def build_aggregate_2(settings):
"""Example function for building aggregate no. 2"""
mol_l = []
mod_l = []
with qr.energy_units("1/cm"):
for ind in range(settings["Nmol"]):
mol = Molecule([0.0, settings["E1"]])
# mol1.set_dipole(0,1,[1.0, 0.0, 0.0])
# mol1.set_transition_width((0,1), width)
mod = Mode(settings["omega"])
mol.add_Mode(mod)
mod.set_nmax(0, settings["Nvib_0"])
mod.set_nmax(1, settings["Nvib_1"])
mod.set_HR(1, settings["HR"])
mol_l.append(mol)
mod_l.append(mod)
agg = Aggregate(molecules=mol_l)
for ind in range(settings["Nmol"] - 1):
agg.set_resonance_coupling(ind, ind + 1, settings["JJ"])
# agg.set_resonance_coupling(settings["Nmol"]-1, 0, settings["JJ"])
agg.build(mult=1)
return agg
def build_testing_aggregate():
"""Testing aggregate for unit tests."""
# Number of molecules
Nmol = 2
# energy of molecule one
E1 = 12500.0
# energy gap to molecule two
Edelta = 100.0
# coupling between the two molecules
JJ = 30.0
# frequency of the vibrational mode
omega = 110.0
# Huan-Rhys factor
HR = 0.01
# transition width
width = 80
# max nvib states
Nvib_0 = 3
Nvib_1 = 3
mol_l = []
mod_l = []
with qr.energy_units("1/cm"):
for ind in range(Nmol):
mol = Molecule([0.0, E1])
mol.set_dipole(0, 1, [1.0, 0.0, 0.0])
mol.set_transition_width((0, 1), width)
mod = Mode(omega)
mol.add_Mode(mod)
mod.set_nmax(0, Nvib_0)
mod.set_nmax(1, Nvib_1)
mod.set_HR(1, HR)
mol_l.append(mol)
mod_l.append(mod)
agg = Aggregate(molecules=mol_l)
for ind in range(Nmol - 1):
agg.set_resonance_coupling(ind, ind + 1, JJ)
agg.set_resonance_coupling(Nmol - 1, 0, JJ)
agg.build(mult=1)
return agg
m1v = Molecule([0.0, 1.0]) m2v = Molecule([0.0, 1.1]) m3v = Molecule([0.0, 1.2]) from quantarhei import Mode mod1 = Mode(0.01) mod2 = Mode(0.01) mod3 = Mode(0.01) Nvib = 2 m1v.add_Mode(mod1) mod1.set_nmax(0, Nvib) mod1.set_nmax(1, Nvib) mod1.set_HR(1, 0.3) m2v.add_Mode(mod2) mod2.set_nmax(0, Nvib) mod2.set_nmax(1, Nvib) mod2.set_HR(1, 0.3) m3v.add_Mode(mod3) mod3.set_nmax(0, Nvib) mod3.set_nmax(1, Nvib) mod3.set_HR(1, 0.3) vagg = Aggregate(molecules=[m1v, m2v, m3v]) vagg.build() from quantarhei.qm import ProjectionOperator
m1v = Molecule([0.0, 1.0]) m2v = Molecule([0.0, 1.1]) m3v = Molecule([0.0, 1.2]) from quantarhei import Mode mod1 = Mode(0.01) mod2 = Mode(0.01) mod3 = Mode(0.01) Nvib = 2 m1v.add_Mode(mod1) mod1.set_nmax(0, Nvib) mod1.set_nmax(1, Nvib) mod1.set_HR(1, 0.3) m2v.add_Mode(mod2) mod2.set_nmax(0, Nvib) mod2.set_nmax(1, Nvib) mod2.set_HR(1, 0.3) m3v.add_Mode(mod3) mod3.set_nmax(0, Nvib) mod3.set_nmax(1, Nvib) mod3.set_HR(1, 0.3) vagg = Aggregate(molecules=[m1v, m2v, m3v]) vagg.build() from quantarhei.qm import ProjectionOperator