def run_():
dirname = os.getcwd().partition('/')[-1]
print "Starting:",dirname.split('/')[-1]
#initial file
dirname = os.getcwd().partition('/')[-1]
print "Starting:",dirname.split('/')[-1]
delta = 10
M=MD.ReadCord()
Lx = M.box_length
Ly = M.box_length_y
Lz = M.box_length_z
L = np.array([Lx, Ly, Lz])
L_cont = M.box_volume()
last = M.frames
x, xcount = util.get_box_size_steps(L_cont)
#x_set = [450,820,1240,2050,2445,2862,3268,3674,4080,
# 4486,4892,5298,5704,6110]
#x_set = [50,70,90,110,130]
#x_set = [50,70,90]
#x_set = [25, 45, 65, 90, 110, 130, 150, 170, 190, 220, 230,
# 250,270,290,310]
#x_set = [25, 45, 65, 90, 110, 130, 150]
x_set = []
n_frames = []
for i in range(len(xcount)):
if xcount[i] > 10:
x_set.append(x[i]+10)
n_frames.append(xcount[i]-10)
polymer_end_2_end(M, L_cont, x_set)
def run_():
dirname = os.getcwd().partition('/')[-1]
print "Starting:",dirname.split('/')[-1]
#initial file
dirname = os.getcwd().partition('/')[-1]
print "Starting:",dirname.split('/')[-1]
delta = 10
M=MD.ReadCord()
Lx = M.box_length
Ly = M.box_length_y
Lz = M.box_length_z
L = np.array([Lx, Ly, Lz])
L_cont = M.box_volume()
last = M.frames
x, xcount = util.get_box_size_steps(L_cont)
x_set = []
n_frames = []
for i in range(len(xcount)):
if xcount[i] > 10:
x_set.append(x[i]+10)
n_frames.append(xcount[i]-10)
print x_set
polymer_end_2_end(M, L_cont, x_set)
def run_():
#setp
dirname = os.getcwd().partition('/')[-1]
print "Starting:",dirname.split('/')[-1]
M=MD.ReadCord()
Lx = M.box_length
Ly = M.box_length_y
Lz = M.box_length_z
L = np.array([Lx, Ly, Lz])
L_cont = M.box_volume()
L_cont[-1] =L_cont[-2]
last = M.frames
new = False
try:
V = util.pickle_load('V.pkl')
if V.shape[0] != last:
print 'generating new pickle'
asdf
#Z = util.pickle_load('Z.pkl')
except:
#V=M.cord_auto(['V','W'])
new = True
V=M.cord_auto(['V'])
if V.shape[1] < 1:
V=M.cord_auto(['A','A0','A1'])
#Z=M.cord_auto(['Z'])
#VW_index=M.get_names(['V','W'])
#Z_index=M.get_names(['Z'])
#V = drift_remove(V,L,VW_index)
#Z = drift_remove(Z,L,Z_index)
#dump_xyz(V)
#dump_xyz(Z)
util.pickle_dump(V,'V.pkl')
#util.pickle_dump(Z,'Z.pkl')
# if (os.path.isfile('msd.pkl') is False):
# msd(V,L)
print V
asdf
x, xcount = util.get_box_size_steps(L_cont)
print x
x_set = []
n_frames = []
print xcount
print x
#F = filter(lambda x: x > 10, xcount)
for i in range(len(xcount)):
if xcount[i] > 10:
x_set.append(x[i])
n_frames.append(xcount[i]-10)
print n_frames
print x_set
f = h5py.File('../pmf_dist.hdf5','w')
for j,i in enumerate(x_set):
if i + n_frames[j] <= V.shape[0]:
if L_cont[i] == L_cont[i+n_frames[j]]:
print "L = ",L_cont[i][0]
print "rho = ",V.shape[1]/L_cont[i][0]**3
print "frame = ", i
print "n_frame", n_frames[j]
PMF(f, V,L_cont[i],n_start=i,n_frames=n_frames[j])
else:
print "L is not the same reduce the n_frames"
f.close()