def __init__(self, n):
phi = (1 + np.sqrt(5)) / 2 # the golden ratio
long_incr = 2*np.pi / phi # how much to increment the longitude
dz = 2.0 / float(n) # a unit sphere has diameter 2
bands = np.arange(n) # each band will have one point placed on it
z = bands * dz - 1 + (dz/2) # the height z of each band/point
r = np.sqrt(1 - z*z) # project onto xy-plane
az = bands * long_incr # azimuthal angle of point modulo 2 pi
x = r * np.cos(az)
y = r * np.sin(az)
points = np.column_stack((x, y, z))
from mbuild.port import Port
ports = list()
for point in points:
port = Port()
ports.append(port)
# Make the top of the port point toward the positive x axis.
rotate_around_z(port, -np.pi/2)
# Raise up (or down) the top of the port in the z direction.
rotate_around_y(port, -np.arcsin(point[2]))
# Rotate the Port along the z axis.
rotate_around_z(port, np.arctan2(point[1], point[0]))
# Move the Port a bit away from the surface of the Sphere.
#translate(port, point + 0.07)
super(SpherePattern, self).__init__(points=points,
orientations={'normal': ports})
def __init__(self, anchor=None):
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, 0, 0], port_particle=True), 'middle')
up.add(Particle(name='G', pos=[0, 0.02, 0], port_particle=True), 'top')
up.add(Particle(name='G', pos=[-0.02, -0.01, 0], port_particle=True), 'left')
up.add(Particle(name='G', pos=[0.0, -0.02, 0.01], port_particle=True), 'right')
down = clone(up)
rotate_around_z(down, np.pi)
self.add(up, 'up')
self.add(down, 'down')
def __init__(self, anchor=None):
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, 0, 0], port_particle=True), 'middle')
up.add(Particle(name='G', pos=[0, 0.02, 0], port_particle=True), 'top')
up.add(Particle(name='G', pos=[-0.02, -0.01, 0], port_particle=True), 'left')
up.add(Particle(name='G', pos=[0.0, -0.02, 0.01], port_particle=True), 'right')
down = clone(up)
rotate_around_z(down, np.pi)
self.add(up, 'up')
self.add(down, 'down')
self.used = False
if anchor:
translate_to(self, anchor.pos)
def test_rotate_around_z_away_from_origin(self, sixpoints):
before = sixpoints.xyz_with_ports
rotate_around_z(sixpoints, np.pi)
after = sixpoints.xyz_with_ports
assert (np.allclose(before[:, 1], -1 * after[:, 1], atol=1e-16)
and np.allclose(before[:, 0], -1 * after[:, 0], atol=1e-16))
def test_rotate_around_z(self, ch2):
before = ch2.xyz_with_ports
rotate_around_z(ch2, np.pi)
after = ch2.xyz_with_ports
assert (np.allclose(before[:, 0], -1 * after[:, 0], atol=1e-16)
and np.allclose(before[:, 1], -1 * after[:, 1], atol=1e-16))
def test_warn_rotate_z(self, methane):
with pytest.warns(DeprecationWarning):
rotate_around_z(methane, np.pi)
def test_rotate_around_z(self, ch2):
before = ch2.xyz_with_ports
rotate_around_z(ch2, np.pi)
after = ch2.xyz_with_ports
def test_error_rotate_z(self, methane):
with pytest.raises(RemovedFuncError):
rotate_around_z(methane, np.pi)
def test_rotate_around_z_away_from_origin(self, sixpoints):
before = sixpoints.xyz_with_ports
rotate_around_z(sixpoints, np.pi)
after = sixpoints.xyz_with_ports
assert ( np.allclose(before[:, 1], -1*after[:, 1], atol=1e-16)
and np.allclose(before[:, 0], -1*after[:, 0], atol=1e-16))
def test_rotate_around_z(self, ch2):
before = ch2.xyz_with_ports
rotate_around_z(ch2, np.pi)
after = ch2.xyz_with_ports
assert ( np.allclose(before[:, 0], -1*after[:, 0], atol=1e-16)
and np.allclose(before[:, 1], -1*after[:, 1], atol=1e-16))
def test_warn_rotate_z(self, methane):
with pytest.warns(DeprecationWarning):
rotate_around_z(methane, np.pi)
def test_rotate_around_z(self, ch2):
before = ch2.xyz_with_ports
rotate_around_z(ch2, np.pi)
after = ch2.xyz_with_ports
