for nb in nbs:
print ' ', nb
vec = np.array([nb.at.x, nb.at.y, nb.at.z]) - np.array([at_x.x, at_x.y, at_x.z])
#print vec, ln.norm(vec)
vecs.append(vec)
val = []
for i, j in (0,1), (1,2), (0,2):
#print vecs[i], vecs[j]
angle = np.degrees(np.arccos( np.dot(vecs[i], vecs[j]) / (ln.norm(vecs[i]) * ln.norm(vecs[j]))) )
val.append( angle)
print ' angle = ', angle
val = sum(val)/3.
angs.append(val)
A0 = get_A0(bdimer, c)
As.append(fabs(A0))
plt.scatter(angs, As, edgecolor='0.1', linewidths=2, s=250, facecolor='none')
plt.gca().xaxis.set_minor_locator(MultipleLocator(5))
plt.gca().yaxis.set_tick_params(which='major', length=10, width=2)
plt.gca().xaxis.set_tick_params(which='major', length=10, width=2, labelsize=15)
plt.gca().xaxis.set_tick_params(which='minor', length=5, width=2, labelsize=15)
#plt.gca().tick_params(width=2, labelsize=15)
for tick in plt.gca().xaxis.get_major_ticks()+plt.gca().yaxis.get_major_ticks():
tick.label1.set_fontweight('bold')
for x in ['top', 'bottom', 'left', 'right']:
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
plt.scatter(Ds, As, edgecolor='0.1', linewidths=2, s=250, facecolor='none')
plt.gca().xaxis.set_minor_locator(MultipleLocator(5))
plt.gca().yaxis.set_tick_params(which='major', length=10, width=2)
plt.gca().xaxis.set_tick_params(which='major', length=10, width=2, labelsize=15)
plt.gca().xaxis.set_tick_params(which='minor', length=5, width=2, labelsize=15)
#plt.gca().tick_params(width=2, labelsize=15)
for tick in plt.gca().xaxis.get_major_ticks()+plt.gca().yaxis.get_major_ticks():
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)
plt.gca().xaxis.set_tick_params(which='major', length=10, width=2, labelsize=15)
plt.gca().xaxis.set_tick_params(which='minor', length=5, width=2, labelsize=15)
#plt.gca().tick_params(width=2, labelsize=15)
for tick in plt.gca().xaxis.get_major_ticks()+plt.gca().yaxis.get_major_ticks():
tick.label1.set_fontweight('bold')
'c4': [65, 119],
'c5': [82, 102],
'c6': [66, 101, 119],
'c2ox': [72],
'c3ox': [65],
'c5ox': [65],
}
print 'Eprimes'
for c, eprimes in eprime_dict.items():
print c
for eprime in eprimes:
print '\t', eprime,
s_m = get_spin_mom(eprime, c)
#print '(s = ', s_m,
A0 = get_A0(eprime, c)
#print 'A ', A0, ')'
epr ,= plt.plot(s_m, 0.5, 'g.', label="$E'$")
print 'Dimers'
for c, dimers in dimer_dict.items():
print c
for dimer in dimers:
print '\t', dimer,
s_m = get_spin_mom(dimer, c)
#print '(s = ', s_m,
A0 = get_A0(dimer, c)
#print 'A ', A0, ')'
dim_,= plt.plot(s_m, 0.0, 'b.', label="dimer")
import matplotlib.pyplot as plt
from matplotlib.ticker import MultipleLocator
c1 = ReadStruct('../crystal_files/INPUT_hfo2si_c1')
c1ox = ReadStruct('../crystal_files/INPUT_hfo2si_c1ox')
c2ox = ReadStruct('../crystal_files/INPUT_hfo2si_c2ox')
c3ox = ReadStruct('../crystal_files/INPUT_hfo2si_c3ox')
pos_graph = {'Hf':0.5, 'Si':-0.5, 'O':0.}
scatter = {'Hf':[], 'O':[], 'Si':[]}
x, y = [], []
print 'cell 1'
for no, at in enumerate(c1.atoms):
A0 = get_A0(no+1, 'hfo2si_c1')
if math.fabs(A0) > 10:
print no+1, at, A0
y.append(pos_graph[at.species])
scatter[at.species].append(A0)
x.append(A0)
print 'cell 1 ox'
for no, at in enumerate(c1ox.atoms):
A0 = get_A0(no+1, 'hfo2si_c1ox')
if math.fabs(A0) > 10:
print no+1, at, A0
y.append(pos_graph[at.species])
scatter[at.species].append(A0)
x.append(A0)
