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.
spin_z(port, -np.pi / 2)
# Raise up (or down) the top of the port in the z direction.
spin_y(port, -np.arcsin(point[2]))
# Rotate the Port along the z axis.
spin_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, n, **kwargs):
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(int(n)) # each band will have one point placed on it
z = bands * dz - 1.0 + (dz / 2.0) # the height z of each band/point
r = np.sqrt(1.0 - 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
if kwargs.get("orientations") is None:
ports = list()
for point in points:
port = Port()
ports.append(port)
# Make the top of the port point toward the positive x axis.
port.spin(-np.pi / 2, [0, 0, 1])
# Raise up (or down) the top of the port in the z direction.
port.spin(-np.arcsin(point[2]), [0, 1, 0])
# Rotate the Port along the z axis.
port.spin(np.arctan2(point[1], point[0]), [0, 0, 1])
# Move the Port a bit away from the surface of the Sphere.
# translate(port, point + 0.07)
kwargs["orientations"] = {"normal": ports}
else:
raise NotImplementedError(
"Custom orientation support is not yet implemented.")
super(SpherePattern, self).__init__(points=points, **kwargs)
def _add_port(compound,
label,
idx,
separation,
orientation=None,
replace=True):
"""Add the ports to the compound at the specified particle index.
The port will either use that particle as an anchor or replace it entirely.
"""
if replace:
atom_bonds = [b for b in compound.bonds() if compound[idx] in b][0]
anchor = [p for p in atom_bonds if p != compound[idx]][0]
if orientation is None:
orientation = compound[idx].pos - anchor.pos
if separation is None:
separation = np.linalg.norm(compound[idx].pos - anchor.pos)
else:
anchor = compound[idx]
port = Port(
anchor=anchor,
orientation=orientation,
separation=separation / 2,
)
compound.add(port, label=label)
return separation