API documentation

This chapter contains automatically generated API documentation, including a list of QuantumDNA’s public classes and functions.

• Classes
  • Linear Combination of Atomic Orbitals
    • Base
    • BasePair
    • Dimer
  • DNA Sequence
    • DNA_Seq
  • Tight-binding Model
    • TB_Model
  • Tight-binding Hamiltonian
    • TB_Ham
  • Lindblad Dissipator
    • Lindblad_Diss
  • Master Equation Solver
    • ME_Solver
• Functions
  • Calculate Tight-Binding Parameters
    • calc_orbital_energy()
    • calc_orbital_overlap()
    • load_xyz()
    • convert_json_to_xyz()
    • convert_pdb_to_xyz()
    • calc_tb_energies_monomers()
    • calc_tb_params_dimer()
    • calc_tb_params()
  • Save and Load Tight-Binding Parameters
    • save_tb_params()
    • load_tb_params()
    • wrap_save_tb_params()
    • wrap_load_tb_params()
  • Tight-Binding Basis
    • get_tb_basis()
    • get_eh_basis()
    • get_eh_distance()
    • get_particle_eh_states()
    • basis_change()
    • local_to_global()
    • global_to_local()
  • Tight-Binding Configuration
    • get_tb_config()
  • DNA sequences
    • create_upper_strands()
  • Tight-Binding Hamiltonian
    • set_matrix_element()
    • tb_ham_1P()
    • tb_ham_2P()
    • add_groundstate()
    • delete_groundstate()
    • add_interaction()
  • Lindblad rates
    • debye_spectral_density()
    • ohmic_spectral_density()
    • bose_einstein_distrib()
    • dephasing_rate()
  • Lindblad operators
    • get_relax_op()
    • get_glob_therm_op()
    • get_glob_therm_ops()
    • get_loc_therm_op()
    • get_loc_therm_ops()
    • get_loc_deph_ops()
    • get_glob_deph_ops()
    • get_loc_deph_p_ops()
    • get_glob_deph_p_ops()
  • Master Equation Solver
    • get_me_solver()
  • Reduced Density Matrix
    • get_reduced_dm()
    • get_reduced_dm_eigs()
  • Exciton Observables
    • calc_lifetime()
    • calc_lifetime_dict()
    • calc_dipole()
    • calc_dipole_wrapper()
    • calc_dipole_dict()
  • Observables
    • get_tb_observable()
    • get_eh_observable()
    • get_pop_particle()
    • get_coh_particle()
  • Equilibrium states
    • get_therm_eq_state()
    • get_deph_eq_state()
• Utilities
  • Unit Conversion
    • get_conversion()
    • get_all_conversions()
    • get_conversion_dict()
  • Hamiltonian Analysis
    • calc_average_pop()
    • calc_amplitudes()
    • calc_frequencies()
    • get_pop_fourier()
    • calc_ipr_hamiltonian()
  • Density Matrix Analysis
    • calc_trace_distance()
    • calc_purity()
    • calc_coherence()
    • calc_ipr_dm()
• Visualization
  • Plot DNA Base Frequency
    • plot_dna_base_frequency()
  • Plot Eigenspectrum
    • plot_eigv()
    • plot_eigs()
  • Plot Fourier Analysis
    • plot_fourier()
    • plot_average_pop()
  • Plot Populations and Coherences
    • plot_pop_fourier()
    • plot_pop()
    • plot_pops()
    • plot_pops_heatmap()
    • plot_coh()
    • plot_test_fourier()