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 structure_factor(VW, L, n_frames=10, n_start=1,
filters=0.05, dh=0.05,save='sf',l=10):
import MD.analysis.sfactor as sf
#Find Structure Factor
A = Average(VW,L,n_start,n_frames)
#A = VW[n_start]
stmp,qx = sf.sfactor(np.array([A]),L=L[n_start],l=l)
S,Q,primitive_vectors = sf.sort_sfpeaks(stmp,qx)
fid = open('sftotal.txt','w')
fid.write('S Q\n')
for i in range(len(S)):
fid.write('%.5f %.5f\n'%(S[i],Q[i]))
fid.close()
#Plot the graph
xlabel = '$|\\vec{q}$ $|$'
ylabel = '$S(\\vec{q}$ $)$ '
#sp4 = 0.634698
#sp12 = 0.530493
#sc 1.121997
#pyplot_eps.plot_sf(Q, S,0.552381, linestyle='', marker='x',
#xlabel=xlabel, ylabel=ylabel, save=save,xlen=20)
pyplot.plot_sf(Q, S,0.552381, linestyle='', marker='x',
xlabel=xlabel, ylabel=ylabel, save=save,xlen=20)
util.pickle_dump(Q,'Vsfx%i.pkl'%n_start)
util.pickle_dump(S,'Vsfy%i.pkl'%n_start)
print 'finished reconstruction'
#if len(QQ)>500:
# bars,height = sf.sf_max(QQ,qpeaks=8)
# db_x,db_y = sf.dbfactor(msdr=5)
# pyplot.plot_bar(bars, height, xlabel=xlabel, ylabel=ylabel,
# save=save)
# pyplot.plot(db_x, db_y, linestyle='--', xlabel=xlabel, ylabel=ylabel,
# save=save)
# #return q, s, bars, height, db_x, db_y
# return Q, S, primitive_vectors
#filter out the noise
Q, S, primitive_vectors = sf.sf_filter(Q, S, primitive_vectors,
filters=filters,save=save)
import MD.analysis.reconstruct_lattice as rl
import MD.unit.make_bcc as mb
con = True
while con:
a1,a2,a3 = rl.reconstruct_lattice(Q,primitive_vectors,save+'recipricol.txt')
print a1,a2,a3
mb.make_bcc(a1,a2,a3,A[0],L[n_start])
if raw_input('Reselect? (y)/N') == 'N':
con = False
return Q, S, primitive_vectors
import os
import sys
import numpy as np
sys.path.append('/home/cdknorow/Dropbox/Software')
import MD
import MD.unit.make_bcc as make_bcc
b1 = np.array([0.0,0.0,0.0])
p1 = np.array([-5.164,12.86,5.1])
p2 = np.array([9.311,10.361,4.205])
p3 = np.array([-4.126,10.339,-9.335])
a1 = p1-b1
a2 = p2-b1
a3 = p3-b1
b1 = np.array([-6.58,-3.91,7.6])
basis = b1
count = 0
for basis in [b1]:
L = [67,67,67]
VW, VW_names = make_bcc.make_bcc(a1,a2,a3,basis,L,S=5,name='bcc_unit%i.xyz'%count)
count+=1
import pickle
output = open('bcc_unit.pkl','wb')
S=pickle.dump(VW,output)
output.close()