wavefunction_analysis package

• wavefunction_analysis.dynamics package
  • Submodules
  • wavefunction_analysis.dynamics.dimers_in_crystal module
    • add_molecule()
    • add_molecules_cell()
    • cal_dipole_interactions()
    • dipole_dipole_interaction()
    • get_center_of_mass()
    • read_unit_cell_info()
    • translate_molecule()
    • write_eda_files()
    • write_xyz_files()
  • wavefunction_analysis.dynamics.electronic_dynamics_gs module
    • CurvyElectronicDynamicsStep
      • CurvyElectronicDynamicsStep.cal_electronic_energy_force()
      • CurvyElectronicDynamicsStep.cy_get_mass_on_basis()
      • CurvyElectronicDynamicsStep.cy_orbital_response()
      • CurvyElectronicDynamicsStep.cy_update_delta()
      • CurvyElectronicDynamicsStep.cy_update_density()
      • CurvyElectronicDynamicsStep.euler_step()
      • CurvyElectronicDynamicsStep.get_electronic_kinetic_energy()
      • CurvyElectronicDynamicsStep.init_electronic_density_static()
      • CurvyElectronicDynamicsStep.leapfrog_step()
      • CurvyElectronicDynamicsStep.update_electronic_density_static()
      • CurvyElectronicDynamicsStep.update_electronic_density_static2()
      • CurvyElectronicDynamicsStep.velocity_verlet_step()
    • ElectronicDynamicsStep
      • ElectronicDynamicsStep.cal_electronic_force()
      • ElectronicDynamicsStep.get_ortho_basis()
      • ElectronicDynamicsStep.init_electronic_density_static()
      • ElectronicDynamicsStep.setup_electronic_basis()
      • ElectronicDynamicsStep.update_electronic_density_dynamics()
      • ElectronicDynamicsStep.update_electronic_density_static()
    • ExtendedLagElectronicDynamicsStep
      • ExtendedLagElectronicDynamicsStep.init_electronic_density_static()
      • ExtendedLagElectronicDynamicsStep.init_xl_variables()
      • ExtendedLagElectronicDynamicsStep.static_extended_lagrange()
      • ExtendedLagElectronicDynamicsStep.update_electronic_density_static()
      • ExtendedLagElectronicDynamicsStep.xl_auxiliary_density_dotdot()
      • ExtendedLagElectronicDynamicsStep.xl_build_fock()
      • ExtendedLagElectronicDynamicsStep.xl_build_fock_init()
    • GrassmannElectronicDynamicsStep
      • GrassmannElectronicDynamicsStep.init_electronic_density_static()
      • GrassmannElectronicDynamicsStep.interpolation()
      • GrassmannElectronicDynamicsStep.update_electronic_density_static()
      • GrassmannElectronicDynamicsStep.update_gamma_lagrange()
    • cal_electronic_energy1()
    • cal_electronic_energy2()
    • cal_electronic_force()
    • cal_idempotency()
    • cal_pulay_force()
    • density_purification()
    • run_pyscf_gs()
  • wavefunction_analysis.dynamics.exciton_dynamics module
    • Dynamics
      • Dynamics.kernel()
      • Dynamics.plot_time_variables()
    • ExcitonDynamicsStep
      • ExcitonDynamicsStep.analyze_wf_property()
      • ExcitonDynamicsStep.cal_energy()
      • ExcitonDynamicsStep.cal_force()
      • ExcitonDynamicsStep.cal_ipr_value()
      • ExcitonDynamicsStep.cal_r_correlation()
      • ExcitonDynamicsStep.check_sanity()
      • ExcitonDynamicsStep.convert_parameter_units()
      • ExcitonDynamicsStep.get_exciton_couplings()
      • ExcitonDynamicsStep.get_exciton_diagonal()
      • ExcitonDynamicsStep.get_exciton_hamiltonian()
      • ExcitonDynamicsStep.get_exciton_hamiltonian0()
      • ExcitonDynamicsStep.get_exciton_hamiltonian1()
      • ExcitonDynamicsStep.get_exciton_hamiltonian2()
      • ExcitonDynamicsStep.get_initial_coefficients()
      • ExcitonDynamicsStep.get_unit_cell_info()
      • ExcitonDynamicsStep.process_parameters()
      • ExcitonDynamicsStep.update_coefficients()
    • ExcitonDynamicsStep3D
      • ExcitonDynamicsStep3D.cal_force()
      • ExcitonDynamicsStep3D.get_exciton_couplings()
      • ExcitonDynamicsStep3D.process_parameters()
    • OscillatorDynamicsStep
      • OscillatorDynamicsStep.convert_parameter_units()
      • OscillatorDynamicsStep.get_phonon_hamiltonian()
    • get_boltzmann_beta()
  • wavefunction_analysis.dynamics.molecular_dynamics module
    • MolecularDynamics
      • MolecularDynamics.plot_time_variables()
      • MolecularDynamics.run_dynamics()
      • MolecularDynamics.set_electronic_step()
      • MolecularDynamics.set_nuclear_step()
      • MolecularDynamics.set_photon_step()
    • plot_time_variables()
  • wavefunction_analysis.dynamics.oscillator_dynamics module
    • NuclearDynamicsStep
      • NuclearDynamicsStep.convert_parameter_units()
      • NuclearDynamicsStep.get_potential_energy()
      • NuclearDynamicsStep.init_coordinate_velocity()
      • NuclearDynamicsStep.init_velocity_random()
      • NuclearDynamicsStep.init_velocity_thermo()
      • NuclearDynamicsStep.project_force()
      • NuclearDynamicsStep.project_velocity()
      • NuclearDynamicsStep.update_coordinate_velocity()
    • angular_property()
    • get_boltzmann_beta()
    • harmonic_oscillator
      • harmonic_oscillator.euler_step()
      • harmonic_oscillator.get_energy()
      • harmonic_oscillator.get_kinetic_energy()
      • harmonic_oscillator.get_potential_energy()
      • harmonic_oscillator.init_coordinate_velocity()
      • harmonic_oscillator.leapfrog_step()
      • harmonic_oscillator.recursive_exploration_step()
      • harmonic_oscillator.update_coordinate_velocity()
      • harmonic_oscillator.velocity_verlet_step()
    • remove_trans_rotat_force()
    • remove_trans_rotat_velocity()
  • wavefunction_analysis.dynamics.photon_dynamics module
    • PhotonDynamicsStep
      • PhotonDynamicsStep.get_initial_density()
      • PhotonDynamicsStep.update_density()
    • PhotonDynamicsStep2
      • PhotonDynamicsStep2.convert_parameter_units()
      • PhotonDynamicsStep2.get_minimim_displacement()
      • PhotonDynamicsStep2.update_density()
    • get_trans_amplitude()
  • Module contents
• wavefunction_analysis.embedding package
  • Submodules
  • wavefunction_analysis.embedding.fci_thermal module
  • wavefunction_analysis.embedding.fragment_entangle module
    • EmbeddingMeanField
      • EmbeddingMeanField.emb_basis_dmet()
      • EmbeddingMeanField.get_eomf()
    • fragment_localization()
    • get_embedding_energy()
    • get_embedding_orbital()
    • get_embedding_system()
    • get_localized_orbital()
    • get_localized_orbital_rdm()
  • wavefunction_analysis.embedding.mol_lo_tools module
    • lo_weight_on_ao()
    • lo_weight_on_atom()
    • lo_weight_on_frag()
    • partition_lo_to_atms()
    • partition_lo_to_frags()
    • partition_lo_to_imps()
  • wavefunction_analysis.embedding.orbital_entropy module
    • get_1rdm()
    • get_2rdm()
    • get_orbital_entropy_info()
    • get_rdm_entropy()
    • normalize_wf()
  • wavefunction_analysis.embedding.td_embeddinng module
  • Module contents
• wavefunction_analysis.opt package
  • Submodules
  • wavefunction_analysis.opt.grassmann module
    • Grassmann
      • Grassmann.barzilai_borwein_step()
      • Grassmann.init_guess()
      • Grassmann.kernel()
      • Grassmann.polak_ribiere_step()
    • Involution_Grassmann
      • Involution_Grassmann.init_guess()
      • Involution_Grassmann.project_tangent_space()
      • Involution_Grassmann.update()
    • Projection_Grassmann
      • Projection_Grassmann.init_guess()
      • Projection_Grassmann.project_tangent_space()
    • Quotient_Grassmann
      • Quotient_Grassmann.conjugate_gradient_step()
      • Quotient_Grassmann.init_guess()
      • Quotient_Grassmann.project_tangent_space()
      • Quotient_Grassmann.tangent_parallel_transport()
      • Quotient_Grassmann.update()
    • cs_decompose()
    • geodesic_exp()
    • geodesic_svd()
    • geodesic_svd_compact()
  • wavefunction_analysis.opt.optimization module
    • cg_fletcher_reeves()
    • cg_polak_ribiere()
    • choose_direction()
    • conjugate_gradient()
    • gradient_descent()
    • line_search()
    • ls_armijo()
    • ls_backtracking()
    • ls_newton_raphson()
    • ls_steepest()
    • newton_2nd()
    • trust_region()
  • wavefunction_analysis.opt.riemannian module
    • Grassmann()
    • Grassmann_Quotient
      • Grassmann_Quotient.check_sanity()
      • Grassmann_Quotient.check_tangent()
      • Grassmann_Quotient.dimension
      • Grassmann_Quotient.dist
      • Grassmann_Quotient.exp()
      • Grassmann_Quotient.get_tangent()
      • Grassmann_Quotient.horizontal_lift()
      • Grassmann_Quotient.inverse_retraction_polar()
      • Grassmann_Quotient.log()
      • Grassmann_Quotient.newton_2nd()
      • Grassmann_Quotient.projection()
      • Grassmann_Quotient.retraction_polar()
      • Grassmann_Quotient.retraction_qr()
      • Grassmann_Quotient.tangent_solver()
      • Grassmann_Quotient.transport()
      • Grassmann_Quotient.weingarten()
    • OrthogonalGroup
      • OrthogonalGroup.check_sanity()
      • OrthogonalGroup.eigenvalue
      • OrthogonalGroup.exp()
      • OrthogonalGroup.func()
      • OrthogonalGroup.func_grad()
      • OrthogonalGroup.log()
      • OrthogonalGroup.projection()
      • OrthogonalGroup.retraction_cayley()
      • OrthogonalGroup.retraction_norm()
      • OrthogonalGroup.retraction_polar()
      • OrthogonalGroup.retraction_qr()
    • Riemannian
      • Riemannian.check_tangent()
      • Riemannian.conjugate_gradient()
      • Riemannian.dimension
      • Riemannian.dist
      • Riemannian.exp()
      • Riemannian.geodesic()
      • Riemannian.gradient_descent()
      • Riemannian.inverse_retraction()
      • Riemannian.log()
      • Riemannian.norm
      • Riemannian.projection()
      • Riemannian.retraction()
      • Riemannian.riemannian_gradient()
      • Riemannian.riemannian_hessian()
      • Riemannian.to_tangent_space()
      • Riemannian.transport()
      • Riemannian.weingarten()
    • Stiefel
      • Stiefel.check_sanity()
      • Stiefel.check_tangent()
      • Stiefel.dimension
      • Stiefel.dist
      • Stiefel.exp()
      • Stiefel.inverse_retraction_polar()
      • Stiefel.inverse_retraction_qr()
      • Stiefel.log()
      • Stiefel.projection()
      • Stiefel.retraction_polar()
      • Stiefel.retraction_qr()
      • Stiefel.weingarten()
    • get_random_matrix()
    • solve_sylvester()
  • Module contents
• wavefunction_analysis.plot package
  • Submodules
  • wavefunction_analysis.plot.plot_iteration module
  • wavefunction_analysis.plot.plot_orbital_property module
    • plot_orbital_property()
  • wavefunction_analysis.plot.plot_wave_energy_temperature module
    • plot_wave_energy_frequency()
  • wavefunction_analysis.plot.utils module
    • add_colorbar_map()
    • broadening()
    • brokenaxes()
    • fit_val()
    • get_kwargs()
    • gradient_color_line()
    • make_line_segments()
  • wavefunction_analysis.plot.vibrational_spectra module
    • autocorrelation()
    • cal_spectra()
    • fft_acf()
    • get_dipole_dev()
    • infrared()
    • plot_spectra()
    • smooth()
  • Module contents
• wavefunction_analysis.polariton package
  • Submodules
  • wavefunction_analysis.polariton.condensate module
    • bose_einstein_distribution()
  • wavefunction_analysis.polariton.greens_func module
    • absorption_spectra()
    • density_of_states_e()
    • density_of_states_p()
    • greens_func_e()
    • greens_func_e0_gauss()
    • greens_func_e0_lorentz()
    • greens_func_p()
    • plot_sigma()
    • self_energy_same_coupling()
  • wavefunction_analysis.polariton.qed_ks module
    • get_dse_2e()
    • get_dse_2e_xyz()
    • get_dse_elec_nuc()
    • get_energy_nuc_dip()
    • get_lambda2()
    • get_multipole_matrix()
    • get_nuclear_dipoles()
    • get_scaled_lambda()
    • polariton
      • polariton.get_multipole_matrix()
      • polariton.nuc_grad_method()
    • polariton_cs
      • polariton_cs.Gradients()
      • polariton_cs.Hessian()
      • polariton_cs.energy_elec()
      • polariton_cs.gen_response()
      • polariton_cs.get_coupling_energy()
      • polariton_cs.get_hcore()
      • polariton_cs.get_veff()
    • polariton_ns
      • polariton_ns.Gradients()
      • polariton_ns.energy_elec()
      • polariton_ns.energy_nuc()
      • polariton_ns.get_coupling_energy()
      • polariton_ns.get_hcore()
      • polariton_ns.get_veff()
    • print_qed_dse_energy()
  • wavefunction_analysis.polariton.qed_ks_grad module
    • Gradients
      • Gradients.dse_fock_d1()
      • Gradients.get_veff()
    • Gradients2
      • Gradients2.dse_fock_d1()
      • Gradients2.grad_nuc()
    • cal_multipole_matrix_d1()
    • cal_multipole_matrix_fd()
    • finite_difference()
    • get_dse_2e()
    • get_dse_elec_nuc_d1()
    • get_dse_elec_nuc_grad()
    • get_grad_nuc_dip()
    • get_multipole_matrix_d1()
    • get_nuclear_dipoles_d1()
  • wavefunction_analysis.polariton.qed_ks_hess module
    • Hessian
      • Hessian.make_h1()
      • Hessian.partial_hess_elec()
    • dse_fock_d1_s()
    • fd_orbital_rotation_mo1()
    • get_dse_2e_a()
    • get_multipole_matrix_d2()
    • make_h1()
    • partial_hess_elec()
    • resemble_deriv_on_atoms()
  • wavefunction_analysis.polariton.qed_ks_response module
    • cphf_with_freq()
    • get_polarizability()
  • wavefunction_analysis.polariton.qed_thermo module
    • get_g1_d1()
    • harmonic_analysis()
    • project_trans_rotation()
  • wavefunction_analysis.polariton.td_gks_soc module
    • GHF
      • GHF.gen_response()
    • get_ab()
    • make_h01_soc1e()
  • Module contents
• wavefunction_analysis.property package
  • Submodules
  • wavefunction_analysis.property.delta_scf module
    • Delta_UKS
      • Delta_UKS.get_init_guess()
      • Delta_UKS.get_occ()
      • Delta_UKS.get_veff()
      • Delta_UKS.init_guess_by_aufbau()
      • Delta_UKS.require_spin_image()
    • get_occ()
    • pick_orbital_from_mom()
  • wavefunction_analysis.property.energy_density_plot module
    • EnergyDensity
      • EnergyDensity.becke_partition()
      • EnergyDensity.cal_density_matrices()
      • EnergyDensity.cal_excitation_lambda_factor()
      • EnergyDensity.cal_excited_state()
      • EnergyDensity.cal_overlap_detach_attach_density()
      • EnergyDensity.check_energy_core()
      • EnergyDensity.check_energy_coulomb_exchange()
      • EnergyDensity.check_energy_functional()
      • EnergyDensity.check_energy_jk()
      • EnergyDensity.check_energy_xc()
      • EnergyDensity.check_transtion_density()
      • EnergyDensity.creat_mesh_grids()
      • EnergyDensity.decompose_energy_density()
      • EnergyDensity.decompose_energy_density_es()
      • EnergyDensity.decompose_energy_density_gs()
      • EnergyDensity.density_on_grids()
      • EnergyDensity.energy_density_core()
      • EnergyDensity.energy_density_coulomb_exchange()
      • EnergyDensity.energy_density_coulomb_only()
      • EnergyDensity.energy_density_exchange_rsh()
      • EnergyDensity.energy_density_functional()
      • EnergyDensity.energy_density_j_only()
      • EnergyDensity.energy_density_jk()
      • EnergyDensity.energy_density_k_rsh()
      • EnergyDensity.energy_density_xc()
      • EnergyDensity.grab_es_density_on_grids()
      • EnergyDensity.grab_gs_density_on_grids()
      • EnergyDensity.group_hirshfeld_partition()
      • EnergyDensity.mayer_bond_order()
      • EnergyDensity.partition_energy_or_charge()
      • EnergyDensity.plot_es_energy_density()
      • EnergyDensity.plot_gs_energy_density()
      • EnergyDensity.relaxed_z_kernel()
      • EnergyDensity.sum_energy_density_component()
      • EnergyDensity.use_auxilary_basis()
  • wavefunction_analysis.property.epr module
    • cal_epr()
    • hamil_hyperfine_coupling()
    • hamil_nuclear_gyromagnetic()
    • hamil_spin()
    • hamil_spin_spin_coupling()
    • hamil_zeeman()
  • wavefunction_analysis.property.gtensor module
  • wavefunction_analysis.property.orbital_property module
    • cal_orbital_property()
    • cal_property_from_scratch()
  • wavefunction_analysis.property.rdm_analysis module
    • cal_dipoles()
    • cal_rdm1()
    • get_attach_dm()
    • get_detach_dm()
    • get_difference_dm()
    • get_dipoles()
    • get_transition_dm()
  • wavefunction_analysis.property.sapt_dispersion module
    • build_trans_density()
    • cal_sapt()
    • cal_sapt_r()
    • cal_sapt_u()
    • get_xys_in_ao()
    • reshape_xys()
    • run_tddft()
  • Module contents
• wavefunction_analysis.spins package
  • Submodules
  • wavefunction_analysis.spins.circuit module
    • beta_layer()
    • create_circuit()
    • create_qubits_2d()
    • gamma_layer()
  • wavefunction_analysis.spins.infinite_mps_block module
    • apply_gate_on_mps()
    • build_evolution_gate()
    • contract_from_left()
    • contract_from_right()
    • evaluate_energy_mps()
    • evaluate_energy_rdm()
    • get_mps_2rdm()
    • normalize_mps()
    • normalize_mps_2()
    • run_tebd()
    • update_ortho_mps()
  • wavefunction_analysis.spins.matrix_product_state module
    • dmrg_opt_gs()
    • dmrg_sweep()
    • get_hamil_from_mpo()
    • mpo_hamil_disordered()
    • mpo_hamil_uniform()
    • mpo_spin_correlation()
    • mps_canonical()
    • mps_canonical_left()
    • mps_canonical_right()
    • zipper_from_left()
    • zipper_from_right()
  • wavefunction_analysis.spins.qaoa module
    • QAOA
      • QAOA.draw_circuit
      • QAOA.energy_evaluation()
      • QAOA.energy_expectation()
      • QAOA.fd_gradient_evaluation()
      • QAOA.optimizer()
      • QAOA.resolve_circuit_params()
    • QAOA_Ising
      • QAOA_Ising.energy_expectation()
      • QAOA_Ising.resolve_circuit_params()
  • wavefunction_analysis.spins.spin_hamil module
    • get_prod_spin_list()
    • get_spin()
    • get_spin_mat()
    • get_spins()
    • hamil_heisenberg_1d()
    • hamil_x_1d()
    • hamil_xxz_1d()
    • hamil_xyz_1d()
    • hamil_zeeman_1d()
  • Module contents
• wavefunction_analysis.utils package
  • Submodules
  • wavefunction_analysis.utils.cg_coeffs module
    • clebsch_gordan_coeff_direct()
    • clebsch_gordan_coeff_recur()
    • ladder_coeff()
    • print_cg_coeff()
  • wavefunction_analysis.utils.chiral_geom module
    • run_gtensor()
    • spin_square_biortho()
    • swap_atoms_coords()
  • wavefunction_analysis.utils.fdiff module
    • change_matrix_phase_c()
    • change_matrix_phase_rc()
    • change_number_phase()
    • change_wf_phase()
    • fdiff
      • fdiff.coeff
      • fdiff.compute()
      • fdiff.get_d()
      • fdiff.get_x()
  • wavefunction_analysis.utils.get_cx module
  • wavefunction_analysis.utils.monitor_performance module
    • monitor_performance()
    • set_performance_log()
  • wavefunction_analysis.utils.ortho_basis module
    • get_ortho_basis()
    • get_ortho_basis_deriv()
  • wavefunction_analysis.utils.print_matrix module
    • print_matrix()
  • wavefunction_analysis.utils.pyscf_parser module
    • build_atom()
    • build_molecule()
    • convert_string()
    • final_print_energy()
    • find_oscillator_strength()
    • find_transition_dipole()
    • get_basis_info()
    • get_center_of_mass()
    • get_frgm_idx()
    • get_jobtype()
    • get_photon_info()
    • get_rem_info()
    • justify_photon_info()
    • parser()
    • read_keyword_block()
    • read_molecule()
    • run_pyscf_dft()
    • run_pyscf_dft_tddft()
    • run_pyscf_final()
    • run_pyscf_tddft()
    • run_pyscf_tdqed()
  • wavefunction_analysis.utils.read_files module
    • istype()
    • read_array()
    • read_matrix()
    • read_number()
    • read_time()
  • wavefunction_analysis.utils.sec_mole module
    • align_principal_axes()
    • cal_dihedral_angle()
    • get_center_property()
    • get_charge_or_mass()
    • get_molecular_center()
    • get_moment_of_inertia()
    • get_rotation_matrix()
    • get_symbols_coords()
    • read_geometries_standard()
    • read_geometry()
    • read_symbols_coords()
    • rotate_molecule()
    • standard_orientation()
    • standard_orientation2()
    • switch_atoms()
    • translate_molecule()
    • write_geometry()
    • write_mol_info()
    • write_mol_info_geometry()
    • write_rem_info()
    • write_symbols_coords()
  • wavefunction_analysis.utils.sec_rem module
    • put_keys_kwargs_to_object()
    • put_keys_to_kwargs()
    • put_keys_to_object()
    • put_kwargs_to_keys()
    • put_kwargs_to_object()
  • wavefunction_analysis.utils.unit_conversion module
    • convert_different_units()
    • convert_other_property()
    • convert_property_to_energy()
    • convert_same_units()
    • convert_units()
    • default_unit_index()
    • find_properties()
  • wavefunction_analysis.utils.utils module
    • ishermitian()
    • random_matrix()
    • swap_largest_to_diagonal()
  • wavefunction_analysis.utils.wf_overlap module
    • assemble_amplitudes()
    • cal_wf_overlap()
    • cal_wf_overlap_r()
    • cal_wf_overlap_r0()
    • cal_wf_overlap_sf()
    • cal_wf_overlap_u()
    • change_phase()
    • sign_fixing()
  • Module contents