for i in range(copolymer_frac):
copolymer.append('a')
for i in range(copolymer_frac):
copolymer.append('b')
sequence_range = 10
num_walks = 15
for i in range(num_walks):
box.uniform_chain(size,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
termination='soften',
bead_sequence=copolymer,
srate=0.99,
suppress=False,
sequence_range=5,
retraction_limit=0,
danger=1.09)
print(f"{i+1} random walked")
while box.dead_walks > 0:
reattempts = box.dead_walks
box.dead_walks = 0
for i in range(reattempts):
box.uniform_chain(size,
rw_kval,
rw_cutoff,
print(f"Density file read in. Time taken: {t1 - t0}")
#----------------------------------------------------------------------------------------
# RANDOM WALK ASSIGNMENT
#----------------------------------------------------------------------------------------
total_time = 0
for i in range(num_walks):
t0 = time.time()
box.uniform_chain(size,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
bead_sequence=copolymer,
meanfield=True,
termination='soften',
srate=0.98,
suppress=False,
danger=1.03,
initial_failures=15000,
walk_failures=15000,
retraction_limit=10,
sequence_range=int(0.9 * asize * size))
t1 = time.time()
print(f"Walk {i} complete. Time taken: {t1-t0} seconds.")
total_time += t1 - t0
print(f"Walks complete. Total time: {total_time} seconds")
t0 = time.time()
box.mdsim.structure(f"structure-{ret}.in")
for i in range(b_bead):
copolymer.append('b')
for i in range(a_bead):
copolymer.append('a')
print(a_bead)
print(b_bead)
print(a_bead + b_bead)
total_time = 0
for i in range(num_walks):
t0 = time.time()
box.uniform_chain(size,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
bead_sequence=copolymer,
sequence_range=int(seq_frac * a_bead),
meanfield=True)
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.mdsim.structure(f"struc{seq_frac}.in")
t1 = time.time()
# block = 100
copolymer = []
for i in range(400):
copolymer.append('a')
for i in range(400):
copolymer.append('b')
total_time = 0
for i in range(num_walks):
t0 = time.time()
box.uniform_chain(size,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
bead_sequence=copolymer,
meanfield=True)
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.mdsim.structure("test_structure2.in")
t1 = time.time()
copolymer_frac = 5
copolymer = []
for i in range(copolymer_frac):
copolymer.append('a')
for i in range(copolymer_frac):
copolymer.append('b')
random_copolymer = []
num_walks = 15
for i in range(num_walks):
box.uniform_chain(size,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
termination='soften',
bead_sequence=copolymer,
srate=0.99,
suppress=False,
danger=1.09)
print(f"{i+1} random walked")
print(f"Walk completed in {t1-t0} seconds")
box.mdsim.structure("test_structure.in")
box.mdsim.settings("test_settings.in", prebuilt="test_structure.in")
timestep = 0.01
desc1 = "testing"
box.meanfield.density_file("rgrid", [15, 15, 15])
print(f"Density file read in. Time taken: {t1 - t0}")
#----------------------------------------------------------------------------------------
# RANDOM WALK ASSIGNMENT
#----------------------------------------------------------------------------------------
total_time = 0
for i in range(num_walks):
t0 = time.time()
box.uniform_chain(size,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
bead_sequence=copolymer,
meanfield=True,
srate=0.99,
suppress=False,
initial_failures=1000,
sequence_range=sequence_range,
walk_failures=5000)
t1 = time.time()
print(f"Walk {i} complete. Time taken: {t1-t0} seconds.")
total_time += t1 - t0
total_time += t1 - t0
print(f"Walks complete. Total time: {total_time} seconds")
t0 = time.time()
box.mdsim.structure(f"structure-{sequence_range}.in")
box.mdsim.settings(f"settings-{sequence_range}.in",
print(f"Density file read in. Time taken: {t1 - t0}")
#----------------------------------------------------------------------------------------
# RANDOM WALK ASSIGNMENT
#----------------------------------------------------------------------------------------
total_time = 0
for i in range(num_walks):
t0 = time.time()
box.uniform_chain(size,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
bead_sequence = copolymer,
meanfield = True,
srate = 0.99,
suppress= False,
danger = 1.03,
initial_failures=15000,
walk_failures=15000,
sequence_range=int(0.125*size))
t1 = time.time()
print(f"Walk {i} complete. Time taken: {t1-t0} seconds.")
total_time+= t1-t0
print(f"Walks complete. Total time: {total_time} seconds")
t0 = time.time()
box.mdsim.structure(f"structure-{stretch_val}.in")
box.mdsim.settings(f"settings-{stretch_val}.in", nskin=4.0, nlist=[10,10000])
for i in range(int(0.25 * size)):
copolymer.append('a')
for i in range(int(0.75 * size)):
copolymer.append('b')
print(int(0.25 * size))
print(int(0.75 * size))
total_time = 0
for i in range(num_walks):
t0 = time.time()
box.uniform_chain(size,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
bead_sequence=copolymer,
meanfield=True,
srate=0.85,
sequence_range=75,
suppress=False)
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.mdsim.structure(f"test_structure{cellnums}.in")
copolymer = []
for i in range(10):
copolymer.append('a')
for i in range(10):
copolymer.append('b')
random_copolymer = []
for i in range(1):
box.uniform_chain(size,
rw_kval,
rw_cutoff,
rw_epsilon,
rw_sigma,
copolymer,
mini=1.1,
suppress=False,
termination='soften',
sequence_range=3,
srate=0.95,
danger=1.0,
initial_failures=100,
walk_failures=1000)
print(f"{i+1} random walked")
print(f"Walk completed in {t1-t0} seconds")
print(f"Number of retractions: {box.retractions}")
box.mdsim.structure("test_structure.in")
box.mdsim.settings("test_settings.in")