AggregateSpectroscopy

Class comprising the aggregate methods for support of spectroscopic simulations

Class Details

class quantarhei.builders.aggregate_spectroscopy.AggregateSpectroscopy(molecules=None, name='')

Class comprising the aggregate methods for support of spectroscopic simulations

Methods

add_Mode_by_name(name, mode)
add_Molecule(mono)	Adds monomer to the aggregate
allstates([mult, mode, all_vibronic, …])	Generator of all aggregate states
build([mult, sbi_for_higher_ex, …])	Builds aggregate properties
calculate_resonance_coupling([method, params])	Sets resonance coupling calculated by a given method
cast_to_vibronic(KK)	Casts an electronic operator to a vibronic basis
clean()	Cleans the aggregate object of anything built
convert_to_DensityMatrix(psi[, …])	Converts StateVector into DensityMatrix (possibly reduced one)
copy()	Returns a shallow copy of the self
coupling(state1, state2[, full])	Coupling between two aggregate states
deepcopy()	Returns a deep copy of the self
diagonalize()	Transforms some internal quantities into diagonal basis
dipole_dipole_coupling(kk, ll[, epsr, delta])	Calculates dipole-dipole coupling
elsignatures([mult, mode, emax])	Generator of electronic signatures
elstates([mult, mode, save_indices])	Generator of electronic states
fc_factor(state1, state2)	Franck-Condon factors between two vibrational states
get_DensityMatrix([condition_type, …])	Returns density matrix according to specified condition
get_ElectronicState(sig[, index])	Returns electronic state corresponding to this aggregate
get_FoersterRateMatrix()	Returns Förster rate matrix for the open system
get_Hamiltonian()	Returns the aggregate Hamiltonian
get_KTHierarchy([depth])	Returns the Kubo-Tanimura hierarchy of an open system
get_KTHierarchyPropagator([depth])	Returns a propagator based on the Kubo-Tanimura hierarchy
get_RWA_suggestion()	Returns average transition energy
get_RedfieldRateMatrix()	Returns Redfield rate matrix
get_ReducedDensityMatrixPropagator(timeaxis)	Returns propagator of the density matrix
get_RelaxationTensor(timeaxis[, …])	Returns a relaxation tensor corresponding to the system
get_SystemBathInteraction()	Returns the aggregate SystemBathInteraction object
get_TransitionDipoleMoment()	Returns the aggregate transition dipole moment operator
get_VibronicState(esig, vsig)	Returns vibronic state corresponding to the two specified signatures
get_dipole_by_name(name, N, M)
get_electronic_Hamiltonian([full])	Returns the aggregate electronic Hamiltonian
get_electronic_groundstate()	Indices of states in electronic ground state
get_energy_by_name(name, N)	Electronic energy
get_excited_density_matrix([condition, …])	Returns the density matrix corresponding to excitation condition
get_excitonic_band([band])	Indices of states in a given excitonic band.
get_lindich_axes()
get_max_excitations()	Returns a list of maximum number of excitations on each monomer
get_nearest_Molecule(molecule)	Returns a molecule nearest in the aggregate to a given molecule
get_resonance_coupling(i, j)	Returns resonance coupling value between two sites
get_temperature()	Returns temperature associated with this aggregate
get_thermal_ReducedDensityMatrix()	Returns equilibrium density matrix for a give temparature
get_transition(Nf, Ni)	Returns relevant info about the energetic transition
get_transition_dephasing(state1[, state2])	Returns phenomenological dephasing of a given transition
get_transition_width(state1[, state2])	Returns phenomenological width of a given transition
get_width(n, N, M)
has_SystemBathInteraction()	Returns True if the Aggregate is embedded in a defined environment
init_coupling_matrix()	Nullifies coupling matrix
liouville_pathways_1([eUt, ham, dtol, ptol, …])	Generator of the first order Liouville pathways
liouville_pathways_3([ptype, dtol, ptol, …])	Generator of Liouville pathways
liouville_pathways_3T([ptype, eUt, ham, t2, …])	Generator of Liouville pathways with energy transfer
load(filename[, test])	Loads an object from a file and returns it
loaddir(dirname)	Returns a directory of objects saved into a directory
number_of_electronic_states_in_band([band])	Number of states in a given excitonic band
number_of_states_in_band([band, …])	Number of states in a given excitonic band
rebuild([mult, sbi_for_higher_ex, …])	Cleans the object and rebuilds it
save(filename[, comment, test])	Saves the object with all its content into a file
savedir(dirname[, tag, comment, test])	Saves an object into directory containing a file with unique name
scopy()	Creates a copy of the object by saving and loading it
set_SystemBathInteraction(sbi)	Sets the SystemBathInteraction operator for this aggregate
set_coupling_by_dipole_dipole([epsr, delta])	Sets resonance coupling by dipole-dipole interaction
set_egcf_matrix(cm)	Sets a matrix describing system bath interaction
set_lindich_axes(axis_orthog_membrane)	Creates a coordinate system with one axis supplied by the user (typically an axis orthogonal to the membrane), and two other axes, all of which are orthonormal.
set_resonance_coupling(i, j, coupling[, …])	Sets resonance coupling value between two sites
set_resonance_coupling_matrix(coupmat)	Sets resonance coupling values from a matrix
total_number_of_electronic_states([mult])	Total number of electronic states in the aggregate
total_number_of_states([mult, …])	Total number of states in the aggregate
trace_over_vibrations(operator[, Nt])	Average an operator over vibrational degrees of freedom
transition_dipole(state1, state2)	Transition dipole moment between two states
vibsignatures(elsignature[, approx])	Generator of vibrational signatures
wipe_out()	Removes everything except of name attribute

convert_energy_2_current_u
convert_energy_2_internal_u
convert_length_2_current_u
convert_length_2_internal_u
get_Mode_by_name
get_Molecule_by_name
get_Molecule_index
get_dipole
remove_Molecule
unit_repr
unit_repr_latex

liouville_pathways_1(eUt=None, ham=None, dtol=0.01, ptol=0.001, etol=1e-06, verbose=0, lab=None)

Generator of the first order Liouville pathways

Generator of the pathways for an absorption spectrum calculation.

Parameters:eUt (EvolutionSuperOperator) – Evolution superoperator representing the evolution of optical coherence in the system

dtol : float

Minimum acceptable strength of the transition from ground to excited state, relative to the maximum dipole strength available in the system

ptol : float

Minimum acceptable population of the ground state (e.g. states not thermally populated are excluded)

lab : LaboratorySetup

Object representing laboratory setup - number of pulses, polarization etc.

Returns:lst – List of LiouvillePathway objects Return type:list

liouville_pathways_3(ptype='R3g', dtol=0.01, ptol=0.001, lab=None, verbose=0)

Generator of Liouville pathways

liouville_pathways_3T(ptype='R3g', eUt=None, ham=None, t2=0.0, dtol=1e-12, ptol=0.001, etol=1e-06, verbose=0, lab=None)

Generator of Liouville pathways with energy transfer

Parameters:

• ptype (tuple, list, str) – List of strings or a string representing one or more Liouville pathway types that are to be calculated
• eUt (EvolutionSuperOperator) – Evolution superoperator representing the energy transfer in the system
• t2 (float) – Waiting time at which the spectrum is calculated
• dtol (float) – Minimum acceptable strength of the transition from ground to excited state, relative to the maximum dipole strength available in the system
• ptol (float) – Minimum acceptable population of the ground state (e.g. states not thermally populated are excluded)
• lab (LaboratorySetup) – Object representing laboratory setup - number of pulses, polarization etc.

Returns:

lst – List of LiouvillePathway objects

Return type:

list