Index

_

__call__() (yaff.analysis.hook.AnalysisHook method) (yaff.pes.generator.D3BJGenerator method) (yaff.pes.generator.DampDispGenerator method) (yaff.pes.generator.ExpRepGenerator method) (yaff.pes.generator.FixedChargeGenerator method) (yaff.pes.generator.Generator method) (yaff.pes.generator.LJGenerator method) (yaff.pes.generator.MM3Generator method) (yaff.pes.generator.ValenceCrossGenerator method) (yaff.pes.generator.ValenceGenerator method) (yaff.pes.parameters.Complain method) (yaff.sampling.io.HDF5Writer method) (yaff.sampling.io.RestartWriter method) (yaff.sampling.io.XYZWriter method) (yaff.sampling.iterative.Hook method) (yaff.sampling.opt.OptScreenLog method) (yaff.sampling.trajectory.TrajScreenLog method) (yaff.sampling.verlet.VerletHook method) (yaff.sampling.verlet.VerletScreenLog method) (yaff.tune.cost.CostFunction method) (yaff.tune.cost.Simulation method) (yaff.tune.cost.Test method) (yaff.tune.transform.ModifierRule method) (yaff.tune.transform.ParameterModifier method) (yaff.tune.transform.ParameterTransform method)

A

add_delta() (yaff.pes.dlist.DeltaList method) add_electrostatic_parts() (yaff.pes.generator.FFArgs method) add_ic() (yaff.pes.iclist.InternalCoordinateList method) add_part() (yaff.pes.ff.ForceField method) add_press_cont() (yaff.sampling.npt.MTKBarostat method) (yaff.sampling.npt.PRBarostat method) (yaff.sampling.npt.TadmorBarostat method) add_term() (yaff.pes.ff.ForcePartValence method) (yaff.pes.vlist.ValenceList method) align_cell() (yaff.system.System method) allow_superposition (yaff.pes.generator.Generator attribute) (yaff.pes.generator.OopAngleGenerator attribute) (yaff.pes.generator.OopCosGenerator attribute) (yaff.pes.generator.OopDistGenerator attribute) (yaff.pes.generator.OopMeanAngleGenerator attribute) (yaff.pes.generator.OopMeanCosGenerator attribute) (yaff.pes.generator.TorsionGenerator attribute)

AnalysisHook (class in yaff.analysis.hook) AnalysisInput (class in yaff.analysis.hook) AndersenThermostat (class in yaff.sampling.nvt) angular_moment() (in module yaff.sampling.utils) AnisoCellDOF (class in yaff.sampling.dof) apply() (yaff.pes.generator.D3BJGenerator method) (yaff.pes.generator.DampDispGenerator method) (yaff.pes.generator.ExpRepGenerator method) (yaff.pes.generator.FixedChargeGenerator method) (yaff.pes.generator.LJGenerator method) (yaff.pes.generator.MM3Generator method) (yaff.pes.generator.ValenceCrossGenerator method) (yaff.pes.generator.ValenceGenerator method) apply_generators() (in module yaff.pes.generator) atsel_compile() (in module yaff.atselect) AttributeStateItem (class in yaff.sampling.iterative)

B

back() (yaff.pes.dlist.DeltaList method) (yaff.pes.iclist.InternalCoordinateList method) (yaff.pes.vlist.ValenceList method) baro() (yaff.sampling.npt.LangevinBarostat method) (yaff.sampling.npt.MTKBarostat method) (yaff.sampling.npt.PRBarostat method) (yaff.sampling.npt.TadmorBarostat method) BaseCellDOF (class in yaff.sampling.dof) BaseOptimizer (class in yaff.sampling.opt) BendAngle (class in yaff.pes.iclist) BendAngleHarmGenerator (class in yaff.pes.generator) BendCos (class in yaff.pes.iclist) BendCosGenerator (class in yaff.pes.generator) BendCosHarmGenerator (class in yaff.pes.generator)

BendGenerator (class in yaff.pes.generator) BendGroup (class in yaff.tune.cost) BerendsenBarostat (class in yaff.sampling.npt) BerendsenThermostat (class in yaff.sampling.nvt) BFGSHessianModel (class in yaff.sampling.opt) blav() (in module yaff.analysis.blav) Bond (class in yaff.pes.iclist) BondDoubleWell (class in yaff.pes.vlist) BondDoubleWell2Generator (class in yaff.pes.generator) BondDoubleWellGenerator (class in yaff.pes.generator) BondFuesGenerator (class in yaff.pes.generator) BondGenerator (class in yaff.pes.generator) BondGroup (class in yaff.tune.cost) BondHarmGenerator (class in yaff.pes.generator) BondMorseGenerator (class in yaff.pes.generator)

C

calc_cov_mat() (in module yaff.analysis.pca) calc_cov_mat_internal() (in module yaff.analysis.pca) calc_pca() (in module yaff.analysis.pca) call_hooks() (yaff.sampling.iterative.Iterative method) call_verlet_hooks() (yaff.sampling.verlet.VerletIntegrator method) CartesianDOF (class in yaff.sampling.dof) cell_symmetrize() (in module yaff.sampling.utils) CellStateItem (class in yaff.sampling.iterative) CGOptimizer (class in yaff.sampling.opt) Chebychev1 (class in yaff.pes.vlist) Chebychev2 (class in yaff.pes.vlist) Chebychev3 (class in yaff.pes.vlist) Chebychev4 (class in yaff.pes.vlist) Chebychev6 (class in yaff.pes.vlist) check() (yaff.pes.nlist.NeighborList method) check_convergence() (yaff.sampling.dof.BaseCellDOF method) (yaff.sampling.dof.CartesianDOF method) check_delta() (yaff.sampling.dof.DOF method) check_mic() (yaff.pes.scaling.Scalings method) check_name() (in module yaff.atselect) check_suffixes() (yaff.pes.generator.Generator method) check_trajectory_rows() (in module yaff.conversion.common) clean_momenta() (in module yaff.sampling.utils) clear() (yaff.pes.ff.ForcePart method) Complain (class in yaff.pes.parameters) compute() (yaff.pes.ff.ForcePart method) compute_derived() (yaff.analysis.diffusion.Diffusion method) (yaff.analysis.hook.AnalysisHook method) (yaff.analysis.rdf.RDF method) (yaff.analysis.spectrum.Spectrum method) compute_error() (yaff.tune.cost.FCTest method) (yaff.tune.cost.ICTest method) (yaff.tune.cost.Test method)

compute_fc() (yaff.tune.cost.FCTest method) compute_ic() (yaff.tune.cost.ICGroup method) compute_iteration() (yaff.analysis.diffusion.Diffusion method) (yaff.analysis.hook.AnalysisHook method) (yaff.analysis.rdf.RDF method) (yaff.analysis.spectrum.Spectrum method) compute_offline() (yaff.analysis.hook.AnalysisHook method) compute_properties() (yaff.sampling.verlet.VerletIntegrator method) compute_tangent() (yaff.tune.cost.ICGroup method) configure_offline() (yaff.analysis.diffusion.Diffusion method) (yaff.analysis.hook.AnalysisHook method) (yaff.analysis.rdf.RDF method) (yaff.analysis.spectrum.Spectrum method) configure_online() (yaff.analysis.diffusion.Diffusion method) (yaff.analysis.hook.AnalysisHook method) (yaff.analysis.rdf.RDF method) (yaff.analysis.spectrum.Spectrum method) ConsErrTracker (class in yaff.sampling.verlet) copy() (yaff.pes.parameters.ParameterDefinition method) (yaff.pes.parameters.ParameterSection method) (yaff.pes.parameters.Parameters method) (yaff.sampling.iterative.AttributeStateItem method) (yaff.sampling.iterative.StateItem method) (yaff.sampling.npt.MTKAttributeStateItem method) (yaff.sampling.nvt.NHCAttributeStateItem method) Cosine (class in yaff.pes.vlist) CostFunction (class in yaff.tune.cost) cp2k_ener_to_hdf5() (in module yaff.conversion.cp2k) cpar_info (yaff.pes.generator.DampDispGenerator attribute) Cross (class in yaff.pes.vlist) CrossGenerator (class in yaff.pes.generator) CSVRThermostat (class in yaff.sampling.nvt) cut_bonds() (yaff.system.System method)

D

D3BJGenerator (class in yaff.pes.generator) DampDispGenerator (class in yaff.pes.generator) default_state (yaff.sampling.iterative.Iterative attribute) (yaff.sampling.opt.BaseOptimizer attribute) (yaff.sampling.trajectory.RefTrajectory attribute) (yaff.sampling.verlet.VerletIntegrator attribute) DeltaList (class in yaff.pes.dlist) detect_bonds() (yaff.system.System method) detect_ffatypes() (yaff.system.System method)

Diffusion (class in yaff.analysis.diffusion) DihedAngle (class in yaff.pes.iclist) DihedCos (class in yaff.pes.iclist) DipoleStateItem (class in yaff.sampling.iterative) DipoleVelStateItem (class in yaff.sampling.iterative) dlpoly_history_to_hdf5() (in module yaff.conversion.dlpoly) DOF (class in yaff.sampling.dof) dump_restart() (yaff.sampling.io.RestartWriter method) dump_system() (yaff.sampling.io.HDF5Writer method) (yaff.sampling.io.RestartWriter method)

E

EpotBendsStateItem (class in yaff.sampling.iterative) EpotBondsStateItem (class in yaff.sampling.iterative) EPotContribStateItem (class in yaff.sampling.iterative) EpotDihedsStateItem (class in yaff.sampling.iterative) estimate_cart_hessian() (in module yaff.sampling.harmonic)

estimate_elastic() (in module yaff.sampling.harmonic) estimate_hessian() (in module yaff.sampling.harmonic) expects_call() (yaff.sampling.iterative.Hook method) expectscall() (yaff.sampling.npt.TBCombination method) ExpRepGenerator (class in yaff.pes.generator)

F

FCTest (class in yaff.tune.cost) FFArgs (class in yaff.pes.generator) filter_results() (yaff.tune.cost.Test method) finalize() (yaff.sampling.iterative.Iterative method) (yaff.sampling.opt.BaseOptimizer method) (yaff.sampling.trajectory.RefTrajectory method) (yaff.sampling.verlet.VerletIntegrator method) find_first() (in module yaff.atselect) FixedBCDOF (class in yaff.sampling.dof) FixedChargeGenerator (class in yaff.pes.generator) FixedVolOrthoCellDOF (class in yaff.sampling.dof) ForceField (class in yaff.pes.ff) ForcePart (class in yaff.pes.ff) ForcePartEwaldCorrection (class in yaff.pes.ff) ForcePartEwaldCorrectionDD (class in yaff.pes.ff) ForcePartEwaldNeutralizing (class in yaff.pes.ff)

ForcePartEwaldReciprocal (class in yaff.pes.ff) ForcePartEwaldReciprocalDD (class in yaff.pes.ff) ForcePartGrid (class in yaff.pes.ff) ForcePartPair (class in yaff.pes.ff) ForcePartPressure (class in yaff.pes.ff) ForcePartValence (class in yaff.pes.ff) forward() (yaff.pes.dlist.DeltaList method) (yaff.pes.iclist.InternalCoordinateList method) (yaff.pes.vlist.ValenceList method) from_file() (yaff.pes.parameters.Parameters class method) (yaff.system.System class method) from_hdf5() (yaff.system.System class method) Fues (class in yaff.pes.vlist) FullCellDOF (class in yaff.sampling.dof) fun() (yaff.sampling.dof.BaseCellDOF method) (yaff.sampling.dof.CartesianDOF method) (yaff.sampling.opt.BaseOptimizer method)

G

g09log_to_hdf5() (in module yaff.conversion.gaussian) generate() (yaff.pes.ff.ForceField class method) Generator (class in yaff.pes.generator) GeoOptHessianSimulation (class in yaff.tune.cost) GeoOptSimulation (class in yaff.tune.cost) get() (yaff.sampling.verlet.ConsErrTracker method) get_conversion() (yaff.pes.iclist.BendAngle method) (yaff.pes.iclist.BendCos method) (yaff.pes.iclist.Bond method) (yaff.pes.iclist.DihedAngle method) (yaff.pes.iclist.DihedCos method) (yaff.pes.iclist.InternalCoordinate method) (yaff.pes.iclist.OopAngle method) (yaff.pes.iclist.OopCos method) (yaff.pes.iclist.OopDist method) (yaff.pes.iclist.OopMeanAngle method) (yaff.pes.iclist.OopMeanCos method) (yaff.pes.iclist.UreyBradley method) get_ffatype() (yaff.system.System method) get_ic_indexes() (yaff.pes.vlist.ValenceTerm method) get_indexes() (yaff.system.System method) get_indexes0() (yaff.pes.generator.CrossGenerator method) (yaff.pes.generator.ValenceCrossGenerator method) get_indexes1() (yaff.pes.generator.CrossGenerator method) (yaff.pes.generator.ValenceCrossGenerator method) get_indexes2() (yaff.pes.generator.CrossGenerator method) (yaff.pes.generator.ValenceCrossGenerator method) get_init() (yaff.tune.transform.IncrementRule method) (yaff.tune.transform.ModifierRule method) (yaff.tune.transform.ParameterModifier method) (yaff.tune.transform.ParameterTransform method) (yaff.tune.transform.ScaleRule method) get_last_trajectory_row() (in module yaff.conversion.common) get_log() (yaff.pes.iclist.InternalCoordinate method) (yaff.pes.vlist.BondDoubleWell method) (yaff.pes.vlist.Chebychev1 method) (yaff.pes.vlist.Chebychev2 method) (yaff.pes.vlist.Chebychev3 method) (yaff.pes.vlist.Chebychev4 method) (yaff.pes.vlist.Chebychev6 method) (yaff.pes.vlist.Cosine method) (yaff.pes.vlist.Cross method) (yaff.pes.vlist.Fues method) (yaff.pes.vlist.Harmonic method) (yaff.pes.vlist.MM3Bend method) (yaff.pes.vlist.MM3Quartic method) (yaff.pes.vlist.Morse method) (yaff.pes.vlist.PolyFour method) (yaff.pes.vlist.PolySix method) (yaff.pes.vlist.ValenceTerm method)

get_ndof_baro() (in module yaff.sampling.utils) get_ndof_internal_md() (in module yaff.sampling.utils) get_nlist() (yaff.pes.generator.FFArgs method) get_part() (yaff.pes.generator.FFArgs method) get_part_pair() (yaff.pes.generator.FFArgs method) get_part_valence() (yaff.pes.generator.FFArgs method) get_random_vel() (in module yaff.sampling.utils) get_random_vel_press() (in module yaff.sampling.utils) get_rows_signs() (yaff.pes.iclist.InternalCoordinate method) get_scope() (yaff.system.System method) get_slice() (in module yaff.analysis.utils) get_trajectory_datasets() (in module yaff.conversion.common) get_trajectory_group() (in module yaff.conversion.common) get_value() (yaff.sampling.iterative.AttributeStateItem method) (yaff.sampling.iterative.CellStateItem method) (yaff.sampling.iterative.DipoleStateItem method) (yaff.sampling.iterative.DipoleVelStateItem method) (yaff.sampling.iterative.EPotContribStateItem method) (yaff.sampling.iterative.EpotBendsStateItem method) (yaff.sampling.iterative.EpotBondsStateItem method) (yaff.sampling.iterative.EpotDihedsStateItem method) (yaff.sampling.iterative.PosStateItem method) (yaff.sampling.iterative.StateItem method) (yaff.sampling.iterative.VolumeStateItem method) (yaff.sampling.npt.MTKAttributeStateItem method) (yaff.sampling.nvt.NHCAttributeStateItem method) (yaff.sampling.verlet.TemperatureStateItem method) get_vterm() (yaff.pes.generator.OopCosGenerator method) (yaff.pes.generator.OopMeanCosGenerator method) (yaff.pes.generator.TorsionGenerator method) (yaff.pes.generator.ValenceGenerator method) getR() (yaff.sampling.npt.LangevinBarostat method) GLEThermostat (class in yaff.sampling.nvt) globalpar_info (yaff.pes.generator.D3BJGenerator attribute)

H

Harmonic (class in yaff.pes.vlist)

HDF5Writer (class in yaff.sampling.io) Hook (class in yaff.sampling.iterative)

I

ICClass (yaff.pes.generator.BendAngleHarmGenerator attribute) (yaff.pes.generator.BendCosGenerator attribute) (yaff.pes.generator.BendCosHarmGenerator attribute) (yaff.pes.generator.BendGenerator attribute) (yaff.pes.generator.BondDoubleWell2Generator attribute) (yaff.pes.generator.BondDoubleWellGenerator attribute) (yaff.pes.generator.BondGenerator attribute) (yaff.pes.generator.BondMorseGenerator attribute) (yaff.pes.generator.MM3BendGenerator attribute) (yaff.pes.generator.OopAngleGenerator attribute) (yaff.pes.generator.OopCosGenerator attribute) (yaff.pes.generator.OopDistGenerator attribute) (yaff.pes.generator.OopMeanAngleGenerator attribute) (yaff.pes.generator.OopMeanCosGenerator attribute) (yaff.pes.generator.TorsionCos2HarmGenerator attribute) (yaff.pes.generator.TorsionCosHarmGenerator attribute) (yaff.pes.generator.TorsionGenerator attribute) (yaff.pes.generator.UreyBradleyHarmGenerator attribute) (yaff.pes.generator.ValenceGenerator attribute) ICClass0 (yaff.pes.generator.CrossGenerator attribute) (yaff.pes.generator.ValenceCrossGenerator attribute) ICClass1 (yaff.pes.generator.CrossGenerator attribute) (yaff.pes.generator.ValenceCrossGenerator attribute) ICClass2 (yaff.pes.generator.CrossGenerator attribute) (yaff.pes.generator.ValenceCrossGenerator attribute) ICGroup (class in yaff.tune.cost) ICTest (class in yaff.tune.cost) IncrementRule (class in yaff.tune.transform) inefficiency() (in module yaff.analysis.blav) init() (yaff.sampling.npt.BerendsenBarostat method) (yaff.sampling.npt.LangevinBarostat method) (yaff.sampling.npt.MTKBarostat method) (yaff.sampling.npt.McDonaldBarostat method) (yaff.sampling.npt.PRBarostat method) (yaff.sampling.npt.TBCombination method) (yaff.sampling.npt.TadmorBarostat method) (yaff.sampling.nvt.AndersenThermostat method) (yaff.sampling.nvt.BerendsenThermostat method) (yaff.sampling.nvt.CSVRThermostat method) (yaff.sampling.nvt.GLEThermostat method) (yaff.sampling.nvt.LangevinThermostat method) (yaff.sampling.nvt.NHCThermostat method) (yaff.sampling.verlet.KineticAnnealing method) (yaff.sampling.verlet.VerletHook method) init_first() (yaff.analysis.diffusion.Diffusion method) (yaff.analysis.hook.AnalysisHook method) (yaff.analysis.rdf.RDF method) (yaff.analysis.spectrum.Spectrum method) init_online() (yaff.analysis.hook.AnalysisHook method) (yaff.analysis.spectrum.Spectrum method) init_state() (yaff.sampling.io.RestartWriter method) init_timestep() (yaff.analysis.diffusion.Diffusion method) (yaff.analysis.hook.AnalysisHook method) (yaff.analysis.spectrum.Spectrum method) init_trajectory() (yaff.sampling.io.HDF5Writer method) (yaff.sampling.io.RestartWriter method)

initialize() (yaff.sampling.iterative.Iterative method) (yaff.sampling.opt.BaseOptimizer method) (yaff.sampling.opt.CGOptimizer method) (yaff.sampling.opt.QNOptimizer method) (yaff.sampling.trajectory.RefTrajectory method) (yaff.sampling.verlet.VerletIntegrator method) InternalCoordinate (class in yaff.pes.iclist) InternalCoordinateList (class in yaff.pes.iclist) IsoCellDOF (class in yaff.sampling.dof) iter_angles() (yaff.system.System method) iter_attrs() (yaff.sampling.iterative.EPotContribStateItem method) (yaff.sampling.iterative.StateItem method) (yaff.sampling.verlet.TemperatureStateItem method) iter_atts() (yaff.sampling.iterative.EpotBendsStateItem method) (yaff.sampling.iterative.EpotBondsStateItem method) (yaff.sampling.iterative.EpotDihedsStateItem method) iter_bonds() (yaff.system.System method) iter_dihedrals() (yaff.system.System method) iter_equiv_keys_and_pars() (yaff.pes.generator.BendGenerator method) (yaff.pes.generator.BondDoubleWell2Generator method) (yaff.pes.generator.BondDoubleWellGenerator method) (yaff.pes.generator.BondGenerator method) (yaff.pes.generator.BondMorseGenerator method) (yaff.pes.generator.CrossGenerator method) (yaff.pes.generator.D3BJGenerator method) (yaff.pes.generator.DampDispGenerator method) (yaff.pes.generator.ExpRepGenerator method) (yaff.pes.generator.Generator method) (yaff.pes.generator.OopAngleGenerator method) (yaff.pes.generator.OopCosGenerator method) (yaff.pes.generator.OopDistGenerator method) (yaff.pes.generator.OopMeanAngleGenerator method) (yaff.pes.generator.OopMeanCosGenerator method) (yaff.pes.generator.TorsionCos2HarmGenerator method) (yaff.pes.generator.TorsionCosHarmGenerator method) (yaff.pes.generator.TorsionGenerator method) iter_indexes() (yaff.pes.generator.BendGenerator method) (yaff.pes.generator.BondDoubleWell2Generator method) (yaff.pes.generator.BondDoubleWellGenerator method) (yaff.pes.generator.BondGenerator method) (yaff.pes.generator.BondMorseGenerator method) (yaff.pes.generator.CrossGenerator method) (yaff.pes.generator.OopAngleGenerator method) (yaff.pes.generator.OopCosGenerator method) (yaff.pes.generator.OopDistGenerator method) (yaff.pes.generator.OopMeanAngleGenerator method) (yaff.pes.generator.OopMeanCosGenerator method) (yaff.pes.generator.TorsionCos2HarmGenerator method) (yaff.pes.generator.TorsionCosHarmGenerator method) (yaff.pes.generator.TorsionGenerator method) (yaff.pes.generator.ValenceCrossGenerator method) (yaff.pes.generator.ValenceGenerator method) iter_matches() (in module yaff.atselect) (yaff.system.System method) iter_oops() (yaff.system.System method) iter_paths() (in module yaff.pes.scaling) Iterative (class in yaff.sampling.iterative)

K

kind (yaff.pes.iclist.BendAngle attribute) (yaff.pes.iclist.BendCos attribute) (yaff.pes.iclist.Bond attribute) (yaff.pes.iclist.DihedAngle attribute) (yaff.pes.iclist.DihedCos attribute) (yaff.pes.iclist.InternalCoordinate attribute) (yaff.pes.iclist.OopAngle attribute) (yaff.pes.iclist.OopCos attribute) (yaff.pes.iclist.OopDist attribute) (yaff.pes.iclist.OopMeanAngle attribute) (yaff.pes.iclist.OopMeanCos attribute) (yaff.pes.iclist.UreyBradley attribute) (yaff.pes.vlist.BondDoubleWell attribute) (yaff.pes.vlist.Chebychev1 attribute) (yaff.pes.vlist.Chebychev2 attribute) (yaff.pes.vlist.Chebychev3 attribute) (yaff.pes.vlist.Chebychev4 attribute) (yaff.pes.vlist.Chebychev6 attribute) (yaff.pes.vlist.Cosine attribute) (yaff.pes.vlist.Cross attribute) (yaff.pes.vlist.Fues attribute) (yaff.pes.vlist.Harmonic attribute) (yaff.pes.vlist.MM3Bend attribute) (yaff.pes.vlist.MM3Quartic attribute) (yaff.pes.vlist.Morse attribute) (yaff.pes.vlist.PolyFour attribute) (yaff.pes.vlist.PolySix attribute) (yaff.pes.vlist.ValenceTerm attribute) (yaff.sampling.iterative.Hook attribute) (yaff.sampling.npt.BerendsenBarostat attribute) (yaff.sampling.npt.LangevinBarostat attribute) (yaff.sampling.npt.MTKBarostat attribute) (yaff.sampling.npt.McDonaldBarostat attribute) (yaff.sampling.npt.PRBarostat attribute) (yaff.sampling.npt.TadmorBarostat attribute) (yaff.sampling.nvt.AndersenThermostat attribute) (yaff.sampling.nvt.BerendsenThermostat attribute) (yaff.sampling.nvt.CSVRThermostat attribute) (yaff.sampling.nvt.GLEThermostat attribute) (yaff.sampling.nvt.LangevinThermostat attribute) (yaff.sampling.nvt.NHCThermostat attribute)

KineticAnnealing (class in yaff.sampling.verlet)

L

LangevinBarostat (class in yaff.sampling.npt) LangevinThermostat (class in yaff.sampling.nvt) lex_find() (in module yaff.atselect) lex_split() (in module yaff.atselect) LJGenerator (class in yaff.pes.generator) log() (yaff.sampling.dof.BaseCellDOF method) (yaff.sampling.dof.DOF method) log_name (yaff.sampling.iterative.Iterative attribute) (yaff.sampling.opt.BaseOptimizer attribute) (yaff.sampling.opt.CGOptimizer attribute) (yaff.sampling.opt.QNOptimizer attribute) (yaff.sampling.trajectory.RefTrajectory attribute) (yaff.sampling.verlet.VerletIntegrator attribute)

lookup_atoms() (yaff.pes.dlist.DeltaList method) (yaff.pes.iclist.InternalCoordinateList method) (yaff.pes.vlist.ValenceList method)

M

make_step() (yaff.sampling.opt.QNOptimizer method) McDonaldBarostat (class in yaff.sampling.npt) method (yaff.sampling.iterative.Hook attribute) (yaff.sampling.npt.BerendsenBarostat attribute) (yaff.sampling.npt.LangevinBarostat attribute) (yaff.sampling.npt.MTKBarostat attribute) (yaff.sampling.npt.McDonaldBarostat attribute) (yaff.sampling.npt.PRBarostat attribute) (yaff.sampling.npt.TadmorBarostat attribute) (yaff.sampling.nvt.AndersenThermostat attribute) (yaff.sampling.nvt.BerendsenThermostat attribute) (yaff.sampling.nvt.CSVRThermostat attribute) (yaff.sampling.nvt.GLEThermostat attribute) (yaff.sampling.nvt.LangevinThermostat attribute) (yaff.sampling.nvt.NHCThermostat attribute)

mixing_rules (yaff.pes.generator.ExpRepGenerator attribute) (yaff.pes.generator.NonbondedGenerator attribute) MM3Bend (class in yaff.pes.vlist) MM3BendGenerator (class in yaff.pes.generator) MM3Generator (class in yaff.pes.generator) MM3Quartic (class in yaff.pes.vlist) MM3QuarticGenerator (class in yaff.pes.generator) ModifierRule (class in yaff.tune.transform) modify_value() (yaff.tune.transform.IncrementRule method) (yaff.tune.transform.ModifierRule method) (yaff.tune.transform.ScaleRule method) Morse (class in yaff.pes.vlist) MTKAttributeStateItem (class in yaff.sampling.npt) MTKBarostat (class in yaff.sampling.npt)

N

name (yaff.sampling.iterative.Hook attribute) (yaff.sampling.npt.BerendsenBarostat attribute) (yaff.sampling.npt.LangevinBarostat attribute) (yaff.sampling.npt.MTKBarostat attribute) (yaff.sampling.npt.McDonaldBarostat attribute) (yaff.sampling.npt.PRBarostat attribute) (yaff.sampling.npt.TBCombination attribute) (yaff.sampling.npt.TadmorBarostat attribute) (yaff.sampling.nvt.AndersenThermostat attribute) (yaff.sampling.nvt.BerendsenThermostat attribute) (yaff.sampling.nvt.CSVRThermostat attribute) (yaff.sampling.nvt.GLEThermostat attribute) (yaff.sampling.nvt.LangevinThermostat attribute) (yaff.sampling.nvt.NHCThermostat attribute) natom (yaff.system.System attribute) (yaff.tune.cost.BendGroup attribute) (yaff.tune.cost.BondGroup attribute) (yaff.tune.cost.ICGroup attribute) nbond (yaff.system.System attribute) ncelldof (yaff.sampling.dof.BaseCellDOF attribute) ncellvar (yaff.sampling.dof.BaseCellDOF attribute) ndof (yaff.sampling.dof.DOF attribute)

NeighborList (class in yaff.pes.nlist) nffatype (yaff.pes.generator.BendGenerator attribute) (yaff.pes.generator.BondDoubleWell2Generator attribute) (yaff.pes.generator.BondDoubleWellGenerator attribute) (yaff.pes.generator.BondGenerator attribute) (yaff.pes.generator.BondMorseGenerator attribute) (yaff.pes.generator.CrossGenerator attribute) (yaff.pes.generator.MM3BendGenerator attribute) (yaff.pes.generator.OopAngleGenerator attribute) (yaff.pes.generator.OopCosGenerator attribute) (yaff.pes.generator.OopDistGenerator attribute) (yaff.pes.generator.OopMeanAngleGenerator attribute) (yaff.pes.generator.OopMeanCosGenerator attribute) (yaff.pes.generator.TorsionCos2HarmGenerator attribute) (yaff.pes.generator.TorsionCosHarmGenerator attribute) (yaff.pes.generator.TorsionGenerator attribute) (yaff.pes.generator.ValenceCrossGenerator attribute) (yaff.pes.generator.ValenceGenerator attribute) (yaff.system.System attribute) NHCAttributeStateItem (class in yaff.sampling.nvt) NHCThermostat (class in yaff.sampling.nvt) NonbondedGenerator (class in yaff.pes.generator)

O

offline_loop() (yaff.analysis.hook.AnalysisHook method) (yaff.analysis.spectrum.Spectrum method) OopAngle (class in yaff.pes.iclist) OopAngleGenerator (class in yaff.pes.generator) OopCos (class in yaff.pes.iclist) OopCosGenerator (class in yaff.pes.generator) OopDist (class in yaff.pes.iclist)

OopDistGenerator (class in yaff.pes.generator) OopMeanAngle (class in yaff.pes.iclist) OopMeanAngleGenerator (class in yaff.pes.generator) OopMeanCos (class in yaff.pes.iclist) OopMeanCosGenerator (class in yaff.pes.generator) OptScreenLog (class in yaff.sampling.opt) overlap_bsize() (yaff.analysis.diffusion.Diffusion method)

P

pairpar_info (yaff.pes.generator.D3BJGenerator attribute) par_info (yaff.pes.generator.BendAngleHarmGenerator attribute) (yaff.pes.generator.BendCosGenerator attribute) (yaff.pes.generator.BendCosHarmGenerator attribute) (yaff.pes.generator.BondDoubleWell2Generator attribute) (yaff.pes.generator.BondDoubleWellGenerator attribute) (yaff.pes.generator.BondGenerator attribute) (yaff.pes.generator.BondMorseGenerator attribute) (yaff.pes.generator.CrossGenerator attribute) (yaff.pes.generator.D3BJGenerator attribute) (yaff.pes.generator.DampDispGenerator attribute) (yaff.pes.generator.ExpRepGenerator attribute) (yaff.pes.generator.FixedChargeGenerator attribute) (yaff.pes.generator.Generator attribute) (yaff.pes.generator.LJGenerator attribute) (yaff.pes.generator.MM3BendGenerator attribute) (yaff.pes.generator.MM3Generator attribute) (yaff.pes.generator.OopAngleGenerator attribute) (yaff.pes.generator.OopCosGenerator attribute) (yaff.pes.generator.OopDistGenerator attribute) (yaff.pes.generator.OopMeanAngleGenerator attribute) (yaff.pes.generator.OopMeanCosGenerator attribute) (yaff.pes.generator.TorsionCos2HarmGenerator attribute) (yaff.pes.generator.TorsionCosHarmGenerator attribute) (yaff.pes.generator.TorsionGenerator attribute) (yaff.pes.generator.UreyBradleyHarmGenerator attribute) ParameterDefinition (class in yaff.pes.parameters) ParameterModifier (class in yaff.tune.transform) Parameters (class in yaff.pes.parameters) ParameterSection (class in yaff.pes.parameters) ParameterTransform (class in yaff.tune.transform) pca_convergence() (in module yaff.analysis.pca) pca_projection() (in module yaff.analysis.pca) pca_similarity() (in module yaff.analysis.pca) plot() (yaff.analysis.diffusion.Diffusion method) (yaff.analysis.rdf.RDF method) (yaff.analysis.spectrum.Spectrum method) plot_ac() (yaff.analysis.spectrum.Spectrum method) plot_angle() (in module yaff.analysis.basic) plot_cell_pars() (in module yaff.analysis.basic) plot_density() (in module yaff.analysis.basic) plot_dihedral() (in module yaff.analysis.basic) plot_energies() (in module yaff.analysis.basic) plot_epot_contribs() (in module yaff.analysis.basic) plot_press_dist() (in module yaff.analysis.basic) plot_pressure() (in module yaff.analysis.basic) plot_temp_dist() (in module yaff.analysis.basic) plot_temperature() (in module yaff.analysis.basic) plot_volume_dist() (in module yaff.analysis.basic) PolyFour (class in yaff.pes.vlist) PolySix (class in yaff.pes.vlist) PosStateItem (class in yaff.sampling.iterative) post() (yaff.sampling.npt.BerendsenBarostat method) (yaff.sampling.npt.LangevinBarostat method) (yaff.sampling.npt.MTKBarostat method) (yaff.sampling.npt.McDonaldBarostat method) (yaff.sampling.npt.PRBarostat method) (yaff.sampling.npt.TBCombination method) (yaff.sampling.npt.TadmorBarostat method) (yaff.sampling.nvt.AndersenThermostat method) (yaff.sampling.nvt.BerendsenThermostat method) (yaff.sampling.nvt.CSVRThermostat method) (yaff.sampling.nvt.GLEThermostat method) (yaff.sampling.nvt.LangevinThermostat method) (yaff.sampling.nvt.NHCThermostat method) (yaff.sampling.verlet.KineticAnnealing method) (yaff.sampling.verlet.VerletHook method)

PRBarostat (class in yaff.sampling.npt) pre() (yaff.sampling.npt.BerendsenBarostat method) (yaff.sampling.npt.LangevinBarostat method) (yaff.sampling.npt.MTKBarostat method) (yaff.sampling.npt.McDonaldBarostat method) (yaff.sampling.npt.PRBarostat method) (yaff.sampling.npt.TBCombination method) (yaff.sampling.npt.TadmorBarostat method) (yaff.sampling.nvt.AndersenThermostat method) (yaff.sampling.nvt.BerendsenThermostat method) (yaff.sampling.nvt.CSVRThermostat method) (yaff.sampling.nvt.GLEThermostat method) (yaff.sampling.nvt.LangevinThermostat method) (yaff.sampling.nvt.NHCThermostat method) (yaff.sampling.verlet.KineticAnnealing method) (yaff.sampling.verlet.VerletHook method) prefix (yaff.pes.generator.BendAngleHarmGenerator attribute) (yaff.pes.generator.BendCosGenerator attribute) (yaff.pes.generator.BendCosHarmGenerator attribute) (yaff.pes.generator.BondDoubleWell2Generator attribute) (yaff.pes.generator.BondDoubleWellGenerator attribute) (yaff.pes.generator.BondFuesGenerator attribute) (yaff.pes.generator.BondHarmGenerator attribute) (yaff.pes.generator.BondMorseGenerator attribute) (yaff.pes.generator.CrossGenerator attribute) (yaff.pes.generator.D3BJGenerator attribute) (yaff.pes.generator.DampDispGenerator attribute) (yaff.pes.generator.ExpRepGenerator attribute) (yaff.pes.generator.FixedChargeGenerator attribute) (yaff.pes.generator.Generator attribute) (yaff.pes.generator.LJGenerator attribute) (yaff.pes.generator.MM3BendGenerator attribute) (yaff.pes.generator.MM3Generator attribute) (yaff.pes.generator.MM3QuarticGenerator attribute) (yaff.pes.generator.OopAngleGenerator attribute) (yaff.pes.generator.OopCosGenerator attribute) (yaff.pes.generator.OopDistGenerator attribute) (yaff.pes.generator.OopMeanAngleGenerator attribute) (yaff.pes.generator.OopMeanCosGenerator attribute) (yaff.pes.generator.TorsionCos2HarmGenerator attribute) (yaff.pes.generator.TorsionCosHarmGenerator attribute) (yaff.pes.generator.TorsionGenerator attribute) (yaff.pes.generator.UreyBradleyHarmGenerator attribute) process_atoms() (yaff.pes.generator.FixedChargeGenerator method) process_bonds() (yaff.pes.generator.FixedChargeGenerator method) process_dielectric() (yaff.pes.generator.FixedChargeGenerator method) process_mix() (yaff.pes.generator.NonbondedGenerator method) process_pars() (yaff.pes.generator.BondDoubleWell2Generator method) (yaff.pes.generator.Generator method) (yaff.pes.generator.TorsionCos2HarmGenerator method) process_scales() (yaff.pes.generator.NonbondedGenerator method) process_units() (yaff.pes.generator.Generator method) propagate() (yaff.sampling.iterative.Iterative method) (yaff.sampling.opt.BaseOptimizer method) (yaff.sampling.opt.CGOptimizer method) (yaff.sampling.opt.QNOptimizer method) (yaff.sampling.trajectory.RefTrajectory method) (yaff.sampling.verlet.VerletIntegrator method)

Q

QNOptimizer (class in yaff.sampling.opt)

R

RDF (class in yaff.analysis.rdf) read_offline() (yaff.analysis.diffusion.Diffusion method) (yaff.analysis.hook.AnalysisHook method) (yaff.analysis.rdf.RDF method) read_online() (yaff.analysis.diffusion.Diffusion method) (yaff.analysis.hook.AnalysisHook method) (yaff.analysis.rdf.RDF method) (yaff.analysis.spectrum.Spectrum method) RefTrajectory (class in yaff.sampling.trajectory)

remove_angular_moment() (in module yaff.sampling.utils) remove_com_moment() (in module yaff.sampling.utils) remove_duplicate() (yaff.system.System method) request_rcut() (yaff.pes.nlist.NeighborList method) reset() (yaff.sampling.dof.DOF method) RestartWriter (class in yaff.sampling.io) run() (yaff.sampling.iterative.Iterative method) (yaff.tune.cost.GeoOptHessianSimulation method) (yaff.tune.cost.GeoOptSimulation method) (yaff.tune.cost.Simulation method)

S

ScaleRule (class in yaff.tune.transform) Scalings (class in yaff.pes.scaling) set_standard_masses() (yaff.system.System method) Simulation (class in yaff.tune.cost) solve_trust_radius() (in module yaff.sampling.opt) Spectrum (class in yaff.analysis.spectrum) SR1HessianModel (class in yaff.sampling.opt) stabilized_cholesky_decomp() (in module yaff.sampling.utils) StateItem (class in yaff.sampling.iterative) StrainCellDOF (class in yaff.sampling.dof) subsystem() (yaff.system.System method)

suffixes (yaff.pes.generator.D3BJGenerator attribute) (yaff.pes.generator.DampDispGenerator attribute) (yaff.pes.generator.ExpRepGenerator attribute) (yaff.pes.generator.FixedChargeGenerator attribute) (yaff.pes.generator.Generator attribute) (yaff.pes.generator.LJGenerator attribute) (yaff.pes.generator.MM3Generator attribute) (yaff.pes.generator.ValenceCrossGenerator attribute) (yaff.pes.generator.ValenceGenerator attribute) supercell() (yaff.system.System method) System (class in yaff.system)

T

TadmorBarostat (class in yaff.sampling.npt) TBCombination (class in yaff.sampling.npt) TemperatureStateItem (class in yaff.sampling.verlet) Test (class in yaff.tune.cost) thermo() (yaff.sampling.nvt.GLEThermostat method) (yaff.sampling.nvt.LangevinThermostat method)

to_dictionary() (yaff.pes.nlist.NeighborList method) to_file() (yaff.system.System method) to_hdf5() (yaff.system.System method) TorsionCos2HarmGenerator (class in yaff.pes.generator) TorsionCosHarmGenerator (class in yaff.pes.generator) TorsionGenerator (class in yaff.pes.generator) TrajScreenLog (class in yaff.sampling.trajectory)

U

update() (yaff.pes.nlist.NeighborList method) (yaff.sampling.iterative.StateItem method) (yaff.sampling.opt.BFGSHessianModel method) (yaff.sampling.opt.SR1HessianModel method) (yaff.sampling.verlet.ConsErrTracker method) update_gmax() (yaff.pes.ff.ForcePartEwaldReciprocal method) (yaff.pes.ff.ForcePartEwaldReciprocalDD method) update_msd() (yaff.analysis.diffusion.Diffusion method)

update_pos() (yaff.pes.ff.ForceField method) (yaff.pes.ff.ForcePart method) update_rmax() (yaff.pes.nlist.NeighborList method) update_rvecs() (yaff.pes.ff.ForceField method) (yaff.pes.ff.ForcePart method) (yaff.pes.ff.ForcePartEwaldReciprocal method) (yaff.pes.ff.ForcePartEwaldReciprocalDD method) UreyBradley (class in yaff.pes.iclist) UreyBradleyHarmGenerator (class in yaff.pes.generator)

V

ValenceCrossGenerator (class in yaff.pes.generator) ValenceGenerator (class in yaff.pes.generator) ValenceList (class in yaff.pes.vlist) ValenceTerm (class in yaff.pes.vlist) VClass (yaff.pes.generator.BendCosGenerator attribute) (yaff.pes.generator.BendGenerator attribute) (yaff.pes.generator.BondDoubleWell2Generator attribute) (yaff.pes.generator.BondDoubleWellGenerator attribute) (yaff.pes.generator.BondFuesGenerator attribute) (yaff.pes.generator.BondGenerator attribute) (yaff.pes.generator.BondHarmGenerator attribute) (yaff.pes.generator.BondMorseGenerator attribute) (yaff.pes.generator.MM3BendGenerator attribute) (yaff.pes.generator.MM3QuarticGenerator attribute) (yaff.pes.generator.OopAngleGenerator attribute) (yaff.pes.generator.OopCosGenerator attribute) (yaff.pes.generator.OopDistGenerator attribute) (yaff.pes.generator.OopMeanAngleGenerator attribute) (yaff.pes.generator.OopMeanCosGenerator attribute) (yaff.pes.generator.TorsionCos2HarmGenerator attribute) (yaff.pes.generator.TorsionCosHarmGenerator attribute) (yaff.pes.generator.TorsionGenerator attribute) (yaff.pes.generator.ValenceGenerator attribute)

VClass01 (yaff.pes.generator.CrossGenerator attribute) (yaff.pes.generator.ValenceCrossGenerator attribute) VClass02 (yaff.pes.generator.CrossGenerator attribute) (yaff.pes.generator.ValenceCrossGenerator attribute) VClass12 (yaff.pes.generator.CrossGenerator attribute) (yaff.pes.generator.ValenceCrossGenerator attribute) verify() (yaff.sampling.npt.TBCombination method) VerletHook (class in yaff.sampling.verlet) VerletIntegrator (class in yaff.sampling.verlet) VerletScreenLog (class in yaff.sampling.verlet) VolumeStateItem (class in yaff.sampling.iterative)

W

write_principal_mode() (in module yaff.analysis.pca)

write_to_dataset() (in module yaff.conversion.common) write_to_file() (yaff.pes.parameters.Parameters method)

X

xyz_to_hdf5() (in module yaff.conversion.xyz)

XYZWriter (class in yaff.sampling.io)

Y

yaff.analysis.basic (module) yaff.analysis.blav (module) yaff.analysis.diffusion (module) yaff.analysis.hook (module) yaff.analysis.pca (module) yaff.analysis.rdf (module) yaff.analysis.spectrum (module) yaff.analysis.utils (module) yaff.atselect (module) yaff.conversion.common (module) yaff.conversion.cp2k (module) yaff.conversion.dlpoly (module) yaff.conversion.gaussian (module) yaff.conversion.xyz (module) yaff.log (module) yaff.pes.dlist (module) yaff.pes.ff (module) yaff.pes.generator (module)

yaff.pes.iclist (module) yaff.pes.nlist (module) yaff.pes.parameters (module) yaff.pes.scaling (module) yaff.pes.vlist (module) yaff.sampling.dof (module) yaff.sampling.harmonic (module) yaff.sampling.io (module) yaff.sampling.iterative (module) yaff.sampling.npt (module) yaff.sampling.nvt (module) yaff.sampling.opt (module) yaff.sampling.trajectory (module) yaff.sampling.utils (module) yaff.sampling.verlet (module) yaff.system (module) yaff.tune.cost (module) yaff.tune.transform (module) yaff.version (module)