Classes

Linear Combination of Atomic Orbitals

class qDNA.lcao.Base(xyz_identifier, xyz_data)

A class to represent a molecular system and perform various calculations on it.

Parameters:

xyz_identifierstr: Identifier for the xyz data.
xyz_datapandas.DataFrame: DataFrame containing the xyz coordinates and atom types.

Attributes:

xyz_datapandas.DataFrame: DataFrame containing the xyz coordinates and atom types.
identifierstr: Identifier for the xyz data.
atomslist of str: List of atoms in the molecule.
num_atomsint: Number of atoms in the molecule.
atom_identifierslist of str: List of atom identifiers (e.g., ‘C_0’, ‘H_1’).
atom_coordinatesnumpy.ndarray: Array of atom coordinates.
atom_distance_matrixnumpy.ndarray: Matrix of distances between atoms.
atom_bond_matrixnumpy.ndarray: Matrix indicating bonds between atoms.
num_atom_orbitalsdict: Dictionary mapping atom types to the number of orbitals.
orbitalslist of Orbital: List of orbitals in the molecule.
num_orbitalsint: Number of orbitals in the molecule.
orbital_identifierslist of str: List of orbital identifiers (e.g., ‘C_0_pz’, ‘H_1_s’).
orbital_coordinatesnumpy.ndarray: Array of orbital coordinates.
orbital_distance_matrixnumpy.ndarray: Matrix of distances between orbitals.
orbital_bond_matrixnumpy.ndarray: Matrix indicating bonds between orbitals.
atom_massesdict: Dictionary mapping atom types to their masses.
massfloat: Total mass of the molecule.
center_of_massnumpy.ndarray: Coordinates of the center of mass of the molecule.
relative_atom_coordinatesnumpy.ndarray: Atom coordinates relative to the center of mass.
relative_orbital_coordinatesnumpy.ndarray: Orbital coordinates relative to the center of mass.
num_atom_electronsdict: Dictionary mapping atom types to the number of valence electrons.
num_electronsint: Number of valence electrons in the molecule.
Hnumpy.ndarray: LCAO Hamiltonian matrix.
eigvnumpy.ndarray: Eigenvalues of the Hamiltonian matrix.
eigsnumpy.ndarray: Eigenvectors of the Hamiltonian matrix.
E_HOMOfloat: Energy of the highest occupied molecular orbital (HOMO).
HOMOnumpy.ndarray: Highest occupied molecular orbital (HOMO).
HOMO_occupationnumpy.ndarray: Occupation of the HOMO.
HOMO_typestr: Type of the HOMO (sigma, pi, n).
HOMO_type_occupationlist of float: Occupation of the HOMO by type.
E_HOMO_1float: Energy of the HOMO-1.
HOMO_1numpy.ndarray: HOMO-1.
HOMO_occupation_1numpy.ndarray: Occupation of the HOMO-1.
HOMO_type_1str: Type of the HOMO-1 (sigma, pi, n).
HOMO_type_occupation_1list of float: Occupation of the HOMO-1 by type.
E_HOMO_2float: Energy of the HOMO-2.
HOMO_2numpy.ndarray: HOMO-2.
HOMO_occupation_2numpy.ndarray: Occupation of the HOMO-2.
HOMO_type_2str: Type of the HOMO-2 (sigma, pi, n).
HOMO_type_occupation_2list of float: Occupation of the HOMO-2 by type.
E_LUMOfloat: Energy of the lowest unoccupied molecular orbital (LUMO).
LUMOnumpy.ndarray: Lowest unoccupied molecular orbital (LUMO).
LUMO_occupationnumpy.ndarray: Occupation of the LUMO.
LUMO_typestr: Type of the LUMO (sigma, pi, n).
LUMO_type_occupationlist of float: Occupation of the LUMO by type.
E_LUMO_1float: Energy of the LUMO+1.
LUMO_1numpy.ndarray: LUMO+1.
LUMO_occupation_1numpy.ndarray: Occupation of the LUMO+1.
LUMO_type_1str: Type of the LUMO+1 (sigma, pi, n).
LUMO_type_occupation_1list of float: Occupation of the LUMO+1 by type.
E_LUMO_2float: Energy of the LUMO+2.
LUMO_2numpy.ndarray: LUMO+2.
LUMO_occupation_2numpy.ndarray: Occupation of the LUMO+2.
LUMO_type_2str: Type of the LUMO+2 (sigma, pi, n).
LUMO_type_occupation_2list of float: Occupation of the LUMO+2 by type.
MO_typesdict: Dictionary mapping molecular orbital types to their identifiers.
E_excfloat: Excitation energy (HOMO-LUMO gap).
dipole_momentfloat: Dipole moment of the molecule.
oscillator_strengthfloat: Oscillator strength of the molecule.

Methods

save_results(directory=’results’)	Saves the results to a JSON file.
*calc_dipole_moment(MO_1=None, MO_2=None, unit=’CoulombAngstrom’)**	Calculates the dipole moment between two molecular orbitals.
calc_oscillator_strength(dipole_moment)	Calculates the dimensionless oscillator strength.
calc_MO(identifier, deviation=0)	Returns properties of the molecular orbital.

calc_MO(identifier, deviation=0)

Calculate the Molecular Orbital (MO) properties.

Parameters:

identifierstr: The identifier for the MO to calculate. Should be either “HOMO” (Highest Occupied Molecular Orbital) or “LUMO” (Lowest Unoccupied Molecular Orbital).
deviationint, optional: The deviation from the HOMO or LUMO level to calculate. Default is 0.

Returns:

E_MOfloat: The energy of the specified MO.
MOnumpy.ndarray: The molecular orbital eigenvector.
MO_occupationnumpy.ndarray: The occupation of the molecular orbital.
MO_typestr: The type of the molecular orbital.
MO_type_occupationfloat: The occupation of the molecular orbital type.

calc_dipole_moment(MO_1=None, MO_2=None, unit='Coulomb*Angstrom')

Calculate the dipole moment between two molecular orbitals: one from the HOMO, the other one from the LUMO. The function weigthens the overlap by the relative vector with respect to the center of mass.

Parameters:

MO_1numpy.ndarray, optional: Molecular orbital coefficients for the first orbital. If None, defaults to HOMO.
MO_2numpy.ndarray, optional: Molecular orbital coefficients for the second orbital. If None, defaults to LUMO.
unitstr, optional: Unit of the dipole moment. Options are “Coulomb*Angstrom”, “Debye”, and “atomic_units”. Default is “Coulomb*Angstrom”.

Returns:

float: The dipole moment in the specified unit.

Notes

Note

The dipole moment is calculated using \(d = \sqrt{d_x^2 + d_y^2 + d_z^2}\) where dipole_x, dipole_y, and dipole_z are the components of the dipole moment along the x, y, and z axes, respectively. The conversion factors used are:

“Coulomb*Angstrom”: No conversion needed.
“Debye”: dipole * c.c / 1e-11
“atomic_units”: dipole * 1e-10 / (c.physical_constants[“Bohr radius”][0] * c.e)

calc_oscillator_strength(dipole_moment)

Calculate the oscillator strength of a transition.

Parameters:

dipole_momentfloat: The dipole moment of the transition in Coulomb*Angstrom.

Returns:

float: The oscillator strength of the transition.

save_results(directory='results')

Save the calculation results to a JSON file.

Parameters:

directorystr, optional: The directory where the results file will be saved. Default is “results”.

Notes

Note

The results are saved in a JSON file named “results_<identifier>.json” where <identifier> is a unique identifier for the calculation. The file contains the following keys:

“E_HOMO”: The energy of the highest occupied molecular orbital (HOMO), rounded to 4 decimal places.
“E_LUMO”: The energy of the lowest unoccupied molecular orbital (LUMO), rounded to 4 decimal places.
“HOMO”: The list of HOMO values.
“LUMO”: The list of LUMO values.
“dipole_moment”: The dipole moment, rounded to 4 decimal places.
“oscillator_strength”: The oscillator strength, rounded to 4 decimal places.

class qDNA.lcao.BasePair(base1, base2, identifier=None)

A class to represent a base pair in a DNA molecule.

Attributes:

base1object: The first base in the pair.
base2object: The second base in the pair.
identifierstr, optional: An identifier for the base pair (default is None).
atomslist: List of atoms in the base pair.
num_atomsint: Total number of atoms in the base pair.
atom_identifierslist: List of atom identifiers in the base pair.
atom_coordinatesndarray: Coordinates of atoms in the base pair.
atom_distance_matrixndarray: Matrix of distances between atoms in the base pair.
orbitalslist: List of orbitals in the base pair.
num_orbitalsint: Total number of orbitals in the base pair.
orbital_identifierslist: List of orbital identifiers in the base pair.
orbital_coordinatesndarray: Coordinates of orbitals in the base pair.
orbital_distance_matrixndarray: Matrix of distances between orbitals in the base pair.
massfloat: Mass of the base pair.
center_of_massndarray: Center of mass of the base pair.
relative_atom_coordinatesndarray: Atom coordinates relative to the center of mass.
relative_orbital_coordinatesndarray: Orbital coordinates relative to the center of mass.
num_electronsint: Total number of valence electrons in the base pair.
Hndarray: LCAO Hamiltonian matrix for the base pair.
eigvndarray: Eigenvalues of the Hamiltonian matrix.
eigsndarray: Eigenvectors of the Hamiltonian matrix.
E_HOMOfloat: Energy of the highest occupied molecular orbital (HOMO).
HOMOndarray: Highest occupied molecular orbital (HOMO).
HOMO_occupationndarray: Occupation of the HOMO.
HOMO_typestr: Type of the HOMO (sigma, pi, or n).
HOMO_type_occupationlist: Occupation of the HOMO by type.
E_HOMO_1float: Energy of the HOMO-1.
HOMO_1ndarray: HOMO-1.
HOMO_occupation_1ndarray: Occupation of the HOMO-1.
HOMO_type_1str: Type of the HOMO-1 (sigma, pi, or n).
HOMO_type_occupation_1list: Occupation of the HOMO-1 by type.
E_HOMO_2float: Energy of the HOMO-2.
HOMO_2ndarray: HOMO-2.
HOMO_occupation_2ndarray: Occupation of the HOMO-2.
HOMO_type_2str: Type of the HOMO-2 (sigma, pi, or n).
HOMO_type_occupation_2list: Occupation of the HOMO-2 by type.
E_LUMOfloat: Energy of the lowest unoccupied molecular orbital (LUMO).
LUMOndarray: Lowest unoccupied molecular orbital (LUMO).
LUMO_occupationndarray: Occupation of the LUMO.
LUMO_typestr: Type of the LUMO (sigma, pi, or n).
LUMO_type_occupationlist: Occupation of the LUMO by type.
E_LUMO_1float: Energy of the LUMO+1.
LUMO_1ndarray: LUMO+1.
LUMO_occupation_1ndarray: Occupation of the LUMO+1.
LUMO_type_1str: Type of the LUMO+1 (sigma, pi, or n).
LUMO_type_occupation_1list: Occupation of the LUMO+1 by type.
E_LUMO_2float: Energy of the LUMO+2.
LUMO_2ndarray: LUMO+2.
LUMO_occupation_2ndarray: Occupation of the LUMO+2.
LUMO_type_2str: Type of the LUMO+2 (sigma, pi, or n).
LUMO_type_occupation_2list: Occupation of the LUMO+2 by type.
MO_typesdict: Dictionary of molecular orbital types.
E_excfloat: Excitation energy (HOMO-LUMO gap).

Methods

save_results(directory=”results”):	Saves the results to a JSON file.
calc_MO(identifier, deviation=0):	Returns properties of the molecular orbital (MO).

calc_MO(identifier, deviation=0)

Calculate the Molecular Orbital (MO) properties.

Parameters:

identifierstr: The identifier for the MO to calculate. Should be either “HOMO” (Highest Occupied Molecular Orbital) or “LUMO” (Lowest Unoccupied Molecular Orbital).
deviationint, optional: The deviation from the HOMO or LUMO level to calculate. Default is 0.

Returns:

E_MOfloat: The energy of the specified MO.
MOnumpy.ndarray: The molecular orbital eigenvector.
MO_occupationnumpy.ndarray: The occupation of the molecular orbital.
MO_typestr: The type of the molecular orbital.
MO_type_occupationfloat: The occupation of the molecular orbital type.

save_results(directory='results')

Save the calculation results to a JSON file.

Parameters:

directorystr, optional: The directory where the results file will be saved. Default is “results”.

Notes

Note

The results are saved in a JSON file named “results_<identifier>.json” where <identifier> is a unique identifier for the calculation. The file contains the following keys:

“E_HOMO”: The energy of the highest occupied molecular orbital (HOMO), rounded to 4 decimal places.
“E_LUMO”: The energy of the lowest unoccupied molecular orbital (LUMO), rounded to 4 decimal places.
“HOMO”: The list of HOMO values.
“LUMO”: The list of LUMO values.

class qDNA.lcao.Dimer(molecule1, molecule2, identifier=None)

A class to represent a dimer consisting of two molecules.

Parameters:

molecule1Molecule: The first molecule in the dimer.
molecule2Molecule: The second molecule in the dimer.
identifierstr, optional: An identifier for the dimer. If not provided, it is generated from the identifiers of the two molecules.

Attributes:

molecule1Molecule: The first molecule in the dimer.
molecule2Molecule: The second molecule in the dimer.
identifierstr, optional: An identifier for the dimer. If not provided, it is generated from the identifiers of the two molecules.
H_intnumpy.ndarray: The interaction Hamiltonian matrix between the two molecules.
t_HOMOfloat: The hopping parameter for the highest occupied molecular orbital (HOMO).
t_HOMO_1float: The hopping parameter for the first HOMO-1.
t_HOMO_2float: The hopping parameter for the second HOMO-2.
t_LUMOfloat: The hopping parameter for the lowest unoccupied molecular orbital (LUMO).
t_LUMO_1float: The hopping parameter for the first LUMO-1.
t_LUMO_2float: The hopping parameter for the second LUMO-2.

Methods

save_results(directory=”results”):

Saves the results of the calculation to a JSON file.

save_results(directory='results')

Save the results of the calculation to a JSON file.

Parameters:

directorystr, optional: The directory where the results file will be saved (default is “results”).

Notes

Note

The results include the HOMO and LUMO energies of two molecules and their coupling terms. The results are saved in a JSON file named after the identifier of the object.

DNA Sequence

class qDNA.DNA_Seq(upper_strand, tb_model_name, methylated=True, lower_strand='auto_complete')

A class to represent a DNA sequence and its properties based on a tight- binding model.

Parameters:

upper_strandstr: The upper strand of the DNA sequence.
tb_model_namestr: The name of the tight-binding model.
methylatedbool, optional: Indicates whether the DNA sequence is methylated (default is True).
lower_strandstr, optional: The lower strand of the DNA sequence (default is ‘auto_complete’).

Attributes:

upper_strandstr: The upper strand of the DNA sequence.
lower_strandstr: The lower strand of the DNA sequence.
methylatedbool: Indicates whether the DNA sequence is methylated.
tb_model_namestr: The name of the tight-binding model.
tb_model_propsdict: Properties of the tight-binding model.
backbonebool: Indicates whether the model includes a backbone.
double_strandedbool: Indicates whether the DNA is double-stranded.
num_strandsint: Number of strands in the DNA sequence.
num_sites_per_strandint: Number of sites per strand in the DNA sequence.
tb_dimstuple: Dimensions of the tight-binding model.
complementary_base_dictdict: Dictionary mapping each base to its complementary base.
dna_seqtuple: The generated DNA sequence.

Tight-binding Model

class qDNA.model.TB_Model(tb_model_name, tb_dims)

A class to define a predefined tight-binding model.

Parameters:

tb_model_namestr: The name of the predefined tight-binding model.
tb_dimstuple: A tuple specifying the dimensions of the model (number of strands, number of sites per strand).

Attributes:

tb_model_namestr: The name of the predefined tight-binding model.
tb_dimstuple: The dimensions of the model (number of strands, number of sites per strand).
num_strandsint: The number of strands in the model.
num_sites_per_strandint: The number of sites per strand.
num_sitesint: The total number of sites in the model.
tb_model_propsdict: The properties of the predefined tight-binding model.
tb_configlist of tuple: The configurations of the model.
tb_basislist of str: The basis states of the model.
eh_basislist of str: The electron-hole basis states of the model.
verbosebool: Verbose mode for printing debug information.

Tight-binding Hamiltonian

class qDNA.hamiltonian.TB_Ham(dna_seq, **ham_kwargs)

A class used to represent the tight-binding Hamiltonian for DNA sequences.

Parameters:

dna_seqDNA_Seq: The DNA sequence object containing the sequence and model information.
ham_kwargsdict: Additional keyword arguments for the Hamiltonian construction.

Attributes:

dna_seqDNA_Seq: The DNA sequence object containing the sequence and model information.
tb_modelTB_Model: The tight-binding model associated with the DNA sequence.
tb_basislist: The tight-binding basis states.
tb_sites_flattenedlist: The flattened list of tight-binding sites.
tb_basis_sites_dictdict: Dictionary mapping the TB basis to the TB sites.
tb_sitesnp.ndarray: The array of TB sites.
descriptionstr: Description of the Hamiltonian (e.g., ‘1P’ or ‘2P’).
particleslist: List of particles considered (e.g., [‘electron’, ‘hole’]).
sourcestr: Source of the tight-binding parameters.
unitstr: Unit of the Hamiltonian parameters.
tb_params_electrondict: Tight-binding parameters for electrons.
tb_params_holedict: Tight-binding parameters for holes.
relaxationbool: Flag indicating if relaxation is considered.
coulomb_paramfloat: Coulomb interaction parameter for the Hamiltonian.
exchange_paramfloat: Exchange interaction parameter for the Hamiltonian.
eh_basislist: Electron-hole basis states.
nn_cutoffbool: Nearest-neighbor cutoff for interactions.
matrixnp.ndarray: The Hamiltonian matrix.
matrix_dimint: Dimension of the Hamiltonian matrix.
backbonebool: Flag indicating if the model has a backbone.

Methods

get_param_dict(particle)	Retrieves the tight-binding parameters.
get_eigensystem()	Computes and returns the eigenvalues and eigenvectors of the Hamiltonian.
get_matrix()	Computes and returns the Hamiltonian matrix.
get_fourier(init_state, end_state, quantities)	Computes Fourier components of the Hamiltonian for given states.
get_amplitudes(init_state, end_state)	Computes and returns the amplitudes for given states.
get_frequencies(init_state, end_state)	Computes and returns the frequencies for given states.
get_average_pop(init_state, end_state)	Computes and returns the average population for given states.
get_backbone_pop(init_state)	Computes and returns the population of particles on the backbone sites.

get_backbone_pop(init_state)

Calculate the population of particles on the backbone sites of a Fishbone model.

Parameters:

init_statestr: The initial state of the system.

Returns:

dict: A dictionary where keys are particle identifiers and values are the population of each particle on the backbone sites.

Raises:

AssertionError: If the model is not a Fishbone model.

get_eigensystem()

Compute the eigenvalues and eigenvectors of the matrix. This method computes the eigenvalues and eigenvectors of the matrix associated with the instance. If the description is “2P” and relaxation is enabled, the ground state is deleted from the matrix before computing the eigensystem.

Returns:

tuple

eigenvaluesndarray: The eigenvalues of the matrix.
eigenvectorsndarray: The eigenvectors of the matrix.

get_fourier(init_state, end_state, quantities)

Calculate the Fourier components of the transition between initial and end states.

Parameters:

init_statestr: The initial state from which the transition starts.
end_statestr: The end state to which the transition occurs.
quantitieslist of str: List of quantities to calculate. Possible values are “amplitude”, “frequency”, and “average_pop”.

Returns:

amplitudes_dictdict: Dictionary containing the amplitudes for each particle.
frequencies_dictdict: Dictionary containing the frequencies for each particle.
average_pop_dictdict: Dictionary containing the average population for each particle.

Raises:

AssertionError: If end_state is not in self.tb_basis. If init_state is not in self.eh_basis or self.tb_basis depending on the description.

get_matrix()

Generate the tight-binding Hamiltonian matrix based on the system description.

Returns:

matrixnumpy.ndarray: The Hamiltonian matrix for the system.

Raises:

ValueError: If the description attribute is not “2P” or “1P”.

Notes

Note

For a “2P” description, the Hamiltonian matrix is generated using tb_ham_2P and may include interaction and relaxation terms if specified.
For a “1P” description, the Hamiltonian matrix is generated using tb_ham_1P for either electrons or holes based on the particles attribute.

get_param_dict(particle)

Retrieves the tight-binding parameters for the selected particle. This method loads the tight-binding parameters from the specified source and model name. If the unit of the loaded parameters does not match the expected unit, it converts the parameters to the expected unit.

Parameters:

particlestr: The particle for which to retrieve the tight-binding parameters.

Returns:

tuple

tb_paramsdict: The tight-binding parameters.

Lindblad Dissipator

class qDNA.environment.Lindblad_Diss(tb_ham, **diss_kwargs)

Provides the operators of the form \(\sqrt{\gamma} a\) that are used in the Lindblad dissipator of the master equation.

Parameters:

tb_hamTBHamType: The tight-binding Hamiltonian.
diss_kwargsdict: Additional keyword arguments for the dissipator.

Attributes:

tb_hamTBHamType: The tight-binding Hamiltonian.
num_sitesint: Number of sites in the tight-binding model.
loc_deph_ratefloat: Local dephasing rate.
glob_deph_ratefloat: Global dephasing rate.
uniform_relaxationbool: Flag for uniform relaxation.
relax_ratesdict: Relaxation rates for each DNA base.
loc_thermbool: Flag for local thermalization.
glob_thermbool: Flag for global thermalization.
deph_ratefloat: Dephasing rate.
cutoff_freqfloat: Cutoff frequency.
reorg_energyfloat: Reorganization energy.
temperaturefloat: Temperature in Kelvin.
spectral_densitystr: Type of spectral density (‘debye’ or ‘ohmic’).
exponentfloat: Exponent for the Ohmic spectral density.
relax_opslist: List of relaxation operators.
deph_opslist: List of dephasing operators.
therm_opslist: List of thermalizing operators.
c_opslist: List of collapse operators.
num_c_opsint: Number of collapse operators.
e_opstuple: Tuple containing population, coherence, and ground state population operators.
pop_opsdict: Population operators.
coh_opsdict: Coherence operators.
groundstate_pop_opsdict: Ground state population operators.
unitstr: Unit of the operators.

Master Equation Solver

class qDNA.dynamics.ME_Solver(tb_ham, lindblad_diss, **me_kwargs)

A class used to solve master equations using the tight-binding Hamiltonian and Lindblad dissipator.

This class provides methods to initialize the solver, set up the Hamiltonian and Lindblad dissipator, and compute various properties such as populations, coherences, and ground state populations over time.

Parameters:

tb_hamTB_Ham: The tight-binding Hamiltonian.
lindblad_dissLindblad_Diss: The Lindblad dissipator.
me_kwargsdict, optional: Additional keyword arguments for the master equation solver.

Attributes:

me_kwargsdict: Keyword arguments for the master equation solver.
verbosebool: Flag for verbose output.
t_stepsint: Number of time steps.
t_endint: End time.
timesnp.ndarray: Array of time points.
t_unitstr: Time unit.
tb_hamTB_Ham: The tight-binding Hamiltonian.
tb_modelTB_Model: The tight-binding model.
lindblad_dissLindblad_Diss: The Lindblad dissipator.
init_statetuple or str: Initial state depending on the Hamiltonian description.
init_matrixqutip.Qobj: Initial density matrix.
resultlist: List to store the results.
groundstate_popdict: Dictionary to store ground state population.
popdict: Dictionary to store population of states.
cohdict: Dictionary to store coherence of states.

Methods

get_init_matrix()	Generate the initial state matrix for the quantum system based on the Hamiltonian description.
get_result()	Calculate and return the result of the master equation solver.
get_result_particle(particle)	Retrieve the reduced density matrix for a specified particle.
get_pop()	Calculate and return the population of particles in the system.
get_coh()	Calculate and return the coherence of the system.
get_groundstate_pop()	Calculate and return the ground state population.
reset()	Resets the solver’s state by clearing results and initializing dictionaries for populations and coherences.

get_coh()

Calculate and return the coherence of the system. This method computes the coherence of the system based on the Hamiltonian description and the Lindblad dissipation operators. It supports two types of Hamiltonian descriptions: “2P” and “1P”. For “2P” description, it uses the coherence operators from the Lindblad dissipation. For “1P” description, it constructs the coherence operators based on the tensor basis permutations. The method then solves the master equation using the QuTiP qutip.mesolve function and calculates the coherence for each particle in the system.

Returns:

dict: A dictionary where the keys are particle identifiers and the values are the computed coherence values.

get_groundstate_pop()

Calculate and return the ground state population. This function computes the ground state population of a system described by a two- particle (2P) Hamiltonian with relaxation. If the ground state population has already been computed, it returns the cached result.

Returns:

dict: A dictionary containing the ground state population with the key “groundstate”.

Raises:

AssertionError: If the Hamiltonian description is not “2P”.
AssertionError: If relaxation is not enabled in the Hamiltonian.

get_init_matrix()

Generate the initial state matrix for the quantum system based on the Hamiltonian description. The method supports two types of descriptions for the tight-binding Hamiltonian (tb_ham): “2P” (two- particle) and “1P” (one- particle). Depending on the description and the initialization parameters, the initial state matrix is constructed either as a delocalized state over all exciton states or as a localized state on a single exciton state.

Returns:

qutip.Qobj: The initial state matrix of the quantum system as a Qobj instance from the QuTiP library.

Raises:

ValueError: If the Hamiltonian description is not recognized.

get_pop()

Calculate and return the population of particles in the system. This method computes the population of particles based on the Hamiltonian description and the Lindblad dissipation operators. It uses the QuTiP library to solve the master equation and obtain the expectation values of the population operators.

Returns:

dict: A dictionary where the keys are particle-site combinations and the values are the corresponding population expectation values.

Notes

Note

If the population self.pop is already computed, it returns the cached result.
The method supports two types of Hamiltonian descriptions: “2P” and “1P”.
For “2P” description, it uses the population operators from self.lindblad_diss.pop_ops.
For “1P” description, it constructs the population operators based on the tight-binding basis self.tb_ham.tb_basis.
The master equation is solved using qutip.mesolve with the Hamiltonian matrix, initial state, time points, collapse operators, and population operators.

get_result()

Calculate and return the result of the master equation solver. This method checks if the result has already been calculated. If not, it constructs the Hamiltonian matrix and solves the master equation using QuTiP’s qutip.mesolve function. The result is then stored and returned.

Returns:

list: A list of quantum states representing the solution of the master equation at different time points.

get_result_particle(particle)

Retrieve the reduced density matrix for a specified particle. This method checks if the result has already been calculated. If not, it calculates the result. Then, it checks if the reduced density matrix for the specified particle has been calculated. If not, it calculates the reduced density matrix for the specified particle and stores it.

Parameters:

particlestr: The particle for which the reduced density matrix is to be retrieved.

Returns:

list: A list of reduced density matrices for the specified particle.

reset()

Resets the solver’s state by clearing results and initializing dictionaries for populations and coherences.

Notes

Note

Clears the result list (for the full the all reduced density matrices).
Initializes groundstate_pop, pop, and coh dictionaries.