np.allclose(
Rmat(angle=angle), rotation_matrix(angle=angle, axis=axis)))
for angle in np.linspace(0.0, 2 * np.pi, np.pi / 4)]
for Rmat, axis in zip((Rx, Ry, Rz), ('x', 'y', 'z'))]
assert_true(np.allclose(rotation_matrix(angle=np.pi / 2),
rotation_matrix(from_vector=[1, 0],
to_vector=[0, 1])))
assert_true(np.allclose(rotation_matrix(angle=-np.pi / 2),
rotation_matrix(from_vector=[0, 1],
to_vector=[1, 0])))
assert_true(np.allclose(
rotation_matrix(angle=np.pi / 2, axis=[0, 0, 1]),
rotation_matrix(from_vector=[1, 0, 0], to_vector=[0, 1, 0])))
assert_true(np.allclose(
rotation_matrix(angle=-np.pi / 2, axis=[0, 0, 1]),
rotation_matrix(from_vector=[0, 1, 0], to_vector=[1, 0, 0])))
def test11():
a = np.sqrt(3) * aCC
dlattice = Crystal3DLattice(a=a, b=a, c=2 * r_CC_vdw,
alpha=90, beta=90, gamma=120)
orientation_matrix = rotation_matrix(angle=np.pi / 6, axis=zhat)
rlattice = \
Reciprocal3DLattice(a_star=dlattice.reciprocal_lattice.a_star,
b_star=dlattice.reciprocal_lattice.b_star,
c_star=dlattice.reciprocal_lattice.c_star,
alpha_star=dlattice.reciprocal_lattice.alpha_star,
beta_star=dlattice.reciprocal_lattice.beta_star,
gamma_star=dlattice.reciprocal_lattice.gamma_star,
orientation_matrix=orientation_matrix)
print('\ndlattice.reciprocal_lattice.matrix:\n{}'.format(
dlattice.reciprocal_lattice.matrix))
print('\nrlattice.matrix:\n{}'.format(rlattice.matrix))
print('\ndlattice.matrix:\n{}'.format(dlattice.matrix))
print('\nrlattice.reciprocal_lattice.matrix:\n{}'.format(
rlattice.reciprocal_lattice.matrix))
# assert_equal(dlattice.reciprocal_lattice, rlattice)
assert_true(np.allclose(dlattice.reciprocal_lattice.matrix,
rlattice.matrix))
assert_true(np.allclose(dlattice.matrix,
rlattice.reciprocal_lattice.matrix))
# print('\n{}'.format(np.linalg.inv(dlattice.matrix)))
# print(np.linalg.inv(dlattice.matrix) * dlattice.matrix)
# print(np.linalg.inv(dlattice.matrix).T)
# print(dlattice.reciprocal_lattice.matrix)
# print(dlattice.reciprocal_lattice.b1)
# print(dlattice.reciprocal_lattice.b2)
# print(dlattice.reciprocal_lattice.b3)
# print(rlattice.matrix)
# print(rlattice.b1)
# print(rlattice.b2)
# print(rlattice.b3)
assert_equal(dlattice.reciprocal_lattice, rlattice)
assert_equal(dlattice.reciprocal_lattice.b1, rlattice.b1)
assert_equal(dlattice.reciprocal_lattice.b2, rlattice.b2)
assert_equal(dlattice.reciprocal_lattice.b3, rlattice.b3)
assert_true(np.allclose(dlattice.reciprocal_lattice.matrix,
rlattice.matrix))
assert_true(np.allclose(dlattice.reciprocal_lattice.metric_tensor,
rlattice.metric_tensor))
pmg_dlattice = pmg.Lattice(dlattice.matrix)
print('\npmg_dlattice.matrix:\n{}'.format(pmg_dlattice.matrix))
print('\ndlattice.matrix:\n{}'.format(dlattice.matrix))
print('\npmg_dlattice.reciprocal_lattice.matrix:\n{}'.format(
pmg_dlattice.reciprocal_lattice.matrix))
print('\ndlattice.reciprocal_lattice.matrix:\n{}'.format(
dlattice.reciprocal_lattice.matrix))
assert_true(np.allclose(dlattice.a, pmg_dlattice.a))
assert_true(np.allclose(dlattice.b, pmg_dlattice.b))
assert_true(np.allclose(dlattice.c, pmg_dlattice.c))
assert_true(np.allclose(np.asarray(dlattice.a1), pmg_dlattice.matrix[0]))
assert_true(np.allclose(np.asarray(dlattice.a2), pmg_dlattice.matrix[1]))
assert_true(np.allclose(np.asarray(dlattice.a3), pmg_dlattice.matrix[2]))
assert_true(np.allclose(dlattice.matrix, pmg_dlattice.matrix))
assert_true(np.allclose(dlattice.ortho_matrix.T,
pmg.Lattice(dlattice.ortho_matrix.T).matrix))
assert_true(np.allclose(pmg.Lattice(dlattice.matrix).metric_tensor,
dlattice.metric_tensor))
assert_true(np.allclose(pmg.Lattice(dlattice.ortho_matrix.T).metric_tensor,
dlattice.metric_tensor))
assert_true(np.allclose(pmg.Lattice(dlattice.matrix).matrix,
dlattice.matrix))
assert_true(np.allclose(pmg.Lattice(dlattice.ortho_matrix.T).matrix,
dlattice.matrix))
# print('latt_from_inv_latt_matrix_transpose:\n{}\n'.format(
# latt_from_inv_latt_matrix_transpose.matrix))
# print('rlattice.reciprocal_lattice.matrix:\n{}'.format(
# rlattice.reciprocal_lattice.matrix))
assert_true(np.allclose(pmg.Lattice(dlattice.matrix).matrix,
rlattice.reciprocal_lattice.matrix))
# print('rlattice.reciprocal_lattice.matrix:\n{}'.format(
# rlattice.reciprocal_lattice.matrix))
# print('pmg.Lattice(np.linalg.inv(dlattice.matrix).T).'
# 'reciprocal_lattice_crystallographic.matrix:\n{}'
# .format(pmg.Lattice(np.linalg.inv(dlattice.matrix).T)
# .reciprocal_lattice_crystallographic.matrix))
# print('pmg.Lattice.from_parameters(...):\n{}\n'.format(
# rezero_array(pmg.Lattice.from_parameters(
# dlattice.reciprocal_lattice.a_star,
# dlattice.reciprocal_lattice.b_star,
# dlattice.reciprocal_lattice.c_star,
# dlattice.reciprocal_lattice.alpha_star,
# dlattice.reciprocal_lattice.beta_star,
# dlattice.reciprocal_lattice.gamma_star)
# .reciprocal_lattice_crystallographic.matrix)))
# print('dlattice.ortho_matrix:\n{}'.format(dlattice.ortho_matrix))
# print('np.linalg.inv(dlattice.matrix).T:\n{}'.format(np.linalg.inv(
# dlattice.matrix).T))
# print('rlattice.reciprocal_lattice.ortho_matrix:\n{}'
# .format(rlattice.reciprocal_lattice.ortho_matrix))
# print('rlattice.reciprocal_lattice.ortho_matrix:\n{}\n'.
# format(rlattice.reciprocal_lattice.ortho_matrix))
# print('dlattice.reciprocal_lattice.ortho_matrix:\n{}'.format(
# dlattice.reciprocal_lattice.ortho_matrix))
# print('rlattice.ortho_matrix:\n{}'.format(
# rlattice.ortho_matrix))
# print('rlattice.ortho_matrix:\n{}\n'.format(
# rlattice.ortho_matrix))
assert_true(np.allclose(dlattice.ortho_matrix,
rlattice.reciprocal_lattice.
ortho_matrix))
assert_true(np.allclose(dlattice.reciprocal_lattice.ortho_matrix,
rlattice.ortho_matrix))
assert_equal(dlattice, rlattice.reciprocal_lattice)
assert_equal(dlattice.reciprocal_lattice, rlattice)
print(dlattice.matrix * rlattice.matrix.T)
assert_true(np.allclose(dlattice.matrix * rlattice.matrix.T,
np.eye(3)))
def test_rotation_matrix():
assert_true(
np.allclose(rotation_matrix(angle=np.pi / 2),
np.array([[0.0, -1.0], [1.0, 0.0]])))
sqrt2 = np.sqrt(2)
assert_true(
np.allclose(
rotation_matrix(angle=np.pi / 4),
np.array([[1 / sqrt2, -1 / sqrt2], [1 / sqrt2, 1 / sqrt2]])))
sqrt3 = np.sqrt(3)
assert_true(
np.allclose(
rotation_matrix(angle=np.pi / 2, axis=Vector(np.ones(3))),
np.array([[1 / 3, 1 / 3 - 1 / sqrt3, 1 / 3 + 1 / sqrt3],
[1 / 3 + 1 / sqrt3, 1 / 3, 1 / 3 - 1 / sqrt3],
[1 / 3 - 1 / sqrt3, 1 / 3 + 1 / sqrt3, 1 / 3]])))
[[
assert_true(
np.allclose(Rmat(angle=angle),
rotation_matrix(angle=angle, axis=axis)))
for angle in np.linspace(0.0, 2 * np.pi, np.pi / 4)
] for Rmat, axis in zip((Rx, Ry, Rz), ('x', 'y', 'z'))]
assert_true(
np.allclose(rotation_matrix(angle=np.pi / 2),
rotation_matrix(from_vector=[1, 0], to_vector=[0, 1])))
assert_true(
np.allclose(rotation_matrix(angle=-np.pi / 2),
rotation_matrix(from_vector=[0, 1], to_vector=[1, 0])))
assert_true(
np.allclose(
rotation_matrix(angle=np.pi / 2, axis=[0, 0, 1]),
rotation_matrix(from_vector=[1, 0, 0], to_vector=[0, 1, 0])))
assert_true(
np.allclose(
rotation_matrix(angle=-np.pi / 2, axis=[0, 0, 1]),
rotation_matrix(from_vector=[0, 1, 0], to_vector=[1, 0, 0])))
def test11():
a = np.sqrt(3) * aCC
dlattice = Crystal3DLattice(a=a,
b=a,
c=2 * r_CC_vdw,
alpha=90,
beta=90,
gamma=120)
orientation_matrix = rotation_matrix(angle=np.pi / 6, axis=zhat)
rlattice = \
Reciprocal3DLattice(a_star=dlattice.reciprocal_lattice.a_star,
b_star=dlattice.reciprocal_lattice.b_star,
c_star=dlattice.reciprocal_lattice.c_star,
alpha_star=dlattice.reciprocal_lattice.alpha_star,
beta_star=dlattice.reciprocal_lattice.beta_star,
gamma_star=dlattice.reciprocal_lattice.gamma_star,
orientation_matrix=orientation_matrix)
print('\ndlattice.reciprocal_lattice.matrix:\n{}'.format(
dlattice.reciprocal_lattice.matrix))
print('\nrlattice.matrix:\n{}'.format(rlattice.matrix))
print('\ndlattice.matrix:\n{}'.format(dlattice.matrix))
print('\nrlattice.reciprocal_lattice.matrix:\n{}'.format(
rlattice.reciprocal_lattice.matrix))
# assert_equal(dlattice.reciprocal_lattice, rlattice)
assert_true(
np.allclose(dlattice.reciprocal_lattice.matrix, rlattice.matrix))
assert_true(
np.allclose(dlattice.matrix, rlattice.reciprocal_lattice.matrix))
# print('\n{}'.format(np.linalg.inv(dlattice.matrix)))
# print(np.linalg.inv(dlattice.matrix) * dlattice.matrix)
# print(np.linalg.inv(dlattice.matrix).T)
# print(dlattice.reciprocal_lattice.matrix)
# print(dlattice.reciprocal_lattice.b1)
# print(dlattice.reciprocal_lattice.b2)
# print(dlattice.reciprocal_lattice.b3)
# print(rlattice.matrix)
# print(rlattice.b1)
# print(rlattice.b2)
# print(rlattice.b3)
assert_equal(dlattice.reciprocal_lattice, rlattice)
assert_equal(dlattice.reciprocal_lattice.b1, rlattice.b1)
assert_equal(dlattice.reciprocal_lattice.b2, rlattice.b2)
assert_equal(dlattice.reciprocal_lattice.b3, rlattice.b3)
assert_true(
np.allclose(dlattice.reciprocal_lattice.matrix, rlattice.matrix))
assert_true(
np.allclose(dlattice.reciprocal_lattice.metric_tensor,
rlattice.metric_tensor))
pmg_dlattice = pmg.Lattice(dlattice.matrix)
print('\npmg_dlattice.matrix:\n{}'.format(pmg_dlattice.matrix))
print('\ndlattice.matrix:\n{}'.format(dlattice.matrix))
print('\npmg_dlattice.reciprocal_lattice.matrix:\n{}'.format(
pmg_dlattice.reciprocal_lattice.matrix))
print('\ndlattice.reciprocal_lattice.matrix:\n{}'.format(
dlattice.reciprocal_lattice.matrix))
assert_true(np.allclose(dlattice.a, pmg_dlattice.a))
assert_true(np.allclose(dlattice.b, pmg_dlattice.b))
assert_true(np.allclose(dlattice.c, pmg_dlattice.c))
assert_true(np.allclose(np.asarray(dlattice.a1), pmg_dlattice.matrix[0]))
assert_true(np.allclose(np.asarray(dlattice.a2), pmg_dlattice.matrix[1]))
assert_true(np.allclose(np.asarray(dlattice.a3), pmg_dlattice.matrix[2]))
assert_true(np.allclose(dlattice.matrix, pmg_dlattice.matrix))
assert_true(
np.allclose(dlattice.ortho_matrix.T,
pmg.Lattice(dlattice.ortho_matrix.T).matrix))
assert_true(
np.allclose(
pmg.Lattice(dlattice.matrix).metric_tensor,
dlattice.metric_tensor))
assert_true(
np.allclose(
pmg.Lattice(dlattice.ortho_matrix.T).metric_tensor,
dlattice.metric_tensor))
assert_true(
np.allclose(pmg.Lattice(dlattice.matrix).matrix, dlattice.matrix))
assert_true(
np.allclose(
pmg.Lattice(dlattice.ortho_matrix.T).matrix, dlattice.matrix))
# print('latt_from_inv_latt_matrix_transpose:\n{}\n'.format(
# latt_from_inv_latt_matrix_transpose.matrix))
# print('rlattice.reciprocal_lattice.matrix:\n{}'.format(
# rlattice.reciprocal_lattice.matrix))
assert_true(
np.allclose(
pmg.Lattice(dlattice.matrix).matrix,
rlattice.reciprocal_lattice.matrix))
# print('rlattice.reciprocal_lattice.matrix:\n{}'.format(
# rlattice.reciprocal_lattice.matrix))
# print('pmg.Lattice(np.linalg.inv(dlattice.matrix).T).'
# 'reciprocal_lattice_crystallographic.matrix:\n{}'
# .format(pmg.Lattice(np.linalg.inv(dlattice.matrix).T)
# .reciprocal_lattice_crystallographic.matrix))
# print('pmg.Lattice.from_parameters(...):\n{}\n'.format(
# rezero_array(pmg.Lattice.from_parameters(
# dlattice.reciprocal_lattice.a_star,
# dlattice.reciprocal_lattice.b_star,
# dlattice.reciprocal_lattice.c_star,
# dlattice.reciprocal_lattice.alpha_star,
# dlattice.reciprocal_lattice.beta_star,
# dlattice.reciprocal_lattice.gamma_star)
# .reciprocal_lattice_crystallographic.matrix)))
# print('dlattice.ortho_matrix:\n{}'.format(dlattice.ortho_matrix))
# print('np.linalg.inv(dlattice.matrix).T:\n{}'.format(np.linalg.inv(
# dlattice.matrix).T))
# print('rlattice.reciprocal_lattice.ortho_matrix:\n{}'
# .format(rlattice.reciprocal_lattice.ortho_matrix))
# print('rlattice.reciprocal_lattice.ortho_matrix:\n{}\n'.
# format(rlattice.reciprocal_lattice.ortho_matrix))
# print('dlattice.reciprocal_lattice.ortho_matrix:\n{}'.format(
# dlattice.reciprocal_lattice.ortho_matrix))
# print('rlattice.ortho_matrix:\n{}'.format(
# rlattice.ortho_matrix))
# print('rlattice.ortho_matrix:\n{}\n'.format(
# rlattice.ortho_matrix))
assert_true(
np.allclose(dlattice.ortho_matrix,
rlattice.reciprocal_lattice.ortho_matrix))
assert_true(
np.allclose(dlattice.reciprocal_lattice.ortho_matrix,
rlattice.ortho_matrix))
assert_equal(dlattice, rlattice.reciprocal_lattice)
assert_equal(dlattice.reciprocal_lattice, rlattice)
print(dlattice.matrix * rlattice.matrix.T)
assert_true(np.allclose(dlattice.matrix * rlattice.matrix.T, np.eye(3)))