def average_position_simple(M):
A = np.zeros((M.shape[1],3))
for i in range(M.shape[1]):
count = 1
p = np.array([0.0,0.0,0.0])
p += M[0][i]
for j in range(1,M.shape[0]):
if points.dist_np(M[0][i],M[j][i])[0] < 5:
p += M[j][i]
count += 1
p = p/count
A[i] = p
return A
def msd(A,L,step=1):
#find the drift
print A.shape
Drift = drift_position(A,L)[0]
#find msd
num = A[0].shape[0]
print num
frames=A.shape[0]
print "Calculating MSD"
MSD=np.zeros((frames-1))
B = np.zeros((num,3))
for k in range(frames-1):
r_sum=0
for i in range(num):
B[i] = boundary_cross(A[k][i], A[k+1][i], L, B[i])
d = points.dist_np(A[0][i][0:3] + Drift[k], A[k+1][i][0:3] - B[i] * L)
r_sum = d[0]**2 / num + r_sum
MSD[k] = r_sum
x = np.arange(0, A.shape[0] * step - step, step)
return x,MSD
def write_qmap_xyz(VW,Q6,Q4,frame,rcut):
# counter bcc, hcp, fcc, mrco, liqid
counter = [0,0,0,0,0]
fid = open('%s.q6q4.xyz'%frame,'w')
bcc_cut = .055
bcc = np.array([.475,.03 ])
hcp_cut = .035
hcp = np.array([.475,.1 ])
fcc_cut = .075
fcc = np.array([.5,.17 ])
Liq_cut = .1
Liq = np.array([.2,.04])
C = np.array([200,200,200])
fid.write('%i\n\n'%(5*len(VW)))
Qx = [[] for n in range(5)]
Qy = [[] for n in range(5)]
for j in range(len(VW)):
w = [False for n in range(5)]
#bcc
if points.dist_np(bcc,np.array([Q6[j],Q4[j]]))[0] < bcc_cut:
w[0] = True
counter[0] = counter[0] + 1
#hcp
elif points.dist_np(hcp,np.array([Q6[j],Q4[j]]))[0] < hcp_cut:
w[1] = True
counter[1] = counter[1] + 1
#fcc
elif points.dist_np(fcc,np.array([Q6[j],Q4[j]]))[0] < fcc_cut:
w[2] = True
counter[2] = counter[2] + 1
#liq
elif points.dist_np(Liq,np.array([Q6[j],Q4[j]]))[0] < Liq_cut:
w[3] = True
counter[3] = counter[3] + 1
#Interface
else:
w[4] = True
counter[4] = counter[4] + 1
if w[0] == True:
fid.write(('B %.4f %.4f %.4f\n'%(VW[j][0],
VW[j][1],VW[j][2])))
Qx[0].append(Q4[j])
Qy[0].append(Q6[j])
else:
fid.write(('B %.4f %.4f %.4f\n'%(C[0],C[1],C[2])))
if w[1] == True:
fid.write(('H %.4f %.4f %.4f\n'%(VW[j][0],
VW[j][1],VW[j][2])))
Qx[1].append(Q4[j])
Qy[1].append(Q6[j])
else:
fid.write(('H %.4f %.4f %.4f\n'%(C[0],C[1],C[2])))
if w[2] == True:
fid.write(('F %.4f %.4f %.4f\n'%(VW[j][0],
VW[j][1],VW[j][2])))
Qx[2].append(Q4[j])
Qy[2].append(Q6[j])
else:
fid.write(('F %.4f %.4f %.4f\n'%(C[0],C[1],C[2])))
if w[3] == True:
fid.write(('L %.4f %.4f %.4f\n'%(VW[j][0],
VW[j][1],VW[j][2])))
Qx[3].append(Q4[j])
Qy[3].append(Q6[j])
else:
fid.write(('L %.4f %.4f %.4f\n'%(C[0],C[1],C[2])))
if w[4] == True:
fid.write(('I %.4f %.4f %.4f\n'%(VW[j][0],
VW[j][1],VW[j][2])))
Qx[4].append(Q4[j])
Qy[4].append(Q6[j])
else:
fid.write(('I %.4f %.4f %.4f\n'%(C[0],C[1],C[2])))
xlabel = 'q4_avg'
ylabel = 'q6_avg'
Label = ['bcc','hcp','fcc','liq','int']
#pyplot.plot_multi(Qx,Qy,Label,
# xlabel=xlabel,ylabel=ylabel,save=('Qmap_frame%i_rcut%.2f'%(frame,rcut)),
# limx=(0,.2),limy=(0,.6),make_marker=True)
fid.close()
return counter, [Qx,Qy]
