def connected_angles(VW,Z,L,connections, N_nodes, vertex_points=1, cut = 5):
Cube = [[[] for j in range(N_nodes[0])] for l in range(len(connections))]
for k,i in enumerate(connections):
for j in i:
#find the two connections
#we need to + Adivide by the number of sites to get the right
#major particle index
A=j[0]
B=j[1]+N_nodes[0]
Cube[k][A].append(B)
counter = np.zeros((len(Cube),4))
for k in range(len(Cube)):
count_face = 0
count_all = 0
count_face_less = 0
count_all_less = 0
for i in range(len(Cube[k])):
for j in points.unique(Cube[k][i]):
if Cube[k][i].count(j)>=cut:
count_all += 1
if angle.face_check(VW,Z,k,i,j,1,1,L):
count_face += 1
else:
count_all_less += 1
if angle.face_check(VW,Z,k,i,j,1,1,L):
count_face_less += 1
counter[k] = [count_face,count_all,count_face_less,count_all_less]
print 'finished counting'
return counter
def sides_faces_mod(VW,Z,L,connections, N_nodes, vertex_points=1, cut = 5):
A_points = vertex_points[0]*N_nodes[0]
Cube = [[[] for j in range(sum(N_nodes))] for l in range(len(connections))]
for k,i in enumerate(connections):
for j in i:
#find the two connections
#we need to + Adivide by the number of sites to get the right
#major particle index
A=j[0]
B=j[1]+N_nodes[0]
#This provides the position of sides which are connected
Cube[k][A].append(B)
#add the connections to a list
counter = np.zeros((len(Cube),3))
for k in range(len(Cube)):
count_face = 0
count_all = 0
for j in range(len(Cube[k])):
if len(Cube[k][j]) in cut:
for N in points.unique(Cube[k][j]):
count_all += 1
a = angle.face_check(VW,Z,k,j,N,L)
if a+b==2:
count_face += 1
if count_all == 0:
counter[k] = [ 0,0,0]
else:
counter[k] = [count_face,count_all,count_face/float(count_all)]
print 'finished counting'
return counter
def nearpart_remove():
#print out directory
fid = open('dna_2nuc.xyz','r')
N_atoms = fid.readline()
fid.readline()
M = fid.readlines()
V = []
count = 0
NP_center = []
#NP_center = index of center of particle
#V = numpy array of all particle positions
#index = "name of particle at each index'
index = []
for line in M:
index.append(line.split()[0])
V.append([float(line.split()[1]),float(line.split()[2]),float(line.split()[3])])
if line.split()[0] == 'V' or line.split()[0] == 'W':
NP_center.append(count)
count += 1
fid.close()
V = np.array(V)
Lx = 220
Ly = 110
Lz = 110
L = np.array([Lx, Ly, Lz])
print L
#the center of the partilcl
too_close = []
print NP_center
C = NP_center[0]
NP_size = NP_center[1] - NP_center[0]
for i in NP_center:
print i/NP_size
for j in NP_center:
if i != j:
if points.dist(V[i],V[j],L)[0]<12:
too_close.append([min(i,j),max(i,j)])
too_close = points.unique(too_close)
remove = []
for i in too_close:
remove.append(i[0])
#remove the NP which are too_close!
#to do and write the new dna.xyz file
print 'writing dna.xyz'
out = open('dna_close_remove.xyz','w')
out.write(('%i\n\n')%(V.shape[0]))
count = 0
for i in range(V.shape[0]):
if i in remove:
i+=1
if count>=V.shape[0]-1:
print 'breaking'
break
for j in range(NP_size):
count = i * NP_size + j
out.write(('%s %.2f %.2f %.2f\n')%(index[count],V[count][0],V[count][1],V[count][2]))
def search(connected,A,B):
add=False
for i in range(len(connected)):
#is it in there already
if connected[i].count(A)==1:
if connected[i].count(B)==0:
connected[i].append(B)
if connected[i].count(B)==1:
if connected[i].count(A)==0:
connected[i].append(A)
#look through connectd if there is an intersection, take the union and
#delete what was there
for i in range(len(connected)):
for j in range(len(connected)):
if intersection(connected[i],connected[j])!=[]:
connected[i]=union(connected[i],connected[j])
connected[j]=connected[i]
#Removed any doubles
connected=unique(connected)
return connected
def find_defects_mod(CV,CW,VW,V,W,L,n_finish=1,n_start=0,delta=20,filters=0.2):
from MD.analysis.nearest_neighbor import ws_neighbors_point
from MD.analysis.nearest_neighbor import close_neighbors_point
#######
debug = False
x = np.arange(n_start,n_finish,delta)
lattice = []
for i in range(CV.shape[0]):
lattice.append(int(points.dist(CV[0],CV[i],L)[0]))
for i in range(CW.shape[0]):
lattice.append(int(points.dist(CV[0],CW[i],L)[0]))
points.unique(lattice)
lattice.sort()
print lattice
rmin = lattice[1] / 2.0
rmax = lattice[2] / 2.0 +1
#for interstitial
s = min(W.shape[1],V.shape[1])
#for vacancy
#s = max(W.shape[1],V.shape[1])
DW = np.zeros((len(x),CW.shape[0]))
DV = np.zeros((len(x),CV.shape[0]))
vac_count = np.zeros((len(x),1))
int_count = np.zeros((len(x),1))
fid = open('defects.txt','w')
master = [[],[]]
particle_frame = []
for index,k in enumerate(x):
print 'frame',k
# Identify the points on the bcc Lattice which belong to A and B type
#lets look at one point first
# Assign each point to its place on the lattice
#find the closest point
#####################
N = []
N_V = []
N_W = []
Vn = []
Wn = []
for i in V[k]:
if abs(i[0]) < L[0]:
Vn.append(i)
for i in W[k]:
if abs(i[0]) < L[0]:
Wn.append(i)
print 'Wn',len(Wn)
print 'Vn',len(Vn)
particle_frame.append(len(Wn)+len(Vn))
Wn = np.array(Wn)
Vn = np.array(Vn)
for i in range(CV.shape[0]):
N = ws_neighbors_point(Vn,CV[i],L,i,rmin=rmin,rmax=rmax)[0]
N_V.extend(N)
num = len(N)
if num == 0:
N2 = ws_neighbors_point(Wn,CV[i],L,i,rmin=rmin,rmax=rmax)[0]
N_W.extend(N2)
num = -len(N2)
DV[index][i] = num
###########################
for i in range(CW.shape[0]):
N = ws_neighbors_point(Wn,CW[i],L,i+W.shape[1],rmin=rmin,rmax=rmax)[0]
N_W.extend(N)
num = len(N)
if num == 0:
N2 = ws_neighbors_point(Vn,CW[i],L,i+V.shape[1],rmin=rmin,rmax=rmax)[0]
N_V.extend(N2)
num = -len(N2)
DW[index][i] = num
#find the atoms that haven't been placed on the lattice yet
IV = points.difference(range(Vn.shape[0]),N_V)
IW = points.difference(range(Wn.shape[0]),N_W)
##
if debug:
print 'atoms not added listed after first sorting'
print IV, IW
print DW[index]
print DV[index]
for i in IV:
#find closest lattice point
nw, dw = close_neighbors_point(CW,Vn[i],L)
nv, dv = close_neighbors_point(CV,Vn[i],L)
if dw <= dv:
#check to see if there is already an atom at that point
if DW[index][nw] == 1 or DW[index][nw] == -1:
if DV[index][nv] == 0:
DV[index][nv] = 1
N_V.extend([i])
else:
DW[index][nw] = -2
N_V.extend([i])
if DW[index][nw] == 0:
DW[index][nw] = -1
N_V.extend([i])
#check to see if there is already an atom at that point
else:
if DV[index][nv] == 1 or DV[index][nv] == -1:
#if there isn't one at the other point add it
if DW[index][nw] == 0:
DW[index][nw] = -1
N_V.extend([i])
else:
if DV[index][nv] == 1:
DV[index][nv] = 2
if DV[index][nv] == -1:
DV[index][nv] = -2
N_V.extend([i])
if DV[index][nv] == 0:
DV[index][nv] = 1
N_V.extend([i])
for i in IW:
nw, dw = close_neighbors_point(CW,Wn[i],L)
nv, dv = close_neighbors_point(CV,Wn[i],L)
if dv <= dw:
if DV[index][nv] == 1 or DV[index][nv] == -1:
if DW[index][nw] == 0:
DW[index][nw] = 1
N_W.extend([i])
else:
DV[index][nv] = -2
N_W.extend([i])
if DV[index][nv] == 0:
DV[index][nv] = -1
N_W.extend([i])
else:
if DW[index][nw] == 1 or DW[index][nw] == -1:
if DV[index][nv] == 0:
DV[index][nv] = -1
N_W.extend([i])
else:
DW[index][nw] = 2
N_W.extend([i])
if DW[index][nw] == 0:
DW[index][nw] = 1
N_W.extend([i])
#find the atoms that haven't been placed on the lattice yet
IV = points.difference(range(Vn.shape[0]),N_V)
IW = points.difference(range(Wn.shape[0]),N_W)
##
if debug:
print 'atoms not added list for debugging'
print IV, IW
print DW[index]
print DV[index]
print 'Defect list for lattice'
#print out the vacency, substitutions
def out_defect(A, index, fid, def_list, C=0):
for i in range(A.shape[1]):
if A[index][i] == 0:
pr = 'vacecy at '+ str(i+C)+ '\n'
try:
def_list[0].extend(i+C)
except:
def_list[0].append(i+C)
if debug:
print pr
fid.write(pr)
if A[index][i] == -1:
pr = 'substitution ' + str(i+C)+ '\n'
if debug:
print pr
fid.write(pr)
if A[index][i] == -2:
pr = 'interstitial ' + str(i + C)+ '\n'
try:
def_list[1].extend(i+C)
except:
def_list[1].append(i+C)
if debug:
print pr
fid.write(pr)
if A[index][i] == 2:
pr = 'interstitial ' + str(i + C)+ '\n'
try:
def_list[1].extend(i+C)
except:
def_list[1].append(i+C)
if debug:
print pr
fid.write(pr)
frame = 'Frame ' + str(k) + '\n'
fid.write(frame)
def_list = [[],[]]
out_defect(DV, index, fid, def_list)
out_defect(DW, index, fid, def_list, C = DV.shape[1])
if len(points.difference(def_list[0], master[0])) != 0:
vac_count[index] += len(points.difference(def_list[1],master[1]))
master[0] = def_list[0]
if len(points.difference(def_list[1],master[1])) != 0:
int_count[index] += len(points.difference(def_list[1],master[1]))
master[1] = def_list[1]
#find the atoms that haven't been placed on the lattice yet
IV = points.difference(range(V.shape[1]),N_V)
IW = points.difference(range(W.shape[1]),N_W)
# Identify the defects surrounding each point
#The total number of frames we are going to look at
# Find the number of defects in each frame
count = 0
substitutions = []
vacancies = []
intersticial = []
def count_def(A,check):
count = 0
for i in A:
if i == check:
count +=1
return count
def count_ldef(A,check):
count = 0
for i in A:
if i < check:
count +=1
return count
def count_adef(A,check):
count = 0
for i in A:
if abs(i) == check:
count +=1
return count
for k in range(DW.shape[0]):
#find the points that are nearest neighbor that are different
substitutions.append(count_ldef(DW[k],0)+count_ldef(DV[k],0))
vacancies.append(count_def(DW[k],0)+count_def(DV[k],0))
intersticial.append(count_adef(DW[k],2.0)+count_adef(DV[k],2.0))
print 'substitions'
print substitutions
print 'vacancies'
print vacancies
print 'interstitials'
print intersticial
util.pickle_dump(DV,'DV_s.pkl')
util.pickle_dump(DW,'DW_s.pkl')
util.pickle_dump([substitutions, vacancies, intersticial, x],'plot_def_s.pkl')
pyplot.plot3(x, substitutions, x, particle_frame, x, intersticial,
label1='substitutions',label2='number of particles',label3='intersticial',
save='defects_per_frame_surface',showleg=True)
#pyplot.plot(x, vac_count, save='defect_vac_diffusion_count')
#pyplot.plot(x, int_count, save='defect_int_diffusion_count')
return DV, DW, [substitutions, vacancies, intersticial, x]
