def test_of_correlation_function_addition(self):
"""(CorrelationFunction) Testing addition of CorrelationFunction objects """
t = TimeAxis(0.0, 1000, 1.0)
params1 = dict(ftype="OverdampedBrownian",
reorg = 30.0,
cortime = 100.0,
T = 300.0)
params2 = dict(ftype="OverdampedBrownian",
reorg = 40.0,
cortime = 100.0,
T = 300.0)
with energy_units("1/cm"):
f1 = CorrelationFunction(t, params1)
f2 = CorrelationFunction(t, params2)
#
# normal addition
#
f = f1 + f2
sum_data = f1.data + f2.data
sum_lamb = f1.lamb + f2.lamb
sum_cutoff = max(f1.cutoff_time, f2.cutoff_time)
sum_temp = f1.temperature
self.assertEqual(f.lamb, sum_lamb)
numpy.testing.assert_allclose(f.data, sum_data)
self.assertEqual(f.cutoff_time, sum_cutoff)
self.assertEqual(f.temperature, sum_temp)
#self.assertFalse(f.is_analytical())
self.assertTrue(f._is_composed)
self.assertFalse(f._is_empty)
#
# inplace addition by function
#
f1.add_to_data(f2)
self.assertEqual(f1.lamb, sum_lamb)
numpy.testing.assert_allclose(f1.data, sum_data)
self.assertEqual(f1.cutoff_time, sum_cutoff)
self.assertEqual(f1.temperature, sum_temp)
#self.assertFalse(f1.is_analytical())
self.assertTrue(f1._is_composed)
self.assertFalse(f1._is_empty)
#
# inplace addition by += operator
#
with energy_units("1/cm"):
f1 = CorrelationFunction(t, params1) # new object
fs = f1
f1 += f2
self.assertEqual(f1.lamb, sum_lamb)
numpy.testing.assert_allclose(f1.data, sum_data)
self.assertEqual(f1.cutoff_time, sum_cutoff)
self.assertEqual(f1.temperature, sum_temp)
#self.assertFalse(f1.is_analytical())
self.assertTrue(f1._is_composed)
self.assertFalse(f1._is_empty)
# test if inplace addition really happend
self.assertEqual(fs, f1)
# System-bath interaction
#
tsbi = TimeAxis(0.0, 3 * Nr, 2.0)
params = dict(ftype="OverdampedBrownian", T=300, reorg=70.0, cortime=100.0)
with energy_units('1/cm'):
cf = CorrelationFunction(tsbi, params)
params2 = dict(ftype="UnderdampedBrownian",
T=300,
reorg=10.0,
freq=150.0,
gamma=1.0 / 10000.0)
with energy_units('1/cm'):
cf2 = CorrelationFunction(tsbi, params2)
cf.add_to_data(cf2)
#
# Set system-bath interaction
#
mol1.set_transition_environment((0, 1), cf)
mol2.set_transition_environment((0, 1), cf)
#
# Creating aggregate
#
agg = Aggregate("Dimer", molecules=[mol1, mol2])
agg.set_coupling_by_dipole_dipole()
with energy_units("1/cm"):
print(agg.get_resonance_coupling(0, 1))
agg.build(mult=2)
lab.set_laser_polarizations(a_0,a_0,a_0,a_0)
#
# System-bath interaction
#
tsbi = TimeAxis(0.0, 3*Nr, 2.0)
params = dict(ftype="OverdampedBrownian", T=300, reorg=70.0, cortime=100.0)
with energy_units('1/cm'):
cf = CorrelationFunction(tsbi, params)
params2 = dict(ftype="UnderdampedBrownian", T=300, reorg=10.0, freq=150.0,
gamma=1.0/10000.0)
with energy_units('1/cm'):
cf2 = CorrelationFunction(tsbi, params2)
cf.add_to_data(cf2)
#
# Set system-bath interaction
#
mol1.set_transition_environment((0,1),cf)
mol2.set_transition_environment((0,1),cf)
#
# Creating aggregate
#
agg = Aggregate(name="Dimer", molecules=[mol1, mol2])
agg.set_coupling_by_dipole_dipole()
with energy_units("1/cm"):
print(agg.get_resonance_coupling(0,1))
agg.build(mult=2)