def absorption_spectrum_trimer(self):
dd1 = [0.0,3.0,0.0]
dd2 = [0.0,1.0,2.0]
dd3 = [0.0,1.0,1.0]
cf = world.cf
with energy_units("1/cm"):
m1 = Molecule([0.0, 12100])
m1.set_dipole(0,1,dd1)
m1.set_transition_environment((0,1), cf)
m2 = Molecule([0.0, 11800])
m2.set_dipole(0,1,dd2)
m2.set_transition_environment((0,1), cf)
m3 = Molecule([0.0, 12500])
m3.set_dipole(0,1,dd3)
m3.set_transition_environment((0,1), cf)
m1.position = [0.0,0.0,0.0]
m2.position = [5.0,0.0,0.0]
m3.position = [0.0,5.0,0.0]
AG = Aggregate(name="TestAggregate")
AG.add_Molecule(m1)
AG.add_Molecule(m2)
AG.add_Molecule(m3)
AG.set_coupling_by_dipole_dipole(epsr=3.0)
AG.build()
(RRr,hamr) = AG.get_RelaxationTensor(world.ta,
relaxation_theory="standard_Redfield",
time_dependent=True)
ac = AbsSpectrumCalculator(world.ta,AG,
relaxation_tensor=RRr,
effective_hamiltonian=hamr)
with energy_units("1/cm"):
ac.bootstrap(rwa=12000)
a1 = ac.calculate(raw=True)
with energy_units("1/cm"):
world.abs = numpy.zeros((len(a1.data),2))
for kk in range(len(a1.data)):
world.abs[kk,0] = a1.axis.data[kk] #frequency[kk]
world.abs[kk,1] = a1.data[kk]
def absorption_spectrum_trimer(self):
dd1 = [0.0, 3.0, 0.0]
dd2 = [0.0, 1.0, 2.0]
dd3 = [0.0, 1.0, 1.0]
cf = world.cf
with energy_units("1/cm"):
m1 = Molecule([0.0, 12100])
m1.set_dipole(0, 1, dd1)
m1.set_transition_environment((0, 1), cf)
m2 = Molecule([0.0, 11800])
m2.set_dipole(0, 1, dd2)
m2.set_transition_environment((0, 1), cf)
m3 = Molecule([0.0, 12500])
m3.set_dipole(0, 1, dd3)
m3.set_transition_environment((0, 1), cf)
m1.position = [0.0, 0.0, 0.0]
m2.position = [5.0, 0.0, 0.0]
m3.position = [0.0, 5.0, 0.0]
AG = Aggregate(name="TestAggregate")
AG.add_Molecule(m1)
AG.add_Molecule(m2)
AG.add_Molecule(m3)
AG.set_coupling_by_dipole_dipole(epsr=3.0)
AG.build()
(RRr,
hamr) = AG.get_RelaxationTensor(world.ta,
relaxation_theory="standard_Redfield",
time_dependent=True)
ac = AbsSpectrumCalculator(world.ta,
AG,
relaxation_tensor=RRr,
effective_hamiltonian=hamr)
with energy_units("1/cm"):
ac.bootstrap(rwa=12000)
a1 = ac.calculate()
with energy_units("1/cm"):
world.abs = numpy.zeros((len(a1.data), 2))
for kk in range(len(a1.data)):
world.abs[kk, 0] = a1.axis.data[kk] #frequency[kk]
world.abs[kk, 1] = a1.data[kk]
def absorption_spectrum_dimer(self):
dd1 = [0.0,3.0,0.0]
dd2 = [0.0,1.0,1.0]
cf = world.cf
#cm = CorrelationFunctionMatrix(world.ta,2,1)
#cm.set_correlation_function(cf,[(1,1),(0,0)])
with energy_units("1/cm"):
m1 = Molecule([0.0, 12100])
m1.set_dipole(0,1,dd1)
m1.set_transition_environment((0,1), cf)
m2 = Molecule([0.0, 12000])
m2.set_dipole(0,1,dd2)
m2.set_transition_environment((0,1), cf)
#m1.set_egcf([0,1],cf)
#m2.set_egcf([0,1],cf)
#m1.set_egcf_mapping((0,1),cm,0)
#m2.set_egcf_mapping((0,1),cm,1)
m1.position = [0.0,0.0,0.0]
m2.position = [5.0,0.0,0.0]
AG = Aggregate(name="TestAggregate")
#AG.set_egcf_matrix(cm)
AG.add_Molecule(m1)
AG.add_Molecule(m2)
AG.set_coupling_by_dipole_dipole()
AG.build()
ac = AbsSpectrumCalculator(world.ta,AG)
with energy_units("1/cm"):
ac.bootstrap(rwa=12000)
a1 = ac.calculate(raw=True)
with energy_units("1/cm"):
world.abs = numpy.zeros((len(a1.data),2))
for kk in range(len(a1.data)):
world.abs[kk,0] = a1.axis.data[kk] #frequency[kk]
world.abs[kk,1] = a1.data[kk]
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)
with energy_units("1/cm"):
rwa_cm = agg.get_RWA_suggestion()
rwa = agg.get_RWA_suggestion()
#
# Prepare for calculation of 2D spectra
#
# TimeAxis for t2 waiting time
t2s = TimeAxis(0.0, 5, 20.0)
class AggregateTest(unittest.TestCase):
"""Tests for the Manager class
"""
def setUp(self):
m1 = Molecule(name="Molecule 1", elenergies=[0.0, 1.0])
m2 = Molecule(name="Molecule 2", elenergies=[0.0, 1.0])
time = TimeAxis(0.0, 1000, 1.0)
params = dict(ftype="OverdampedBrownian", reorg=20, cortime=100, T=300)
with energy_units("1/cm"):
fc = CorrelationFunction(time, params)
m1.set_transition_environment((0, 1), fc)
m1.position = [0.0, 0.0, 0.0]
m1.set_dipole(0, 1, [10.0, 0.0, 0.0])
m2.set_transition_environment((0, 1), fc)
m2.position = [10.0, 0.0, 0.0]
m2.set_dipole(0, 1, [10.0, 0.0, 0.0])
self.agg = Aggregate(name="TestAgg", molecules=[m1, m2])
self.agg.set_coupling_by_dipole_dipole()
self.agg.build()
m3 = Molecule(name="Molecule 1", elenergies=[0.0, 1.0])
m4 = Molecule(name="Molecule 2", elenergies=[0.0, 1.0])
m3.add_Mode(Mode(0.01))
m4.add_Mode(Mode(0.01))
mod3 = m3.get_Mode(0)
mod4 = m4.get_Mode(0)
mod3.set_nmax(0, 4)
mod3.set_nmax(1, 4)
mod3.set_HR(1, 0.1)
mod4.set_nmax(0, 4)
mod4.set_nmax(1, 4)
mod4.set_HR(1, 0.3)
self.vagg = Aggregate(molecules=[m3, m4])
self.vagg.build()
#########################################################################
#
# TESTS
#
#########################################################################
def test_saving_of_aggregate(self):
"""(Aggregate) Testing its saving capability
"""
use_temporary_file = True
if use_temporary_file:
#drv = "core"
#bcs = False
#with h5py.File('tempfile.hdf5',
# driver=drv,
# backing_store=bcs) as f:
with tempfile.TemporaryFile() as f:
self.agg.save(f, test=True) #,report_unsaved=True)
# reread it
agg = Aggregate()
agg = agg.load(f, test=True)
else:
#with h5py.File('tempfile.hdf5') as f:
with open('tempfile.qrp', 'wb') as f:
self.agg.save(f)
#with h5py.File('tempfile.hdf5') as f:
with open('tempfile.qrp', 'rb') as f:
agg = Aggregate()
agg.load(f)
self.assertEqual(self.agg.nmono, agg.nmono)
self.assertEqual(self.agg.mult, agg.mult)
self.assertEqual(self.agg.sbi_mult, agg.sbi_mult)
self.assertEqual(self.agg.name, agg.name)
self.assertEqual(self.agg._has_egcf_matrix, agg._has_egcf_matrix)
self.assertEqual(self.agg._has_system_bath_interaction,
agg._has_system_bath_interaction)
self.assertEqual(self.agg.coupling_initiated, agg.coupling_initiated)
self.assertEqual(self.agg._has_relaxation_tensor,
agg._has_relaxation_tensor)
self.assertEqual(self.agg._relaxation_theory, agg._relaxation_theory)
self.assertEqual(self.agg._built, agg._built)
self.assertEqual(self.agg.Nel, agg.Nel)
self.assertEqual(self.agg.Ntot, agg.Ntot)
numpy.testing.assert_array_equal(self.agg.Nb, agg.Nb)
for key in agg.mnames.keys():
self.assertEqual(self.agg.mnames[key], agg.mnames[key])
numpy.testing.assert_array_equal(self.agg.resonance_coupling,
agg.resonance_coupling)
mnames = ["Molecule 1", "Molecule 2"]
for k in range(agg.nmono):
m = agg.monomers[k]
self.assertIn(m.name, mnames)
mnames.remove(m.name)
def test_trace_over_vibrations(self):
"""(Aggregate) Testing trace over vibrational DOF
"""
agg = self.vagg
ham = agg.get_Hamiltonian()
rho = ReducedDensityMatrix(dim=ham.dim)
rho._data[5, 5] = 1.0
redr = agg.trace_over_vibrations(rho)
numpy.testing.assert_almost_equal(numpy.trace(redr._data),
1.0,
decimal=7)
N = agg.Nb[0]
rho = ReducedDensityMatrix(dim=ham.dim)
rho._data[N + 5, N + 5] = 1.0
redr = agg.trace_over_vibrations(rho)
numpy.testing.assert_almost_equal(numpy.trace(redr._data),
1.0,
decimal=3)
N = agg.Nb[1]
rho = ReducedDensityMatrix(dim=ham.dim)
rho._data[N + 5, N + 5] = 1.0
redr = agg.trace_over_vibrations(rho)
numpy.testing.assert_almost_equal(numpy.trace(redr._data),
1.0,
decimal=2)
def test_get_Density_Matrix_thermal(self):
"""(Aggregate) Testing the get_Densitymatrix method with `thermal` condition type
"""
from quantarhei.core.units import kB_intK
vagg = self.vagg
H = vagg.get_Hamiltonian()
N = H.data.shape[0]
# zero temperature
rho0 = vagg.get_DensityMatrix(condition_type="thermal")
tst0 = numpy.zeros((N, N), dtype=qr.COMPLEX)
tst0[0, 0] = 1.0
numpy.testing.assert_almost_equal(rho0.data, tst0)
# room temperature
rho0 = vagg.get_DensityMatrix(condition_type="thermal",
temperature=300)
# cannonical balance between neighboring states is tested
kbT = kB_intK * 300.0
for k in range(N - 1):
E2 = H.data[k + 1, k + 1]
E1 = H.data[k, k]
ratio = numpy.exp(-(E2 - E1) / kbT)
numpy.testing.assert_almost_equal(
ratio, rho0.data[k + 1, k + 1] / rho0.data[k, k])
def test_get_Density_Matrix_thermal_excited(self):
"""(Aggregate) Testing the get_Densitymatrix method with `thermal_excited_state` condition type
"""
from quantarhei.core.units import kB_intK
vagg = self.vagg
H = vagg.get_Hamiltonian()
N = H.data.shape[0]
Nb0 = vagg.Nb[0]
# zero temperature
rho0 = vagg.get_DensityMatrix(condition_type="thermal_excited_state")
tst0 = numpy.zeros((N, N), dtype=qr.COMPLEX)
tst0[Nb0, Nb0] = 1.0
numpy.testing.assert_almost_equal(rho0.data, tst0)
# room temperature
kbT = kB_intK * 300.0
H = self.agg.get_Hamiltonian()
N = H.data.shape[0]
Nb0 = self.agg.Nb[0]
with qr.eigenbasis_of(H):
rho0 = self.agg.get_DensityMatrix(
condition_type="thermal_excited_state", temperature=300)
tst0 = numpy.zeros((N, N), dtype=qr.COMPLEX)
with qr.eigenbasis_of(H):
ssum = 0.0
for i in range(Nb0, N):
tst0[i,
i] = numpy.exp(-(H.data[i, i] - H.data[Nb0, Nb0]) / kbT)
ssum += tst0[i, i]
tst0 = tst0 / ssum
numpy.testing.assert_almost_equal(rho0.data, tst0)
# ssum = 0.0
# for i in range(N):
# tst0[i,i] = numpy.exp(-H.data[i,i]/kbT)
# ssum += tst0[i,i]
# tst0 = tst0/ssum
#
# DD = vagg.TrDMOp.data
# # abs value of the transition dipole moment
# dabs = numpy.sqrt(DD[:,:,0]**2 + \
# DD[:,:,1]**2 + DD[:,:,2]**2)
# # excitation from bra and ket
# tst0 = numpy.dot(dabs, numpy.dot(tst0,dabs))
#
# numpy.testing.assert_almost_equal(rho0.data, tst0)
def test_get_temperature(self):
"""(Aggregate) Testing temperature retrieval
"""
agg = self.agg
T = agg.get_temperature()
numpy.testing.assert_almost_equal(T, 300.0)
def test_init_coupling_matrix(self):
"""(Aggregate) Testing coupling matrix initialization
"""
agg = TestAggregate(name="dimer-2-env")
self.assertFalse(agg.coupling_initiated)
agg.init_coupling_matrix()
self.assertTrue(agg.coupling_initiated)
self.assertAlmostEqual(0.0, agg.resonance_coupling[0, 1])
def test_set_resonance_coupling(self):
"""(Aggregate) Testing resonance coupling setting with different units
"""
agg = TestAggregate(name="dimer-2-env")
agg.init_coupling_matrix()
agg.set_resonance_coupling(0, 1, 1.0)
self.assertAlmostEqual(1.0, agg.resonance_coupling[0, 1])
self.assertAlmostEqual(1.0, agg.resonance_coupling[1, 0])
with qr.energy_units("1/cm"):
agg.set_resonance_coupling(0, 1, 100.0)
self.assertAlmostEqual(qr.convert(100.0, "1/cm", "int"),
agg.resonance_coupling[0, 1])
self.assertAlmostEqual(qr.convert(100.0, "1/cm", "int"),
agg.resonance_coupling[1, 0])
def test_get_resonance_coupling(self):
"""(Aggregate) Testing resonance coupling retrieval in different units
"""
agg = TestAggregate(name="dimer-2-env")
agg.init_coupling_matrix()
agg.set_resonance_coupling(0, 1, 1.0)
coup = agg.get_resonance_coupling(1, 0)
self.assertAlmostEqual(coup, 1.0)
with qr.energy_units("1/cm"):
coup = agg.get_resonance_coupling(1, 0)
self.assertAlmostEqual(coup, qr.convert(1.0, "int", "1/cm"))
with qr.energy_units("eV"):
coup = agg.get_resonance_coupling(1, 0)
self.assertAlmostEqual(coup, qr.convert(1.0, "int", "eV"))
with qr.energy_units("THz"):
coup = agg.get_resonance_coupling(1, 0)
self.assertAlmostEqual(coup, qr.convert(1.0, "int", "THz"))
def test_set_resonance_coupling_matrix(self):
"""(Aggregate) Testing setting the whole resonance coupling matrix
"""
agg = TestAggregate(name="dimer-2-env")
mat = [[0.0, 1.0], [1.0, 0.0]]
agg.set_resonance_coupling_matrix(mat)
self.assertAlmostEqual(agg.resonance_coupling[1, 0], 1.0)
self.assertAlmostEqual(agg.resonance_coupling[0, 1], 1.0)
self.assertAlmostEqual(agg.resonance_coupling[0, 0], 0.0)
self.assertAlmostEqual(agg.resonance_coupling[1, 1], 0.0)
mat = ((0.0, 500.0), (500.0, 0.0))
with qr.energy_units("1/cm"):
agg.set_resonance_coupling_matrix(mat)
inint = qr.convert(500, "1/cm", "int")
self.assertAlmostEqual(agg.resonance_coupling[1, 0], inint)
self.assertAlmostEqual(agg.resonance_coupling[0, 1], inint)
self.assertAlmostEqual(agg.resonance_coupling[0, 0], 0.0)
self.assertAlmostEqual(agg.resonance_coupling[1, 1], 0.0)
def test_dipole_dipole_coupling(self):
"""(Aggregate) Testing dipole-dipole coupling calculation
"""
agg = TestAggregate(name="dimer-2-env")
coup1 = agg.dipole_dipole_coupling(0, 1)
coup2 = agg.dipole_dipole_coupling(0, 1, epsr=2.0)
self.assertAlmostEqual(coup1, coup2 * 2.0)
with qr.energy_units("1/cm"):
coup = agg.dipole_dipole_coupling(0, 1)
self.assertAlmostEqual(qr.convert(coup1, "int", "1/cm"), coup)
def test_set_coupling_by_dipole_dipole(self):
"""(Aggregate) Testing dipole-dipole coupling calculation for the whole agregate
"""
agg = TestAggregate(name="dimer-2-env")
agg.set_coupling_by_dipole_dipole()
coup1 = agg.dipole_dipole_coupling(0, 1)
self.assertAlmostEqual(coup1, agg.resonance_coupling[0, 1])
with qr.energy_units("1/cm"):
agg.set_coupling_by_dipole_dipole()
coup1 = agg.dipole_dipole_coupling(0, 1)
self.assertAlmostEqual(coup1, agg.resonance_coupling[0, 1])
def test_calculate_resonance_coupling(self):
"""(Aggregate) Testing resonance coupling calculation by various methods
"""
agg = TestAggregate(name="dimer-2-env")
agg.calculate_resonance_coupling(method="dipole-dipole")
coup1 = agg.dipole_dipole_coupling(0, 1)
self.assertEqual(coup1, agg.resonance_coupling[1, 0])
with qr.energy_units("1/cm"):
agg.calculate_resonance_coupling(method="dipole-dipole")
self.assertEqual(coup1, agg.resonance_coupling[1, 0])
def test_add_Molecule(self):
"""(Aggregate) Testing add_Molecule() method
"""
agg = TestAggregate(name="dimer-2-env")
mol = qr.Molecule(elenergies=[0.0, 1.0])
nmols1 = agg.nmono
agg.add_Molecule(mol)
nmols2 = agg.nmono
self.assertEqual(nmols1 + 1, nmols2)
self.assertEqual(len(agg.monomers), nmols2)
self.assertLessEqual(len(agg.mnames), nmols2)
class AggregateTest(unittest.TestCase):
"""Tests for the Manager class
"""
def setUp(self):
m1 = Molecule(name="Molecule 1", elenergies=[0.0, 1.0])
m2 = Molecule(name="Molecule 2", elenergies=[0.0, 1.0])
time = TimeAxis(0.0, 1000, 1.0)
params = dict(ftype="OverdampedBrownian", reorg=20, cortime=100, T=300)
with energy_units("1/cm"):
fc = CorrelationFunction(time, params)
m1.set_transition_environment((0,1), fc)
m1.position = [0.0, 0.0, 0.0]
m1.set_dipole(0,1,[10.0, 0.0, 0.0])
m2.set_transition_environment((0,1), fc)
m2.position = [10.0, 0.0, 0.0]
m2.set_dipole(0,1,[10.0, 0.0, 0.0])
self.agg = Aggregate(name="TestAgg", molecules=[m1,m2])
self.agg.set_coupling_by_dipole_dipole()
self.agg.build()
m3 = Molecule(name="Molecule 1", elenergies=[0.0, 1.0])
m4 = Molecule(name="Molecule 2", elenergies=[0.0, 1.0])
m3.add_Mode(Mode(0.01))
m4.add_Mode(Mode(0.01))
mod3 = m3.get_Mode(0)
mod4 = m4.get_Mode(0)
mod3.set_nmax(0, 4)
mod3.set_nmax(1, 4)
mod3.set_HR(1, 0.1)
mod4.set_nmax(0, 4)
mod4.set_nmax(1, 4)
mod4.set_HR(1, 0.3)
self.vagg = Aggregate(molecules=[m3, m4])
self.vagg.build()
#########################################################################
#
# TESTS
#
#########################################################################
def test_saving_of_aggregate(self):
"""(Aggregate) Testing its saving capability
"""
use_temporary_file = True
if use_temporary_file:
#drv = "core"
#bcs = False
#with h5py.File('tempfile.hdf5',
# driver=drv,
# backing_store=bcs) as f:
with tempfile.TemporaryFile() as f:
self.agg.save(f, test=True) #,report_unsaved=True)
# reread it
agg = Aggregate()
agg = agg.load(f, test=True)
else:
#with h5py.File('tempfile.hdf5') as f:
with open('tempfile.qrp','wb') as f:
self.agg.save(f)
#with h5py.File('tempfile.hdf5') as f:
with open('tempfile.qrp','rb') as f:
agg = Aggregate()
agg.load(f)
self.assertEqual(self.agg.nmono, agg.nmono)
self.assertEqual(self.agg.mult, agg.mult)
self.assertEqual(self.agg.sbi_mult, agg.sbi_mult)
self.assertEqual(self.agg.name, agg.name)
self.assertEqual(self.agg._has_egcf_matrix, agg._has_egcf_matrix)
self.assertEqual(self.agg._has_system_bath_interaction,
agg._has_system_bath_interaction)
self.assertEqual(self.agg.coupling_initiated, agg.coupling_initiated)
self.assertEqual(self.agg._has_relaxation_tensor,
agg._has_relaxation_tensor)
self.assertEqual(self.agg._relaxation_theory, agg._relaxation_theory)
self.assertEqual(self.agg._built, agg._built)
self.assertEqual(self.agg.Nel,agg.Nel)
self.assertEqual(self.agg.Ntot,agg.Ntot)
numpy.testing.assert_array_equal(self.agg.Nb,agg.Nb)
for key in agg.mnames.keys():
self.assertEqual(self.agg.mnames[key],agg.mnames[key])
numpy.testing.assert_array_equal(self.agg.resonance_coupling,
agg.resonance_coupling)
mnames = ["Molecule 1", "Molecule 2"]
for k in range(agg.nmono):
m = agg.monomers[k]
self.assertIn(m.name, mnames)
mnames.remove(m.name)
def test_trace_over_vibrations(self):
"""(Aggregate) Testing trace over vibrational DOF
"""
agg = self.vagg
ham = agg.get_Hamiltonian()
rho = ReducedDensityMatrix(dim=ham.dim)
rho._data[5, 5] = 1.0
redr = agg.trace_over_vibrations(rho)
numpy.testing.assert_almost_equal(numpy.trace(redr._data), 1.0,
decimal=7)
N = agg.Nb[0]
rho = ReducedDensityMatrix(dim=ham.dim)
rho._data[N+5, N+5] = 1.0
redr = agg.trace_over_vibrations(rho)
numpy.testing.assert_almost_equal(numpy.trace(redr._data), 1.0,
decimal=3)
N = agg.Nb[1]
rho = ReducedDensityMatrix(dim=ham.dim)
rho._data[N+5, N+5] = 1.0
redr = agg.trace_over_vibrations(rho)
numpy.testing.assert_almost_equal(numpy.trace(redr._data), 1.0,
decimal=2)
def test_get_Density_Matrix_thermal(self):
"""(Aggregate) Testing the get_Densitymatrix method with `thermal` condition type
"""
from quantarhei.core.units import kB_intK
vagg = self.vagg
H = vagg.get_Hamiltonian()
N = H.data.shape[0]
# zero temperature
rho0 = vagg.get_DensityMatrix(condition_type="thermal")
tst0 = numpy.zeros((N,N),dtype=qr.COMPLEX)
tst0[0,0] = 1.0
numpy.testing.assert_almost_equal(rho0.data, tst0)
# room temperature
rho0 = vagg.get_DensityMatrix(condition_type="thermal",
temperature=300)
# cannonical balance between neighboring states is tested
kbT = kB_intK*300.0
for k in range(N-1):
E2 = H.data[k+1,k+1]
E1 = H.data[k,k]
ratio = numpy.exp(-(E2-E1)/kbT)
numpy.testing.assert_almost_equal(ratio,
rho0.data[k+1,k+1]/rho0.data[k,k])
def test_get_Density_Matrix_thermal_excited(self):
"""(Aggregate) Testing the get_Densitymatrix method with `thermal_excited_state` condition type
"""
from quantarhei.core.units import kB_intK
vagg = self.vagg
H = vagg.get_Hamiltonian()
N = H.data.shape[0]
Nb0 = vagg.Nb[0]
# zero temperature
rho0 = vagg.get_DensityMatrix(condition_type="thermal_excited_state")
tst0 = numpy.zeros((N,N),dtype=qr.COMPLEX)
tst0[Nb0,Nb0] = 1.0
numpy.testing.assert_almost_equal(rho0.data, tst0)
# room temperature
kbT = kB_intK*300.0
H = self.agg.get_Hamiltonian()
N = H.data.shape[0]
Nb0 = self.agg.Nb[0]
with qr.eigenbasis_of(H):
rho0 = self.agg.get_DensityMatrix(condition_type="thermal_excited_state",
temperature=300)
tst0 = numpy.zeros((N,N),dtype=qr.COMPLEX)
with qr.eigenbasis_of(H):
ssum = 0.0
for i in range(Nb0, N):
tst0[i,i] = numpy.exp(-(H.data[i,i]-H.data[Nb0,Nb0])/kbT)
ssum += tst0[i,i]
tst0 = tst0/ssum
numpy.testing.assert_almost_equal(rho0.data, tst0)
# ssum = 0.0
# for i in range(N):
# tst0[i,i] = numpy.exp(-H.data[i,i]/kbT)
# ssum += tst0[i,i]
# tst0 = tst0/ssum
#
# DD = vagg.TrDMOp.data
# # abs value of the transition dipole moment
# dabs = numpy.sqrt(DD[:,:,0]**2 + \
# DD[:,:,1]**2 + DD[:,:,2]**2)
# # excitation from bra and ket
# tst0 = numpy.dot(dabs, numpy.dot(tst0,dabs))
#
# numpy.testing.assert_almost_equal(rho0.data, tst0)
def test_get_temperature(self):
"""(Aggregate) Testing temperature retrieval
"""
agg = self.agg
T = agg.get_temperature()
numpy.testing.assert_almost_equal(T, 300.0)
def test_init_coupling_matrix(self):
"""(Aggregate) Testing coupling matrix initialization
"""
agg = TestAggregate(name="dimer-2-env")
self.assertFalse(agg.coupling_initiated)
agg.init_coupling_matrix()
self.assertTrue(agg.coupling_initiated)
self.assertAlmostEqual(0.0, agg.resonance_coupling[0,1])
def test_set_resonance_coupling(self):
"""(Aggregate) Testing resonance coupling setting with different units
"""
agg = TestAggregate(name="dimer-2-env")
agg.init_coupling_matrix()
agg.set_resonance_coupling(0, 1, 1.0)
self.assertAlmostEqual(1.0, agg.resonance_coupling[0,1])
self.assertAlmostEqual(1.0, agg.resonance_coupling[1,0])
with qr.energy_units("1/cm"):
agg.set_resonance_coupling(0, 1, 100.0)
self.assertAlmostEqual(qr.convert(100.0, "1/cm", "int"),
agg.resonance_coupling[0,1])
self.assertAlmostEqual(qr.convert(100.0, "1/cm", "int"),
agg.resonance_coupling[1,0])
def test_get_resonance_coupling(self):
"""(Aggregate) Testing resonance coupling retrieval in different units
"""
agg = TestAggregate(name="dimer-2-env")
agg.init_coupling_matrix()
agg.set_resonance_coupling(0, 1, 1.0)
coup = agg.get_resonance_coupling(1,0)
self.assertAlmostEqual(coup, 1.0)
with qr.energy_units("1/cm"):
coup = agg.get_resonance_coupling(1,0)
self.assertAlmostEqual(coup, qr.convert(1.0, "int", "1/cm"))
with qr.energy_units("eV"):
coup = agg.get_resonance_coupling(1,0)
self.assertAlmostEqual(coup, qr.convert(1.0, "int", "eV"))
with qr.energy_units("THz"):
coup = agg.get_resonance_coupling(1,0)
self.assertAlmostEqual(coup, qr.convert(1.0, "int", "THz"))
def test_set_resonance_coupling_matrix(self):
"""(Aggregate) Testing setting the whole resonance coupling matrix
"""
agg = TestAggregate(name="dimer-2-env")
mat = [[0.0, 1.0],
[1.0, 0.0]]
agg.set_resonance_coupling_matrix(mat)
self.assertAlmostEqual(agg.resonance_coupling[1,0], 1.0)
self.assertAlmostEqual(agg.resonance_coupling[0,1], 1.0)
self.assertAlmostEqual(agg.resonance_coupling[0,0], 0.0)
self.assertAlmostEqual(agg.resonance_coupling[1,1], 0.0)
mat = ((0.0, 500.0),
(500.0, 0.0))
with qr.energy_units("1/cm"):
agg.set_resonance_coupling_matrix(mat)
inint = qr.convert(500, "1/cm", "int")
self.assertAlmostEqual(agg.resonance_coupling[1,0], inint)
self.assertAlmostEqual(agg.resonance_coupling[0,1], inint)
self.assertAlmostEqual(agg.resonance_coupling[0,0], 0.0)
self.assertAlmostEqual(agg.resonance_coupling[1,1], 0.0)
def test_dipole_dipole_coupling(self):
"""(Aggregate) Testing dipole-dipole coupling calculation
"""
agg = TestAggregate(name="dimer-2-env")
coup1 = agg.dipole_dipole_coupling(0,1)
coup2 = agg.dipole_dipole_coupling(0,1, epsr=2.0)
self.assertAlmostEqual(coup1, coup2*2.0)
with qr.energy_units("1/cm"):
coup = agg.dipole_dipole_coupling(0,1)
self.assertAlmostEqual(qr.convert(coup1,"int","1/cm"), coup)
def test_set_coupling_by_dipole_dipole(self):
"""(Aggregate) Testing dipole-dipole coupling calculation for the whole agregate
"""
agg = TestAggregate(name="dimer-2-env")
agg.set_coupling_by_dipole_dipole()
coup1 = agg.dipole_dipole_coupling(0,1)
self.assertAlmostEqual(coup1, agg.resonance_coupling[0,1])
with qr.energy_units("1/cm"):
agg.set_coupling_by_dipole_dipole()
coup1 = agg.dipole_dipole_coupling(0,1)
self.assertAlmostEqual(coup1, agg.resonance_coupling[0,1])
def test_calculate_resonance_coupling(self):
"""(Aggregate) Testing resonance coupling calculation by various methods
"""
agg = TestAggregate(name="dimer-2-env")
agg.calculate_resonance_coupling(method="dipole-dipole")
coup1 = agg.dipole_dipole_coupling(0,1)
self.assertEqual(coup1, agg.resonance_coupling[1,0])
with qr.energy_units("1/cm"):
agg.calculate_resonance_coupling(method="dipole-dipole")
self.assertEqual(coup1, agg.resonance_coupling[1,0])
def test_add_Molecule(self):
"""(Aggregate) Testing add_Molecule() method
"""
agg = TestAggregate(name="dimer-2-env")
mol = qr.Molecule(elenergies=[0.0, 1.0])
nmols1 = agg.nmono
agg.add_Molecule(mol)
nmols2 = agg.nmono
self.assertEqual(nmols1 + 1, nmols2)
self.assertEqual(len(agg.monomers), nmols2)
self.assertLessEqual(len(agg.mnames), nmols2)
class TestAggregate(unittest.TestCase):
"""Tests for the Manager class
"""
def setUp(self):
m1 = Molecule(name="Molecule 1", elenergies=[0.0, 1.0])
m2 = Molecule(name="Molecule 2", elenergies=[0.0, 1.0])
time = TimeAxis(0.0, 1000, 1.0)
params = dict(ftype="OverdampedBrownian", reorg=20, cortime=100, T=300)
with energy_units("1/cm"):
fc = CorrelationFunction(time, params)
m1.set_transition_environment((0,1), fc)
m1.position = [0.0, 0.0, 0.0]
m1.set_dipole(0,1,[10.0, 0.0, 0.0])
m2.set_transition_environment((0,1), fc)
m2.position = [10.0, 0.0, 0.0]
m2.set_dipole(0,1,[10.0, 0.0, 0.0])
self.agg = Aggregate(name="TestAgg", molecules=[m1,m2])
self.agg.set_coupling_by_dipole_dipole()
self.agg.build()
m3 = Molecule(name="Molecule 1", elenergies=[0.0, 1.0])
m4 = Molecule(name="Molecule 2", elenergies=[0.0, 1.0])
m3.add_Mode(Mode(0.01))
m4.add_Mode(Mode(0.01))
mod3 = m3.get_Mode(0)
mod4 = m4.get_Mode(0)
mod3.set_nmax(0, 4)
mod3.set_nmax(1, 4)
mod3.set_HR(1, 0.1)
mod4.set_nmax(0, 4)
mod4.set_nmax(1, 4)
mod4.set_HR(1, 0.3)
self.vagg = Aggregate(molecules=[m3, m4])
self.vagg.build()
def test_saving_of_aggregate(self):
"""Testing the saving capability of the Aggregate class
"""
use_temporary_file = True
if use_temporary_file:
drv = "core"
bcs = False
with h5py.File('tempfile.hdf5',
driver=drv,
backing_store=bcs) as f:
self.agg.save(f,report_unsaved=True)
# reread it
agg = Aggregate()
agg.load(f)
else:
with h5py.File('tempfile.hdf5') as f:
self.agg.save(f)
with h5py.File('tempfile.hdf5') as f:
agg = Aggregate()
agg.load(f)
self.assertEqual(self.agg.nmono, agg.nmono)
self.assertEqual(self.agg.mult, agg.mult)
self.assertEqual(self.agg.sbi_mult, agg.sbi_mult)
self.assertEqual(self.agg.name, agg.name)
self.assertEqual(self.agg._has_egcf_matrix, agg._has_egcf_matrix)
self.assertEqual(self.agg._has_system_bath_interaction,
agg._has_system_bath_interaction)
self.assertEqual(self.agg.coupling_initiated, agg.coupling_initiated)
self.assertEqual(self.agg._has_relaxation_tensor,
agg._has_relaxation_tensor)
self.assertEqual(self.agg._relaxation_theory, agg._relaxation_theory)
self.assertEqual(self.agg._built, agg._built)
self.assertEqual(self.agg.Nel,agg.Nel)
self.assertEqual(self.agg.Ntot,agg.Ntot)
numpy.testing.assert_array_equal(self.agg.Nb,agg.Nb)
for key in agg.mnames.keys():
self.assertEqual(self.agg.mnames[key],agg.mnames[key])
numpy.testing.assert_array_equal(self.agg.resonance_coupling,
agg.resonance_coupling)
mnames = ["Molecule 1", "Molecule 2"]
for k in range(agg.nmono):
m = agg.monomers[k]
self.assertIn(m.name, mnames)
mnames.remove(m.name)
def test_trace_over_vibrations(self):
"""Testing trace over vibrational DOF
"""
agg = self.vagg
ham = agg.get_Hamiltonian()
rho = ReducedDensityMatrix(dim=ham.dim)
rho._data[5, 5] = 1.0
redr = agg.trace_over_vibrations(rho)
numpy.testing.assert_almost_equal(numpy.trace(redr._data), 1.0,
decimal=7)
N = agg.Nb[0]
rho = ReducedDensityMatrix(dim=ham.dim)
rho._data[N+5, N+5] = 1.0
redr = agg.trace_over_vibrations(rho)
numpy.testing.assert_almost_equal(numpy.trace(redr._data), 1.0,
decimal=3)
N = agg.Nb[1]
rho = ReducedDensityMatrix(dim=ham.dim)
rho._data[N+5, N+5] = 1.0
redr = agg.trace_over_vibrations(rho)
numpy.testing.assert_almost_equal(numpy.trace(redr._data), 1.0,
decimal=2)
m.set_energy(1, 12466.0)
m = agg.get_Molecule_by_name("BChl3")
m.set_energy(1, 12129.0)
m = agg.get_Molecule_by_name("BChl4")
m.set_energy(1, 12410.0)
m = agg.get_Molecule_by_name("BChl5")
m.set_energy(1, 12320.0)
m = agg.get_Molecule_by_name("BChl6")
m.set_energy(1, 12593.0)
m = agg.get_Molecule_by_name("BChl7")
m.set_energy(1, 12353.0)
#
# Set resonance coupling by dipole-dipole method
#
agg.set_coupling_by_dipole_dipole(epsr=1.21)
#
# Build the aggregate
#
agg.build()
#
# Now we can start simulations
#
H = agg.get_Hamiltonian()
with energy_units("1/cm"):
print("\nExcited state Hamiltonian (energies in 1/cm):\n")
# for i in range(1, H.dim):
# for j in range(i,H.dim):
AG.add_Molecule(m5)
AG.add_Molecule(m6)
AG.add_Molecule(m7)
AG.add_Molecule(m8)
AG.add_Molecule(m9)
AG.add_Molecule(m10)
AG.add_Molecule(m11)
AG.add_Molecule(m12)
print(AG._has_egcf_matrix)
print(AG._has_system_bath_interaction)
# setting coupling by dipole-dipole formula
AG.set_coupling_by_dipole_dipole(prefac=0.0147520827152)
print (AG.resonance_coupling[1,2]/cm2int)
# building aggregate
print("Building aggregate... ")
start = tm.time()
AG.build()
print("...done in ",tm.time()-start)
with energy_units("1/cm"):
anth = Molecule("Anth",[0.0,11380]) #*cm2int],[d0,d1])
anth.set_dipole(0,1,d1)
anth.set_egcf((0,1),cfce1)
# FIXME: use with construct
m.set_energy(1, 12466.0)
m = agg.get_Molecule_by_name("BChl3")
m.set_energy(1, 12129.0)
m = agg.get_Molecule_by_name("BChl4")
m.set_energy(1, 12410.0)
m = agg.get_Molecule_by_name("BChl5")
m.set_energy(1, 12320.0)
m = agg.get_Molecule_by_name("BChl6")
m.set_energy(1, 12593.0)
m = agg.get_Molecule_by_name("BChl7")
m.set_energy(1, 12353.0)
#
# Set resonance coupling by dipole-dipole method
#
agg.set_coupling_by_dipole_dipole(epsr=1.21)
# Setting spectral density to all molecules
tmax = qr.TimeAxis(0.0, 1000, 1.0)
param = dict(ftype="OverdampedBrownian", reorg=50,
cortime=50, T=300)
with qr.energy_units("1/cm"):
cfce = qr.CorrelationFunction(tmax, param)
for mol in agg.monomers:
mol.set_transition_environment((0,1), cfce)
#
# Build the aggregate
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)
with energy_units("1/cm"):
rwa_cm = agg.get_RWA_suggestion()
rwa = agg.get_RWA_suggestion()
#
# Prepare for calculation of 2D spectra
#
# TimeAxis for t2 waiting time
t2s = TimeAxis(0.0, 5, 20.0)
def get_Aggregate(self, name="dimer-1"):
if name == "dimer-1":
agg = Aggregate(name=name)
elif name == "trimer-1":
agg = Aggregate(name=name)
with energy_units("1/cm"):
m1 = Molecule("Mol 1", [0.0, 10100.0])
m2 = Molecule("Mol 2", [0.0, 10050.0])
m3 = Molecule("Mol 3", [0.0, 10000.0])
m1.position = [0.0, 0.0, 0.0]
m2.position = [15.0, 0.0, 0.0]
m3.position = [10.0, 10.0, 0.0]
m1.set_dipole(0, 1, [5.8, 0.0, 0.0])
m2.set_dipole(0, 1, [5.8, 0.0, 0.0])
m3.set_dipole(0, 1, [numpy.sqrt(12.0), 0.0, 0.0])
agg.add_Molecule(m1)
agg.add_Molecule(m2)
agg.add_Molecule(m3)
self.molecules = [m1, m2, m3]
# m4 = Molecule("Mol 4", [0.0, 11000.0])
# m5 = Molecule("Mol 5", [0.0, 11000.0])
# m4.position = [15.0, 15.0, 0.0]
# m5.position = [15.0, 10.0, 0.0]
# m4.set_dipole(0,1,[5.8, 0.0, 0.0])
# m5.set_dipole(0,1,[5.8, 0.0, 0.0])
# agg.add_Molecule(m4)
# agg.add_Molecule(m5)
agg.set_coupling_by_dipole_dipole()
elif name == "pentamer-1":
agg = Aggregate(name=name)
with energy_units("1/cm"):
m1 = Molecule("Mol 1", [0.0, 10100.0])
m2 = Molecule("Mol 2", [0.0, 10050.0])
m3 = Molecule("Mol 3", [0.0, 10000.0])
m4 = Molecule("Mol 4", [0.0, 10200.0])
m5 = Molecule("Mol 5", [0.0, 10070.0])
m1.position = [0.0, 0.0, 0.0]
m2.position = [15.0, 0.0, 0.0]
m3.position = [10.0, 10.0, 0.0]
m4.position = [15.0, 15.0, 0.0]
m5.position = [0, 10.0, 10.0]
m1.set_dipole(0, 1, [5.8, 0.0, 0.0])
m2.set_dipole(0, 1, [5.8, 0.0, 0.0])
m3.set_dipole(0, 1, [numpy.sqrt(12.0), 0.0, 0.0])
m4.set_dipole(0, 1, [5.8, 0.0, 0.0])
m5.set_dipole(0, 1, [5.8, 0.0, 0.0])
agg.add_Molecule(m1)
agg.add_Molecule(m2)
agg.add_Molecule(m3)
agg.add_Molecule(m4)
agg.add_Molecule(m5)
self.molecules = [m1, m2, m3, m4, m5]
agg.set_coupling_by_dipole_dipole()
else:
raise Exception("Unknown model name %s" % name)
return agg