Index

_

__init__() (pysisyphus.calculators.AFIR method) (pysisyphus.calculators.AFIR.AFIR method), [1] (pysisyphus.calculators.AtomAtomTransTorque method) (pysisyphus.calculators.AtomAtomTransTorque.AtomAtomTransTorque method) (pysisyphus.calculators.Calculator.Calculator method), [1] (pysisyphus.calculators.CFOUR method) (pysisyphus.calculators.CFOUR.CFOUR method) (pysisyphus.calculators.EnergyMin method) (pysisyphus.calculators.EnergyMin.EnergyMin method) (pysisyphus.calculators.ExternalPotential.LogFermi method) (pysisyphus.calculators.ExternalPotential.RMSD method) (pysisyphus.calculators.FreeEndNEBPot.FreeEndNEBPot method) (pysisyphus.calculators.HardSphere method) (pysisyphus.calculators.HardSphere.HardSphere method) (pysisyphus.calculators.HardSphere.PWHardSphere method) (pysisyphus.calculators.LEPSExpr.LEPSExpr method) (pysisyphus.calculators.ONIOM method) (pysisyphus.calculators.ONIOMv2.ONIOM method), [1] (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] (pysisyphus.calculators.TransTorque method) (pysisyphus.calculators.TransTorque.TransTorque method) (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] (pysisyphus.cos.AdaptiveNEB.AdaptiveNEB method), [1] (pysisyphus.cos.FreeEndNEB.FreeEndNEB method), [1] (pysisyphus.dynamics.Gaussian.Gaussian method) (pysisyphus.Geometry.Geometry method), [1] (pysisyphus.irc.DWI.DWI method) (pysisyphus.irc.IRC.IRC method), [1] (pysisyphus.line_searches.Backtracking method) (pysisyphus.line_searches.Backtracking.Backtracking method) (pysisyphus.line_searches.StrongWolfe method) (pysisyphus.line_searches.StrongWolfe.StrongWolfe method) (pysisyphus.modefollow.NormalMode method) (pysisyphus.modefollow.NormalMode.NormalMode method) (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer method), [1] (pysisyphus.optimizers.LBFGS.LBFGS method), [1] (pysisyphus.optimizers.Optimizer.Optimizer method), [1] (pysisyphus.optimizers.PreconLBFGS.PreconLBFGS method), [1] (pysisyphus.optimizers.RFOptimizer.RFOptimizer method), [1] (pysisyphus.tsoptimizers.TSHessianOptimizer.TSHessianOptimizer method), [1]

A

a (pysisyphus.io.zmat.ZLine attribute) a8() (in module pysisyphus.io.crd) action() (pysisyphus.irc.Instanton.Instanton method) action_gradient() (pysisyphus.irc.Instanton.Instanton method) action_hessian() (pysisyphus.irc.Instanton.Instanton method) adapt_this_cycle() (pysisyphus.cos.AdaptiveNEB.AdaptiveNEB method), [1] AdaptiveNEB (class in pysisyphus.cos.AdaptiveNEB), [1] add_gaussian() (pysisyphus.calculators.Dimer method) (pysisyphus.calculators.Dimer.Dimer method), [1], [2] adjust_alpha() (pysisyphus.optimizers.StabilizedQNMethod.StabilizedQNMethod method) adjust_alpha_stretch() (pysisyphus.optimizers.StabilizedQNMethod.StabilizedQNMethod method) AFIR (class in pysisyphus.calculators) (class in pysisyphus.calculators.AFIR), [1] afir_closure() (in module pysisyphus.calculators.AFIR), [1] afir_fd_hessian_wrapper() (pysisyphus.calculators.AFIR method) (pysisyphus.calculators.AFIR.AFIR method), [1] AFIRPath (class in pysisyphus.drivers.afir) aHOH (pysisyphus.calculators.TIP3P attribute) (pysisyphus.calculators.TIP3P.TIP3P attribute), [1] aind (pysisyphus.io.zmat.ZLine attribute) align() (in module pysisyphus.trj) align_coords() (in module pysisyphus.helpers) align_geoms() (in module pysisyphus.helpers) align_on_subset() (in module pysisyphus.drivers.merge) align_principal_axes() (pysisyphus.Geometry.Geometry method), [1] ALL (pysisyphus.calculators.Calculator.KeepKind attribute), [1] all_coords (pysisyphus.irc.IRCDummy.IRCDummy attribute) all_energies (pysisyphus.Geometry.Geometry property), [1] all_geoms_to_trj() (pysisyphus.interpolate.Interpolator.Interpolator method) all_overlaps() (pysisyphus.calculators.WFOWrapper2.WFOWrapper2 method) 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) analyze_afir_path() (in module pysisyphus.drivers.afir) AnaPot (class in pysisyphus.calculators.AnaPot) AnaPot2 (class in pysisyphus.calculators.AnaPot2) AnaPot2_ (class in pysisyphus.calculators.AnaPot2) AnaPot3 (class in pysisyphus.calculators.AnaPot3) AnaPot4 (class in pysisyphus.calculators.AnaPot4) AnaPotBase (class in pysisyphus.calculators.AnaPotBase), [1] AnaPotCBM (class in pysisyphus.calculators.AnaPotCBM) anim_coords() (pysisyphus.calculators.AnaPotBase.AnaPotBase method), [1] anim_cos() (in module pysisyphus.plot) anim_opt() (pysisyphus.calculators.AnaPotBase.AnaPotBase method), [1] animate() (pysisyphus.plotters.AnimPlot.AnimPlot method) AnimPlot (class in pysisyphus.plotters.AnimPlot)

append() (in module pysisyphus.trj) append_control() (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] apply_keep_kind() (pysisyphus.calculators.Calculator.Calculator method), [1] apply_set_plans() (pysisyphus.calculators.Calculator.Calculator method), [1] apply_transform() (in module pysisyphus.stocastic.align) approx_float() (in module pysisyphus.helpers_pure) approximate_radius() (pysisyphus.Geometry.Geometry method), [1] arc_dims (pysisyphus.cos.GrowingChainOfStates.GrowingChainOfStates property), [1] are_collinear() (in module pysisyphus.intcoords.valid) as_ase_atoms() (pysisyphus.Geometry.Geometry method), [1] as_calculator() (pysisyphus.calculators.ONIOMv2.Model method), [1] as_g98_list() (pysisyphus.Geometry.Geometry method), [1] as_geom() (pysisyphus.calculators.ONIOMv2.Model method), [1] as_html5() (pysisyphus.plotters.AnimPlot.AnimPlot method) as_pdb() (in module pysisyphus.pack) as_xyz() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] (pysisyphus.cos.FreezingString.FreezingString method) (pysisyphus.cos.GrowingNT.GrowingNT method) (pysisyphus.Geometry.Geometry method), [1] (pysisyphus.irc.Instanton.Instanton method) assert_cart_coords() (pysisyphus.Geometry.Geometry method), [1] assert_compatibility() (pysisyphus.Geometry.Geometry method), [1] atom (pysisyphus.calculators.ONIOMv2.Link attribute), [1] (pysisyphus.io.zmat.ZLine attribute) atom_indices() (pysisyphus.Geometry.Geometry method), [1] atom_inds_in_layer() (pysisyphus.calculators.ONIOM method) (pysisyphus.calculators.ONIOMv2.ONIOM method), [1] atom_inds_to_cart_inds() (in module pysisyphus.calculators.ONIOMv2), [1] atom_types (pysisyphus.Geometry.Geometry property), [1] atom_xyz_iter() (pysisyphus.Geometry.Geometry method), [1] AtomAtomTransTorque (class in pysisyphus.calculators) (class in pysisyphus.calculators.AtomAtomTransTorque) atomic_numbers (pysisyphus.Geometry.Geometry property), [1] atoms (pysisyphus.cos.ChainOfStates.ChainOfStates property), [1] (pysisyphus.cos.GrowingNT.GrowingNT property) (pysisyphus.drivers.afir.AFIRPath attribute) (pysisyphus.irc.IRCDummy.IRCDummy attribute) atoms_are_too_close() (pysisyphus.stocastic.Pipeline.Pipeline method) atoms_coords_to_crd_str() (in module pysisyphus.io.crd) atoms_coords_to_pdb_str() (in module pysisyphus.io.pdb) augment_bonds() (in module pysisyphus.intcoords.augment_bonds) augment_primitives() (in module pysisyphus.intcoords.eval) automatic_fragmentation() (in module pysisyphus.drivers.afir) AUX_BOND (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) AUX_INTERFRAG_BOND (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) aux_interfrag_bonds (pysisyphus.intcoords.setup.CoordInfo attribute) available() (in module pysisyphus.testing) available_potentials (pysisyphus.calculators.ExternalPotential attribute) (pysisyphus.calculators.ExternalPotential.ExternalPotential attribute)

B

B (pysisyphus.intcoords.DLC property) (pysisyphus.intcoords.DLC.DLC property) (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] 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] backtrack() (pysisyphus.optimizers.BacktrackingOptimizer.BacktrackingOptimizer method) Backtracking (class in pysisyphus.line_searches) (class in pysisyphus.line_searches.Backtracking) BacktrackingOptimizer (class in pysisyphus.optimizers.BacktrackingOptimizer) backtransform_hessian() (pysisyphus.intcoords.DLC method) (pysisyphus.intcoords.DLC.DLC method) (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] backward (pysisyphus.irc.IRCDummy.IRCDummy attribute) barrier (pysisyphus.drivers.rates.ReactionRates attribute) barrier_si (pysisyphus.drivers.rates.ReactionRates attribute) base_cmd (pysisyphus.calculators.MOPAC attribute) (pysisyphus.calculators.MOPAC.MOPAC attribute), [1] bell_corr() (in module pysisyphus.drivers.rates) 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) BFGS (class in pysisyphus.optimizers.BFGS) bfgs_multiply() (in module pysisyphus.optimizers.closures)

bfgs_update() (in module pysisyphus.optimizers.hessian_updates) (pysisyphus.optimizers.BFGS.BFGS method) bio_mode() (pysisyphus.optimizers.StabilizedQNMethod.StabilizedQNMethod method) birkholz_interpolation() (in module pysisyphus.drivers.birkholz) bisect() (pysisyphus.line_searches.HagerZhang method) (pysisyphus.line_searches.HagerZhang.HagerZhang method) block_davidson() (in module pysisyphus.modefollow.davidson) bofill_update() (in module pysisyphus.optimizers.hessian_updates) 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_order() (in module pysisyphus.drivers.birkholz) bond_orders() (in module pysisyphus.drivers.birkholz) bond_orders_for_geom() (in module pysisyphus.drivers.birkholz) 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.BondedFragment) bonds (pysisyphus.intcoords.setup.CoordInfo attribute) bool_color() (in module pysisyphus.color) 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_gateway_str() (pysisyphus.calculators.OpenMolcas method) (pysisyphus.calculators.OpenMolcas.OpenMolcas method), [1] build_mcpdft_str() (pysisyphus.calculators.OpenMolcas method) (pysisyphus.calculators.OpenMolcas.OpenMolcas method), [1] build_rasscf_str() (pysisyphus.calculators.OpenMolcas method) (pysisyphus.calculators.OpenMolcas.OpenMolcas method), [1] build_rassi_str() (pysisyphus.calculators.OpenMolcas method) (pysisyphus.calculators.OpenMolcas.OpenMolcas method), [1] build_set_plans() (pysisyphus.calculators.Calculator.Calculator method), [1] build_str_from_dict() (pysisyphus.calculators.OpenMolcas method) (pysisyphus.calculators.OpenMolcas.OpenMolcas method), [1]

C

C (pysisyphus.calculators.Dimer property) (pysisyphus.calculators.Dimer.Dimer property), [1], [2] (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] cache_arrays() (in module pysisyphus.helpers_pure) calc() (pysisyphus.calculators.DFTD3.DFTD3 method) (pysisyphus.calculators.ExternalPotential.HarmonicSphere method) (pysisyphus.calculators.ExternalPotential.LogFermi method) (pysisyphus.calculators.ExternalPotential.Restraint method) (pysisyphus.calculators.ExternalPotential.RMSD method) calc_angle() (pysisyphus.irc.ParamPlot.ParamPlot method) calc_bond() (pysisyphus.irc.ParamPlot.ParamPlot method) calc_cdd_cube() (pysisyphus.calculators.OverlapCalculator.OverlapCalculator method), [1] calc_centroid() (in module pysisyphus.calculators.CFOUR) calc_double_ao_overlap() (pysisyphus.Geometry.Geometry method), [1] calc_energy_and_forces() (pysisyphus.Geometry.Geometry method), [1] calc_getter (pysisyphus.run.RunResult attribute) calc_hessian_for() (pysisyphus.cos.GrowingNT.GrowingNT method) calc_ipi_client() (in module pysisyphus.calculators.IPIClient) calc_layer() (pysisyphus.calculators.ONIOM method) (pysisyphus.calculators.ONIOMv2.ONIOM method), [1] calc_prim_restraint() (pysisyphus.calculators.ExternalPotential.Restraint static method) calc_rot_matrix() (in module pysisyphus.calculators.CFOUR) CALC_TYPES (pysisyphus.calculators.MOPAC attribute) (pysisyphus.calculators.MOPAC.MOPAC attribute), [1] calced_geoms (pysisyphus.run.RunResult attribute) calced_results (pysisyphus.run.RunResult attribute) calcs_from_dict() (in module pysisyphus.calculators.MultiCalc) calculate() (pysisyphus.calculators.LennardJones method) (pysisyphus.calculators.LennardJones.LennardJones method), [1] (pysisyphus.calculators.TIP3P method) (pysisyphus.calculators.TIP3P.TIP3P method), [1] (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_forces() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] Calculator (class in pysisyphus.calculators.Calculator), [1] calculator (pysisyphus.cos.ChainOfStates.ChainOfStates property), [1] call_jmol() (in module pysisyphus.wrapper.jmol) call_mwfn() (in module pysisyphus.wrapper.mwfn) call_packmol() (in module pysisyphus.wrapper.packmol) can_bias_f0 (pysisyphus.calculators.Dimer property) (pysisyphus.calculators.Dimer.Dimer property), [1], [2] can_bias_f1 (pysisyphus.calculators.Dimer property) (pysisyphus.calculators.Dimer.Dimer property), [1], [2] cap_fragment() (in module pysisyphus.calculators.ONIOMv2), [1] capped_atoms_coords() (pysisyphus.calculators.ONIOMv2.Model method), [1] 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_coords (pysisyphus.cos.ChainOfStates.ChainOfStates property), [1] (pysisyphus.cos.GrowingNT.GrowingNT property) (pysisyphus.drivers.afir.AFIRPath attribute) (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.irc.Instanton.Instanton property) 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_hessian (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.irc.Instanton.Instanton property) Cartesian (class in pysisyphus.intcoords.Cartesian) CARTESIAN (pysisyphus.intcoords.PrimTypes.PrimTypes 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) CDD_PNG_FNS (in module pysisyphus.plot) center() (in module pysisyphus.trj) (pysisyphus.Geometry.Geometry method), [1] center_fragments() (in module pysisyphus.drivers.precon_pos_rot) center_of_mass (pysisyphus.Geometry.Geometry property), [1] center_of_mass_at() (pysisyphus.Geometry.Geometry method), [1] centerm() (in module pysisyphus.trj) centroid (pysisyphus.Geometry.Geometry property), [1] CerjanMiller (class in pysisyphus.calculators.CerjanMiller) CFOUR (class in pysisyphus.calculators) (class in pysisyphus.calculators.CFOUR) cg_step() (pysisyphus.optimizers.MicroOptimizer method) (pysisyphus.optimizers.MicroOptimizer.MicroOptimizer method) ChainOfStates (class in pysisyphus.cos.ChainOfStates), [1] charge (pysisyphus.calculators.AFIR property) (pysisyphus.calculators.AFIR.AFIR property), [1] (pysisyphus.calculators.ONIOM property) (pysisyphus.calculators.ONIOMv2.LayerCalc property), [1] (pysisyphus.calculators.ONIOMv2.ONIOM property), [1] (pysisyphus.db.molecules.Molecule attribute) (pysisyphus.drivers.afir.AFIRPath attribute) charges (pysisyphus.calculators.TIP3P attribute) (pysisyphus.calculators.TIP3P.TIP3P attribute), [1] check_alpha() (pysisyphus.line_searches.LineSearch.LineSearch method) check_asserts() (in module pysisyphus.run) check_convergence() (pysisyphus.cos.GrowingNT.GrowingNT method) (pysisyphus.optimizers.LayerOpt.LayerOpt method), [1] (pysisyphus.optimizers.Optimizer.Optimizer method), [1] (pysisyphus.optimizers.StringOptimizer.StringOptimizer method) check_for_climbing_start() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] check_for_end_sign() (in module pysisyphus.helpers) check_mem() (in module pysisyphus.helpers_pure) check_primitives() (in module pysisyphus.intcoords.eval) check_termination() (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] (pysisyphus.calculators.XTB static method) (pysisyphus.calculators.XTB.XTB static method), [1] check_typed_prims() (in module pysisyphus.intcoords.valid) chunks() (in module pysisyphus.helpers_pure) ci_coeffs_above_thresh() (pysisyphus.calculators.WFOWrapper.WFOWrapper method) (pysisyphus.calculators.WFOWrapper2.WFOWrapper2 method) cid_from_name() (in module pysisyphus.io.pubchem)

CIQuantities (class in pysisyphus.calculators.ConicalIntersection) clean() (in module pysisyphus.db.generate_db) (pysisyphus.calculators.Calculator.Calculator method), [1] clean_tmp() (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] clear() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] (pysisyphus.Geometry.Geometry method), [1] (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] clear_passed() (pysisyphus.cos.GrowingNT.GrowingNT method) coeffs (pysisyphus.optimizers.gdiis.DIISResult attribute) Colvar (class in pysisyphus.dynamics.colvars) comment (pysisyphus.Geometry.Geometry property), [1] compare_to_geometric() (in module pysisyphus.intcoords.Rotation) compatible() (pysisyphus.drivers.afir.AFIRPath method) complete_fragments() (in module pysisyphus.helpers) Composite (class in pysisyphus.calculators) (class in pysisyphus.calculators.Composite) compute() (pysisyphus.calculators.Dalton.Dalton method), [1] concurrent_force_calcs() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] condition() (pysisyphus.calculators.Calculator.SetPlan method), [1] conf_key (pysisyphus.calculators.Calculator.Calculator attribute), [1] (pysisyphus.calculators.CFOUR attribute) (pysisyphus.calculators.CFOUR.CFOUR attribute) (pysisyphus.calculators.Dalton.Dalton attribute), [1] (pysisyphus.calculators.DFTBp attribute) (pysisyphus.calculators.DFTBp.DFTBp attribute), [1] (pysisyphus.calculators.DFTD3.DFTD3 attribute) (pysisyphus.calculators.Gaussian09 attribute) (pysisyphus.calculators.Gaussian09.Gaussian09 attribute), [1] (pysisyphus.calculators.Gaussian16 attribute) (pysisyphus.calculators.Gaussian16.Gaussian16 attribute), [1] (pysisyphus.calculators.MOPAC attribute) (pysisyphus.calculators.MOPAC.MOPAC attribute), [1] (pysisyphus.calculators.OpenMolcas attribute) (pysisyphus.calculators.OpenMolcas.OpenMolcas attribute), [1] (pysisyphus.calculators.ORCA attribute) (pysisyphus.calculators.ORCA.ORCA attribute), [1] (pysisyphus.calculators.ORCA5 attribute) (pysisyphus.calculators.ORCA5.ORCA5 attribute) (pysisyphus.calculators.Psi4 attribute) (pysisyphus.calculators.Psi4.Psi4 attribute), [1] (pysisyphus.calculators.Turbomole attribute) (pysisyphus.calculators.Turbomole.Turbomole attribute), [1] (pysisyphus.calculators.XTB attribute) (pysisyphus.calculators.XTB.XTB attribute), [1] conf_thresh (pysisyphus.calculators.OverlapCalculator.OverlapCalculator attribute), [1] (pysisyphus.calculators.WFOWrapper.WFOWrapper property) confirm_input() (in module pysisyphus.helpers) ConicalIntersection (class in pysisyphus.calculators) (class in pysisyphus.calculators.ConicalIntersection) ConjugateGradient (class in pysisyphus.optimizers.ConjugateGradient) 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) control_from_simple_input() (in module pysisyphus.calculators.Turbomole), [1] conv_dict (pysisyphus.calculators.OBabel attribute) (pysisyphus.calculators.OBabel.OBabel attribute), [1] converged (pysisyphus.line_searches.LineSearch.LineSearchResult attribute) (pysisyphus.modefollow.davidson.DavidsonResult attribute) ConvInfo (class in pysisyphus.optimizers.Optimizer), [1] coord_types (pysisyphus.Geometry.Geometry attribute), [1] coordinates_similar() (in module pysisyphus.drivers.afir) CoordInfo (class in pysisyphus.intcoords.setup) coords (pysisyphus.cos.ChainOfStates.ChainOfStates property), [1] (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.irc.IRC.IRC property), [1] (pysisyphus.optimizers.gdiis.DIISResult attribute) coords0 (pysisyphus.calculators.Dimer property) (pysisyphus.calculators.Dimer.Dimer property), [1], [2] coords1 (pysisyphus.calculators.Dimer property) (pysisyphus.calculators.Dimer.Dimer property), [1], [2] coords3d (pysisyphus.cos.ChainOfStates.ChainOfStates property), [1] (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.intcoords.CartesianCoords property) (pysisyphus.intcoords.CartesianCoords.CartesianCoords property) (pysisyphus.intcoords.Coords.CoordSys property) (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] coords_by_type (pysisyphus.Geometry.Geometry property), [1] 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] copy_yaml_and_geometries() (in module pysisyphus.run) correct_dihedrals() (in module pysisyphus.intcoords.update) corrector_step() (pysisyphus.irc.EulerPC method) (pysisyphus.irc.EulerPC.EulerPC method), [1] cos (pysisyphus.run.RunResult attribute) cos_opt (pysisyphus.run.RunResult attribute) cost_function() (pysisyphus.interpolate.LST.LST method) coulomb() (pysisyphus.calculators.TIP3P method) (pysisyphus.calculators.TIP3P.TIP3P method), [1] covalent_radii (pysisyphus.Geometry.Geometry property), [1] CovRadiiSumZero, [1] create_bond_vec_getters() (pysisyphus.calculators.ONIOMv2.Model method), [1] create_links() (pysisyphus.calculators.ONIOMv2.Model method), [1] cross3() (in module pysisyphus.linalg) csvr_closure() (in module pysisyphus.dynamics.thermostats) csvr_closure_2() (in module pysisyphus.dynamics.thermostats) 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) CubicNewton (class in pysisyphus.optimizers) (class in pysisyphus.optimizers.CubicNewton) cur_cycle (pysisyphus.modefollow.davidson.DavidsonResult attribute) (pysisyphus.optimizers.Optimizer.ConvInfo attribute), [1] curvature() (pysisyphus.calculators.Dimer method) (pysisyphus.calculators.Dimer.Dimer method), [1], [2] curvature_condition() (pysisyphus.line_searches.LineSearch.LineSearch method) 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) 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) Dalton (class in pysisyphus.calculators.Dalton), [1] damp_velocity() (pysisyphus.irc.DampedVelocityVerlet method) (pysisyphus.irc.DampedVelocityVerlet.DampedVelocityVerlet method), [1] damped_bfgs_update() (in module pysisyphus.optimizers.hessian_updates) (pysisyphus.optimizers.BFGS.BFGS method) DampedVelocityVerlet (class in pysisyphus.irc) (class in pysisyphus.irc.DampedVelocityVerlet), [1] data_funcs (pysisyphus.benchmarks.Benchmark.Benchmark attribute) data_model (pysisyphus.calculators.OverlapCalculator.OverlapCalculator property), [1] DavidsonResult (class in pysisyphus.modefollow.davidson) decrease_distance() (in module pysisyphus.drivers.afir) del_atoms() (pysisyphus.Geometry.Geometry method), [1] density (pysisyphus.db.molecules.Molecule attribute) describe() (in module pysisyphus.helpers_pure) (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] (pysisyphus.Geometry.Geometry method), [1] desired_eigval_structure (pysisyphus.optimizers.Optimizer.ConvInfo attribute), [1] detect_paths() (in module pysisyphus.config) determine_target_pairs() (in module pysisyphus.drivers.afir) determine_target_pairs_for_geom() (in module pysisyphus.drivers.afir) df_evals (pysisyphus.line_searches.LineSearch.LineSearchResult attribute) DFTBp (class in pysisyphus.calculators) (class in pysisyphus.calculators.DFTBp), [1] DFTD3 (class in pysisyphus.calculators.DFTD3) DFTD4 (class in pysisyphus.calculators) dict_to_mol2_string() (in module pysisyphus.io.mol2) 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_result() (in module pysisyphus.optimizers.gdiis) DIISResult (class in pysisyphus.optimizers.gdiis) Dimer (class in pysisyphus.calculators) (class in pysisyphus.calculators.Dimer), [1], [2] dind (pysisyphus.io.zmat.ZLine attribute) direct_cycle() (in module pysisyphus.drivers.pka) direct_rotation() (pysisyphus.calculators.Dimer method) (pysisyphus.calculators.Dimer.Dimer method), [1], [2]

DISTANCE_FUNCTION (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) DistanceFunction (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.DistanceFunction) DLC (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.DLC) do_calculations() (pysisyphus.calculators.EnergyMin method) (pysisyphus.calculators.EnergyMin.EnergyMin method) do_clean() (in module pysisyphus.run) do_dimer_rotations() (pysisyphus.calculators.Dimer method) (pysisyphus.calculators.Dimer.Dimer method), [1], [2] do_endopt_ts_barriers() (in module pysisyphus.drivers.barriers) do_final_hessian() (in module pysisyphus.helpers) do_line_search() (pysisyphus.tsoptimizers.TSHessianOptimizer.TSHessianOptimizer static method), [1] do_parent() (pysisyphus.calculators.ONIOMv2.LayerCalc method), [1] do_rmsds() (in module pysisyphus.run) double_damp() (in module pysisyphus.optimizers.hessian_updates) double_damped_bfgs_update() (pysisyphus.optimizers.BFGS.BFGS method) double_secant() (pysisyphus.line_searches.HagerZhang method) (pysisyphus.line_searches.HagerZhang.HagerZhang method) downhill (pysisyphus.irc.IRCDummy.IRCDummy attribute) 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_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) ds (pysisyphus.irc.initial_displ.ThirdDerivResult attribute) Dummy (class in pysisyphus.calculators) (class in pysisyphus.calculators.Dummy) dummy_hessian_update() (in module pysisyphus.optimizers.HessianOptimizer), [1] 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) DummyMark (class in pysisyphus.testing) DummyTorsion (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.DummyTorsion) dump() (pysisyphus.dynamics.Gaussian.Gaussian method) (pysisyphus.irc.DWI.DWI method) dump_coords() (in module pysisyphus.dynamics.helpers) dump_data() (pysisyphus.irc.IRC.IRC method), [1] dump_ends() (pysisyphus.irc.IRC.IRC method), [1] dump_geoms() (in module pysisyphus.trj) dump_h5() (pysisyphus.calculators.AFIR method) (pysisyphus.calculators.AFIR.AFIR method), [1] dump_overlap_data() (pysisyphus.calculators.OverlapCalculator.OverlapCalculator method), [1] dump_progress() (pysisyphus.interpolate.Redund.Redund method) dump_restart_info() (pysisyphus.optimizers.Optimizer.Optimizer method), [1] dump_trj() (pysisyphus.drivers.afir.AFIRPath method) dump_xyz() (pysisyphus.Geometry.Geometry method), [1] DWI (class in pysisyphus.irc.DWI)

E

E_tot (pysisyphus.dynamics.driver.MDResult attribute) eckart_corr() (in module pysisyphus.drivers.rates) eckart_corr_brown() (in module pysisyphus.drivers.rates) eckart_projection() (pysisyphus.Geometry.Geometry method), [1] EGO (class in pysisyphus.calculators) (class in pysisyphus.calculators.EGO) eigval_to_wavenumber() (in module pysisyphus.helpers_pure) eigvals (pysisyphus.helpers.FinalHessianResult attribute) eigvec_grad() (in module pysisyphus.linalg) embeddings (pysisyphus.calculators.ONIOM attribute) (pysisyphus.calculators.ONIOMv2.ONIOM attribute), [1] end_geoms (pysisyphus.run.RunResult attribute) energies (pysisyphus.drivers.afir.AFIRPath attribute) energy (pysisyphus.calculators.ConicalIntersection.CIQuantities attribute) (pysisyphus.cos.ChainOfStates.ChainOfStates property), [1] (pysisyphus.cos.FreezingString.FreezingString property) (pysisyphus.cos.GrowingNT.GrowingNT property) (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.irc.Instanton.Instanton property) (pysisyphus.irc.IRC.IRC property), [1] (pysisyphus.optimizers.gdiis.DIISResult attribute) energy() (pysisyphus.calculators.Dimer.Gaussian method), [1], [2] energy0 (pysisyphus.calculators.Dimer property) (pysisyphus.calculators.Dimer.Dimer property), [1], [2] energy1 (pysisyphus.calculators.ConicalIntersection.CIQuantities attribute) energy2 (pysisyphus.calculators.ConicalIntersection.CIQuantities attribute) energy_converged (pysisyphus.optimizers.Optimizer.ConvInfo attribute), [1] energy_diff (pysisyphus.calculators.ConicalIntersection.CIQuantities attribute)

energy_forces_getter_closure() (in module pysisyphus.dynamics.helpers) energy_from_results() (pysisyphus.calculators.ONIOMv2.LayerCalc static method), [1] energy_minus (pysisyphus.irc.initial_displ.ThirdDerivResult attribute) energy_plus (pysisyphus.irc.initial_displ.ThirdDerivResult attribute) EnergyMin (class in pysisyphus.calculators) (class in pysisyphus.calculators.EnergyMin) epsilon (pysisyphus.calculators.TIP3P attribute) (pysisyphus.calculators.TIP3P.TIP3P attribute), [1] estimate() (in module pysisyphus.helpers_pure) estimate_error() (pysisyphus.irc.DampedVelocityVerlet method) (pysisyphus.irc.DampedVelocityVerlet.DampedVelocityVerlet method), [1] Euler (class in pysisyphus.irc) (class in pysisyphus.irc.Euler), [1] EulerPC (class in pysisyphus.irc) (class in pysisyphus.irc.EulerPC), [1] 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] eval_B() (in module pysisyphus.intcoords.eval) eval_primitives() (in module pysisyphus.intcoords.eval) every() (in module pysisyphus.trj) expand() (in module pysisyphus.helpers_pure) ExternalPotential (class in pysisyphus.calculators) (class in pysisyphus.calculators.ExternalPotential) eye (pysisyphus.optimizers.BFGS.BFGS property) eyring_rate() (in module pysisyphus.drivers.rates)

F

f0 (pysisyphus.calculators.Dimer property) (pysisyphus.calculators.Dimer.Dimer property), [1], [2] (pysisyphus.intcoords.generate_derivatives.FuncResult attribute) f1 (pysisyphus.calculators.Dimer property) (pysisyphus.calculators.Dimer.Dimer property), [1], [2] (pysisyphus.intcoords.generate_derivatives.FuncResult attribute) f1_bias (pysisyphus.calculators.Dimer property) (pysisyphus.calculators.Dimer.Dimer property), [1], [2] f2 (pysisyphus.calculators.Dimer property) (pysisyphus.calculators.Dimer.Dimer property), [1], [2] (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) fail (pysisyphus.calculators.Calculator.SetPlan attribute), [1] fake_turbo_mos() (pysisyphus.calculators.WFOWrapper.WFOWrapper method) (pysisyphus.calculators.WFOWrapper2.WFOWrapper2 static method) FakeASE (class in pysisyphus.calculators) (class in pysisyphus.calculators.FakeASE), [1] fd_coords3d_gen() (pysisyphus.Geometry.Geometry method), [1] file_or_str() (in module pysisyphus.helpers_pure) filter_fixture_store() (in module pysisyphus.helpers_pure) filter_small_eigvals() (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer method), [1] fin_diff_B() (in module pysisyphus.intcoords.findiffs) fin_diff_prim() (in module pysisyphus.intcoords.findiffs) final_modes (pysisyphus.modefollow.davidson.DavidsonResult attribute) final_summary() (pysisyphus.optimizers.Optimizer.Optimizer method), [1] 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_candidates() (in module pysisyphus.drivers.afir) find_closest_sequence() (in module pysisyphus.helpers_pure) find_dihedrals() (in module pysisyphus.intcoords.setup_fast) find_missing_bonds_by_projection() (in module pysisyphus.intcoords.augment_bonds) find_missing_strong_bonds() (in module pysisyphus.intcoords.augment_bonds) finite_difference_hessian() (in module pysisyphus.linalg) FIRE (class in pysisyphus.optimizers.FIRE) fischer_guess() (in module pysisyphus.optimizers.guess_hessians) fit_grad_and_energies() (pysisyphus.irc.IMKMod method) (pysisyphus.irc.IMKMod.IMKMod method), [1] fit_parabola() (pysisyphus.irc.IMKMod method) (pysisyphus.irc.IMKMod.IMKMod method), [1] fit_rigid() (in module pysisyphus.helpers) (pysisyphus.optimizers.Optimizer.Optimizer method), [1] FitResult (class in pysisyphus.optimizers.poly_fit)

flowchart_update() (in module pysisyphus.optimizers.hessian_updates) fmt_k() (pysisyphus.cos.NEB.NEB method), [1] fn (pysisyphus.db.molecules.Molecule attribute) (pysisyphus.drivers.opt.OptResult attribute) force_num_hessian() (pysisyphus.calculators.Calculator.Calculator method), [1] forces (pysisyphus.calculators.ConicalIntersection.CIQuantities attribute) (pysisyphus.cos.AdaptiveNEB.AdaptiveNEB property), [1] (pysisyphus.cos.ChainOfStates.ChainOfStates property), [1] (pysisyphus.cos.FreezingString.FreezingString property) (pysisyphus.cos.GrowingNT.GrowingNT property) (pysisyphus.cos.GrowingString.GrowingString property), [1] (pysisyphus.cos.NEB.NEB property), [1] (pysisyphus.drivers.afir.AFIRPath attribute) (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.irc.Instanton.Instanton property) (pysisyphus.optimizers.gdiis.DIISResult attribute) forces() (pysisyphus.calculators.Dimer.Gaussian method), [1], [2] forces_fin_diff() (in module pysisyphus.modefollow.davidson) form_A() (in module pysisyphus.drivers.precon_pos_rot) form_coordinate_union() (in module pysisyphus.intcoords.helpers) forward (pysisyphus.irc.IRCDummy.IRCDummy attribute) fourier_rotation() (pysisyphus.calculators.Dimer method) (pysisyphus.calculators.Dimer.Dimer method), [1], [2] FourWellAnaPot (class in pysisyphus.calculators.FourWellAnaPot) frag_sort() (in module pysisyphus.trj) FragmentKick (class in pysisyphus.stocastic) (class in pysisyphus.stocastic.FragmentKick) fragments (pysisyphus.intcoords.setup.CoordInfo attribute) FreeEndNEB (class in pysisyphus.cos.FreeEndNEB), [1] FreeEndNEBPot (class in pysisyphus.calculators.FreeEndNEBPot) freeze_primitives() (pysisyphus.intcoords.DLC method) (pysisyphus.intcoords.DLC.DLC method) FreezingString (class in pysisyphus.cos.FreezingString) from_ (pysisyphus.drivers.rates.ReactionRates attribute) from_coeffs() (in module pysisyphus.optimizers.gdiis) from_h5() (pysisyphus.irc.DWI.DWI static method) from_instanton() (pysisyphus.irc.Instanton.Instanton class method) from_oniom_calculator() (pysisyphus.optimizers.LayerOpt.Layers class method), [1] from_overlap_data() (pysisyphus.calculators.OverlapCalculator.OverlapCalculator static method), [1] from_ts() (pysisyphus.irc.Instanton.Instanton class method) full_expand() (in module pysisyphus.helpers_pure) full_name() (in module pysisyphus.db.helpers) full_string_image_inds (pysisyphus.cos.GrowingString.GrowingString property), [1] fully_grown (pysisyphus.cos.FreezingString.FreezingString property) (pysisyphus.cos.GrowingString.GrowingString property), [1] func() (pysisyphus.plotters.AnimPlot.AnimPlot method) FuncResult (class in pysisyphus.intcoords.generate_derivatives)

G

g (pysisyphus.calculators.ONIOMv2.Link attribute), [1] G() (pysisyphus.calculators.LEPSExpr.LEPSExpr method) G_aq_from_h5_hessian() (in module pysisyphus.drivers.pka) g_new (pysisyphus.line_searches.LineSearch.LineSearchResult attribute) G_vec (pysisyphus.irc.initial_displ.ThirdDerivResult attribute) gamma (pysisyphus.drivers.afir.AFIRPath attribute) Gaussian (class in pysisyphus.calculators.Dimer), [1], [2] (class in pysisyphus.dynamics.Gaussian) Gaussian09 (class in pysisyphus.calculators) (class in pysisyphus.calculators.Gaussian09), [1] Gaussian16 (class in pysisyphus.calculators) (class in pysisyphus.calculators.Gaussian16), [1] gdiis() (in module pysisyphus.optimizers.gdiis) Gdimer() (pysisyphus.calculators.LEPSExpr.LEPSExpr method) gediis() (in module pysisyphus.optimizers.gdiis) gen_solutions() (in module pysisyphus.optimizers.poly_fit) generate_all_dets() (pysisyphus.calculators.WFOWrapper.WFOWrapper method) (pysisyphus.calculators.WFOWrapper2.WFOWrapper2 method) generate_db() (in module pysisyphus.db.generate_db) generate_random_union() (in module pysisyphus.drivers.afir) generate_random_union_ref() (in module pysisyphus.drivers.afir) generate_wilson() (in module pysisyphus.intcoords.generate_derivatives) geom (pysisyphus.drivers.opt.OptResult attribute) 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_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) 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.zmat) geom_from_zmat_str() (in module pysisyphus.io.zmat) geom_is_close_in_energy() (pysisyphus.stocastic.Pipeline.Pipeline method) geom_is_new() (pysisyphus.stocastic.Pipeline.Pipeline method) geom_is_valid() (pysisyphus.stocastic.Pipeline.Pipeline method) 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_similar() (in module pysisyphus.drivers.afir) geom_to_crd_str() (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_from_inline_xyz() (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() (in module pysisyphus.trj) get_active_set() (pysisyphus.intcoords.DLC method) (pysisyphus.intcoords.DLC.DLC method) get_additional_print() (pysisyphus.cos.GrowingNT.GrowingNT method) (pysisyphus.cos.GrowingString.GrowingString method), [1] (pysisyphus.irc.Instanton.Instanton method) (pysisyphus.irc.ModeKill method) (pysisyphus.irc.ModeKill.ModeKill method) get_alpha_step() (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer method), [1] get_atoms_coords() (pysisyphus.calculators.FakeASE method) (pysisyphus.calculators.FakeASE.FakeASE method), [1] get_augmented_hessian() (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer method), [1] get_baker_data() (in module pysisyphus.benchmarks.data) get_baker_ts_data() (in module pysisyphus.benchmarks.data) get_bend_candidates() (in module pysisyphus.intcoords.setup_fast) get_bend_inds() (in module pysisyphus.intcoords.setup) get_beta() (pysisyphus.optimizers.ConjugateGradient.ConjugateGradient method) get_birkholz_rx_data() (in module pysisyphus.benchmarks.data) get_block_str() (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] 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_subgeom() (in module pysisyphus.drivers.replace) 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_calc_closure() (in module pysisyphus.run) get_calculator() (pysisyphus.calculators.PyXTB method) (pysisyphus.calculators.PyXTB.PyXTB method) get_charges() (pysisyphus.calculators.OpenMM.OpenMM method) get_chkfiles() (pysisyphus.calculators.EnergyMin method) (pysisyphus.calculators.EnergyMin.EnergyMin method) (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] get_ci_coeffs_for() (pysisyphus.calculators.OverlapCalculator.OverlapCalculator method), [1] get_ci_quantities() (pysisyphus.calculators.ConicalIntersection method) (pysisyphus.calculators.ConicalIntersection.ConicalIntersection method) get_climbing_forces() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] get_climbing_indices() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] get_clock() (in module pysisyphus.helpers_pure) get_cmd() (in module pysisyphus.config) (pysisyphus.calculators.Calculator.Calculator method), [1] get_colvar() (in module pysisyphus.dynamics.colvars) 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_conv_fact() (pysisyphus.irc.IRC.IRC method), [1] get_convergence() (pysisyphus.optimizers.Optimizer.ConvInfo method), [1] get_coords3d_and_indices_ext() (pysisyphus.intcoords.DummyImproper static method) (pysisyphus.intcoords.DummyTorsion static method) (pysisyphus.intcoords.DummyTorsion.DummyTorsion static method) get_coords_diffs() (in module pysisyphus.helpers) get_cosmo_data_groups() (in module pysisyphus.calculators.Turbomole), [1] get_cubic_crystal() (in module pysisyphus.helpers_pure) get_cur_param_density() (pysisyphus.cos.GrowingString.GrowingString method), [1] get_curv_vec() (in module pysisyphus.irc.initial_displ) get_dask_client() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] get_data_model() (in module pysisyphus.calculators.AFIR), [1] (in module pysisyphus.calculators.OverlapCalculator), [1] (in module pysisyphus.dynamics.driver) (in module pysisyphus.optimizers.Optimizer), [1] get_defaults() (in module pysisyphus.run) get_dihedral_inds() (in module pysisyphus.intcoords.setup) get_dimer() (pysisyphus.calculators.LEPSExpr.LEPSExpr method) get_dipole_moment() (pysisyphus.calculators.OpenMM.OpenMM method) get_dispersion() (pysisyphus.calculators.DFTD4 method) get_dist_func() (in module pysisyphus.intcoords.PrimTypes) get_embedding_charges() (in module pysisyphus.calculators.ONIOMv2), [1] get_en_conv() (in module pysisyphus.plot) get_endpoint_and_ts_geoms() (pysisyphus.irc.IRC.IRC method), [1] get_energy() (pysisyphus.calculators.AFIR method) (pysisyphus.calculators.AFIR.AFIR method), [1] (pysisyphus.calculators.AnaPot2.AnaPot2_ method) (pysisyphus.calculators.AnaPotBase.AnaPotBase method), [1] (pysisyphus.calculators.Calculator.Calculator method), [1] (pysisyphus.calculators.CFOUR method) (pysisyphus.calculators.CFOUR.CFOUR method) (pysisyphus.calculators.Composite method) (pysisyphus.calculators.Composite.Composite method) (pysisyphus.calculators.ConicalIntersection method) (pysisyphus.calculators.ConicalIntersection.ConicalIntersection method) (pysisyphus.calculators.Dalton.Dalton method), [1] (pysisyphus.calculators.DFTBp method) (pysisyphus.calculators.DFTBp.DFTBp method), [1] (pysisyphus.calculators.DFTD4 method) (pysisyphus.calculators.Dummy method) (pysisyphus.calculators.Dummy.Dummy method) (pysisyphus.calculators.EGO method) (pysisyphus.calculators.EGO.EGO method) (pysisyphus.calculators.EnergyMin method) (pysisyphus.calculators.EnergyMin.EnergyMin method) (pysisyphus.calculators.ExternalPotential method) (pysisyphus.calculators.ExternalPotential.ExternalPotential method) (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] (pysisyphus.calculators.IPIServer method) (pysisyphus.calculators.IPIServer.IPIServer method) (pysisyphus.calculators.LennardJones method) (pysisyphus.calculators.LennardJones.LennardJones method), [1] (pysisyphus.calculators.MOPAC method) (pysisyphus.calculators.MOPAC.MOPAC method), [1] (pysisyphus.calculators.OBabel method) (pysisyphus.calculators.OBabel.OBabel method), [1] (pysisyphus.calculators.ONIOM method) (pysisyphus.calculators.ONIOMv2.LayerCalc method), [1] (pysisyphus.calculators.ONIOMv2.Model method), [1] (pysisyphus.calculators.ONIOMv2.ModelDummyCalc method), [1] (pysisyphus.calculators.ONIOMv2.ONIOM method), [1] (pysisyphus.calculators.OpenMM.OpenMM method) (pysisyphus.calculators.OpenMolcas method) (pysisyphus.calculators.OpenMolcas.OpenMolcas method), [1] (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] (pysisyphus.calculators.Psi4 method) (pysisyphus.calculators.Psi4.Psi4 method), [1] (pysisyphus.calculators.PyXTB method) (pysisyphus.calculators.PyXTB.PyXTB method) (pysisyphus.calculators.Remote method) (pysisyphus.calculators.Remote.Remote method) (pysisyphus.calculators.SocketCalc.SocketCalc method) (pysisyphus.calculators.TIP3P method) (pysisyphus.calculators.TIP3P.TIP3P method), [1] (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB 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_exc_ens_fosc() (in module pysisyphus.calculators.ORCA), [1] get_excited_state_str() (pysisyphus.calculators.DFTBp static method) (pysisyphus.calculators.DFTBp.DFTBp static method), [1] get_expr() (pysisyphus.calculators.LEPSExpr.LEPSExpr method) get_fchk_str() (pysisyphus.calculators.Psi4 method) (pysisyphus.calculators.Psi4.Psi4 method), [1] get_fg() (pysisyphus.line_searches.LineSearch.LineSearch method) get_fh_logger() (in module pysisyphus.init_logging) get_final_energy() (pysisyphus.calculators.Composite method) (pysisyphus.calculators.Composite.Composite method) get_fixed_indices() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] get_fmts() (in module pysisyphus.socket_helper) get_force_unit() (in module pysisyphus.plot) get_forces() (pysisyphus.calculators.AFIR method) (pysisyphus.calculators.AFIR.AFIR method), [1] (pysisyphus.calculators.AnaPotBase.AnaPotBase method), [1] (pysisyphus.calculators.AtomAtomTransTorque method) (pysisyphus.calculators.AtomAtomTransTorque.AtomAtomTransTorque method) (pysisyphus.calculators.Calculator.Calculator method), [1] (pysisyphus.calculators.CFOUR method) (pysisyphus.calculators.CFOUR.CFOUR method) (pysisyphus.calculators.Composite method) (pysisyphus.calculators.Composite.Composite method) (pysisyphus.calculators.ConicalIntersection method) (pysisyphus.calculators.ConicalIntersection.ConicalIntersection method) (pysisyphus.calculators.Dalton.Dalton method), [1] (pysisyphus.calculators.DFTBp method) (pysisyphus.calculators.DFTBp.DFTBp method), [1] (pysisyphus.calculators.DFTD4 method) (pysisyphus.calculators.Dimer method) (pysisyphus.calculators.Dimer.Dimer method), [1], [2] (pysisyphus.calculators.Dummy method) (pysisyphus.calculators.Dummy.Dummy method) (pysisyphus.calculators.EGO method) (pysisyphus.calculators.EGO.EGO method) (pysisyphus.calculators.EnergyMin method) (pysisyphus.calculators.EnergyMin.EnergyMin method) (pysisyphus.calculators.ExternalPotential method) (pysisyphus.calculators.ExternalPotential.ExternalPotential method) (pysisyphus.calculators.FakeASE method) (pysisyphus.calculators.FakeASE.FakeASE method), [1] (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] (pysisyphus.calculators.HardSphere method) (pysisyphus.calculators.HardSphere.HardSphere method) (pysisyphus.calculators.HardSphere.PWHardSphere method) (pysisyphus.calculators.IDPPCalculator.IDPPCalculator method) (pysisyphus.calculators.IPIServer method) (pysisyphus.calculators.IPIServer.IPIServer method) (pysisyphus.calculators.LennardJones method) (pysisyphus.calculators.LennardJones.LennardJones method), [1] (pysisyphus.calculators.MOPAC method) (pysisyphus.calculators.MOPAC.MOPAC method), [1] (pysisyphus.calculators.OBabel method) (pysisyphus.calculators.OBabel.OBabel method), [1] (pysisyphus.calculators.ONIOM method) (pysisyphus.calculators.ONIOMv2.LayerCalc method), [1] (pysisyphus.calculators.ONIOMv2.Model method), [1] (pysisyphus.calculators.ONIOMv2.ModelDummyCalc method), [1] (pysisyphus.calculators.ONIOMv2.ONIOM method), [1] (pysisyphus.calculators.OpenMM.OpenMM method) (pysisyphus.calculators.OpenMolcas method) (pysisyphus.calculators.OpenMolcas.OpenMolcas method), [1] (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] (pysisyphus.calculators.Psi4 method) (pysisyphus.calculators.Psi4.Psi4 method), [1] (pysisyphus.calculators.PyPsi4 method) (pysisyphus.calculators.PyPsi4.PyPsi4 method) (pysisyphus.calculators.PyXTB method) (pysisyphus.calculators.PyXTB.PyXTB method) (pysisyphus.calculators.Remote method) (pysisyphus.calculators.Remote.Remote method) (pysisyphus.calculators.SocketCalc.SocketCalc method) (pysisyphus.calculators.TIP3P method) (pysisyphus.calculators.TIP3P.TIP3P method), [1] (pysisyphus.calculators.TransTorque method) (pysisyphus.calculators.TransTorque.TransTorque method) (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1]

get_forces_naive() (pysisyphus.calculators.TransTorque method) (pysisyphus.calculators.TransTorque.TransTorque method) get_fourth_coords() (pysisyphus.intcoords.DummyTorsion static method) (pysisyphus.intcoords.DummyTorsion.DummyTorsion static method) get_fragments() (in module pysisyphus.intcoords.setup) (pysisyphus.Geometry.Geometry method), [1] (pysisyphus.stocastic.FragmentKick method) (pysisyphus.stocastic.FragmentKick.FragmentKick method) get_fragments_and_bonds() (in module pysisyphus.drivers.precon_pos_rot) get_from_to_sets() (pysisyphus.calculators.WFOWrapper.WFOWrapper method) get_full_irc_data() (pysisyphus.irc.IRC.IRC method), [1] get_g_value() (in module pysisyphus.calculators.ONIOMv2), [1] get_gaussian_energies() (pysisyphus.calculators.Dimer method) (pysisyphus.calculators.Dimer.Dimer method), [1], [2] get_gaussian_forces() (pysisyphus.calculators.Dimer method) (pysisyphus.calculators.Dimer.Dimer method), [1], [2] get_gen_str() (pysisyphus.calculators.DFTBp static method) (pysisyphus.calculators.DFTBp.DFTBp static method), [1] get_geom() (pysisyphus.calculators.AnaPotBase.AnaPotBase class method), [1] get_geom_getter() (in module pysisyphus.helpers) get_geom_kwargs() (in module pysisyphus.optimizers.LayerOpt), [1] get_geoms() (in module pysisyphus.trj) (pysisyphus.benchmarks.Benchmark.Benchmark method) get_geoms_from_stored_coords() (pysisyphus.calculators.AnaPotBase.AnaPotBase method), [1] get_gs_line() (pysisyphus.calculators.WFOWrapper.WFOWrapper method) get_guess_hessian() (in module pysisyphus.optimizers.guess_hessians) get_h5_group() (in module pysisyphus.io.hdf5) (pysisyphus.calculators.OverlapCalculator.OverlapCalculator method), [1] get_harmonic() (pysisyphus.calculators.LEPSExpr.LEPSExpr method) get_hei_index() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] get_hessian() (pysisyphus.calculators.AFIR method) (pysisyphus.calculators.AFIR.AFIR method), [1] (pysisyphus.calculators.AnaPotBase.AnaPotBase method), [1] (pysisyphus.calculators.Calculator.Calculator method), [1] (pysisyphus.calculators.Composite method) (pysisyphus.calculators.Composite.Composite method) (pysisyphus.calculators.ConicalIntersection method) (pysisyphus.calculators.ConicalIntersection.ConicalIntersection method) (pysisyphus.calculators.Dimer method) (pysisyphus.calculators.Dimer.Dimer method), [1], [2] (pysisyphus.calculators.Dummy method) (pysisyphus.calculators.Dummy.Dummy method) (pysisyphus.calculators.EnergyMin method) (pysisyphus.calculators.EnergyMin.EnergyMin method) (pysisyphus.calculators.ExternalPotential method) (pysisyphus.calculators.ExternalPotential.ExternalPotential method) (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] (pysisyphus.calculators.IPIServer method) (pysisyphus.calculators.IPIServer.IPIServer method) (pysisyphus.calculators.MOPAC method) (pysisyphus.calculators.MOPAC.MOPAC method), [1] (pysisyphus.calculators.ONIOM method) (pysisyphus.calculators.ONIOMv2.LayerCalc method), [1] (pysisyphus.calculators.ONIOMv2.Model method), [1] (pysisyphus.calculators.ONIOMv2.ONIOM method), [1] (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] (pysisyphus.calculators.Psi4 method) (pysisyphus.calculators.Psi4.Psi4 method), [1] (pysisyphus.calculators.Remote method) (pysisyphus.calculators.Remote.Remote method) (pysisyphus.calculators.SocketCalc.SocketCalc method) (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB 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_image_calc_counter_sum() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] get_index_of_typed_prim() (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] get_indices() (pysisyphus.calculators.OverlapCalculator.OverlapCalculator method), [1] get_input() (in module pysisyphus.helpers_pure) get_input_geom() (pysisyphus.stocastic.FragmentKick method) (pysisyphus.stocastic.FragmentKick.FragmentKick method) (pysisyphus.stocastic.Kick method) (pysisyphus.stocastic.Kick.Kick method) (pysisyphus.stocastic.Pipeline.Pipeline method) get_integration_length_func() (pysisyphus.irc.EulerPC method) (pysisyphus.irc.EulerPC.EulerPC method), [1] get_interactively() (in module pysisyphus.trj) get_irc_data() (pysisyphus.irc.IRC.IRC method), [1] get_iteration() (pysisyphus.calculators.WFOWrapper2.WFOWrapper2 method) get_jacobian() (pysisyphus.calculators.ONIOMv2.Model method), [1] get_k() (pysisyphus.irc.RK4 method) (pysisyphus.irc.RK4.RK4 method), [1] get_K_matrix() (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] get_kick() (pysisyphus.stocastic.Kick method) (pysisyphus.stocastic.Kick.Kick method) get_last_calc_cycle() (in module pysisyphus.run) get_layer_calc() (pysisyphus.calculators.ONIOM method) (pysisyphus.calculators.ONIOMv2.ONIOM method), [1] get_lbfgs_step() (pysisyphus.optimizers.LBFGS.LBFGS method), [1] get_leps() (pysisyphus.calculators.LEPSExpr.LEPSExpr method) get_lindh_alpha() (in module pysisyphus.optimizers.guess_hessians) get_lindh_k() (in module pysisyphus.optimizers.precon) get_lindh_precon() (in module pysisyphus.optimizers.precon) get_linear_bend_inds() (in module pysisyphus.intcoords.setup) get_loader() (in module pysisyphus.yaml_mods) 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_mdrestart_str() (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] get_minima() (pysisyphus.calculators.AnaPotBase.AnaPotBase method), [1] get_minimum() (in module pysisyphus.optimizers.poly_fit) get_mo_norms() (pysisyphus.calculators.OverlapCalculator.OverlapCalculator static method), [1] get_model() (pysisyphus.calculators.DFTD4 method) get_mods() (pysisyphus.calculators.EGO method) (pysisyphus.calculators.EGO.EGO method) get_moinp_str() (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] get_molecular_radius() (in module pysisyphus.helpers_pure) get_molecules_levels() (in module pysisyphus.db.helpers) get_mwfn_exc_str() (in module pysisyphus.wrapper.mwfn) get_N_raw_from_hessian() (pysisyphus.calculators.Dimer method) (pysisyphus.calculators.Dimer.Dimer method), [1], [2] get_name() (in module pysisyphus.calculators.ORCA), [1] get_new_image() (pysisyphus.cos.FreezingString.FreezingString method) (pysisyphus.cos.GrowingString.GrowingString method), [1] get_new_image_from_coords() (pysisyphus.cos.GrowingChainOfStates.GrowingChainOfStates method), [1] get_newton_step() (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer static method), [1] get_newton_step_on_trust() (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer method), [1] get_normal_modes() (pysisyphus.Geometry.Geometry method), [1] get_num_hessian() (pysisyphus.calculators.Calculator.Calculator method), [1] get_opt_cls() (in module pysisyphus.optimizers.cls_map) get_opt_kwargs() (in module pysisyphus.optimizers.LayerOpt), [1] get_optimal_bias() (in module pysisyphus.drivers.opt) get_orbital_matrices() (pysisyphus.calculators.OverlapCalculator.OverlapCalculator method), [1] get_origin() (pysisyphus.stocastic.FragmentKick method) (pysisyphus.stocastic.FragmentKick.FragmentKick method) get_P() (in module pysisyphus.calculators.ConicalIntersection) get_pair_covalent_radii() (in module pysisyphus.intcoords.setup) get_pal_env() (pysisyphus.calculators.OpenMolcas method) (pysisyphus.calculators.OpenMolcas.OpenMolcas method), [1] (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] get_parallel_forces() (pysisyphus.cos.NEB.NEB method), [1] get_param() (pysisyphus.irc.ParamPlot.ParamPlot method) get_parser() (in module pysisyphus.io.pdb) get_path() (in module pysisyphus.db.helpers) (pysisyphus.calculators.AnaPotBase.AnaPotBase method), [1] (pysisyphus.cos.GrowingNT.GrowingNT method) get_path_for_fn() (pysisyphus.irc.IRC.IRC method), [1] (pysisyphus.optimizers.Optimizer.Optimizer method), [1] get_perpendicular_forces() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] get_phi_dphi() (pysisyphus.line_searches.LineSearch.LineSearch method) get_potential_energy() (pysisyphus.calculators.ExternalPotential method) (pysisyphus.calculators.ExternalPotential.ExternalPotential method) (pysisyphus.calculators.FakeASE method) (pysisyphus.calculators.FakeASE.FakeASE method), [1] get_potential_forces() (pysisyphus.calculators.ExternalPotential method) (pysisyphus.calculators.ExternalPotential.ExternalPotential method) get_precon_getter() (pysisyphus.optimizers.PreconLBFGS.PreconLBFGS method), [1] get_precon_pos_rot_data() (in module pysisyphus.benchmarks.data) get_prim_internals_by_indices() (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] get_primitives() (in module pysisyphus.intcoords.setup) get_quenched_dneb_forces() (pysisyphus.cos.NEB.NEB method), [1] get_r() (pysisyphus.cos.GrowingNT.GrowingNT static method) get_r0s() (in module pysisyphus.drivers.birkholz) get_random_path() (in module pysisyphus.helpers_pure) get_rates() (in module pysisyphus.drivers.rates) get_rates_for_geoms() (in module pysisyphus.drivers.rates) get_rates_for_hessians() (in module pysisyphus.drivers.rates) get_ratio() (in module pysisyphus.helpers_pure) get_ref_mos() (pysisyphus.calculators.OverlapCalculator.OverlapCalculator method), [1] get_restart_info() (pysisyphus.calculators.Calculator.Calculator method), [1] (pysisyphus.Geometry.Geometry method), [1] (pysisyphus.optimizers.Optimizer.Optimizer method), [1] get_retry_args() (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] get_ricc2_root() (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] get_root() (pysisyphus.calculators.OpenMolcas method) (pysisyphus.calculators.OpenMolcas.OpenMolcas method), [1] get_rot_coord() (in module pysisyphus.intcoords.PrimTypes) get_rot_mat() (in module pysisyphus.drivers.precon_pos_rot) (in module pysisyphus.linalg) get_rot_mat_for_coords() (in module pysisyphus.linalg) get_rs_step() (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer method), [1] get_s22_data() (in module pysisyphus.benchmarks.data) get_saddles() (pysisyphus.calculators.AnaPotBase.AnaPotBase method), [1] get_sao_from_mo_coeffs() (pysisyphus.calculators.OverlapCalculator.OverlapCalculator static method), [1] get_scale_max() (in module pysisyphus.optimizers.restrict_step) get_shifted_step_trans() (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer static method), [1] get_sparse_jacobian() (pysisyphus.calculators.ONIOMv2.Model method), [1] get_sphere_radius() (pysisyphus.Geometry.Geometry method), [1] get_splined_hei() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] get_spring_forces() (pysisyphus.cos.NEB.NEB method), [1] get_stable_wavefunction() (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] get_step() (in module pysisyphus.intcoords.helpers) get_step_func() (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer method), [1] get_steps_to_active_atom_mean() (in module pysisyphus.drivers.precon_pos_rot) get_subgeom() (pysisyphus.Geometry.Geometry method), [1] get_subgeom_without() (pysisyphus.Geometry.Geometry method), [1] get_tangent() (in module pysisyphus.intcoords.helpers) (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] (pysisyphus.cos.FreezingString.FreezingString method) (pysisyphus.cos.GrowingString.GrowingString method), [1] get_tangent_trj_str() (in module pysisyphus.helpers) get_tangents() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] get_tden_overlaps() (pysisyphus.calculators.OverlapCalculator.OverlapCalculator method), [1] 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_differences() (pysisyphus.calculators.OverlapCalculator.OverlapCalculator method), [1] get_tot() (pysisyphus.calculators.LEPSExpr.LEPSExpr method) get_trans_rot_projector() (in module pysisyphus.Geometry), [1] (pysisyphus.Geometry.Geometry method), [1] get_trans_rot_vectors() (in module pysisyphus.Geometry), [1] get_trans_torque_forces() (in module pysisyphus.calculators.TransTorque) get_unique_geometries() (pysisyphus.stocastic.Pipeline.Pipeline method) get_unique_internals() (in module pysisyphus.filtertrj) get_update_mu_reg() (in module pysisyphus.optimizers.closures) get_valid_index_set() (pysisyphus.stocastic.Pipeline.Pipeline method) get_weighted_bond_mode() (in module pysisyphus.intcoords.helpers) get_weighted_bond_mode_getter() (in module pysisyphus.intcoords.helpers) get_which_frag() (in module pysisyphus.drivers.precon_pos_rot) 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) GonzalezSchlegel (class in pysisyphus.irc) (class in pysisyphus.irc.GonzalezSchlegel), [1] got_alpha_phi_dphi() (pysisyphus.line_searches.LineSearch.LineSearch method) GotNoGeometryException gradient (pysisyphus.cos.ChainOfStates.ChainOfStates property), [1] (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.irc.Instanton.Instanton property) (pysisyphus.irc.IRC.IRC property), [1] gradient() (pysisyphus.dynamics.colvars.Colvar method) (pysisyphus.dynamics.Gaussian.Gaussian method) gradient1 (pysisyphus.calculators.ConicalIntersection.CIQuantities attribute) gradient2 (pysisyphus.calculators.ConicalIntersection.CIQuantities attribute) gradient_diff (pysisyphus.calculators.ConicalIntersection.CIQuantities attribute) gradient_mean (pysisyphus.calculators.ConicalIntersection.CIQuantities attribute) gram_schmidt() (in module pysisyphus.linalg) green() (in module pysisyphus.color) grow_image() (pysisyphus.cos.GrowingNT.GrowingNT method) GrowingChainOfStates (class in pysisyphus.cos.GrowingChainOfStates), [1] GrowingNT (class in pysisyphus.cos.GrowingNT) GrowingString (class in pysisyphus.cos.GrowingString), [1]

H

H5_MAP (pysisyphus.calculators.OverlapCalculator.OverlapCalculator attribute), [1] 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) HardSphere (class in pysisyphus.calculators) (class in pysisyphus.calculators.HardSphere) hardsphere_merge() (in module pysisyphus.drivers.merge) (in module pysisyphus.trj) harmonic_tst_rate() (in module pysisyphus.drivers.rates) HarmonicSphere (class in pysisyphus.calculators.ExternalPotential) hash_args() (in module pysisyphus.helpers_pure) hash_arr() (in module pysisyphus.helpers_pure) HDLC (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.DLC)

header (pysisyphus.TableFormatter.TableFormatter property) HEIIsFirstOrLastException hessian (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.irc.Instanton.Instanton property) HessianOptimizer (class in pysisyphus.optimizers.HessianOptimizer), [1] HessKind (class in pysisyphus.calculators.Calculator), [1] highlight_text() (in module pysisyphus.helpers_pure) housekeeping() (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer method), [1] hubbard_derivs (pysisyphus.calculators.DFTBp attribute) (pysisyphus.calculators.DFTBp.DFTBp attribute), [1] 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) IDPP (class in pysisyphus.interpolate.IDPP) IDPPCalculator (class in pysisyphus.calculators.IDPPCalculator) imag_fns (pysisyphus.helpers.FinalHessianResult attribute) imag_frequency (pysisyphus.drivers.rates.ReactionRates attribute) imag_modes_from_geom() (in module pysisyphus.helpers) imag_wavenumber (pysisyphus.drivers.rates.ReactionRates attribute) image_coords (pysisyphus.cos.ChainOfStates.ChainOfStates property), [1] image_inds (pysisyphus.cos.ChainOfStates.ChainOfStates property), [1] (pysisyphus.cos.GrowingString.GrowingString property), [1] IMKMod (class in pysisyphus.irc) (class in pysisyphus.irc.IMKMod), [1] IMPROPER_DIHEDRAL (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) improper_dihedrals (pysisyphus.intcoords.setup.CoordInfo attribute) improved_guess() (in module pysisyphus.optimizers.guess_hessians) increment_fn() (in module pysisyphus.helpers_pure) ind (pysisyphus.calculators.ONIOMv2.Link attribute), [1] 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) index_array_from_overlaps() (in module pysisyphus.helpers) index_strs_for_atoms() (in module pysisyphus.calculators.Turbomole), [1] inds_from_prim_types() (in module pysisyphus.intcoords.update) inertia_tensor (pysisyphus.Geometry.Geometry property), [1] inertia_tensor() (in module pysisyphus.Geometry), [1] init_h5_group() (in module pysisyphus.io.hdf5) (pysisyphus.calculators.AFIR method) (pysisyphus.calculators.AFIR.AFIR method), [1] init_logging() (in module pysisyphus.init_logging) init_logging_base() (in module pysisyphus.init_logging) initial() (pysisyphus.line_searches.HagerZhang method) (pysisyphus.line_searches.HagerZhang.HagerZhang method) initial_displacement() (pysisyphus.irc.IRC.IRC method), [1]

initialize() (pysisyphus.cos.GrowingNT.GrowingNT method) instant_pressure() (pysisyphus.calculators.ExternalPotential.HarmonicSphere method) Instanton (class in pysisyphus.irc.Instanton) 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() (in module pysisyphus.interpolate.helpers) (pysisyphus.interpolate.IDPP.IDPP method) (pysisyphus.interpolate.Interpolator.Interpolator method) (pysisyphus.interpolate.LST.LST method) (pysisyphus.interpolate.Redund.Redund method) (pysisyphus.irc.DWI.DWI method) interpolate_all() (in module pysisyphus.interpolate.helpers) (pysisyphus.interpolate.Interpolator.Interpolator method) interpolate_colors() (in module pysisyphus.helpers_pure) Interpolator (class in pysisyphus.interpolate.Interpolator) 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) ipi_client() (in module pysisyphus.calculators.IPIClient) IPIServer (class in pysisyphus.calculators) (class in pysisyphus.calculators.IPIServer) IRC (class in pysisyphus.irc.IRC), [1] irc (pysisyphus.run.RunResult attribute) irc() (pysisyphus.irc.IRC.IRC method), [1] irc_geom (pysisyphus.run.RunResult attribute) IRCDummy (class in pysisyphus.irc.IRCDummy) is_analytical_2d (pysisyphus.Geometry.Geometry property), [1] is_analytical_2d() (pysisyphus.irc.Instanton.Instanton method) is_converged() (pysisyphus.optimizers.Optimizer.ConvInfo method), [1]

J

J() (pysisyphus.calculators.LEPSExpr.LEPSExpr method) jacobian() (pysisyphus.intcoords.LinearBend method) (pysisyphus.intcoords.LinearBend.LinearBend method) (pysisyphus.intcoords.LinearDisplacement method) (pysisyphus.intcoords.LinearDisplacement.LinearDisplacement method) (pysisyphus.intcoords.Primitive.Primitive method)

jmol() (pysisyphus.Geometry.Geometry method), [1] join_format() (pysisyphus.TableFormatter.TableFormatter method) json_to_results() (in module pysisyphus.helpers_pure)

K

kappa_bell (pysisyphus.drivers.rates.ReactionRates attribute) kappa_eckart (pysisyphus.drivers.rates.ReactionRates attribute) kappa_eyring (pysisyphus.drivers.rates.ReactionRates attribute) kappa_wigner (pysisyphus.drivers.rates.ReactionRates attribute) keep() (pysisyphus.calculators.Calculator.Calculator method), [1] (pysisyphus.calculators.CFOUR method) (pysisyphus.calculators.CFOUR.CFOUR method) KeepKind (class in pysisyphus.calculators.Calculator), [1]

key (pysisyphus.calculators.Calculator.SetPlan attribute), [1] key_is_tsopt() (in module pysisyphus.optimizers.cls_map) Kick (class in pysisyphus.stocastic) (class in pysisyphus.stocastic.Kick) kick_fragment() (pysisyphus.stocastic.FragmentKick method) (pysisyphus.stocastic.FragmentKick.FragmentKick method) kill_dir() (in module pysisyphus.helpers_pure) kinetic_energy_for_temperature() (in module pysisyphus.dynamics.helpers) kinetic_energy_from_velocities() (in module pysisyphus.dynamics.helpers)

L

l_mw (pysisyphus.modefollow.NormalMode property) (pysisyphus.modefollow.NormalMode.NormalMode property) lambdas (pysisyphus.calculators.OverlapCalculator.NTOs attribute), [1] lanczos() (in module pysisyphus.modefollow.lanczos) last_index (pysisyphus.cos.ChainOfStates.ChainOfStates property), [1] last_two_coords (pysisyphus.calculators.WFOWrapper2.WFOWrapper2 property) LATEST (pysisyphus.calculators.Calculator.KeepKind attribute), [1] layer_num (pysisyphus.optimizers.LayerOpt.LayerOpt property), [1] LayerCalc (class in pysisyphus.calculators.ONIOMv2), [1] LayerOpt (class in pysisyphus.optimizers.LayerOpt), [1] Layers (class in pysisyphus.optimizers.LayerOpt), [1] layers (pysisyphus.Geometry.Geometry property), [1] LBFGS (class in pysisyphus.optimizers.LBFGS), [1] lbfgs_closure() (in module pysisyphus.optimizers.closures) lbfgs_step() (pysisyphus.optimizers.MicroOptimizer method) (pysisyphus.optimizers.MicroOptimizer.MicroOptimizer method) left_frontier (pysisyphus.cos.FreezingString.FreezingString property) left_size (pysisyphus.cos.GrowingString.GrowingString property), [1] length_for_bond_order() (in module pysisyphus.drivers.birkholz) LennardJones (class in pysisyphus.calculators) (class in pysisyphus.calculators.LennardJones), [1] LEPSBase (class in pysisyphus.calculators.LEPSBase) LEPSExpr (class in pysisyphus.calculators.LEPSExpr) lf_ind (pysisyphus.cos.GrowingString.GrowingString property), [1] lincs_closure() (in module pysisyphus.dynamics.lincs) lindh_guess() (in module pysisyphus.optimizers.guess_hessians) lindh_style_guess() (in module pysisyphus.optimizers.guess_hessians) line() (pysisyphus.TableFormatter.TableFormatter method) 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) Link (class in pysisyphus.calculators.ONIOMv2), [1] list_h5_groups() (in module pysisyphus.plot) listen_for() (pysisyphus.calculators.IPIServer method) (pysisyphus.calculators.IPIServer.IPIServer method) (pysisyphus.calculators.SocketCalc.SocketCalc method)

listen_for_client_atom_num() (pysisyphus.calculators.IPIServer method) (pysisyphus.calculators.IPIServer.IPIServer method) listen_for_energy() (pysisyphus.calculators.IPIServer method) (pysisyphus.calculators.IPIServer.IPIServer method) listen_for_forces() (pysisyphus.calculators.IPIServer method) (pysisyphus.calculators.IPIServer.IPIServer method) listen_for_hessian() (pysisyphus.calculators.IPIServer method) (pysisyphus.calculators.IPIServer.IPIServer method) listen_kinds (pysisyphus.calculators.IPIServer attribute) (pysisyphus.calculators.IPIServer.IPIServer attribute) load_h5() (in module pysisyphus.plot) load_run_dict() (in module pysisyphus.run) log() (in module pysisyphus.helpers_pure) (in module pysisyphus.optimizers.gdiis) (in module pysisyphus.wrapper.mwfn) (pysisyphus.calculators.Calculator.Calculator method), [1] (pysisyphus.calculators.ONIOMv2.Model method), [1] (pysisyphus.calculators.WFOWrapper.WFOWrapper method) (pysisyphus.calculators.WFOWrapper2.WFOWrapper2 method) (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] (pysisyphus.cos.GrowingNT.GrowingNT method) (pysisyphus.intcoords.Primitive.Primitive method) (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] (pysisyphus.irc.IRC.IRC method), [1] (pysisyphus.line_searches.LineSearch.LineSearch method) (pysisyphus.optimizers.MicroOptimizer method) (pysisyphus.optimizers.MicroOptimizer.MicroOptimizer method) (pysisyphus.optimizers.Optimizer.Optimizer method), [1] (pysisyphus.stocastic.Pipeline.Pipeline method) log_dbg() (pysisyphus.intcoords.Primitive.Primitive method) log_fragments() (pysisyphus.calculators.AFIR method) (pysisyphus.calculators.AFIR.AFIR method), [1] log_int_grad_msg() (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] log_negative_eigenvalues() (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer method), [1] log_progress() (in module pysisyphus.irc.Instanton) LogFermi (class in pysisyphus.calculators.ExternalPotential) logger (pysisyphus.calculators.WFOWrapper.WFOWrapper attribute) (pysisyphus.calculators.WFOWrapper2.WFOWrapper2 attribute) (pysisyphus.cos.ChainOfStates.ChainOfStates attribute), [1] (pysisyphus.cos.GrowingNT.GrowingNT attribute) LQA (class in pysisyphus.irc) (class in pysisyphus.irc.LQA), [1] LST (class in pysisyphus.interpolate.LST) lstsqs_with_reference() (in module pysisyphus.drivers.afir)

M

m_sqrt (pysisyphus.irc.IRC.IRC property), [1] main() (in module pysisyphus.run) make_cdd() (in module pysisyphus.wrapper.mwfn) make_conv_dict() (pysisyphus.optimizers.Optimizer.Optimizer method), [1] make_deriv_funcs() (in module pysisyphus.intcoords.generate_derivatives) make_det_string() (pysisyphus.calculators.WFOWrapper.WFOWrapper method) (pysisyphus.calculators.WFOWrapper2.WFOWrapper2 method) make_dets_header() (pysisyphus.calculators.WFOWrapper.WFOWrapper method) (pysisyphus.calculators.WFOWrapper2.WFOWrapper2 method) make_exc_str() (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] make_fchk() (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] make_float_class() (in module pysisyphus.calculators.parser) make_fn() (pysisyphus.calculators.Calculator.Calculator method), [1] make_full_dets_list() (pysisyphus.calculators.WFOWrapper.WFOWrapper method) (pysisyphus.calculators.WFOWrapper2.WFOWrapper2 method) make_gbs_str() (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] make_input() (in module pysisyphus.wrapper.packmol) make_molden() (pysisyphus.calculators.Turbomole static method) (pysisyphus.calculators.Turbomole.Turbomole static method), [1] make_py_func() (in module pysisyphus.intcoords.generate_derivatives) make_sym_mat() (in module pysisyphus.calculators.ORCA), [1] 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) mass_weigh_hessian() (pysisyphus.Geometry.Geometry method), [1] (pysisyphus.irc.IRC.IRC method), [1] masses (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.intcoords.CartesianCoords property) (pysisyphus.intcoords.CartesianCoords.CartesianCoords property) masses_rep (pysisyphus.cos.ChainOfStates.ChainOfStates property), [1] (pysisyphus.Geometry.Geometry property), [1] masses_sqrt (pysisyphus.intcoords.CartesianCoords property) (pysisyphus.intcoords.CartesianCoords.CartesianCoords property) match() (in module pysisyphus.trj) match_geom_atoms() (in module pysisyphus.stocastic.align) match_geoms() (in module pysisyphus.helpers) matched_rmsd() (in module pysisyphus.stocastic.align) matrix_power() (in module pysisyphus.linalg) matrix_types (pysisyphus.calculators.WFOWrapper.WFOWrapper attribute) (pysisyphus.calculators.WFOWrapper2.WFOWrapper2 attribute) max_ang_moms (pysisyphus.calculators.DFTBp attribute) (pysisyphus.calculators.DFTBp.DFTBp attribute), [1] max_force_converged (pysisyphus.optimizers.Optimizer.ConvInfo attribute), [1] max_image_num (pysisyphus.cos.ChainOfStates.ChainOfStates property), [1] (pysisyphus.cos.GrowingChainOfStates.GrowingChainOfStates property), [1] max_step_converged (pysisyphus.optimizers.Optimizer.ConvInfo attribute), [1] md() (in module pysisyphus.dynamics.driver) mdp() (in module pysisyphus.dynamics.mdp) mdp_result (pysisyphus.run.RunResult attribute) MDPResult (in module pysisyphus.dynamics.mdp) MDResult (class in pysisyphus.dynamics.driver) merge_coordinate_definitions() (in module pysisyphus.intcoords.helpers) merge_geoms() (in module pysisyphus.drivers.merge) merge_opt() (in module pysisyphus.drivers.merge) merge_sets() (in module pysisyphus.helpers_pure) merge_with_frozen_geom() (in module pysisyphus.drivers.merge) METHODS (pysisyphus.calculators.MOPAC attribute) (pysisyphus.calculators.MOPAC.MOPAC attribute), [1] micro_step() (pysisyphus.irc.GonzalezSchlegel method) (pysisyphus.irc.GonzalezSchlegel.GonzalezSchlegel method), [1] MicroOptimizer (class in pysisyphus.optimizers) (class in pysisyphus.optimizers.MicroOptimizer) min_width_fmts() (pysisyphus.TableFormatter.TableFormatter method) mm_inv (pysisyphus.Geometry.Geometry property), [1] mm_sqrt_inv (pysisyphus.Geometry.Geometry property), [1] mod_flowchart_update() (in module pysisyphus.optimizers.hessian_updates) mode_inds (pysisyphus.modefollow.davidson.DavidsonResult attribute) ModeKill (class in pysisyphus.irc) (class in pysisyphus.irc.ModeKill) Model (class in pysisyphus.calculators.ONIOMv2), [1] model_iter (pysisyphus.calculators.ONIOM property) (pysisyphus.calculators.ONIOMv2.ONIOM property), [1] model_opt (pysisyphus.optimizers.LayerOpt.LayerOpt property), [1] ModelDummyCalc (class in pysisyphus.calculators.ONIOMv2), [1] 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 pysisyphus.calculators.AFIR, [1] pysisyphus.calculators.AnaPot pysisyphus.calculators.AnaPot2 pysisyphus.calculators.AnaPot3 pysisyphus.calculators.AnaPot4 pysisyphus.calculators.AnaPotBase, [1] pysisyphus.calculators.AnaPotCBM pysisyphus.calculators.AtomAtomTransTorque pysisyphus.calculators.Calculator, [1] pysisyphus.calculators.CerjanMiller pysisyphus.calculators.CFOUR pysisyphus.calculators.Composite pysisyphus.calculators.ConicalIntersection pysisyphus.calculators.Dalton, [1] pysisyphus.calculators.DFTBp, [1] pysisyphus.calculators.DFTD3 pysisyphus.calculators.Dimer, [1], [2] pysisyphus.calculators.Dummy pysisyphus.calculators.EGO pysisyphus.calculators.EnergyMin pysisyphus.calculators.ExternalPotential pysisyphus.calculators.ExternalPotential.ExternalPotential pysisyphus.calculators.ExternalPotential.HarmonicSphere pysisyphus.calculators.ExternalPotential.LogFermi pysisyphus.calculators.ExternalPotential.Restraint pysisyphus.calculators.FakeASE, [1] pysisyphus.calculators.FourWellAnaPot pysisyphus.calculators.FreeEndNEBPot pysisyphus.calculators.Gaussian09, [1] pysisyphus.calculators.Gaussian16, [1] pysisyphus.calculators.HardSphere pysisyphus.calculators.IDPPCalculator pysisyphus.calculators.IPIClient pysisyphus.calculators.IPIServer pysisyphus.calculators.LennardJones, [1] pysisyphus.calculators.LEPSBase pysisyphus.calculators.LEPSExpr pysisyphus.calculators.MOPAC, [1] pysisyphus.calculators.MullerBrownSympyPot pysisyphus.calculators.MultiCalc pysisyphus.calculators.OBabel, [1] pysisyphus.calculators.ONIOMv2, [1] pysisyphus.calculators.OpenMM pysisyphus.calculators.OpenMolcas, [1] pysisyphus.calculators.ORCA, [1] pysisyphus.calculators.ORCA5 pysisyphus.calculators.OverlapCalculator, [1] pysisyphus.calculators.parser pysisyphus.calculators.Psi4, [1] pysisyphus.calculators.PyPsi4 pysisyphus.calculators.PyXTB pysisyphus.calculators.Rastrigin pysisyphus.calculators.Remote pysisyphus.calculators.Rosenbrock pysisyphus.calculators.SocketCalc pysisyphus.calculators.TIP3P, [1] pysisyphus.calculators.TransTorque pysisyphus.calculators.Turbomole, [1] pysisyphus.calculators.WFOWrapper pysisyphus.calculators.WFOWrapper2 pysisyphus.calculators.XTB, [1] pysisyphus.color pysisyphus.config pysisyphus.constants pysisyphus.cos pysisyphus.cos.AdaptiveNEB, [1] pysisyphus.cos.ChainOfStates, [1] pysisyphus.cos.FreeEndNEB, [1] pysisyphus.cos.FreezingString pysisyphus.cos.GrowingChainOfStates, [1] pysisyphus.cos.GrowingNT pysisyphus.cos.GrowingString, [1] pysisyphus.cos.NEB, [1] pysisyphus.cos.SimpleZTS, [1] pysisyphus.db pysisyphus.db.generate_db pysisyphus.db.helpers pysisyphus.db.level pysisyphus.db.molecules pysisyphus.drivers pysisyphus.drivers.afir pysisyphus.drivers.barriers pysisyphus.drivers.birkholz pysisyphus.drivers.merge pysisyphus.drivers.opt pysisyphus.drivers.perf pysisyphus.drivers.pka pysisyphus.drivers.precon_pos_rot pysisyphus.drivers.rates pysisyphus.drivers.replace pysisyphus.drivers.scan pysisyphus.drivers.thermo 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.elem_data pysisyphus.exceptions pysisyphus.filtertrj pysisyphus.Geometry, [1] pysisyphus.helpers pysisyphus.helpers_pure 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.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.mp_derivatives pysisyphus.intcoords.OutOfPlane pysisyphus.intcoords.Primitive pysisyphus.intcoords.PrimTypes pysisyphus.intcoords.RedundantCoords, [1] 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.interpolate pysisyphus.interpolate.helpers pysisyphus.interpolate.IDPP pysisyphus.interpolate.Interpolator pysisyphus.interpolate.LST pysisyphus.interpolate.Redund pysisyphus.io pysisyphus.io.cjson pysisyphus.io.crd pysisyphus.io.hdf5 pysisyphus.io.hessian pysisyphus.io.mol2 pysisyphus.io.molden pysisyphus.io.pdb pysisyphus.io.pubchem pysisyphus.io.sdf pysisyphus.io.xyz pysisyphus.io.zmat pysisyphus.irc pysisyphus.irc.DampedVelocityVerlet, [1] pysisyphus.irc.DWI pysisyphus.irc.Euler, [1] pysisyphus.irc.EulerPC, [1] pysisyphus.irc.GonzalezSchlegel, [1] pysisyphus.irc.IMKMod, [1] pysisyphus.irc.initial_displ pysisyphus.irc.Instanton pysisyphus.irc.IRC, [1] pysisyphus.irc.IRCDummy pysisyphus.irc.LQA, [1] pysisyphus.irc.ModeKill pysisyphus.irc.ParamPlot pysisyphus.irc.RK4, [1] pysisyphus.linalg pysisyphus.line_searches pysisyphus.line_searches.Backtracking pysisyphus.line_searches.HagerZhang pysisyphus.line_searches.interpol pysisyphus.line_searches.LineSearch pysisyphus.line_searches.StrongWolfe pysisyphus.modefollow pysisyphus.modefollow.davidson pysisyphus.modefollow.lanczos pysisyphus.modefollow.NormalMode pysisyphus.optimizers pysisyphus.optimizers.BacktrackingOptimizer pysisyphus.optimizers.BFGS pysisyphus.optimizers.closures pysisyphus.optimizers.cls_map pysisyphus.optimizers.ConjugateGradient pysisyphus.optimizers.CubicNewton pysisyphus.optimizers.exceptions pysisyphus.optimizers.FIRE pysisyphus.optimizers.gdiis pysisyphus.optimizers.guess_hessians pysisyphus.optimizers.hessian_updates pysisyphus.optimizers.HessianOptimizer, [1] pysisyphus.optimizers.LayerOpt, [1] pysisyphus.optimizers.LBFGS, [1] pysisyphus.optimizers.MicroOptimizer pysisyphus.optimizers.NCOptimizer pysisyphus.optimizers.Optimizer, [1] pysisyphus.optimizers.poly_fit pysisyphus.optimizers.precon pysisyphus.optimizers.PreconLBFGS, [1] pysisyphus.optimizers.PreconSteepestDescent pysisyphus.optimizers.QuickMin pysisyphus.optimizers.restrict_step pysisyphus.optimizers.RFOptimizer, [1] pysisyphus.optimizers.RSA pysisyphus.optimizers.StabilizedQNMethod pysisyphus.optimizers.SteepestDescent pysisyphus.optimizers.StringOptimizer pysisyphus.pack pysisyphus.peakdetect pysisyphus.plot pysisyphus.plotters pysisyphus.plotters.AnimPlot pysisyphus.run pysisyphus.socket_helper pysisyphus.stocastic pysisyphus.stocastic.align pysisyphus.stocastic.FragmentKick pysisyphus.stocastic.Kick pysisyphus.stocastic.Pipeline pysisyphus.TableFormatter pysisyphus.TablePrinter pysisyphus.testing pysisyphus.tests pysisyphus.thermo pysisyphus.trj pysisyphus.tsoptimizers pysisyphus.tsoptimizers.RSIRFOptimizer, [1] pysisyphus.tsoptimizers.RSPRFOptimizer, [1] pysisyphus.tsoptimizers.TRIM, [1] pysisyphus.tsoptimizers.TSHessianOptimizer, [1] pysisyphus.version pysisyphus.wrapper pysisyphus.wrapper.jmol pysisyphus.wrapper.mwfn pysisyphus.wrapper.packmol pysisyphus.xyzloader pysisyphus.yaml_mods

module_available() (in module pysisyphus.testing) molecular_volume() (in module pysisyphus.helpers_pure) Molecule (class in pysisyphus.db.molecules) MOPAC (class in pysisyphus.calculators) (class in pysisyphus.calculators.MOPAC), [1] moving_atoms (pysisyphus.Geometry.Geometry property), [1] moving_atoms_jmol() (pysisyphus.Geometry.Geometry method), [1] moving_images (pysisyphus.cos.ChainOfStates.ChainOfStates property), [1] moving_indices (pysisyphus.cos.ChainOfStates.ChainOfStates property), [1] MullerBrownPot (class in pysisyphus.calculators.MullerBrownSympyPot) mult (pysisyphus.calculators.AFIR property) (pysisyphus.calculators.AFIR.AFIR property), [1] (pysisyphus.calculators.ONIOM property) (pysisyphus.calculators.ONIOMv2.LayerCalc property), [1] (pysisyphus.calculators.ONIOMv2.ONIOM property), [1] (pysisyphus.db.molecules.Molecule attribute) (pysisyphus.drivers.afir.AFIRPath attribute) MULT_STRS (pysisyphus.calculators.MOPAC attribute) (pysisyphus.calculators.MOPAC.MOPAC attribute), [1] multi_component_sym_mat() (in module pysisyphus.linalg) MultiCalc (class in pysisyphus.calculators) (class in pysisyphus.calculators.MultiCalc) mw_coords (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.irc.IRC.IRC property), [1] mw_grad_to_acc() (pysisyphus.irc.DampedVelocityVerlet method) (pysisyphus.irc.DampedVelocityVerlet.DampedVelocityVerlet method), [1] mw_gradient (pysisyphus.Geometry.Geometry property), [1] (pysisyphus.irc.IRC.IRC 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.calculators.Dimer property) (pysisyphus.calculators.Dimer.Dimer property), [1], [2] (pysisyphus.optimizers.gdiis.DIISResult attribute) n_hist (pysisyphus.optimizers.StabilizedQNMethod.StabilizedQNMethod property) name (pysisyphus.calculators.Calculator.Calculator property), [1] (pysisyphus.calculators.Calculator.SetPlan attribute), [1] (pysisyphus.db.molecules.Molecule attribute) NCOptimizer (class in pysisyphus.optimizers.NCOptimizer) NEB (class in pysisyphus.cos.NEB), [1] NeedNewInternalsException neg_eigvals (pysisyphus.helpers.FinalHessianResult attribute) new_node_coords() (pysisyphus.cos.GrowingChainOfStates.GrowingChainOfStates method), [1] nodes_missing (pysisyphus.cos.GrowingString.GrowingString property), [1] NONE (pysisyphus.calculators.Calculator.KeepKind attribute), [1] norm3() (in module pysisyphus.linalg)

norm_inf() (pysisyphus.line_searches.HagerZhang method) (pysisyphus.line_searches.HagerZhang.HagerZhang method) norm_max_rms() (in module pysisyphus.helpers) normalize_prim_input() (in module pysisyphus.intcoords.PrimTypes) normalize_prim_inputs() (in module pysisyphus.intcoords.PrimTypes) normalize_replacements() (in module pysisyphus.drivers.replace) NormalMode (class in pysisyphus.modefollow) (class in pysisyphus.modefollow.NormalMode) np_print() (in module pysisyphus.helpers) NTOs (class in pysisyphus.calculators.OverlapCalculator), [1] ntos (pysisyphus.calculators.OverlapCalculator.NTOs attribute), [1] nuc_charges_for_atoms() (in module pysisyphus.elem_data) NUMERICAL (pysisyphus.calculators.Calculator.HessKind attribute), [1] nus (pysisyphus.helpers.FinalHessianResult attribute) (pysisyphus.modefollow.davidson.DavidsonResult attribute)

O

OBabel (class in pysisyphus.calculators) (class in pysisyphus.calculators.OBabel), [1] on_keypress() (pysisyphus.plotters.AnimPlot.AnimPlot method) ONIOM (class in pysisyphus.calculators) (class in pysisyphus.calculators.ONIOMv2), [1] OpenMM (class in pysisyphus.calculators.OpenMM) OpenMolcas (class in pysisyphus.calculators) (class in pysisyphus.calculators.OpenMolcas), [1] opt (pysisyphus.drivers.opt.OptResult attribute) (pysisyphus.run.RunResult attribute) opt_afir_path() (in module pysisyphus.drivers.afir) opt_davidson() (in module pysisyphus.drivers.opt) opt_geom (pysisyphus.calculators.XTB.OptResult attribute), [1] (pysisyphus.run.RunResult attribute) opt_is_converged (pysisyphus.drivers.afir.AFIRPath attribute) opt_log (pysisyphus.calculators.XTB.OptResult attribute), [1] OptimizationError optimize() (pysisyphus.optimizers.BFGS.BFGS method) (pysisyphus.optimizers.ConjugateGradient.ConjugateGradient method) (pysisyphus.optimizers.CubicNewton method) (pysisyphus.optimizers.CubicNewton.CubicNewton method) (pysisyphus.optimizers.FIRE.FIRE method) (pysisyphus.optimizers.LayerOpt.LayerOpt method), [1] (pysisyphus.optimizers.LBFGS.LBFGS method), [1] (pysisyphus.optimizers.MicroOptimizer method) (pysisyphus.optimizers.MicroOptimizer.MicroOptimizer method) (pysisyphus.optimizers.NCOptimizer.NCOptimizer method) (pysisyphus.optimizers.Optimizer.Optimizer method), [1] (pysisyphus.optimizers.PreconLBFGS.PreconLBFGS method), [1] (pysisyphus.optimizers.QuickMin.QuickMin method) (pysisyphus.optimizers.RFOptimizer.RFOptimizer method), [1] (pysisyphus.optimizers.RSA.RSA method) (pysisyphus.optimizers.StabilizedQNMethod.StabilizedQNMethod method) (pysisyphus.optimizers.SteepestDescent.SteepestDescent method) (pysisyphus.optimizers.StringOptimizer.StringOptimizer method) (pysisyphus.tsoptimizers.RSIRFOptimizer method) (pysisyphus.tsoptimizers.RSIRFOptimizer.RSIRFOptimizer method), [1] (pysisyphus.tsoptimizers.RSPRFOptimizer method) (pysisyphus.tsoptimizers.RSPRFOptimizer.RSPRFOptimizer method), [1] (pysisyphus.tsoptimizers.TRIM method) (pysisyphus.tsoptimizers.TRIM.TRIM method), [1]

Optimizer (class in pysisyphus.optimizers.Optimizer), [1] OptResult (class in pysisyphus.calculators.XTB), [1] (class in pysisyphus.drivers.opt) ORCA (class in pysisyphus.calculators) (class in pysisyphus.calculators.ORCA), [1] ORCA5 (class in pysisyphus.calculators) (class in pysisyphus.calculators.ORCA5) OrderedEnum (class in pysisyphus.helpers_pure) ORG (pysisyphus.calculators.Calculator.HessKind attribute), [1] origin() (in module pysisyphus.trj) orthogonalize_against() (in module pysisyphus.linalg) 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] OverlapCalculator (class in pysisyphus.calculators.OverlapCalculator), [1] OVLP_TYPE_VERBOSE (pysisyphus.calculators.OverlapCalculator.OverlapCalculator attribute), [1]

P

P (pysisyphus.calculators.ConicalIntersection.CIQuantities attribute) (pysisyphus.cos.GrowingNT.GrowingNT property) (pysisyphus.intcoords.RedundantCoords property) (pysisyphus.intcoords.RedundantCoords.RedundantCoords property), [1] (pysisyphus.irc.Instanton.Instanton property) P_bh (pysisyphus.irc.Instanton.Instanton attribute) par_image_calc() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] parallel() (pysisyphus.intcoords.Primitive.Primitive static method) parallel_forces (pysisyphus.cos.NEB.NEB property), [1] ParamPlot (class in pysisyphus.irc.ParamPlot) parent_ind (pysisyphus.calculators.ONIOMv2.Link attribute), [1] parse_635r_dump() (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] parse_all_energies() (pysisyphus.calculators.DFTBp method) (pysisyphus.calculators.DFTBp.DFTBp method), [1] (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] parse_args() (in module pysisyphus.config) (in module pysisyphus.db.generate_db) (in module pysisyphus.drivers.merge) (in module pysisyphus.drivers.replace) (in module pysisyphus.drivers.thermo) (in module pysisyphus.filtertrj) (in module pysisyphus.pack) (in module pysisyphus.plot) (in module pysisyphus.run) (in module pysisyphus.trj) parse_atom_name() (in module pysisyphus.io.pdb) parse_atoms_coords() (pysisyphus.calculators.ORCA static method) (pysisyphus.calculators.ORCA.ORCA static method), [1] parse_cc2_vectors() (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] parse_cfour_energy() (in module pysisyphus.calculators.CFOUR) parse_cfour_gradient() (in module pysisyphus.calculators.CFOUR) parse_charges() (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] (pysisyphus.calculators.ONIOMv2.Model method), [1] (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] parse_charges_from_json() (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] parse_ci_coeffs() (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] parse_cis() (pysisyphus.calculators.ORCA static method) (pysisyphus.calculators.ORCA.ORCA static method), [1] parse_cjson() (in module pysisyphus.io.cjson) parse_coord_line() (in module pysisyphus.io.sdf) parse_double_mol() (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] parse_energies() (pysisyphus.calculators.OpenMolcas method) (pysisyphus.calculators.OpenMolcas.OpenMolcas method), [1] parse_energy() (pysisyphus.calculators.CFOUR method) (pysisyphus.calculators.CFOUR.CFOUR method) (pysisyphus.calculators.DFTBp method) (pysisyphus.calculators.DFTBp.DFTBp method), [1] (pysisyphus.calculators.DFTD3.DFTD3 method) (pysisyphus.calculators.MOPAC method) (pysisyphus.calculators.MOPAC.MOPAC method), [1] (pysisyphus.calculators.OpenMolcas method) (pysisyphus.calculators.OpenMolcas.OpenMolcas method), [1] (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] (pysisyphus.calculators.Psi4 method) (pysisyphus.calculators.Psi4.Psi4 method), [1] (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] parse_energy_from_aux() (pysisyphus.calculators.MOPAC static method) (pysisyphus.calculators.MOPAC.MOPAC static method), [1] parse_engrad() (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] parse_engrad_info() (pysisyphus.calculators.ORCA static method) (pysisyphus.calculators.ORCA.ORCA static method), [1] parse_exc_dat() (pysisyphus.calculators.DFTBp static method) (pysisyphus.calculators.DFTBp.DFTBp static method), [1] parse_fchk() (pysisyphus.calculators.Gaussian16 static method) (pysisyphus.calculators.Gaussian16.Gaussian16 static method), [1] parse_filter() (in module pysisyphus.filtertrj) parse_force() (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] parse_forces() (pysisyphus.calculators.DFTBp method) (pysisyphus.calculators.DFTBp.DFTBp method), [1] parse_gbw() (pysisyphus.calculators.ORCA static method) (pysisyphus.calculators.ORCA.ORCA static method), [1] parse_grad() (pysisyphus.calculators.MOPAC method) (pysisyphus.calculators.MOPAC.MOPAC method), [1] (pysisyphus.calculators.Psi4 method) (pysisyphus.calculators.Psi4.Psi4 method), [1] parse_gradient() (pysisyphus.calculators.CFOUR method) (pysisyphus.calculators.CFOUR.CFOUR method) (pysisyphus.calculators.DFTD3.DFTD3 method) (pysisyphus.calculators.OpenMolcas method) (pysisyphus.calculators.OpenMolcas.OpenMolcas method), [1] (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] parse_gs_energy() (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] parse_hess_file() (pysisyphus.calculators.ORCA static method) (pysisyphus.calculators.ORCA.ORCA static method), [1] parse_hessian() (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] (pysisyphus.calculators.MOPAC method) (pysisyphus.calculators.MOPAC.MOPAC method), [1] (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] (pysisyphus.calculators.Psi4 method) (pysisyphus.calculators.Psi4.Psi4 method), [1] (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] parse_hessian_from_aux() (pysisyphus.calculators.MOPAC static method) (pysisyphus.calculators.MOPAC.MOPAC static method), [1] parse_keyword() (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] parse_log() (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] parse_md() (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] parse_mo() (in module pysisyphus.calculators.DFTBp), [1] (in module pysisyphus.io.molden) parse_mo_numbers() (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] parse_molden_atoms() (in module pysisyphus.io.molden) parse_mos() (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] parse_opt() (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] parse_orca_cis() (in module pysisyphus.calculators.ORCA), [1] parse_orca_gbw() (in module pysisyphus.calculators.ORCA), [1] parse_rassi_track() (pysisyphus.calculators.OpenMolcas method) (pysisyphus.calculators.OpenMolcas.OpenMolcas method), [1] parse_raw_term_func() (in module pysisyphus.dynamics.mdp) parse_raw_term_funcs() (in module pysisyphus.dynamics.mdp) parse_results() (pysisyphus.calculators.Remote method) (pysisyphus.calculators.Remote.Remote method) parse_sdf() (in module pysisyphus.io.sdf) parse_stable() (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] parse_td_vectors() (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] parse_tddft() (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] parse_tddft_tden() (pysisyphus.calculators.Turbomole static method) (pysisyphus.calculators.Turbomole.Turbomole static method), [1] parse_topo() (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] parse_total_energy() (pysisyphus.calculators.DFTBp method) (pysisyphus.calculators.DFTBp.DFTBp method), [1] parse_trj_file() (in module pysisyphus.xyzloader) parse_trj_str() (in module pysisyphus.xyzloader) parse_turbo_ccre0_ascii() (in module pysisyphus.calculators.parser) parse_turbo_exstates() (in module pysisyphus.calculators.parser) parse_turbo_exstates_re() (in module pysisyphus.calculators.parser) parse_turbo_gradient() (in module pysisyphus.calculators.parser) parse_turbo_mos() (in module pysisyphus.calculators.parser) parse_wfoverlap_out() (pysisyphus.calculators.WFOWrapper.WFOWrapper method) (pysisyphus.calculators.WFOWrapper2.WFOWrapper2 method) parse_xplusy() (in module pysisyphus.calculators.DFTBp), [1] parse_xyz_file() (in module pysisyphus.xyzloader) parse_xyz_str() (in module pysisyphus.xyzloader) path_indices (pysisyphus.drivers.afir.AFIRPath attribute) path_length (pysisyphus.irc.Instanton.Instanton 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) perf_results (pysisyphus.run.RunResult attribute) perp_comp() (in module pysisyphus.linalg) perp_component() (pysisyphus.irc.GonzalezSchlegel method) (pysisyphus.irc.GonzalezSchlegel.GonzalezSchlegel method), [1] perpendicular_forces (pysisyphus.cos.ChainOfStates.ChainOfStates property), [1] pick_image_inds() (in module pysisyphus.helpers) Pipeline (class in pysisyphus.stocastic.Pipeline) pivoted_cholesky() (in module pysisyphus.linalg) pivoted_cholesky2() (in module pysisyphus.linalg) plot() (pysisyphus.calculators.AnaPotBase.AnaPotBase method), [1] (pysisyphus.irc.ParamPlot.ParamPlot method) plot3d() (pysisyphus.calculators.AnaPotBase.AnaPotBase method), [1] plot_afir() (in module pysisyphus.plot) plot_all_energies() (in module pysisyphus.plot) plot_coords() (pysisyphus.calculators.AnaPotBase.AnaPotBase method), [1] plot_cos_energies() (in module pysisyphus.plot) plot_cos_forces() (in module pysisyphus.plot) plot_cycle() (in module pysisyphus.plot) plot_eigenvalue_structure() (pysisyphus.calculators.AnaPotBase.AnaPotBase method), [1] plot_gau() (in module pysisyphus.plot) plot_geoms() (pysisyphus.calculators.AnaPotBase.AnaPotBase method), [1] plot_irc() (in module pysisyphus.plot) (pysisyphus.calculators.AnaPotBase.AnaPotBase method), [1] plot_irc_h5() (in module pysisyphus.plot) plot_md() (in module pysisyphus.plot) plot_opt() (in module pysisyphus.plot) (pysisyphus.calculators.AnaPotBase.AnaPotBase method), [1] plot_overlaps() (in module pysisyphus.plot) plot_scan() (in module pysisyphus.plot) plot_trj_energies() (in module pysisyphus.plot) poly_line_search() (in module pysisyphus.optimizers.poly_fit) polys (pysisyphus.optimizers.poly_fit.FitResult attribute) popen() (pysisyphus.calculators.Calculator.Calculator method), [1] postprocess() (pysisyphus.irc.GonzalezSchlegel method) (pysisyphus.irc.GonzalezSchlegel.GonzalezSchlegel method), [1] (pysisyphus.irc.IRC.IRC method), [1] (pysisyphus.irc.ModeKill method) (pysisyphus.irc.ModeKill.ModeKill method) postprocess_opt() (pysisyphus.optimizers.CubicNewton method) (pysisyphus.optimizers.CubicNewton.CubicNewton method) (pysisyphus.optimizers.LayerOpt.LayerOpt method), [1] (pysisyphus.optimizers.LBFGS.LBFGS method), [1] (pysisyphus.optimizers.Optimizer.Optimizer method), [1] (pysisyphus.optimizers.RFOptimizer.RFOptimizer method), [1] precon_getter() (in module pysisyphus.optimizers.precon) precon_pos_rot() (in module pysisyphus.drivers.precon_pos_rot) precondition_gradient() (pysisyphus.optimizers.StabilizedQNMethod.StabilizedQNMethod method) PreconLBFGS (class in pysisyphus.optimizers.PreconLBFGS), [1] PreconSteepestDescent (class in pysisyphus.optimizers.PreconSteepestDescent) preopt_first_geom (pysisyphus.run.RunResult attribute) preopt_last_geom (pysisyphus.run.RunResult attribute) prepare() (pysisyphus.calculators.Calculator.Calculator method), [1] (pysisyphus.calculators.CFOUR method) (pysisyphus.calculators.CFOUR.CFOUR method) (pysisyphus.irc.DampedVelocityVerlet method) (pysisyphus.irc.DampedVelocityVerlet.DampedVelocityVerlet method), [1] (pysisyphus.irc.EulerPC method) (pysisyphus.irc.EulerPC.EulerPC method), [1] (pysisyphus.irc.IRC.IRC method), [1] (pysisyphus.irc.ModeKill method) (pysisyphus.irc.ModeKill.ModeKill method) prepare_add_args() (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] prepare_coords() (pysisyphus.calculators.Calculator.Calculator method), [1] (pysisyphus.calculators.CFOUR method) (pysisyphus.calculators.CFOUR.CFOUR method) (pysisyphus.calculators.MOPAC method) (pysisyphus.calculators.MOPAC.MOPAC method), [1] (pysisyphus.calculators.OpenMolcas method) (pysisyphus.calculators.OpenMolcas.OpenMolcas method), [1] (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] prepare_input() (pysisyphus.calculators.Calculator.Calculator method), [1] (pysisyphus.calculators.CFOUR method) (pysisyphus.calculators.CFOUR.CFOUR method) (pysisyphus.calculators.Dalton.Dalton method), [1] (pysisyphus.calculators.DFTBp method) (pysisyphus.calculators.DFTBp.DFTBp method), [1] (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] (pysisyphus.calculators.MOPAC method) (pysisyphus.calculators.MOPAC.MOPAC method), [1] (pysisyphus.calculators.OpenMolcas method) (pysisyphus.calculators.OpenMolcas.OpenMolcas method), [1] (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] (pysisyphus.calculators.Psi4 method) (pysisyphus.calculators.Psi4.Psi4 method), [1] (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] prepare_line_search() (pysisyphus.line_searches.HagerZhang method) (pysisyphus.line_searches.HagerZhang.HagerZhang method) (pysisyphus.line_searches.LineSearch.LineSearch method) prepare_mc_afir() (in module pysisyphus.drivers.afir) prepare_merge() (in module pysisyphus.drivers.merge) prepare_opt() (pysisyphus.optimizers.BFGS.BFGS method) (pysisyphus.optimizers.ConjugateGradient.ConjugateGradient method) (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer method), [1] (pysisyphus.optimizers.Optimizer.Optimizer method), [1] (pysisyphus.optimizers.PreconLBFGS.PreconLBFGS method), [1] (pysisyphus.optimizers.QuickMin.QuickMin method) (pysisyphus.optimizers.StabilizedQNMethod.StabilizedQNMethod method) (pysisyphus.optimizers.SteepestDescent.SteepestDescent method) (pysisyphus.optimizers.StringOptimizer.StringOptimizer method) (pysisyphus.tsoptimizers.TSHessianOptimizer.TSHessianOptimizer method), [1] prepare_opt_cycle() (pysisyphus.cos.AdaptiveNEB.AdaptiveNEB method), [1] (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] (pysisyphus.cos.GrowingChainOfStates.GrowingChainOfStates method), [1] prepare_overlap_data() (pysisyphus.calculators.DFTBp method) (pysisyphus.calculators.DFTBp.DFTBp method), [1] (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] (pysisyphus.calculators.OverlapCalculator.OverlapCalculator method), [1] (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] prepare_path() (pysisyphus.calculators.Calculator.Calculator method), [1] prepare_pattern() (pysisyphus.calculators.Calculator.Calculator method), [1] prepare_point_charges() (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] prepare_sc_afir() (in module pysisyphus.drivers.afir) prepare_td() (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] prepare_turbo_coords() (pysisyphus.calculators.Calculator.Calculator method), [1] prepare_xyz_string() (pysisyphus.calculators.Calculator.Calculator method), [1] prev_eigvec_max (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer property), [1] prev_eigvec_min (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer property), [1] 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_bibtex() (in module pysisyphus.run) print_capabilities() (pysisyphus.calculators.Calculator.Calculator method), [1] print_fragments() (pysisyphus.stocastic.FragmentKick method) (pysisyphus.stocastic.FragmentKick.FragmentKick method) print_header() (in module pysisyphus.run) (pysisyphus.TablePrinter.TablePrinter method) print_info() (in module pysisyphus.pack) print_internal_vals() (in module pysisyphus.trj) print_internals() (in module pysisyphus.trj) print_opt_progress() (pysisyphus.optimizers.LayerOpt.LayerOpt method), [1] (pysisyphus.optimizers.Optimizer.Optimizer method), [1] print_out_fn() (pysisyphus.calculators.Calculator.Calculator method), [1] print_perf_results() (in module pysisyphus.drivers.perf) print_row() (pysisyphus.TablePrinter.TablePrinter method) print_sep() (pysisyphus.TablePrinter.TablePrinter 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) (pysisyphus.optimizers.Optimizer.Optimizer method), [1] 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) psb_update() (in module pysisyphus.optimizers.hessian_updates) Psi4 (class in pysisyphus.calculators) (class in pysisyphus.calculators.Psi4), [1] PT (in module pysisyphus.intcoords.PrimTypes) PWHardSphere (class in pysisyphus.calculators.HardSphere) PyPsi4 (class in pysisyphus.calculators) (class in pysisyphus.calculators.PyPsi4) pysisyphus module pysisyphus.benchmarks module pysisyphus.benchmarks.Benchmark module pysisyphus.benchmarks.data module pysisyphus.calculators module pysisyphus.calculators.AFIR module, [1] pysisyphus.calculators.AnaPot module pysisyphus.calculators.AnaPot2 module pysisyphus.calculators.AnaPot3 module pysisyphus.calculators.AnaPot4 module pysisyphus.calculators.AnaPotBase module, [1] pysisyphus.calculators.AnaPotCBM module pysisyphus.calculators.AtomAtomTransTorque module pysisyphus.calculators.Calculator module, [1] pysisyphus.calculators.CerjanMiller module pysisyphus.calculators.CFOUR module pysisyphus.calculators.Composite module pysisyphus.calculators.ConicalIntersection module pysisyphus.calculators.Dalton module, [1] pysisyphus.calculators.DFTBp module, [1] pysisyphus.calculators.DFTD3 module pysisyphus.calculators.Dimer module, [1], [2] pysisyphus.calculators.Dummy module pysisyphus.calculators.EGO module pysisyphus.calculators.EnergyMin module pysisyphus.calculators.ExternalPotential module pysisyphus.calculators.ExternalPotential.ExternalPotential module pysisyphus.calculators.ExternalPotential.HarmonicSphere module pysisyphus.calculators.ExternalPotential.LogFermi module pysisyphus.calculators.ExternalPotential.Restraint module pysisyphus.calculators.FakeASE module, [1] pysisyphus.calculators.FourWellAnaPot module pysisyphus.calculators.FreeEndNEBPot module

pysisyphus.calculators.Gaussian09 module, [1] pysisyphus.calculators.Gaussian16 module, [1] pysisyphus.calculators.HardSphere module pysisyphus.calculators.IDPPCalculator module pysisyphus.calculators.IPIClient module pysisyphus.calculators.IPIServer module pysisyphus.calculators.LennardJones module, [1] pysisyphus.calculators.LEPSBase module pysisyphus.calculators.LEPSExpr module pysisyphus.calculators.MOPAC module, [1] pysisyphus.calculators.MullerBrownSympyPot module pysisyphus.calculators.MultiCalc module pysisyphus.calculators.OBabel module, [1] pysisyphus.calculators.ONIOMv2 module, [1] pysisyphus.calculators.OpenMM module pysisyphus.calculators.OpenMolcas module, [1] pysisyphus.calculators.ORCA module, [1] pysisyphus.calculators.ORCA5 module pysisyphus.calculators.OverlapCalculator module, [1] pysisyphus.calculators.parser module pysisyphus.calculators.Psi4 module, [1] pysisyphus.calculators.PyPsi4 module pysisyphus.calculators.PyXTB module pysisyphus.calculators.Rastrigin module pysisyphus.calculators.Remote module pysisyphus.calculators.Rosenbrock module pysisyphus.calculators.SocketCalc module pysisyphus.calculators.TIP3P module, [1] pysisyphus.calculators.TransTorque module pysisyphus.calculators.Turbomole module, [1] pysisyphus.calculators.WFOWrapper module pysisyphus.calculators.WFOWrapper2 module pysisyphus.calculators.XTB module, [1] pysisyphus.color module pysisyphus.config module pysisyphus.constants module pysisyphus.cos module pysisyphus.cos.AdaptiveNEB module, [1] pysisyphus.cos.ChainOfStates module, [1] pysisyphus.cos.FreeEndNEB module, [1] pysisyphus.cos.FreezingString module pysisyphus.cos.GrowingChainOfStates module, [1] pysisyphus.cos.GrowingNT module pysisyphus.cos.GrowingString module, [1] pysisyphus.cos.NEB module, [1] pysisyphus.cos.SimpleZTS module, [1] pysisyphus.db module pysisyphus.db.generate_db module pysisyphus.db.helpers module pysisyphus.db.level module pysisyphus.db.molecules module pysisyphus.drivers module pysisyphus.drivers.afir module pysisyphus.drivers.barriers module pysisyphus.drivers.birkholz module pysisyphus.drivers.merge module pysisyphus.drivers.opt module pysisyphus.drivers.perf module pysisyphus.drivers.pka module pysisyphus.drivers.precon_pos_rot module pysisyphus.drivers.rates module pysisyphus.drivers.replace module pysisyphus.drivers.scan module pysisyphus.drivers.thermo 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.elem_data module pysisyphus.exceptions module pysisyphus.filtertrj module pysisyphus.Geometry module, [1] pysisyphus.helpers module pysisyphus.helpers_pure 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.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.mp_derivatives module pysisyphus.intcoords.OutOfPlane module pysisyphus.intcoords.Primitive module pysisyphus.intcoords.PrimTypes module pysisyphus.intcoords.RedundantCoords module, [1] 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.interpolate module pysisyphus.interpolate.helpers module pysisyphus.interpolate.IDPP module pysisyphus.interpolate.Interpolator module pysisyphus.interpolate.LST module pysisyphus.interpolate.Redund module pysisyphus.io module pysisyphus.io.cjson module pysisyphus.io.crd module pysisyphus.io.hdf5 module pysisyphus.io.hessian module pysisyphus.io.mol2 module pysisyphus.io.molden module pysisyphus.io.pdb module pysisyphus.io.pubchem module pysisyphus.io.sdf module pysisyphus.io.xyz module pysisyphus.io.zmat module pysisyphus.irc module pysisyphus.irc.DampedVelocityVerlet module, [1] pysisyphus.irc.DWI module pysisyphus.irc.Euler module, [1] pysisyphus.irc.EulerPC module, [1] pysisyphus.irc.GonzalezSchlegel module, [1] pysisyphus.irc.IMKMod module, [1] pysisyphus.irc.initial_displ module pysisyphus.irc.Instanton module pysisyphus.irc.IRC module, [1] pysisyphus.irc.IRCDummy module pysisyphus.irc.LQA module, [1] pysisyphus.irc.ModeKill module pysisyphus.irc.ParamPlot module pysisyphus.irc.RK4 module, [1] pysisyphus.linalg 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.modefollow module pysisyphus.modefollow.davidson module pysisyphus.modefollow.lanczos module pysisyphus.modefollow.NormalMode module pysisyphus.optimizers module pysisyphus.optimizers.BacktrackingOptimizer module pysisyphus.optimizers.BFGS module pysisyphus.optimizers.closures module pysisyphus.optimizers.cls_map module pysisyphus.optimizers.ConjugateGradient module pysisyphus.optimizers.CubicNewton module pysisyphus.optimizers.exceptions module pysisyphus.optimizers.FIRE module pysisyphus.optimizers.gdiis module pysisyphus.optimizers.guess_hessians module pysisyphus.optimizers.hessian_updates module pysisyphus.optimizers.HessianOptimizer module, [1] pysisyphus.optimizers.LayerOpt module, [1] pysisyphus.optimizers.LBFGS module, [1] pysisyphus.optimizers.MicroOptimizer module pysisyphus.optimizers.NCOptimizer module pysisyphus.optimizers.Optimizer module, [1] pysisyphus.optimizers.poly_fit module pysisyphus.optimizers.precon module pysisyphus.optimizers.PreconLBFGS module, [1] pysisyphus.optimizers.PreconSteepestDescent module pysisyphus.optimizers.QuickMin module pysisyphus.optimizers.restrict_step module pysisyphus.optimizers.RFOptimizer module, [1] pysisyphus.optimizers.RSA module pysisyphus.optimizers.StabilizedQNMethod module pysisyphus.optimizers.SteepestDescent module pysisyphus.optimizers.StringOptimizer module pysisyphus.pack module pysisyphus.peakdetect module pysisyphus.plot module pysisyphus.plotters module pysisyphus.plotters.AnimPlot module pysisyphus.run module pysisyphus.socket_helper module pysisyphus.stocastic module pysisyphus.stocastic.align module pysisyphus.stocastic.FragmentKick module pysisyphus.stocastic.Kick module pysisyphus.stocastic.Pipeline module pysisyphus.TableFormatter module pysisyphus.TablePrinter module pysisyphus.testing module pysisyphus.tests module pysisyphus.thermo module pysisyphus.trj module pysisyphus.tsoptimizers module pysisyphus.tsoptimizers.RSIRFOptimizer module, [1] pysisyphus.tsoptimizers.RSPRFOptimizer module, [1] pysisyphus.tsoptimizers.TRIM module, [1] pysisyphus.tsoptimizers.TSHessianOptimizer module, [1] pysisyphus.version module pysisyphus.wrapper module pysisyphus.wrapper.jmol module pysisyphus.wrapper.mwfn module pysisyphus.wrapper.packmol module pysisyphus.xyzloader module pysisyphus.yaml_mods module PyXTB (class in pysisyphus.calculators) (class in pysisyphus.calculators.PyXTB)

Q

Q() (pysisyphus.calculators.LEPSExpr.LEPSExpr method) 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) qH (pysisyphus.calculators.TIP3P attribute) (pysisyphus.calculators.TIP3P.TIP3P attribute), [1] qO (pysisyphus.calculators.TIP3P attribute) (pysisyphus.calculators.TIP3P.TIP3P attribute), [1] qs (pysisyphus.modefollow.davidson.DavidsonResult attribute) quadratic_model() (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer static method), [1] quartic_fit() (in module pysisyphus.optimizers.poly_fit) quaternion_to_rot_mat() (in module pysisyphus.linalg) QuickMin (class in pysisyphus.optimizers.QuickMin) quintic_fit() (in module pysisyphus.optimizers.poly_fit)

R

r (pysisyphus.cos.GrowingNT.GrowingNT property) (pysisyphus.io.zmat.ZLine attribute) raise_exception() (pysisyphus.calculators.Dummy method) (pysisyphus.calculators.Dummy.Dummy method) Rastrigin (class in pysisyphus.calculators.Rastrigin) rate_bell (pysisyphus.drivers.rates.ReactionRates attribute) rate_eckart (pysisyphus.drivers.rates.ReactionRates attribute) rate_eyring (pysisyphus.drivers.rates.ReactionRates attribute) rate_wigner (pysisyphus.drivers.rates.ReactionRates attribute) rattle_closure() (in module pysisyphus.dynamics.rattle) ReactionRates (class in pysisyphus.drivers.rates) read_aux() (pysisyphus.calculators.MOPAC method) (pysisyphus.calculators.MOPAC.MOPAC method), [1] read_cfour_geom() (in module pysisyphus.calculators.CFOUR) read_geoms() (in module pysisyphus.trj) reattach() (pysisyphus.calculators.OpenMolcas method) (pysisyphus.calculators.OpenMolcas.OpenMolcas method), [1] (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] RebuiltInternalsException 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) Redund (class in pysisyphus.interpolate.Redund) RedundantCoords (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.RedundantCoords), [1] ref_hessian (pysisyphus.calculators.EGO property) (pysisyphus.calculators.EGO.EGO property) relax_afir_path() (in module pysisyphus.drivers.afir) relaxed_1d_scan() (in module pysisyphus.drivers.scan) relaxed_scan() (in module pysisyphus.drivers.scan) Remote (class in pysisyphus.calculators) (class in pysisyphus.calculators.Remote) remove_com_velocity() (in module pysisyphus.dynamics.helpers) remove_duplicates() (in module pysisyphus.helpers_pure) remove_translation() (pysisyphus.calculators.Dimer method) (pysisyphus.calculators.Dimer.Dimer method), [1], [2] render_cdd_cube() (in module pysisyphus.wrapper.jmol) (pysisyphus.calculators.OverlapCalculator.OverlapCalculator method), [1] render_cdds() (in module pysisyphus.plot) render_data_groups() (in module pysisyphus.calculators.Turbomole), [1] render_geom_and_charges() (in module pysisyphus.wrapper.jmol) render_rx_rates() (in module pysisyphus.drivers.rates) render_xyz() (in module pysisyphus.io.mol2) renorm_mos() (pysisyphus.calculators.OverlapCalculator.OverlapCalculator static method), [1] reparam_cart() (pysisyphus.cos.GrowingString.GrowingString method), [1] reparam_dlc() (pysisyphus.cos.GrowingString.GrowingString method), [1] reparametrize() (pysisyphus.cos.FreezingString.FreezingString method) (pysisyphus.cos.GrowingNT.GrowingNT method) (pysisyphus.cos.GrowingString.GrowingString method), [1] (pysisyphus.cos.SimpleZTS.SimpleZTS method), [1] (pysisyphus.Geometry.Geometry method), [1] replace_atom() (in module pysisyphus.drivers.replace) replace_atoms() (in module pysisyphus.drivers.replace) report_bonds() (pysisyphus.irc.IRC.IRC method), [1] report_charges() (pysisyphus.calculators.OpenMM.OpenMM method) report_conv_thresholds() (pysisyphus.irc.IRC.IRC method), [1] (pysisyphus.optimizers.Optimizer.Optimizer method), [1] report_frags() (in module pysisyphus.drivers.precon_pos_rot) report_frozen_atoms() (in module pysisyphus.helpers_pure) report_isotopes() (in module pysisyphus.helpers_pure) report_mats() (in module pysisyphus.drivers.precon_pos_rot) res_rms (pysisyphus.modefollow.davidson.DavidsonResult attribute) reset() (pysisyphus.optimizers.BacktrackingOptimizer.BacktrackingOptimizer method) (pysisyphus.optimizers.ConjugateGradient.ConjugateGradient method) (pysisyphus.optimizers.FIRE.FIRE method) (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer method), [1] (pysisyphus.optimizers.LBFGS.LBFGS method), [1] (pysisyphus.optimizers.QuickMin.QuickMin method) (pysisyphus.optimizers.StringOptimizer.StringOptimizer method) reset_client_connection() (pysisyphus.calculators.IPIServer method) (pysisyphus.calculators.IPIServer.IPIServer method) reset_constraints() (pysisyphus.intcoords.DLC method) (pysisyphus.intcoords.DLC.DLC method) reset_coords() (pysisyphus.Geometry.Geometry method), [1] reset_geometries() (pysisyphus.cos.GrowingString.GrowingString method), [1] resize_h5_group() (in module pysisyphus.io.hdf5) resname (pysisyphus.db.molecules.Molecule attribute) restart_interpolate() (pysisyphus.interpolate.Redund.Redund method) restore_org_hessian() (pysisyphus.calculators.Calculator.Calculator method), [1] Restraint (class in pysisyphus.calculators.ExternalPotential) restrict_step() (in module pysisyphus.optimizers.restrict_step) restrict_step_components() (pysisyphus.optimizers.StringOptimizer.StringOptimizer method) results (pysisyphus.cos.ChainOfStates.ChainOfStates property), [1] results_to_json() (in module pysisyphus.helpers_pure) retried_listen_for() (pysisyphus.calculators.IPIServer method) (pysisyphus.calculators.IPIServer.IPIServer method) return_inds() (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] reuse_data() (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] rf_ind (pysisyphus.cos.GrowingString.GrowingString property), [1] rfo_dict (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer attribute), [1] rfo_model() (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer static method), [1] RFOptimizer (class in pysisyphus.optimizers.RFOptimizer), [1] rho() (pysisyphus.intcoords.Primitive.Primitive static method) right_frontier (pysisyphus.cos.FreezingString.FreezingString property) right_size (pysisyphus.cos.GrowingString.GrowingString property), [1] rind (pysisyphus.io.zmat.ZLine attribute) RK4 (class in pysisyphus.irc) (class in pysisyphus.irc.RK4), [1] rms() (in module pysisyphus.helpers_pure) (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] rms_force_converged (pysisyphus.optimizers.Optimizer.ConvInfo attribute), [1] rms_step_converged (pysisyphus.optimizers.Optimizer.ConvInfo attribute), [1] RMSD (class in pysisyphus.calculators.ExternalPotential) rmsd() (pysisyphus.Geometry.Geometry method), [1] rmsd_grad() (in module pysisyphus.linalg) ROBUST_TORSION1 (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) ROBUST_TORSION2 (pysisyphus.intcoords.PrimTypes.PrimTypes attribute) RobustTorsion1 (class in pysisyphus.intcoords) RobustTorsion2 (class in pysisyphus.intcoords) rOH (pysisyphus.calculators.TIP3P attribute) (pysisyphus.calculators.TIP3P.TIP3P attribute), [1] root (pysisyphus.tsoptimizers.TSHessianOptimizer.TSHessianOptimizer property), [1] roots (pysisyphus.tsoptimizers.TSHessianOptimizer.TSHessianOptimizer property), [1] Rosenbrock (class in pysisyphus.calculators.Rosenbrock) rot_force (pysisyphus.calculators.Dimer property) (pysisyphus.calculators.Dimer.Dimer property), [1], [2] rot_quaternion() (in module pysisyphus.linalg) rotate() (pysisyphus.Geometry.Geometry method), [1]

rotate_coords1() (pysisyphus.calculators.Dimer method) (pysisyphus.calculators.Dimer.Dimer method), [1], [2] rotate_gradient() (in module pysisyphus.calculators.CFOUR) rotate_inplace() (in module pysisyphus.drivers.precon_pos_rot) 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) 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) RotationConverged, [1], [2] RSA (class in pysisyphus.optimizers.RSA) RSIRFOptimizer (class in pysisyphus.tsoptimizers) (class in pysisyphus.tsoptimizers.RSIRFOptimizer), [1] RSPRFOptimizer (class in pysisyphus.tsoptimizers) (class in pysisyphus.tsoptimizers.RSPRFOptimizer), [1] run() (in module pysisyphus.db.generate_db) (in module pysisyphus.drivers.replace) (in module pysisyphus.filtertrj) (in module pysisyphus.pack) (in module pysisyphus.plot) (in module pysisyphus.run) (in module pysisyphus.TableFormatter) (in module pysisyphus.trj) (pysisyphus.calculators.Calculator.Calculator method), [1] (pysisyphus.drivers.precon_pos_rot.SteepestDescent method) (pysisyphus.irc.IRC.IRC method), [1] (pysisyphus.line_searches.LineSearch.LineSearch method) (pysisyphus.optimizers.MicroOptimizer method) (pysisyphus.optimizers.MicroOptimizer.MicroOptimizer method) (pysisyphus.optimizers.Optimizer.Optimizer method), [1] (pysisyphus.stocastic.Pipeline.Pipeline method) run_afir_path() (in module pysisyphus.drivers.afir) run_afir_paths() (in module pysisyphus.drivers.afir) run_after() (pysisyphus.calculators.Calculator.Calculator method), [1] (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] run_calculation() (pysisyphus.calculators.CFOUR method) (pysisyphus.calculators.CFOUR.CFOUR method) (pysisyphus.calculators.Composite method) (pysisyphus.calculators.Composite.Composite method) (pysisyphus.calculators.DFTBp method) (pysisyphus.calculators.DFTBp.DFTBp method), [1] (pysisyphus.calculators.Dummy method) (pysisyphus.calculators.Dummy.Dummy method) (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] (pysisyphus.calculators.MOPAC method) (pysisyphus.calculators.MOPAC.MOPAC method), [1] (pysisyphus.calculators.MultiCalc method) (pysisyphus.calculators.MultiCalc.MultiCalc method) (pysisyphus.calculators.ONIOM method) (pysisyphus.calculators.ONIOMv2.ONIOM method), [1] (pysisyphus.calculators.OpenMolcas method) (pysisyphus.calculators.OpenMolcas.OpenMolcas method), [1] (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] (pysisyphus.calculators.Psi4 method) (pysisyphus.calculators.Psi4.Psi4 method), [1] (pysisyphus.calculators.Remote method) (pysisyphus.calculators.Remote.Remote method) (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] run_calculations() (in module pysisyphus.run) (pysisyphus.calculators.ONIOM method) (pysisyphus.calculators.ONIOMv2.LayerCalc method), [1] (pysisyphus.calculators.ONIOMv2.ONIOM method), [1] run_cycle() (pysisyphus.stocastic.Kick method) (pysisyphus.stocastic.Kick.Kick method) run_detect_paths() (in module pysisyphus.config) run_double_mol_calculation() (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] run_endopt() (in module pysisyphus.run) run_from_dict() (in module pysisyphus.run) run_geom_opt() (pysisyphus.stocastic.Pipeline.Pipeline method) run_irc() (in module pysisyphus.run) 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_mc_afir_paths() (in module pysisyphus.drivers.afir) run_md() (in module pysisyphus.dynamics.mdp) (in module pysisyphus.run) (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] run_mdp() (in module pysisyphus.run) run_merge() (in module pysisyphus.drivers.merge) run_opt() (in module pysisyphus.drivers.opt) (in module pysisyphus.drivers.replace) (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] run_perf() (in module pysisyphus.drivers.perf) run_precontr() (in module pysisyphus.drivers.precon_pos_rot) run_preopt() (in module pysisyphus.run) run_rwfdump() (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] run_sc_afir_paths() (in module pysisyphus.drivers.afir) run_scan() (in module pysisyphus.run) run_stable() (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] run_stocastic() (in module pysisyphus.run) run_thermo() (in module pysisyphus.drivers.thermo) run_topo() (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] run_tsopt_from_cos() (in module pysisyphus.run) RunResult (class in pysisyphus.run)

S

s (pysisyphus.calculators.EGO property) (pysisyphus.calculators.EGO.EGO property) (pysisyphus.dynamics.Gaussian.Gaussian property) save() (pysisyphus.irc.ParamPlot.ParamPlot method) save_coords() (pysisyphus.irc.ParamPlot.ParamPlot method) save_hessian() (in module pysisyphus.io) (in module pysisyphus.io.hessian) (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer method), [1] save_orca_pc_file() (in module pysisyphus.calculators.ORCA), [1] save_third_deriv() (in module pysisyphus.io) (in module pysisyphus.io.hessian) scale_by_max_step() (in module pysisyphus.optimizers.restrict_step) (pysisyphus.optimizers.Optimizer.Optimizer method), [1] scale_max_element() (pysisyphus.optimizers.PreconLBFGS.PreconLBFGS method), [1] scale_velocities_to_energy() (in module pysisyphus.dynamics.helpers) scale_velocities_to_temperatue() (in module pysisyphus.dynamics.helpers) scan_energies (pysisyphus.run.RunResult attribute) scan_geoms (pysisyphus.run.RunResult attribute) scan_vals (pysisyphus.run.RunResult attribute) scipy_corrector_step() (pysisyphus.irc.EulerPC method) (pysisyphus.irc.EulerPC.EulerPC method), [1] sd_step() (pysisyphus.optimizers.MicroOptimizer method) (pysisyphus.optimizers.MicroOptimizer.MicroOptimizer method) sdf_from_cid() (in module pysisyphus.io.pubchem) secant() (pysisyphus.line_searches.HagerZhang method) (pysisyphus.line_searches.HagerZhang.HagerZhang method) 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 method) (pysisyphus.calculators.AFIR.AFIR method), [1] set_calculator() (pysisyphus.Geometry.Geometry method), [1] set_chkfiles() (pysisyphus.calculators.EnergyMin method) (pysisyphus.calculators.EnergyMin.EnergyMin method) (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] set_climbing_forces() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] set_coord() (pysisyphus.Geometry.Geometry method), [1] set_coords() (pysisyphus.cos.GrowingString.GrowingString method), [1] (pysisyphus.Geometry.Geometry method), [1] set_coords_at() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] set_cross_vec() (pysisyphus.intcoords.Primitive.Primitive method) set_data() (pysisyphus.calculators.WFOWrapper2.WFOWrapper2 method) (pysisyphus.irc.IRC.IRC method), [1] set_from_nested_list() (pysisyphus.calculators.WFOWrapper.WFOWrapper method) (pysisyphus.calculators.WFOWrapper2.WFOWrapper2 method) set_h5_hessian() (pysisyphus.Geometry.Geometry method), [1] set_images() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] set_inds_from_typed_prims() (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] set_mo_coeffs() (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] set_mo_coeffs_in_gbw() (pysisyphus.calculators.ORCA static method) (pysisyphus.calculators.ORCA.ORCA static method), [1] set_N_invs() (pysisyphus.calculators.TransTorque method) (pysisyphus.calculators.TransTorque.TransTorque method) set_N_raw() (pysisyphus.calculators.Dimer method) (pysisyphus.calculators.Dimer.Dimer method), [1], [2] set_new_frontier_nodes() (pysisyphus.cos.FreezingString.FreezingString method) set_new_node() (pysisyphus.cos.GrowingChainOfStates.GrowingChainOfStates method), [1] set_new_trust_radius() (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer method), [1] set_occ_and_mo_nums() (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] set_primitive_indices() (pysisyphus.intcoords.RedundantCoords method) (pysisyphus.intcoords.RedundantCoords.RedundantCoords method), [1] set_restart_info() (pysisyphus.calculators.Calculator.Calculator method), [1] (pysisyphus.Geometry.Geometry method), [1] (pysisyphus.optimizers.Optimizer.Optimizer method), [1] set_results() (pysisyphus.Geometry.Geometry method), [1] set_variable_springs() (pysisyphus.cos.NEB.NEB method), [1] set_vector() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] set_zero_forces_for_fixed_images() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] SetPlan (class in pysisyphus.calculators.Calculator), [1] setup() (pysisyphus.calculators.OBabel method) (pysisyphus.calculators.OBabel.OBabel method), [1] setup_redundant() (in module pysisyphus.intcoords.setup) setup_redundant_from_geom() (in module pysisyphus.intcoords.setup)

setup_run_dict() (in module pysisyphus.run) shake() (in module pysisyphus.trj) shake_coords() (in module pysisyphus.helpers) should_bias_f0 (pysisyphus.calculators.Dimer property) (pysisyphus.calculators.Dimer.Dimer property), [1], [2] should_bias_f1 (pysisyphus.calculators.Dimer property) (pysisyphus.calculators.Dimer.Dimer property), [1], [2] show() (pysisyphus.irc.ParamPlot.ParamPlot method) sigma (pysisyphus.calculators.TIP3P attribute) (pysisyphus.calculators.TIP3P.TIP3P attribute), [1] simple_guess() (in module pysisyphus.optimizers.guess_hessians) simple_peaks() (in module pysisyphus.helpers) SimpleZTS (class in pysisyphus.cos.SimpleZTS), [1] slugify_worker() (in module pysisyphus.helpers) small_lbfgs_closure() (in module pysisyphus.optimizers.closures) SocketCalc (class in pysisyphus.calculators.SocketCalc) solve_rfo() (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer method), [1] sort_by_central() (in module pysisyphus.helpers_pure) sort_by_prim_type() (in module pysisyphus.intcoords.setup) sphere_radius_from_volume() (in module pysisyphus.pack) spline() (pysisyphus.cos.GrowingString.GrowingString method), [1] spline_plot_cycles() (in module pysisyphus.plot) spline_redistribute() (in module pysisyphus.trj) split_xyz_str() (in module pysisyphus.xyzloader) sr1_update() (in module pysisyphus.optimizers.hessian_updates) StabilizedQNMethod (class in pysisyphus.optimizers.StabilizedQNMethod) standard_orientation() (in module pysisyphus.trj) (pysisyphus.Geometry.Geometry method), [1] standard_state_corr() (in module pysisyphus.helpers_pure) standardize_geoms() (in module pysisyphus.trj) statistics() (pysisyphus.calculators.AnaPotBase.AnaPotBase method), [1] SteepestDescent (class in pysisyphus.drivers.precon_pos_rot) (class in pysisyphus.optimizers.SteepestDescent) step (pysisyphus.dynamics.driver.MDResult attribute) step() (pysisyphus.irc.DampedVelocityVerlet method) (pysisyphus.irc.DampedVelocityVerlet.DampedVelocityVerlet method), [1] (pysisyphus.irc.Euler method) (pysisyphus.irc.Euler.Euler method), [1] (pysisyphus.irc.EulerPC method) (pysisyphus.irc.EulerPC.EulerPC method), [1] (pysisyphus.irc.GonzalezSchlegel method) (pysisyphus.irc.GonzalezSchlegel.GonzalezSchlegel method), [1] (pysisyphus.irc.IMKMod method) (pysisyphus.irc.IMKMod.IMKMod method), [1] (pysisyphus.irc.LQA method) (pysisyphus.irc.LQA.LQA method), [1] (pysisyphus.irc.ModeKill method) (pysisyphus.irc.ModeKill.ModeKill method) (pysisyphus.irc.RK4 method) (pysisyphus.irc.RK4.RK4 method), [1] step_along_tangent() (pysisyphus.interpolate.Redund.Redund method) step_and_grad_from_line_search() (pysisyphus.tsoptimizers.TSHessianOptimizer.TSHessianOptimizer method), [1] stocastic (pysisyphus.run.RunResult attribute) store_and_track() (pysisyphus.calculators.DFTBp method) (pysisyphus.calculators.DFTBp.DFTBp method), [1] (pysisyphus.calculators.Gaussian16 method) (pysisyphus.calculators.Gaussian16.Gaussian16 method), [1] (pysisyphus.calculators.ORCA method) (pysisyphus.calculators.ORCA.ORCA method), [1] (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] store_overlap_data() (pysisyphus.calculators.OverlapCalculator.OverlapCalculator method), [1] stored_calculations (pysisyphus.calculators.OverlapCalculator.OverlapCalculator property), [1] Stretch (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.Stretch) string_size (pysisyphus.cos.GrowingString.GrowingString property), [1] StringOptimizer (class in pysisyphus.optimizers.StringOptimizer) 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) sub_control() (pysisyphus.calculators.Turbomole method) (pysisyphus.calculators.Turbomole.Turbomole method), [1] sufficiently_decreased() (pysisyphus.line_searches.LineSearch.LineSearch method) sum_formula (pysisyphus.Geometry.Geometry property), [1] sum_noises() (in module pysisyphus.dynamics.thermostats) surface_area (pysisyphus.calculators.ExternalPotential.HarmonicSphere property) svd_inv() (in module pysisyphus.linalg) swart_guess() (in module pysisyphus.optimizers.guess_hessians) sym_mat_from_tril() (in module pysisyphus.linalg) sym_mat_from_triu() (in module pysisyphus.linalg)

T

T (pysisyphus.dynamics.driver.MDResult attribute) 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) TableFormatter (class in pysisyphus.TableFormatter) TablePrinter (class in pysisyphus.TablePrinter) take_quad_step() (pysisyphus.line_searches.HagerZhang method) (pysisyphus.line_searches.HagerZhang.HagerZhang method) take_step() (pysisyphus.optimizers.MicroOptimizer method) (pysisyphus.optimizers.MicroOptimizer.MicroOptimizer method) taylor() (in module pysisyphus.irc.DWI) taylor_closure() (in module pysisyphus.irc.initial_displ) taylor_grad() (in module pysisyphus.irc.DWI) temperature (pysisyphus.drivers.rates.ReactionRates attribute) 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) timed() (in module pysisyphus.helpers_pure) TIP3P (class in pysisyphus.calculators) (class in pysisyphus.calculators.TIP3P), [1] tmp_xyz_handle() (pysisyphus.Geometry.Geometry method), [1] TMTRIC (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.RedundantCoords), [1] to_float() (in module pysisyphus.calculators.parser) to_sets() (in module pysisyphus.helpers_pure) to_subscript_num() (in module pysisyphus.helpers_pure) Torsion (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.Torsion) Torsion2 (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.Torsion2) total_mass (pysisyphus.Geometry.Geometry property), [1] touch() (in module pysisyphus.helpers_pure) track_root() (pysisyphus.calculators.OverlapCalculator.OverlapCalculator method), [1] 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] translate() (in module pysisyphus.trj) 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_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) TransTorque (class in pysisyphus.calculators) (class in pysisyphus.calculators.TransTorque) TRIC (class in pysisyphus.intcoords) (class in pysisyphus.intcoords.RedundantCoords), [1] TRIM (class in pysisyphus.tsoptimizers) (class in pysisyphus.tsoptimizers.TRIM), [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) ts_geom (pysisyphus.run.RunResult attribute) ts_hessian() (in module pysisyphus.optimizers.guess_hessians) ts_opt (pysisyphus.run.RunResult attribute) TSHessianOptimizer (class in pysisyphus.tsoptimizers.TSHessianOptimizer), [1] tunl() (in module pysisyphus.drivers.rates) Turbomole (class in pysisyphus.calculators) (class in pysisyphus.calculators.Turbomole), [1] type (pysisyphus.optimizers.gdiis.DIISResult attribute) 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.intcoords.DLC property) (pysisyphus.intcoords.DLC.DLC property) unlink() (pysisyphus.calculators.IPIServer method) (pysisyphus.calculators.IPIServer.IPIServer method) unscaled_velocity_distribution() (in module pysisyphus.dynamics.helpers) unweight_mw_hessian() (pysisyphus.Geometry.Geometry method), [1] unweight_vec() (pysisyphus.irc.IRC.IRC method), [1] update() (pysisyphus.irc.DWI.DWI method) update_adapt_thresh() (pysisyphus.cos.AdaptiveNEB.AdaptiveNEB method), [1] update_hessian() (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer method), [1]

update_internals() (in module pysisyphus.intcoords.update) update_mw_down_step() (pysisyphus.irc.ModeKill method) (pysisyphus.irc.ModeKill.ModeKill method) update_orientation() (pysisyphus.calculators.Dimer method) (pysisyphus.calculators.Dimer.Dimer method), [1], [2] update_springs() (pysisyphus.cos.NEB.NEB method), [1] update_trust_radius() (pysisyphus.optimizers.HessianOptimizer.HessianOptimizer method), [1] update_ts_mode() (pysisyphus.tsoptimizers.TSHessianOptimizer.TSHessianOptimizer method), [1] update_y() (in module pysisyphus.calculators.ConicalIntersection) using() (in module pysisyphus.testing)

V

V_dimer() (pysisyphus.calculators.LEPSExpr.LEPSExpr method) V_harmonic() (pysisyphus.calculators.LEPSExpr.LEPSExpr method) V_LEPS() (pysisyphus.calculators.LEPSExpr.LEPSExpr method) V_tot() (pysisyphus.calculators.LEPSExpr.LEPSExpr method) VALID_CDDS (pysisyphus.calculators.OverlapCalculator.OverlapCalculator attribute), [1] valid_coord_types (pysisyphus.cos.ChainOfStates.ChainOfStates attribute), [1] valid_diis_direction() (in module pysisyphus.optimizers.gdiis) valid_displs (pysisyphus.irc.IRC.IRC attribute), [1] VALID_KEYS (pysisyphus.calculators.OverlapCalculator.OverlapCalculator attribute), [1] valid_requests (pysisyphus.calculators.SocketCalc.SocketCalc attribute) valid_updates (pysisyphus.tsoptimizers.TSHessianOptimizer.TSHessianOptimizer attribute), [1] VALID_XY (pysisyphus.calculators.OverlapCalculator.OverlapCalculator attribute), [1]

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) verbose_bond_difference() (in module pysisyphus.intcoords.helpers) verify_chkfiles() (pysisyphus.calculators.Calculator.Calculator method), [1] view_cdd_cube() (in module pysisyphus.wrapper.jmol) volume_for_density() (in module pysisyphus.pack)

W

w (pysisyphus.dynamics.Gaussian.Gaussian property) weight() (pysisyphus.intcoords.Primitive.Primitive method) weight_function() (in module pysisyphus.drivers.afir) wf_overlap() (pysisyphus.calculators.WFOWrapper.WFOWrapper method) (pysisyphus.calculators.WFOWrapper2.WFOWrapper2 method) WFOWrapper (class in pysisyphus.calculators.WFOWrapper) WFOWrapper2 (class in pysisyphus.calculators.WFOWrapper2) wigner_corr() (in module pysisyphus.drivers.rates) without_hydrogens() (pysisyphus.Geometry.Geometry method), [1] wolfe_condition() (pysisyphus.line_searches.LineSearch.LineSearch method)

wrap_stdin() (in module pysisyphus.wrapper.mwfn) write_cycle_to_file() (pysisyphus.optimizers.Optimizer.Optimizer method), [1] write_fragment_geoms() (pysisyphus.calculators.AFIR method) (pysisyphus.calculators.AFIR.AFIR method), [1] write_geoms_to_trj() (in module pysisyphus.xyzloader) (pysisyphus.stocastic.Pipeline.Pipeline method) write_image_trjs() (pysisyphus.optimizers.Optimizer.Optimizer method), [1] write_mdrestart() (pysisyphus.calculators.XTB method) (pysisyphus.calculators.XTB.XTB method), [1] write_results() (pysisyphus.optimizers.Optimizer.Optimizer method), [1] write_to_out_dir() (pysisyphus.optimizers.Optimizer.Optimizer method), [1]

X

x (pysisyphus.calculators.ConicalIntersection.CIQuantities attribute) (pysisyphus.optimizers.poly_fit.FitResult attribute)

XTB (class in pysisyphus.calculators) (class in pysisyphus.calculators.XTB), [1] xtb_hessian() (in module pysisyphus.optimizers.guess_hessians)

Y

y (pysisyphus.calculators.ConicalIntersection.CIQuantities attribute) (pysisyphus.optimizers.poly_fit.FitResult attribute)

Z

zero_crossings() (in module pysisyphus.peakdetect) zero_crossings_sine_fit() (in module pysisyphus.peakdetect) zero_fixed_vector() (pysisyphus.cos.ChainOfStates.ChainOfStates method), [1] 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)