types = {1: 1.0, 2: 1.0, 3: 1.0}
nums = 2 # number of random walks
size = 10 # size of the chain
rw_kval = 30.0
rw_cutoff = 3.5
rw_epsilon = 0.05
rw_sigma = 0.5
total_time = 0
for i in range(nums):
t0 = time.time()
box.random_walk(size,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
bead_types=types,
termination="retract")
t1 = time.time()
total_time += t1 - t0
print(f"Random walks: attempt {i+1} successful. Time taken: {t1 - t0}")
print(f"Total time taken for random walk configuration: {total_time}")
num_links = 1 # number of crosslinks
mass = 3.0 # mass of crosslinker bead
cl_kval = rw_kval
cl_epsilon = rw_epsilon
cl_sigma = rw_sigma
)
print(f" SAMPLE NUMBER: {sample}")
print(
"--------------------------------------------------------------------------------------"
)
box = PolyLattice(celllen, cellnums, pair_cutoff, pair_sigma,
pair_epsilon)
t0 = time.time()
for j in range(num_walks):
current_walks = box.num_walks
while True:
try:
box.random_walk(j,
size,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
bead_types=types)
if box.num_walks == current_walks + 1:
print(
f"Simulation {i}_{sample}: Random walk {j} complete"
)
break
except:
print("Oooops! Random walk crashed!")
for cell in box.Cells:
cell.beads = [
bead for bead in cell.beads if bead[0] != j
]
cl_kval,
cl_cutoff,
cl_epsilon,
cl_sigma,
allowed_types=None,
style='fene',
prob=0.8,
ibonds=2)
for i in range(nums):
t0 = time.time()
# use cell_num to control where walk starts
box.random_walk(size,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
bead_types=types,
termination="retract",
allowed_failures=50000)
t1 = time.time()
total_time += t1 - t0
print(f"Random walks: attempt {i+1} successful. Time taken: {t1 - t0}")
print(f"Total time taken for random walk configuration: {total_time}")
box.unbonded_crosslinks(50,
mass,
cl_kval,
cl_cutoff,
cl_epsilon,
cl_sigma,
allowed=['a', 'b'])
copolymer = []
for i in range(copolymer_frac):
copolymer.append('a')
for i in range(copolymer_frac):
copolymer.append('b')
random_copolymer = []
total_time = 0
t0 = time.time()
box.random_walk(size,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
bead_sequence=copolymer,
termination="retract")
t1 = time.time()
total_time += t1 - t0
print(f"Walk completed in {t1-t0} seconds")
t0 = time.time()
box.random_walk(size,
0.9 * rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
bead_sequence=['b', 'c'],