def i():
p, zpe, spec, bonds, offd, angs, torp, hbs = read_lib(libfile='ffield')
fj = open('ffield.json', 'w')
j = {'p': p, 'm': [], 'eb_layer': []}
js.dump(j, fj, sort_keys=True, indent=2)
fj.close()
def plro(lab='sigma'):
p,zpe,spec,bonds,offd,angs,torp,hbs= \
read_lib(libfile='ffield',zpe=False)
r = np.arange(0.0001, 3.0, 0.1)
ro = np.arange(0.75, 1.85, 0.15)
plt.figure()
plt.ylabel('Uncorrected ' + lab + 'Bond Order')
plt.xlabel(r'$Radius$ $(Angstrom)$')
plt.xlim(0, 3.0)
plt.ylim(0, 1.01)
bd = 'C-C'
# for i,bd in enumerate(bonds):
b = bd.split('-')
bdn = b[0] if b[0] == b[1] else bd
for i, rosi in enumerate(ro):
b = get_bo(r, rosi=rosi, bo1=p['bo1_' + bd], bo2=p['bo2_' + bd])
plt.plot(r,
b,
label=r'$r_{sigma}=%f$' % rosi,
color=colors[i % len(colors)],
linewidth=2,
linestyle='--')
plt.legend()
plt.savefig('bovsro.eps')
plt.close()
def plbo3d(lab='sigma'):
p,zpe,spec,bonds,offd,angs,torp,hbs= \
read_lib(libfile='ffield',zpe=False)
r = np.linspace(0.0001, 3.0, 50)
bo2_ = np.linspace(0.001, 18.0, 50)
bo1_ = np.linspace(-0.9, -0.0001, 50)
bo1_, bo2_ = np.meshgrid(bo1_, bo2_)
bd = 'C-C'
b = bd.split('-')
bdn = b[0] if b[0] == b[1] else bd
b = get_bo(r, rosi=p['rosi_' + bdn], bo1=bo1_, bo2=bo2_)
fig = plt.figure()
ax = Axes3D(fig)
# plt.xlabel("Delta'")
ax = plt.subplot(111, projection='3d')
ax.plot_surface(bo1_, bo2_, b, cmap=plt.get_cmap('rainbow'))
ax.contourf(bo1_,
bo2_,
b,
zdir='z',
offset=0.0,
cmap=plt.get_cmap('rainbow'))
plt.savefig('bovsbo23d.eps')
plt.close()
def plbo(lab='sigma'):
p,zpe,spec,bonds,offd,angs,torp,hbs= \
read_lib(libfile='ffield',zpe=False)
r = np.arange(0.0001, 3.0, 0.1)
plt.figure()
plt.ylabel('Uncorrected ' + lab + 'Bond Order')
plt.xlabel(r'$Radius$ $(Angstrom)$')
# plt.xlim(0,2.5)
# plt.ylim(0,1.01)
for i, bd in enumerate(bonds):
b = bd.split('-')
bdn = b[0] if b[0] == b[1] else bd
if lab == 'sigma':
bo_ = get_bo(r,
rosi=p['rosi_' + bdn],
bo1=p['bo1_' + bd],
bo2=p['bo2_' + bd])
bo = sigmoid(p['bosiw1_' + bd] * bo_ + p['bosib1_' + bd])
elif lab == 'pi':
bo_ = get_bo(r,
rosi=p['ropi_' + bdn],
bo1=p['bo3_' + bd],
bo2=p['bo4_' + bd])
bo = sigmoid(bo_ * p['bopiw1_' + bd] + p['bopib1_' + bd])
elif lab == 'pp':
bo_ = get_bo(r,
rosi=p['ropp_' + bdn],
bo1=p['bo5_' + bd],
bo2=p['bo6_' + bd])
bo = sigmoid(bo_ * p['boppw1_' + bd] + p['boppb1_' + bd])
plt.plot(r,
bo,
label=r'$%s$' % bd,
color=colors[i % len(colors)],
linewidth=2,
linestyle='--')
plt.legend()
plt.savefig('bo_%s.eps' % lab)
plt.close()
def jj():
lf = open('ffield.json', 'r')
j = js.load(lf)
p_ = j['p']
m_ = j['m']
bo_layer = j['bo_layer']
ea_layer = j['ea_layer']
eb_layer = j['eb_layer']
lf.close()
spec, bonds, offd, angs, torp, hbs = init_bonds(p_)
p, zpe, spec, bonds, offd, angs, torp, hbs = read_lib(libfile='ffield')
system('mv ffield.json ffield_.json')
fj = open('ffield.json', 'w')
j = {
'p': p,
'm': m_,
'bo_layer': bo_layer,
'ea_layer': ea_layer,
'eb_layer': eb_layer
}
js.dump(j, fj, sort_keys=True, indent=2)
fj.close()
def plf4():
''' get parameters from ffield '''
p,zpe,spec,bonds,offd,angs,torp,hbs= \
read_lib(libfile='ffield',zpe=False)
df4 = np.linspace(-2.500, -1.0, 100)
plt.figure()
plt.ylabel('f4')
plt.xlabel(r'bo - $\Delta$')
for i, bd in enumerate(bonds):
f4_ = get_f4(boc3=p['boc3_' + bd], boc4=p['boc4_' + bd], D=df4)
f4 = sigmoid(p['f4w1_' + bd] * f4_ + p['f4b1_' + bd])
plt.plot(df4,
f4,
label=r'$%s$' % bd,
color=colors[i % len(colors)],
linewidth=2,
linestyle='--')
plt.legend()
plt.savefig('f4.eps')
plt.close()
def ii():
p, zpe, spec, bonds, offd, angs, torp, hbs = read_lib(libfile='ffield')
write_lib(p_, spec, bonds, offd, angs, torp, hbs, libfile='ffield_')
def q(gen='packed.gen'):
p, zpe, spec, bonds, offd, angs, torp, hbs = read_lib(libfile='ffield')
A = read(gen)
q = qeq(p=p, atoms=A)
q.calc()