# try :
# A0 = get_A0(i, c)
# except:
# break
#
# full, = plt.plot(fabs(A0), 0.5, 'ko', fillstyle='none', markersize=12, label='all')
#
print 'Eprimes'
Ds, As = [], []
for c, dimers in dimer_dict.items():
s = ReadStruct('../crystal_files/INPUT_'+c)
for dimer in dimers:
#at_x = s.atoms[dimer-1]
nbs = neighbours_from_file(dimer, c)
print c, dimer, len([n for n in nbs if (n.length < 2.5 and n.atom_type=='Si')])
nb2 = [n.length for n in nbs if (n.length < 2.5 and n.atom_type=='Si')]
print nb2
#d = sum(nb2)/len(nb2)
d = max(nb2)
Ds.append(d)
for nb in nbs:
print ' ', nb.atom_type, nb.length
A0 = get_A0(dimer, c)
As.append(fabs(A0))
#epr ,= plt.plot(fabs(A0), 0.5, 'yo', markersize=12, label="$E'$")
print Ds, As
for i, nm in enumerate(nms):
s = ReadStruct('../../crystal_files/INPUT_'+nm)
o = lambda k : k - offsets[nm]['VBM']
fig[i].axvspan(-1, 0, facecolor='0.85', linewidth=0)
fig[i].axvspan(offsets[nm]['CBM']-offsets[nm]['VBM'], 3, facecolor='0.85', linewidth=0)
E, up, down = get_at_pdos(nm, 3, total=True)
fig[i].plot(o(E), up, '-', color='slateblue', linewidth=3)
fig[i].plot(o(E), down, '-', color='slateblue', linewidth=3)
p1, p2 = np.zeros(600), np.zeros(600)
for ii, at in enumerate(s.atoms):
nbs = neighbours_from_file(ii+1, nm)
nbs = [nb for nb in nbs if (nb.atom_type == 'Hf' and nb.length < 3.)]
if at.species == 'Si' and nbs:
print [(nb.atom_type, nb.length) for nb in nbs]
_, u, d = get_at_pdos(nm, ii+1)
p1 += u
p2 += d
fig[i].plot(o(E), p1, '-', color='#66FFCC', linewidth=3)
fig[i].plot(o(E), p2, '-', color='#66FFCC', linewidth=3)
print 'Done plotting!'
plt.subplots_adjust(hspace=0)
plt.gcf().set_size_inches(20., 4*3.5)
plt.xlabel('Energy [eV]', fontweight='bold', fontsize=25)
# A0 = get_A0(i, c)
# except:
# break
#
# full, = plt.plot(fabs(A0), 0.5, 'ko', fillstyle='none', markersize=12, label='all')
#
print 'Eprimes'
Ds, As = [], []
for c, eprimes in eprime_dict.items():
s = ReadStruct('../crystal_files/INPUT_'+c)
for eprime in eprimes:
at_x = s.atoms[eprime-1]
nbs = neighbours_from_file(eprime, c)
print c, eprime
Ds.append((nbs[0].length + nbs[1].length + nbs[2].length)/3)
for nb in nbs:
print ' ', nb.atom_type, nb.length
A0 = get_A0(eprime, c)
As.append(fabs(A0))
#epr ,= plt.plot(fabs(A0), 0.5, 'yo', markersize=12, label="$E'$")
plt.scatter(Ds, As, edgecolor='0.1', linewidths=2, s=100, facecolor='none')
plt.gca().xaxis.set_minor_locator(MultipleLocator(5))
plt.gca().yaxis.set_tick_params(which='major', length=10, width=2)
#nms = ['hfo2si_c1']
nms = ['hfo2si_c1', 'hfo2si_c1ox', 'hfo2si_c2ox', 'hfo2si_c3ox']
a = np.zeros(12, dtype=int)
r=3.0
for nm in nms:
s = ReadStruct('../../crystal_files/INPUT_'+nm)
it = (i+1 for i in range(len(s)))
for at in it:
if s.atoms[at-1].species == 'Hf':
nbs = neighbours_from_file(at, nm)
#nbs = [nb for nb in nbs if (nb.length < 2.5 and nb.atom_type == 'O')]
nbs = [nb for nb in nbs if (nb.length < r and nb.atom_type == 'O')]
a[len(nbs)] +=1
print a
a = a*100/float(sum(a))
print a
# bulk amorphous
b = np.zeros(12, dtype=int)
s = ReadStruct('../../crystal_files/INPUT_aHfO2')
it = (i+1 for i in range(len(s)))