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diffusion2particle.py
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import numpy
a=[198,182,160,156,153,150,153,132,125,130,122,122,121,126,104,99,96,91,62,167]
size=a+a
noc=len(size)+1
csize=numpy.cumsum(size)
atoms=sum(size)
print "number of atoms",atoms
startPos=4001
endPos=10001+1
noOfFrame=0
timestep=0.005
chromosome=numpy.zeros((endPos-startPos,atoms+1,3),dtype=numpy.float)
for filen in range(startPos,endPos,1):
noOfFrame+=1
name='my/file'+str(filen)+'.dat'
f=open(name)
cont=f.readlines()
time=cont[1][0:-1]
#print filen, "Time", time
for i in range(5,len(cont)): ###8 check this line
l=cont[i].split()
if len(l)==6:
chromosome[filen-startPos][int(l[0])]=[float(l[3]),float(l[4]),float(l[5])]
'''
if filen==startPos:
initPos=chromosome[monomer]
initTime=float(time)
if filen>startPos:
dist=numpy.linalg.norm(chromosome[monomer]-initPos)
Dcoef = (dist**2)/( (float(time)-initTime) * timestep )
#ff.write(str(time)+'\t'+str(chromosome[monomer][0])+'\t'+str(chromosome[monomer][1])+'\t'+str(chromosome[monomer][2])+'\t'+str(Dcoef)+'\n')
'''
N=noOfFrame
print N
m1=[1013,1052,1363,1346,1013, 1052,1052,1306,1226,1306, 1306,1329,544,1005,1052, 545,610,1106,1026,25, 52,26,50,1012,1052, 870,919,870,919, 26, 52]
m2=[1052,1148,1408,1408,1148, 1106,1134,1363,1278,1329, 1405,1405,657,1052,1142, 657,657,1142,1134,180, 146,179,149,1052,1141, 972,972,965,965, 180, 149]
monomer1=[]
monomer2=[]
n=sum(a)
for i in range(len(m1)):
monomer1.append(n+m1[i])
monomer1.append(m1[i])
monomer2.append(n+m2[i])
monomer2.append(m2[i])
for mo in range(len(monomer1)):
fy=open('TAG/MSD_'+str(monomer1[mo])+'-'+str(monomer2[mo])+'.dat','w')
fx=open('TAG/displacement_'+str(monomer1[mo])+'-'+str(monomer2[mo])+'.dat','w')
for tau in range(1,300):
MSD_3D=0.0
MSD_xy=0.0
MSD_yz=0.0
MSD_zx=0.0
for i in range(N-tau):
disp_3D=numpy.linalg.norm(chromosome[i+tau][monomer1[mo]]-chromosome[i][monomer2[mo]]) ## 3D
#print chromosome[i+tau][monomer1]
disp_xy=numpy.linalg.norm(chromosome[i+tau][monomer1[mo]][[0,1]] - chromosome[i][monomer2[mo]][[0,1]])
disp_yz=numpy.linalg.norm(chromosome[i+tau][monomer1[mo]][[1,2]] - chromosome[i][monomer2[mo]][[1,2]])
disp_zx=numpy.linalg.norm(chromosome[i+tau][monomer1[mo]][[0,2]] - chromosome[i][monomer2[mo]][[0,2]])
MSD_3D+= disp_3D**2;
MSD_xy+= disp_xy**2;
MSD_yz+= disp_yz**2;
MSD_zx+= disp_zx**2;
if tau<6:
fx.write(str(tau)+'\t'+str(disp_3D)+'\t'+str(disp_xy)+'\t'+str(disp_yz)+'\t'+str(disp_zx)+'\n')
value1=MSD_3D/(N-tau)
value2=MSD_xy/(N-tau)
value3=MSD_yz/(N-tau)
value4=MSD_zx/(N-tau)
fy.write(str(tau)+'\t'+str(value1)+'\t'+str(value2)+'\t'+str(value3)+'\t'+str(value4)+'\n')
if tau%50==0:
print tau
#value/30
# MSD(i)=(norm(chromosome[i+tau][monomer]-chromosome[i][monomer]))^2; # single particle
'''
1052 - 1013 # 53 -14 # 12 - 10 # chr 7 # 153
1052 - 1148 # 53 -149 # 12 - 10 # chr 7
1363 - 1408 # 79 -124 # 12 - 10 # chr 9 # 125
1346 - 1408 # 62 -124 # 10 - 10 # chr 9
1013 - 1148 # 14 -149 # 10 - 10 # chr 7
1106 - 1052 # 107-53 # 8 - 12 # chr 7
1134 - 1052 # 135 -53 # 8 - 12 # chr 7
1306 - 1363 # 22 - 79 # 8 - 12 # chr 9
1226 - 1278 # 74 -126 # 8 - 8 # chr 8
1329 - 1306 # 45 - 22 # 8 - 8 # chr 9
1306 - 1405 # 22 - 121# 8 - 8 # chr 9
1329 - 1405 # 45 - 121# 8 - 8 # chr 9
657 - 544 # 117 - 4 # 10-8 # chr 4
965 - 972 # 116 -123 # 8-10 # chr 6
1052-1005 # 53-6 # 12-6
1052-1026 # 53-27
1052-1142 # 53-143
657-545 # 117-5 # 10-6
657-582 # 117-42
657-610 # 117-70
657-635 # 117-95
1106-1142 # 107-143 #8-6
1134-1026 # 135-27
25-180 #6-6
52-146
26-179 #1-1
50-149
1052-1012 #12-1
1052-1141
972-870 #10-1
972-919
965-870 #8-1
965-919
180-26 #6-1
52-149
'''