def test_spin_relative_compound_coordinates(self, sixpoints):
"""Check compounds's relative coordinates don't change upon spinning"""
np.random.seed(0)
angles_before = np.asarray([
angle(a, b, c) for (a, b, c) in itt.combinations(sixpoints.xyz, 3)
])
sixpoints.spin(np.pi * 0.1234569789, np.random.rand(3))
angles_after = np.asarray([
angle(a, b, c) for (a, b, c) in itt.combinations(sixpoints.xyz, 3)
])
assert np.allclose(angles_before, angles_after, atol=1e-15)
def test_spin_relative_compound_coordinates(self, sixpoints):
"""Check compounds's relative coordinates don't change upon spinning"""
np.random.seed(0)
angles_before = np.asarray(
[angle(a, b, c)
for (a, b, c) in itt.combinations(sixpoints.xyz, 3)])
sixpoints.spin(np.pi*0.1234569789, np.random.rand(3))
angles_after = np.asarray(
[angle(a, b, c)
for (a, b, c) in itt.combinations(sixpoints.xyz, 3)])
assert np.allclose(angles_before, angles_after, atol=1e-15)
def __init__(self, anchor=None, orientation=None, separation=0):
super(Port, self).__init__(name='Port', port_particle=True)
self.anchor = anchor
up = Compound(name='subport', port_particle=True)
up.add(
Particle(name='G',
pos=[0.005, 0.0025, -0.0025],
port_particle=True), 'middle')
up.add(
Particle(name='G',
pos=[0.005, 0.0225, -0.0025],
port_particle=True), 'top')
up.add(
Particle(name='G',
pos=[-0.015, -0.0075, -0.0025],
port_particle=True), 'left')
up.add(
Particle(name='G',
pos=[0.005, -0.0175, 0.0075],
port_particle=True), 'right')
down = clone(up)
down.rotate(np.pi, [0, 0, 1])
self.add(up, 'up')
self.add(down, 'down')
self.used = False
if orientation is None:
orientation = [0, 1, 0]
default_direction = [0, 1, 0]
if np.array_equal(np.asarray(default_direction),
unit_vector(-np.asarray(orientation))):
self.rotate(np.pi, [1, 0, 0])
elif np.array_equal(np.asarray(default_direction),
unit_vector(np.asarray(orientation))):
pass
else:
normal = np.cross(default_direction, orientation)
self.rotate(angle(default_direction, orientation), normal)
if anchor:
self.translate_to(anchor.pos)
self.translate(separation * unit_vector(orientation))
def calc_dihedral(point1, point2, point3, point4):
"""Calculate a dihedral angle.
Here, two planes are defined by (point1, point2, point3) and (point2,
point3, point4). The angle between them is returned.
Parameters
----------
point1, point2, point3, point4 : array-like, shape=(3,), dtype=float
Four points that define two planes
Returns
-------
float
The dihedral angle between the two planes defined by the four points.
"""
points = np.array([point1, point2, point3, point4])
x = np.cross(points[1] - points[0], points[2] - points[1])
y = np.cross(points[2] - points[1], points[3] - points[2])
return angle(x, y)
def update_orientation(self, orientation):
"""
Change the direction between a port and its anchor particle
orientation : array-like, shape=(3,), required
Vector along which to orient the port
"""
if self.used:
warn("This port is already being used and changing its orientation"
" will have no effect on the direction between particles.")
orientation = np.asarray(orientation).reshape(3, )
init_separation = self.separation
normal = np.cross(self.direction, orientation)
#Move to origin to perform rotation
self.translate_to((0, 0, 0))
self.rotate(angle(self.direction, orientation), normal)
self.labels['down'].rotate(np.pi, normal)
self.labels['up'].rotate(np.pi, normal)
#Move back to it's anchor particle
self.update_separation(init_separation)
def calc_dihedral(point1, point2, point3, point4):
"""Calculates a dihedral angle
Here, two planes are defined by (point1, point2, point3) and
(point2, point3, point4). The angle between them is returned.
Parameters
----------
point1, point2, point3, point4 : array-like, shape=(3,), dtype=float
Four points that define two planes
Returns
-------
float
The dihedral angle between the two planes defined by the four
points.
"""
points = np.array([point1, point2, point3, point4])
x = np.cross(points[1] - points[0], points[2] - points[1])
y = np.cross(points[2] - points[1], points[3] - points[2])
return angle(x, y)
def __init__(self, anchor=None, orientation=None, separation=0):
super(Port, self).__init__(name='Port', port_particle=True)
self.anchor = anchor
up = Compound(name='subport', port_particle=True)
up.add(Particle(name='G', pos=[0.005, 0.0025, -0.0025],
port_particle=True), 'middle')
up.add(Particle(name='G', pos=[0.005, 0.0225, -0.0025],
port_particle=True), 'top')
up.add(Particle(name='G', pos=[-0.015, -0.0075, -0.0025],
port_particle=True), 'left')
up.add(Particle(name='G', pos=[0.005, -0.0175, 0.0075],
port_particle=True), 'right')
down = clone(up)
down.rotate(np.pi, [0, 0, 1])
self.add(up, 'up')
self.add(down, 'down')
self.used = False
if orientation is None:
orientation = [0, 1, 0]
default_direction = [0, 1, 0]
if np.array_equal(
np.asarray(default_direction), unit_vector(-np.asarray(orientation))):
self.rotate(np.pi, [1, 0, 0])
elif np.array_equal(
np.asarray(default_direction), unit_vector(np.asarray(orientation))):
pass
else:
normal = np.cross(default_direction, orientation)
self.rotate(angle(default_direction, orientation), normal)
if anchor:
self.translate_to(anchor.pos)
self.translate(separation*unit_vector(orientation))
def __init__(self, anchor=None, orientation=None, separation=0):
super(Port, self).__init__(name="Port", port_particle=True)
self.anchor = anchor
default_direction = np.array([0, 1, 0])
if orientation is None:
orientation = [0, 1, 0]
orientation = np.asarray(orientation)
up = Compound(name="subport", port_particle=True)
pos = [0.005, 0.0025, -0.0025]
up.add(Particle(name="G", pos=pos, port_particle=True), "middle")
pos = [0.005, 0.0225, -0.0025]
up.add(Particle(name="G", pos=pos, port_particle=True), "top")
pos = [-0.015, -0.0075, -0.0025]
up.add(Particle(name="G", pos=pos, port_particle=True), "left")
pos = [0.005, -0.0175, 0.0075]
up.add(Particle(name="G", pos=pos, port_particle=True), "right")
down = clone(up)
self.add(up, "up")
self.add(down, "down")
self.used = False
if np.allclose(default_direction, unit_vector(-orientation)):
down.rotate(np.pi, [0, 0, 1])
self.rotate(np.pi, [0, 0, 1])
elif np.allclose(default_direction, unit_vector(orientation)):
down.rotate(np.pi, [0, 0, 1])
else:
normal = np.cross(default_direction, orientation)
self.rotate(angle(default_direction, orientation), normal)
down.rotate(np.pi, normal)
if anchor:
self.translate_to(anchor.pos)
self.translate(separation * unit_vector(orientation))
