Index

A

a (MPIMap attribute) ABELIAN_GROUP_OPS (in module oqp.library.symmetry_detect) action (BaekAEvaluation attribute) (Diagnostic attribute) active (NAMD attribute) (NAMD_SOC attribute) (NAMD_SOC_QMMM attribute) add() (CheckReport method) align (OQPNEBOpt attribute) align_mo() (BasisOverlap method) align_type (BasisOverlap attribute) align_x() (NACME method) ALL_RUNTYPES (in module oqp.utils.input_checker) alpha (BaekAObjective attribute) (BaekAState attribute) (MECIOpt attribute) (OQPBaekAOpt attribute) alternative_scf (SinglePoint attribute) amplitude_matrix() (MRSFExcitedStates method) AMU_TO_AU (in module oqp.library.namd) AMU_to_KG (in module oqp.utils.constants) analytic_hessian_capability() (in module oqp.utils.input_checker) analytical_ground_state_hess() (Hessian method) analytical_hess() (Hessian method) analytical_mrsf_hess() (Hessian method) analytical_nac() (NAC method) analytical_sf_hess() (Hessian method) analytical_tddft_hess() (Hessian method) Angle (class in oqp.library.oqp_coords) ANGSTROM_TO_BOHR (in module oqp.library.libgeometric) (in module oqp.library.liboqp) (in module oqp.library.oqp_coords) (in module oqp.utils.constants) ao (CubeExporter attribute) ao_atom (AOBasis attribute)

ao_index (AOBasis attribute) ao_to_mo_1body() (in module oqp.quantum.integrals) ao_to_mo_2body() (in module oqp.quantum.integrals) AOBasis (class in oqp.analysis.gto_grid) applies() (RegKey method) apply() (in module oqp.utils.perf_levels) apply_config() (OQPData method) apply_dftb_model_default() (in module oqp.utils.input_checker) args (CallSpec attribute) ArrayLike (in module oqp.library.baeka) as_dict() (OneElectronBlockLeakSummary method) assemble_embedding_sites() (in module oqp.library.qmmm_connectivity) assign_mo_irreps() (in module oqp.library.symmetry) assign_mode_irreps() (in module oqp.library.symmetry) assign_state_irreps() (in module oqp.library.symmetry) ATMOS (in module oqp.utils.constants) atom_xyz (BasisData attribute) atoms (Angle attribute) (BasisData attribute) (Bond attribute) (Dihedral attribute) (MEP attribute) (Optimizer attribute) (OQPEngine attribute) (QMMM_MD attribute) attach_detection_metadata() (in module oqp.library.symmetry_detect) attachment_detachment() (in module oqp.analysis.density_diff) attachment_detachment_cubes() (CubeExporter method) attr_value (in module oqp) AU_TO_DEBYE (in module oqp.utils.dftb_trace) average_energy (BaekAObjective attribute) average_gradient (BaekAObjective attribute) AVOGADRO_CONSTANT (in module oqp.utils.constants) axis (RotationComponent attribute) (TranslationComponent attribute)

B

b_matrix() (CartesianCoordinates method) (DelocalizedInternalCoordinates method) (RedundantInternalCoordinates method) back_door (BasisOverlap attribute) (Molecule attribute) back_door() (Runner method) back_door_data (OpenQPEngine attribute) back_transform() (CartesianCoordinates method) (DelocalizedInternalCoordinates method) (RedundantInternalCoordinates method) baeka (OQPBaekAOpt attribute) baeka_objective() (in module oqp.library.baeka) baeka_optimizer (OQPAutoMECIOpt attribute) BaekAEvaluation (class in oqp.library.baeka) BaekAJumpScheduleExhausted BaekAObjective (class in oqp.library.baeka) BaekAState (class in oqp.library.baeka) barostat_interval (QMMM_MD attribute) barray() (in module oqp.molecule.oqpdata) barrier() (MPIManager method) base_test_dir (OQPTester attribute) basis (CalculationSpec attribute) (SinglePoint attribute)

basis_names (BasisData attribute) basis_search_paths() (in module oqp.runtime) BasisData (class in oqp.library.set_basis) BasisOverlap (class in oqp.library.single_point) bcast() (MPIManager method) beta_schedule (BaekAState attribute) BOHR (in module oqp.utils.constants) BOHR_TO_ANGSTROM (in module oqp.library.libgeometric) (in module oqp.library.neb_utils) (in module oqp.library.oqp_coords) BOHR_TO_NM (in module oqp.library.namd) bohr_to_nm (in module oqp.utils.qmmm) BOLTZMANN_CONSTANT (in module oqp.utils.constants) Bond (class in oqp.library.oqp_coords) bonded_info (in module oqp.utils.qmmm) bp (NAC attribute) build_coordinates() (in module oqp.library.oqp_coords) build_full_group_blocks() (in module oqp.library.symmetry) build_kw_map() (in module oqp.utils.kword_map) build_pyscf_mol() (in module oqp.export.fcidump) build_reduction_maps() (in module oqp.library.symmetry) build_symmetry_adapted_transform() (in module oqp.library.symmetry) builtin_geometry() (in module oqp.utils.geometry) BUILTIN_TEMPLATES (in module oqp.SimulationManager)

C

C (MRSFExcitedStates attribute) calc() (GeometricEngine method) calc_new() (GeometricEngine method) calculate_max_workers() (OQPTester method) calculation_request_lines() (in module oqp.utils.state_labels) CalculationSpec (class in oqp.utils.oqp_input) Calculator (class in oqp.library.single_point) CallSpec (class in oqp.utils.oqp_input) canonical_dftb_type() (in module oqp.utils.state_labels) canonical_text (OQPResolution attribute) cart_rmsd() (CartesianCoordinates method) (DelocalizedInternalCoordinates method) (RedundantInternalCoordinates method) CartesianCoordinates (class in oqp.library.oqp_coords) CHARACTER_TABLES (in module oqp.library.symmetry_detect) charge (Molecule attribute) (VirtualCharge attribute) check() (Molecule method) check_convergence() (ConstrainOpt method) (MECIOpt method) (MECPOpt method) (Optimizer method) (OQPBaekAOpt method) (QMMMOpt method) check_dependencies() (SimulationManager static method) check_input_values() (in module oqp.utils.input_checker) check_mep() (MEP method) check_ref() (Molecule method) CheckReport (class in oqp.utils.input_checker) clean (Hessian attribute) (NAC attribute) clearCalcs() (GeometricEngine method) climb_fmax (NEB attribute) (OQPNEBOpt attribute) climbing (NEB attribute) (OQPNEBOpt attribute) close() (MPIPool method) coef (NAMD attribute) (NAMD_SOC attribute) (NAMD_SOC_MCH attribute) (NAMD_SOC_MCH_QMMM attribute) (NAMD_SOC_QMMM attribute) collapse_repeats() (in module oqp.utils.dftb_trace) compare_data() (in module oqp.molecule.molecule) compare_results() (in module oqp.interop.compare) compile_natural_request() (in module oqp.utils.oqp_input) compute() (LastStep method) compute_alpha_beta_electrons() (in module oqp.molecule.oqpdata) compute_bp() (NAC static method)

compute_data() (in module oqp.library.runfunc) compute_energy() (in module oqp.library.runfunc) compute_force() (OpenQpQMMM method) compute_geom() (in module oqp.library.runfunc) compute_grad() (in module oqp.library.runfunc) compute_hess() (in module oqp.library.runfunc) compute_md() (in module oqp.library.runfunc) compute_nac() (in module oqp.library.runfunc) compute_nacme() (in module oqp.library.runfunc) compute_namd() (in module oqp.library.runfunc) compute_properties() (in module oqp.library.runfunc) compute_scf_prop() (in module oqp.library.runfunc) compute_soc() (in module oqp.library.runfunc) compute_thermo() (in module oqp.library.runfunc) config (Molecule attribute) (OpenQPDFTBAdapter attribute) (OpenQPEngine attribute) (PyRAI2MDEngine attribute) config_str (OPENQP attribute) (OpenQP attribute) config_tag (Molecule attribute) config_typed (OPENQP attribute) (OpenQP attribute) configs (SimulationManager attribute) ConstrainOpt (class in oqp.library.libscipy) constraints (in module oqp.utils.qmmm) control (Molecule attribute) (OpenQP attribute) conv (SinglePoint attribute) converged (BaekAEvaluation attribute) ConvergenceSignal converger_type (SinglePoint attribute) coordinates_angstrom (NEBImage attribute) coords (AOBasis attribute) (CubeExporter attribute) (OQPEngine attribute) coordsys (GeometricNEBOpt attribute) (OQPEngine attribute) core_energy (MolecularHamiltonian attribute) correlation() (SinglePoint method) COVALENT_RADII (in module oqp.library.qmmm_connectivity) covalent_radii (in module oqp.utils.qmmm) covalent_radius() (in module oqp.library.qmmm_connectivity) covalent_radius_bohr() (in module oqp.library.oqp_coords) create_shell_data() (BasisData method) create_template() (SimulationManager static method) CubeExporter (class in oqp.export.cubegen) cutoff (NAMD_QMMM attribute) Cutoff (OpenQpQMMM attribute) cutoff (QMMM_MD attribute)

D

DampingParam() (in module oqp.utils.matrix) data (BaekAEvaluation attribute) (Molecule attribute) data_allocate() (Molecule method) data_deallocate() (Molecule method) dcm (Molecule attribute) decoherence (NAMD attribute) DEFAULT_TOLERANCE (in module oqp.quantum.fcidump) DelocalizedInternalCoordinates (class in oqp.library.oqp_coords) delta_beta (BaekAState attribute) (OQPBaekAOpt attribute) delta_f (BaekAEvaluation attribute) derivatives() (Angle method) (Bond method) (Dihedral method) (RotationComponent method) (TranslationComponent method) detect_dft() (GeometricEngine method) detect_link_atoms() (in module oqp.library.qmmm_connectivity) detect_point_group() (in module oqp.library.symmetry_detect) dft() (OpenQP method) dftb (OpenQP property) (OpenQPDFTBAdapter attribute) DFTB_BACKENDS (in module oqp.utils.input_checker) DFTB_CAP_SCC_FINAL_TRUST (in module oqp.utils.state_labels) DFTB_CAP_STATE_SPECTRUM (in module oqp.utils.state_labels) DFTB_CAP_STRUCTURED_TRACE (in module oqp.utils.state_labels) DFTB_KNOWN_PRESETS (in module oqp.utils.state_labels) dftb_method_name() (in module oqp.utils.state_labels) DFTB_MODEL_DEFAULT_MRSF (in module oqp.utils.input_checker) DFTB_MODEL_DEFAULT_OPEN_SHELL (in module oqp.utils.input_checker) DFTB_MODEL_LOCKED_KEYS (in module oqp.utils.input_checker) DFTB_MODELS (in module oqp.utils.input_checker)

DFTB_NATIVE_ONLY_KEYS (in module oqp.utils.input_checker) dftb_overlap() (BasisOverlap method) dftb_reference_description() (in module oqp.utils.state_labels) DFTB_SCC_MIXERS (in module oqp.utils.input_checker) dftb_soc() (in module oqp.library.openqp_dftb) dftb_states_overlap() (NACME method) dftb_target_description() (in module oqp.utils.state_labels) DFTB_TYPES (in module oqp.utils.input_checker) dftd4_native_disp() (in module oqp.library.single_point) dftd_installed (in module oqp.library.single_point) Diagnostic (class in oqp.utils.input_checker) diagnostics (CheckReport attribute) diff_density_mo() (MRSFExcitedStates method) Dihedral (class in oqp.library.oqp_coords) DIIS_TYPES (in module oqp.utils.input_checker) dip_oqp (MRSFExcitedStates attribute) dir (IRC attribute) DispersionModel (class in oqp.utils.matrix) do_d4 (LastStep attribute) driver (CalculationSpec attribute) (NAMD_QMMM attribute) DRIVER_OPTIONS (in module oqp.utils.oqp_input) dt (NACME attribute) (NAMD attribute) dt_adaptive (NAMD attribute) dt_fs (NAMD attribute) dt_max (NAMD attribute) dt_min (NAMD attribute) dump_data() (in module oqp.utils.file_utils) dump_fcidump() (in module oqp.export.fcidump) dump_log() (in module oqp.utils.file_utils) dump_strings_from_parser() (in module oqp.openqp) dV (CubeExporter attribute) dx_max (NAMD attribute)

E

e0 (NAMD_SOC attribute) (NAMD_SOC_QMMM attribute) e_ref (NAMD_SOC attribute) (NAMD_SOC_QMMM attribute) econs (NAMD_SOC attribute) (NAMD_SOC_QMMM attribute) ecp (BasisData attribute) edc_c (NAMD attribute) effective_sigma (BaekAObjective attribute) electrostatic_potential() (OpenQpQMMM method) elem (Molecule attribute) ELEMENT_TO_Z (in module oqp.SimulationManager) ELEMENTS (in module oqp.periodic_table) ELEMENTS_LONG_NAME (in module oqp.periodic_table) ELEMENTS_NAME (in module oqp.periodic_table) Embedding (OpenQpQMMM attribute) embedding (QMMM_MD attribute) end_fmax (OQPNEBOpt attribute) end_time (OQPTester attribute) energies (BaekAObjective attribute) (Molecule attribute) (MRSFExcitedStates attribute) (NEB attribute)

energy() (OpenQPDFTBAdapter method) (SinglePoint method) energy_file (QMMM_MD attribute) energy_func (SinglePoint attribute) energy_gap (Optimizer attribute) energy_shift (Optimizer attribute) ensemble (QMMM_MD attribute) enumerate_full_group() (in module oqp.library.symmetry_detect) eri_ao() (in module oqp.library.ints_2e) errors (CheckReport property) espf_full (OpenQpQMMM attribute) eval_ao() (AOBasis method) eval_orbitals() (AOBasis method) evaluate() (BaekAState method) exception (Calculator attribute) excitation() (OpenQPDFTBAdapter method) (SinglePoint method) exclude_runtypes (RegKey attribute) EXEMPT_FLAGS (in module oqp.utils.regression) expected (Diagnostic attribute) explicit (CallSpec attribute) explicit_scf_props() (Molecule method) export (Calculator attribute) export_title (Calculator attribute)

F

farray() (in module oqp.molecule.oqpdata) feature_coverage() (in module oqp.utils.regression) feature_coverage_cli() (in module oqp.pyoqp) ffi (in module oqp) field() (RegKey method) file (MoldenWriter attribute) filename (MoldenReader attribute) final_energy() (LastStep method) final_energy_annotation() (in module oqp.utils.dftb_trace) final_energy_header() (in module oqp.utils.dftb_trace) final_energy_label() (in module oqp.utils.dftb_trace) final_grad() (LastStep method) finalize_mpi() (MPIManager method) find_vec_order() (BasisOverlap static method) FINE_STRUCTURE (in module oqp.library.openqp_dftb) folder (SimulationManager attribute) follow_mode (OQPEngine attribute) force_field (in module oqp.utils.qmmm) forced_attempt (SinglePoint attribute) forcefield (NAMD_QMMM attribute) (OpenQpQMMM attribute) (QMMM_MD attribute) forcefield0 (in module oqp.utils.qmmm) forces_mm() (OpenQpQMMM method) forces_qm_openqp() (OpenQpQMMM method) form_gradient_qmmm() (in module oqp.utils.qmmm) format_calculation_request() (in module oqp.utils.state_labels) format_charge_block() (in module oqp.utils.dftb_trace) format_davidson_block() (in module oqp.utils.dftb_trace) format_davidson_summary_line() (in module oqp.utils.dftb_trace) format_dftb_settings() (in module oqp.utils.state_labels) format_energy_components() (in module oqp.utils.dftb_trace) format_excited_state_summary() (in module oqp.utils.dftb_trace)

format_mo_table() (in module oqp.utils.dftb_trace) format_other_lines() (in module oqp.utils.dftb_trace) format_report() (in module oqp.utils.perf_levels) format_resolved_options() (in module oqp.utils.dftb_trace) format_scc_block() (in module oqp.utils.dftb_trace) format_scc_pass() (in module oqp.utils.dftb_trace) format_scc_post_update() (in module oqp.utils.dftb_trace) format_scc_recoveries() (in module oqp.utils.dftb_trace) format_scc_summary_lines() (in module oqp.utils.dftb_trace) format_state_configurations() (in module oqp.utils.dftb_trace) format_step_timing() (in module oqp.utils.dftb_trace) format_table() (in module oqp.interop.compare) format_time() (OQPTester method) format_zvector_block() (in module oqp.utils.dftb_trace) format_zvector_dense_block() (in module oqp.utils.dftb_trace) frag (RotationComponent attribute) (TranslationComponent attribute) fragment_ct_matrix() (in module oqp.analysis.descriptors) FREQ_TO_INV_CM (in module oqp.utils.constants) freqs (Molecule attribute) friction (QMMM_MD attribute) from_geometry() (RedundantInternalCoordinates class method) from_openqp() (in module oqp.quantum.hamiltonian) from_pyscf() (OpenQP class method) from_ric() (DelocalizedInternalCoordinates class method) from_template() (SimulationManager class method) frontier_scheme (OpenQpQMMM attribute) (QMMM_MD attribute) frozen_distances (OQPEngine attribute) FS_TO_AU (in module oqp.library.namd) func (MPIMap attribute) functional (CalculationSpec attribute) (LastStep attribute) (SinglePoint attribute)

G

g (LinkAtom attribute) gamma_ref_mo (MRSFExcitedStates attribute) gap_converged (BaekAEvaluation attribute) gap_gradients (BaekAObjective attribute) gap_tol (BaekAState attribute) gap_weight (BaekAState attribute) gaps (BaekAObjective attribute) GAS_CONSTANT (in module oqp.utils.constants) generate_reference_cli() (in module oqp.pyoqp) generate_report() (OQPTester method) GENERIC_SCHEMA_KEYS (in module oqp.utils.oqp_input) geometric_config (GeometricNEBOpt attribute) GeometricEngine (class in oqp.library.libgeometric) GeometricIRCOpt (class in oqp.library.libgeometric) GeometricMECIOpt (class in oqp.library.libgeometric) GeometricMECPOpt (class in oqp.library.libgeometric) GeometricNEBOpt (class in oqp.library.libgeometric) GeometricOpt (class in oqp.library.libgeometric) GeometricTSOpt (class in oqp.library.libgeometric) geometry_from_sdf() (in module oqp.utils.geometry) GEOMETRY_UNSTABLE_RUNTYPES (in module oqp.utils.regression) GeometryLookupError get_atoms() (Molecule method) get_atoms2() (Molecule method) get_basis() (OQPData method) get_basis_data() (BasisData method) get_basislist() (BasisData method) get_config() (Molecule method) get_coord() (in module oqp.molecule.molecule) (Molecule method) get_data() (Molecule method) get_data_from_back_door() (Molecule method) get_dispersion() (DispersionModel method) (LastStep method) get_geometry() (in module oqp.utils.geometry)

get_git_branch_info() (OQPTester method) get_git_commit_info() (OQPTester method) get_grad() (Molecule method) get_hess() (Molecule method) get_mass() (Molecule method) get_mrsf_ekt_results() (Molecule method) get_nac() (Molecule method) get_optimizer() (in module oqp.library.runfunc) get_results() (Molecule method) get_scf_energy() (Molecule method) get_soc() (Molecule method) get_system() (Molecule method) grad (Optimizer attribute) (QMMM_MD attribute) grad_func (Gradient attribute) GRAD_RUNTYPES (in module oqp.utils.regression) grad_to_q() (CartesianCoordinates method) (DelocalizedInternalCoordinates method) (RedundantInternalCoordinates method) grad_wrapper() (in module oqp.library.single_point) gradient (BaekAObjective attribute) Gradient (class in oqp.library.single_point) gradient() (Gradient method) (OpenQPDFTBAdapter method) gradient_qmmm (in module oqp.utils.qmmm) gradients (BaekAObjective attribute) (NEB attribute) grads (Gradient attribute) (Molecule attribute) ground_dftb() (OpenQP method) guess() (in module oqp.library.guess) guess_hessian() (CartesianCoordinates method) (DelocalizedInternalCoordinates method) (RedundantInternalCoordinates method) GUESS_TYPES (in module oqp.utils.input_checker)

H

HA_TO_WAVENUM (in module oqp.library.namd) HA_TO_WAVENUMBER (in module oqp.library.openqp_dftb) HABOHR_TO_KJMOLNM (in module oqp.library.namd) HARTREE_TO_EV (in module oqp.utils.dftb_trace) hess_type (Hessian attribute) Hessian (class in oqp.library.single_point) hessian (Molecule attribute)

hessian() (Hessian method) HESSIAN_CACHE_VERSION (in module oqp.molecule.molecule) hessian_metadata (Molecule attribute) hf() (OpenQP method) host_row (LinkAtom attribute) hosts (VirtualCharge attribute) how_long() (in module oqp.utils.file_utils) hybrid() (MECIOpt method)

I

iarray() (in module oqp.molecule.oqpdata) IDENTITY_KEYS (in module oqp.utils.regression) idx (Molecule attribute) images (NEB attribute) imaginary_mode() (in module oqp.library.oqp_irc) imap_unordered() (MPIPool method) imult (Optimizer attribute) incre (MECIOpt attribute) inertia (Molecule attribute) infrared_intensities (Molecule attribute) infrared_intensities() (in module oqp.library.frequency) infrared_mode_dipole_derivatives (Molecule attribute) init_basis (SinglePoint attribute) init_conv (SinglePoint attribute) init_energy (ConstrainOpt attribute) (QMMMOpt attribute) init_it (SinglePoint attribute) init_library (SinglePoint attribute) init_scf (Optimizer attribute) (QMMM_MD attribute) (SinglePoint attribute) INIT_SCF_TYPES (in module oqp.utils.input_checker) init_state (NAMD_SOC attribute) (NAMD_SOC_QMMM attribute) init_temp (NAMD attribute)

init_xyz (ConstrainOpt attribute) (QMMMOpt attribute) initialize_symmetry_metadata() (Molecule method) input_dict (OpenQPEngine attribute) input_file (Molecule attribute) input_format (OQPTester attribute) integrate_density() (CubeExporter method) integrate_orbital_sq() (CubeExporter method) INTENTIONALLY_FORBIDDEN_SCHEMA_KEYS (in module oqp.utils.oqp_input) interpolate_xyz_endpoints() (in module oqp.library.neb_utils) ints_1e() (in module oqp.library.ints_1e) ints_2e() (in module oqp.library.ints_2e) IR_INTENSITY_CONVERSION_KM_MOL (in module oqp.library.frequency) IRC (class in oqp.library.oqp_irc) irc_direction (GeometricIRCOpt attribute) irc_sign (OQPIRCOpt attribute) irc_step (OQPIRCOpt attribute) is_mrsf() (in module oqp.utils.state_labels) is_phase_invariant() (in module oqp.utils.regression) ispher_mode() (in module oqp.molecule.oqpdata) istate (in module oqp.utils.qmmm) (MEP attribute) (Optimizer attribute) itr (Optimizer attribute) ixcore_shift() (SinglePoint method)

J

J_TO_AU (in module oqp.utils.constants) J_TO_INV_CM (in module oqp.utils.constants) jmult (Optimizer attribute) json_array() (in module oqp.utils.json_utils)

jstate (Optimizer attribute) jump (BaekAEvaluation attribute) jump_index (BaekAEvaluation attribute) (BaekAState attribute) jump_schedule (OQPBaekAOpt attribute)

K

k (NEB attribute) k_spring (OQPNEBOpt attribute) kabsch_align() (in module oqp.library.neb_utils) KB_HARTREE (in module oqp.library.namd) key (RegKey attribute) keys_to_compare() (in module oqp.utils.regression) kind (Angle attribute) (Bond attribute) (Dihedral attribute) (RotationComponent attribute) (TranslationComponent attribute)

kj_per_mol_to_hartree (in module oqp.utils.qmmm) KJMOL_TO_HARTREE (in module oqp.library.namd) KNOBS (in module oqp.utils.perf_levels) KNOWN_UNCOVERED (in module oqp.utils.regression) kstate (Optimizer attribute) KW_MAP_PURE (in module oqp.utils.kword_map) kwargs (CallSpec attribute)

L

label (StateRef attribute) label_excited_states() (Molecule method) label_molecular_orbitals() (Molecule method) label_normal_modes() (Molecule method) last_energy (ConstrainOpt attribute) (QMMMOpt attribute) last_radius (ConstrainOpt attribute) (QMMMOpt attribute) last_xyz (ConstrainOpt attribute) (QMMMOpt attribute) LastStep (class in oqp.library.single_point) LEAN_JSON_ENV (in module oqp.molecule.molecule) lean_keep() (in module oqp.utils.regression) legacy_config (OQPResolution attribute) LEGACY_ONLY_SCHEMA_KEYS (in module oqp.utils.oqp_input) library (SinglePoint attribute) library_suffix() (in module oqp.runtime) link_atom_position() (in module oqp.library.qmmm_connectivity) link_atoms (OpenQpQMMM attribute) link_g_factor() (in module oqp.library.qmmm_connectivity)

LinkAtom (class in oqp.library.qmmm_connectivity) list2string() (in module oqp.molecule.molecule) list_templates() (SimulationManager static method) load_config() (Molecule method) load_data() (Molecule method) load_dict() (OQPConfigParser method) load_guess_files() (GeometricEngine method) load_previous_data() (BasisOverlap method) local_stationary (BaekAEvaluation attribute) log (Molecule attribute) (OpenQP attribute) log() (OQPTester method) log_file (QMMM_MD attribute) log_path (Molecule attribute) logger (IRC attribute) (NEB attribute) (OQPEngine attribute) looks_canonical() (in module oqp.utils.oqp_input) lower_to_legacy() (in module oqp.utils.oqp_input) ls (Optimizer attribute)

M

M (GeometricEngine attribute) m_all (NAMD_QMMM attribute) main() (in module oqp.pyoqp) make_box_grid() (in module oqp.analysis.gto_grid) map_spectrum_label() (in module oqp.utils.dftb_trace) mass (ConstrainOpt attribute) (Molecule attribute) (NAMD attribute) MASSES (in module oqp.periodic_table) max_grad (Optimizer attribute) max_off_block_abs (OneElectronBlockLeakSummary attribute) max_off_block_indices (OneElectronBlockLeakSummary attribute) max_step (Optimizer attribute) max_workers (OQPTester attribute) maxit (Optimizer attribute) maxiter (OQPEngine attribute) maxmove (OQPNEBOpt attribute) md (in module oqp.library.qmmm_md) MECI_SEARCH (in module oqp.utils.input_checker) meci_search (MECIOpt attribute) MECIOpt (class in oqp.library.libscipy) mecp_search (MECPOpt attribute) MECPOpt (class in oqp.library.libscipy) MEP (class in oqp.library.libscipy) mep_energies (MEP attribute) mep_itr (MEP attribute) mep_maxit (MEP attribute) (Optimizer attribute) mep_step (OQPMEPOpt attribute) message (ConstrainOpt attribute) (Diagnostic attribute) (QMMMOpt attribute) METADATA_KEYS (in module oqp.utils.regression) method (Gradient attribute) (MECIOpt attribute) (MECPOpt attribute) (SinglePoint attribute) (StateSpecificOpt attribute) METHODS (in module oqp.utils.input_checker) metrics (Optimizer attribute) (OQPAutoMECIOpt attribute) missing_required() (in module oqp.utils.regression) mm (NAMD_QMMM attribute) mm_index (LinkAtom attribute) mm_systems (OpenQpQMMM attribute) (QMMM_MD attribute) mo (MEP attribute) mo_cube() (CubeExporter method) mo_density_ao() (MRSFExcitedStates method) mode (OQPBaekAOpt attribute) (OQPEngine attribute) (OQPMECIOpt attribute) (OQPMECPOpt attribute) (OQPOpt attribute) (OQPTCIOpt attribute) (OQPTSOpt attribute) (PyRAI2MDEngine attribute) (SimulationManager attribute) model (CalculationSpec attribute) model_options (CalculationSpec attribute) modes (Molecule attribute) modifiers (CalculationSpec attribute) module oqp oqp.analysis oqp.analysis.density_diff oqp.analysis.descriptors oqp.analysis.gto_grid oqp.analysis.nto oqp.analysis.transition_density oqp.export oqp.export.cubegen oqp.export.fcidump oqp.export.qcschema oqp.interop oqp.interop.compare oqp.interop.parsers oqp.library oqp.library.baeka oqp.library.frequency oqp.library.guess oqp.library.ints_1e oqp.library.ints_2e oqp.library.libgeometric oqp.library.libopenmm oqp.library.liboqp oqp.library.libscipy oqp.library.namd oqp.library.neb_utils oqp.library.openqp_dftb oqp.library.oqp_coords oqp.library.oqp_engine oqp.library.oqp_irc oqp.library.oqp_neb oqp.library.project_basis oqp.library.qmmm_connectivity oqp.library.qmmm_driver oqp.library.qmmm_md oqp.library.runfunc oqp.library.scf_selector_model oqp.library.set_basis oqp.library.single_point oqp.library.solvent oqp.library.symmetry oqp.library.symmetry_detect oqp.molden oqp.molden.moldenreader oqp.molden.moldenwriter oqp.molecule oqp.molecule.molecule oqp.molecule.oqpdata oqp.openqp oqp.periodic_table oqp.pyoqp oqp.quantum oqp.quantum.fcidump oqp.quantum.hamiltonian oqp.quantum.integrals oqp.runtime oqp.SimulationManager oqp.utils oqp.utils.constants oqp.utils.dftb_trace oqp.utils.file_utils oqp.utils.geometry oqp.utils.input_checker oqp.utils.input_parser oqp.utils.json_utils oqp.utils.kword_map oqp.utils.matrix oqp.utils.mpi_utils oqp.utils.oqp_input oqp.utils.oqp_tester oqp.utils.perf_levels oqp.utils.qmmm oqp.utils.regression oqp.utils.state_labels

mol (BasisData attribute) (BasisOverlap attribute) (Calculator attribute) (ConstrainOpt attribute) (GeometricNEBOpt attribute) (Gradient attribute) (Hessian attribute) (MEP attribute) (MRSFExcitedStates attribute) (NAC attribute) (NACME attribute) (NAMD attribute) (OPENQP attribute) (OpenQP attribute) (OpenQPDFTBAdapter attribute) (Optimizer attribute) (OQPAutoMECIOpt attribute) (QMMM_MD attribute), [1] (QMMMOpt attribute) (Runner attribute) (SinglePoint attribute) mol2 (OQPData attribute) mol_energy (Molecule attribute) molden_unique_name() (SinglePoint static method) MoldenReader (class in oqp.molden.moldenreader) MoldenWriter (class in oqp.molden.moldenwriter) MolecularHamiltonian (class in oqp.quantum.hamiltonian) Molecule (class in oqp.molecule.molecule) molecule() (OpenQP method) mp2() (OpenQP method) MP2_VARIANT_SCALES (in module oqp.library.single_point) MP2_VARIANTS (in module oqp.utils.input_checker) mpi4py_available (in module oqp.utils.mpi_utils) mpi4py_available() (MPIManager method) mpi_dump() (in module oqp.utils.mpi_utils) mpi_get_attr() (in module oqp.utils.mpi_utils) mpi_manager (BasisData attribute) (Calculator attribute) (Molecule attribute) (MPIMap attribute) (OQPTester attribute) (Runner attribute) mpi_update_attr() (in module oqp.utils.mpi_utils) MPIManager (class in oqp.utils.mpi_utils) MPIMap (class in oqp.utils.mpi_utils) MPIPool (class in oqp.utils.mpi_utils) mrsf() (OpenQP method) mrsf_ekt_results_by_kind (Molecule attribute) mrsf_tddftb() (OpenQP method) MRSFExcitedStates (class in oqp.analysis.transition_density) ms2 (MolecularHamiltonian attribute) mult (Molecule attribute) multiplicity (StateRef property)

N

n (TranslationComponent attribute) n_elec (MRSFExcitedStates attribute) n_electrons (MolecularHamiltonian attribute) n_orbitals (MolecularHamiltonian property) n_steps (QMMM_MD attribute) na (MRSFExcitedStates attribute) NAC (class in oqp.library.single_point) nac (Molecule attribute) nac() (NAC method) nac_dim (NACME attribute) nac_func (NAC attribute) nac_states (NAC attribute) nac_type (NAC attribute) NACME (class in oqp.library.single_point) nacme() (NACME method) nacme_wrapper() (in module oqp.library.single_point) NAMD (class in oqp.library.namd) NAMD_QMMM (class in oqp.library.namd) NAMD_SOC (class in oqp.library.namd) NAMD_SOC_MCH (class in oqp.library.namd) NAMD_SOC_MCH_QMMM (class in oqp.library.namd) NAMD_SOC_QMMM (class in oqp.library.namd) name (CallSpec attribute) native_hess_func (Hessian attribute) natom (BasisOverlap attribute) (CartesianCoordinates attribute) (DelocalizedInternalCoordinates attribute) (DispersionModel attribute) (Gradient attribute) (LastStep attribute) (NAC attribute) (NAMD attribute) (OpenQPDFTBAdapter attribute) (Optimizer attribute) (QMMM_MD attribute) (RedundantInternalCoordinates attribute) natom_all (NAMD_QMMM attribute) nb (MRSFExcitedStates attribute) nbf (AOBasis attribute) (MRSFExcitedStates attribute) NBFS (MoldenWriter attribute) ndim (CartesianCoordinates attribute) (DelocalizedInternalCoordinates attribute) (RedundantInternalCoordinates attribute) NEB (class in oqp.library.oqp_neb) neb_config (GeometricNEBOpt attribute)

neb_dt (OQPNEBOpt attribute) neb_fmax (OQPNEBOpt attribute) neb_frms (OQPNEBOpt attribute) neb_output (OQPNEBOpt attribute) NEBImage (class in oqp.library.neb_utils) needs_excited (RegKey attribute) needs_prop (RegKey attribute) NEW_INPUT_KEYS (in module oqp.utils.perf_levels) next_sigma (BaekAEvaluation attribute) nimage (GeometricNEBOpt attribute) (NEB attribute) (OQPNEBOpt attribute) NM_TO_BOHR (in module oqp.library.namd) NMR_GAUGES (in module oqp.utils.input_checker) nonbondedMethod (in module oqp.utils.qmmm) nonfinite_step_rejections (OQPEngine attribute) normal_mode() (in module oqp.library.frequency) normalize_system() (in module oqp.utils.geometry) NORMS (MoldenWriter attribute) NOT_AVAILABLE_RUNTYPES (in module oqp.utils.input_checker) ns (NAMD_SOC attribute) (NAMD_SOC_QMMM attribute) nstate (BasisOverlap attribute) (Gradient attribute) (NAC attribute) (NAMD attribute) (OpenQPDFTBAdapter attribute) (Optimizer attribute) (QMMM_MD attribute) (SinglePoint attribute) nstate_mrsf (NAMD_SOC attribute) (NAMD_SOC_QMMM attribute) nstate_soc (NAMD_SOC attribute) (NAMD_SOC_QMMM attribute) nstates (MRSFExcitedStates attribute) nstep (NAMD attribute) nSteps (in module oqp.utils.qmmm) (QMMM_MD attribute) nt (NAMD_SOC attribute) (NAMD_SOC_QMMM attribute) nto_cube() (CubeExporter method) nto_excitation() (in module oqp.analysis.nto) nto_transition() (in module oqp.analysis.nto) num_atoms (BasisData attribute) number_output() (GeometricEngine method) numerical_hess() (Hessian method) numerical_nac() (NAC method)

O

objective (BaekAObjective attribute) off_block_element_count (OneElectronBlockLeakSummary attribute) ok (CheckReport property) omp_threads (OQPTester attribute) one_body (MolecularHamiltonian attribute) one_electron_block_diagnostics() (in module oqp.library.symmetry) one_step() (ConstrainOpt method) (MECIOpt method) (MECPOpt method) (Optimizer method) (OQPBaekAOpt method) (OQPTCIOpt method) (QMMMOpt method) (StateSpecificOpt method) (TemplateOpt method) OneElectronBlockLeakSummary (class in oqp.library.symmetry) op (OpenQpQMMM attribute) openmm_dump() (in module oqp.utils.qmmm) openmm_energy() (in module oqp.utils.qmmm) openmm_gradient() (in module oqp.utils.qmmm) openmm_info() (in module oqp.utils.qmmm) openmm_init() (in module oqp.utils.qmmm) openmm_potential() (in module oqp.utils.qmmm) openmm_system() (in module oqp.utils.qmmm) openmm_update_system() (in module oqp.utils.qmmm) OPENQP (class in oqp.openqp) OpenQP (class in oqp.openqp) openqp (SimulationManager attribute) OpenQPDFTBAdapter (class in oqp.library.openqp_dftb) OpenQPEngine (class in oqp.SimulationManager) OpenQpQMMM (class in oqp.library.qmmm_driver) opt_ends (OQPNEBOpt attribute) opt_func() (Optimizer method) OPT_LIBS (in module oqp.utils.input_checker) opt_status (ConstrainOpt attribute) (QMMMOpt attribute) optimize() (GeometricNEBOpt method) (MEP method) (Optimizer method) (OQPAutoMECIOpt method) (OQPBaekAOpt method) (OQPIRCOpt method) (OQPMEPOpt method) (OQPNEBOpt method) Optimizer (class in oqp.library.libscipy) optimizer (GeometricEngine attribute) (MEP attribute) (Optimizer attribute) OPTIMIZER_RUNTYPES (in module oqp.openqp) OPTIONAL_SCF_CONVERGERS (in module oqp.utils.input_checker) optional_string() (in module oqp.molecule.oqpdata) options (CalculationSpec attribute) oqp module OQP (in module oqp.openqp) oqp.analysis module oqp.analysis.density_diff module oqp.analysis.descriptors module oqp.analysis.gto_grid module oqp.analysis.nto module oqp.analysis.transition_density module oqp.export module oqp.export.cubegen module oqp.export.fcidump module oqp.export.qcschema module oqp.interop module oqp.interop.compare module oqp.interop.parsers module oqp.library module oqp.library.baeka module oqp.library.frequency module oqp.library.guess module oqp.library.ints_1e module oqp.library.ints_2e module oqp.library.libgeometric module oqp.library.libopenmm module oqp.library.liboqp module oqp.library.libscipy module oqp.library.namd module oqp.library.neb_utils module oqp.library.openqp_dftb module oqp.library.oqp_coords module oqp.library.oqp_engine module oqp.library.oqp_irc module oqp.library.oqp_neb module oqp.library.project_basis module

oqp.library.qmmm_connectivity module oqp.library.qmmm_driver module oqp.library.qmmm_md module oqp.library.runfunc module oqp.library.scf_selector_model module oqp.library.set_basis module oqp.library.single_point module oqp.library.solvent module oqp.library.symmetry module oqp.library.symmetry_detect module oqp.molden module oqp.molden.moldenreader module oqp.molden.moldenwriter module oqp.molecule module oqp.molecule.molecule module oqp.molecule.oqpdata module oqp.openqp module oqp.periodic_table module oqp.pyoqp module oqp.quantum module oqp.quantum.fcidump module oqp.quantum.hamiltonian module oqp.quantum.integrals module oqp.runtime module oqp.SimulationManager module oqp.utils module oqp.utils.constants module oqp.utils.dftb_trace module oqp.utils.file_utils module oqp.utils.geometry module oqp.utils.input_checker module oqp.utils.input_parser module oqp.utils.json_utils module oqp.utils.kword_map module oqp.utils.matrix module oqp.utils.mpi_utils module oqp.utils.oqp_input module oqp.utils.oqp_tester module oqp.utils.perf_levels module oqp.utils.qmmm module oqp.utils.regression module oqp.utils.state_labels module oqp_cfg (QMMM_MD attribute) OQP_CONFIG_SCHEMA (in module oqp.molecule.oqpdata) oqp_driver (QMMM_MD attribute) oqp_qmmm_single_point() (QMMM_MD method) OQP_SCHEMA_KEYS (in module oqp.utils.oqp_input) OQPAutoMECIOpt (class in oqp.library.liboqp) OQPBaekAOpt (class in oqp.library.liboqp) OQPConfigParser (class in oqp.utils.input_parser) OQPData (class in oqp.molecule.oqpdata) OQPEngine (class in oqp.library.oqp_engine) OQPInputError OQPIRCOpt (class in oqp.library.liboqp) OQPMECIOpt (class in oqp.library.liboqp) OQPMECPOpt (class in oqp.library.liboqp) OQPMEPOpt (class in oqp.library.liboqp) OQPNEBOpt (class in oqp.library.liboqp) OQPOpt (class in oqp.library.liboqp) OQPResolution (class in oqp.utils.oqp_input) OQPTCIOpt (class in oqp.library.liboqp) OQPTester (class in oqp.utils.oqp_tester) OQPTSOpt (class in oqp.library.liboqp) orb_to_dens() (in module oqp.utils.matrix) orbsym (MolecularHamiltonian attribute) ORDERS (MoldenWriter attribute) orthogonality_max_deviation (OneElectronBlockLeakSummary attribute) orthogonality_ok (OneElectronBlockLeakSummary attribute) oscillator_strength() (MRSFExcitedStates method) output_dir (OQPTester attribute) overlap() (BasisOverlap method) overlap_analytic() (AOBasis method) overlap_func (BasisOverlap attribute)

P

pack_lower_tri_single() (in module oqp.library.qmmm_driver) pack_matrix() (in module oqp.utils.matrix) pack_molden_name() (SinglePoint method) parallel_gradient (BaekAObjective attribute) parallel_norm (BaekAObjective attribute) parallel_scaled_norm (BaekAObjective attribute) parray() (in module oqp.molecule.oqpdata) parse_canonical_oqp() (in module oqp.utils.oqp_input) parse_frozen_distance_spec() (in module oqp.library.oqp_engine) parse_ini_to_config() (in module oqp.library.qmmm_md) parse_jump_schedule() (in module oqp.library.baeka) parse_native_trace() (in module oqp.utils.dftb_trace) parse_oqp() (in module oqp.interop.parsers) parse_output() (in module oqp.interop.parsers) parse_pyscf_tddft() (in module oqp.interop.parsers) parse_section() (OQPData method) participation_ratio() (in module oqp.analysis.descriptors) path (Diagnostic attribute) path() (in module oqp.molecule.oqpdata) path_gtol (OQPIRCOpt attribute) (OQPMEPOpt attribute) PCM_BACKEND_MODELS (in module oqp.utils.input_checker) PCM_BACKENDS (in module oqp.utils.input_checker) PCM_MODELS (in module oqp.utils.input_checker) PCM_MODES (in module oqp.utils.input_checker) pdb (NAMD_QMMM attribute) (QMMM_MD attribute) pdb0 (in module oqp.utils.qmmm) pdb_file (in module oqp.utils.qmmm) penalty (BaekAObjective attribute) penalty() (MECIOpt method) penalty_gradient (BaekAObjective attribute) penalty_optimizer (OQPAutoMECIOpt attribute) penalty_projector() (in module oqp.library.baeka) penalty_subspace() (in module oqp.library.baeka) periodic (NAMD_QMMM attribute) perpendicular_gradient (BaekAObjective attribute) perpendicular_norm (BaekAObjective attribute) phase_invariant (RegKey attribute) physical_index (StateRef property) physical_method (CalculationSpec property) plan_image_directories() (GeometricNEBOpt method)

PLANCK_CONSTANT (in module oqp.utils.constants) point_charge_dipole() (in module oqp.utils.dftb_trace) positions (OpenQpQMMM attribute) pre_coord (Optimizer attribute) (QMMMOpt attribute) pre_energy (Optimizer attribute) predict() (in module oqp.library.scf_selector_model) prefix (GeometricNEBOpt attribute) prepare() (OpenQPEngine method) (PyRAI2MDEngine method) (SimulationManager method) prepare_mm() (OpenQpQMMM method) pressure (QMMM_MD attribute) prev_data (NAMD attribute) prev_xyz (NAMD attribute) primitives (CartesianCoordinates attribute) (DelocalizedInternalCoordinates attribute) (RedundantInternalCoordinates attribute) print_config() (OQPConfigParser method) processes (MPIMap attribute) (MPIPool attribute) product (OQPNEBOpt attribute) product_irrep() (in module oqp.library.symmetry) project (OpenQP attribute) (OpenQPEngine attribute) project_basis() (in module oqp.library.project_basis) project_global_rigid_modes (OQPEngine attribute) project_link_gradient() (in module oqp.library.qmmm_connectivity) project_name (Molecule attribute) projector_atol (BaekAState attribute) projector_basis (BaekAObjective attribute) projector_rank (BaekAObjective attribute) projector_rtol (BaekAState attribute) projector_singular_values (BaekAObjective attribute) provisional_ddx_external_charges() (in module oqp.library.solvent) provisional_ddx_reaction_field_inputs() (in module oqp.library.solvent) pubchem_geometry() (in module oqp.utils.geometry) public_method_name() (in module oqp.utils.state_labels) public_state_label() (in module oqp.utils.state_labels) put_data() (Molecule method) pyrai2md (SimulationManager attribute) PyRAI2MDEngine (class in oqp.SimulationManager)

Q

q() (CartesianCoordinates method) (DelocalizedInternalCoordinates method) (RedundantInternalCoordinates method) q_displacement() (CartesianCoordinates method) (DelocalizedInternalCoordinates method) (RedundantInternalCoordinates method) q_ref (DelocalizedInternalCoordinates attribute) qm_atoms (in module oqp.utils.qmmm) (NAMD_QMMM attribute) (OpenQpQMMM attribute) (QMMM_MD attribute)

qm_index (LinkAtom attribute) qm_mass (NAMD_QMMM attribute) qmmm() (OpenQP method) qmmm_ext (QMMM_MD attribute) QMMM_MD (class in oqp.library.libopenmm) (class in oqp.library.qmmm_md) QMMMOpt (class in oqp.library.libscipy) quad() (MECPOpt method)

R

R (MRSFExcitedStates attribute) r_all (NAMD_QMMM attribute) raman_activities (Molecule attribute) raman_activities() (in module oqp.library.frequency) raman_mode_polarizability_derivatives (Molecule attribute) read (Hessian attribute) read_basis_fmt() (BasisData method) read_fcidump() (in module oqp.quantum.fcidump) read_freqs() (Molecule method) read_mo() (MoldenReader method) read_system() (in module oqp.molecule.oqpdata) read_xyz() (in module oqp.library.qmmm_driver) rebase_previous_objective() (OQPEngine method) redistribute_frontier_charges() (in module oqp.library.qmmm_connectivity) RedundantInternalCoordinates (class in oqp.library.oqp_coords) ref (RotationComponent attribute) ref_coord (ConstrainOpt attribute) reference() (OpenQPDFTBAdapter method) (SinglePoint method) reference_description() (in module oqp.utils.state_labels) reference_method (CalculationSpec property) reference_multiplicity (CalculationSpec property) reference_scf_pcm_energy_terms() (in module oqp.library.solvent) reference_scf_phi_cav_inputs() (in module oqp.library.solvent) reference_scf_reaction_field_contract() (in module oqp.library.solvent) reference_scf_total_density() (in module oqp.library.solvent) REGISTRY (in module oqp.utils.regression) RegKey (class in oqp.utils.regression) regression_context() (Molecule method) reload() (Runner method) ReLU() (in module oqp.library.libscipy) render_canonical_oqp() (in module oqp.utils.oqp_input) reorient_for_integral_symmetry() (Molecule method) report_file (OQPTester attribute) report_interval (QMMM_MD attribute) requested_states() (in module oqp.utils.state_labels) required (RegKey attribute) res (LastStep attribute) resolve() (in module oqp.utils.perf_levels) resolve_oqp_file() (in module oqp.utils.oqp_input) resolve_oqp_root() (in module oqp.runtime) resolve_oqp_text() (in module oqp.utils.oqp_input) resolve_param_key() (in module oqp.utils.kword_map) resolved_dftb_type() (in module oqp.utils.state_labels) resolved_path (OQPResolution attribute)

response_type() (in module oqp.utils.state_labels) restart (Hessian attribute) (NAC attribute) results (OpenQPEngine attribute) (OQPTester attribute) results() (Runner method) ric (DelocalizedInternalCoordinates attribute) rigidWater (in module oqp.utils.qmmm) rmsd_grad (Optimizer attribute) rmsd_step (Optimizer attribute) rng (NAMD attribute) root (StateRef attribute) RotationComponent (class in oqp.library.oqp_coords) ROUTE_DRIVER_SCHEMA_KEYS (in module oqp.utils.oqp_input) RTLD (in module oqp) rtol (RegKey attribute) run() (IRC method) (NAMD method) (NAMD_QMMM method) (NAMD_SOC method) (NAMD_SOC_MCH method) (NAMD_SOC_MCH_QMMM method) (NAMD_SOC_QMMM method) (NEB method) (OPENQP method) (OpenQP method) (OpenQPEngine method) (OQPEngine method) (OQPTester method) (PyRAI2MDEngine method) (QMMM_MD method) (Runner method) (SimulationManager method) run_func (Runner attribute) run_md() (QMMM_MD method) run_qmmm() (OpenQPEngine method) run_single_test() (OQPTester method) run_tests() (in module oqp.pyoqp) (OQPTester method) Runner (class in oqp.pyoqp) runner (OPENQP attribute) (OpenQP attribute) Runner (OpenQPEngine attribute) runtype (SinglePoint attribute) RUNTYPE_SECTIONS (in module oqp.openqp) runtypes (RegKey attribute)

S

S (MRSFExcitedStates attribute) sarray() (in module oqp.molecule.oqpdata) save_data() (Molecule method) save_freqs() (Molecule method) save_guess_files() (GeometricEngine method) save_mol (Calculator attribute) save_molden (SinglePoint attribute) save_template() (SimulationManager method) scf() (SinglePoint method) SCF_CONVERGERS (in module oqp.utils.input_checker) scf_grad() (Gradient method) scf_maxit (SinglePoint attribute) scf_mult (SinglePoint attribute) SCF_PROPS (in module oqp.utils.input_checker) scf_type (SinglePoint attribute) SCF_TYPES (in module oqp.utils.input_checker) SCFnotConverged schema (OQPConfigParser attribute) SCHEMA_KEY_OWNERS (in module oqp.utils.oqp_input) SCIPY_OPTIMIZERS (in module oqp.utils.input_checker) section() (OpenQP method) sections (MoldenReader attribute) seed (NAMD attribute) set() (OPENQP method) (OpenQP method) set_basis() (in module oqp.library.set_basis) set_basis_data() (BasisData method) set_conf_threshold() (OQPData method) set_config() (SimulationManager method) set_config_json() (Molecule method) set_dft_functional() (OQPData method) set_dftgrid_ang_npts() (OQPData method) set_dftgrid_ao_pruned() (OQPData method) set_dftgrid_ao_threshold() (OQPData method) set_dftgrid_cam_alpha() (OQPData method) set_dftgrid_cam_beta() (OQPData method) set_dftgrid_cam_flag() (OQPData method) set_dftgrid_cam_mu() (OQPData method) set_dftgrid_hfscale() (OQPData method) set_dftgrid_partfun() (OQPData method) set_dftgrid_pruned() (OQPData method) set_dftgrid_pruned_ao_sparsity_ratio() (OQPData method) set_dftgrid_rad_npts() (OQPData method) set_dftgrid_rad_type() (OQPData method) set_ecp_data() (BasisData method) set_hessian_result() (Molecule method) set_log() (Molecule method) set_mol_charge() (OQPData method) set_mol_multiplicity() (OQPData method) set_mp2_opposite_spin_scale() (OQPData method) set_mp2_same_spin_scale() (OQPData method) set_mpi_comm() (MPIManager method) set_namd_config() (SimulationManager method) set_param() (LastStep method) set_pcm_enabled() (OQPData method) set_pcm_epsilon() (OQPData method) set_pdb() (SimulationManager method) set_qmmm_constraints() (OQPData method) set_qmmm_flag() (OQPData method) set_qmmm_forcefield() (OQPData method) set_qmmm_istate() (OQPData method) set_qmmm_nonbondedmethod() (OQPData method) set_qmmm_nsteps() (OQPData method) set_qmmm_rigidwater() (OQPData method) set_qmmm_timestep() (OQPData method) set_scf_active_basis() (OQPData method) set_scf_cdiis_switch() (OQPData method) set_scf_conv() (OQPData method) set_scf_converger_type() (OQPData method) set_scf_diis_reset_conv() (OQPData method) set_scf_diis_reset_mod() (OQPData method) set_scf_diis_type() (OQPData method) set_scf_grad_cutoff() (OQPData method) set_scf_incremental() (OQPData method) set_scf_maxdiis() (OQPData method) set_scf_maxit() (OQPData method) set_scf_mom() (OQPData method) set_scf_mom_switch() (OQPData method) set_scf_pfon() (OQPData method) set_scf_pfon_cooling_rate() (OQPData method) set_scf_pfon_nsmear() (OQPData method) set_scf_pfon_start_temp() (OQPData method) set_scf_pscreen() (OQPData method) set_scf_pscreen_cap() (OQPData method) set_scf_pscreen_grid_ang() (OQPData method) set_scf_pscreen_grid_rad() (OQPData method) set_scf_pscreen_k() (OQPData method) set_scf_pscreen_tight() (OQPData method) set_scf_pscreen_xc_aocut() (OQPData method) set_scf_pscreen_xc_dcut() (OQPData method) set_scf_rstctmo() (OQPData method) set_scf_scal_rel() (OQPData method) set_scf_type() (OQPData method) set_scf_vdiis_vshift_switch() (OQPData method) set_scf_verbose() (OQPData method) set_scf_vshift() (OQPData method) set_scf_xc_c2f() (OQPData method) set_scf_xc_incdft() (OQPData method) set_scf_xc_phi_cache() (OQPData method) set_sd_scf() (OQPData method) set_soc_2e() (OQPData method) set_soscf_lvl_shift() (OQPData method) set_subsystem_solver() (OQPData method) set_system() (OQPData method) set_system2() (OQPData method) set_tdhf_cam_alpha() (OQPData method) set_tdhf_cam_beta() (OQPData method) set_tdhf_cam_mu() (OQPData method) set_tdhf_conv() (OQPData method) set_tdhf_fp32() (OQPData method) set_tdhf_gmres_dim() (OQPData method) set_tdhf_hfscale() (OQPData method) set_tdhf_ixcore() (OQPData method)

set_tdhf_maxit() (OQPData method) set_tdhf_maxit_zv() (OQPData method) set_tdhf_multiplicity() (OQPData method) set_tdhf_nstate() (OQPData method) set_tdhf_nvdav() (OQPData method) set_tdhf_resp_cutoff() (OQPData method) set_tdhf_spc_coco() (OQPData method) set_tdhf_spc_coov() (OQPData method) set_tdhf_spc_ovov() (OQPData method) set_tdhf_target() (OQPData method) set_tdhf_tlf() (OQPData method) set_tdhf_type() (OQPData method) set_tdhf_z_solver() (OQPData method) set_tdhf_zv_warmstart() (OQPData method) set_tdhf_zvconv() (OQPData method) set_trah_global_red_factor() (OQPData method) set_trah_impl() (OQPData method) set_trah_jacobi_davidson_start() (OQPData method) set_trah_line_search() (OQPData method) set_trah_local_red_factor() (OQPData method) set_trah_n_micro() (OQPData method) set_trah_n_random_trial_vectors() (OQPData method) set_trah_stability() (OQPData method) set_trah_start_trust_radius() (OQPData method) set_xyz() (SimulationManager method) settings (OpenQP attribute) setup() (QMMM_MD method) setup_files() (PyRAI2MDEngine method) setup_input() (OpenQPEngine method) setup_input_with_xyz() (OpenQPEngine method) severity (Diagnostic attribute) sf_tddft() (OpenQP method) sf_tddftb() (OpenQP method) shell_num (BasisData attribute) SHELL_TYPES (MoldenWriter attribute) shells (AOBasis attribute) shells_data (BasisData attribute) show_config() (SimulationManager method) sidecar_field (RegKey attribute) sidecar_keys() (in module oqp.utils.regression) sigma (BaekAObjective attribute) (BaekAState attribute) (MECIOpt attribute) sign (IRC attribute) SIGN_OPERATIONS (in module oqp.library.symmetry_detect) silent (Molecule attribute) (OpenQP attribute) (OQPData attribute) simulation_md (QMMM_MD attribute) SimulationManager (class in oqp.SimulationManager) SinglePoint (class in oqp.library.single_point) skip_sub (RegKey attribute) skip_sub_keys() (in module oqp.utils.regression) skip_tag (Molecule attribute) snapshot_mrsf_ekt_results() (Molecule method) soc (Molecule attribute) soc() (OpenQP method) soc_du_dt_corr (NAMD_SOC attribute) (NAMD_SOC_QMMM attribute) soc_matrix() (OpenQPDFTBAdapter method) soc_tdc_grad_corr (NAMD_SOC attribute) (NAMD_SOC_QMMM attribute) source (RegKey attribute) source_path (OQPResolution attribute) source_text (CalculationSpec attribute) sp (OPENQP property) (Optimizer attribute) (QMMM_MD attribute) span (BaekAObjective attribute) spans_internal_space() (RedundantInternalCoordinates method) spec (OQPResolution attribute) spectrum_from_ground() (in module oqp.utils.dftb_trace) SPEED_OF_LIGHT (in module oqp.utils.constants) SPH_NBFS (MoldenWriter attribute) SPH_ORDERS (MoldenWriter attribute) spin_flip_pair() (in module oqp.utils.dftb_trace) spin_name() (in module oqp.utils.state_labels) sqm (IRC attribute) sqrt_cartesian_mass (OQPEngine attribute) st (CubeExporter attribute) stability (SinglePoint attribute) stage_integral_symmetry_maps() (Molecule method) stage_response_symmetry() (Molecule method) start_time (Molecule attribute) (OQPTester attribute) state (Hessian attribute) state_density_ao() (MRSFExcitedStates method) state_density_cube() (CubeExporter method) state_density_mo() (MRSFExcitedStates method) StateRef (class in oqp.utils.oqp_input) states (OQPBaekAOpt attribute) states_overlap() (OpenQPDFTBAdapter method) StateSpecificOpt (class in oqp.library.libscipy) status (OneElectronBlockLeakSummary attribute) (OQPTester attribute) step (IRC attribute) step() (QMMM_MD method) step_size (Optimizer attribute) step_tol (Optimizer attribute) stored_calcs (GeometricEngine attribute) string() (in module oqp.molecule.oqpdata) string_config() (in module oqp.molecule.molecule) strip_schema() (OQPConfigParser method) substep (NAMD attribute) SUPPORTED_RUNTYPES (in module oqp.utils.input_checker) swapmo() (SinglePoint method) symbol (in module oqp.periodic_table) SYMBOL_MAP (in module oqp.periodic_table) SYMBOL_MAP_1 (in module oqp.periodic_table) symbols (NEBImage attribute) symmetrize_gradient() (Molecule method) symmetry_metadata (Molecule attribute) system0 (in module oqp.utils.qmmm) system_md (QMMM_MD attribute)

T

TA_DIMENSIONS_LENGTH (in module oqp.molecule.oqpdata) tag (Molecule attribute) td (Gradient attribute) (SinglePoint attribute) td_prop (Gradient attribute) tdc_scheme (NAMD attribute) tddft() (OpenQP method) (SinglePoint method) tddft_grad() (Gradient method) tddftb() (OpenQP method) TDHF_TYPES (in module oqp.utils.input_checker) tdm_ao() (MRSFExcitedStates method) tdm_mo() (MRSFExcitedStates method) TDnotConverged temperature (Hessian attribute) (QMMM_MD attribute) TemplateOpt (class in oqp.library.libscipy) test() (Runner method) tested_data (BaekAEvaluation attribute) tested_sigma (BaekAEvaluation attribute) theory (OpenQP attribute) thermal_analysis() (in module oqp.library.frequency) thrshe (NAMD attribute) timeStep (in module oqp.utils.qmmm) (QMMM_MD attribute) timestep (QMMM_MD attribute) title (SimulationManager attribute) tmass (ConstrainOpt attribute) (QMMMOpt attribute)

tmax (GeometricNEBOpt attribute) to_fcidump() (MolecularHamiltonian method) to_input_dict() (OpenQP method) to_qcschema() (in module oqp.export.qcschema) to_text() (CheckReport method) (Diagnostic method) tol_f (BaekAState attribute) tol_g (BaekAState attribute) topology (OpenQpQMMM attribute) total_cpus (OQPTester attribute) tozer_lambda() (in module oqp.analysis.descriptors) trajectory_file (QMMM_MD attribute) trajectory_format (QMMM_MD attribute) trans_den_from_amplitudes() (MRSFExcitedStates method) transition_density_cube() (CubeExporter method) transition_dipole() (MRSFExcitedStates method) TranslationComponent (class in oqp.library.oqp_coords) trivial (NAMD attribute) trivial_thresh (NAMD attribute) trust (GeometricNEBOpt attribute) (OQPEngine attribute) trust_max (OQPEngine attribute) trust_min (OQPEngine attribute) try_basis() (in module oqp.utils.file_utils) try_data_file() (in module oqp.utils.file_utils) two_body (MolecularHamiltonian attribute) typemap (OQPData property)

U

U (DelocalizedInternalCoordinates attribute) ubp() (MECIOpt method) unit (OpenQP attribute) unit_charge (in module oqp.utils.qmmm) unpack_lower_tri_multi() (in module oqp.library.qmmm_driver) unpack_lower_tri_single() (in module oqp.library.qmmm_driver) unpack_symmetric() (in module oqp.utils.matrix) unpack_triangular() (in module oqp.quantum.integrals) UNSET (in module oqp.utils.perf_levels)

update() (OpenQP method) update_config_json() (Molecule method) update_guess() (in module oqp.library.guess) update_mol() (Molecule method) update_one_electron_block_diagnostics() (in module oqp.library.symmetry) update_system() (Molecule method) use_ecp (BasisData attribute) use_mol (OpenQpQMMM attribute) usempi (Molecule attribute) (OpenQP attribute)

V

v_all (NAMD_QMMM attribute) VALID_MODES (SimulationManager attribute) validate() (in module oqp.utils.perf_levels) (OQPConfigParser method) validate_examples() (in module oqp.utils.regression) validate_examples_cli() (in module oqp.pyoqp) validate_qcschema() (in module oqp.export.qcschema) value (Diagnostic attribute) value() (Angle method) (Bond method) (Dihedral method) (RotationComponent method) (TranslationComponent method)

var (MPIMap attribute) vel (NAMD attribute) velocity_source (NAMD attribute) verify_fcidump_fci() (in module oqp.export.fcidump) vibrational_intensity_metadata (Molecule attribute) VirtualCharge (class in oqp.library.qmmm_connectivity)

W

warnings (CheckReport property) was_natural (OQPResolution attribute) weights (MECIOpt attribute) (MECPOpt attribute) (OQPBaekAOpt attribute) (VirtualCharge attribute) what_is_time() (in module oqp.utils.file_utils) wiki (Diagnostic attribute) WIKI_HELP (in module oqp.utils.input_checker) within_tolerance (OneElectronBlockLeakSummary attribute) work_func (MECIOpt attribute) (MECPOpt attribute)

workdir (OpenQPEngine attribute) workflow (OpenQP attribute) write_atoms() (MoldenWriter method) write_basis() (MoldenWriter method) write_config() (in module oqp.utils.file_utils) write_fcidump() (in module oqp.quantum.fcidump) write_frequency() (in module oqp.molden.moldenwriter) write_grad() (in module oqp.utils.file_utils) write_mo() (MoldenWriter method) write_molden() (Molecule method) write_neb_xyz() (in module oqp.library.neb_utils) write_spherical_markers() (MoldenWriter method) write_xyz() (in module oqp.utils.file_utils)

X

x (MECIOpt attribute) (OQPEngine attribute)

x_ts (IRC attribute) xyz (Molecule attribute)

Y

y (MECIOpt attribute)

Z

Z (CubeExporter attribute)

zvec_func (Gradient attribute) ZVnotConverged