def diffusion(M,Z,L,index=0,t0=0,tfinal=1):
theta = []
v1 = []
sides = Z.shape[1]/M.shape[1]
for i in range(t0,tfinal):
v1.append(points.unit(points.vector1d(M[i][index],Z[i][index*sides],L[i])))
for i in range(tfinal-t0):
theta.append(np.dot(v1[0],v1[i]))
return theta
fid.readline()
fid.readline()
for line in fid.readlines():
if line.split()[0] == 'R':
x = float(line.split()[1])
y = float(line.split()[2])
z = float(line.split()[3])
positions.append([x,y,z])
fid.close()
#Transform
L = np.array([50,50,50])
w = np.array([[1,0,0],[0,1,0],[0,0,1]])
V = np.array([0,0,0])
x_r = points.unit(np.array(orientations[1]))
y_r = points.unit(np.array(orientations[2]))
z_r = points.unit(np.array(orientations[3]))
v = np.array([x_r,y_r,z_r])
print points
R = points.reference_rotation(w,v)
location = []
for i in range(len(P)):
d = points.dist(V,P[i],L)[0]
c_r = points.unit(points.vector1d(V,P[i],L))
location.append(points.unit(np.dot(R,np.transpose(c_r)))*d)
#write out
positions.extend([0,0,0])
fid.open('cube_unit_cell.xyz','w')
fid.write('%i \n\n'%(len(positions)*len(location)))
def cube_vectors(V,E,L):
vec = []
for i in E:
vec.append(points.unit(points.vector1d(V,i,L)))
return vec
def old_cubatic_order(M,Z,L,select=0):
#Choose references cube
ref = M[0][select]
us = points.unit(points.vector1d(ref,Z[0][select*6],L))
ws = points.unit(points.vector1d(ref,Z[0][select*6+1],L))
vs = points.unit(points.vector1d(ref,Z[0][select*6+4],L))
####################################################
#Create u,w,v based on best alignment with reference cube
u = []
v = []
w = []
for k in range(M.shape[0]):
for i in range(M.shape[1]):
if i != select:
vc = cube_vectors(M[k][i],Z[k][i*6:i*6+6],L)
usmall = 0
vsmall = 0
wsmall = 0
for j in range(1,len(vc)):
if points.angle_between(us,vc[j])<=points.angle_between(us,vc[usmall]):
usmall = j
if points.angle_between(ws,vc[j])<=points.angle_between(ws,vc[wsmall]):
wsmall = j
if points.angle_between(vs,vc[j])<=points.angle_between(vs,vc[vsmall]):
vsmall = j
u.append(vc[usmall])
v.append(vc[vsmall])
w.append(vc[wsmall])
else:
u.append(ws)
v.append(us)
w.append(vs)
#Find Ordering Tesnors
Quu = np.zeros((3,3))
Qww = np.zeros((3,3))
Qvv = np.zeros((3,3))
for N in range(len(u)):
for i in range(3):
for j in range(3):
Quu[i,j] += 3. * u[N][i]*u[N][j] - delta(i,j)
Qvv[i,j] += 3. * v[N][i]*v[N][j] - delta(i,j)
Qww[i,j] += 3. * w[N][i]*w[N][j] - delta(i,j)
Quu = Quu / (2.*len(u))
Qvv = Qvv / (2.*len(v))
Qww = Qww / (2.*len(w))
#Find eigenvalues
e_w = np.linalg.eig(Qww)
e_u = np.linalg.eig(Quu)
e_v = np.linalg.eig(Qvv)
#Identify Laboratory Z,Y and X axis
#print e_w,'\n',e_u,'\n',e_v
def find_max(e):
evalue = e[0][0]
index = 0
if e[0][1] > evalue:
evalue = e[0][1]
index = 1
if e[0][2] > evalue:
evalue = e[0][2]
index = 2
return evalue, index
#get index of eigenvector and evalue
e_plus_v = find_max(e_v)
e_plus_u = find_max(e_u)
e_plus_w = find_max(e_w)
#find Z
s = []
if e_plus_v[0] == max(e_plus_v[0],e_plus_u[0],e_plus_w[0]):
z = e_v[1][e_plus_v[1]]
Qz = Qvv
s.append(0)
if e_plus_v[0] == min(e_plus_v[0],e_plus_u[0],e_plus_w[0]):
x = e_v[1][e_plus_v[1]]
Qx = Qvv
s.append(0)
if e_plus_u[0] == max(e_plus_v[0],e_plus_u[0],e_plus_w[0]):
z = e_u[1][e_plus_u[1]]
Qz = Quu
s.append(1)
if e_plus_u[0] == min(e_plus_v[0],e_plus_u[0],e_plus_w[0]):
x = e_u[1][e_plus_u[1]]
Qx = Quu
s.append(1)
if e_plus_w[0] == max(e_plus_v[0],e_plus_u[0],e_plus_w[0]):
z = e_w[1][e_plus_w[1]]
Qz = Qww
s.append(2)
if e_plus_w[0] == min(e_plus_v[0],e_plus_u[0],e_plus_w[0]):
x = e_w[1][e_plus_w[1]]
Qx = Qww
s.append(2)
if len(s) != 2:
print 'error too Qx and Qz were not selected properly'
asdfasdf
if 0 not in s:
y = e_v[1][e_plus_v[1]]
Qy = Qvv
s.append(0)
if 1 not in s:
y = e_u[1][e_plus_u[1]]
Qy = Quu
s.append(1)
if 2 not in s:
y = e_w[1][e_plus_w[1]]
Qy = Qww
s.append(2)
x = np.cross(z,y)
#print 'angles between Laboratory'
print points.angle_between(z,y)
#Find Q22 and Q00
Q00 = np.dot(np.dot(z,Qz),z)
#Q00 = (np.dot(np.dot(z,Qz),z)+np.dot(np.dot(y,Qy),y)+np.dot(np.dot(x,Qx),x))/3.
Q22 = (np.dot(np.dot(x,Qx),x) + np.dot(np.dot(y,Qy),y) -
np.dot(np.dot(x,Qy),x) - np.dot(np.dot(y,Qx),y))/3.
return Q00, Q22
def ssDNA_gauss(M,VW, Z,L, frames, rcut=1.0, step=5e4):
try:
#V = util.pickle_load('V.pkl')
P = util.pickle_load('SSDNA.pkl')
except:
P = M.cord_auto(['K','T'])
util.pickle_dump(P,'SSDNA.pkl')
gauss_map = []
w = np.array([[1,0,0],[0,1,0],[0,0,1]])
ndna = P.shape[1]/VW.shape[1]
print P.shape
for k in frames:
location = []
print k
try:
for i in range(VW.shape[1]):
#we must rotate about a specific cube reference frame
if i in range(20):
V = VW[k][i]
x_r = points.unit(points.vector1d(V,Z[k][i*6+1],L[k]))
y_r = points.unit(points.vector1d(V,Z[k][i*6+2],L[k]))
z_r = points.unit(points.vector1d(V,Z[k][i*6+5],L[k]))
dd = points.dist(V,Z[k][i*6+5],L[k])[0]
v = np.array([x_r,y_r,z_r])
R = points.reference_rotation(v,w)
for j in range(ndna):
d = points.dist(V,P[k][j+i*ndna],L[k])[0]
c_r = points.unit(points.vector1d(V,P[k][j+i*ndna],L[k]))
location.append(points.unit(np.dot(R,np.transpose(c_r)))*d)
except:
print 'something went wrong here'
gauss_map.append(location)
#########
fid = open('gaussmap_dna.xyz','w')
max_gauss = 0
for k in gauss_map:
if len(k) > max_gauss:
max_gauss = len(k)
for k in range(len(gauss_map)):
fid.write('%i\n%i\n'%(max_gauss+4,frames[k]))
fid.write('E %.2f 0 0\n'%dd)
fid.write('E 0 %.2f 0\n'%dd)
fid.write('E 0 0 %.2f\n'%dd)
fid.write('V 0 0 0\n')
for i in gauss_map[k]:
fid.write('N %.3f %.3f %.3f\n'%(i[0],i[1],i[2]))
for i in range(max_gauss - len(gauss_map[k])):
fid.write('N 0 0 0\n')
fid.close()
###########
fid = open('gaussmap_dna_step.xyz','w')
max_gauss = 0
step = 10
for k in gauss_map:
if len(k) > max_gauss:
max_gauss = len(k)
max_gauss = max_gauss*step
for s in range(0,len(gauss_map)-step,step):
fid.write('%i\n\n'%(max_gauss+4))
fid.write('E 1 0 0\n')
fid.write('E 0 1 0\n')
fid.write('E 0 0 1\n')
fid.write('V 0 0 0\n')
count = 4
for k in range(s,s+step):
for i in gauss_map[k]:
fid.write('N %.3f %.3f %.3f\n'%(i[0],i[1],i[2]))
count+=1
for i in range(max_gauss+4 - count):
fid.write('N 0 0 0\n')
fid.close()
def polymer_gauss(M,VW, Z,L, frames, rcut=1.0, step=5e4):
#\brief find the gauss map of polymers surrounding NC
try:
#V = util.pickle_load('V.pkl')
P = util.pickle_load('M.pkl')
except:
P = M.cord_auto(['M'])
util.pickle_dump(P,'M.pkl')
A = VW.shape[1]/2
gauss_map = []
w = np.array([[1,0,0],[0,1,0],[0,0,1]])
ndna = P.shape[1]/VW.shape[1]
print P.shape
for k in frames:
location = []
print k
try:
for i in range(VW.shape[1]):
#we must rotate about a specific cube reference frame
if i in range(1):
V = VW[k][i]
x_r = points.unit(points.vector1d(V,Z[k][i*6+1],L[k]))
y_r = points.unit(points.vector1d(V,Z[k][i*6+2],L[k]))
z_r = points.unit(points.vector1d(V,Z[k][i*6+5],L[k]))
v = np.array([x_r,y_r,z_r])
R = points.reference_rotation(v,w)
for j in range(1,ndna,2):
d = points.dist(V,P[k][j+i*ndna],L[k])[0]
c_r = points.unit(points.vector1d(V,P[k][j+i*ndna],L[k]))
location.append(points.unit(np.dot(R,np.transpose(c_r)))*d)
except:
print 'something went wrong here'
gauss_map.append(location)
#########
#fid = open('gaussmap_polymer.xyz','w')
#max_gauss = 0
#for k in gauss_map:
# if len(k) > max_gauss:
# max_gauss = len(k)
#for k in range(len(gauss_map)):
# fid.write('%i\n%i\n'%(max_gauss+4,frames[k]))
# fid.write('E 1 0 0\n')
# fid.write('E 0 1 0\n')
# fid.write('E 0 0 1\n')
# fid.write('V 0 0 0\n')
# for i in gauss_map[k]:
# fid.write('N %.3f %.3f %.3f\n'%(i[0],i[1],i[2]))
# for i in range(max_gauss - len(gauss_map[k])):
# fid.write('N 0 0 0\n')
#fid.close()
###########
fid = open('gaussmap_polymers_total.xyz','w')
max_gauss = 0
for k in gauss_map:
if len(k) > max_gauss:
max_gauss = len(k)
max_gauss = max_gauss*len(gauss_map)
fid.write('%i\n\n'%(max_gauss+4))
fid.write('E 1 0 0\n')
fid.write('E 0 1 0\n')
fid.write('E 0 0 1\n')
fid.write('V 0 0 0\n')
count = 4
for k in range(len(gauss_map)):
for i in gauss_map[k]:
fid.write('N %.3f %.3f %.3f\n'%(i[0],i[1],i[2]))
count+=1
fid.close()
