Index

_

__init__() (pysisyphus.calculators.AFIR.AFIR method), [1] (pysisyphus.calculators.AtomAtomTransTorque.AtomAtomTransTorque method) (pysisyphus.calculators.Calculator.Calculator method), [1] (pysisyphus.dynamics.Gaussian.Gaussian method) (pysisyphus.Geometry.Geometry method), [1] (pysisyphus.line_searches.Backtracking method) (pysisyphus.line_searches.Backtracking.Backtracking method) (pysisyphus.line_searches.LineSearch.LineSearch method) (pysisyphus.line_searches.StrongWolfe method) (pysisyphus.line_searches.StrongWolfe.StrongWolfe method) (pysisyphus.modefollow.NormalMode method) (pysisyphus.modefollow.NormalMode.NormalMode method) (pysisyphus.wavefunction.DIIS.DIIS method)

A

a (pysisyphus.io.zmat.ZLine attribute) a8() (in module pysisyphus.io.crd) AB (pysisyphus.wavefunction.gen_ints.TwoCenter1d property) accumulate_multipoles() (in module pysisyphus.wavefunction.dma) action() (pysisyphus.irc.Instanton.Instanton method) action_gradient() (pysisyphus.irc.Instanton.Instanton method) action_hessian() (pysisyphus.irc.Instanton.Instanton method) add_pyscf_to_dict() (in module pysisyphus.calculators.pyscf_lazy) adia_ens (pysisyphus.diabatization.results.DiabatizationResult attribute) AFIR (class in pysisyphus.calculators.AFIR), [1] afir_closure() (in module pysisyphus.calculators.AFIR), [1] afir_fd_hessian_wrapper() (pysisyphus.calculators.AFIR.AFIR method), [1] aind (pysisyphus.io.zmat.ZLine attribute) align_coords() (in module pysisyphus.helpers) align_geoms() (in module pysisyphus.helpers) align_principal_axes() (pysisyphus.Geometry.Geometry method), [1] ALL (pysisyphus.calculators.Calculator.KeepKind attribute), [1] all_energies (pysisyphus.Geometry.Geometry property), [1] all_energies_from_fchk_data() (in module pysisyphus.io.fchk) allcoords (pysisyphus.cos.FreezingString.FreezingString property) alpha (pysisyphus.line_searches.LineSearch.LineSearchResult attribute) alpha_new_from_phi() (pysisyphus.line_searches.Backtracking method) (pysisyphus.line_searches.Backtracking.Backtracking method) alpha_new_from_phi_dphi() (pysisyphus.line_searches.Backtracking method) (pysisyphus.line_searches.Backtracking.Backtracking method) alpha_spin_pop (pysisyphus.wavefunction.pop_analysis.PopAnalysis property) Am() (in module pysisyphus.wavefunction.solid_harmonics) anharmonic_classic_partfunc() (in module pysisyphus.partfuncs.partfuncs) anim_cos() (in module pysisyphus.plot) ao_center_map (pysisyphus.wavefunction.wavefunction.Wavefunction property) ao_centers (pysisyphus.wavefunction.wavefunction.Wavefunction property) AOMixShells (class in pysisyphus.wavefunction.shells) apply_cloudpickle() (in module pysisyphus.executors) apply_keep_kind() (pysisyphus.calculators.Calculator.Calculator method), [1] apply_set_plans() (pysisyphus.calculators.Calculator.Calculator method), [1] approx_float() (in module pysisyphus.helpers_pure) approximate_radius() (pysisyphus.Geometry.Geometry method), [1] are_collinear() (in module pysisyphus.intcoords.valid) (in module pysisyphus.linalg) argsort() (in module pysisyphus.helpers_pure) arrow() (in module pysisyphus.wrapper.jmol) as_arrays() (pysisyphus.wavefunction.shells.Shells method) as_ascii_art() (pysisyphus.Geometry.Geometry method), [1] as_ase_atoms() (pysisyphus.Geometry.Geometry method), [1]

as_g98_list() (pysisyphus.Geometry.Geometry method), [1] as_gau_gbs() (pysisyphus.wavefunction.shells.Shells method) as_numba_shells() (pysisyphus.wavefunction.shells.Shells method) as_numba_shellstructs() (pysisyphus.wavefunction.shells.Shells method) as_tuple() (pysisyphus.wavefunction.shells.Shell method) (pysisyphus.wavefunction.shells.Shells method) as_wavenums_and_ang_tuple() (pysisyphus.marcus_dim.types.MarcusModel method) as_xyz() (pysisyphus.cos.FreezingString.FreezingString method) (pysisyphus.cos.GrowingNT.GrowingNT method) (pysisyphus.Geometry.Geometry method), [1] (pysisyphus.irc.Instanton.Instanton method) as_xyzs() (pysisyphus.hindered_rotor.RotorInfo.RotorInfo method) assert_cart_coords() (pysisyphus.Geometry.Geometry method), [1] assert_compatibility() (pysisyphus.Geometry.Geometry method), [1] atom (pysisyphus.io.zmat.ZLine attribute) atom_indices() (pysisyphus.Geometry.Geometry method), [1] atom_num (pysisyphus.wavefunction.wavefunction.Wavefunction property) atom_types (pysisyphus.Geometry.Geometry property), [1] atom_xyz_iter() (pysisyphus.Geometry.Geometry method), [1] AtomAtomTransTorque (class in pysisyphus.calculators.AtomAtomTransTorque) atomic_numbers (pysisyphus.Geometry.Geometry property), [1] atomic_numbers_for_atoms() (in module pysisyphus.elem_data) atoms (pysisyphus.cos.GrowingNT.GrowingNT property) (pysisyphus.hindered_rotor.RotorInfo.RotorInfo attribute) (pysisyphus.io.Cube attribute) (pysisyphus.io.cube.Cube attribute) atoms_coords3d (pysisyphus.wavefunction.shells.Shells property) atoms_coords_to_crd_str() (in module pysisyphus.io.crd) atoms_coords_to_pdb_str() (in module pysisyphus.io.pdb) atoms_from_data() (in module pysisyphus.io.fchk) augment_bonds() (in module pysisyphus.intcoords.augment_bonds) augment_matrix() (in module pysisyphus.linalg_affine3) augment_primitives() (in module pysisyphus.intcoords.eval) augment_vector() (in module pysisyphus.linalg_affine3) augment_vectors() (in module pysisyphus.linalg_affine3) AUX_BOND (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) AUX_INTERFRAG_BOND (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) aux_interfrag_bonds (pysisyphus.intcoords.setup.CoordInfo attribute) aux_vrr (pysisyphus.wavefunction.gen_ints.ThreeCenterTwoElectron attribute) (pysisyphus.wavefunction.gen_ints.ThreeCenterTwoElectronSph attribute) available() (in module pysisyphus.testing) axes (pysisyphus.io.Cube attribute) (pysisyphus.io.cube.Cube attribute) AxisSwitch (class in pysisyphus.franckcondon.duschinsky)

B

B (pysisyphus.intcoords.DLC property) (pysisyphus.intcoords.DLC.DLC property) (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] B0 (pysisyphus.franckcondon.duschinsky.AxisSwitch attribute) B_inv (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] B_inv_prim (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] B_prim (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] backend_module (pysisyphus.wavefunction.shells.Shells attribute) Backtracking (class in pysisyphus.line_searches) (class in pysisyphus.line_searches.Backtracking) backtransform_hessian() (pysisyphus.intcoords.DLC method) (pysisyphus.intcoords.DLC.DLC method) (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] Basis (class in pysisyphus.wavefunction.Basis) basis_from_json() (in module pysisyphus.wavefunction.Basis) basis_from_orca_str() (in module pysisyphus.wavefunction.Basis) basis_from_pyscf_str() (in module pysisyphus.wavefunction.Basis) batch_pals (pysisyphus.cos.distributed.ParallelData attribute) batch_sizes (pysisyphus.cos.distributed.ParallelData attribute) Benchmark (class in pysisyphus.benchmarks.Benchmark) Bend (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.Bend) BEND (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) Bend2 (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.Bend2) BEND2 (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) bend_atom_indices (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] bend_indices (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] bend_valid() (in module pysisyphus.intcoords.valid)

bends (pysisyphus.intcoords.setup.CoordInfo attribute) berendsen_closure() (in module pysisyphus.dynamics.thermostats) beta_spin_pop (pysisyphus.wavefunction.pop_analysis.PopAnalysis property) bf_ind_key() (in module pysisyphus.wavefunction.shells_molcas) bfgs_multiply() (in module pysisyphus.optimizers.closures) bfgs_update() (in module pysisyphus.optimizers.hessian_updates) BFType (class in pysisyphus.wavefunction.helpers) bisect() (pysisyphus.line_searches.HagerZhang method) (pysisyphus.line_searches.HagerZhang.HagerZhang method) block_davidson() (in module pysisyphus.modefollow.davidson) Bm() (in module pysisyphus.wavefunction.solid_harmonics) boettger_factors2d() (in module pysisyphus.wavefunction.so_coupling) bofill_update() (in module pysisyphus.optimizers.hessian_updates) bond (pysisyphus.hindered_rotor.RotorInfo.RotorInfo attribute) BOND (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) bond_atom_indices (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] bond_indices (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] bond_sets (pysisyphus.Geometry.Geometry property), [1] bond_typed_prims (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] BONDED_FRAGMENT (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) BondedFragment (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.BondedFragment) bonds (pysisyphus.intcoords.setup.CoordInfo attribute) bool_color() (in module pysisyphus.color) boys (class in pysisyphus.wavefunction.gen_ints) boys() (in module pysisyphus.wavefunction.ints.boys) bracket() (pysisyphus.line_searches.HagerZhang method) (pysisyphus.line_searches.HagerZhang.HagerZhang method) Bt_inv (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] Bt_inv_prim (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] build_set_plans() (pysisyphus.calculators.Calculator.Calculator method), [1]

C

C (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] (pysisyphus.wavefunction.localization.JacobiSweepResult attribute) C() (in module pysisyphus.wavefunction.solid_harmonics) C_occ (pysisyphus.wavefunction.wavefunction.Wavefunction property) C_virt (pysisyphus.wavefunction.wavefunction.Wavefunction property) Ca (pysisyphus.MOCoeffs.MOCoeffs attribute) cache_arrays() (in module pysisyphus.helpers_pure) calc_double_ao_overlap() (pysisyphus.Geometry.Geometry method), [1] calc_energy() (pysisyphus.Geometry.Geometry method), [1] calc_energy_and_forces() (pysisyphus.Geometry.Geometry method), [1] calc_hessian_for() (pysisyphus.cos.GrowingNT.GrowingNT method) calc_pals (pysisyphus.cos.distributed.ParallelData attribute) calc_relaxed_density() (pysisyphus.Geometry.Geometry method), [1] calc_wavefunction() (pysisyphus.Geometry.Geometry method), [1] calcEholo_vert() (in module pysisyphus.cos.stiffness) calculate() (pysisyphus.dynamics.Gaussian.Gaussian method) (pysisyphus.intcoords.LinearBend method) (pysisyphus.intcoords.LinearBend.LinearBend method) (pysisyphus.intcoords.LinearDisplacement method) (pysisyphus.intcoords.LinearDisplacement.LinearDisplacement method) (pysisyphus.intcoords.Primitive.Primitive method) calculate_property() (in module pysisyphus.marcus_dim.fit) CalculationFailedException Calculator (class in pysisyphus.calculators.Calculator), [1] call_jmol() (in module pysisyphus.wrapper.jmol) call_mwfn() (in module pysisyphus.wrapper.mwfn) call_packmol() (in module pysisyphus.wrapper.packmol) callback() (in module pysisyphus.diabatization.coulomb_eta) can_get_coeffs() (pysisyphus.wavefunction.DIIS.DIIS method) canonical_order() (in module pysisyphus.wavefunction.backend_numba_multipole) (in module pysisyphus.wavefunction.gen_ints) (in module pysisyphus.wavefunction.helpers) cart2ang_moms() (in module pysisyphus.wavefunction.helpers) cart2sph_coeff() (in module pysisyphus.wavefunction.cart2sph) cart2sph_coeffs (pysisyphus.wavefunction.shells.Shells property) (pysisyphus.wavefunction.shells_molcas.MolcasShells property) cart2sph_coeffs() (in module pysisyphus.wavefunction.cart2sph) cart2sph_coeffs_for() (in module pysisyphus.wavefunction.cart2sph) cart2sph_nlms() (in module pysisyphus.wavefunction.cart2sph) cart2spherical() (in module pysisyphus.wavefunction.gen_ints) cart_ao_centers (pysisyphus.wavefunction.shells.Shells property) cart_axis (pysisyphus.intcoords.Cartesian.CartesianX attribute) (pysisyphus.intcoords.Cartesian.CartesianY attribute) (pysisyphus.intcoords.Cartesian.CartesianZ attribute) (pysisyphus.intcoords.CartesianX attribute) (pysisyphus.intcoords.CartesianY attribute) (pysisyphus.intcoords.CartesianZ attribute) (pysisyphus.intcoords.Translation.TranslationX attribute) (pysisyphus.intcoords.Translation.TranslationY attribute) (pysisyphus.intcoords.Translation.TranslationZ attribute) (pysisyphus.intcoords.TranslationX attribute) (pysisyphus.intcoords.TranslationY attribute) (pysisyphus.intcoords.TranslationZ attribute) cart_bf_num (pysisyphus.wavefunction.shells.Shells property) cart_coords (pysisyphus.cos.GrowingNT.GrowingNT property) (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.irc.Instanton.Instanton property) cart_displs_to_vib_normal_modes() (in module pysisyphus.io.hessian) cart_forces (pysisyphus.cos.GrowingNT.GrowingNT property) (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.irc.Instanton.Instanton property) cart_gradient (pysisyphus.Geometry.Geometry property), [1] cart_gto3d_0() (in module pysisyphus.wavefunction.ints.cart_gto3d) cart_gto3d_1() (in module pysisyphus.wavefunction.ints.cart_gto3d) cart_gto3d_2() (in module pysisyphus.wavefunction.ints.cart_gto3d) cart_gto3d_3() (in module pysisyphus.wavefunction.ints.cart_gto3d) cart_gto3d_4() (in module pysisyphus.wavefunction.ints.cart_gto3d) cart_gto3d_rel() (in module pysisyphus.wavefunction.density_numba) cart_hessian (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.irc.Instanton.Instanton property) cart_order (pysisyphus.wavefunction.shells.AOMixShells attribute) (pysisyphus.wavefunction.shells.FCHKShells attribute) (pysisyphus.wavefunction.shells.MoldenShells attribute) (pysisyphus.wavefunction.shells_trexio.TrexIOShells attribute) cart_powers (pysisyphus.wavefunction.shells.Shell property) cart_Ps (pysisyphus.wavefunction.shells_pyscf.PySCFShells attribute) cart_size (pysisyphus.wavefunction.shells.Shell property) (pysisyphus.wavefunction.shells.Shells property) cart_size() (in module pysisyphus.wavefunction.density_numba) (in module pysisyphus.wavefunction.helpers) Cartesian (class in pysisyphus.intcoords.Cartesian) CARTESIAN (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) (pysisyphus.wavefunction.helpers.BFType attribute) cartesian_indices (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] cartesian_inds (pysisyphus.intcoords.setup.CoordInfo attribute) CARTESIAN_X (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) CARTESIAN_Y (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) CARTESIAN_Z (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) CartesianCoords (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.CartesianCoords) CartesianX (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.Cartesian) CartesianY (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.Cartesian) CartesianZ (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.Cartesian) CartGTO3d (class in pysisyphus.wavefunction.gen_ints) CartGTOShell (class in pysisyphus.wavefunction.gen_ints) Cb (pysisyphus.MOCoeffs.MOCoeffs attribute) cca_order() (in module pysisyphus.wavefunction.helpers) CDD_PNG_FNS (in module pysisyphus.plot) center() (in module pysisyphus.TablePrinter) (pysisyphus.Geometry.Geometry method), [1] center_of_mass (pysisyphus.Geometry.Geometry property), [1] center_of_mass_at() (pysisyphus.Geometry.Geometry method), [1] center_shell_iter() (pysisyphus.wavefunction.shells.Shells method) centers (pysisyphus.numint.molint.MolGrid attribute) centroid (pysisyphus.Geometry.Geometry property), [1] charge (pysisyphus.calculators.AFIR.AFIR property), [1] charges (pysisyphus.wavefunction.pop_analysis.PopAnalysis property) chebyshev_2nd_kind() (in module pysisyphus.numint.radint) check_alpha() (pysisyphus.line_searches.LineSearch.LineSearch method) check_convergence() (pysisyphus.cos.GrowingNT.GrowingNT method) check_for_end_sign() (in module pysisyphus.helpers) check_mem() (in module pysisyphus.helpers_pure) check_primitives() (in module pysisyphus.intcoords.eval) check_sanity() (pysisyphus.wavefunction.wavefunction.Wavefunction method) check_typed_prims() (in module pysisyphus.intcoords.valid) cholesky() (in module pysisyphus.wavefunction.localization) chunks() (in module pysisyphus.helpers_pure) cid_from_name() (in module pysisyphus.io.pubchem) CLASS1 (pysisyphus.marcus_dim.types.RobinDay attribute) CLASS2 (pysisyphus.marcus_dim.types.RobinDay attribute) CLASS3 (pysisyphus.marcus_dim.types.RobinDay attribute) class_type (pysisyphus.wavefunction.backend_numba.NumbaShell attribute) classical_particle_density() (in module pysisyphus.partfuncs.partfuncs)

clean() (pysisyphus.calculators.Calculator.Calculator method), [1] clear() (pysisyphus.Geometry.Geometry method), [1] (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] clear_passed() (pysisyphus.cos.GrowingNT.GrowingNT method) closest_sites_and_weights() (in module pysisyphus.wavefunction.dma) CloudpickleProcessPoolExecutor (class in pysisyphus.executors) coeffs (pysisyphus.optimizers.gdiis.DIISResult attribute) Colvar (class in pysisyphus.dynamics.colvars) com (pysisyphus.hessian_proj.Orientation attribute) combine_grids() (in module pysisyphus.numint.atomint) comment (pysisyphus.Geometry.Geometry property), [1] comment1 (pysisyphus.io.Cube attribute) (pysisyphus.io.cube.Cube attribute) comment2 (pysisyphus.io.Cube attribute) (pysisyphus.io.cube.Cube attribute) compare_to_geometric() (in module pysisyphus.intcoords.Rotation) complete_fragments() (in module pysisyphus.helpers) condition() (pysisyphus.calculators.Calculator.SetPlan method), [1] conf_key (pysisyphus.calculators.Calculator.Calculator attribute), [1] confirm_input() (in module pysisyphus.helpers) connect_fragments() (in module pysisyphus.intcoords.setup) connect_fragments_ahlrichs() (in module pysisyphus.intcoords.setup) connect_fragments_kmeans() (in module pysisyphus.intcoords.setup) constrained_indices (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] constraints (pysisyphus.intcoords.DLC property) (pysisyphus.intcoords.DLC.DLC property) contr_depth (pysisyphus.wavefunction.shells.Shell property) converged (pysisyphus.line_searches.LineSearch.LineSearchResult attribute) (pysisyphus.modefollow.davidson.DavidsonResult attribute) coord_types (pysisyphus.Geometry.Geometry attribute), [1] CoordInfo (class in pysisyphus.intcoords.setup) coords (pysisyphus.cos.FreezingString.FreezingString property) (pysisyphus.cos.GrowingNT.GrowingNT property) (pysisyphus.dynamics.driver.MDResult attribute) (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.intcoords.CartesianCoords property) (pysisyphus.intcoords.CartesianCoords.CartesianCoords property) (pysisyphus.intcoords.Coords.CoordSys property) (pysisyphus.intcoords.DLC property) (pysisyphus.intcoords.DLC.DLC property) (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] (pysisyphus.irc.Instanton.Instanton property) (pysisyphus.marcus_dim.types.MarcusDimScanResult attribute) (pysisyphus.optimizers.gdiis.DIISResult attribute) coords3d (pysisyphus.dynamics.wigner.WignerSample attribute) (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.hessian_proj.Orientation attribute) (pysisyphus.hindered_rotor.RotorInfo.RotorInfo attribute) (pysisyphus.intcoords.CartesianCoords property) (pysisyphus.intcoords.CartesianCoords.CartesianCoords property) (pysisyphus.intcoords.Coords.CoordSys property) (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] (pysisyphus.io.Cube attribute) (pysisyphus.io.cube.Cube attribute) (pysisyphus.wavefunction.wavefunction.Wavefunction property) coords3d_eq (pysisyphus.dynamics.wigner.WignerSample attribute) coords3d_final (pysisyphus.franckcondon.duschinsky.AxisSwitch attribute) coords3d_init (pysisyphus.franckcondon.duschinsky.AxisSwitch attribute) coords3d_init_rot (pysisyphus.franckcondon.duschinsky.AxisSwitch attribute) coords3d_org (pysisyphus.hessian_proj.Orientation attribute) coords_by_type (pysisyphus.Geometry.Geometry property), [1] coords_last (pysisyphus.dynamics.driver.MDResult attribute) coords_minus (pysisyphus.irc.initial_displ.ThirdDerivResult attribute) coords_plus (pysisyphus.irc.initial_displ.ThirdDerivResult attribute) coords_to_trj() (in module pysisyphus.xyzloader) CoordSys (class in pysisyphus.intcoords.Coords) copy() (pysisyphus.Geometry.Geometry method), [1] copy_all() (pysisyphus.Geometry.Geometry method), [1] correct_dihedrals() (in module pysisyphus.intcoords.update) Coulomb (class in pysisyphus.wavefunction.gen_ints) coulomb3d_00() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_01() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_02() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_03() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_04() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_10() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_11() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_12() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_13() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_14() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_20() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_21() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_22() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_23() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_24() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_30() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_31() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_32() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_33() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_34() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_40() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_41() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_42() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_43() (in module pysisyphus.wavefunction.ints.coulomb3d) coulomb3d_44() (in module pysisyphus.wavefunction.ints.coulomb3d) CoulombShell (class in pysisyphus.wavefunction.gen_ints) coupling (pysisyphus.marcus_dim.types.MarcusModel attribute) couplings (pysisyphus.diabatization.results.DiabatizationResult property) covalent_radii (pysisyphus.Geometry.Geometry property), [1] CovRadiiSumZero, [1] create_correlation_plots() (in module pysisyphus.marcus_dim.fit) create_marcus_coefficient_plot() (in module pysisyphus.marcus_dim.fit) cross3() (in module pysisyphus.linalg) csvr_closure() (in module pysisyphus.dynamics.thermostats) csvr_closure_2() (in module pysisyphus.dynamics.thermostats) ct_numbers() (in module pysisyphus.wavefunction.excited_states) ct_numbers_for_states() (in module pysisyphus.wavefunction.excited_states) Cube (class in pysisyphus.io) (class in pysisyphus.io.cube) cube_to_str() (in module pysisyphus.io.cube) cubic_displ() (in module pysisyphus.irc.initial_displ) cubic_displ_for_geom() (in module pysisyphus.irc.initial_displ) cubic_displ_for_h5() (in module pysisyphus.irc.initial_displ) cubic_fit() (in module pysisyphus.optimizers.poly_fit) cur_cycle (pysisyphus.diabatization.results.DiabatizationResult attribute) (pysisyphus.modefollow.davidson.DavidsonResult attribute) (pysisyphus.wavefunction.localization.JacobiSweepResult attribute) current_density() (pysisyphus.wavefunction.wavefunction.Wavefunction method) curvature_at_image() (in module pysisyphus.optimizers.hessian_updates) curvature_condition() (pysisyphus.line_searches.LineSearch.LineSearch method) curvature_tangent_update() (in module pysisyphus.optimizers.hessian_updates) CVBend (class in pysisyphus.dynamics.colvars) CVDistance (class in pysisyphus.dynamics.colvars) CVTorsion (class in pysisyphus.dynamics.colvars)

D

d (pysisyphus.io.zmat.ZLine attribute) (pysisyphus.marcus_dim.types.MarcusModel attribute) d0 (pysisyphus.intcoords.generate_derivatives.FuncResult attribute) d1 (pysisyphus.intcoords.generate_derivatives.FuncResult attribute) d2 (pysisyphus.intcoords.generate_derivatives.FuncResult attribute) d2q_a() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) d2q_a2() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) d2q_b() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) d2q_d() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) d2q_d2() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) d2q_lb() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) d2q_ld() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) d2q_oop() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) d2q_rd1() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) d2q_rd2() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) damped_bfgs_update() (in module pysisyphus.optimizers.hessian_updates) data_funcs (pysisyphus.benchmarks.Benchmark.Benchmark attribute) DavidsonResult (class in pysisyphus.modefollow.davidson) default_assumptions (pysisyphus.wavefunction.gen_ints.boys attribute) (pysisyphus.wavefunction.gen_ints.CartGTO3d attribute) (pysisyphus.wavefunction.gen_ints.CartGTOShell attribute) (pysisyphus.wavefunction.gen_ints.Coulomb attribute) (pysisyphus.wavefunction.gen_ints.CoulombShell attribute) (pysisyphus.wavefunction.gen_ints.DiagQuadrupole3dShell attribute) (pysisyphus.wavefunction.gen_ints.ERI attribute) (pysisyphus.wavefunction.gen_ints.ERIShell attribute) (pysisyphus.wavefunction.gen_ints.Kinetic1d attribute) (pysisyphus.wavefunction.gen_ints.Kinetic3d attribute) (pysisyphus.wavefunction.gen_ints.Kinetic3dShell attribute) (pysisyphus.wavefunction.gen_ints.Multipole1d attribute) (pysisyphus.wavefunction.gen_ints.Multipole3d attribute) (pysisyphus.wavefunction.gen_ints.Multipole3dShell attribute) (pysisyphus.wavefunction.gen_ints.Overlap1d attribute) (pysisyphus.wavefunction.gen_ints.Overlap3dShell attribute) (pysisyphus.wavefunction.gen_ints.SpinOrbit attribute) (pysisyphus.wavefunction.gen_ints.SpinOrbitShell attribute) (pysisyphus.wavefunction.gen_ints.ThreeCenterTwoElectron attribute) (pysisyphus.wavefunction.gen_ints.ThreeCenterTwoElectronBase attribute) (pysisyphus.wavefunction.gen_ints.ThreeCenterTwoElectronShell attribute) (pysisyphus.wavefunction.gen_ints.ThreeCenterTwoElectronSph attribute) (pysisyphus.wavefunction.gen_ints.ThreeCenterTwoElectronSphShell attribute) (pysisyphus.wavefunction.gen_ints.TwoCenter1d attribute) (pysisyphus.wavefunction.gen_ints.TwoCenterTwoElectron attribute) (pysisyphus.wavefunction.gen_ints.TwoCenterTwoElectronShell attribute) del_atoms() (pysisyphus.Geometry.Geometry method), [1] dens_cub_call() (in module pysisyphus.diabatization.chimerabatch) densities (pysisyphus.wavefunction.wavefunction.Wavefunction property) DensityType (class in pysisyphus.wavefunction.wavefunction) describe() (in module pysisyphus.helpers_pure) (pysisyphus.Geometry.Geometry method), [1] det_att_call() (in module pysisyphus.diabatization.chimerabatch) detachment_attachment_density() (in module pysisyphus.wavefunction.excited_states) detect_paths() (in module pysisyphus.config) df_evals (pysisyphus.line_searches.LineSearch.LineSearchResult attribute) dG (pysisyphus.marcus_dim.types.MarcusModel attribute) dia_result_from_jac_result() (in module pysisyphus.diabatization.results) DiabatizationResult (class in pysisyphus.diabatization.results) diabatize_path() (in module pysisyphus.diabatization.driver_yaml) diag_quadrupole3d_00() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_01() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_02() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_03() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_04() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_10() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_11() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_12() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_13() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_14() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_20() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_21() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_22() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_23() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_24() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_30() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_31() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_32() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_33() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_34() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_40() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_41() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_42() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_43() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) diag_quadrupole3d_44() (in module pysisyphus.wavefunction.ints.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) DiagQuadrupole3dShell (class in pysisyphus.wavefunction.gen_ints) dict_to_mol2_string() (in module pysisyphus.io.mol2) DifferentAtomOrdering DifferentCoordLengthsException

DifferentPrimitivesException dihedral_atom_indices (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] dihedral_indices (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] dihedral_valid() (in module pysisyphus.intcoords.valid) dihedrals_are_valid() (in module pysisyphus.intcoords.valid) DIIS (class in pysisyphus.wavefunction.DIIS) diis_result() (in module pysisyphus.optimizers.gdiis) DIISResult (class in pysisyphus.optimizers.gdiis) dind (pysisyphus.io.zmat.ZLine attribute) dip_mom_tensor (pysisyphus.diabatization.results.DiabatizationResult attribute) dipole3d_00() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_01() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_02() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_03() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_04() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_10() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_11() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_12() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_13() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_14() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_20() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_21() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_22() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_23() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_24() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_30() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_31() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_32() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_33() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_34() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_40() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_41() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_42() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_43() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole3d_44() (in module pysisyphus.wavefunction.ints.dipole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) dipole_ints() (pysisyphus.wavefunction.wavefunction.Wavefunction method) dipole_moment (pysisyphus.wavefunction.wavefunction.Wavefunction property) DISTANCE_FUNCTION (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) DistanceFunction (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.DistanceFunction) distributed_calculations() (in module pysisyphus.cos.distributed) DLC (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.DLC) dln_sos_partfunc_dT() (in module pysisyphus.partfuncs.partfuncs) dma() (in module pysisyphus.wavefunction.dma) do_final_hessian() (in module pysisyphus.helpers) double_damp() (in module pysisyphus.optimizers.hessian_updates) double_secant() (pysisyphus.line_searches.HagerZhang method) (pysisyphus.line_searches.HagerZhang.HagerZhang method) dphi0 (pysisyphus.line_searches.LineSearch.LineSearchResult attribute) dq_a() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) dq_a2() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) dq_b() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) dq_d() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) dq_d2() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) dq_diabatization() (in module pysisyphus.diabatization.multipole) dq_diabatization_from_run_dict() (in module pysisyphus.diabatization.driver_yaml) dq_jacobi_sweeps() (in module pysisyphus.diabatization.multipole) dq_lb() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) dq_ld() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) dq_oop() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) dq_rd1() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) dq_rd2() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) draw_state_graph() (in module pysisyphus.diabatization.plot) ds (pysisyphus.irc.initial_displ.ThirdDerivResult attribute) DUMMY_IMPROPER (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) DUMMY_TORSION (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) DummyColvar (class in pysisyphus.dynamics.Gaussian) DummyImproper (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.DummyImproper) DummyMark (class in pysisyphus.testing) DummyTorsion (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.DummyTorsion) dump() (pysisyphus.dynamics.Gaussian.Gaussian method) dump_coords() (in module pysisyphus.dynamics.helpers) dump_h5() (pysisyphus.calculators.AFIR.AFIR method), [1] dump_marcus_dim_xyz_trj() (in module pysisyphus.marcus_dim.fit) dump_scan_result() (in module pysisyphus.marcus_dim.run) dump_to_h5_group() (pysisyphus.wavefunction.shells.Shells method) dump_trj() (pysisyphus.Geometry.Geometry method), [1] (pysisyphus.hindered_rotor.RotorInfo.RotorInfo method) dump_xyz() (pysisyphus.Geometry.Geometry method), [1] duschinsky() (in module pysisyphus.franckcondon.duschinsky) DuschinskyRef (class in pysisyphus.franckcondon.duschinsky) DuschinskyResult (class in pysisyphus.franckcondon.duschinsky)

E

E_tot (pysisyphus.dynamics.driver.MDResult attribute) eckart_projection() (pysisyphus.Geometry.Geometry method), [1] edmiston_ruedenberg() (in module pysisyphus.wavefunction.localization) edmiston_ruedenberg_cost_func() (in module pysisyphus.wavefunction.localization) edmiston_ruedenberg_diabatization() (in module pysisyphus.diabatization.coulomb) edmiston_ruedenberg_diabatization_df() (in module pysisyphus.diabatization.coulomb) edmiston_ruedenberg_diabatization_jacobi() (in module pysisyphus.diabatization.coulomb) edmiston_ruedenberg_eta_diabatization() (in module pysisyphus.diabatization.coulomb_eta) edmiston_ruedenberg_grad() (in module pysisyphus.wavefunction.localization) edmiston_ruedenberg_jacobi_sweeps() (in module pysisyphus.diabatization.coulomb) EEXC (pysisyphus.marcus_dim.types.Property attribute) eigval_to_wavenumber() (in module pysisyphus.helpers_pure) eigvals (pysisyphus.helpers.FinalHessianResult attribute) eigvec_grad() (in module pysisyphus.linalg) en_exc_property() (in module pysisyphus.marcus_dim.fit) energies (pysisyphus.marcus_dim.types.MarcusDimScanResult attribute) energy (pysisyphus.cos.FreezingString.FreezingString property) (pysisyphus.cos.GrowingNT.GrowingNT property) (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.irc.Instanton.Instanton property) (pysisyphus.optimizers.gdiis.DIISResult attribute) energy_forces_getter_closure() (in module pysisyphus.dynamics.helpers) energy_minus (pysisyphus.irc.initial_displ.ThirdDerivResult attribute) energy_plus (pysisyphus.irc.initial_displ.ThirdDerivResult attribute) ensa (pysisyphus.MOCoeffs.MOCoeffs attribute) ensb (pysisyphus.MOCoeffs.MOCoeffs attribute) epos_from_wf() (in module pysisyphus.marcus_dim.fit) EPOS_IAO (pysisyphus.marcus_dim.types.Property attribute) EPOS_MULLIKEN (pysisyphus.marcus_dim.types.Property attribute) epos_property() (in module pysisyphus.marcus_dim.fit) epos_property_iao() (in module pysisyphus.marcus_dim.fit) epos_property_mulliken() (in module pysisyphus.marcus_dim.fit) epots (pysisyphus.diabatization.results.DiabatizationResult attribute) er_eta() (in module pysisyphus.diabatization.coulomb_eta) ERI (class in pysisyphus.wavefunction.gen_ints) ERIShell (class in pysisyphus.wavefunction.gen_ints) estimate() (in module pysisyphus.helpers_pure) estimate_runtime() (in module pysisyphus.timing) euler_maclaurin_dma() (in module pysisyphus.numint.radint)

eval() (pysisyphus.dynamics.colvars.Colvar method) (pysisyphus.dynamics.Gaussian.DummyColvar method) (pysisyphus.dynamics.Gaussian.Gaussian method) (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] (pysisyphus.wavefunction.gen_ints.CartGTO3d class method) (pysisyphus.wavefunction.gen_ints.CartGTOShell class method) (pysisyphus.wavefunction.gen_ints.Coulomb method) (pysisyphus.wavefunction.gen_ints.CoulombShell class method) (pysisyphus.wavefunction.gen_ints.DiagQuadrupole3dShell class method) (pysisyphus.wavefunction.gen_ints.ERI class method) (pysisyphus.wavefunction.gen_ints.ERIShell class method) (pysisyphus.wavefunction.gen_ints.Kinetic1d method) (pysisyphus.wavefunction.gen_ints.Kinetic3d class method) (pysisyphus.wavefunction.gen_ints.Kinetic3dShell class method) (pysisyphus.wavefunction.gen_ints.Multipole1d method) (pysisyphus.wavefunction.gen_ints.Multipole3d class method) (pysisyphus.wavefunction.gen_ints.Multipole3dShell class method) (pysisyphus.wavefunction.gen_ints.Overlap1d method) (pysisyphus.wavefunction.gen_ints.Overlap3dShell class method) (pysisyphus.wavefunction.gen_ints.SpinOrbit class method) (pysisyphus.wavefunction.gen_ints.SpinOrbitShell class method) (pysisyphus.wavefunction.gen_ints.ThreeCenterTwoElectronBase class method) (pysisyphus.wavefunction.gen_ints.ThreeCenterTwoElectronShell class method) (pysisyphus.wavefunction.gen_ints.ThreeCenterTwoElectronSphShell class method) (pysisyphus.wavefunction.gen_ints.TwoCenterTwoElectron class method) (pysisyphus.wavefunction.gen_ints.TwoCenterTwoElectronShell class method) (pysisyphus.wavefunction.shells.Shells method) eval_B() (in module pysisyphus.intcoords.eval) eval_density() (in module pysisyphus.wavefunction.density_numba) (pysisyphus.wavefunction.wavefunction.Wavefunction method) eval_esp() (pysisyphus.wavefunction.wavefunction.Wavefunction method) eval_prim_density() (in module pysisyphus.wavefunction.density_numba) eval_primitives() (in module pysisyphus.intcoords.eval) expand() (in module pysisyphus.helpers_pure) expand_sph_quantum_numbers() (in module pysisyphus.wavefunction.cart2sph) expect() (in module pysisyphus.io.bson) expect_byte() (in module pysisyphus.io.bson) exps_coeffs_iter() (pysisyphus.wavefunction.shells.Shell method)

F

f (pysisyphus.marcus_dim.types.MarcusModel attribute) f0 (pysisyphus.intcoords.generate_derivatives.FuncResult attribute) f1 (pysisyphus.intcoords.generate_derivatives.FuncResult attribute) f2 (pysisyphus.intcoords.generate_derivatives.FuncResult attribute) f20() (in module pysisyphus.io.crd) f_evals (pysisyphus.line_searches.LineSearch.LineSearchResult attribute) f_new (pysisyphus.line_searches.LineSearch.LineSearchResult attribute) factorial2() (in module pysisyphus.wavefunction.backend_numba_multipole) (in module pysisyphus.wavefunction.normalization) factorial_boys() (in module pysisyphus.wavefunction.ints.boys) factors (pysisyphus.marcus_dim.types.MarcusDimScanResult attribute) fail (pysisyphus.calculators.Calculator.SetPlan attribute), [1] FCHKShells (class in pysisyphus.wavefunction.shells) fd_coords3d_gen() (pysisyphus.Geometry.Geometry method), [1] fd_rmsd_hessian() (in module pysisyphus.linalg) file_or_str() (in module pysisyphus.helpers_pure) filter_ens() (in module pysisyphus.MOCoeffs) filter_fixture_store() (in module pysisyphus.helpers_pure) fin_diff_B() (in module pysisyphus.intcoords.findiffs) fin_diff_prim() (in module pysisyphus.intcoords.findiffs) FINAL (pysisyphus.franckcondon.duschinsky.DuschinskyRef attribute) final_modes (pysisyphus.modefollow.davidson.DavidsonResult attribute) FinalHessianResult (class in pysisyphus.helpers) find_bends() (in module pysisyphus.intcoords.setup_fast) find_bonds() (in module pysisyphus.intcoords.setup_fast) find_bonds_bends() (in module pysisyphus.intcoords.setup_fast) find_bonds_for_geom() (in module pysisyphus.intcoords.setup_fast) find_closest_sequence() (in module pysisyphus.helpers_pure) find_dihedrals() (in module pysisyphus.intcoords.setup_fast) find_minima() (in module pysisyphus.marcus_dim.param) find_missing_bonds_by_projection() (in module pysisyphus.intcoords.augment_bonds) find_missing_strong_bonds() (in module pysisyphus.intcoords.augment_bonds) finite_difference_gradient() (in module pysisyphus.finite_diffs) finite_difference_hessian() (in module pysisyphus.finite_diffs) finite_difference_hessian_mp() (in module pysisyphus.finite_diffs) fit_marcus_dim() (in module pysisyphus.marcus_dim.fit) fit_marcus_dim_batched() (in module pysisyphus.marcus_dim.fit) fit_rigid() (in module pysisyphus.helpers) FitResult (class in pysisyphus.optimizers.poly_fit) flowchart_update() (in module pysisyphus.optimizers.hessian_updates) fmt_tensor() (in module pysisyphus.diabatization.helpers) force_num_hessian() (pysisyphus.calculators.Calculator.Calculator method), [1] forces (pysisyphus.cos.FreezingString.FreezingString property) (pysisyphus.cos.GrowingNT.GrowingNT property) (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.irc.Instanton.Instanton property) (pysisyphus.optimizers.gdiis.DIISResult attribute)

forces_fin_diff() (in module pysisyphus.modefollow.davidson) form_coordinate_union() (in module pysisyphus.intcoords.helpers) format_vib() (in module pysisyphus.io.hessian) format_xyz() (in module pysisyphus.io.hessian) foster_boys() (in module pysisyphus.wavefunction.localization) Fragment (class in pysisyphus.hindered_rotor.RotorInfo) fragment_ao_map() (pysisyphus.wavefunction.shells.Shells method) fragment_geom() (in module pysisyphus.hindered_rotor.fragment) fragment_left (pysisyphus.hindered_rotor.RotorInfo.RotorInfo property) fragment_right (pysisyphus.hindered_rotor.RotorInfo.RotorInfo property) fragments (pysisyphus.intcoords.setup.CoordInfo attribute) freeze_atoms (pysisyphus.cos.GrowingNT.GrowingNT property) freeze_primitives() (pysisyphus.intcoords.DLC method) (pysisyphus.intcoords.DLC.DLC method) FreezingString (class in pysisyphus.cos.FreezingString) from_aomix() (pysisyphus.wavefunction.shells.Shells static method) (pysisyphus.wavefunction.wavefunction.Wavefunction static method) from_basis() (pysisyphus.wavefunction.shells.Shells method) from_coeffs() (in module pysisyphus.optimizers.gdiis) from_cube_and_vol_data() (pysisyphus.io.Cube static method) (pysisyphus.io.cube.Cube static method) from_fchk() (pysisyphus.wavefunction.shells.Shells static method) (pysisyphus.wavefunction.wavefunction.Wavefunction static method) from_file() (pysisyphus.io.Cube static method) (pysisyphus.io.cube.Cube static method) (pysisyphus.wavefunction.wavefunction.Wavefunction static method) from_geom() (pysisyphus.line_searches.LineSearch.LineSearch method) from_instanton() (pysisyphus.irc.Instanton.Instanton class method) from_molden() (pysisyphus.wavefunction.wavefunction.Wavefunction static method) from_orca_bson() (pysisyphus.wavefunction.wavefunction.Wavefunction static method) from_orca_json() (pysisyphus.wavefunction.shells.Shells static method) (pysisyphus.wavefunction.wavefunction.Wavefunction static method) from_orca_molden() (pysisyphus.wavefunction.wavefunction.Wavefunction static method) from_pyscf_mol() (pysisyphus.wavefunction.shells.Shells static method) from_shells() (pysisyphus.wavefunction.shells.Shells class method) from_sympleints_arrays() (pysisyphus.wavefunction.shells.Shells static method) from_sympleints_h5() (pysisyphus.wavefunction.shells.Shells static method) from_torsion() (pysisyphus.hindered_rotor.RotorInfo.RotorInfo static method) from_trexio() (pysisyphus.wavefunction.wavefunction.Wavefunction static method) from_ts() (pysisyphus.irc.Instanton.Instanton class method) from_wf_and_grid() (pysisyphus.io.Cube static method) (pysisyphus.io.cube.Cube static method) Fstiffness_k() (in module pysisyphus.cos.stiffness) full_expand() (in module pysisyphus.helpers_pure) fully_grown (pysisyphus.cos.FreezingString.FreezingString property) FuncResult (class in pysisyphus.intcoords.generate_derivatives)

G

G_adiabatic() (pysisyphus.marcus_dim.types.MarcusModel method) G_diabatic() (pysisyphus.marcus_dim.types.MarcusModel method) g_new (pysisyphus.line_searches.LineSearch.LineSearchResult attribute) G_vec (pysisyphus.irc.initial_displ.ThirdDerivResult attribute) gamma() (in module pysisyphus.wavefunction.solid_harmonics) Gaussian (class in pysisyphus.dynamics.Gaussian) gdiis() (in module pysisyphus.optimizers.gdiis) gediis() (in module pysisyphus.optimizers.gdiis) gen_integral_exprs() (in module pysisyphus.wavefunction.gen_ints) gen_solutions() (in module pysisyphus.optimizers.poly_fit) generate_wilson() (in module pysisyphus.intcoords.generate_derivatives) geom_davidson() (in module pysisyphus.modefollow) (in module pysisyphus.modefollow.davidson) geom_from_cjson() (in module pysisyphus.io) (in module pysisyphus.io.cjson) geom_from_crd() (in module pysisyphus.io) (in module pysisyphus.io.crd) geom_from_cube() (in module pysisyphus.io) geom_from_fchk() (in module pysisyphus.io) geom_from_fn() (pysisyphus.calculators.Calculator.Calculator class method), [1] geom_from_hessian() (in module pysisyphus.io) (in module pysisyphus.io.hessian) geom_from_missing_ext() (in module pysisyphus.helpers) geom_from_mol2() (in module pysisyphus.io) (in module pysisyphus.io.mol2) geom_from_pdb() (in module pysisyphus.io) (in module pysisyphus.io.pdb) geom_from_pubchem_name() (in module pysisyphus.io) (in module pysisyphus.io.pubchem) geom_from_qcschema() (in module pysisyphus.io) (in module pysisyphus.io.qcschema) geom_from_sdf() (in module pysisyphus.io.sdf) geom_from_xyz() (in module pysisyphus.io.xyz) geom_from_xyz_file() (in module pysisyphus.helpers) geom_from_zmat() (in module pysisyphus.io) (in module pysisyphus.io.zmat) geom_from_zmat_fn() (in module pysisyphus.io) (in module pysisyphus.io.zmat) geom_from_zmat_str() (in module pysisyphus.io.zmat) geom_iter (pysisyphus.benchmarks.Benchmark.Benchmark property) geom_lanczos() (in module pysisyphus.modefollow) (in module pysisyphus.modefollow.lanczos) geom_loader() (in module pysisyphus.helpers) geom_to_crd_str() (in module pysisyphus.io) (in module pysisyphus.io.crd) geom_to_pdb_str() (in module pysisyphus.io.pdb) Geometry (class in pysisyphus.Geometry), [1] geoms (pysisyphus.benchmarks.Benchmark.Benchmark property) geoms_and_comments_from_xyz() (in module pysisyphus.io.xyz) geoms_from_inline_xyz() (in module pysisyphus.io) (in module pysisyphus.io.xyz) geoms_from_molden() (in module pysisyphus.io) (in module pysisyphus.io.molden) geoms_from_trj() (in module pysisyphus.helpers) geoms_from_xyz() (in module pysisyphus.io) (in module pysisyphus.io.xyz) get() (pysisyphus.wavefunction.DIIS.DIIS method) get_1el_ints_cart() (in module pysisyphus.wavefunction.backend_numba) (in module pysisyphus.wavefunction.backend_numba_multipole) (in module pysisyphus.wavefunction.backend_python) (pysisyphus.wavefunction.shells.Shells method) get_1el_ints_sph() (pysisyphus.wavefunction.shells.Shells method) get_2c2el_ints_cart() (pysisyphus.wavefunction.shells.Shells method) get_2c2el_ints_sph() (pysisyphus.wavefunction.shells.Shells method) get_2c_ints_cart() (in module pysisyphus.wavefunction.backend_numba) get_3c2el_ints_cart() (in module pysisyphus.wavefunction.backend_python) (pysisyphus.wavefunction.shells.Shells method) get_3c2el_ints_sph() (pysisyphus.wavefunction.shells.Shells method) get_A() (in module pysisyphus.numerov.driver) get_A1() (in module pysisyphus.partfuncs.partfuncs) get_A2() (in module pysisyphus.partfuncs.partfuncs) get_A_periodic() (in module pysisyphus.numerov.driver) get_A_periodic_sparse() (in module pysisyphus.numerov.driver) get_A_sparse() (in module pysisyphus.numerov.driver) get_active_set() (pysisyphus.intcoords.DLC method) (pysisyphus.intcoords.DLC.DLC method) get_additional_print() (pysisyphus.cos.GrowingNT.GrowingNT method) (pysisyphus.irc.Instanton.Instanton method) get_atomic_grid() (in module pysisyphus.numint.atomint) get_axis_switch() (in module pysisyphus.franckcondon.duschinsky) get_baker_data() (in module pysisyphus.benchmarks.data) get_baker_ts_data() (in module pysisyphus.benchmarks.data) get_batch_calc_func() (in module pysisyphus.marcus_dim.fit) get_batch_calc_func_from_npz() (in module pysisyphus.marcus_dim.fit) get_bend_candidates() (in module pysisyphus.intcoords.setup_fast) get_bend_inds() (in module pysisyphus.intcoords.setup) get_binom_lmkq() (in module pysisyphus.wavefunction.dma) get_birkholz_rx_data() (in module pysisyphus.benchmarks.data) get_bond_difference() (in module pysisyphus.intcoords.helpers) get_bond_differences_verbose() (in module pysisyphus.intcoords.helpers) get_bond_mat() (in module pysisyphus.intcoords.setup) get_bond_sets() (in module pysisyphus.intcoords.setup) get_bond_vec_getter() (in module pysisyphus.intcoords.setup_fast) get_bonded_frag_coord() (in module pysisyphus.intcoords.PrimTypes) get_box() (in module pysisyphus.helpers_pure) get_box_grid() (in module pysisyphus.io.cube) get_C() (in module pysisyphus.wavefunction.dma) get_cart_norms() (in module pysisyphus.wavefunction.so_coupling) get_center() (in module pysisyphus.wavefunction.gen_ints) get_centers() (in module pysisyphus.wavefunction.gen_ints) get_classII_scan_info() (in module pysisyphus.marcus_dim.scan) get_clock() (in module pysisyphus.helpers_pure) get_cmd() (in module pysisyphus.config) (pysisyphus.calculators.Calculator.Calculator method), [1] get_coeffs() (pysisyphus.wavefunction.DIIS.DIIS method) get_colvar() (in module pysisyphus.dynamics.colvars) get_com() (in module pysisyphus.hindered_rotor.inertmom) get_conect_lines() (in module pysisyphus.io.pdb) get_constrained_U() (pysisyphus.intcoords.DLC method) (pysisyphus.intcoords.DLC.DLC method) get_constructor() (in module pysisyphus.yaml_mods) get_coord_factor() (in module pysisyphus.io.orca) get_coords3d_and_indices_ext() (pysisyphus.intcoords.DummyImproper static method) (pysisyphus.intcoords.DummyImproper.DummyImproper static method) (pysisyphus.intcoords.DummyTorsion static method) (pysisyphus.intcoords.DummyTorsion.DummyTorsion static method) get_coords_diffs() (in module pysisyphus.helpers) get_crossec_integrand() (in module pysisyphus.franckcondon.imdho) get_cubic_crystal() (in module pysisyphus.helpers_pure) get_current_density() (pysisyphus.wavefunction.wavefunction.Wavefunction method) get_current_total_density() (pysisyphus.wavefunction.wavefunction.Wavefunction method) get_curv_vec() (in module pysisyphus.irc.initial_displ) get_data_model() (in module pysisyphus.calculators.AFIR), [1] (in module pysisyphus.dynamics.driver) get_diag_quadrupole_ints_cart() (pysisyphus.wavefunction.shells.Shells method) get_diag_quadrupole_ints_sph() (pysisyphus.wavefunction.shells.Shells method) get_diffuse_density_numba() (in module pysisyphus.wavefunction.gdma_int) get_dihedral_inds() (in module pysisyphus.intcoords.setup) get_dipole_ints_cart() (pysisyphus.wavefunction.shells.Shells method) get_dipole_ints_sph() (pysisyphus.wavefunction.shells.Shells method) get_dipole_moment() (pysisyphus.wavefunction.wavefunction.Wavefunction method) get_displaced_coordinates() (in module pysisyphus.marcus_dim.fit) get_dist_func() (in module pysisyphus.intcoords.PrimTypes) get_effective_charge() (in module pysisyphus.wavefunction.so_coupling) get_en_conv() (in module pysisyphus.plot) get_energy() (pysisyphus.calculators.AFIR.AFIR method), [1] (pysisyphus.calculators.Calculator.Calculator method), [1] get_energy_and_cart_forces_at() (pysisyphus.Geometry.Geometry method), [1] get_energy_and_cart_hessian_at() (pysisyphus.Geometry.Geometry method), [1] get_energy_and_forces_at() (pysisyphus.cos.GrowingNT.GrowingNT method) (pysisyphus.Geometry.Geometry method), [1] get_energy_at() (pysisyphus.cos.GrowingNT.GrowingNT method) (pysisyphus.Geometry.Geometry method), [1] get_energy_at_cart_coords() (pysisyphus.Geometry.Geometry method), [1] get_extra_n_rad() (in module pysisyphus.numint.atomint) get_fb_ab_func() (in module pysisyphus.wavefunction.localization) get_fb_contract() (in module pysisyphus.wavefunction.localization) get_fb_cost_func() (in module pysisyphus.wavefunction.localization) get_fermion_atomic_grid() (in module pysisyphus.numint.atomint) get_fg() (pysisyphus.line_searches.LineSearch.LineSearch method) get_fh_logger() (in module pysisyphus.init_logging) get_fmts() (in module pysisyphus.socket_helper) get_force_unit() (in module pysisyphus.plot) get_forces() (pysisyphus.calculators.AFIR.AFIR method), [1] (pysisyphus.calculators.AtomAtomTransTorque.AtomAtomTransTorque method) (pysisyphus.calculators.Calculator.Calculator method), [1] get_fourth_coords() (pysisyphus.intcoords.DummyTorsion static method) (pysisyphus.intcoords.DummyTorsion.DummyTorsion static method)

get_fragment() (pysisyphus.hindered_rotor.RotorInfo.RotorInfo method) get_fragment_xyzs() (in module pysisyphus.helpers) get_fragments() (in module pysisyphus.intcoords.setup) (pysisyphus.Geometry.Geometry method), [1] get_func_data() (in module pysisyphus.wavefunction.backend_numba) (in module pysisyphus.wavefunction.backend_numba_multipole) (in module pysisyphus.wavefunction.backend_python) get_func_dict() (in module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.dipole3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) get_gdma_atomic_grid() (in module pysisyphus.numint.atomint) get_geom_getter() (in module pysisyphus.helpers) get_geoms() (pysisyphus.benchmarks.Benchmark.Benchmark method) get_grid() (in module pysisyphus.io.cube) get_grid_with_spacing() (in module pysisyphus.io.cube) get_grids_for_fermion_kind() (in module pysisyphus.numint.atomint) get_h5_group() (in module pysisyphus.io.hdf5) get_hessian() (pysisyphus.calculators.AFIR.AFIR method), [1] (pysisyphus.calculators.Calculator.Calculator method), [1] get_hessian_projector() (in module pysisyphus.hessian_proj) (pysisyphus.Geometry.Geometry method), [1] get_hydrogen_bond_inds() (in module pysisyphus.intcoords.setup) get_hydrogen_bond_inds_v2() (in module pysisyphus.intcoords.setup) get_imag_frequencies() (pysisyphus.Geometry.Geometry method), [1] get_index_maps() (in module pysisyphus.wavefunction.dma) get_index_of_typed_prim() (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] get_input() (in module pysisyphus.helpers_pure) get_K_matrix() (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] get_l() (in module pysisyphus.wavefunction.helpers) get_lebedev_grid() (in module pysisyphus.numint.angint) get_linear_bend_inds() (in module pysisyphus.intcoords.setup) get_lmn_factors() (in module pysisyphus.wavefunction.normalization) get_loader() (in module pysisyphus.yaml_mods) get_map() (in module pysisyphus.wavefunction.gen_ints) get_marcus_dim() (in module pysisyphus.marcus_dim.fit) get_mass() (in module pysisyphus.marcus_dim.fit) get_max_bond_dists() (in module pysisyphus.intcoords.setup_fast) get_maximum() (in module pysisyphus.optimizers.poly_fit) get_mb_velocities() (in module pysisyphus.dynamics.helpers) get_mb_velocities_for_geom() (in module pysisyphus.dynamics.helpers) get_minimum() (in module pysisyphus.optimizers.poly_fit) get_mins_maxs() (in module pysisyphus.io.cube) get_mol_grid() (in module pysisyphus.numint.molint) get_molcas_P_sph() (in module pysisyphus.wavefunction.shells_molcas) get_molecular_radius() (in module pysisyphus.helpers_pure) get_multipole_ints_cart() (in module pysisyphus.wavefunction.backend_numba_multipole) get_multipole_ints_cart_numba() (in module pysisyphus.wavefunction.backend_numba_multipole) get_multipole_ints_sph() (in module pysisyphus.wavefunction.backend_numba_multipole) get_multipole_moment() (in module pysisyphus.wavefunction.multipole) get_mwfn_exc_str() (in module pysisyphus.wrapper.mwfn) get_new_image() (pysisyphus.cos.FreezingString.FreezingString method) get_normal_modes() (pysisyphus.Geometry.Geometry method), [1] get_num_hessian() (pysisyphus.calculators.Calculator.Calculator method), [1] get_origin() (pysisyphus.wavefunction.wavefunction.Wavefunction method) get_original_charge() (in module pysisyphus.wavefunction.so_coupling) get_pair_covalent_radii() (in module pysisyphus.intcoords.setup) get_parser() (in module pysisyphus.io.pdb) get_path() (pysisyphus.cos.GrowingNT.GrowingNT method) get_permut_matrix() (pysisyphus.wavefunction.wavefunction.Wavefunction method) get_permut_matrix_native() (pysisyphus.wavefunction.wavefunction.Wavefunction method) get_phi_dphi() (pysisyphus.line_searches.LineSearch.LineSearch method) get_precon_pos_rot_data() (in module pysisyphus.benchmarks.data) get_prim_data() (in module pysisyphus.wavefunction.gdma_int) get_prim_internals_by_indices() (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] get_primitives() (in module pysisyphus.intcoords.setup) get_projector() (in module pysisyphus.hessian_proj) get_pyscf_P() (in module pysisyphus.wavefunction.shells_pyscf) get_quadrupole_ints_cart() (pysisyphus.wavefunction.shells.Shells method) get_quadrupole_ints_sph() (pysisyphus.wavefunction.shells.Shells method) get_quadrupole_moment() (pysisyphus.wavefunction.wavefunction.Wavefunction method) get_r() (pysisyphus.cos.GrowingNT.GrowingNT static method) get_radii() (in module pysisyphus.wavefunction.dma) get_random_path() (in module pysisyphus.helpers_pure) get_random_U() (in module pysisyphus.diabatization.helpers) get_ratio() (in module pysisyphus.helpers_pure) get_rd_class() (in module pysisyphus.marcus_dim.types) get_redistribution_func() (in module pysisyphus.wavefunction.dma) get_relaxed_density() (in module pysisyphus.io.fchk) (pysisyphus.calculators.Calculator.Calculator method), [1] (pysisyphus.wavefunction.wavefunction.Wavefunction method) get_restart_info() (pysisyphus.calculators.Calculator.Calculator method), [1] (pysisyphus.Geometry.Geometry method), [1] get_root_energy() (pysisyphus.Geometry.Geometry method), [1] get_rot_coord() (in module pysisyphus.intcoords.PrimTypes) get_rot_mat() (in module pysisyphus.linalg) get_rot_mat_for_coords() (in module pysisyphus.linalg) get_s22_data() (in module pysisyphus.benchmarks.data) get_S_cart() (pysisyphus.wavefunction.shells.Shells method) get_S_sph() (pysisyphus.wavefunction.shells.Shells method) get_scale_max() (in module pysisyphus.optimizers.restrict_step) get_scan_factors_and_steps() (in module pysisyphus.marcus_dim.scan) get_soc_oscs() (in module pysisyphus.wavefunction.so_coupling) get_soc_states() (in module pysisyphus.wavefunction.so_coupling) get_soc_tdms() (in module pysisyphus.wavefunction.so_coupling) get_sphere_radius() (pysisyphus.Geometry.Geometry method), [1] get_standard_orientation() (in module pysisyphus.hessian_proj) get_state_label() (in module pysisyphus.helpers_pure) get_state_to_state_transition_density() (in module pysisyphus.wavefunction.excited_states) get_step() (in module pysisyphus.intcoords.helpers) get_stiff_stress() (in module pysisyphus.cos.stiffness) get_stored_wavefunction() (pysisyphus.calculators.Calculator.Calculator method), [1] get_subgeom() (pysisyphus.Geometry.Geometry method), [1] get_subgeom_without() (pysisyphus.Geometry.Geometry method), [1] get_T_cart() (pysisyphus.wavefunction.shells.Shells method) get_T_sph() (pysisyphus.wavefunction.shells.Shells method) get_tangent() (in module pysisyphus.intcoords.helpers) (pysisyphus.cos.FreezingString.FreezingString method) get_tangent_trj_str() (in module pysisyphus.helpers) get_temporary_coords() (pysisyphus.Geometry.Geometry method), [1] get_thermoanalysis() (pysisyphus.Geometry.Geometry method), [1] get_thermoanalysis_from_hess_h5() (in module pysisyphus.thermo) get_tm_indices() (in module pysisyphus.elem_data) get_top_moment_of_inertia() (in module pysisyphus.hindered_rotor.inertmom) get_total_relaxed_density() (pysisyphus.wavefunction.wavefunction.Wavefunction method) get_tr_projector() (in module pysisyphus.intcoords.RedundantCoords), [1] get_trans_rot_projector() (in module pysisyphus.hessian_proj) (pysisyphus.Geometry.Geometry method), [1] get_trans_rot_vectors() (in module pysisyphus.hessian_proj) get_transition_dipole_moment() (pysisyphus.wavefunction.wavefunction.Wavefunction method) get_transition_multipole_moment() (in module pysisyphus.wavefunction.multipole) (pysisyphus.wavefunction.wavefunction.Wavefunction method) get_transition_quadrupole_moment() (pysisyphus.wavefunction.wavefunction.Wavefunction method) get_unique_internals() (in module pysisyphus.filtertrj) get_unit_orientation() (in module pysisyphus.hessian_proj) get_update_mu_reg() (in module pysisyphus.optimizers.closures) get_V() (pysisyphus.wavefunction.wavefunction.Wavefunction method) get_V_cart() (pysisyphus.wavefunction.shells.Shells method) get_V_sph() (pysisyphus.wavefunction.shells.Shells method) get_vib_state() (in module pysisyphus.dynamics.wigner) get_W() (in module pysisyphus.wavefunction.dma) get_wavefunction() (pysisyphus.calculators.Calculator.Calculator method), [1] get_wavenumber() (in module pysisyphus.marcus_dim.fit) get_wavenumber_from_coeffs() (in module pysisyphus.marcus_dim.fit) get_weighted_bond_mode() (in module pysisyphus.intcoords.helpers) get_weighted_bond_mode_getter() (in module pysisyphus.intcoords.helpers) get_wigner_sampler() (in module pysisyphus.dynamics.wigner) get_xtb_nuc_charges() (in module pysisyphus.io.molden) get_xtb_rx_data() (in module pysisyphus.benchmarks.data) get_zimmerman_data() (in module pysisyphus.benchmarks.data) get_zimmerman_xtb_data() (in module pysisyphus.benchmarks.data) got_alpha_phi_dphi() (pysisyphus.line_searches.LineSearch.LineSearch method) grad_func() (in module pysisyphus.finite_diffs) gradient (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.irc.Instanton.Instanton property) gradient() (pysisyphus.dynamics.colvars.Colvar method) (pysisyphus.dynamics.Gaussian.Gaussian method) gram_schmidt() (in module pysisyphus.linalg) green() (in module pysisyphus.color) Grid (class in pysisyphus.plot_ascii) grid_iter() (pysisyphus.numint.molint.MolGrid method) grow_image() (pysisyphus.cos.GrowingNT.GrowingNT method) GrowingNT (class in pysisyphus.cos.GrowingNT)

H

H_minus (pysisyphus.irc.initial_displ.ThirdDerivResult attribute) H_plus (pysisyphus.irc.initial_displ.ThirdDerivResult attribute) HagerZhang (class in pysisyphus.line_searches) (class in pysisyphus.line_searches.HagerZhang) harmonic_classic_partfunc() (in module pysisyphus.partfuncs.partfuncs) harmonic_quantum_partfunc() (in module pysisyphus.partfuncs.partfuncs) has_all_energies() (pysisyphus.Geometry.Geometry method), [1] has_energy (pysisyphus.Geometry.Geometry property), [1] has_forces (pysisyphus.Geometry.Geometry property), [1] has_hessian() (pysisyphus.Geometry.Geometry method), [1] has_shells (pysisyphus.wavefunction.wavefunction.Wavefunction property) hash_args() (in module pysisyphus.helpers_pure) hash_arr() (in module pysisyphus.helpers_pure) HDLC (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.DLC)

HEIIsFirstOrLastException hess_func() (in module pysisyphus.diabatization.coulomb_eta) hessian (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.irc.Instanton.Instanton property) HessKind (class in pysisyphus.calculators.Calculator), [1] highlight_text() (in module pysisyphus.helpers_pure) homoa (pysisyphus.MOCoeffs.MOCoeffs property) homob (pysisyphus.MOCoeffs.MOCoeffs property) householder_reflection_matrix() (in module pysisyphus.linalg_affine3) HybridRedundantCoords (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.RedundantCoords), [1] HYDROGEN_BOND (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) hydrogen_bonds (pysisyphus.intcoords.setup.CoordInfo attribute)

I

i10() (in module pysisyphus.io.crd) iao_charges() (in module pysisyphus.wavefunction.pop_analysis) imag_fns (pysisyphus.helpers.FinalHessianResult attribute) imag_modes_from_geom() (in module pysisyphus.helpers) imdho_abs_cross_section() (in module pysisyphus.franckcondon.imdho) imom (pysisyphus.hindered_rotor.RotorInfo.Fragment attribute) imom_left (pysisyphus.hindered_rotor.RotorInfo.RotorInfo attribute) imom_right (pysisyphus.hindered_rotor.RotorInfo.RotorInfo attribute) IMPROPER_DIHEDRAL (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) improper_dihedrals (pysisyphus.intcoords.setup.CoordInfo attribute) improved_mayer_bond_order() (in module pysisyphus.wavefunction.bond_order) increment_fn() (in module pysisyphus.helpers_pure) index (pysisyphus.intcoords.Rotation.Rotation attribute) (pysisyphus.intcoords.Rotation.RotationA attribute) (pysisyphus.intcoords.Rotation.RotationB attribute) (pysisyphus.intcoords.Rotation.RotationC attribute) (pysisyphus.intcoords.RotationA attribute) (pysisyphus.intcoords.RotationB attribute) (pysisyphus.intcoords.RotationC attribute) (pysisyphus.wavefunction.shells.Shell property) index_array_from_overlaps() (in module pysisyphus.helpers) indices (pysisyphus.hindered_rotor.RotorInfo.Fragment attribute) (pysisyphus.hindered_rotor.RotorInfo.RotorInfo attribute) indices_left (pysisyphus.hindered_rotor.RotorInfo.RotorInfo attribute) indices_right (pysisyphus.hindered_rotor.RotorInfo.RotorInfo attribute) inds_from_prim_types() (in module pysisyphus.intcoords.update) inertia_1n() (in module pysisyphus.hindered_rotor.inertmom) inertia_tensor (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.hessian_proj.Orientation property) inertia_tensor() (in module pysisyphus.hessian_proj) init_h5_group() (in module pysisyphus.io.hdf5) (pysisyphus.calculators.AFIR.AFIR method), [1] init_logging() (in module pysisyphus.init_logging) init_logging_base() (in module pysisyphus.init_logging) INITIAL (pysisyphus.franckcondon.duschinsky.DuschinskyRef attribute) initial() (pysisyphus.line_searches.HagerZhang method) (pysisyphus.line_searches.HagerZhang.HagerZhang method) initialize() (pysisyphus.cos.GrowingNT.GrowingNT method) Instanton (class in pysisyphus.irc.Instanton) int2c2e3d_00() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_01() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_02() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_03() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_04() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_10() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_11() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_12() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_13() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_14() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_20() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_21() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_22() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_23() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_24() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_30() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_31() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_32() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_33() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_34() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_40() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_41() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_42() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_43() (in module pysisyphus.wavefunction.ints.int2c2e3d) int2c2e3d_44() (in module pysisyphus.wavefunction.ints.int2c2e3d) int3c2e3d_sph_000() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_001() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_002() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_003() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_004() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_010() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_011() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_012() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_013() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_014() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_020() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_021() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_022() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_023() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_024() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_030() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_031() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_032() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_033() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph)

int3c2e3d_sph_034() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_100() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_101() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_102() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_103() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_104() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_110() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_111() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_112() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_113() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_114() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_120() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_121() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_122() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_123() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_124() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_130() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_131() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_132() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_133() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_134() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_200() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_201() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_202() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_203() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_204() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_210() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_211() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_212() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_213() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_214() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_220() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_221() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_222() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_223() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_224() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_230() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_231() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_232() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_233() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_234() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_300() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_301() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_302() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_303() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_304() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_310() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_311() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_312() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_313() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_314() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_320() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_321() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_322() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_323() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_324() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_330() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_331() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_332() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_333() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) int3c2e3d_sph_334() (in module pysisyphus.wavefunction.ints.int3c2e3d_sph) IntegralBackend (class in pysisyphus.wavefunction.shells) INTERFRAG_BOND (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) interfrag_bonds (pysisyphus.intcoords.setup.CoordInfo attribute) interfragment_distance() (in module pysisyphus.intcoords.helpers) interpol_alpha_cubic() (in module pysisyphus.line_searches.interpol) interpol_alpha_quad() (in module pysisyphus.line_searches.interpol) interpolate_colors() (in module pysisyphus.helpers_pure) interval_update() (pysisyphus.line_searches.HagerZhang method) (pysisyphus.line_searches.HagerZhang.HagerZhang method) inv_B() (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] inv_Bt() (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] inv_masses_rep_sqrt (pysisyphus.intcoords.CartesianCoords property) (pysisyphus.intcoords.CartesianCoords.CartesianCoords property) inv_translation_matrix() (in module pysisyphus.linalg_affine3) is_analytical_2d (pysisyphus.Geometry.Geometry property), [1] is_analytical_2d() (pysisyphus.irc.Instanton.Instanton method) is_cartesian (pysisyphus.wavefunction.wavefunction.Wavefunction property) is_converged (pysisyphus.diabatization.results.DiabatizationResult attribute) (pysisyphus.wavefunction.localization.JacobiSweepResult attribute) is_linear (pysisyphus.Geometry.Geometry property), [1]

J

J (pysisyphus.franckcondon.duschinsky.DuschinskyResult attribute) jac_func() (in module pysisyphus.diabatization.coulomb_eta) jacobi_sweeps() (in module pysisyphus.wavefunction.localization) jacobian() (pysisyphus.intcoords.LinearBend method) (pysisyphus.intcoords.LinearBend.LinearBend method) (pysisyphus.intcoords.LinearDisplacement method) (pysisyphus.intcoords.LinearDisplacement.LinearDisplacement method) (pysisyphus.intcoords.Primitive.Primitive method)

JacobiSweepResult (class in pysisyphus.wavefunction.localization) jmol() (pysisyphus.Geometry.Geometry method), [1] json_to_results() (in module pysisyphus.helpers_pure)

K

K (pysisyphus.franckcondon.duschinsky.DuschinskyResult attribute) (pysisyphus.wavefunction.gen_ints.TwoCenter1d property) keep() (pysisyphus.calculators.Calculator.Calculator method), [1] KeepKind (class in pysisyphus.calculators.Calculator), [1] key (pysisyphus.calculators.Calculator.SetPlan attribute), [1] (pysisyphus.hindered_rotor.RotorInfo.Fragment attribute) kill_dir() (in module pysisyphus.helpers_pure) kind (pysisyphus.diabatization.results.DiabatizationResult attribute) Kinetic1d (class in pysisyphus.wavefunction.gen_ints) Kinetic3d (class in pysisyphus.wavefunction.gen_ints) kinetic3d_00() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_01() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_02() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_03() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_04() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_10() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_11() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_12() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_13() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_14() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_20() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d)

kinetic3d_21() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_22() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_23() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_24() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_30() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_31() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_32() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_33() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_34() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_40() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_41() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_42() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_43() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) kinetic3d_44() (in module pysisyphus.wavefunction.ints.kinetic3d) (in module pysisyphus.wavefunction.ints_numba.kinetic3d) Kinetic3dShell (class in pysisyphus.wavefunction.gen_ints) kinetic_energy_for_temperature() (in module pysisyphus.dynamics.helpers) kinetic_energy_from_velocities() (in module pysisyphus.dynamics.helpers)

L

l_max (pysisyphus.wavefunction.shells.Shells property) l_mw (pysisyphus.modefollow.NormalMode property) (pysisyphus.modefollow.NormalMode.NormalMode property) L_tensor (pysisyphus.diabatization.results.DiabatizationResult attribute) lanczos() (in module pysisyphus.modefollow.lanczos) LATEST (pysisyphus.calculators.Calculator.KeepKind attribute), [1] layers (pysisyphus.Geometry.Geometry property), [1] lbfgs_closure() (in module pysisyphus.optimizers.closures) left_frontier (pysisyphus.cos.FreezingString.FreezingString property) lincs_closure() (in module pysisyphus.dynamics.lincs) LINEAR_BEND (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) LINEAR_BEND_COMPLEMENT (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) linear_bend_complements (pysisyphus.intcoords.setup.CoordInfo attribute) linear_bend_indices (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] linear_bends (pysisyphus.intcoords.setup.CoordInfo attribute) LINEAR_DISPLACEMENT (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) LINEAR_DISPLACEMENT_COMPLEMENT (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) LinearBend (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.LinearBend) LinearDisplacement (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.LinearDisplacement) LineSearch (class in pysisyphus.line_searches.LineSearch) LineSearchConverged LineSearchNotConverged

LineSearchResult (class in pysisyphus.line_searches.LineSearch) list_h5_groups() (in module pysisyphus.plot) lm_iter() (in module pysisyphus.wavefunction.helpers) lmn_factors() (in module pysisyphus.wavefunction.backend_numba_multipole) load() (in module pysisyphus.io.bson) load_h5() (in module pysisyphus.plot) load_wavefunction_from_file() (pysisyphus.calculators.Calculator.Calculator method), [1] loads() (in module pysisyphus.io.bson) log() (in module pysisyphus.helpers_pure) (in module pysisyphus.wrapper.mwfn) (pysisyphus.calculators.Calculator.Calculator method), [1] (pysisyphus.cos.GrowingNT.GrowingNT method) (pysisyphus.intcoords.Primitive.Primitive method) (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] (pysisyphus.line_searches.LineSearch.LineSearch method) log_dbg() (pysisyphus.intcoords.Primitive.Primitive method) log_fragments() (pysisyphus.calculators.AFIR.AFIR method), [1] log_int_grad_msg() (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] log_progress() (in module pysisyphus.irc.Instanton) logger (pysisyphus.cos.GrowingNT.GrowingNT attribute) lq2_abs_cross_sec() (in module pysisyphus.franckcondon.lq2) lumoa (pysisyphus.MOCoeffs.MOCoeffs property) lumob (pysisyphus.MOCoeffs.MOCoeffs property)

M

m (pysisyphus.hindered_rotor.RotorInfo.RotorInfo attribute) make_array() (in module pysisyphus.diabatization.driver_yaml) make_boys_table() (in module pysisyphus.wavefunction.ints.boys) make_c_func() (in module pysisyphus.wavefunction.gen_ints) make_cdd() (in module pysisyphus.wrapper.mwfn) make_density_matrices_for_root() (in module pysisyphus.wavefunction.excited_states) make_deriv_funcs() (in module pysisyphus.intcoords.generate_derivatives) make_fn() (pysisyphus.calculators.Calculator.Calculator method), [1] make_iaos() (in module pysisyphus.wavefunction.pop_analysis) make_input() (in module pysisyphus.wrapper.packmol) make_mo_density_matrix_for_root() (in module pysisyphus.wavefunction.excited_states) make_py_func() (in module pysisyphus.intcoords.generate_derivatives) (in module pysisyphus.wavefunction.gen_ints) make_trj_str() (in module pysisyphus.xyzloader) make_trj_str_from_geoms() (in module pysisyphus.xyzloader) make_unit_vec() (in module pysisyphus.linalg) make_xyz_str() (in module pysisyphus.xyzloader) make_xyz_str_au() (in module pysisyphus.xyzloader) map_array_to_interval() (in module pysisyphus.diabatization.plot) MarcusDimScanResult (class in pysisyphus.marcus_dim.types) MarcusModel (class in pysisyphus.marcus_dim.types) mass_weigh_hessian() (pysisyphus.Geometry.Geometry method), [1] masses (pysisyphus.franckcondon.duschinsky.AxisSwitch attribute) (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.hessian_proj.Orientation attribute) (pysisyphus.hindered_rotor.RotorInfo.RotorInfo attribute) (pysisyphus.intcoords.CartesianCoords property) (pysisyphus.intcoords.CartesianCoords.CartesianCoords property) (pysisyphus.wavefunction.wavefunction.Wavefunction property) masses_for_atoms() (in module pysisyphus.elem_data) masses_rep (pysisyphus.Geometry.Geometry property), [1] masses_sqrt (pysisyphus.intcoords.CartesianCoords property) (pysisyphus.intcoords.CartesianCoords.CartesianCoords property) match_geoms() (in module pysisyphus.helpers) matrix_power() (in module pysisyphus.linalg) MaybeScheduler (class in pysisyphus.executors) md() (in module pysisyphus.dynamics.driver) mdp() (in module pysisyphus.dynamics.mdp) MDPResult (in module pysisyphus.dynamics.mdp) MDResult (class in pysisyphus.dynamics.driver) mean_est (pysisyphus.timing.RuntimeEstimation attribute) median_est (pysisyphus.timing.RuntimeEstimation attribute) merge_coordinate_definitions() (in module pysisyphus.intcoords.helpers) merge_sets() (in module pysisyphus.helpers_pure) mm_inv (pysisyphus.Geometry.Geometry property), [1] mm_sqrt_inv (pysisyphus.Geometry.Geometry property), [1] mo_coeffs_from_fchk_data() (in module pysisyphus.io.fchk) mo_inds_from_tden() (in module pysisyphus.wavefunction.excited_states) mo_num (pysisyphus.wavefunction.wavefunction.Wavefunction property) MOCoeffs (class in pysisyphus.MOCoeffs) mod_flowchart_update() (in module pysisyphus.optimizers.hessian_updates) mode_inds (pysisyphus.modefollow.davidson.DavidsonResult attribute) modes3d() (pysisyphus.Geometry.Geometry method), [1] modified_broyden_closure() (in module pysisyphus.optimizers.closures) module pysisyphus pysisyphus.benchmarks pysisyphus.benchmarks.Benchmark pysisyphus.benchmarks.data pysisyphus.calculators.AFIR, [1] pysisyphus.calculators.AtomAtomTransTorque pysisyphus.calculators.Calculator, [1] pysisyphus.calculators.pyscf_lazy pysisyphus.color pysisyphus.config pysisyphus.constants pysisyphus.cos pysisyphus.cos.distributed pysisyphus.cos.FreezingString pysisyphus.cos.GrowingNT pysisyphus.cos.stiffness pysisyphus.diabatization pysisyphus.diabatization.chimerabatch pysisyphus.diabatization.coulomb pysisyphus.diabatization.coulomb_eta pysisyphus.diabatization.driver_yaml pysisyphus.diabatization.helpers pysisyphus.diabatization.multipole pysisyphus.diabatization.plot pysisyphus.diabatization.results pysisyphus.dynamics pysisyphus.dynamics.colvars pysisyphus.dynamics.driver pysisyphus.dynamics.Gaussian pysisyphus.dynamics.helpers pysisyphus.dynamics.lincs pysisyphus.dynamics.mdp pysisyphus.dynamics.rattle pysisyphus.dynamics.thermostats pysisyphus.dynamics.wigner pysisyphus.elem_data pysisyphus.exceptions pysisyphus.executors pysisyphus.filtertrj pysisyphus.finite_diffs pysisyphus.franckcondon pysisyphus.franckcondon.duschinsky pysisyphus.franckcondon.helpers pysisyphus.franckcondon.imdho pysisyphus.franckcondon.lq2 pysisyphus.Geometry, [1] pysisyphus.helpers pysisyphus.helpers_pure pysisyphus.hessian_proj pysisyphus.hindered_rotor pysisyphus.hindered_rotor.fragment pysisyphus.hindered_rotor.inertmom pysisyphus.hindered_rotor.RotorInfo pysisyphus.hindered_rotor.types pysisyphus.init_logging pysisyphus.intcoords pysisyphus.intcoords.augment_bonds pysisyphus.intcoords.Bend pysisyphus.intcoords.Bend2 pysisyphus.intcoords.BondedFragment pysisyphus.intcoords.Cartesian pysisyphus.intcoords.CartesianCoords pysisyphus.intcoords.Coords pysisyphus.intcoords.derivatives pysisyphus.intcoords.DistanceFunction pysisyphus.intcoords.DLC pysisyphus.intcoords.DummyImproper pysisyphus.intcoords.DummyTorsion pysisyphus.intcoords.eval pysisyphus.intcoords.exceptions pysisyphus.intcoords.findiffs pysisyphus.intcoords.generate_derivatives pysisyphus.intcoords.helpers pysisyphus.intcoords.LinearBend pysisyphus.intcoords.LinearDisplacement pysisyphus.intcoords.logging_conf pysisyphus.intcoords.mp_derivatives pysisyphus.intcoords.OutOfPlane pysisyphus.intcoords.Primitive pysisyphus.intcoords.PrimTypes pysisyphus.intcoords.RedundantCoords, [1] pysisyphus.intcoords.RobustTorsion pysisyphus.intcoords.Rotation pysisyphus.intcoords.setup pysisyphus.intcoords.setup_fast pysisyphus.intcoords.Stretch pysisyphus.intcoords.Torsion pysisyphus.intcoords.Torsion2 pysisyphus.intcoords.Translation pysisyphus.intcoords.update pysisyphus.intcoords.valid pysisyphus.io pysisyphus.io.aomix pysisyphus.io.bson pysisyphus.io.cjson pysisyphus.io.coord pysisyphus.io.crd pysisyphus.io.cube pysisyphus.io.fchk pysisyphus.io.hdf5 pysisyphus.io.hessian pysisyphus.io.mol2 pysisyphus.io.molcas pysisyphus.io.molden pysisyphus.io.orca pysisyphus.io.pdb pysisyphus.io.psf pysisyphus.io.pubchem pysisyphus.io.qcschema pysisyphus.io.sdf pysisyphus.io.xyz pysisyphus.io.zmat pysisyphus.irc.initial_displ pysisyphus.irc.Instanton pysisyphus.linalg pysisyphus.linalg_affine3 pysisyphus.line_searches pysisyphus.line_searches.Backtracking pysisyphus.line_searches.HagerZhang pysisyphus.line_searches.interpol pysisyphus.line_searches.LineSearch pysisyphus.line_searches.StrongWolfe pysisyphus.marcus_dim pysisyphus.marcus_dim.config pysisyphus.marcus_dim.fit pysisyphus.marcus_dim.param pysisyphus.marcus_dim.run pysisyphus.marcus_dim.scan pysisyphus.marcus_dim.types pysisyphus.MOCoeffs pysisyphus.modefollow pysisyphus.modefollow.davidson pysisyphus.modefollow.lanczos pysisyphus.modefollow.NormalMode pysisyphus.numerov pysisyphus.numerov.driver pysisyphus.numint pysisyphus.numint.angint pysisyphus.numint.atomint pysisyphus.numint.molint pysisyphus.numint.radint pysisyphus.optimizers pysisyphus.optimizers.closures pysisyphus.optimizers.exceptions pysisyphus.optimizers.gdiis pysisyphus.optimizers.hessian_updates pysisyphus.optimizers.poly_fit pysisyphus.optimizers.restrict_step pysisyphus.partfuncs.partfuncs pysisyphus.peakdetect pysisyphus.plot pysisyphus.plot_ascii pysisyphus.plotters pysisyphus.socket_helper pysisyphus.TablePrinter pysisyphus.testing pysisyphus.tests pysisyphus.thermo pysisyphus.timing pysisyphus.version pysisyphus.wavefunction pysisyphus.wavefunction.backend_numba pysisyphus.wavefunction.backend_numba_multipole pysisyphus.wavefunction.backend_python pysisyphus.wavefunction.Basis pysisyphus.wavefunction.bond_order pysisyphus.wavefunction.cart2sph pysisyphus.wavefunction.density_numba pysisyphus.wavefunction.DIIS pysisyphus.wavefunction.dma pysisyphus.wavefunction.excited_states pysisyphus.wavefunction.gdma_int pysisyphus.wavefunction.gen_ints pysisyphus.wavefunction.helpers pysisyphus.wavefunction.ints pysisyphus.wavefunction.ints.boys pysisyphus.wavefunction.ints.cart_gto3d pysisyphus.wavefunction.ints.coulomb3d pysisyphus.wavefunction.ints.diag_quadrupole3d pysisyphus.wavefunction.ints.dipole3d pysisyphus.wavefunction.ints.int2c2e3d pysisyphus.wavefunction.ints.int3c2e3d_sph pysisyphus.wavefunction.ints.kinetic3d pysisyphus.wavefunction.ints.multipole3d_sph pysisyphus.wavefunction.ints.ovlp3d pysisyphus.wavefunction.ints.quadrupole3d pysisyphus.wavefunction.ints_numba pysisyphus.wavefunction.ints_numba.diag_quadrupole3d pysisyphus.wavefunction.ints_numba.dipole3d pysisyphus.wavefunction.ints_numba.kinetic3d pysisyphus.wavefunction.ints_numba.multipole3d_sph pysisyphus.wavefunction.ints_numba.ovlp3d pysisyphus.wavefunction.ints_numba.quadrupole3d pysisyphus.wavefunction.localization pysisyphus.wavefunction.multipole pysisyphus.wavefunction.normalization pysisyphus.wavefunction.pop_analysis pysisyphus.wavefunction.shells pysisyphus.wavefunction.shells_molcas pysisyphus.wavefunction.shells_pyscf pysisyphus.wavefunction.shells_trexio pysisyphus.wavefunction.so_coupling pysisyphus.wavefunction.solid_harmonics pysisyphus.wavefunction.wavefunction pysisyphus.wrapper pysisyphus.wrapper.exceptions pysisyphus.wrapper.jmol pysisyphus.wrapper.mwfn pysisyphus.wrapper.packmol pysisyphus.xyzloader pysisyphus.yaml_mods

module_available() (in module pysisyphus.testing) MolcasShells (class in pysisyphus.wavefunction.shells_molcas) MoldenError MoldenShells (class in pysisyphus.wavefunction.shells) molecular_volume() (in module pysisyphus.helpers_pure) MolGrid (class in pysisyphus.numint.molint) move_multipoles() (in module pysisyphus.wavefunction.dma) move_multipoles_gen() (in module pysisyphus.wavefunction.dma) moving_atoms (pysisyphus.cos.GrowingNT.GrowingNT property) (pysisyphus.Geometry.Geometry property), [1] moving_atoms_jmol() (pysisyphus.Geometry.Geometry method), [1] mp_cart2sph_coeff() (in module pysisyphus.wavefunction.cart2sph) mu (pysisyphus.wavefunction.gen_ints.TwoCenter1d property) mulliken_charges() (in module pysisyphus.wavefunction.pop_analysis) mult (pysisyphus.calculators.AFIR.AFIR property), [1] multi_component_sym_mat() (in module pysisyphus.linalg) Multipole1d (class in pysisyphus.wavefunction.gen_ints) multipole1d() (in module pysisyphus.wavefunction.backend_numba_multipole) multipole1d_() (in module pysisyphus.wavefunction.backend_numba_multipole) Multipole3d (class in pysisyphus.wavefunction.gen_ints) multipole3d() (in module pysisyphus.wavefunction.backend_numba_multipole) multipole3d_sph_00() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_01() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_02() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_03() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_04() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_10() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_11() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_12() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_13() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_14() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_20() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_21() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_22() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_23() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_24() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_30() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_31() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_32() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_33() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_34() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_40() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_41() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_42() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_43() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) multipole3d_sph_44() (in module pysisyphus.wavefunction.ints.multipole3d_sph) (in module pysisyphus.wavefunction.ints_numba.multipole3d_sph) Multipole3dShell (class in pysisyphus.wavefunction.gen_ints) mw_coords (pysisyphus.Geometry.Geometry property), [1] mw_gradient (pysisyphus.Geometry.Geometry property), [1] mw_hessian (pysisyphus.Geometry.Geometry property), [1] mw_norm_for_norm() (pysisyphus.modefollow.NormalMode method) (pysisyphus.modefollow.NormalMode.NormalMode method) MWCartesianCoords (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.CartesianCoords)

N

n (pysisyphus.hindered_rotor.RotorInfo.RotorInfo attribute) N (pysisyphus.optimizers.gdiis.DIISResult attribute) name (pysisyphus.calculators.Calculator.Calculator property), [1] (pysisyphus.calculators.Calculator.SetPlan attribute), [1] (pysisyphus.wavefunction.gen_ints.boys attribute) natoms (pysisyphus.hindered_rotor.RotorInfo.Fragment attribute) (pysisyphus.hindered_rotor.RotorInfo.RotorInfo property) nbatches (pysisyphus.cos.distributed.ParallelData attribute) ncalcs (pysisyphus.cos.distributed.ParallelData attribute) ncores (pysisyphus.cos.distributed.ParallelData attribute) NeedNewInternalsException neg_eigvals (pysisyphus.helpers.FinalHessianResult attribute) neville() (in module pysisyphus.wavefunction.ints.boys) neville_boys() (in module pysisyphus.wavefunction.ints.boys) neville_gen5() (in module pysisyphus.wavefunction.ints.boys) nfields (pysisyphus.TablePrinter.TablePrinter property) NONE (pysisyphus.calculators.Calculator.KeepKind attribute), [1] norm3() (in module pysisyphus.linalg) norm_cgto_lmn() (in module pysisyphus.wavefunction.normalization) norm_ci_coeffs() (in module pysisyphus.wavefunction.excited_states) norm_inf() (pysisyphus.line_searches.HagerZhang method) (pysisyphus.line_searches.HagerZhang.HagerZhang method) norm_max_rms() (in module pysisyphus.helpers) norm_pgto() (in module pysisyphus.wavefunction.normalization) normal_mode_reduced_masses() (in module pysisyphus.dynamics.wigner) normal_modes_to_molden() (in module pysisyphus.io.hessian)

normalize_atoms() (in module pysisyphus.Geometry), [1] normalize_prim_input() (in module pysisyphus.intcoords.PrimTypes) normalize_prim_inputs() (in module pysisyphus.intcoords.PrimTypes) NormalMode (class in pysisyphus.modefollow) (class in pysisyphus.modefollow.NormalMode) np_print() (in module pysisyphus.helpers) npoints (pysisyphus.io.Cube attribute) (pysisyphus.io.cube.Cube attribute) (pysisyphus.numint.molint.MolGrid property) nprims (pysisyphus.wavefunction.shells.Shells property) nremain (pysisyphus.timing.RuntimeEstimation attribute) nstates (pysisyphus.diabatization.results.DiabatizationResult property) nto_overlaps() (in module pysisyphus.wavefunction.excited_states) nu2angfreq_au() (in module pysisyphus.franckcondon.helpers) nu2eV() (in module pysisyphus.franckcondon.helpers) nuc_charges (pysisyphus.wavefunction.pop_analysis.PopAnalysis attribute) (pysisyphus.wavefunction.wavefunction.Wavefunction property) nuc_charges_for_atoms() (in module pysisyphus.elem_data) NUMBA (pysisyphus.wavefunction.shells.IntegralBackend attribute) NUMBA_MULTIPOLE (pysisyphus.wavefunction.shells.IntegralBackend attribute) numba_shells (pysisyphus.wavefunction.shells.Shells property) numba_shellstructs (pysisyphus.wavefunction.shells.Shells property) NumbaShell (class in pysisyphus.wavefunction.backend_numba) NUMERICAL (pysisyphus.calculators.Calculator.HessKind attribute), [1] nus (pysisyphus.helpers.FinalHessianResult attribute) (pysisyphus.modefollow.davidson.DavidsonResult attribute)

O

occ_from_occs() (in module pysisyphus.MOCoeffs) occa (pysisyphus.MOCoeffs.MOCoeffs property) occb (pysisyphus.MOCoeffs.MOCoeffs property) occsa (pysisyphus.MOCoeffs.MOCoeffs attribute) occsb (pysisyphus.MOCoeffs.MOCoeffs attribute) off_diag_indices() (in module pysisyphus.numerov.driver) ol_as_tuple() (in module pysisyphus.wavefunction.backend_numba) ol_cart_size() (in module pysisyphus.wavefunction.backend_numba) ol_sph_size() (in module pysisyphus.wavefunction.backend_numba) OptimizationError optional_on_line() (in module pysisyphus.io.mol2) ORCAMoldenShells (class in pysisyphus.wavefunction.shells) ORCAShells (class in pysisyphus.wavefunction.shells) OrderedEnum (class in pysisyphus.helpers_pure) ORG (pysisyphus.calculators.Calculator.HessKind attribute), [1] Orientation (class in pysisyphus.hessian_proj) origin (pysisyphus.io.Cube attribute) (pysisyphus.io.cube.Cube attribute) orthogonalize_against() (in module pysisyphus.linalg) oscillator_strength() (pysisyphus.wavefunction.wavefunction.Wavefunction method) OUT_OF_PLANE (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) OutOfPlane (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.OutOfPlane) outofplane_indices (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] Overlap1d (class in pysisyphus.wavefunction.gen_ints) Overlap3dShell (class in pysisyphus.wavefunction.gen_ints) ovlp() (in module pysisyphus.wavefunction.excited_states) ovlp3d_00() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_01() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_02() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_03() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_04() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_10() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d)

ovlp3d_11() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_12() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_13() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_14() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_20() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_21() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_22() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_23() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_24() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_30() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_31() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_32() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_33() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_34() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_40() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_41() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_42() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_43() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d) ovlp3d_44() (in module pysisyphus.wavefunction.ints.ovlp3d) (in module pysisyphus.wavefunction.ints_numba.ovlp3d)

P

P (pysisyphus.cos.GrowingNT.GrowingNT property) (pysisyphus.diabatization.results.DiabatizationResult attribute) (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] (pysisyphus.irc.Instanton.Instanton property) (pysisyphus.wavefunction.gen_ints.TwoCenter1d property) p (pysisyphus.wavefunction.gen_ints.TwoCenter1d property) P (pysisyphus.wavefunction.localization.JacobiSweepResult attribute) (pysisyphus.wavefunction.wavefunction.Wavefunction property) P_bh (pysisyphus.irc.Instanton.Instanton attribute) P_cart (pysisyphus.wavefunction.shells.Shells property) (pysisyphus.wavefunction.shells_pyscf.PySCFShells property) P_cart_native (pysisyphus.wavefunction.shells.Shells property) P_exc() (pysisyphus.wavefunction.wavefunction.Wavefunction method) P_sph (pysisyphus.wavefunction.shells.Shells property) (pysisyphus.wavefunction.shells_molcas.MolcasShells property) (pysisyphus.wavefunction.shells_pyscf.PySCFShells property) P_sph_native (pysisyphus.wavefunction.shells.Shells property) P_tot (pysisyphus.wavefunction.wavefunction.Wavefunction property) PA (pysisyphus.wavefunction.gen_ints.TwoCenter1d property) pal_values_for_parallel_calcs() (in module pysisyphus.cos.distributed) parallel() (pysisyphus.intcoords.Primitive.Primitive static method) ParallelData (class in pysisyphus.cos.distributed) param_marcus() (in module pysisyphus.marcus_dim.param) parse_args() (in module pysisyphus.config) (in module pysisyphus.diabatization.coulomb_eta) (in module pysisyphus.diabatization.driver_yaml) (in module pysisyphus.diabatization.plot) (in module pysisyphus.dynamics.wigner) (in module pysisyphus.filtertrj) (in module pysisyphus.plot) (in module pysisyphus.wavefunction.cart2sph) (in module pysisyphus.wavefunction.gen_ints) (in module pysisyphus.wavefunction.ints.boys) parse_atom_name() (in module pysisyphus.io.pdb) parse_cjson() (in module pysisyphus.io.cjson) parse_coord_line() (in module pysisyphus.io.sdf) parse_cube() (in module pysisyphus.io) parse_document() (in module pysisyphus.io.bson) parse_element() (in module pysisyphus.io.bson) parse_filter() (in module pysisyphus.filtertrj) parse_fstring() (in module pysisyphus.TablePrinter) parse_mo() (in module pysisyphus.io.molden) parse_molden_atoms() (in module pysisyphus.io.molden) parse_raw_term_func() (in module pysisyphus.dynamics.mdp) parse_raw_term_funcs() (in module pysisyphus.dynamics.mdp) parse_sdf() (in module pysisyphus.io.sdf) parse_tden() (in module pysisyphus.wavefunction.excited_states) parse_trj_file() (in module pysisyphus.xyzloader) parse_trj_str() (in module pysisyphus.xyzloader) parse_xyz() (in module pysisyphus.io) parse_xyz_file() (in module pysisyphus.xyzloader) parse_xyz_str() (in module pysisyphus.xyzloader) path_length (pysisyphus.irc.Instanton.Instanton property) PB (pysisyphus.wavefunction.gen_ints.TwoCenter1d property) PC (pysisyphus.wavefunction.gen_ints.TwoCenter1d property) peakdetect() (in module pysisyphus.peakdetect) peakdetect_fft() (in module pysisyphus.peakdetect) peakdetect_parabola() (in module pysisyphus.peakdetect) peakdetect_sine() (in module pysisyphus.peakdetect) peakdetect_sine_locked() (in module pysisyphus.peakdetect) peakdetect_spline() (in module pysisyphus.peakdetect) peakdetect_zero_crossing() (in module pysisyphus.peakdetect) periodic_fd_2_8() (in module pysisyphus.finite_diffs) periodic_finite_difference() (in module pysisyphus.finite_diffs) permut_for_order() (in module pysisyphus.wavefunction.helpers) perp_comp() (in module pysisyphus.linalg) pick_image_inds() (in module pysisyphus.helpers) pipek_mezey() (in module pysisyphus.wavefunction.localization) pivoted_cholesky() (in module pysisyphus.linalg) pivoted_cholesky2() (in module pysisyphus.linalg) plane_normal() (in module pysisyphus.linalg_affine3) plot() (in module pysisyphus.plot_ascii) (pysisyphus.marcus_dim.types.MarcusModel method) plot_afir() (in module pysisyphus.plot) plot_all_energies() (in module pysisyphus.plot) plot_calculations() (in module pysisyphus.plot) plot_cos_energies() (in module pysisyphus.plot) plot_cos_forces() (in module pysisyphus.plot) plot_cycle() (in module pysisyphus.plot) plot_dia_res() (in module pysisyphus.diabatization.driver_yaml) plot_distances() (in module pysisyphus.dynamics.wigner) plot_gau() (in module pysisyphus.plot) plot_irc() (in module pysisyphus.plot) plot_irc_h5() (in module pysisyphus.plot) plot_md() (in module pysisyphus.plot) plot_mo_energies() (pysisyphus.MOCoeffs.MOCoeffs method) plot_normal_coords() (in module pysisyphus.dynamics.wigner) plot_opt() (in module pysisyphus.plot) plot_overlaps() (in module pysisyphus.plot) plot_scan() (in module pysisyphus.marcus_dim.scan) (in module pysisyphus.plot) plot_trj_energies() (in module pysisyphus.plot) plot_wrapper() (in module pysisyphus.plot_ascii) poly_line_search() (in module pysisyphus.optimizers.poly_fit) polys (pysisyphus.optimizers.poly_fit.FitResult attribute) pop_a (pysisyphus.wavefunction.pop_analysis.PopAnalysis attribute) pop_b (pysisyphus.wavefunction.pop_analysis.PopAnalysis attribute) PopAnalysis (class in pysisyphus.wavefunction.pop_analysis) popen() (pysisyphus.calculators.Calculator.Calculator method), [1] PopKind (in module pysisyphus.marcus_dim.types) prefacts() (in module pysisyphus.wavefunction.density_numba) prefix (pysisyphus.optimizers.gdiis.DIISResult attribute) prepare() (pysisyphus.calculators.Calculator.Calculator method), [1] prepare_coords() (pysisyphus.calculators.Calculator.Calculator method), [1] prepare_input() (pysisyphus.calculators.Calculator.Calculator method), [1] prepare_line_search() (pysisyphus.line_searches.HagerZhang method) (pysisyphus.line_searches.HagerZhang.HagerZhang method) (pysisyphus.line_searches.LineSearch.LineSearch method) prepare_path() (pysisyphus.calculators.Calculator.Calculator method), [1] prepare_pattern() (pysisyphus.calculators.Calculator.Calculator method), [1] prepare_rotor_info() (in module pysisyphus.hindered_rotor.RotorInfo) prepare_turbo_coords() (pysisyphus.calculators.Calculator.Calculator method), [1] prepare_xyz_string() (pysisyphus.calculators.Calculator.Calculator method), [1] preprocess_fields() (pysisyphus.wavefunction.backend_numba.ShellStructType method) pretty() (pysisyphus.marcus_dim.types.MarcusModel method) prim_coords (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] prim_for_human() (in module pysisyphus.intcoords.PrimTypes) prim_indices_set (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] prim_internals (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] PrimInternal (class in pysisyphus.intcoords.eval) Primitive (class in pysisyphus.intcoords.Primitive) PrimitiveNotDefinedException, [1] primitives (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] prims_from_prim_inputs() (in module pysisyphus.intcoords.PrimTypes) PrimTypes (class in pysisyphus.intcoords.PrimTypes) principal_axes_are_aligned() (pysisyphus.Geometry.Geometry method), [1] print() (pysisyphus.TablePrinter.TablePrinter method) print_barrier() (in module pysisyphus.helpers) print_capabilities() (pysisyphus.calculators.Calculator.Calculator method), [1] print_coeffs() (in module pysisyphus.wavefunction.cart2sph) print_header() (pysisyphus.TablePrinter.TablePrinter method) print_out_fn() (pysisyphus.calculators.Calculator.Calculator method), [1] print_row() (pysisyphus.TablePrinter.TablePrinter method) print_rows() (pysisyphus.TablePrinter.TablePrinter method) print_sep() (pysisyphus.TablePrinter.TablePrinter method) print_shells() (pysisyphus.wavefunction.shells.Shells method) print_thermoanalysis() (in module pysisyphus.thermo) print_typed_prims() (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] procrustes() (in module pysisyphus.helpers) project_hessian() (pysisyphus.intcoords.CartesianCoords method) (pysisyphus.intcoords.CartesianCoords.CartesianCoords method) (pysisyphus.intcoords.Coords.CoordSys method) (pysisyphus.intcoords.DLC method) (pysisyphus.intcoords.DLC.DLC method) (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] project_primitive_on_active_set() (pysisyphus.intcoords.DLC method) (pysisyphus.intcoords.DLC.DLC method) project_vector() (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] PROPER_DIHEDRAL (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) PROPER_DIHEDRAL2 (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) proper_dihedrals (pysisyphus.intcoords.setup.CoordInfo attribute) properties (pysisyphus.marcus_dim.types.MarcusDimScanResult attribute) Property (class in pysisyphus.marcus_dim.types) ps (pysisyphus.dynamics.wigner.WignerSample attribute) ps_nodim (pysisyphus.dynamics.wigner.WignerSample attribute) psb_update() (in module pysisyphus.optimizers.hessian_updates) PT (in module pysisyphus.intcoords.PrimTypes) PURE_SPHERICAL (pysisyphus.wavefunction.helpers.BFType attribute) put() (pysisyphus.plot_ascii.Grid method) pyscf_cart_order() (in module pysisyphus.wavefunction.shells_pyscf) PySCFShells (class in pysisyphus.wavefunction.shells_pyscf) pysisyphus module pysisyphus.benchmarks module pysisyphus.benchmarks.Benchmark module pysisyphus.benchmarks.data module pysisyphus.calculators.AFIR module, [1] pysisyphus.calculators.AtomAtomTransTorque module pysisyphus.calculators.Calculator module, [1] pysisyphus.calculators.pyscf_lazy module pysisyphus.color module pysisyphus.config module pysisyphus.constants module pysisyphus.cos module pysisyphus.cos.distributed module pysisyphus.cos.FreezingString module pysisyphus.cos.GrowingNT module pysisyphus.cos.stiffness module pysisyphus.diabatization module pysisyphus.diabatization.chimerabatch module pysisyphus.diabatization.coulomb module pysisyphus.diabatization.coulomb_eta module pysisyphus.diabatization.driver_yaml module pysisyphus.diabatization.helpers module pysisyphus.diabatization.multipole module pysisyphus.diabatization.plot module pysisyphus.diabatization.results module pysisyphus.dynamics module pysisyphus.dynamics.colvars module pysisyphus.dynamics.driver module pysisyphus.dynamics.Gaussian module pysisyphus.dynamics.helpers module pysisyphus.dynamics.lincs module pysisyphus.dynamics.mdp module pysisyphus.dynamics.rattle module pysisyphus.dynamics.thermostats module pysisyphus.dynamics.wigner module pysisyphus.elem_data module pysisyphus.exceptions module pysisyphus.executors module pysisyphus.filtertrj module pysisyphus.finite_diffs module pysisyphus.franckcondon module pysisyphus.franckcondon.duschinsky module pysisyphus.franckcondon.helpers module pysisyphus.franckcondon.imdho module pysisyphus.franckcondon.lq2 module pysisyphus.Geometry module, [1] pysisyphus.helpers module pysisyphus.helpers_pure module pysisyphus.hessian_proj module pysisyphus.hindered_rotor module pysisyphus.hindered_rotor.fragment module pysisyphus.hindered_rotor.inertmom module pysisyphus.hindered_rotor.RotorInfo module pysisyphus.hindered_rotor.types module pysisyphus.init_logging module pysisyphus.intcoords module pysisyphus.intcoords.augment_bonds module pysisyphus.intcoords.Bend module pysisyphus.intcoords.Bend2 module pysisyphus.intcoords.BondedFragment module pysisyphus.intcoords.Cartesian module pysisyphus.intcoords.CartesianCoords module pysisyphus.intcoords.Coords module pysisyphus.intcoords.derivatives module

pysisyphus.intcoords.DistanceFunction module pysisyphus.intcoords.DLC module pysisyphus.intcoords.DummyImproper module pysisyphus.intcoords.DummyTorsion module pysisyphus.intcoords.eval module pysisyphus.intcoords.exceptions module pysisyphus.intcoords.findiffs module pysisyphus.intcoords.generate_derivatives module pysisyphus.intcoords.helpers module pysisyphus.intcoords.LinearBend module pysisyphus.intcoords.LinearDisplacement module pysisyphus.intcoords.logging_conf module pysisyphus.intcoords.mp_derivatives module pysisyphus.intcoords.OutOfPlane module pysisyphus.intcoords.Primitive module pysisyphus.intcoords.PrimTypes module pysisyphus.intcoords.RedundantCoords module, [1] pysisyphus.intcoords.RobustTorsion module pysisyphus.intcoords.Rotation module pysisyphus.intcoords.setup module pysisyphus.intcoords.setup_fast module pysisyphus.intcoords.Stretch module pysisyphus.intcoords.Torsion module pysisyphus.intcoords.Torsion2 module pysisyphus.intcoords.Translation module pysisyphus.intcoords.update module pysisyphus.intcoords.valid module pysisyphus.io module pysisyphus.io.aomix module pysisyphus.io.bson module pysisyphus.io.cjson module pysisyphus.io.coord module pysisyphus.io.crd module pysisyphus.io.cube module pysisyphus.io.fchk module pysisyphus.io.hdf5 module pysisyphus.io.hessian module pysisyphus.io.mol2 module pysisyphus.io.molcas module pysisyphus.io.molden module pysisyphus.io.orca module pysisyphus.io.pdb module pysisyphus.io.psf module pysisyphus.io.pubchem module pysisyphus.io.qcschema module pysisyphus.io.sdf module pysisyphus.io.xyz module pysisyphus.io.zmat module pysisyphus.irc.initial_displ module pysisyphus.irc.Instanton module pysisyphus.linalg module pysisyphus.linalg_affine3 module pysisyphus.line_searches module pysisyphus.line_searches.Backtracking module pysisyphus.line_searches.HagerZhang module pysisyphus.line_searches.interpol module pysisyphus.line_searches.LineSearch module pysisyphus.line_searches.StrongWolfe module pysisyphus.marcus_dim module pysisyphus.marcus_dim.config module pysisyphus.marcus_dim.fit module pysisyphus.marcus_dim.param module pysisyphus.marcus_dim.run module pysisyphus.marcus_dim.scan module pysisyphus.marcus_dim.types module pysisyphus.MOCoeffs module pysisyphus.modefollow module pysisyphus.modefollow.davidson module pysisyphus.modefollow.lanczos module pysisyphus.modefollow.NormalMode module pysisyphus.numerov module pysisyphus.numerov.driver module pysisyphus.numint module pysisyphus.numint.angint module pysisyphus.numint.atomint module pysisyphus.numint.molint module pysisyphus.numint.radint module pysisyphus.optimizers module pysisyphus.optimizers.closures module pysisyphus.optimizers.exceptions module pysisyphus.optimizers.gdiis module pysisyphus.optimizers.hessian_updates module pysisyphus.optimizers.poly_fit module pysisyphus.optimizers.restrict_step module pysisyphus.partfuncs.partfuncs module pysisyphus.peakdetect module pysisyphus.plot module pysisyphus.plot_ascii module pysisyphus.plotters module pysisyphus.socket_helper module pysisyphus.TablePrinter module pysisyphus.testing module pysisyphus.tests module pysisyphus.thermo module pysisyphus.timing module pysisyphus.version module pysisyphus.wavefunction module pysisyphus.wavefunction.backend_numba module pysisyphus.wavefunction.backend_numba_multipole module pysisyphus.wavefunction.backend_python module pysisyphus.wavefunction.Basis module pysisyphus.wavefunction.bond_order module pysisyphus.wavefunction.cart2sph module pysisyphus.wavefunction.density_numba module pysisyphus.wavefunction.DIIS module pysisyphus.wavefunction.dma module pysisyphus.wavefunction.excited_states module pysisyphus.wavefunction.gdma_int module pysisyphus.wavefunction.gen_ints module pysisyphus.wavefunction.helpers module pysisyphus.wavefunction.ints module pysisyphus.wavefunction.ints.boys module pysisyphus.wavefunction.ints.cart_gto3d module pysisyphus.wavefunction.ints.coulomb3d module pysisyphus.wavefunction.ints.diag_quadrupole3d module pysisyphus.wavefunction.ints.dipole3d module pysisyphus.wavefunction.ints.int2c2e3d module pysisyphus.wavefunction.ints.int3c2e3d_sph module pysisyphus.wavefunction.ints.kinetic3d module pysisyphus.wavefunction.ints.multipole3d_sph module pysisyphus.wavefunction.ints.ovlp3d module pysisyphus.wavefunction.ints.quadrupole3d module pysisyphus.wavefunction.ints_numba module pysisyphus.wavefunction.ints_numba.diag_quadrupole3d module pysisyphus.wavefunction.ints_numba.dipole3d module pysisyphus.wavefunction.ints_numba.kinetic3d module pysisyphus.wavefunction.ints_numba.multipole3d_sph module pysisyphus.wavefunction.ints_numba.ovlp3d module pysisyphus.wavefunction.ints_numba.quadrupole3d module pysisyphus.wavefunction.localization module pysisyphus.wavefunction.multipole module pysisyphus.wavefunction.normalization module pysisyphus.wavefunction.pop_analysis module pysisyphus.wavefunction.shells module pysisyphus.wavefunction.shells_molcas module pysisyphus.wavefunction.shells_pyscf module pysisyphus.wavefunction.shells_trexio module pysisyphus.wavefunction.so_coupling module pysisyphus.wavefunction.solid_harmonics module pysisyphus.wavefunction.wavefunction module pysisyphus.wrapper module pysisyphus.wrapper.exceptions module pysisyphus.wrapper.jmol module pysisyphus.wrapper.mwfn module pysisyphus.wrapper.packmol module pysisyphus.xyzloader module pysisyphus.yaml_mods module PYTHON (pysisyphus.wavefunction.shells.IntegralBackend attribute)

Q

Q() (in module pysisyphus.wavefunction.so_coupling) q_a() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) q_a2() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) q_b() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) q_d() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) q_d2() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) q_lb() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) q_ld() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) q_oop() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) q_rd1() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) q_rd2() (in module pysisyphus.intcoords.derivatives) (in module pysisyphus.intcoords.mp_derivatives) qs (pysisyphus.dynamics.wigner.WignerSample attribute) (pysisyphus.modefollow.davidson.DavidsonResult attribute) qs_nodim (pysisyphus.dynamics.wigner.WignerSample attribute) quad_mom_tensor (pysisyphus.diabatization.results.DiabatizationResult attribute) quadrupole3d_00() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_01() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_02() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_03() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_04() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_10() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_11() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_12() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d)

quadrupole3d_13() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_14() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_20() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_21() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_22() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_23() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_24() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_30() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_31() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_32() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_33() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_34() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_40() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_41() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_42() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_43() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole3d_44() (in module pysisyphus.wavefunction.ints.quadrupole3d) (in module pysisyphus.wavefunction.ints_numba.quadrupole3d) quadrupole_ints() (pysisyphus.wavefunction.wavefunction.Wavefunction method) quadrupole_moment (pysisyphus.wavefunction.wavefunction.Wavefunction property) quartic_fit() (in module pysisyphus.optimizers.poly_fit) quaternion_to_rot_mat() (in module pysisyphus.linalg) quintic_fit() (in module pysisyphus.optimizers.poly_fit)

R

r (pysisyphus.cos.GrowingNT.GrowingNT property) (pysisyphus.io.zmat.ZLine attribute) R (pysisyphus.marcus_dim.types.MarcusModel attribute) r_diff() (in module pysisyphus.wavefunction.excited_states) R_tensor (pysisyphus.diabatization.results.DiabatizationResult attribute) rAB() (in module pysisyphus.wavefunction.excited_states) radial_integral() (in module pysisyphus.io.molden) radint() (in module pysisyphus.numint.radint) rattle_closure() (in module pysisyphus.dynamics.rattle) read_ename() (in module pysisyphus.io.bson) read_float64() (in module pysisyphus.io.bson) read_int32() (in module pysisyphus.io.bson) read_string() (in module pysisyphus.io.bson) RebuiltInternalsException recursive_extract() (in module pysisyphus.helpers_pure) recursive_update() (in module pysisyphus.helpers_pure) recv_closure() (in module pysisyphus.socket_helper) red() (in module pysisyphus.color) red_mass (pysisyphus.modefollow.NormalMode property) (pysisyphus.modefollow.NormalMode.NormalMode property) RedundantCoords (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.RedundantCoords), [1] ref (pysisyphus.franckcondon.duschinsky.DuschinskyResult attribute) reflect_coords() (in module pysisyphus.linalg_affine3) reflection_matrix() (in module pysisyphus.linalg_affine3) RELAXED (pysisyphus.wavefunction.wavefunction.DensityType attribute) remove_com_velocity() (in module pysisyphus.dynamics.helpers) remove_duplicates() (in module pysisyphus.helpers_pure) render() (in module pysisyphus.timing) render_c_funcs() (in module pysisyphus.wavefunction.gen_ints) render_cdd_cube() (in module pysisyphus.wrapper.jmol) render_cdds() (in module pysisyphus.plot) render_geom_and_charges() (in module pysisyphus.wrapper.jmol) render_mean() (pysisyphus.timing.RuntimeEstimation method) render_median() (pysisyphus.timing.RuntimeEstimation method) render_py_funcs() (in module pysisyphus.wavefunction.gen_ints) render_report() (pysisyphus.diabatization.results.DiabatizationResult method) (pysisyphus.hindered_rotor.RotorInfo.RotorInfo method) render_sp_stats() (in module pysisyphus.helpers_pure) render_xyz() (in module pysisyphus.io.mol2) reorg_en (pysisyphus.marcus_dim.types.MarcusModel attribute) reparametrize() (pysisyphus.cos.FreezingString.FreezingString method) (pysisyphus.cos.GrowingNT.GrowingNT method) (pysisyphus.Geometry.Geometry method), [1] report_bond_orders() (in module pysisyphus.wavefunction.bond_order) report_correlations() (in module pysisyphus.marcus_dim.fit) report_frozen_atoms() (in module pysisyphus.helpers_pure) report_isotopes() (in module pysisyphus.helpers_pure) report_marcus_coefficients() (in module pysisyphus.marcus_dim.fit) report_singlet_trans_moms() (in module pysisyphus.wavefunction.so_coupling) report_so_couplings() (in module pysisyphus.wavefunction.so_coupling) report_so_states() (in module pysisyphus.wavefunction.so_coupling) report_so_trans_moms() (in module pysisyphus.wavefunction.so_coupling) res_rms (pysisyphus.modefollow.davidson.DavidsonResult attribute) res_to_fstring() (in module pysisyphus.TablePrinter) reset() (pysisyphus.wavefunction.DIIS.DIIS method) reset_constraints() (pysisyphus.intcoords.DLC method) (pysisyphus.intcoords.DLC.DLC method) reset_coords() (pysisyphus.Geometry.Geometry method), [1] resize_h5_group() (in module pysisyphus.io.hdf5) restore_org_hessian() (pysisyphus.calculators.Calculator.Calculator method), [1] restrict_step() (in module pysisyphus.optimizers.restrict_step) restricted (pysisyphus.MOCoeffs.MOCoeffs property) results_to_json() (in module pysisyphus.helpers_pure) return_inds() (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] rho() (pysisyphus.intcoords.Primitive.Primitive static method) right_frontier (pysisyphus.cos.FreezingString.FreezingString property)

rind (pysisyphus.io.zmat.ZLine attribute) Rlm() (in module pysisyphus.wavefunction.solid_harmonics) rms() (in module pysisyphus.helpers_pure) rmsd() (pysisyphus.Geometry.Geometry method), [1] rmsd_grad() (in module pysisyphus.linalg) RobinDay (class in pysisyphus.marcus_dim.types) ROBUST_TORSION1 (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) ROBUST_TORSION2 (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) RobustTorsion1 (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.RobustTorsion) RobustTorsion2 (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.RobustTorsion) root_spin_ms_from_row() (in module pysisyphus.wavefunction.so_coupling) rot_inplace() (in module pysisyphus.wavefunction.localization) rot_mat (pysisyphus.hessian_proj.Orientation attribute) rot_mat_from_er_eta() (in module pysisyphus.diabatization.coulomb_eta) rot_mat_from_skew_sym() (in module pysisyphus.diabatization.coulomb_eta) rot_quaternion() (in module pysisyphus.linalg) rotate() (pysisyphus.Geometry.Geometry method), [1] rotate_fragment_around_bond() (in module pysisyphus.hindered_rotor.fragment) rotate_gradient() (pysisyphus.hessian_proj.Orientation method) Rotation (class in pysisyphus.intcoords.Rotation) ROTATION (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) ROTATION_A (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) ROTATION_B (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) ROTATION_C (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) rotation_indices (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] rotation_inds (pysisyphus.intcoords.setup.CoordInfo attribute) rotation_matrix_for_rot_around_vec() (in module pysisyphus.linalg_affine3) rotation_matrix_for_vec_align() (in module pysisyphus.linalg_affine3) RotationA (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.Rotation) RotationB (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.Rotation) RotationC (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.Rotation) RotorInfo (class in pysisyphus.hindered_rotor.RotorInfo) run() (in module pysisyphus.diabatization.coulomb_eta) (in module pysisyphus.diabatization.driver_yaml) (in module pysisyphus.diabatization.plot) (in module pysisyphus.dynamics.wigner) (in module pysisyphus.filtertrj) (in module pysisyphus.numerov.driver) (in module pysisyphus.plot) (in module pysisyphus.wavefunction.cart2sph) (in module pysisyphus.wavefunction.gen_ints) (in module pysisyphus.wavefunction.ints.boys) (in module pysisyphus.wavefunction.so_coupling) (pysisyphus.calculators.Calculator.Calculator method), [1] (pysisyphus.line_searches.LineSearch.LineSearch method) run_after() (pysisyphus.calculators.Calculator.Calculator method), [1] run_batch_calcs() (in module pysisyphus.marcus_dim.fit) run_detect_paths() (in module pysisyphus.config) run_dma() (in module pysisyphus.wavefunction.dma) run_line_search() (pysisyphus.line_searches.Backtracking method) (pysisyphus.line_searches.Backtracking.Backtracking method) (pysisyphus.line_searches.HagerZhang method) (pysisyphus.line_searches.HagerZhang.HagerZhang method) (pysisyphus.line_searches.LineSearch.LineSearch method) (pysisyphus.line_searches.StrongWolfe method) (pysisyphus.line_searches.StrongWolfe.StrongWolfe method) run_marcus_dim() (in module pysisyphus.marcus_dim.run) run_md() (in module pysisyphus.dynamics.mdp) run_param() (in module pysisyphus.marcus_dim.run) run_scan() (in module pysisyphus.marcus_dim.run) run_scan_parallel() (in module pysisyphus.marcus_dim.run) RunAfterCalculationFailedException RuntimeEstimation (class in pysisyphus.timing)

S

s (pysisyphus.dynamics.Gaussian.Gaussian property) S (pysisyphus.wavefunction.wavefunction.Wavefunction property) S() (in module pysisyphus.wavefunction.solid_harmonics) S_cart (pysisyphus.wavefunction.shells.Shells property) S_from_C (pysisyphus.wavefunction.wavefunction.Wavefunction property) S_MO_with() (pysisyphus.wavefunction.wavefunction.Wavefunction method) S_sph (pysisyphus.wavefunction.shells.Shells property) S_with() (pysisyphus.wavefunction.wavefunction.Wavefunction method) S_with_shells() (pysisyphus.wavefunction.wavefunction.Wavefunction method) save_hessian() (in module pysisyphus.io) (in module pysisyphus.io.hessian) save_third_deriv() (in module pysisyphus.io) (in module pysisyphus.io.hessian) savez() (pysisyphus.diabatization.results.DiabatizationResult method) scale_by_max_step() (in module pysisyphus.optimizers.restrict_step) scale_velocities_to_energy() (in module pysisyphus.dynamics.helpers) scale_velocities_to_temperatue() (in module pysisyphus.dynamics.helpers) scan() (in module pysisyphus.marcus_dim.scan) scan_coords_for_max_bond_change() (in module pysisyphus.marcus_dim.scan) scan_dir() (in module pysisyphus.marcus_dim.scan) scan_parallel() (in module pysisyphus.marcus_dim.scan) screen_S() (pysisyphus.wavefunction.shells.Shells static method) sd_call() (in module pysisyphus.diabatization.chimerabatch) sdf_from_cid() (in module pysisyphus.io.pubchem) secant() (pysisyphus.line_searches.HagerZhang method) (pysisyphus.line_searches.HagerZhang.HagerZhang method) SegfaultException send_closure() (in module pysisyphus.socket_helper) set_active_set() (pysisyphus.intcoords.DLC method) (pysisyphus.intcoords.DLC.DLC method) set_atoms_and_funcs() (pysisyphus.calculators.AFIR.AFIR method), [1] set_calculator() (pysisyphus.Geometry.Geometry method), [1] set_coord() (pysisyphus.Geometry.Geometry method), [1] set_coords() (pysisyphus.Geometry.Geometry method), [1] set_cross_vec() (pysisyphus.intcoords.Primitive.Primitive method) set_current_density() (pysisyphus.wavefunction.wavefunction.Wavefunction method) set_executable_flag() (in module pysisyphus.diabatization.chimerabatch) set_h5_hessian() (pysisyphus.Geometry.Geometry method), [1] set_inds_from_typed_prims() (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] set_new_frontier_nodes() (pysisyphus.cos.FreezingString.FreezingString method) set_primitive_indices() (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] set_relaxed_density() (pysisyphus.wavefunction.wavefunction.Wavefunction method) set_restart_info() (pysisyphus.calculators.Calculator.Calculator method), [1] (pysisyphus.Geometry.Geometry method), [1] set_results() (pysisyphus.Geometry.Geometry method), [1] SetPlan (class in pysisyphus.calculators.Calculator), [1] setup_calc_client() (in module pysisyphus.marcus_dim.fit) setup_redundant() (in module pysisyphus.intcoords.setup) setup_redundant_from_geom() (in module pysisyphus.intcoords.setup) shake_coords() (in module pysisyphus.helpers) Shell (class in pysisyphus.wavefunction.shells) shell_index (pysisyphus.wavefunction.shells.Shell property) shell_iter() (in module pysisyphus.wavefunction.gen_ints) Shells (class in pysisyphus.wavefunction.shells) shells_from_aomix_dict() (in module pysisyphus.io.aomix) shells_from_json_dict() (in module pysisyphus.io.orca)

shells_from_molcas_h5() (in module pysisyphus.io.molcas) shells_with_basis() (in module pysisyphus.wavefunction.Basis) ShellStruct (class in pysisyphus.wavefunction.backend_numba) ShellStructType (class in pysisyphus.wavefunction.backend_numba) simple_peaks() (in module pysisyphus.helpers) singlet_triplet_so_couplings() (in module pysisyphus.wavefunction.so_coupling) size (pysisyphus.wavefunction.shells.Shell property) slugify_worker() (in module pysisyphus.helpers) small_lbfgs_closure() (in module pysisyphus.optimizers.closures) solve_marcus() (in module pysisyphus.marcus_dim.param) solve_marcus_wavenums_and_ang() (in module pysisyphus.marcus_dim.param) sort() (pysisyphus.diabatization.results.DiabatizationResult method) sort_by_central() (in module pysisyphus.helpers_pure) sort_by_prim_type() (in module pysisyphus.intcoords.setup) sos_partfunc() (in module pysisyphus.partfuncs.partfuncs) sos_partfunc_trunc() (in module pysisyphus.partfuncs.partfuncs) sph_ao_centers (pysisyphus.wavefunction.shells.Shells property) sph_Ps (pysisyphus.wavefunction.shells.FCHKShells attribute) (pysisyphus.wavefunction.shells.MoldenShells attribute) (pysisyphus.wavefunction.shells.ORCAMoldenShells attribute) (pysisyphus.wavefunction.shells.ORCAShells attribute) (pysisyphus.wavefunction.shells.Shells attribute) (pysisyphus.wavefunction.shells_pyscf.PySCFShells attribute) (pysisyphus.wavefunction.shells_trexio.TrexIOShells attribute) sph_size (pysisyphus.wavefunction.shells.Shell property) (pysisyphus.wavefunction.shells.Shells property) sph_size() (in module pysisyphus.wavefunction.helpers) sph_slice (pysisyphus.wavefunction.shells.Shell property) spin_pop (pysisyphus.wavefunction.pop_analysis.PopAnalysis property) SpinOrbit (class in pysisyphus.wavefunction.gen_ints) SpinOrbitShell (class in pysisyphus.wavefunction.gen_ints) spline_plot_cycles() (in module pysisyphus.plot) split_xyz_str() (in module pysisyphus.xyzloader) sr1_update() (in module pysisyphus.optimizers.hessian_updates) standard_orientation() (pysisyphus.Geometry.Geometry method), [1] standard_state_corr() (in module pysisyphus.helpers_pure) start_inds (pysisyphus.numint.molint.MolGrid attribute) state_graph_from_en_mat() (in module pysisyphus.diabatization.plot) step (pysisyphus.dynamics.driver.MDResult attribute) store() (pysisyphus.wavefunction.DIIS.DIIS method) stratmann_partitioning() (in module pysisyphus.numint.molint) Stretch (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.Stretch) strong_curvature_condition() (pysisyphus.line_searches.LineSearch.LineSearch method) strong_wolfe_condition() (pysisyphus.line_searches.LineSearch.LineSearch method) StrongWolfe (class in pysisyphus.line_searches) (class in pysisyphus.line_searches.StrongWolfe) submit() (pysisyphus.executors.CloudpickleProcessPoolExecutor method) sufficiently_decreased() (pysisyphus.line_searches.LineSearch.LineSearch method) sum_formula (pysisyphus.Geometry.Geometry property), [1] sum_noises() (in module pysisyphus.dynamics.thermostats) svd_inv() (in module pysisyphus.linalg) svd_plane_normal() (in module pysisyphus.linalg_affine3) swap_inplace() (pysisyphus.MOCoeffs.MOCoeffs method) swap_mos() (pysisyphus.MOCoeffs.MOCoeffs method) sym_mat_from_tril() (in module pysisyphus.linalg) sym_mat_from_triu() (in module pysisyphus.linalg) symmetric_orthogonalization() (in module pysisyphus.wavefunction.helpers)

T

T (pysisyphus.dynamics.driver.MDResult attribute) T0 (pysisyphus.franckcondon.duschinsky.AxisSwitch attribute) T_cart (pysisyphus.wavefunction.shells.Shells property) T_crossover_from_eigval() (in module pysisyphus.irc.Instanton) T_crossover_from_ts() (in module pysisyphus.irc.Instanton) t_ps (pysisyphus.dynamics.driver.MDResult attribute) T_sph (pysisyphus.wavefunction.shells.Shells property) TablePrinter (class in pysisyphus.TablePrinter) take_quad_step() (pysisyphus.line_searches.HagerZhang method) (pysisyphus.line_searches.HagerZhang.HagerZhang method) taylor_closure() (in module pysisyphus.irc.initial_displ) taylor_closure_for_geom() (in module pysisyphus.irc.initial_displ) td_1tdms (pysisyphus.Geometry.Geometry property), [1] tden_overlaps() (in module pysisyphus.wavefunction.excited_states) temperature_for_kinetic_energy() (in module pysisyphus.dynamics.helpers) terminated (pysisyphus.dynamics.driver.MDResult attribute) thermo (pysisyphus.helpers.FinalHessianResult attribute) third_deriv_fd() (in module pysisyphus.irc.initial_displ) ThirdDerivResult (class in pysisyphus.irc.initial_displ) ThreeCenterTwoElectron (class in pysisyphus.wavefunction.gen_ints) ThreeCenterTwoElectronBase (class in pysisyphus.wavefunction.gen_ints) ThreeCenterTwoElectronShell (class in pysisyphus.wavefunction.gen_ints) ThreeCenterTwoElectronSph (class in pysisyphus.wavefunction.gen_ints) ThreeCenterTwoElectronSphShell (class in pysisyphus.wavefunction.gen_ints) timed() (in module pysisyphus.helpers_pure) tmp_xyz_handle() (pysisyphus.Geometry.Geometry method), [1] TMTRIC (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.RedundantCoords), [1] to_K_unitless() (pysisyphus.franckcondon.duschinsky.DuschinskyResult method) to_numba_shells() (in module pysisyphus.wavefunction.backend_numba) to_numba_shellstructs() (in module pysisyphus.wavefunction.backend_numba) to_orient() (in module pysisyphus.wavefunction.dma) to_pairs() (in module pysisyphus.wavefunction.excited_states) to_point() (in module pysisyphus.wrapper.jmol) to_pyscf_mol() (pysisyphus.wavefunction.shells.Shells method) to_pyscf_shell() (pysisyphus.wavefunction.shells.Shell method) to_ris_shells() (pysisyphus.wavefunction.shells.Shells method) to_same_basis() (in module pysisyphus.wavefunction.excited_states) to_sap_shell() (pysisyphus.wavefunction.shells.Shell method) to_sap_shells() (pysisyphus.wavefunction.shells.Shells method) to_sets() (in module pysisyphus.helpers_pure) to_str() (pysisyphus.io.Cube method) (pysisyphus.io.cube.Cube method) to_subscript_num() (in module pysisyphus.helpers_pure) to_sympleints_arrays() (pysisyphus.wavefunction.shells.Shells method) to_trexio() (pysisyphus.wavefunction.wavefunction.Wavefunction method) top_differences() (in module pysisyphus.wavefunction.excited_states) Torsion (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.Torsion) Torsion2 (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.Torsion2) tot_charge (pysisyphus.wavefunction.pop_analysis.PopAnalysis property) tot_mass (pysisyphus.hindered_rotor.RotorInfo.Fragment attribute) (pysisyphus.hindered_rotor.RotorInfo.RotorInfo property)

total_mass (pysisyphus.Geometry.Geometry property), [1] touch() (in module pysisyphus.helpers_pure) transform_forces() (pysisyphus.intcoords.CartesianCoords method) (pysisyphus.intcoords.CartesianCoords.CartesianCoords method) (pysisyphus.intcoords.Coords.CoordSys method) (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] transform_hessian() (pysisyphus.intcoords.CartesianCoords method) (pysisyphus.intcoords.CartesianCoords.CartesianCoords method) (pysisyphus.intcoords.Coords.CoordSys method) (pysisyphus.intcoords.DLC method) (pysisyphus.intcoords.DLC.DLC method) (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] transform_int_step() (in module pysisyphus.intcoords.update) (pysisyphus.intcoords.CartesianCoords method) (pysisyphus.intcoords.CartesianCoords.CartesianCoords method) (pysisyphus.intcoords.Coords.CoordSys method) (pysisyphus.intcoords.DLC method) (pysisyphus.intcoords.DLC.DLC method) (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] Translation (class in pysisyphus.intcoords.Translation) TRANSLATION (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) translation_indices (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] translation_inds (pysisyphus.intcoords.setup.CoordInfo attribute) translation_matrix() (in module pysisyphus.linalg_affine3) TRANSLATION_X (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) TRANSLATION_Y (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) TRANSLATION_Z (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) TranslationX (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.Translation) TranslationY (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.Translation) TranslationZ (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.Translation) treutler_m4_map() (in module pysisyphus.numint.radint) TrexIOShells (class in pysisyphus.wavefunction.shells_trexio) TRIC (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.RedundantCoords), [1] ts_bfgs_update() (in module pysisyphus.optimizers.hessian_updates) ts_bfgs_update_org() (in module pysisyphus.optimizers.hessian_updates) ts_bfgs_update_revised() (in module pysisyphus.optimizers.hessian_updates) TwoCenter1d (class in pysisyphus.wavefunction.gen_ints) TwoCenterTwoElectron (class in pysisyphus.wavefunction.gen_ints) TwoCenterTwoElectronShell (class in pysisyphus.wavefunction.gen_ints) type (pysisyphus.optimizers.gdiis.DIISResult property) typed_prims (pysisyphus.intcoords.CartesianCoords property) (pysisyphus.intcoords.CartesianCoords.CartesianCoords property) (pysisyphus.intcoords.Coords.CoordSys property) (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] (pysisyphus.intcoords.setup.CoordInfo attribute)

U

U (pysisyphus.diabatization.results.DiabatizationResult attribute) (pysisyphus.intcoords.DLC property) (pysisyphus.intcoords.DLC.DLC property) unitless_displs_from_eigensystem() (in module pysisyphus.franckcondon.duschinsky) UNRELAXED (pysisyphus.wavefunction.wavefunction.DensityType attribute)

unrestricted (pysisyphus.MOCoeffs.MOCoeffs property) unscaled_velocity_distribution() (in module pysisyphus.dynamics.helpers) unweight_mw_hessian() (pysisyphus.Geometry.Geometry method), [1] update_internals() (in module pysisyphus.intcoords.update) using() (in module pysisyphus.testing)

V

V_cart (pysisyphus.wavefunction.shells.Shells property) v_last (pysisyphus.dynamics.driver.MDResult attribute) V_sph (pysisyphus.wavefunction.shells.Shells property) valid_diis_direction() (in module pysisyphus.optimizers.gdiis) value() (pysisyphus.dynamics.colvars.Colvar method) (pysisyphus.dynamics.colvars.CVBend method) (pysisyphus.dynamics.colvars.CVDistance method) (pysisyphus.dynamics.colvars.CVTorsion method) (pysisyphus.dynamics.Gaussian.Gaussian method) vdw_radii (pysisyphus.Geometry.Geometry property), [1] vdw_volume() (pysisyphus.Geometry.Geometry method), [1] vec (pysisyphus.irc.initial_displ.ThirdDerivResult attribute)

velocities (pysisyphus.dynamics.wigner.WignerSample attribute) verbose_bond_difference() (in module pysisyphus.intcoords.helpers) verify_chkfiles() (pysisyphus.calculators.Calculator.Calculator method), [1] view_cdd() (pysisyphus.io.Cube method) (pysisyphus.io.cube.Cube method) view_cdd_cube() (in module pysisyphus.wrapper.jmol) virt_indsa (pysisyphus.MOCoeffs.MOCoeffs property) virt_indsb (pysisyphus.MOCoeffs.MOCoeffs property) vol_data (pysisyphus.io.Cube attribute) (pysisyphus.io.cube.Cube attribute) vol_element (pysisyphus.io.Cube property) (pysisyphus.io.cube.Cube property)

W

w (pysisyphus.dynamics.Gaussian.Gaussian property) Wavefunction (class in pysisyphus.wavefunction.wavefunction) wavefunction (pysisyphus.Geometry.Geometry property), [1] wavefunction_from_aomix_dict() (in module pysisyphus.io.aomix) wavefunction_from_json_dict() (in module pysisyphus.io.orca) weight() (pysisyphus.intcoords.Primitive.Primitive method) weights (pysisyphus.numint.molint.MolGrid attribute) wigner_kirkwood_partfunc() (in module pysisyphus.partfuncs.partfuncs) WignerSample (class in pysisyphus.dynamics.wigner)

without_hydrogens() (pysisyphus.Geometry.Geometry method), [1] wolfe_condition() (pysisyphus.line_searches.LineSearch.LineSearch method) wrap_stdin() (in module pysisyphus.wrapper.mwfn) write() (pysisyphus.io.Cube method) (pysisyphus.io.cube.Cube method) write_file() (in module pysisyphus.wavefunction.gen_ints) write_fragment_geoms() (pysisyphus.calculators.AFIR.AFIR method), [1] write_geoms_to_trj() (in module pysisyphus.xyzloader) write_inp() (in module pysisyphus.diabatization.chimerabatch) write_render() (in module pysisyphus.wavefunction.gen_ints)

X

x (pysisyphus.optimizers.poly_fit.FitResult attribute)

xyz (pysisyphus.numint.molint.MolGrid attribute)

Y

y (pysisyphus.optimizers.poly_fit.FitResult attribute)

Z

zero_crossings() (in module pysisyphus.peakdetect) zero_crossings_sine_fit() (in module pysisyphus.peakdetect) zero_frozen_forces() (pysisyphus.Geometry.Geometry method), [1] ZeroStepLength ZLine (class in pysisyphus.io.zmat)

zmat_from_fn() (in module pysisyphus.io.zmat) zmat_from_str() (in module pysisyphus.io.zmat) zoom() (pysisyphus.line_searches.StrongWolfe method) (pysisyphus.line_searches.StrongWolfe.StrongWolfe method) zpart() (in module pysisyphus.wavefunction.solid_harmonics)