Index

A

add_groundstate() (in module qDNA.hamiltonian)

add_interaction() (in module qDNA.hamiltonian)

B

Base (class in qDNA.lcao) BasePair (class in qDNA.lcao)

basis_change() (in module qDNA.model) bose_einstein_distrib() (in module qDNA.environment)

C

calc_amplitudes() (in module qDNA.utils) calc_average_pop() (in module qDNA.utils) calc_coherence() (in module qDNA.utils) calc_dipole() (in module qDNA.evaluation) calc_dipole_dict() (in module qDNA.evaluation) calc_dipole_moment() (qDNA.lcao.Base method) calc_dipole_wrapper() (in module qDNA.evaluation) calc_frequencies() (in module qDNA.utils) calc_ipr_dm() (in module qDNA.utils) calc_ipr_hamiltonian() (in module qDNA.utils) calc_lifetime() (in module qDNA.evaluation) calc_lifetime_dict() (in module qDNA.evaluation)

calc_MO() (qDNA.lcao.Base method) (qDNA.lcao.BasePair method) calc_orbital_energy() (in module qDNA.lcao) calc_orbital_overlap() (in module qDNA.lcao) calc_oscillator_strength() (qDNA.lcao.Base method) calc_purity() (in module qDNA.utils) calc_tb_energies_monomers() (in module qDNA.lcao) calc_tb_params() (in module qDNA.lcao) calc_tb_params_dimer() (in module qDNA.lcao) calc_trace_distance() (in module qDNA.utils) convert_json_to_xyz() (in module qDNA.lcao) convert_pdb_to_xyz() (in module qDNA.lcao) create_upper_strands() (in module qDNA)

D

debye_spectral_density() (in module qDNA.environment) delete_groundstate() (in module qDNA.hamiltonian)

dephasing_rate() (in module qDNA.environment) Dimer (class in qDNA.lcao) DNA_Seq (class in qDNA)

G

get_all_conversions() (in module qDNA.utils) get_backbone_pop() (qDNA.hamiltonian.TB_Ham method) get_coh() (qDNA.dynamics.ME_Solver method) get_coh_particle() (in module qDNA.environment) get_conversion() (in module qDNA.utils) get_conversion_dict() (in module qDNA.utils) get_deph_eq_state() (in module qDNA.evaluation) get_eh_basis() (in module qDNA.model) get_eh_distance() (in module qDNA.model) get_eh_observable() (in module qDNA.environment) get_eigensystem() (qDNA.hamiltonian.TB_Ham method) get_fourier() (qDNA.hamiltonian.TB_Ham method) get_glob_deph_ops() (in module qDNA.environment) get_glob_deph_p_ops() (in module qDNA.environment) get_glob_therm_op() (in module qDNA.environment) get_glob_therm_ops() (in module qDNA.environment) get_groundstate_pop() (qDNA.dynamics.ME_Solver method) get_init_matrix() (qDNA.dynamics.ME_Solver method) get_loc_deph_ops() (in module qDNA.environment)

get_loc_deph_p_ops() (in module qDNA.environment) get_loc_therm_op() (in module qDNA.environment) get_loc_therm_ops() (in module qDNA.environment) get_matrix() (qDNA.hamiltonian.TB_Ham method) get_me_solver() (in module qDNA.dynamics) get_param_dict() (qDNA.hamiltonian.TB_Ham method) get_particle_eh_states() (in module qDNA.model) get_pop() (qDNA.dynamics.ME_Solver method) get_pop_fourier() (in module qDNA.utils) get_pop_particle() (in module qDNA.environment) get_reduced_dm() (in module qDNA.dynamics) get_reduced_dm_eigs() (in module qDNA.dynamics) get_relax_op() (in module qDNA.environment) get_result() (qDNA.dynamics.ME_Solver method) get_result_particle() (qDNA.dynamics.ME_Solver method) get_tb_basis() (in module qDNA.model) get_tb_config() (in module qDNA.model) get_tb_observable() (in module qDNA.environment) get_therm_eq_state() (in module qDNA.evaluation) global_to_local() (in module qDNA.model)

L

Lindblad_Diss (class in qDNA.environment) load_tb_params() (in module qDNA.hamiltonian)

load_xyz() (in module qDNA.lcao) local_to_global() (in module qDNA.model)

M

ME_Solver (class in qDNA.dynamics)

O

ohmic_spectral_density() (in module qDNA.environment)

P

plot_average_pop() (in module qDNA.visualization) plot_coh() (in module qDNA.visualization) plot_dna_base_frequency() (in module qDNA.visualization) plot_eigs() (in module qDNA.visualization) plot_eigv() (in module qDNA.visualization)

plot_fourier() (in module qDNA.visualization) plot_pop() (in module qDNA.visualization) plot_pop_fourier() (in module qDNA.visualization) plot_pops() (in module qDNA.visualization) plot_pops_heatmap() (in module qDNA.visualization) plot_test_fourier() (in module qDNA.visualization)

R

reset() (qDNA.dynamics.ME_Solver method)

S

save_results() (qDNA.lcao.Base method) (qDNA.lcao.BasePair method) (qDNA.lcao.Dimer method)

save_tb_params() (in module qDNA.hamiltonian) set_matrix_element() (in module qDNA.hamiltonian)

T

TB_Ham (class in qDNA.hamiltonian) tb_ham_1P() (in module qDNA.hamiltonian)

tb_ham_2P() (in module qDNA.hamiltonian) TB_Model (class in qDNA.model)

W

wrap_load_tb_params() (in module qDNA.hamiltonian)

wrap_save_tb_params() (in module qDNA.hamiltonian)