copolymer = []
for i in range(40):
copolymer.append('a')
for i in range(720):
copolymer.append('b')
for i in range(40):
copolymer.append('a')
total_time = 0
for i in range(num_walks):
t0 = time.time()
box.randomwalk(size,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
bead_sequence=copolymer,
initial_failures=10000,
walk_failures=10000,
soften=True,
termination="soften")
t1 = time.time()
total_time += t1 - t0
print(
f"Walk {i} completed in {t1-t0} seconds. Total time elapsed: {total_time}"
)
total_time += t1 - t0
print(f"Walks complete. Total time: {total_time} seconds")
t0 = time.time()
box.simulation.structure("test_structure.in")
cl_cutoff = 1.1 * rw_cutoff
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.randomwalk(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.randomwalk(size,
0.9 * rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
bead_sequence=['b', 'c'],
for i in range(1500):
copolymer.append('a')
for i in range(1500):
copolymer.append('b')
random_copolymer = []
total_time = 0
for i in range(2):
t0 = time.time()
box.randomwalk(size,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
bead_sequence = ['a'],
initial_failures= 10000,
walk_failures = 10000,
soften=True,
termination="soften")
t1 = time.time()
total_time+= t1-t0
print(f"Walk {box.num_walks} completed in {t1-t0} seconds. Total time elapsed: {total_time}")
for i in range(2):
low_density = box.find_low_density(region=2, quals=1)
print(low_density)
low_density_cell = low_density[0]
t0 = time.time()
box.randomwalk(size,
rw_kval,
size = 100 # size of the chain
rw_kval = 30.0
rw_cutoff = 3.5
rw_epsilon = 0.05
rw_sigma = 0.3
graft_spacing = 20
graft_size = 10
graft_num = 1
total_time = 0
t0 = time.time()
box.randomwalk(size,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
bead_sequence=['a', 'b'],
starting_pos=[5.0, 5.0, 5.0],
termination="retract")
print("Random walk completed.")
for i in range(1, size, graft_spacing):
for j in range(graft_num):
box.graft_chain([1, i],
graft_size,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
bead_sequence=['c'])
print(f"Graft {i} completed.")
# Running random walk
# -------------------------------------------------------------------------
num_walks = 225
rw_kval = 30
rw_cutoff = 1.5
rw_epsilon = 1.0
rw_sigma = 1.0
a
print("Starting walks.")
for i in range(num_walks):
print(f"Walk {i}")
box.randomwalk(500,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
bead_sequence = ['mainbead', 'subbead'],
initial_failures= 10000,
walk_failures = 10000,
soften=True,
termination="soften")
print("Walks complete.")
# -------------------------------------------------------------------------
# Modifying interactions mid simulation
# -------------------------------------------------------------------------
box.interactions.modify_sigma('mainbead', 'mainbead', 1.0)
box.interactions.modify_sigma('subbead', 'subbead', 1.0)
box.interactions.modify_sigma('mainbead', 'subbead', 1.0)
copolymer = []
for i in range(10):
copolymer.append('a')
for i in range(10):
copolymer.append('b')
random_copolymer = []
for i in range(numwalks):
box.randomwalk(size,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
copolymer,
mini=1.1,
suppress = False,
termination='retract',
sequence_range=3,
srate=0.9,
danger = 1.0,
initial_failures = 100,
walk_failures = 50)
print(f"{i+1} random walked")
print(f"Walk completed in {t1-t0} seconds")
print(f"Number of retractions: {box.retractions}")
# for i in box.walk_data():
# print(i, box.mdsim.global_bead_num(i))