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 from_snapshot(snapshot, scale=1.0):
"""Convert a Snapshot to a Compound.
Snapshot can be a hoomd.data.Snapshot or a gsd.hoomd.Snapshot.
Parameters
----------
snapshot : hoomd._hoomd.SnapshotSystemData_float or gsd.hoomd.Snapshot
Snapshot from which to build the mbuild Compound.
scale : float, optional, default 1.0
Value by which to scale the length values
Returns
-------
comp : Compound
Note
----
GSD and HOOMD snapshots center their boxes on the origin (0,0,0), so the
compound is shifted by half the box lengths
"""
comp = Compound()
bond_array = snapshot.bonds.group
n_atoms = snapshot.particles.N
if "SnapshotSystemData_float" in dir(hoomd._hoomd) and isinstance(
snapshot, hoomd._hoomd.SnapshotSystemData_float
):
# hoomd v2
box = snapshot.box
comp.box = Box.from_lengths_tilt_factors(
lengths=np.array([box.Lx, box.Ly, box.Lz]) * scale,
tilt_factors=np.array([box.xy, box.xz, box.yz]),
)
else:
# gsd / hoomd v3
box = snapshot.configuration.box
comp.box = Box.from_lengths_tilt_factors(
lengths=box[:3] * scale, tilt_factors=box[3:]
)
# GSD and HOOMD snapshots center their boxes on the origin (0,0,0)
shift = np.array(comp.box.lengths) / 2
# Add particles
for i in range(n_atoms):
name = snapshot.particles.types[snapshot.particles.typeid[i]]
xyz = snapshot.particles.position[i] * scale + shift
charge = snapshot.particles.charge[i]
atom = Particle(name=name, pos=xyz, charge=charge)
comp.add(atom, label=str(i))
# Add bonds
particle_dict = {idx: p for idx, p in enumerate(comp.particles())}
for i in range(bond_array.shape[0]):
atom1 = int(bond_array[i][0])
atom2 = int(bond_array[i][1])
comp.add_bond([particle_dict[atom1], particle_dict[atom2]])
return comp
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 __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))