# Parameters from the input file
blob_radius = read.blob_radius
periodic_length = read.periodic_length
max_translation = blob_radius * 0.1
weight = 1.0 * read.g
kT = read.kT
# Create rigid bodies
bodies = []
body_types = []
max_body_length = 0.0
for ID, structure in enumerate(read.structures):
print('Creating structures = ', structure[1])
struct_ref_config = read_vertex_file.read_vertex_file(structure[0])
num_bodies_struct, struct_locations, struct_orientations = read_clones_file.read_clones_file(
structure[1])
body_types.append(num_bodies_struct)
# Creat each body of type structure
for i in range(num_bodies_struct):
b = body.Body(struct_locations[i], struct_orientations[i],
struct_ref_config, blob_radius)
b.ID = read.structures_ID[ID]
body_length = b.calc_body_length()
max_body_length = (body_length if body_length > max_body_length
else max_body_length)
bodies.append(b)
bodies = np.array(bodies)
# Set some more variables
num_bodies = bodies.size
Nblobs = sum([x.Nblobs for x in bodies])
# Read input file
read = read_input.ReadInput(input_file)
a = read.blob_radius
structure_names = read.structure_names
n_steps = read.n_steps
n_save = read.n_save
# Create rigid bodies
bodies = []
body_types = []
num_blobs_ID = 0
for ID, structure in enumerate(read.structures):
# print 'Creating structures = ', structure[1]
struct_ref_config = read_vertex_file.read_vertex_file(structure[0])
num_bodies_struct, struct_locations, struct_orientations = read_clones_file.read_clones_file(structure[1])
body_types.append(num_bodies_struct)
# Creat each body of tyoe structure
for i in range(len(struct_orientations)):
b = body.Body(struct_locations[i], struct_orientations[i], struct_ref_config, a)
b.ID = read.structures_ID[ID]
# Append bodies to total bodies list
bodies.append(b)
if b.ID == name_ID:
num_blobs_ID += b.Nblobs
bodies = np.array(bodies)
num_bodies = bodies.size
num_blobs = sum([x.Nblobs for x in bodies])
# Read configuration
with open(config_file, 'r') as f:
