def test_ch4_minfreq(forces_a, relaxed, vibname):
# FC factor for relevant frequencies only
fc = FranckCondon(relaxed, vibname, minfreq=2000)
nrel = 4
# single excitations
FC, freq = fc.get_Franck_Condon_factors(293, forces_a)
assert len(FC[0]) == 2 * nrel + 1
assert len(freq[0]) == 2 * nrel + 1
# include double excitations
FC, freq = fc.get_Franck_Condon_factors(293, forces_a, 2)
assert len(FC[1]) == 2 * nrel
# assert len(FC[2]) == 22 # XXX why? - gives 20 in oldlibs???
for i in range(3):
assert len(freq[i]) == len(FC[i])
def test_ch4_all(forces_a, relaxed, vibname):
"""Evaluate Franck-Condon overlaps in
a molecule suddenly exposed to a different potential"""
# FC factor for all frequencies
fc = FranckCondon(relaxed, vibname)
ndof = 3 * len(relaxed)
# by symmetry only one frequency has a non-vanishing contribution
HR_a, f_a = fc.get_Huang_Rhys_factors(forces_a)
assert len(HR_a) == ndof
assert HR_a[:-1] == approx(0, abs=1e-10)
assert HR_a[-1] == approx(0.859989171)
FC, freq = fc.get_Franck_Condon_factors(293, forces_a)
assert len(FC[0]) == 2 * ndof + 1
assert len(freq[0]) == 2 * ndof + 1
h = 0.3
atoms = Cluster(read_xyz(StringIO.StringIO(butadiene)))
atoms.minimal_box(3.0, h)
atoms.set_calculator(GPAW(h=h))
if 0:
dyn = FIRE(atoms)
dyn.run(fmax=0.05)
atoms.write("butadiene.xyz")
vibname = "fcvib"
vib = Vibrations(atoms, name=vibname)
vib.run()
# Modul
a = FranckCondon(atoms, vibname, minfreq=250)
# excited state forces
F = np.array(
[
[-2.11413, 0.07317, -0.91682],
[3.23569, -0.74520, 0.76758],
[-3.44847, 0.63846, -0.81080],
[2.77345, 0.01272, 0.74811],
[-0.06544, -0.01078, -0.03209],
[-0.01245, -0.01123, -0.00040],
[0.00186, -0.05864, -0.00371],
[-0.00151, 0.05815, 0.00141],
[0.01625, 0.00781, -0.00202],
[0.06253, 0.00902, 0.03381],
]
h = 0.3
atoms = Cluster(read_xyz(StringIO.StringIO(butadiene)))
atoms.minimal_box(3., h)
atoms.set_calculator(GPAW(h=h))
if 0:
dyn = FIRE(atoms)
dyn.run(fmax=0.05)
atoms.write('butadiene.xyz')
vibname = 'fcvib'
vib = Vibrations(atoms, name=vibname)
vib.run()
# Modul
a = FranckCondon(atoms, vibname, minfreq=250)
# excited state forces
F = np.array([[-2.11413, 0.07317, -0.91682], [3.23569, -0.74520, 0.76758],
[-3.44847, 0.63846, -0.81080], [2.77345, 0.01272, 0.74811],
[-0.06544, -0.01078, -0.03209], [-0.01245, -0.01123, -0.00040],
[0.00186, -0.05864, -0.00371], [-0.00151, 0.05815, 0.00141],
[0.01625, 0.00781, -0.00202], [0.06253, 0.00902, 0.03381]])
# Huang-Rhys factors
S, fq = a.get_Huang_Rhys_factors(F)
#Temperature and #quanta taken into account
T = 300
n = 10