Index

A

adjust_hamiltonian() (radicalpy.simulation.HilbertIncoherentProcessBase method) (radicalpy.simulation.LiouvilleIncoherentProcessBase method) adjust_product_probabilities() (radicalpy.kinetics.Exponential method) (radicalpy.simulation.HilbertIncoherentProcessBase method) all_keys (radicalpy.classical.RateEquations property) all_nuclei() (radicalpy.data.Molecule class method) angular_frequency_in_MHz() (in module radicalpy.utils) angular_frequency_to_Gauss() (in module radicalpy.utils) angular_frequency_to_mT() (in module radicalpy.utils) anisotropic (radicalpy.data.Hfc property) anisotropy() (in module radicalpy.experiments)

anisotropy_check() (in module radicalpy.utils) anisotropy_loop() (in module radicalpy.experiments) anisotropy_surface() (in module radicalpy.plot) apply_hilbert_kinetics() (radicalpy.simulation.HilbertSimulation static method) apply_liouville_hamiltonian_modifiers() (radicalpy.simulation.HilbertSimulation method) (radicalpy.tensornetwork.BaseMPSSimulation method) aqueous_glycerol_viscosity() (in module radicalpy.estimations) are_valid_keys() (radicalpy.classical.RateEquations method) autocorrelation() (in module radicalpy.utils) autocorrelation_fit() (in module radicalpy.estimations) available() (radicalpy.data.Isotope class method) (radicalpy.data.Molecule class method)

B

BaseMPSSimulation (class in radicalpy.tensornetwork) Basis (class in radicalpy.simulation) Bhalf_fit() (in module radicalpy.utils) Bhalf_LFEhalf_fit() (in module radicalpy.utils) Bhalf_theoretical_hyperfine() (in module radicalpy.estimations)

Bhalf_theoretical_relaxation() (in module radicalpy.estimations) Bhalf_theoretical_relaxation_delay() (in module radicalpy.estimations) bloch_redfield_liouvillian() (radicalpy.simulation.HilbertSimulation method) bloch_redfield_solver() (radicalpy.simulation.HilbertSimulation method) bloch_redfield_time_evolution() (radicalpy.simulation.HilbertSimulation method)

C

cartesian_to_spherical() (in module radicalpy.utils) check_initial_states() (radicalpy.classical.RateEquations method) cidnp() (in module radicalpy.experiments) cidnp_polarisation_diffusion_model() (in module radicalpy.utils) cidnp_polarisation_exponential_model() (in module radicalpy.utils) cidnp_polarisation_truncated_diffusion_model() (in module radicalpy.utils)

CISS (radicalpy.simulation.State attribute) coherent_control() (in module radicalpy.experiments) Constant (class in radicalpy.shared) convert() (radicalpy.simulation.HilbertSimulation static method) (radicalpy.simulation.LiouvilleSimulation static method) coupling (radicalpy.simulation.HilbertSimulation property) custom (radicalpy.data.Molecule attribute)

D

define_xyz() (in module radicalpy.utils) density_matrix_animation() (in module radicalpy.plot) details (radicalpy.shared.Constant attribute) diffusion_coefficient() (in module radicalpy.estimations) dipolar_hamiltonian() (radicalpy.simulation.HilbertSimulation method) (radicalpy.tensornetwork.BaseMPSSimulation method) (radicalpy.tensornetwork.MPDOSimulation method) dipolar_hamiltonian_1d() (radicalpy.simulation.HilbertSimulation method)

dipolar_hamiltonian_3d() (radicalpy.simulation.HilbertSimulation method) dipolar_interaction_anisotropic() (in module radicalpy.estimations) dipolar_interaction_anisotropic_from_dipolar_vector() (in module radicalpy.estimations) dipolar_interaction_anisotropic_from_dipolar_vector_without_prefactor() (in module radicalpy.estimations) dipolar_interaction_isotropic() (in module radicalpy.estimations) dipolar_interaction_MC() (in module radicalpy.estimations) dipolar_interaction_point_dipole() (in module radicalpy.estimations) DipolarModulation (class in radicalpy.relaxation) double_Lorentzian() (in module radicalpy.utils)

E

effective_hyperfine (radicalpy.data.Molecule property) eigensorter() (in module radicalpy.utils) energy_levels() (in module radicalpy.plot) enumerate_spin_states_from_base() (in module radicalpy.utils) EPR (radicalpy.simulation.State attribute) epr() (in module radicalpy.experiments) EquationRateResult (class in radicalpy.classical) EQUILIBRIUM (radicalpy.simulation.State attribute)

exchange_hamiltonian() (radicalpy.simulation.HilbertSimulation method) (radicalpy.tensornetwork.BaseMPSSimulation method) (radicalpy.tensornetwork.MPDOSimulation method) exchange_interaction_in_protein() (in module radicalpy.estimations) exchange_interaction_in_solution() (in module radicalpy.estimations) exchange_interaction_in_solution_MC() (in module radicalpy.estimations) Exponential (class in radicalpy.kinetics) external_field_mT() (radicalpy.simulation.SemiclassicalSimulation method)

F

field_switching() (in module radicalpy.experiments) from_nuclei() (radicalpy.data.FuseNucleus class method) fromdb() (radicalpy.data.Molecule class method)

fromisotope() (radicalpy.data.Nucleus class method) fromisotopes() (radicalpy.data.Molecule class method) fromjson() (radicalpy.shared.Constant static method) FuseNucleus (class in radicalpy.data)

G

g_tensor_relaxation_rate() (in module radicalpy.estimations) gamma_mT (radicalpy.data.Isotope property) (radicalpy.data.Nucleus property) Gauss_to_angular_frequency() (in module radicalpy.utils) Gauss_to_MHz() (in module radicalpy.utils) Gauss_to_mT() (in module radicalpy.utils) get_angle_between_plane() (in module radicalpy.utils)

get_data() (in module radicalpy.data) get_delta_r() (in module radicalpy.classical) get_eye() (radicalpy.simulation.HilbertSimulation method) (radicalpy.simulation.SparseCholeskyHilbertSimulation method) get_rotation_matrix_euler_angles() (in module radicalpy.utils) GHz_to_meV() (in module radicalpy.utils) GHz_to_mK() (in module radicalpy.utils) GTensorAnisotropy (class in radicalpy.relaxation)

H

Haberkorn (class in radicalpy.kinetics) haberkorn_hamiltonian() (radicalpy.tensornetwork.BaseMPSSimulation method) (radicalpy.tensornetwork.MPDOSimulation method) HaberkornFree (class in radicalpy.kinetics) hamiltonian_size (radicalpy.simulation.HilbertSimulation property) (radicalpy.simulation.LiouvilleSimulation property) Hfc (class in radicalpy.data)

hfc (radicalpy.data.Nucleus attribute) hilbert_to_liouville() (in module radicalpy.utils) HilbertIncoherentProcessBase (class in radicalpy.simulation) HilbertKineticsBase (class in radicalpy.kinetics) HilbertSimulation (class in radicalpy.simulation) hyperfine_hamiltonian() (radicalpy.simulation.HilbertSimulation method) (radicalpy.tensornetwork.BaseMPSSimulation method) (radicalpy.tensornetwork.MPDOSimulation method)

I

infer_bonds() (in module radicalpy.utils) info (radicalpy.data.Molecule attribute) init() (radicalpy.kinetics.Haberkorn method) (radicalpy.kinetics.HaberkornFree method) (radicalpy.kinetics.JonesHore method) (radicalpy.relaxation.DipolarModulation method) (radicalpy.relaxation.GTensorAnisotropy method) (radicalpy.relaxation.RandomFields method) (radicalpy.relaxation.SingletTripletDephasing method) (radicalpy.relaxation.T1Relaxation method) (radicalpy.relaxation.T2Relaxation method) (radicalpy.relaxation.TripletTripletDephasing method) (radicalpy.relaxation.TripletTripletRelaxation method) (radicalpy.simulation.HilbertIncoherentProcessBase method)

initial_density_matrix (radicalpy.data.FuseNucleus property) initial_density_matrix() (radicalpy.simulation.HilbertSimulation method) (radicalpy.simulation.LiouvilleSimulation method) (radicalpy.tensornetwork.BaseMPSSimulation method) is_fast_run() (in module radicalpy.utils) Isotope (class in radicalpy.data) isotropic (radicalpy.data.Hfc property)

J

J_to_meV() (in module radicalpy.utils)

JonesHore (class in radicalpy.kinetics)

K

k_constant() (in module radicalpy.estimations) k_D() (in module radicalpy.estimations) k_electron_transfer() (in module radicalpy.estimations) k_excitation() (in module radicalpy.estimations) k_recombination() (in module radicalpy.estimations)

k_reencounter() (in module radicalpy.estimations) k_ST_mixing() (in module radicalpy.estimations) k_STD() (in module radicalpy.estimations) k_STD_microreactor() (in module radicalpy.estimations) k_triplet_relaxation() (in module radicalpy.estimations) kine_quantum_mary() (in module radicalpy.experiments)

L

label (radicalpy.classical.Rate attribute) latex_eqlist_to_align() (in module radicalpy.classical) latexify() (in module radicalpy.classical) lindblad_liouvillian() (radicalpy.simulation.HilbertSimulation method) linear_energy_levels() (in module radicalpy.plot) liouville_projection_operator() (radicalpy.simulation.LiouvilleSimulation method)

LiouvilleIncoherentProcessBase (class in radicalpy.simulation) LiouvilleKineticsBase (class in radicalpy.kinetics) LiouvilleRelaxationBase (class in radicalpy.relaxation) LiouvilleSimulation (class in radicalpy.simulation) load_molecule_json() (radicalpy.data.Molecule class method) LocallyPurifiedMPSSimulation (class in radicalpy.tensornetwork) Lorentzian() (in module radicalpy.utils)

M

magnetic_field_loop() (in module radicalpy.experiments) magnetic_field_loop_semiclassical() (in module radicalpy.experiments) magnetogyric_ratio (radicalpy.data.Nucleus attribute) make_resonance_sticks() (in module radicalpy.utils) mary() (in module radicalpy.experiments) mary_lfe_hfe() (in module radicalpy.experiments) mary_lorentzian() (in module radicalpy.utils) mary_semiclassical() (in module radicalpy.experiments) matrix_to_vector() (in module radicalpy.utils) max_workers (radicalpy.tensornetwork.StochasticMPSSimulation attribute) meV_to_GHz() (in module radicalpy.utils) meV_to_J() (in module radicalpy.utils) meV_to_mK() (in module radicalpy.utils) MHz_in_angular_frequency() (in module radicalpy.utils) MHz_to_Gauss() (in module radicalpy.utils) MHz_to_mT() (in module radicalpy.utils) mK_to_GHz() (in module radicalpy.utils) mK_to_meV() (in module radicalpy.utils) modulated_mary_brute_force() (in module radicalpy.experiments) modulated_signal() (in module radicalpy.utils) module radicalpy radicalpy.classical radicalpy.data radicalpy.estimations radicalpy.experiments radicalpy.kinetics radicalpy.plot radicalpy.relaxation radicalpy.shared radicalpy.simulation radicalpy.tensornetwork radicalpy.utils

mol_to_plot_arrays() (in module radicalpy.utils) Molecule (class in radicalpy.data) monte_carlo_caged() (in module radicalpy.plot) monte_carlo_free() (in module radicalpy.plot) MPDOSimulation (class in radicalpy.tensornetwork) mT_to_angular_frequency() (in module radicalpy.utils) mT_to_Gauss() (in module radicalpy.utils) mT_to_MHz() (in module radicalpy.utils) multiplicities_spin() (radicalpy.data.FuseNucleus static method) multiplicity (radicalpy.data.Nucleus attribute) multiplicity_to_spin() (in module radicalpy.data)

N

name (radicalpy.data.Molecule attribute) (radicalpy.data.Nucleus attribute) negativity() (in module radicalpy.utils) nmr() (in module radicalpy.experiments) nmr_chemical_shift_imaginary_modulation() (in module radicalpy.utils) nmr_chemical_shift_real_modulation() (in module radicalpy.utils)

nmr_scalar_coupling_modulation() (in module radicalpy.utils) nmr_t2_relaxation() (in module radicalpy.utils) nsamples (radicalpy.tensornetwork.StochasticMPSSimulation attribute) nuclei (radicalpy.data.Molecule attribute) (radicalpy.simulation.HilbertSimulation property) (radicalpy.simulation.SemiclassicalSimulation property) Nucleus (class in radicalpy.data)

O

observable_projection_operator() (radicalpy.simulation.HilbertSimulation method) (radicalpy.simulation.LiouvilleSimulation method) (radicalpy.tensornetwork.BaseMPSSimulation method)

odmr() (in module radicalpy.experiments) omfe() (in module radicalpy.experiments) oop_eseem() (in module radicalpy.experiments)

P

parse_label_xyz_txt() (in module radicalpy.utils) parse_pdb() (in module radicalpy.utils) parse_xyz() (in module radicalpy.utils) particles (radicalpy.simulation.HilbertSimulation property) pauli (radicalpy.data.FuseNucleus property) (radicalpy.data.Nucleus property) pdb_label() (in module radicalpy.utils) plot_3d_results() (in module radicalpy.plot) plot_autocorrelation_fit() (in module radicalpy.plot) plot_bhalf_time() (in module radicalpy.plot) plot_exchange_interaction_in_solution() (in module radicalpy.plot) plot_general() (in module radicalpy.plot) plot_molecule() (in module radicalpy.plot)

plot_sphere() (in module radicalpy.plot) product_operator() (radicalpy.simulation.HilbertSimulation method) product_operator_3d() (radicalpy.simulation.HilbertSimulation method) product_probability() (radicalpy.simulation.HilbertSimulation method) (radicalpy.simulation.SparseCholeskyHilbertSimulation method) (radicalpy.tensornetwork.BaseMPSSimulation method) product_yield() (radicalpy.simulation.HilbertSimulation static method) projection_operator() (radicalpy.simulation.HilbertSimulation method) propagate() (radicalpy.simulation.HilbertSimulation method) (radicalpy.simulation.LiouvilleSimulation method) (radicalpy.simulation.SparseCholeskyHilbertSimulation method) (radicalpy.tensornetwork.BaseMPSSimulation method) purity() (in module radicalpy.utils)

R

radical (radicalpy.data.Molecule attribute) radicalpy module radicalpy.classical module radicalpy.data module radicalpy.estimations module radicalpy.experiments module radicalpy.kinetics module radicalpy.plot module radicalpy.relaxation module radicalpy.shared module radicalpy.simulation module

radicalpy.tensornetwork module radicalpy.utils module radicals (radicalpy.simulation.HilbertSimulation property) random_theta_phi() (in module radicalpy.classical) RandomFields (class in radicalpy.relaxation) randomwalk_3d() (in module radicalpy.classical) Rate (class in radicalpy.classical) rate_constant (radicalpy.kinetics.JonesHore property) (radicalpy.simulation.HilbertIncoherentProcessBase property) RateEquations (class in radicalpy.classical) reaction_scheme() (in module radicalpy.classical) read_lines_utf8_or_utf16le() (in module radicalpy.utils) read_orca_hyperfine() (in module radicalpy.utils) read_trajectory_files() (in module radicalpy.utils) reference_signal() (in module radicalpy.utils) rodrigues_rotation() (in module radicalpy.utils) rotate_axes() (in module radicalpy.utils) rotational_correlation_time_for_molecule() (in module radicalpy.estimations) rotational_correlation_time_for_protein() (in module radicalpy.estimations) rydmr() (in module radicalpy.experiments)

S

s_t0_omega() (in module radicalpy.utils) SECOND_ORDER_POLARISATION (radicalpy.simulation.State attribute) semiclassical_HHs() (radicalpy.simulation.SemiclassicalSimulation method) semiclassical_mary() (in module radicalpy.experiments) semiclassical_std (radicalpy.data.Molecule property) SemiclassicalSimulation (class in radicalpy.simulation) set_equal_aspect() (in module radicalpy.plot) SINGLET (radicalpy.simulation.State attribute) SingletTripletDephasing (class in radicalpy.relaxation) smiles_to_3d() (in module radicalpy.utils) SparseCholeskyHilbertSimulation (class in radicalpy.simulation) spectral_density() (in module radicalpy.utils) spherical_average() (in module radicalpy.utils) spherical_to_cartesian() (in module radicalpy.utils) spin_character() (in module radicalpy.utils)

spin_operator() (radicalpy.simulation.HilbertSimulation method) (radicalpy.simulation.SparseCholeskyHilbertSimulation method) (radicalpy.tensornetwork.BaseMPSSimulation method) spin_orbit_hamiltonian() (radicalpy.simulation.HilbertSimulation method) spin_quantum_number (radicalpy.data.Isotope property) (radicalpy.data.Nucleus property) spin_state_labels() (in module radicalpy.plot) spin_to_multiplicity() (in module radicalpy.data) ST (radicalpy.simulation.Basis attribute) ST_basis() (radicalpy.simulation.HilbertSimulation method) (radicalpy.simulation.SparseCholeskyHilbertSimulation method) (radicalpy.tensornetwork.BaseMPSSimulation method) State (class in radicalpy.simulation) steady_state_mary() (in module radicalpy.experiments) StochasticMPSSimulation (class in radicalpy.tensornetwork)

T

T1_relaxation_rate_g_tensor() (in module radicalpy.estimations) T1_relaxation_rate_hyperfine_tensor() (in module radicalpy.estimations) T1_relaxation_rate_tumbling_motion() (in module radicalpy.estimations) T1Relaxation (class in radicalpy.relaxation) T2_relaxation_rate_g_tensor() (in module radicalpy.estimations) T2_relaxation_rate_hyperfine_tensor() (in module radicalpy.estimations) T2_relaxation_rate_tumbling_motion() (in module radicalpy.estimations) T2Relaxation (class in radicalpy.relaxation) time_evolution() (radicalpy.classical.RateEquations method) (radicalpy.simulation.HilbertSimulation method) (radicalpy.simulation.SparseCholeskyHilbertSimulation method) (radicalpy.tensornetwork.BaseMPSSimulation method) (radicalpy.tensornetwork.LocallyPurifiedMPSSimulation method) (radicalpy.tensornetwork.MPDOSimulation method) (radicalpy.tensornetwork.StochasticMPSSimulation method) total_hamiltonian() (radicalpy.simulation.HilbertSimulation method) (radicalpy.tensornetwork.BaseMPSSimulation method) (radicalpy.tensornetwork.LocallyPurifiedMPSSimulation method) TP_QUINTET (radicalpy.simulation.State attribute) TP_QUINTET_MINUS_ONE (radicalpy.simulation.State attribute) tp_quintet_minus_one_projop() (radicalpy.simulation.HilbertSimulation method) TP_QUINTET_MINUS_TWO (radicalpy.simulation.State attribute) tp_quintet_minus_two_projop() (radicalpy.simulation.HilbertSimulation method) TP_QUINTET_PLUS_ONE (radicalpy.simulation.State attribute) tp_quintet_plus_one_projop() (radicalpy.simulation.HilbertSimulation method)

TP_QUINTET_PLUS_TWO (radicalpy.simulation.State attribute) tp_quintet_plus_two_projop() (radicalpy.simulation.HilbertSimulation method) tp_quintet_projop() (radicalpy.simulation.HilbertSimulation method) TP_QUINTET_ZERO (radicalpy.simulation.State attribute) tp_quintet_zero_projop() (radicalpy.simulation.HilbertSimulation method) TP_SINGLET (radicalpy.simulation.State attribute) tp_singlet_projop() (radicalpy.simulation.HilbertSimulation method) TP_TRIPLET (radicalpy.simulation.State attribute) TP_TRIPLET_MINUS (radicalpy.simulation.State attribute) tp_triplet_minus_projop() (radicalpy.simulation.HilbertSimulation method) TP_TRIPLET_PLUS (radicalpy.simulation.State attribute) tp_triplet_plus_projop() (radicalpy.simulation.HilbertSimulation method) tp_triplet_projop() (radicalpy.simulation.HilbertSimulation method) TP_TRIPLET_ZERO (radicalpy.simulation.State attribute) tp_triplet_zero_projop() (radicalpy.simulation.HilbertSimulation method) Triplet (class in radicalpy.data) TRIPLET (radicalpy.simulation.State attribute) TRIPLET_MINUS (radicalpy.simulation.State attribute) TRIPLET_PLUS (radicalpy.simulation.State attribute) TRIPLET_PLUS_MINUS (radicalpy.simulation.State attribute) TRIPLET_X (radicalpy.simulation.State attribute) TRIPLET_Y (radicalpy.simulation.State attribute) TRIPLET_Z (radicalpy.simulation.State attribute) TRIPLET_ZERO (radicalpy.simulation.State attribute) TripletTripletDephasing (class in radicalpy.relaxation) TripletTripletRelaxation (class in radicalpy.relaxation)

U

unitary_propagator() (radicalpy.simulation.HilbertSimulation static method) (radicalpy.simulation.LiouvilleSimulation static method) (radicalpy.simulation.SparseCholeskyHilbertSimulation method) (radicalpy.tensornetwork.BaseMPSSimulation static method)

V

value (radicalpy.classical.Rate attribute) vector_to_matrix() (in module radicalpy.utils)

visualise_tensor() (in module radicalpy.plot) von_neumann_entropy() (in module radicalpy.utils)

W

write_orca_from_pdb() (in module radicalpy.utils) write_pdb() (in module radicalpy.utils)

write_sdf() (in module radicalpy.utils) write_xyz() (in module radicalpy.utils)

Y

yield_anisotropy() (in module radicalpy.utils)

Z

ZEEMAN (radicalpy.simulation.Basis attribute) zeeman_hamiltonian() (radicalpy.simulation.HilbertSimulation method) (radicalpy.tensornetwork.BaseMPSSimulation method) (radicalpy.tensornetwork.MPDOSimulation method)

zeeman_hamiltonian_1d() (radicalpy.simulation.HilbertSimulation method) zeeman_hamiltonian_3d() (radicalpy.simulation.HilbertSimulation method) zero_field_splitting_hamiltonian() (radicalpy.simulation.HilbertSimulation method) (radicalpy.tensornetwork.BaseMPSSimulation method)