def test_transformation_matrix():
[[assert_true(np.allclose(
Rz(angle=angle), transformation_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(
transformation_matrix(angle=np.pi/2, rot_point=Point([1.0, 1.0])),
np.array([[0.0, -1.0, 2.0], [1.0, 0.0, 0.0], [0.0, 0.0, 1.0]])))
def test_transformation_matrix():
[[
assert_true(
np.allclose(Rz(angle=angle),
transformation_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(
transformation_matrix(angle=np.pi / 2, rot_point=Point([1.0,
1.0])),
np.array([[0.0, -1.0, 2.0], [1.0, 0.0, 0.0], [0.0, 0.0, 1.0]])))
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 `Molecule` position 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 transform_matrix is None:
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)
[molecule.rotate(transform_matrix=transform_matrix)
for molecule in self]
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 `GeometricRegion` :attr:`~GeometricRegion.points` and \
:attr:`~GeometricRegion.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`
See Also
--------
sknano.core.math.rotate
"""
if transform_matrix is None:
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.points.rotate(transform_matrix=transform_matrix)
self.vectors.rotate(transform_matrix=transform_matrix)
def test8():
a = np.sqrt(3) * aCC
latt = Crystal3DLattice(a=a,
b=a,
c=2 * r_CC_vdw,
alpha=90,
beta=90,
gamma=120)
print(latt)
a1 = latt.a1
a2 = latt.a2
a3 = latt.a3
xfrm = transformation_matrix(angle=-np.pi / 6)
rotangle = -np.pi / 6
for v in (a1, a2, a3):
v.rotate(angle=rotangle)
latt.rotate(angle=rotangle, axis='z')
print(latt)
assert_equal(latt.a1, a1)
assert_equal(latt.a2, a2)
assert_equal(latt.a3, a3)
assert_true(np.allclose(latt.orientation_matrix, xfrm))
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 `GeometricRegion` :attr:`~GeometricRegion.points` and \
:attr:`~GeometricRegion.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`
See Also
--------
sknano.core.math.rotate
"""
if transform_matrix is None:
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.points.rotate(transform_matrix=transform_matrix)
self.vectors.rotate(transform_matrix=transform_matrix)
def test4():
a = np.sqrt(3) * aCC
latt = Crystal2DLattice(a=a, b=a, gamma=60)
a1 = latt.a1
a2 = latt.a2
rotated_a1 = a1.copy()
rotated_a2 = a2.copy()
xfrm = transformation_matrix(angle=-np.pi / 6)
rotated_a1.rotate(transform_matrix=xfrm)
rotated_a2.rotate(transform_matrix=xfrm)
latt.rotate(angle=-np.pi / 6)
assert_equal(latt.a1, rotated_a1)
assert_equal(latt.a2, rotated_a2)
assert_true(np.allclose(latt.orientation_matrix, xfrm))
rotated_latt = Crystal2DLattice(a1=rotated_a1, a2=rotated_a2)
assert_equal(rotated_a1, rotated_latt.a1)
assert_equal(rotated_a2, rotated_latt.a2)
assert_true(np.allclose(latt.orientation_matrix,
rotated_latt.orientation_matrix))
def test8():
a = np.sqrt(3) * aCC
latt = Crystal3DLattice(a=a, b=a, c=2 * r_CC_vdw,
alpha=90, beta=90, gamma=120)
print(latt)
a1 = latt.a1
a2 = latt.a2
a3 = latt.a3
xfrm = transformation_matrix(angle=-np.pi / 6)
rotangle = -np.pi / 6
for v in (a1, a2, a3):
v.rotate(angle=rotangle)
latt.rotate(angle=rotangle, axis='z')
print(latt)
assert_equal(latt.a1, a1)
assert_equal(latt.a2, a2)
assert_equal(latt.a3, a3)
assert_true(np.allclose(latt.orientation_matrix, xfrm))
def test4():
a = np.sqrt(3) * aCC
latt = Crystal2DLattice(a=a, b=a, gamma=60)
a1 = latt.a1
a2 = latt.a2
rotated_a1 = a1.copy()
rotated_a2 = a2.copy()
xfrm = transformation_matrix(angle=-np.pi / 6)
rotated_a1.rotate(transform_matrix=xfrm)
rotated_a2.rotate(transform_matrix=xfrm)
latt.rotate(angle=-np.pi / 6)
assert_equal(latt.a1, rotated_a1)
assert_equal(latt.a2, rotated_a2)
assert_true(np.allclose(latt.orientation_matrix, xfrm))
rotated_latt = Crystal2DLattice(a1=rotated_a1, a2=rotated_a2)
assert_equal(rotated_a1, rotated_latt.a1)
assert_equal(rotated_a2, rotated_latt.a2)
assert_true(
np.allclose(latt.orientation_matrix, rotated_latt.orientation_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 `Molecule` position 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 transform_matrix is None:
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)
[
molecule.rotate(transform_matrix=transform_matrix)
for molecule in self
]