def get_log_data(ia, T, key, Wis=range(1, 20)):
path = '/space/tohekorh/ShearSlide/files/%s_%i/%s/' % (ia, T, key)
data = []
print path
for x in os.walk(path):
folder = x[0]
if folder != path:
print folder
if query_yes_no('Take this folder?', default="yes"):
W = int(folder.split('=')[1])
if W in Wis:
for filen in os.listdir(folder):
if filen[-6:] == '.simul':
print filen
if query_yes_no('Take this file?', default="yes"):
fPath = folder + '/' + filen
Wval, L, wi, li, v = read_simul_params_file(
fPath)[:5]
if wi != W: raise
logpath = fPath[:-6] + '.log'
trajpath = fPath[:-6] + '.traj'
atoms = PickleTrajectory(trajpath, 'r')[-1]
natoms = len(atoms)
data.append([
wi, li, Wval, L, natoms, v,
np.loadtxt(logpath)
])
return data
def get_log_data(ia, T, key, Wis=range(1, 20)):
path = "/space/tohekorh/ShearSlide/files/%s_%i/%s/" % (ia, T, key)
data = []
print path
for x in os.walk(path):
folder = x[0]
if folder != path:
print folder
if query_yes_no("Take this folder?", default="yes"):
W = int(folder.split("=")[1])
if W in Wis:
for filen in os.listdir(folder):
if filen[-6:] == ".simul":
print filen
if query_yes_no("Take this file?", default="yes"):
fPath = folder + "/" + filen
Wval, L, wi, li, v = read_simul_params_file(fPath)[:5]
if wi != W:
raise
logpath = fPath[:-6] + ".log"
trajpath = fPath[:-6] + ".traj"
atoms = PickleTrajectory(trajpath, "r")[-1]
natoms = len(atoms)
data.append([wi, li, Wval, L, natoms, v, np.loadtxt(logpath)])
return data
def hyster_study(edge, folder=None):
if folder == None: folder = os.getcwd()
print folder
for fileC in os.listdir(folder):
if fileC[-6:] == '.simul':
fileC = folder + fileC
_, length, _, _, v, T, dt, fric, dtheta, \
thresZ, interval, deltaY, theta, M, edge = read_simul_params_file(fileC)
mdfile = fileC[:-6] + '.traj'
traj = PickleTrajectory(mdfile, 'r')
atoms_init = traj[0]
constraints, _, twist, rend_b, rend_t = get_constraints(atoms_init, edge, \
bond, None, key = 'twist_p')
#constraints, _, rend_b, rend_t = get_constraints(atoms_init, edge, \
# bond, None, key = 'twist_p')
atoms = traj[-1]
atoms.set_constraint(constraints)
vels = (traj[-2].positions - traj[-1].positions) / (interval * dt)
atoms.set_velocities(vels)
calc = LAMMPS(parameters=get_lammps_params())
atoms.set_calculator(calc)
view(atoms)
dyn = Langevin(atoms, dt * units.fs, T * units.kB, fric)
twist.set_angle(theta)
dyn.run(10 * interval)
view(atoms)
traj_new = PickleTrajectory(fileC[:-6] + '_hyst.traj', 'w', atoms)
mdlogf = fileC[:-6] + '_hyst.log'
do_dynamics(mdlogf, atoms, dyn, rend_b, rend_t, v, dt, deltaY, \
theta, dtheta, length, thresZ, \
interval, traj_new, M, twist)
mdhystf = fileC[:-6] + '_hyst.traj'
logfile = fileC[:-6] + '.log'
append_files(logfile, mdlogf, logfile[:-4] + '_comp.log')
call([
'ase-gui', mdfile, mdhystf, '-o', logfile[:-4] + '_comp.traj'
])
def hyster_study(edge, folder = None):
if folder == None: folder = os.getcwd()
print folder
for fileC in os.listdir(folder):
if fileC[-6:] == '.simul':
fileC = folder + fileC
_, length, _, _, v, T, dt, fric, dtheta, \
thresZ, interval, deltaY, theta, M, edge = read_simul_params_file(fileC)
mdfile = fileC[:-6] + '.traj'
traj = PickleTrajectory(mdfile, 'r')
atoms_init = traj[0]
constraints, _, twist, rend_b, rend_t = get_constraints(atoms_init, edge, \
bond, None, key = 'twist_p')
#constraints, _, rend_b, rend_t = get_constraints(atoms_init, edge, \
# bond, None, key = 'twist_p')
atoms = traj[-1]
atoms.set_constraint(constraints)
vels = (traj[-2].positions - traj[-1].positions) / (interval * dt)
atoms.set_velocities(vels)
calc = LAMMPS(parameters=get_lammps_params())
atoms.set_calculator(calc)
view(atoms)
dyn = Langevin(atoms, dt*units.fs, T*units.kB, fric)
twist.set_angle(theta)
dyn.run(10 * interval)
view(atoms)
traj_new= PickleTrajectory(fileC[:-6] + '_hyst.traj', 'w', atoms)
mdlogf = fileC[:-6] + '_hyst.log'
do_dynamics(mdlogf, atoms, dyn, rend_b, rend_t, v, dt, deltaY, \
theta, dtheta, length, thresZ, \
interval, traj_new, M, twist)
mdhystf = fileC[:-6] + '_hyst.traj'
logfile = fileC[:-6] + '.log'
append_files(logfile, mdlogf, logfile[:-4] + '_comp.log')
call(['ase-gui', mdfile, mdhystf, '-o', logfile[:-4] + '_comp.traj'])
def get_datas(ia, T, key):
path = '/space/tohekorh/ShearSlide/files/%s_%i/%s/' % (ia, T, key)
data = []
print path
for x in os.walk(path):
folder = x[0]
if folder != path:
print folder
if query_yes_no('Take this folder?', default="yes"):
W = int(folder.split('=')[1])
for filen in os.listdir(folder):
if filen[-6:] == '.simul':
print filen
if query_yes_no('Take this file?', default="yes"):
fPath = folder + '/' + filen
wf, L, width_i, _, v, _, _, _, _, \
_, _, _, _,_, _ = \
read_simul_params_file(fPath)
if width_i != W:
print width_i, W
raise
logpath = fPath[:-6] + '.log'
with open(logpath, 'r') as f:
lines = f.readlines()
for i in range(0, len(lines)):
line = lines[i]
if line[:7] == '# Kink!':
ne = lines[
i -
1] # you may want to check that i < len(lines)
shift_b, Rad_b, theta_b = ne.split(
' ')[1:4]
Rad_b = float(L) / float(theta_b)
elif line[:15] == '# Kink vanished':
ne = lines[
i -
1] # you may want to check that i < len(lines)
shift_d, Rad_d, theta_d = ne.split(
' ')[1:4]
Rad_d = float(L) / float(theta_d)
break
data.append([wf, L, v, Rad_b, Rad_d])
return data
def get_datas(ia, T, key):
path = "/space/tohekorh/ShearSlide/files/%s_%i/%s/" % (ia, T, key)
data = []
print path
for x in os.walk(path):
folder = x[0]
if folder != path:
print folder
if query_yes_no("Take this folder?", default="yes"):
W = int(folder.split("=")[1])
for filen in os.listdir(folder):
if filen[-6:] == ".simul":
print filen
if query_yes_no("Take this file?", default="yes"):
fPath = folder + "/" + filen
wf, L, width_i, _, v, _, _, _, _, _, _, _, _, _, _ = read_simul_params_file(fPath)
if width_i != W:
print width_i, W
raise
logpath = fPath[:-6] + ".log"
with open(logpath, "r") as f:
lines = f.readlines()
for i in range(0, len(lines)):
line = lines[i]
if line[:7] == "# Kink!":
ne = lines[i - 1] # you may want to check that i < len(lines)
shift_b, Rad_b, theta_b = ne.split(" ")[1:4]
Rad_b = float(L) / float(theta_b)
elif line[:15] == "# Kink vanished":
ne = lines[i - 1] # you may want to check that i < len(lines)
shift_d, Rad_d, theta_d = ne.split(" ")[1:4]
Rad_d = float(L) / float(theta_d)
break
data.append([wf, L, v, Rad_b, Rad_d])
return data