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 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_stick_data(ia, T, key, wi):
path = '/space/tohekorh/ShearSlide/files/%s_%i/%s/w=%i' % (ia, T, key, wi)
#path = '/home/topi/workspace/ShearAndBuckle/data/stick/w=7/'
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"):
r = int(folder.split('=')[-1])
if r % 10 == 0 or r in [12, 14, 16, 18]:
for filen in os.listdir(folder):
if filen[-6:] == '.simul':
print filen
fPath = folder + '/' + filen
width_i, length, length_d, temp, _, _, _, _, _, stick \
= read_stick_simul_params_file(fPath)
if stick:
print 'stick at L_b/L_t = %.2f' % (length_d /
length)
data.append([length, length_d])
if width_i != wi: raise
#trajpath= fPath[:-6] + '.traj'
#atoms = PickleTrajectory(trajpath, 'r')[-1]
return np.array(data)
def get_stick_data(ia, T, key, wi):
path = "/space/tohekorh/ShearSlide/files/%s_%i/%s/w=%i" % (ia, T, key, wi)
# path = '/home/topi/workspace/ShearAndBuckle/data/stick/w=7/'
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"):
r = int(folder.split("=")[-1])
if r % 10 == 0 or r in [12, 14, 16, 18]:
for filen in os.listdir(folder):
if filen[-6:] == ".simul":
print filen
fPath = folder + "/" + filen
width_i, length, length_d, temp, _, _, _, _, _, stick = read_stick_simul_params_file(fPath)
if stick:
print "stick at L_b/L_t = %.2f" % (length_d / length)
data.append([length, length_d])
if width_i != wi:
raise
# trajpath= fPath[:-6] + '.traj'
# atoms = PickleTrajectory(trajpath, 'r')[-1]
return np.array(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
from potentials.KC_imagBottom import make_neighSet, get_setOrig
import numpy as np
import matplotlib.pyplot as plt
pathf = '/space/tohekorh/ShearSlide/files/KC_10/ac_stickTaito/'
width = 7
ratio = 20
Ld_i = 1
edge = 'ac'
bond = 1.39778034758
for filen in os.listdir(pathf + 'w=%i/r=%i/' %(width, ratio)):
if filen[-5:] == '.traj':
print filen
if query_yes_no('Take this file?', default="yes"):
bend, straight, [matchL_idx, matchR_idx, vec], [L_bend, L_straight], [left_idxs, right_idxs]\
= create_bend_stucture(width, ratio, Ld_i, edge, bond)
shift_v = -straight.positions[matchR_idx] + (bend.positions[matchL_idx] + vec)
straight.translate(shift_v)
print matchR_idx
trans_vec = trans_atomsKC(straight.positions[matchR_idx], edge, bond)
print straight.positions[matchR_idx] + trans_vec
rlim = .3
asum_dev = .0 * np.array([np.sqrt(3)/2., 1./2])
m = 0
from plot import plot_posits
from potentials.KC_imagBottom import make_neighSet, get_setOrig
import numpy as np
import matplotlib.pyplot as plt
pathf = '/space/tohekorh/ShearSlide/files/KC_10/ac_stickTaito/'
width = 7
ratio = 20
Ld_i = 1
edge = 'ac'
bond = 1.39778034758
for filen in os.listdir(pathf + 'w=%i/r=%i/' % (width, ratio)):
if filen[-5:] == '.traj':
print filen
if query_yes_no('Take this file?', default="yes"):
bend, straight, [matchL_idx, matchR_idx, vec], [L_bend, L_straight], [left_idxs, right_idxs]\
= create_bend_stucture(width, ratio, Ld_i, edge, bond)
shift_v = -straight.positions[matchR_idx] + (
bend.positions[matchL_idx] + vec)
straight.translate(shift_v)
print matchR_idx
trans_vec = trans_atomsKC(straight.positions[matchR_idx], edge,
bond)
print straight.positions[matchR_idx] + trans_vec
rlim = .3
asum_dev = .0 * np.array([np.sqrt(3) / 2., 1. / 2])