RadicalPy: a toolbox for radical pair spin dynamics
RadicalPy in an intuitive (object-oriented) open-source Python framework specific to radical pair spin dynamics.
To get started take a look at the quick start guide or the examples.
The package is still under development. Basic functionality is implemented, documentation is sparse, testing partial.
Installation
Install simply using pip:
pip install radicalpy
radicalpy
- radicalpy package
- Submodules
- radicalpy.classical module
- radicalpy.data module
- radicalpy.estimations module
Bhalf_theoretical_hyperfine()Bhalf_theoretical_relaxation()Bhalf_theoretical_relaxation_delay()T1_relaxation_rate_g_tensor()T1_relaxation_rate_hyperfine_tensor()T1_relaxation_rate_tumbling_motion()T2_relaxation_rate_g_tensor()T2_relaxation_rate_hyperfine_tensor()T2_relaxation_rate_tumbling_motion()aqueous_glycerol_viscosity()autocorrelation_fit()diffusion_coefficient()dipolar_interaction_MC()dipolar_interaction_anisotropic()dipolar_interaction_anisotropic_from_dipolar_vector()dipolar_interaction_anisotropic_from_dipolar_vector_without_prefactor()dipolar_interaction_isotropic()dipolar_interaction_point_dipole()exchange_interaction_in_protein()exchange_interaction_in_solution()exchange_interaction_in_solution_MC()g_tensor_relaxation_rate()k_D()k_STD()k_STD_microreactor()k_ST_mixing()k_constant()k_electron_transfer()k_excitation()k_recombination()k_reencounter()k_triplet_relaxation()rotational_correlation_time_for_molecule()rotational_correlation_time_for_protein()
- radicalpy.experiments module
anisotropy()anisotropy_loop()cidnp()coherent_control()epr()field_switching()kine_quantum_mary()magnetic_field_loop()magnetic_field_loop_semiclassical()mary()mary_lfe_hfe()mary_semiclassical()modulated_mary_brute_force()nmr()odmr()omfe()oop_eseem()rydmr()semiclassical_mary()steady_state_mary()
- radicalpy.kinetics module
- radicalpy.plot module
anisotropy_surface()density_matrix_animation()energy_levels()linear_energy_levels()monte_carlo_caged()monte_carlo_free()plot_3d_results()plot_autocorrelation_fit()plot_bhalf_time()plot_exchange_interaction_in_solution()plot_general()plot_molecule()plot_sphere()set_equal_aspect()spin_state_labels()visualise_tensor()
- radicalpy.relaxation module
- radicalpy.shared module
- radicalpy.simulation module
BasisHilbertIncoherentProcessBaseHilbertSimulationHilbertSimulation.ST_basis()HilbertSimulation.apply_hilbert_kinetics()HilbertSimulation.apply_liouville_hamiltonian_modifiers()HilbertSimulation.bloch_redfield_liouvillian()HilbertSimulation.bloch_redfield_solver()HilbertSimulation.bloch_redfield_time_evolution()HilbertSimulation.convert()HilbertSimulation.couplingHilbertSimulation.dipolar_hamiltonian()HilbertSimulation.dipolar_hamiltonian_1d()HilbertSimulation.dipolar_hamiltonian_3d()HilbertSimulation.exchange_hamiltonian()HilbertSimulation.get_eye()HilbertSimulation.hamiltonian_sizeHilbertSimulation.hyperfine_hamiltonian()HilbertSimulation.initial_density_matrix()HilbertSimulation.lindblad_liouvillian()HilbertSimulation.nucleiHilbertSimulation.observable_projection_operator()HilbertSimulation.particlesHilbertSimulation.product_operator()HilbertSimulation.product_operator_3d()HilbertSimulation.product_probability()HilbertSimulation.product_yield()HilbertSimulation.projection_operator()HilbertSimulation.propagate()HilbertSimulation.radicalsHilbertSimulation.spin_operator()HilbertSimulation.spin_orbit_hamiltonian()HilbertSimulation.time_evolution()HilbertSimulation.total_hamiltonian()HilbertSimulation.tp_quintet_minus_one_projop()HilbertSimulation.tp_quintet_minus_two_projop()HilbertSimulation.tp_quintet_plus_one_projop()HilbertSimulation.tp_quintet_plus_two_projop()HilbertSimulation.tp_quintet_projop()HilbertSimulation.tp_quintet_zero_projop()HilbertSimulation.tp_singlet_projop()HilbertSimulation.tp_triplet_minus_projop()HilbertSimulation.tp_triplet_plus_projop()HilbertSimulation.tp_triplet_projop()HilbertSimulation.tp_triplet_zero_projop()HilbertSimulation.unitary_propagator()HilbertSimulation.zeeman_hamiltonian()HilbertSimulation.zeeman_hamiltonian_1d()HilbertSimulation.zeeman_hamiltonian_3d()HilbertSimulation.zero_field_splitting_hamiltonian()
LiouvilleIncoherentProcessBaseLiouvilleSimulationSemiclassicalSimulationSparseCholeskyHilbertSimulationSparseCholeskyHilbertSimulation.ST_basis()SparseCholeskyHilbertSimulation.get_eye()SparseCholeskyHilbertSimulation.product_probability()SparseCholeskyHilbertSimulation.propagate()SparseCholeskyHilbertSimulation.spin_operator()SparseCholeskyHilbertSimulation.time_evolution()SparseCholeskyHilbertSimulation.unitary_propagator()
StateState.CISSState.EPRState.EQUILIBRIUMState.SECOND_ORDER_POLARISATIONState.SINGLETState.TP_QUINTETState.TP_QUINTET_MINUS_ONEState.TP_QUINTET_MINUS_TWOState.TP_QUINTET_PLUS_ONEState.TP_QUINTET_PLUS_TWOState.TP_QUINTET_ZEROState.TP_SINGLETState.TP_TRIPLETState.TP_TRIPLET_MINUSState.TP_TRIPLET_PLUSState.TP_TRIPLET_ZEROState.TRIPLETState.TRIPLET_MINUSState.TRIPLET_PLUSState.TRIPLET_PLUS_MINUSState.TRIPLET_XState.TRIPLET_YState.TRIPLET_ZState.TRIPLET_ZERO
- radicalpy.tensornetwork module
BaseMPSSimulationBaseMPSSimulation.ST_basis()BaseMPSSimulation.apply_liouville_hamiltonian_modifiers()BaseMPSSimulation.dipolar_hamiltonian()BaseMPSSimulation.exchange_hamiltonian()BaseMPSSimulation.haberkorn_hamiltonian()BaseMPSSimulation.hyperfine_hamiltonian()BaseMPSSimulation.initial_density_matrix()BaseMPSSimulation.observable_projection_operator()BaseMPSSimulation.product_probability()BaseMPSSimulation.propagate()BaseMPSSimulation.spin_operator()BaseMPSSimulation.time_evolution()BaseMPSSimulation.total_hamiltonian()BaseMPSSimulation.unitary_propagator()BaseMPSSimulation.zeeman_hamiltonian()BaseMPSSimulation.zero_field_splitting_hamiltonian()
LocallyPurifiedMPSSimulationMPDOSimulationStochasticMPSSimulation
- radicalpy.utils module
Bhalf_LFEhalf_fit()Bhalf_fit()GHz_to_mK()GHz_to_meV()Gauss_to_MHz()Gauss_to_angular_frequency()Gauss_to_mT()J_to_meV()Lorentzian()MHz_in_angular_frequency()MHz_to_Gauss()MHz_to_mT()angular_frequency_in_MHz()angular_frequency_to_Gauss()angular_frequency_to_mT()anisotropy_check()autocorrelation()cartesian_to_spherical()cidnp_polarisation_diffusion_model()cidnp_polarisation_exponential_model()cidnp_polarisation_truncated_diffusion_model()define_xyz()double_Lorentzian()eigensorter()enumerate_spin_states_from_base()get_angle_between_plane()get_rotation_matrix_euler_angles()hilbert_to_liouville()infer_bonds()is_fast_run()mK_to_GHz()mK_to_meV()mT_to_Gauss()mT_to_MHz()mT_to_angular_frequency()make_resonance_sticks()mary_lorentzian()matrix_to_vector()meV_to_GHz()meV_to_J()meV_to_mK()modulated_signal()mol_to_plot_arrays()negativity()nmr_chemical_shift_imaginary_modulation()nmr_chemical_shift_real_modulation()nmr_scalar_coupling_modulation()nmr_t2_relaxation()parse_label_xyz_txt()parse_pdb()parse_xyz()pdb_label()purity()read_lines_utf8_or_utf16le()read_orca_hyperfine()read_trajectory_files()reference_signal()rodrigues_rotation()rotate_axes()s_t0_omega()smiles_to_3d()spectral_density()spherical_average()spherical_to_cartesian()spin_character()vector_to_matrix()von_neumann_entropy()write_orca_from_pdb()write_pdb()write_sdf()write_xyz()yield_anisotropy()
- Module contents