velocity = np.zeros((2*num_bodies, 3))
# If scheme == mobility solve mobility problem
if read.scheme == 'mobility':
start_time = time.time()
# Get blobs coordinates
r_vectors_blobs = multi_bodies.get_blobs_r_vectors(bodies, Nblobs)
# Use the code to compute force-torques on bodies if a file was not given
if read.force_file is None:
force_torque = multi_bodies_functions.force_torque_calculator_sort_by_bodies(bodies,
r_vectors_blobs,
g = read.g,
repulsion_strength_wall = read.repulsion_strength_wall,
debye_length_wall = read.debye_length_wall,
repulsion_strength = read.repulsion_strength,
debye_length = read.debye_length,
periodic_length = read.periodic_length,
omega_one_roller = read.omega_one_roller)
# Set right hand side
System_size = Nblobs * 3 + num_bodies * 6
RHS = np.reshape(np.concatenate([slip, -force_torque]), (System_size))
# If prescribed velocity modify RHS
offset = 0
for k, b in enumerate(bodies):
if b.prescribed_kinematics is True:
# Add K*U to Right Hand side
KU = np.dot(b.calc_K_matrix(), b.calc_prescribed_velocity())
RHS[3*offset : 3*(offset+b.Nblobs)] += KU.flatten()
#######################################################################
for k, b in enumerate(bodies):
bodies[k].location[2] -= 2.0
factor = (2 + dist) / 3.0
bodies[k].location *= factor
bodies[k].location[2] += height
print(bodies[k].location)
#######################################################################
r_vectors_blobs = get_blobs_r_vectors(bodies, Nblobs)
slip = np.zeros((Nblobs, 3))
force_torque = multi_bodies_functions.force_torque_calculator_sort_by_bodies(
bodies,
r_vectors_blobs,
g=read.g,
part=1,
comp=0,
sign=-1.0,
repulsion_strength_wall=read.repulsion_strength_wall,
debye_length_wall=read.debye_length_wall,
repulsion_strength=read.repulsion_strength,
debye_length=read.debye_length,
periodic_length=read.periodic_length)
print force_torque
# Set right hand side
System_size = Nblobs * 3 + num_bodies * 6
RHS = np.reshape(np.concatenate([slip, -force_torque]),
(System_size))
# Set linear operators
linear_operator_partial = partial(linear_operator_rigid,
bodies=bodies,
else:
velocity = np.zeros((2*num_bodies, 3))
# If scheme == mobility solve mobility problem
if read.scheme == 'mobility':
start_time = time.time()
# Get blobs coordinates
r_vectors_blobs = multi_bodies.get_blobs_r_vectors(bodies, Nblobs)
# Use the code to compute force-torques on bodies if a file was not given
if read.force_file is None:
force_torque = multi_bodies_functions.force_torque_calculator_sort_by_bodies(bodies,
r_vectors_blobs,
g = read.g,
repulsion_strength_wall = read.repulsion_strength_wall,
debye_length_wall = read.debye_length_wall,
repulsion_strength = read.repulsion_strength,
debye_length = read.debye_length,
periodic_length = read.periodic_length)
# Set right hand side
System_size = Nblobs * 3 + num_bodies * 6
RHS = np.reshape(np.concatenate([slip, -force_torque]), (System_size))
# Set linear operators
linear_operator_partial = partial(multi_bodies.linear_operator_rigid, bodies=bodies, r_vectors=r_vectors_blobs, eta=read.eta, a=read.blob_radius)
A = spla.LinearOperator((System_size, System_size), matvec = linear_operator_partial, dtype='float64')
# Set preconditioner
mobility_inv_blobs = []
mobility_bodies = np.empty((len(bodies), 6, 6))