def find_lattice(MD,VW,L,n_finish=1,n_start=0,delta=20,filters=0.2):
# Identify the bcc lattice as a grid and find the recipricol lattice
#Find Structure Factor
#print VW.shape
redo = True
while redo == True:
stmp,qx = sf.sfactor(VW[-10:-1],L=L,l=10)
S,Q,primitive_vectors = sf.sort_sfpeaks(stmp,qx)
print np.array(Q)
Q, S, primitive_vectors = sf.sf_filter(Q, S, primitive_vectors,
filters=filters, save = 'sffilter')
a,b = MD.analysis.sfactor.recipricol(Q,primitive_vectors)
#Find the best fit for the qlattice at a particular frame by looking
#for the lowest value of the msdr
x = np.arange(n_start,n_finish,delta)
defects = np.zeros((len(x),15))
lowest=10000
for k in x:
for i in range(10):
crystal, c = make.make_bcc(a[0], a[1], a[2], VW[k][i], L[0]+5)
msdr_x = msdr.msd_r(VW[k], crystal, L)
if lowest > msdr_x:
lowest = msdr_x
index = i
frame = k
crystal, cword = make.make_bcc(a[0], a[1], a[2], VW[frame][index], L[0]+5)
print np.array(b)
print np.array(a)
if raw_input('Do you want to retry?[no]/yes ') == 'yes':
redo = True
else:
redo = False
util.pickle_dump(cword,'cword.pkl')
util.pickle_dump(crystal,'ccrystal.pkl')
#filter out the comensurate crystal
C = []
for i in crystal:
#make sure there aren't two that are close due to pbc
if rcut_neighbors_point(np.array(C),i,L,rcut=6) == 0:
C.append(i)
#write out the lattice
fid = open('testlattice.xyz','w')
fid.write(('%i\n')%(len(C)))
fid.write('Atoms\n')
for i in range(len(C)):
fid.write(('%c %f %f %f\n')%('A',C[i][0],C[i][1], C[i][2]))
fid.close()
util.pickle_dump(C,'C.pkl')
return crystal, C
def filter_lattice(C, Vshape, Wshape, L):
import random
#### find the neighbors to a point
def find_neighbors(M,point,L,rcut=17):
neighbors = []
for i in range(len(M)):
if points.dist(M[i],point,L)[0]>1:
if points.dist(M[i],point,L)[0]<rcut:
neighbors.append(M[i])
return neighbors
CB = []
CA = []
point = C[0]
CA.append([point[0],point[1],point[2]])
for i in range(len(C)):
neighbors = find_neighbors(C,point,L)
point = neighbors[random.randint(0,len(neighbors)-1)]
for i in neighbors:
CB.append([i[0],i[1],i[2]])
neighbors = find_neighbors(C,point,L)
point = neighbors[random.randint(0,len(neighbors)-1)]
for i in neighbors:
CA.append([i[0],i[1],i[2]])
CV = np.zeros((len(C)/2,3))
CW = np.zeros((len(C)/2,3))
CV += L[0]*2
CW += L[0]*2
print 'print info'
print CA[0]
print CV.shape
print len(C)
print len(CA)
print Vshape
count = 0
for i, point in enumerate(CA):
if rcut_neighbors_point(CV,point,L,rcut=6) == 0:
print count
CV[count] = point
count += 1
count = 0
for i, point in enumerate(CB):
if rcut_neighbors_point(CW,point,L,rcut=6) == 0:
CW[count] = point
count += 1
print CW.shape
print CV.shape
#write out hte lattice
fid = open('projlattice.xyz','w')
fid.write(('%i\n')%(len(C)))
fid.write('Atoms\n')
for i in range(len(CV)):
if CV[i][0] != 0:
fid.write(('%c %f %f %f\n')%('A',CV[i][0],CV[i][1], CV[i][2]))
for i in range(len(CW)):
#there is a problem with writing one to many when putting in
#interstitials
if CW[i][0] != 0:
fid.write(('%c %f %f %f\n')%('B',CW[i][0],CW[i][1], CW[i][2]))
fid.close()
util.pickle_dump(CV,'CV.pkl')
util.pickle_dump(CW,'CW.pkl')
return CV, CW