def crystal_jump(VW,surface,L,time,delta):
#skip = VW.shape[0]/len(surface)
skip = 1
jump_t = []
jump_d = []
lfilter = 10
for i in range(len(surface[0])):
for k in range(time,time+delta):
if surface[k][i] == 1:
if surface[k-1][i] == 0:
count_before = 0
count_after = 0
for j in range(lfilter):
count_after += surface[k+j][i]
for j in range(lfilter):
count_before += surface[k-j][i]
if (count_before <=2) and (count_after >=8):
spheres = np.zeros((50,1,3))
for f in range(k-50,k):
spheres[f-k] = VW[f*skip][i]
x, MSD = msd_no_drift(spheres,L)
jump_d.append(MSD[-1])
break
print 'number of counts',len(jump_d)
return jump_d
def index_msd(VW,index,L,t,save='msd_index'):
#skip = VW.shape[0]/len(surface)
skip = 1
spheres = np.zeros((t,len(index),3))
for f in range(t):
for i,j in enumerate(index):
spheres[f][i] = VW[f*skip][j]
x, MSD = msd_no_drift(spheres,L)
pyplot_eps.plot(x,MSD,xlabel='t',ylabel=r'$\sqrt{<(r(t)-r(0))^2>}$',save=save)
return x,MSDj
def crystal_msd(VW,surface,L):
#skip = VW.shape[0]/len(surface)
skip = 1
index = []
for i in range(len(surface[0])):
count = 0
for t in range(15):
count += surface[t][i]
if count >= 11:
index.append(i)
spheres = np.zeros((len(surface),len(index),3))
for f in range(len(surface)):
for i in range(len(index)):
spheres[f][i] = VW[f*skip][index[i]]
x, MSD = msd_no_drift(spheres,L)
pyplot.plot(x,MSD,xlabel='time',ylabel='msd cn',save='msd_critical')
def crystal_movement(VW,surface,L):
skip = VW.shape[0]/len(surface)
msd = []
for i in range(10,len(surface[0])):
print i
for k in range(len(surface)):
if surface[k][i] == 1:
count = 0
if surface[k-1][i] == 0:
if k+count >= len(surface)-5:
still_surface = False
else:
still_surface = True
while still_surface == True:
if surface[k+count][i]:
count += 1
elif surface[k+count+1][i]:
count += 2
elif surface[k+count+2][i]:
count += 3
elif surface[k+count+3][i]:
count += 4
else:
still_surface = False
if k+count >= len(surface)-5:
still_surface = False
#find the displacment of the particle from k to count
start = (k-count)*skip
finish = k*skip
if finish - start <=1:
finish += 1
spheres = np.zeros((finish-start,1,3))
for f in range(finish-start):
spheres[f] = VW[f*skip+k*skip][i]
x, MSD = msd_no_drift(spheres,L)
msd.append([MSD,k])
k = k+count
frame = np.zeros((len(surface),1))
MSD = np.zeros((len(surface),1))
for i in msd:
for j in range(len(i[0])):
frame[i[1]+j] += 1
MSD[i[1]+j] += i[0][j]
for i in range(MSD.shape[0]):
MSD[i] = MSD[i] / frame[i]
print MSD
return MSD
def msd(VW,L,step=1,save='MSD_time',time_scale=1):
from MD.analysis.msd import msd_no_drift #Find the msd of the system x,msd=msd_no_drift(VW,L,step=step)
D=0.1
D2=0.03
tau=10
try:
M = util.pickle_load('msd.pkl')
x = M[0][0]
msd = M[1][0]
except:
x, msd = msd_no_drift(VW,L)
x = x*time_scale
util.pickle_dump([[x],[msd]],'msd.pkl')
#msd_fit
fit = []
for i in x:
fit.append((2*3*D2*(i) - tau*(1-math.e**(-i/tau)))**0.5)
msd2 = (6*D*x)**0.5
pyplot.plot(x,msd,xlabel='Time',ylabel='msd',save=save)
