Index

A

add_graph() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) add_masm_info() (in module scine_puffin.utilities.masm_helper) AFIR (scine_puffin.utilities.task_to_readuct_call.SubTaskToReaductCall attribute) analyse_runs() (scine_puffin.utilities.kinetic_modeling_sensitivity_analysis.RMSKineticModelingSensitivityAnalysis method) analyze_side() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) archive() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling method) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization method) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.sleep.Sleep method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.job.Job method) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob method) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders method) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization method) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian method) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint method)

args (scine_puffin.jobs.templates.job.breakable.Break attribute) (scine_puffin.jobs.templates.scine_job.CalculatorNotPresentException attribute) (scine_puffin.utilities.imports.MissingDependencyError attribute) available_models() (scine_puffin.programs.database.Database method) (scine_puffin.programs.gaussian.Gaussian method) (scine_puffin.programs.molassembler.Molassembler method) (scine_puffin.programs.orca.Orca method) (scine_puffin.programs.parrot.Parrot method) (scine_puffin.programs.program.Program method) (scine_puffin.programs.readuct.Readuct method) (scine_puffin.programs.serenity.Serenity method) (scine_puffin.programs.sparrow.Sparrow method) (scine_puffin.programs.utils.Utils method)

B

bond_orders_from_db_bond_orders() (scine_puffin.jobs.conformers.Conformers static method) (scine_puffin.jobs.graph.Graph static method) (scine_puffin.jobs.scine_afir.ScineAfir static method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders static method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization static method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut static method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization static method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization static method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation static method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir static method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt static method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 static method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess static method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob static method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers static method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob static method) (scine_puffin.jobs.templates.scine_react_job.ReactJob static method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob static method)

bootstrap() (in module scine_puffin.bootstrap) breakable (class in scine_puffin.jobs.templates.job) breakable.Break build_reactive_complex() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method)

C

calculate_adjoined_sensitivities() (scine_puffin.utilities.rms_kinetic_model.RMSKineticModel method) calculate_fluxes_and_concentrations() (scine_puffin.utilities.rms_kinetic_model.RMSKineticModel method) calculation_context() (in module scine_puffin.jobs.templates.job) calculation_postprocessing() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) (scine_puffin.utilities.program_helper.Cp2kHelper method) (scine_puffin.utilities.program_helper.ProgramHelper method) calculation_preprocessing() (scine_puffin.utilities.program_helper.Cp2kHelper method) (scine_puffin.utilities.program_helper.ProgramHelper method) calculator_import_resolve() (in module scine_puffin.utilities.imports) CalculatorNotPresentException capture_raw_output() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling method) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization method) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.sleep.Sleep method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.job.Job method) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob method) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders method) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization method) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian method) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint method) check_configuration() (scine_puffin.jobs.conformers.Conformers class method) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 class method) (scine_puffin.jobs.graph.Graph class method) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling class method) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization class method) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling class method) (scine_puffin.jobs.scine_afir.ScineAfir class method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders class method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization class method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft class method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut class method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization class method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization class method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation class method) (scine_puffin.jobs.scine_hessian.ScineHessian class method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan class method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection class method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir class method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt class method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 class method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess class method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint class method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization class method) (scine_puffin.jobs.sleep.Sleep class method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces class method) (scine_puffin.jobs.templates.job.Job class method) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob class method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob class method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob class method) (scine_puffin.jobs.templates.scine_job.ScineJob class method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers class method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob class method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob class method) (scine_puffin.jobs.templates.scine_react_job.ReactJob class method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob class method) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob class method) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders class method) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization class method) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian class method) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint class method) check_duplicate_property() (scine_puffin.jobs.conformers.Conformers static method) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 static method) (scine_puffin.jobs.graph.Graph static method) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling static method) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization static method) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling static method) (scine_puffin.jobs.scine_afir.ScineAfir static method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders static method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization static method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft static method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut static method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization static method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization static method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation static method) (scine_puffin.jobs.scine_hessian.ScineHessian static method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan static method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection static method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir static method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt static method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 static method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess static method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint static method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization static method) (scine_puffin.jobs.sleep.Sleep static method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces static method) (scine_puffin.jobs.templates.job.Job static method) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob static method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob static method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob static method) (scine_puffin.jobs.templates.scine_job.ScineJob static method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers static method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob static method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob static method) (scine_puffin.jobs.templates.scine_react_job.ReactJob static method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob static method) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob static method) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders static method) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization static method) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian static method) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint static method) check_environment() (in module scine_puffin.daemon) check_for_barrierless_reaction() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) check_install() (scine_puffin.programs.database.Database method) (scine_puffin.programs.gaussian.Gaussian method) (scine_puffin.programs.molassembler.Molassembler method) (scine_puffin.programs.orca.Orca method) (scine_puffin.programs.parrot.Parrot method) (scine_puffin.programs.program.Program method) (scine_puffin.programs.readuct.Readuct method) (scine_puffin.programs.serenity.Serenity method) (scine_puffin.programs.sparrow.Sparrow method) (scine_puffin.programs.utils.Utils method) check_mass_balance() (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling method) check_settings_availability() (scine_puffin.utilities.turbomole_helper.TurbomoleHelper method) check_setup() (in module scine_puffin.jobloop) check_structures() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) clear() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling method) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization method) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.sleep.Sleep method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.job.Job method) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob method) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders method) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization method) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian method) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint method)

complete_job() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling method) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization method) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.sleep.Sleep method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.job.Job method) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob method) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders method) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization method) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian method) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint method) concentrations() (scine_puffin.utilities.rms_kinetic_model.RMSKineticModel static method) config (scine_puffin.jobs.conformers.Conformers attribute) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 attribute) (scine_puffin.jobs.graph.Graph attribute) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling attribute) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization attribute) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling attribute) (scine_puffin.jobs.scine_afir.ScineAfir attribute) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders attribute) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization attribute) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft attribute) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut attribute) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization attribute) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization attribute) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation attribute) (scine_puffin.jobs.scine_hessian.ScineHessian attribute) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan attribute) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection attribute) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir attribute) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt attribute) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 attribute) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess attribute) (scine_puffin.jobs.scine_single_point.ScineSinglePoint attribute) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization attribute) (scine_puffin.jobs.sleep.Sleep attribute) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces attribute) (scine_puffin.jobs.templates.job.Job attribute) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob attribute) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob attribute) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob attribute) (scine_puffin.jobs.templates.scine_job.ScineJob attribute) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers attribute) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob attribute) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob attribute) (scine_puffin.jobs.templates.scine_react_job.ReactJob attribute) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob attribute) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob attribute) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders attribute) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization attribute) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian attribute) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint attribute) Configuration (class in scine_puffin.config) configure_run() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling method) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization method) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.sleep.Sleep method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.job.Job method) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob method) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders method) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization method) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian method) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint method) Conformers (class in scine_puffin.jobs.conformers) connectivity_settings (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization attribute) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers attribute) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob attribute) (scine_puffin.jobs.templates.scine_react_job.ReactJob attribute) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob attribute) connectivity_settings_from_only_connectivity_settings() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) ConnectivityJob (class in scine_puffin.jobs.templates.scine_connectivity_job) contains_mm() (in module scine_puffin.utilities.qm_mm_settings) correct_non_applicable_settings() (scine_puffin.utilities.scine_helper.SettingsManager method) Cp2kHelper (class in scine_puffin.utilities.program_helper) create_arrhenius_reaction_entry() (in module scine_puffin.utilities.rms_input_file_creator) create_helpers() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) create_new_structure() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) create_rms_phase_entry() (in module scine_puffin.utilities.rms_input_file_creator) create_rms_reaction_entry() (in module scine_puffin.utilities.rms_input_file_creator) create_rms_units_entry() (in module scine_puffin.utilities.rms_input_file_creator) create_rms_yml_file() (in module scine_puffin.utilities.rms_input_file_creator) create_single_species_entry() (in module scine_puffin.utilities.rms_input_file_creator) create_solvent_entry() (in module scine_puffin.utilities.rms_input_file_creator) create_yml_file() (scine_puffin.utilities.rms_kinetic_model.RMSKineticModel method) cutoff_handling() (scine_puffin.utilities.program_helper.Cp2kHelper method) cutoffs_from_properties() (scine_puffin.utilities.program_helper.Cp2kHelper method)

D

daemon() (scine_puffin.config.Configuration method) Database (class in scine_puffin.programs.database) database() (scine_puffin.config.Configuration method) dependency_addition() (in module scine_puffin.utilities.imports) determine_new_label() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) determine_pes_of_rc() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method)

dict_generator() (in module scine_puffin.config) distance_bond_orders() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) dump() (scine_puffin.config.Configuration method)

E

ensure_non_negative_barriers() (scine_puffin.utilities.rms_kinetic_model.RMSKineticModel method) evaluate_salib_parallel() (scine_puffin.utilities.kinetic_modeling_sensitivity_analysis.RMSKineticModelingSensitivityAnalysis static method) evaluate_spin_mode() (scine_puffin.utilities.turbomole_helper.TurbomoleHelper method) execute() (scine_puffin.utilities.turbomole_helper.TurbomoleHelper static method) execute_hessian_calculation() (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian method) execute_optimization() (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization method) execute_program() (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 method) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization method) execute_single_point_calculation() (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint method) expected_results() (scine_puffin.jobs.conformers.Conformers class method) (scine_puffin.jobs.graph.Graph class method) (scine_puffin.jobs.scine_afir.ScineAfir class method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders class method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization class method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft class method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut class method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization class method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization class method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation class method) (scine_puffin.jobs.scine_hessian.ScineHessian class method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan class method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection class method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir class method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt class method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 class method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess class method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint class method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization class method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces class method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob class method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob class method) (scine_puffin.jobs.templates.scine_job.ScineJob class method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers class method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob class method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob class method) (scine_puffin.jobs.templates.scine_react_job.ReactJob class method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob class method) expected_results_check() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method)

extract_connectivity_settings_from_dict() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) extract_cutoff_optimization_settings() (scine_puffin.utilities.program_helper.Cp2kHelper method)

F

fail_job() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling method) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization method) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.sleep.Sleep method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.job.Job method) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob method) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders method) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization method) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian method) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint method) failed_file() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling method) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization method) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.sleep.Sleep method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.job.Job method) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob method) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders method) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization method) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian method) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint method)

finalize() (scine_puffin.jobs.templates.scine_observers.Observer method) (scine_puffin.jobs.templates.scine_observers.StoreEverythingObserver method) (scine_puffin.jobs.templates.scine_observers.StoreWithFractionObserver method) (scine_puffin.jobs.templates.scine_observers.StoreWithFrequencyObserver method)

G

gather() (scine_puffin.jobs.templates.scine_observers.Observer method) (scine_puffin.jobs.templates.scine_observers.StoreEverythingObserver method) (scine_puffin.jobs.templates.scine_observers.StoreWithFractionObserver method) (scine_puffin.jobs.templates.scine_observers.StoreWithFrequencyObserver method) Gaussian (class in scine_puffin.programs.gaussian) GaussianChargeModel5 (class in scine_puffin.jobs.gaussian_charge_model_5) generate_spline() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) get_aggregate_to_reaction_map() (scine_puffin.utilities.rms_kinetic_model.RMSKineticModel method) get_all_parameters() (scine_puffin.utilities.rms_kinetic_model.RMSKineticModel method) get_analysis() (scine_puffin.utilities.kinetic_modeling_sensitivity_analysis.RMSKineticModelingSensitivityAnalysis method) get_bond_orders() (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders method) get_calc() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) get_calculation() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) get_cbor_graph() (in module scine_puffin.utilities.masm_helper) get_cbor_graph_from_molecule() (in module scine_puffin.utilities.masm_helper) get_charge() (scine_puffin.jobs.conformers.Conformers static method) (scine_puffin.jobs.graph.Graph static method) (scine_puffin.jobs.scine_afir.ScineAfir static method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders static method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization static method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft static method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut static method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization static method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization static method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation static method) (scine_puffin.jobs.scine_hessian.ScineHessian static method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan static method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection static method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir static method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt static method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 static method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess static method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint static method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization static method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces static method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob static method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob static method) (scine_puffin.jobs.templates.scine_job.ScineJob static method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers static method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob static method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob static method) (scine_puffin.jobs.templates.scine_react_job.ReactJob static method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob static method)

get_compound_or_flask() (in module scine_puffin.utilities.compound_and_flask_helpers) get_correct_helper() (scine_puffin.utilities.program_helper.Cp2kHelper class method) (scine_puffin.utilities.program_helper.ProgramHelper class method) get_decision_list_from_molecule() (in module scine_puffin.utilities.masm_helper) get_decision_lists() (in module scine_puffin.utilities.masm_helper) get_default_viscosity() (in module scine_puffin.utilities.rms_input_file_creator) get_energy() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) get_graph_charges_multiplicities() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) get_ideal_dilute_solution() (in module scine_puffin.utilities.rms_input_file_creator) get_ideal_surface() (in module scine_puffin.utilities.rms_input_file_creator) get_initial_conditions() (scine_puffin.utilities.rms_kinetic_model.RMSKineticModel method) get_local_sensitivity_samples() (scine_puffin.utilities.kinetic_modeling_sensitivity_analysis.RMSKineticModelingSensitivityAnalysis method) get_loewdin_charges() (scine_puffin.utilities.turbomole_helper.TurbomoleHelper method) get_molecules_result() (in module scine_puffin.utilities.masm_helper) get_multiplicity() (scine_puffin.jobs.conformers.Conformers static method) (scine_puffin.jobs.graph.Graph static method) (scine_puffin.jobs.scine_afir.ScineAfir static method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders static method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization static method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft static method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut static method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization static method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization static method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation static method) (scine_puffin.jobs.scine_hessian.ScineHessian static method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan static method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection static method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir static method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt static method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 static method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess static method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint static method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization static method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces static method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob static method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob static method) (scine_puffin.jobs.templates.scine_job.ScineJob static method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers static method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob static method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob static method) (scine_puffin.jobs.templates.scine_react_job.ReactJob static method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob static method) get_n_aggregates() (scine_puffin.utilities.rms_kinetic_model.RMSKineticModel method) get_n_parameters() (scine_puffin.utilities.kinetic_modeling_sensitivity_analysis.RMSKineticModelingSensitivityAnalysis method) (scine_puffin.utilities.rms_kinetic_model.RMSKineticModel method) get_n_reactions() (scine_puffin.utilities.rms_kinetic_model.RMSKineticModel method) get_n_total_output() (scine_puffin.utilities.kinetic_modeling_sensitivity_analysis.RMSKineticModelingSensitivityAnalysis method) get_parameter_bounds() (scine_puffin.utilities.kinetic_modeling_sensitivity_analysis.RMSKineticModelingSensitivityAnalysis method) get_parameter_mean_and_std_dev_bounds() (scine_puffin.utilities.kinetic_modeling_sensitivity_analysis.RMSKineticModelingSensitivityAnalysis method) get_qm_atoms() (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces static method) get_reduced_parameter_mapping() (scine_puffin.utilities.kinetic_modeling_sensitivity_analysis.RMSKineticModelingSensitivityAnalysis method) get_slab_dict() (in module scine_puffin.utilities.surface_helper) get_system() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) Graph (class in scine_puffin.jobs.graph)

H

has_wavenumber_below_threshold() (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method)

HessianJob (class in scine_puffin.jobs.templates.scine_hessian_job)

I

initialize() (scine_puffin.programs.database.Database static method) (scine_puffin.programs.gaussian.Gaussian static method) (scine_puffin.programs.molassembler.Molassembler static method) (scine_puffin.programs.orca.Orca static method) (scine_puffin.programs.parrot.Parrot static method) (scine_puffin.programs.program.Program static method) (scine_puffin.programs.readuct.Readuct static method) (scine_puffin.programs.serenity.Serenity static method) (scine_puffin.programs.sparrow.Sparrow static method) (scine_puffin.programs.utils.Utils static method) (scine_puffin.utilities.turbomole_helper.TurbomoleHelper method) install() (scine_puffin.programs.database.Database method) (scine_puffin.programs.gaussian.Gaussian method) (scine_puffin.programs.molassembler.Molassembler method) (scine_puffin.programs.orca.Orca method) (scine_puffin.programs.parrot.Parrot method) (scine_puffin.programs.program.Program method) (scine_puffin.programs.readuct.Readuct method) (scine_puffin.programs.serenity.Serenity method) (scine_puffin.programs.sparrow.Sparrow method) (scine_puffin.programs.utils.Utils method)

integrate_results() (scine_puffin.utilities.rms_kinetic_model.RMSKineticModel method) IRC (scine_puffin.utilities.task_to_readuct_call.SubTaskToReaductCall attribute) irc_sanity_checks_and_analyze_sides() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) IRCOPT (scine_puffin.utilities.task_to_readuct_call.SubTaskToReaductCall attribute) is_configured() (in module scine_puffin.jobs.templates.job) is_qm_mm() (in module scine_puffin.utilities.qm_mm_settings)

J

Job (class in scine_puffin.jobs.templates.job)

job_configuration_wrapper() (in module scine_puffin.jobs.templates.job)

K

kill_daemon() (in module scine_puffin.jobloop)

KineticModelingJob (class in scine_puffin.jobs.templates.kinetic_modeling_jobs) KinetxKineticModeling (class in scine_puffin.jobs.kinetx_kinetic_modeling)

L

load() (scine_puffin.config.Configuration method)

loop() (in module scine_puffin.jobloop)

M

make_bin_str() (in module scine_puffin.utilities.masm_helper) make_bond_orders_from_calc() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) make_decision_lists_from_calc() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) make_graph_from_calc() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) make_masm_result_from_calc() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method)

make_new_cutoff_properties() (scine_puffin.utilities.program_helper.Cp2kHelper method) manage_settings() (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) map_total_indices_to_split_structure_indices() (scine_puffin.utilities.reaction_transfer_helper.ReactionTransferHelper static method) MissingDependency (class in scine_puffin.utilities.imports) MissingDependencyError module scine_puffin.bootstrap scine_puffin.config scine_puffin.daemon scine_puffin.jobloop scine_puffin.jobs scine_puffin.jobs.conformers scine_puffin.jobs.gaussian_charge_model_5 scine_puffin.jobs.graph scine_puffin.jobs.kinetx_kinetic_modeling scine_puffin.jobs.orca_geometry_optimization scine_puffin.jobs.rms_kinetic_modeling scine_puffin.jobs.scine_afir scine_puffin.jobs.scine_bond_orders scine_puffin.jobs.scine_bspline_optimization scine_puffin.jobs.scine_conceptual_dft scine_puffin.jobs.scine_dissociation_cut scine_puffin.jobs.scine_dissociation_cut_with_optimization scine_puffin.jobs.scine_geometry_optimization scine_puffin.jobs.scine_geometry_validation scine_puffin.jobs.scine_hessian scine_puffin.jobs.scine_irc_scan scine_puffin.jobs.scine_qm_region_selection scine_puffin.jobs.scine_react_complex_afir scine_puffin.jobs.scine_react_complex_nt scine_puffin.jobs.scine_react_complex_nt2 scine_puffin.jobs.scine_react_ts_guess scine_puffin.jobs.scine_single_point scine_puffin.jobs.scine_ts_optimization scine_puffin.jobs.sleep scine_puffin.jobs.swoose_qmmm_forces scine_puffin.jobs.templates scine_puffin.jobs.templates.job scine_puffin.jobs.templates.kinetic_modeling_jobs scine_puffin.jobs.templates.scine_connectivity_job scine_puffin.jobs.templates.scine_hessian_job scine_puffin.jobs.templates.scine_job scine_puffin.jobs.templates.scine_job_with_observers scine_puffin.jobs.templates.scine_observers scine_puffin.jobs.templates.scine_optimization_job scine_puffin.jobs.templates.scine_propensity_job scine_puffin.jobs.templates.scine_react_job scine_puffin.jobs.templates.sub_settings_job scine_puffin.jobs.templates.turbomole_job scine_puffin.jobs.turbomole_bond_orders scine_puffin.jobs.turbomole_geometry_optimization scine_puffin.jobs.turbomole_hessian scine_puffin.jobs.turbomole_single_point scine_puffin.programs.program scine_puffin.utilities scine_puffin.utilities.compound_and_flask_helpers scine_puffin.utilities.imports scine_puffin.utilities.kinetic_modeling_sensitivity_analysis scine_puffin.utilities.masm_helper scine_puffin.utilities.program_helper scine_puffin.utilities.properties scine_puffin.utilities.qm_mm_settings scine_puffin.utilities.reaction_transfer_helper scine_puffin.utilities.rms_input_file_creator scine_puffin.utilities.rms_kinetic_model scine_puffin.utilities.scine_helper scine_puffin.utilities.surface_helper scine_puffin.utilities.task_to_readuct_call scine_puffin.utilities.transfer_helper scine_puffin.utilities.turbomole_helper module_exists() (in module scine_puffin.utilities.imports) Molassembler (class in scine_puffin.programs.molassembler) morris_sensitivities() (scine_puffin.utilities.kinetic_modeling_sensitivity_analysis.RMSKineticModelingSensitivityAnalysis method)

N

n_imag_frequencies() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method)

NT (scine_puffin.utilities.task_to_readuct_call.SubTaskToReaductCall attribute) NT2 (scine_puffin.utilities.task_to_readuct_call.SubTaskToReaductCall attribute)

O

observed_readuct_call() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) observed_readuct_call_with_throw() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) Observer (class in scine_puffin.jobs.templates.scine_observers) one_at_a_time_differences() (scine_puffin.utilities.kinetic_modeling_sensitivity_analysis.RMSKineticModelingSensitivityAnalysis method) OPT (scine_puffin.utilities.task_to_readuct_call.SubTaskToReaductCall attribute) optimization_postprocessing() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) OptimizationJob (class in scine_puffin.jobs.templates.scine_optimization_job) optimize_cutoffs() (scine_puffin.utilities.program_helper.Cp2kHelper method) optimize_structures() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method)

Orca (class in scine_puffin.programs.orca) OrcaGeometryOptimization (class in scine_puffin.jobs.orca_geometry_optimization) output() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) own_expected_results (scine_puffin.jobs.conformers.Conformers attribute) (scine_puffin.jobs.graph.Graph attribute) (scine_puffin.jobs.scine_afir.ScineAfir attribute) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders attribute) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization attribute) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft attribute) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut attribute) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization attribute) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization attribute) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation attribute) (scine_puffin.jobs.scine_hessian.ScineHessian attribute) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan attribute) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection attribute) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir attribute) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt attribute) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 attribute) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess attribute) (scine_puffin.jobs.scine_single_point.ScineSinglePoint attribute) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization attribute) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces attribute) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob attribute) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob attribute) (scine_puffin.jobs.templates.scine_job.ScineJob attribute) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers attribute) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob attribute) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob attribute) (scine_puffin.jobs.templates.scine_react_job.ReactJob attribute) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob attribute)

P

Parrot (class in scine_puffin.programs.parrot) parse_energy() (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces static method) parse_energy_file() (scine_puffin.utilities.turbomole_helper.TurbomoleHelper method) parse_forces() (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces static method) parse_output_file() (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 method) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization method) parse_results() (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization method) pip_module_source_install() (scine_puffin.programs.database.Database method) (scine_puffin.programs.gaussian.Gaussian method) (scine_puffin.programs.molassembler.Molassembler method) (scine_puffin.programs.orca.Orca method) (scine_puffin.programs.parrot.Parrot method) (scine_puffin.programs.program.Program method) (scine_puffin.programs.readuct.Readuct method) (scine_puffin.programs.serenity.Serenity method) (scine_puffin.programs.sparrow.Sparrow method) (scine_puffin.programs.utils.Utils method) pip_package_install() (scine_puffin.programs.database.Database static method) (scine_puffin.programs.gaussian.Gaussian static method) (scine_puffin.programs.molassembler.Molassembler static method) (scine_puffin.programs.orca.Orca static method) (scine_puffin.programs.parrot.Parrot static method) (scine_puffin.programs.program.Program static method) (scine_puffin.programs.readuct.Readuct static method) (scine_puffin.programs.serenity.Serenity static method) (scine_puffin.programs.sparrow.Sparrow static method) (scine_puffin.programs.utils.Utils static method) postprocess_calculation_context() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling method) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization method) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.sleep.Sleep method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.job.Job method) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob method) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders method) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization method) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian method) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint method) prepare() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling method) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization method) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.sleep.Sleep method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.job.Job method) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob method) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders method) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization method) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian method) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint method)

prepare_calculation() (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob method) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders method) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization method) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian method) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint method) prepare_define_session() (scine_puffin.utilities.turbomole_helper.TurbomoleHelper method) prepare_optional_settings() (in module scine_puffin.utilities.qm_mm_settings) prepare_readuct_task() (scine_puffin.utilities.scine_helper.SettingsManager method) prepend_to_comment() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) process_output() (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) products_component_map (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization attribute) Program (class in scine_puffin.programs.program) program() (scine_puffin.utilities.program_helper.Cp2kHelper static method) (scine_puffin.utilities.program_helper.ProgramHelper static method) ProgramHelper (class in scine_puffin.utilities.program_helper) programs() (scine_puffin.config.Configuration method)

Q

query_bond_orders() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method)

R

raise_named_exception() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) random_displace_atoms() (scine_puffin.jobs.scine_afir.ScineAfir static method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization static method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut static method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization static method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir static method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt static method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 static method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess static method) (scine_puffin.jobs.templates.scine_react_job.ReactJob static method) RCOPT (scine_puffin.utilities.task_to_readuct_call.SubTaskToReaductCall attribute) react_postprocessing() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) ReactionTransferHelper (class in scine_puffin.utilities.reaction_transfer_helper) reactive_complex_preparations() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) ReactJob (class in scine_puffin.jobs.templates.scine_react_job) read_hessian_matrix() (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian method) read_irc_and_irc_opt_trajectories() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) Readuct (class in scine_puffin.programs.readuct) ref_structure (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization attribute) required_programs() (scine_puffin.jobs.conformers.Conformers static method) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 static method) (scine_puffin.jobs.graph.Graph static method) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling static method) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization static method) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling static method) (scine_puffin.jobs.scine_afir.ScineAfir static method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders static method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization static method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft static method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut static method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization static method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization static method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation static method) (scine_puffin.jobs.scine_hessian.ScineHessian static method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan static method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection static method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir static method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt static method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 static method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess static method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint static method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization static method) (scine_puffin.jobs.sleep.Sleep static method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces static method) (scine_puffin.jobs.templates.job.Job static method) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob static method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob static method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob static method) (scine_puffin.jobs.templates.scine_job.ScineJob static method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers static method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob static method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob static method) (scine_puffin.jobs.templates.scine_react_job.ReactJob static method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob static method) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob static method) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders static method) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization static method) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian static method) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint static method)

requires() (in module scine_puffin.utilities.imports) resolve_rms_phase() (in module scine_puffin.utilities.rms_input_file_creator) resolve_rms_solver() (in module scine_puffin.utilities.rms_input_file_creator) resources() (scine_puffin.config.Configuration method) RMSKineticModel (class in scine_puffin.utilities.rms_kinetic_model) RmsKineticModeling (class in scine_puffin.jobs.rms_kinetic_modeling) RMSKineticModelingSensitivityAnalysis (class in scine_puffin.utilities.kinetic_modeling_sensitivity_analysis) run() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling method) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization method) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.sleep.Sleep method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.job.Job method) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob method) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders method) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization method) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian method) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint method) run_kinetic_modeling() (scine_puffin.utilities.rms_kinetic_model.RMSKineticModel method)

S

salib_wrapped_kinetic_modeling() (scine_puffin.utilities.kinetic_modeling_sensitivity_analysis.RMSKineticModelingSensitivityAnalysis method) save_barrierless_reaction_from_rcopt() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) save_initial_graphs_and_charges() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) save_mep_in_db() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) save_results() (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) scine_module_install() (scine_puffin.programs.database.Database method) (scine_puffin.programs.gaussian.Gaussian method) (scine_puffin.programs.molassembler.Molassembler method) (scine_puffin.programs.orca.Orca method) (scine_puffin.programs.parrot.Parrot method) (scine_puffin.programs.program.Program method) (scine_puffin.programs.readuct.Readuct method) (scine_puffin.programs.serenity.Serenity method) (scine_puffin.programs.sparrow.Sparrow method) (scine_puffin.programs.utils.Utils method) scine_puffin.bootstrap module scine_puffin.config module scine_puffin.daemon module scine_puffin.jobloop module scine_puffin.jobs module scine_puffin.jobs.conformers module scine_puffin.jobs.gaussian_charge_model_5 module scine_puffin.jobs.graph module scine_puffin.jobs.kinetx_kinetic_modeling module scine_puffin.jobs.orca_geometry_optimization module scine_puffin.jobs.rms_kinetic_modeling module scine_puffin.jobs.scine_afir module scine_puffin.jobs.scine_bond_orders module scine_puffin.jobs.scine_bspline_optimization module scine_puffin.jobs.scine_conceptual_dft module scine_puffin.jobs.scine_dissociation_cut module scine_puffin.jobs.scine_dissociation_cut_with_optimization module scine_puffin.jobs.scine_geometry_optimization module scine_puffin.jobs.scine_geometry_validation module scine_puffin.jobs.scine_hessian module scine_puffin.jobs.scine_irc_scan module scine_puffin.jobs.scine_qm_region_selection module scine_puffin.jobs.scine_react_complex_afir module scine_puffin.jobs.scine_react_complex_nt module scine_puffin.jobs.scine_react_complex_nt2 module scine_puffin.jobs.scine_react_ts_guess module scine_puffin.jobs.scine_single_point module scine_puffin.jobs.scine_ts_optimization module scine_puffin.jobs.sleep module scine_puffin.jobs.swoose_qmmm_forces module scine_puffin.jobs.templates module scine_puffin.jobs.templates.job module scine_puffin.jobs.templates.kinetic_modeling_jobs module scine_puffin.jobs.templates.scine_connectivity_job module scine_puffin.jobs.templates.scine_hessian_job module scine_puffin.jobs.templates.scine_job module scine_puffin.jobs.templates.scine_job_with_observers module scine_puffin.jobs.templates.scine_observers module scine_puffin.jobs.templates.scine_optimization_job module scine_puffin.jobs.templates.scine_propensity_job module scine_puffin.jobs.templates.scine_react_job module scine_puffin.jobs.templates.sub_settings_job module scine_puffin.jobs.templates.turbomole_job module scine_puffin.jobs.turbomole_bond_orders module scine_puffin.jobs.turbomole_geometry_optimization module scine_puffin.jobs.turbomole_hessian module scine_puffin.jobs.turbomole_single_point module scine_puffin.programs.program module scine_puffin.utilities module scine_puffin.utilities.compound_and_flask_helpers module scine_puffin.utilities.imports module scine_puffin.utilities.kinetic_modeling_sensitivity_analysis module scine_puffin.utilities.masm_helper module scine_puffin.utilities.program_helper module scine_puffin.utilities.properties module scine_puffin.utilities.qm_mm_settings module scine_puffin.utilities.reaction_transfer_helper module scine_puffin.utilities.rms_input_file_creator module scine_puffin.utilities.rms_kinetic_model module scine_puffin.utilities.scine_helper module scine_puffin.utilities.surface_helper module scine_puffin.utilities.task_to_readuct_call module scine_puffin.utilities.transfer_helper module scine_puffin.utilities.turbomole_helper module ScineAfir (class in scine_puffin.jobs.scine_afir) ScineBondOrders (class in scine_puffin.jobs.scine_bond_orders) ScineBsplineOptimization (class in scine_puffin.jobs.scine_bspline_optimization) ScineConceptualDft (class in scine_puffin.jobs.scine_conceptual_dft) ScineDissociationCut (class in scine_puffin.jobs.scine_dissociation_cut) ScineDissociationCutWithOptimization (class in scine_puffin.jobs.scine_dissociation_cut_with_optimization) ScineGeometryOptimization (class in scine_puffin.jobs.scine_geometry_optimization) ScineGeometryValidation (class in scine_puffin.jobs.scine_geometry_validation) ScineHessian (class in scine_puffin.jobs.scine_hessian) ScineIrcScan (class in scine_puffin.jobs.scine_irc_scan) ScineJob (class in scine_puffin.jobs.templates.scine_job) ScineJobWithObservers (class in scine_puffin.jobs.templates.scine_job_with_observers) ScinePropensityJob (class in scine_puffin.jobs.templates.scine_propensity_job) ScineQmRegionSelection (class in scine_puffin.jobs.scine_qm_region_selection) ScineReactComplexAfir (class in scine_puffin.jobs.scine_react_complex_afir) ScineReactComplexNt (class in scine_puffin.jobs.scine_react_complex_nt) ScineReactComplexNt2 (class in scine_puffin.jobs.scine_react_complex_nt2) ScineReactTsGuess (class in scine_puffin.jobs.scine_react_ts_guess) ScineSinglePoint (class in scine_puffin.jobs.scine_single_point) ScineTsOptimization (class in scine_puffin.jobs.scine_ts_optimization) separate_settings() (scine_puffin.utilities.scine_helper.SettingsManager method) Serenity (class in scine_puffin.programs.serenity) set_analysis_times() (scine_puffin.utilities.kinetic_modeling_sensitivity_analysis.RMSKineticModelingSensitivityAnalysis method) set_prescreening_condition() (scine_puffin.utilities.kinetic_modeling_sensitivity_analysis.RMSKineticModelingSensitivityAnalysis method) setting_is_available() (scine_puffin.utilities.scine_helper.SettingsManager method) settings (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization attribute) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob attribute) (scine_puffin.jobs.templates.scine_react_job.ReactJob attribute) SettingsManager (class in scine_puffin.utilities.scine_helper) setup_automatic_mode_selection() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) setup_environment() (scine_puffin.programs.database.Database method) (scine_puffin.programs.gaussian.Gaussian method) (scine_puffin.programs.molassembler.Molassembler method) (scine_puffin.programs.orca.Orca method) (scine_puffin.programs.parrot.Parrot method) (scine_puffin.programs.program.Program method) (scine_puffin.programs.readuct.Readuct method) (scine_puffin.programs.serenity.Serenity method) (scine_puffin.programs.sparrow.Sparrow method) (scine_puffin.programs.utils.Utils method) shutdown() (in module scine_puffin.daemon) simple_transfer() (scine_puffin.utilities.reaction_transfer_helper.ReactionTransferHelper static method) (scine_puffin.utilities.transfer_helper.TransferHelper static method) simple_transfer_all() (scine_puffin.utilities.reaction_transfer_helper.ReactionTransferHelper static method) (scine_puffin.utilities.transfer_helper.TransferHelper static method) single_particle_energy_from_matrix() (in module scine_puffin.utilities.properties) single_particle_energy_to_matrix() (in module scine_puffin.utilities.properties) slab_dict_name (scine_puffin.utilities.reaction_transfer_helper.ReactionTransferHelper attribute) Sleep (class in scine_puffin.jobs.sleep) slow_connect() (in module scine_puffin.jobloop) sobol_sensitivities() (scine_puffin.utilities.kinetic_modeling_sensitivity_analysis.RMSKineticModelingSensitivityAnalysis method) sort_settings() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) SP (scine_puffin.utilities.task_to_readuct_call.SubTaskToReaductCall attribute) sp_postprocessing() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) Sparrow (class in scine_puffin.programs.sparrow) start_charges (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization attribute) start_daemon() (in module scine_puffin.daemon) start_decision_lists (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization attribute) start_multiplicities (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization attribute) stderr_path (scine_puffin.jobs.conformers.Conformers attribute) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 attribute) (scine_puffin.jobs.graph.Graph attribute) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling attribute) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization attribute) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling attribute) (scine_puffin.jobs.scine_afir.ScineAfir attribute) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders attribute) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization attribute) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft attribute) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut attribute) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization attribute) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization attribute) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation attribute) (scine_puffin.jobs.scine_hessian.ScineHessian attribute) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan attribute) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection attribute) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir attribute) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt attribute) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 attribute) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess attribute) (scine_puffin.jobs.scine_single_point.ScineSinglePoint attribute) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization attribute) (scine_puffin.jobs.sleep.Sleep attribute) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces attribute) (scine_puffin.jobs.templates.job.Job attribute) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob attribute) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob attribute) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob attribute) (scine_puffin.jobs.templates.scine_job.ScineJob attribute) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers attribute) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob attribute) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob attribute) (scine_puffin.jobs.templates.scine_react_job.ReactJob attribute) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob attribute) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob attribute) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders attribute) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization attribute) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian attribute) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint attribute)

stdout_path (scine_puffin.jobs.conformers.Conformers attribute) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 attribute) (scine_puffin.jobs.graph.Graph attribute) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling attribute) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization attribute) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling attribute) (scine_puffin.jobs.scine_afir.ScineAfir attribute) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders attribute) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization attribute) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft attribute) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut attribute) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization attribute) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization attribute) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation attribute) (scine_puffin.jobs.scine_hessian.ScineHessian attribute) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan attribute) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection attribute) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir attribute) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt attribute) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 attribute) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess attribute) (scine_puffin.jobs.scine_single_point.ScineSinglePoint attribute) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization attribute) (scine_puffin.jobs.sleep.Sleep attribute) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces attribute) (scine_puffin.jobs.templates.job.Job attribute) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob attribute) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob attribute) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob attribute) (scine_puffin.jobs.templates.scine_job.ScineJob attribute) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers attribute) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob attribute) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob attribute) (scine_puffin.jobs.templates.scine_react_job.ReactJob attribute) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob attribute) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob attribute) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders attribute) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization attribute) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian attribute) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint attribute) step_direction (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization attribute) stop_daemon() (in module scine_puffin.daemon) store_bond_orders() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) store_energy() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) store_hessian_data() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) store_property() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling method) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization method) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.sleep.Sleep method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.job.Job method) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob method) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders method) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization method) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian method) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint method) store_start_structures() (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) StoreEverythingObserver (class in scine_puffin.jobs.templates.scine_observers) StoreWithFractionObserver (class in scine_puffin.jobs.templates.scine_observers) StoreWithFrequencyObserver (class in scine_puffin.jobs.templates.scine_observers) structure_has_cutoff_properties() (scine_puffin.utilities.program_helper.Cp2kHelper method) SubSettingsJob (class in scine_puffin.jobs.templates.sub_settings_job) SubTaskToReaductCall (class in scine_puffin.utilities.task_to_readuct_call) success_file() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling method) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization method) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.sleep.Sleep method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.job.Job method) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob method) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders method) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization method) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian method) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint method) surface_indices() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) surface_indices_all_structures() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) surface_indices_name (scine_puffin.utilities.reaction_transfer_helper.ReactionTransferHelper attribute) SwooseQmmmForces (class in scine_puffin.jobs.swoose_qmmm_forces) systems (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization attribute)

T

tag_to_label() (scine_puffin.jobs.templates.scine_observers.StoreEverythingObserver static method) (scine_puffin.jobs.templates.scine_observers.StoreWithFractionObserver static method) (scine_puffin.jobs.templates.scine_observers.StoreWithFrequencyObserver static method) throw_if_not_successful() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) transfer_properties() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) (scine_puffin.utilities.reaction_transfer_helper.ReactionTransferHelper method) (scine_puffin.utilities.transfer_helper.TransferHelper method)

transfer_properties_between_multiple() (scine_puffin.utilities.reaction_transfer_helper.ReactionTransferHelper method) (scine_puffin.utilities.transfer_helper.TransferHelper method) TransferHelper (class in scine_puffin.utilities.transfer_helper) translate_minimum_change_to_barriers() (scine_puffin.utilities.rms_kinetic_model.RMSKineticModel method) TSOPT (scine_puffin.utilities.task_to_readuct_call.SubTaskToReaductCall attribute) TurbomoleBondOrders (class in scine_puffin.jobs.turbomole_bond_orders) TurbomoleGeometryOptimization (class in scine_puffin.jobs.turbomole_geometry_optimization) TurbomoleHelper (class in scine_puffin.utilities.turbomole_helper) TurbomoleHessian (class in scine_puffin.jobs.turbomole_hessian) TurbomoleJob (class in scine_puffin.jobs.templates.turbomole_job) TurbomoleSinglePoint (class in scine_puffin.jobs.turbomole_single_point)

U

update_calculator_settings() (scine_puffin.utilities.scine_helper.SettingsManager method) update_model() (in module scine_puffin.utilities.scine_helper)

update_slab_dict() (in module scine_puffin.utilities.surface_helper) use_n_cores() (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling method) Utils (class in scine_puffin.programs.utils)

V

valid_model_solution() (scine_puffin.utilities.rms_kinetic_model.RMSKineticModel method) verify_connection() (scine_puffin.jobs.conformers.Conformers method) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 method) (scine_puffin.jobs.graph.Graph method) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling method) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization method) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling method) (scine_puffin.jobs.scine_afir.ScineAfir method) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders method) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization method) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft method) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut method) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization method) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization method) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation method) (scine_puffin.jobs.scine_hessian.ScineHessian method) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan method) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection method) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir method) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt method) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 method) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess method) (scine_puffin.jobs.scine_single_point.ScineSinglePoint method) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization method) (scine_puffin.jobs.sleep.Sleep method) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces method) (scine_puffin.jobs.templates.job.Job method) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob method) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob method) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob method) (scine_puffin.jobs.templates.scine_job.ScineJob method) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers method) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob method) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob method) (scine_puffin.jobs.templates.scine_react_job.ReactJob method) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob method) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob method) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders method) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization method) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian method) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint method)

W

with_traceback() (scine_puffin.jobs.templates.job.breakable.Break method) (scine_puffin.jobs.templates.scine_job.CalculatorNotPresentException method) (scine_puffin.utilities.imports.MissingDependencyError method) work_dir (scine_puffin.jobs.conformers.Conformers attribute) (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 attribute) (scine_puffin.jobs.graph.Graph attribute) (scine_puffin.jobs.kinetx_kinetic_modeling.KinetxKineticModeling attribute) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization attribute) (scine_puffin.jobs.rms_kinetic_modeling.RmsKineticModeling attribute) (scine_puffin.jobs.scine_afir.ScineAfir attribute) (scine_puffin.jobs.scine_bond_orders.ScineBondOrders attribute) (scine_puffin.jobs.scine_bspline_optimization.ScineBsplineOptimization attribute) (scine_puffin.jobs.scine_conceptual_dft.ScineConceptualDft attribute) (scine_puffin.jobs.scine_dissociation_cut.ScineDissociationCut attribute) (scine_puffin.jobs.scine_dissociation_cut_with_optimization.ScineDissociationCutWithOptimization attribute) (scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization attribute) (scine_puffin.jobs.scine_geometry_validation.ScineGeometryValidation attribute) (scine_puffin.jobs.scine_hessian.ScineHessian attribute) (scine_puffin.jobs.scine_irc_scan.ScineIrcScan attribute) (scine_puffin.jobs.scine_qm_region_selection.ScineQmRegionSelection attribute) (scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir attribute) (scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt attribute) (scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2 attribute) (scine_puffin.jobs.scine_react_ts_guess.ScineReactTsGuess attribute) (scine_puffin.jobs.scine_single_point.ScineSinglePoint attribute) (scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization attribute) (scine_puffin.jobs.sleep.Sleep attribute) (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces attribute) (scine_puffin.jobs.templates.job.Job attribute) (scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob attribute) (scine_puffin.jobs.templates.scine_connectivity_job.ConnectivityJob attribute) (scine_puffin.jobs.templates.scine_hessian_job.HessianJob attribute) (scine_puffin.jobs.templates.scine_job.ScineJob attribute) (scine_puffin.jobs.templates.scine_job_with_observers.ScineJobWithObservers attribute) (scine_puffin.jobs.templates.scine_optimization_job.OptimizationJob attribute) (scine_puffin.jobs.templates.scine_propensity_job.ScinePropensityJob attribute) (scine_puffin.jobs.templates.scine_react_job.ReactJob attribute) (scine_puffin.jobs.templates.sub_settings_job.SubSettingsJob attribute) (scine_puffin.jobs.templates.turbomole_job.TurbomoleJob attribute) (scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders attribute) (scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization attribute) (scine_puffin.jobs.turbomole_hessian.TurbomoleHessian attribute) (scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint attribute)

write_connectivity_file() (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces static method) write_coord_file() (scine_puffin.utilities.turbomole_helper.TurbomoleHelper method) write_input_file() (scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5 method) (scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization method) write_parameter_and_connectivity_file() (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces static method) write_parameter_file() (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces static method) write_partial_charge_file() (scine_puffin.jobs.swoose_qmmm_forces.SwooseQmmmForces static method)