Index

A

abop_potential() (pyiron_contrib.atomistics.atomicrex.potential_factory.ARPotFactory static method) abop_to_tersoff_params() (in module pyiron_contrib.atomistics.atomicrex.potential_factory) ABOPParameters (class in pyiron_contrib.atomistics.atomicrex.potential_factory) ABOPPotential (class in pyiron_contrib.atomistics.atomicrex.potential_factory) AbstractMetaFunction (class in pyiron_contrib.atomistics.atomicrex.function_factory) AbstractPotential (class in pyiron_contrib.atomistics.atomicrex.potential_factory) activate() (pyiron_contrib.image.utils.ModuleScraper method) activate_postprocessing() (pyiron_contrib.atomistics.mlip.mlip.CommandLine method) active_vertex (pyiron_contrib.protocol.generic.Graph attribute) add_coeff() (pyiron_contrib.atomistics.atomicrex.function_factory.PolyCoeffList method) add_constraint() (pyiron_contrib.atomistics.atomicrex.parameter_constraints.ParameterConstraints method) add_event_handler() (pyiron_contrib.protocol.utils.event.Event method) add_FitProperty() (pyiron_contrib.atomistics.atomicrex.fit_properties.ARFitPropertyList method) add_image() (pyiron_contrib.image.job.ImageJob method) add_images() (pyiron_contrib.image.job.ImageJob method) add_job_to_fitting() (pyiron_contrib.atomistics.mlip.mlip.Mlip method) (pyiron_contrib.atomistics.pacemaker.job.PacemakerJob method) add_node() (pyiron_contrib.atomistics.atomicrex.function_factory.NodeList method) add_parameter() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionParameterList method) add_predefined_structure() (pyiron_contrib.atomistics.atomicrex.structure_list.ARStructureContainer method) add_scalar_fit_property() (pyiron_contrib.atomistics.atomicrex.structure_list.ARStructureContainer method) add_structure() (pyiron_contrib.atomistics.atomicrex.structure_list.ARStructureContainer method) (pyiron_contrib.atomistics.atomistics.job.structurelistmasterinteractive.StructureMasterInt method) (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingContainer method) (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingStorage method) add_training_data() (pyiron_contrib.atomistics.atomicrex.structure_list.ARStructureContainer method) (pyiron_contrib.atomistics.ml.potentialfit.PotentialFit method)

add_vector_fit_property() (pyiron_contrib.atomistics.atomicrex.structure_list.ARStructureContainer method) AddDisplacements (class in pyiron_contrib.protocol.compound.qmmm) adp_potential() (pyiron_contrib.atomistics.atomicrex.potential_factory.ARPotFactory static method) ADPotential (class in pyiron_contrib.atomistics.atomicrex.potential_factory) AlgorithmFactory (class in pyiron_contrib.atomistics.atomicrex.general_input) AnyVertex (class in pyiron_contrib.protocol.primitive.two_state) append() (pyiron_contrib.protocol.utils.pointer.Path method) ar_lbfgs() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) ar_spa() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) archive (pyiron_contrib.protocol.generic.Vertex attribute) ARFitProperty (class in pyiron_contrib.atomistics.atomicrex.fit_properties) ARFitPropertyList (class in pyiron_contrib.atomistics.atomicrex.fit_properties) ARPotFactory (class in pyiron_contrib.atomistics.atomicrex.potential_factory) array (pyiron_contrib.protocol.utils.dictionaries.TimelineDict property) ARStructureContainer (class in pyiron_contrib.atomistics.atomicrex.structure_list) as_gray (pyiron_contrib.image.image.Image attribute) Atomicrex (class in pyiron_contrib.atomistics.atomicrex.atomicrex_job) atomicrex_job_object (pyiron_contrib.atomistics.atomicrex.interactive.AtomicrexInteractive property) AtomicrexAlgorithm (class in pyiron_contrib.atomistics.atomicrex.general_input) AtomicrexBase (class in pyiron_contrib.atomistics.atomicrex.base) AtomicrexInteractive (class in pyiron_contrib.atomistics.atomicrex.interactive) AtomsComparer (class in pyiron_contrib.protocol.utils.comparers) AtomTypes (class in pyiron_contrib.atomistics.atomicrex.general_input) Attribute (pyiron_contrib.protocol.utils.pointer.CrumbType attribute) attribute() (pyiron_contrib.protocol.utils.pointer.Crumb static method) attribute_name (pyiron_contrib.image.utils.LockedIfAttributeTrue attribute) (pyiron_contrib.image.utils.ModuleScraper attribute), [1], [2], [3], [4], [5] AutoList (class in pyiron_contrib.protocol.list)

B

BaseFunctionMixin (class in pyiron_contrib.atomistics.atomicrex.function_factory) BerendsenBarostat (class in pyiron_contrib.protocol.primitive.one_state) BoolVertex (class in pyiron_contrib.protocol.primitive.two_state) BOPAbstract (class in pyiron_contrib.atomistics.atomicrex.potential_factory)

BOPParameters (class in pyiron_contrib.atomistics.atomicrex.potential_factory) both_are_int_or_float() (pyiron_contrib.protocol.utils.comparers.Comparer static method) brightness_filter() (in module pyiron_contrib.image.custom_filters) broadcast (pyiron_contrib.protocol.list.ListVertex attribute) BuildMixingPairs (class in pyiron_contrib.protocol.primitive.one_state)

C

calculation_dataframe (pyiron_contrib.atomistics.mlip.mlip.Mlip property) cell() (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingPlots method) CentroidsReparameterization (class in pyiron_contrib.protocol.primitive.fts_vertices) CentroidsRunningAverageMix (class in pyiron_contrib.protocol.primitive.fts_vertices) CentroidsSmoothing (class in pyiron_contrib.protocol.primitive.fts_vertices) Cfg (class in pyiron_contrib.atomistics.mlip.cfgs) cfgparser (class in pyiron_contrib.atomistics.mlip.cfgs) child_type (pyiron_contrib.protocol.list.ListVertex attribute) children (pyiron_contrib.protocol.list.ListVertex attribute) clear_handlers() (pyiron_contrib.protocol.utils.event.Event method) collect_logfiles() (pyiron_contrib.atomistics.mlip.mlip.Mlip method) (pyiron_contrib.atomistics.randspg.randspg.RandSpg method) collect_output() (pyiron_contrib.atomistics.atomicrex.base.AtomicrexBase method) (pyiron_contrib.atomistics.atomistics.job.structurelistmasterinteractive.StructureMasterInt method) (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingContainer method) (pyiron_contrib.atomistics.dft.parametermaster.ParameterMaster method) (pyiron_contrib.atomistics.mlip.lammps.LammpsMlip method) (pyiron_contrib.atomistics.mlip.masters.RandomDisMaster method) (pyiron_contrib.atomistics.mlip.masters.RandomMDMaster method) (pyiron_contrib.atomistics.mlip.mlip.Mlip method) (pyiron_contrib.atomistics.mlip.mlipjob.MlipJob method) (pyiron_contrib.atomistics.mlip.mlipselect.MlipSelect method) (pyiron_contrib.atomistics.pacemaker.job.PacemakerJob method) (pyiron_contrib.atomistics.randspg.randspg.RandSpg method) (pyiron_contrib.image.job.ImageJob method) (pyiron_contrib.protocol.generic.Protocol method) collect_output_log() (pyiron_contrib.atomistics.randspg.randspg.RandSpg method) command() (pyiron_contrib.protocol.compound.qmmm.AddDisplacements method) (pyiron_contrib.protocol.compound.qmmm.PartitionStructure method) (pyiron_contrib.protocol.generic.PrimitiveVertex method) (pyiron_contrib.protocol.list.AutoList method) (pyiron_contrib.protocol.list.ListVertex method) (pyiron_contrib.protocol.list.ParallelList method) (pyiron_contrib.protocol.list.SerialList method) (pyiron_contrib.protocol.primitive.fts_vertices.CentroidsReparameterization method) (pyiron_contrib.protocol.primitive.fts_vertices.CentroidsRunningAverageMix method) (pyiron_contrib.protocol.primitive.fts_vertices.CentroidsSmoothing method) (pyiron_contrib.protocol.primitive.fts_vertices.PositionsRunningAverage method) (pyiron_contrib.protocol.primitive.fts_vertices.StringRecenter method) (pyiron_contrib.protocol.primitive.fts_vertices.StringReflect method) (pyiron_contrib.protocol.primitive.one_state.BerendsenBarostat method) (pyiron_contrib.protocol.primitive.one_state.BuildMixingPairs method) (pyiron_contrib.protocol.primitive.one_state.Compute method) (pyiron_contrib.protocol.primitive.one_state.ComputeFormationEnergy method) (pyiron_contrib.protocol.primitive.one_state.Counter method) (pyiron_contrib.protocol.primitive.one_state.CreateJob method) (pyiron_contrib.protocol.primitive.one_state.CutoffDistance method) (pyiron_contrib.protocol.primitive.one_state.DeleteAtom method) (pyiron_contrib.protocol.primitive.one_state.ExternalHamiltonian method) (pyiron_contrib.protocol.primitive.one_state.FEPExponential method) (pyiron_contrib.protocol.primitive.one_state.GradientDescent method) (pyiron_contrib.protocol.primitive.one_state.HarmonicHamiltonian method) (pyiron_contrib.protocol.primitive.one_state.InitialPositions method) (pyiron_contrib.protocol.primitive.one_state.LangevinThermostat method) (pyiron_contrib.protocol.primitive.one_state.Max method) (pyiron_contrib.protocol.primitive.one_state.MinimizeReferenceJob method) (pyiron_contrib.protocol.primitive.one_state.NEBForces method) (pyiron_contrib.protocol.primitive.one_state.Norm method) (pyiron_contrib.protocol.primitive.one_state.Overwrite method) (pyiron_contrib.protocol.primitive.one_state.RandomVelocity method) (pyiron_contrib.protocol.primitive.one_state.RemoveJob method) (pyiron_contrib.protocol.primitive.one_state.Slice method) (pyiron_contrib.protocol.primitive.one_state.SphereReflection method) (pyiron_contrib.protocol.primitive.one_state.SphereReflectionPerAtom method) (pyiron_contrib.protocol.primitive.one_state.TILDPostProcess method) (pyiron_contrib.protocol.primitive.one_state.Transpose method) (pyiron_contrib.protocol.primitive.one_state.VerletParent method) (pyiron_contrib.protocol.primitive.one_state.VerletPositionUpdate method) (pyiron_contrib.protocol.primitive.one_state.VerletVelocityUpdate method) (pyiron_contrib.protocol.primitive.one_state.VoronoiReflection method) (pyiron_contrib.protocol.primitive.one_state.WeightedSum method) (pyiron_contrib.protocol.primitive.one_state.WelfordOnline method) (pyiron_contrib.protocol.primitive.one_state.Zeros method) (pyiron_contrib.protocol.primitive.two_state.AnyVertex method) (pyiron_contrib.protocol.primitive.two_state.IsGEq method) (pyiron_contrib.protocol.primitive.two_state.IsLEq method) (pyiron_contrib.protocol.primitive.two_state.ModIsZero method)

CommandLine (class in pyiron_contrib.atomistics.mlip.mlip) Comparer (class in pyiron_contrib.protocol.utils.comparers) compatible_types() (pyiron_contrib.protocol.utils.comparers.Comparer method) CompoundVertex (class in pyiron_contrib.protocol.generic) compress() (pyiron_contrib.atomistics.atomicrex.base.AtomicrexBase method) Compute (class in pyiron_contrib.protocol.primitive.one_state) ComputeFormationEnergy (class in pyiron_contrib.protocol.primitive.one_state) ConfinedMD (class in pyiron_contrib.protocol.compound.molecular_dynamics) Constant (class in pyiron_contrib.atomistics.atomicrex.function_factory) constant() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method) Constraint (class in pyiron_contrib.atomistics.atomicrex.parameter_constraints) container (pyiron_contrib.atomistics.atomistics.job.structurelistmasterinteractive.StructureMasterInt property) convergence_check() (pyiron_contrib.atomistics.atomicrex.base.AtomicrexBase method) (pyiron_contrib.atomistics.mlip.lammps.LammpsMlip method) convert_to_acceleration() (pyiron_contrib.protocol.primitive.one_state.VerletParent static method) convert_to_grayscale() (pyiron_contrib.image.image.Image method) coordination() (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingPlots method) copy_final_to_initial_params() (pyiron_contrib.atomistics.atomicrex.function_factory.BaseFunctionMixin method) (pyiron_contrib.atomistics.atomicrex.function_factory.MetaFunctionMixin method) (pyiron_contrib.atomistics.atomicrex.function_factory.Spline method) (pyiron_contrib.atomistics.atomicrex.potential_factory.EAMlikeMixin method) copy_final_to_start_value() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionParameter method) count() (pyiron_contrib.protocol.utils.pointer.Path method) count_local_extrema() (pyiron_contrib.atomistics.atomicrex.potential_factory.EAMPotential method) count_parameters() (pyiron_contrib.atomistics.atomicrex.function_factory.BaseFunctionMixin method) (pyiron_contrib.atomistics.atomicrex.function_factory.MetaFunctionMixin method) (pyiron_contrib.atomistics.atomicrex.function_factory.Spline method) (pyiron_contrib.atomistics.atomicrex.potential_factory.EAMlikeMixin method) count_paths() (in module pyiron_contrib.protocol.utils.pptree) Counter (class in pyiron_contrib.protocol.primitive.one_state) create_from_arrays() (pyiron_contrib.atomistics.atomicrex.function_factory.NodeList method) create_training_dataframe() (pyiron_contrib.atomistics.pacemaker.job.PacemakerJob method) CreateJob (class in pyiron_contrib.protocol.primitive.one_state) Crumb (class in pyiron_contrib.protocol.utils.pointer) crumb_type (pyiron_contrib.protocol.utils.pointer.Crumb property) CrumbType (class in pyiron_contrib.protocol.utils.pointer) cutoff (pyiron_contrib.atomistics.pacemaker.job.PacemakerJob property) CutoffDistance (class in pyiron_contrib.protocol.primitive.one_state)

D

data (pyiron_contrib.image.image.Image attribute) (pyiron_contrib.image.image.Image property) (pyiron_contrib.image.utils.LockedIfAttributeTrue attribute) (pyiron_contrib.image.utils.ModuleScraper attribute), [1], [2], [3], [4], [5] (pyiron_contrib.protocol.utils.dictionaries.TimelineDict property) db_entry() (pyiron_contrib.atomistics.interactive.montecarlo.MonteCarloMaster method) default (pyiron_contrib.image.utils.LockedIfAttributeTrue attribute) (pyiron_contrib.image.utils.ModuleScraper attribute), [1], [2], [3], [4], [5] default() (pyiron_contrib.protocol.utils.comparers.Comparer method) default_whitelist (pyiron_contrib.protocol.generic.CompoundVertex property) DefaultWhitelist (pyiron_contrib.protocol.compound.minimize.Minimize attribute) (pyiron_contrib.protocol.compound.molecular_dynamics.MolecularDynamics attribute) (pyiron_contrib.protocol.compound.qmmm.QMMM attribute) define_execution_flow() (pyiron_contrib.protocol.compound.finite_temperature_string.FTSEvolution method) (pyiron_contrib.protocol.compound.finite_temperature_string.FTSEvolutionParallel method) (pyiron_contrib.protocol.compound.minimize.Minimize method) (pyiron_contrib.protocol.compound.molecular_dynamics.ConfinedMD method) (pyiron_contrib.protocol.compound.molecular_dynamics.HarmonicMD method) (pyiron_contrib.protocol.compound.molecular_dynamics.MolecularDynamics method) (pyiron_contrib.protocol.compound.nudged_elastic_band.NEB method) (pyiron_contrib.protocol.compound.qmmm.QMMM method) (pyiron_contrib.protocol.compound.thermodynamic_integration.HarmonicTILD method) (pyiron_contrib.protocol.compound.thermodynamic_integration.HarmonicTILDParallel method) (pyiron_contrib.protocol.compound.thermodynamic_integration.VacancyFormation method) (pyiron_contrib.protocol.compound.thermodynamic_integration.VacancyTILD method) (pyiron_contrib.protocol.compound.thermodynamic_integration.VacancyTILDParallel method) (pyiron_contrib.protocol.generic.CompoundVertex method) define_information_flow() (pyiron_contrib.protocol.compound.finite_temperature_string.FTSEvolution method) (pyiron_contrib.protocol.compound.finite_temperature_string.FTSEvolutionParallel method) (pyiron_contrib.protocol.compound.minimize.Minimize method) (pyiron_contrib.protocol.compound.molecular_dynamics.ConfinedMD method) (pyiron_contrib.protocol.compound.molecular_dynamics.HarmonicMD method) (pyiron_contrib.protocol.compound.molecular_dynamics.MolecularDynamics method) (pyiron_contrib.protocol.compound.nudged_elastic_band.NEB method) (pyiron_contrib.protocol.compound.qmmm.QMMM method) (pyiron_contrib.protocol.compound.thermodynamic_integration.HarmonicTILD method) (pyiron_contrib.protocol.compound.thermodynamic_integration.HarmonicTILDParallel method) (pyiron_contrib.protocol.compound.thermodynamic_integration.VacancyFormation method) (pyiron_contrib.protocol.compound.thermodynamic_integration.VacancyTILD method) (pyiron_contrib.protocol.compound.thermodynamic_integration.VacancyTILDParallel method) (pyiron_contrib.protocol.generic.CompoundVertex method)

define_vertices() (pyiron_contrib.protocol.compound.finite_temperature_string.FTSEvolution method) (pyiron_contrib.protocol.compound.finite_temperature_string.FTSEvolutionParallel method) (pyiron_contrib.protocol.compound.minimize.Minimize method) (pyiron_contrib.protocol.compound.molecular_dynamics.ConfinedMD method) (pyiron_contrib.protocol.compound.molecular_dynamics.HarmonicMD method) (pyiron_contrib.protocol.compound.molecular_dynamics.MolecularDynamics method) (pyiron_contrib.protocol.compound.nudged_elastic_band.NEB method) (pyiron_contrib.protocol.compound.qmmm.QMMM method) (pyiron_contrib.protocol.compound.thermodynamic_integration.HarmonicTILD method) (pyiron_contrib.protocol.compound.thermodynamic_integration.HarmonicTILDParallel method) (pyiron_contrib.protocol.compound.thermodynamic_integration.VacancyFormation method) (pyiron_contrib.protocol.compound.thermodynamic_integration.VacancyTILD method) (pyiron_contrib.protocol.compound.thermodynamic_integration.VacancyTILDParallel method) (pyiron_contrib.protocol.generic.CompoundVertex method) DeleteAtom (class in pyiron_contrib.protocol.primitive.one_state) desc (pyiron_contrib.atomistics.mlip.cfgs.Cfg attribute) direct (pyiron_contrib.protocol.list.ListVertex attribute) DisplacementJobGenerator (class in pyiron_contrib.atomistics.mlip.masters) DistributingList (class in pyiron_contrib.image.utils)

E

eam_potential() (pyiron_contrib.atomistics.atomicrex.potential_factory.ARPotFactory static method) EAMlikeMixin (class in pyiron_contrib.atomistics.atomicrex.potential_factory) EAMPotential (class in pyiron_contrib.atomistics.atomicrex.potential_factory) Edges (class in pyiron_contrib.protocol.generic) edges (pyiron_contrib.protocol.generic.Graph attribute) elements (pyiron_contrib.atomistics.pacemaker.job.PacemakerJob property) enable_active_learning() (pyiron_contrib.atomistics.mlip.lammps.LammpsMlip method) energy (pyiron_contrib.atomistics.mlip.cfgs.Cfg attribute) energy_pot (pyiron_contrib.atomistics.interactive.mixer.MixingOutput property) energy_scatter_histogram() (pyiron_contrib.atomistics.ml.potentialfit.PotentialPlots method) energy_tot (pyiron_contrib.atomistics.interactive.mixer.MixingOutput property) energy_volume() (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingPlots method) ensure_iterable() (in module pyiron_contrib.protocol.utils.misc) ensure_iterable_tuple() (in module pyiron_contrib.protocol.utils.comparers) equals() (pyiron_contrib.protocol.utils.comparers.AtomsComparer method) (pyiron_contrib.protocol.utils.comparers.Comparer method) (pyiron_contrib.protocol.utils.comparers.ListComparer method) (pyiron_contrib.protocol.utils.comparers.NumpyArrayComparer method) equidistant_spline() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method)

Event (class in pyiron_contrib.protocol.utils.event) EventHandler (class in pyiron_contrib.protocol.utils.event) ExampleInput (class in pyiron_contrib.atomistics.randspg.randspg) execute() (pyiron_contrib.protocol.generic.CompoundVertex method) (pyiron_contrib.protocol.generic.PrimitiveVertex method) (pyiron_contrib.protocol.generic.Protocol method) (pyiron_contrib.protocol.generic.Vertex method) execute_parallel() (pyiron_contrib.protocol.generic.CompoundVertex method) (pyiron_contrib.protocol.generic.PrimitiveVertex method) exp_A_screening() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method) exp_B_screening() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method) exp_gaussian_screening() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method) ExpA (class in pyiron_contrib.atomistics.atomicrex.function_factory) ExpB (class in pyiron_contrib.atomistics.atomicrex.function_factory) ExpGaussian (class in pyiron_contrib.atomistics.atomicrex.function_factory) extend() (pyiron_contrib.protocol.utils.pointer.Path method) ExtendedMishinCuF (class in pyiron_contrib.atomistics.atomicrex.function_factory) extendedMishinCuF() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method) ExternalHamiltonian (class in pyiron_contrib.protocol.primitive.one_state)

F

Factories (class in pyiron_contrib.atomistics.atomicrex.base) FEPExponential (class in pyiron_contrib.protocol.primitive.one_state) final_val (pyiron_contrib.atomistics.atomicrex.fit_properties.FlattenedARScalarProperty property) (pyiron_contrib.atomistics.atomicrex.fit_properties.FlattenedARVectorProperty property) finish() (pyiron_contrib.protocol.generic.Vertex method) (pyiron_contrib.protocol.list.ListVertex method) (pyiron_contrib.protocol.list.ParallelList method) (pyiron_contrib.protocol.primitive.one_state.CreateJob method) (pyiron_contrib.protocol.primitive.one_state.ExternalHamiltonian method) fire() (pyiron_contrib.protocol.utils.event.Event method) fire_handler() (pyiron_contrib.protocol.utils.event.Event method) fit (pyiron_contrib.atomistics.atomicrex.fit_properties.FlattenedARProperty property) fit_dofs_to_xml_element() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionParameterList method) flatten() (in module pyiron_contrib.protocol.utils.misc) FlattenedARProperty (class in pyiron_contrib.atomistics.atomicrex.fit_properties) FlattenedARScalarProperty (class in pyiron_contrib.atomistics.atomicrex.fit_properties) FlattenedARVectorProperty (class in pyiron_contrib.atomistics.atomicrex.fit_properties) force_scatter_histogram() (pyiron_contrib.atomistics.ml.potentialfit.PotentialPlots method) forces (pyiron_contrib.atomistics.interactive.mixer.MixingOutput property) (pyiron_contrib.atomistics.mlip.cfgs.Cfg attribute) forces() (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingPlots method) format_whitelist() (pyiron_contrib.protocol.generic.CompoundVertex method) from_hdf() (pyiron_contrib.atomistics.atomicrex.base.AtomicrexBase method) (pyiron_contrib.atomistics.atomicrex.fit_properties.FlattenedARProperty method) (pyiron_contrib.atomistics.atomicrex.general_input.ScipyAlgorithm method) (pyiron_contrib.atomistics.atomicrex.structure_list.ARStructureContainer method) (pyiron_contrib.atomistics.atomistics.job.structurelistmasterinteractive.StructureMasterInt method) (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingContainer method) (pyiron_contrib.atomistics.dft.parametermaster.ParameterMaster method) (pyiron_contrib.atomistics.interactive.mixer.Mixer method) (pyiron_contrib.atomistics.interactive.montecarlo.MonteCarloMaster method) (pyiron_contrib.atomistics.mlip.lammps.MlipInput method) (pyiron_contrib.atomistics.mlip.mlip.Mlip method) (pyiron_contrib.atomistics.mlip.mlipjob.MlipJob method) (pyiron_contrib.atomistics.mlip.potential.MtpPotential method) (pyiron_contrib.atomistics.pacemaker.job.PacemakerJob method) (pyiron_contrib.atomistics.randspg.randspg.RandSpg method) (pyiron_contrib.image.image.Image method) (pyiron_contrib.image.image.Metadata method) (pyiron_contrib.image.job.ImageJob method) (pyiron_contrib.image.utils.ModuleScraper method) (pyiron_contrib.protocol.generic.CompoundVertex method) (pyiron_contrib.protocol.generic.Edges method) (pyiron_contrib.protocol.generic.Graph method) (pyiron_contrib.protocol.generic.Protocol method) (pyiron_contrib.protocol.generic.Vertex method) (pyiron_contrib.protocol.generic.Vertices method) (pyiron_contrib.protocol.list.ListVertex method) (pyiron_contrib.protocol.utils.dictionaries.IODictionary method)

FTSEvolution (class in pyiron_contrib.protocol.compound.finite_temperature_string) FTSEvolutionParallel (class in pyiron_contrib.protocol.compound.finite_temperature_string) fullname() (in module pyiron_contrib.protocol.utils.misc) (pyiron_contrib.protocol.utils.misc.LoggerMixin method) func (pyiron_contrib.atomistics.atomicrex.function_factory.ExpA property) (pyiron_contrib.atomistics.atomicrex.function_factory.ExpB property) (pyiron_contrib.atomistics.atomicrex.function_factory.ExpGaussian property) (pyiron_contrib.atomistics.atomicrex.function_factory.GaussianFunc property) (pyiron_contrib.atomistics.atomicrex.function_factory.MorseA property) (pyiron_contrib.atomistics.atomicrex.function_factory.MorseB property) (pyiron_contrib.atomistics.atomicrex.function_factory.MorseC property) (pyiron_contrib.atomistics.atomicrex.function_factory.RsMinusRPowN property) (pyiron_contrib.atomistics.atomicrex.function_factory.SpecialFunction property) (pyiron_contrib.atomistics.atomicrex.function_factory.XpowNCutoff property) (pyiron_contrib.protocol.utils.event.EventHandler attribute) FunctionFactory (class in pyiron_contrib.atomistics.atomicrex.function_factory) FunctionParameter (class in pyiron_contrib.atomistics.atomicrex.function_factory) FunctionParameterList (class in pyiron_contrib.atomistics.atomicrex.function_factory)

G

g_mlsl() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) g_mlsl_lds() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) gaussian() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method) GaussianFunc (class in pyiron_contrib.atomistics.atomicrex.function_factory) gaussians_sum() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method) gd_stogo() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) gd_stogo_rand() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) GeneralARInput (class in pyiron_contrib.atomistics.atomicrex.general_input) get_A() (in module pyiron_contrib.atomistics.atomicrex.potential_factory) get_B() (in module pyiron_contrib.atomistics.atomicrex.potential_factory) get_barrier() (pyiron_contrib.protocol.compound.finite_temperature_string.FTSEvolution method) (pyiron_contrib.protocol.compound.nudged_elastic_band.NEB method) get_beta() (in module pyiron_contrib.atomistics.atomicrex.potential_factory) get_classical_harmonic_free_energy() (pyiron_contrib.protocol.compound.thermodynamic_integration.HarmonicTILD method) get_cls() (in module pyiron_contrib.protocol.utils.misc) get_current_potential_filename() (pyiron_contrib.atomistics.pacemaker.job.PacemakerJob method) get_D0() (in module pyiron_contrib.atomistics.atomicrex.potential_factory) get_elements() (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingContainer method) get_fep_free_energy() (pyiron_contrib.protocol.primitive.one_state.TILDPostProcess static method) get_final_potential_filename() (pyiron_contrib.atomistics.pacemaker.job.PacemakerJob method) get_final_potential_filename_ace() (pyiron_contrib.atomistics.pacemaker.job.PacemakerJob method) get_forward_barrier() (pyiron_contrib.protocol.compound.finite_temperature_string.FTSEvolution method) (pyiron_contrib.protocol.compound.nudged_elastic_band.NEB method) get_graph_location() (pyiron_contrib.protocol.generic.Vertex method) get_lam1() (in module pyiron_contrib.atomistics.atomicrex.potential_factory) get_lam2() (in module pyiron_contrib.atomistics.atomicrex.potential_factory) get_lambdas() (pyiron_contrib.protocol.compound.thermodynamic_integration.VacancyFormation method) get_lammps_potential() (pyiron_contrib.atomistics.atomicrex.base.AtomicrexBase method) (pyiron_contrib.atomistics.ml.potentialfit.PotentialFit method) (pyiron_contrib.atomistics.mlip.mlip.Mlip method) (pyiron_contrib.atomistics.pacemaker.job.PacemakerJob method) get_machine_epsilon() (pyiron_contrib.protocol.utils.comparers.NumpyArrayComparer static method) get_neighbors() (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingContainer method) get_output() (pyiron_contrib.protocol.compound.finite_temperature_string.FTSEvolution method) (pyiron_contrib.protocol.compound.minimize.Minimize method) (pyiron_contrib.protocol.compound.molecular_dynamics.HarmonicMD method) (pyiron_contrib.protocol.compound.molecular_dynamics.MolecularDynamics method) (pyiron_contrib.protocol.compound.nudged_elastic_band.NEB method) (pyiron_contrib.protocol.compound.qmmm.QMMM method) (pyiron_contrib.protocol.compound.thermodynamic_integration.HarmonicTILD method) (pyiron_contrib.protocol.compound.thermodynamic_integration.HarmonicTILDParallel method) (pyiron_contrib.protocol.compound.thermodynamic_integration.VacancyFormation method) (pyiron_contrib.protocol.compound.thermodynamic_integration.VacancyTILD method) (pyiron_contrib.protocol.compound.thermodynamic_integration.VacancyTILDParallel method) (pyiron_contrib.protocol.generic.CompoundVertex method)

get_predicted_data() (pyiron_contrib.atomistics.atomicrex.structure_list.ARStructureContainer method) get_quantum_harmonic_free_energy() (pyiron_contrib.protocol.compound.thermodynamic_integration.HarmonicTILD method) get_r0() (in module pyiron_contrib.atomistics.atomicrex.potential_factory) get_reverse_barrier() (pyiron_contrib.protocol.compound.finite_temperature_string.FTSEvolution method) (pyiron_contrib.protocol.compound.nudged_elastic_band.NEB method) get_S() (in module pyiron_contrib.atomistics.atomicrex.potential_factory) get_scalar_property() (pyiron_contrib.atomistics.atomicrex.structure_list.ARStructureContainer method) get_sort_array() (in module pyiron_contrib.atomistics.atomicrex.structure_list) get_structure() (pyiron_contrib.atomistics.mlip.mlip.Mlip method) get_suggested_number_of_configuration() (pyiron_contrib.atomistics.mlip.mlip.Mlip method) get_tild_free_energy() (pyiron_contrib.protocol.primitive.one_state.TILDPostProcess static method) get_tild_integrands() (pyiron_contrib.protocol.compound.thermodynamic_integration.HarmonicTILDParallel method) (pyiron_contrib.protocol.compound.thermodynamic_integration.VacancyFormation method) (pyiron_contrib.protocol.compound.thermodynamic_integration.VacancyTILDParallel method) get_training_data() (pyiron_contrib.atomistics.atomicrex.structure_list.ARStructureContainer method) get_vector_property() (pyiron_contrib.atomistics.atomicrex.structure_list.ARStructureContainer method) gn_crs2_lm() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) gn_direct() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) gn_direct_l() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) gn_esch() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) gn_isres() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) GPA_TO_BAR (in module pyiron_contrib.protocol.primitive.one_state) grade (pyiron_contrib.atomistics.mlip.cfgs.Cfg attribute) GradientDescent (class in pyiron_contrib.protocol.primitive.one_state) Graph (class in pyiron_contrib.protocol.generic) graph_parent (pyiron_contrib.protocol.generic.Vertex attribute)

H

handler_count (pyiron_contrib.protocol.utils.event.Event property) handler_keys (pyiron_contrib.protocol.utils.event.Event property) HarmonicHamiltonian (class in pyiron_contrib.protocol.primitive.one_state)

HarmonicMD (class in pyiron_contrib.protocol.compound.molecular_dynamics) HarmonicTILD (class in pyiron_contrib.protocol.compound.thermodynamic_integration) HarmonicTILDParallel (class in pyiron_contrib.protocol.compound.thermodynamic_integration) has_handler() (pyiron_contrib.protocol.utils.event.Event method)

I

Image (class in pyiron_contrib.image.image) ImageJob (class in pyiron_contrib.image.job) images (pyiron_contrib.image.job.ImageJob attribute) (pyiron_contrib.image.job.ImageJob property) include_dataset() (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingContainer method) (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingStorage method) include_job() (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingContainer method) (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingStorage method) include_structure() (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingContainer method) (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingStorage method) index() (pyiron_contrib.protocol.utils.pointer.Path method) initialize() (pyiron_contrib.protocol.generic.Edges method) InitialPositions (class in pyiron_contrib.protocol.primitive.one_state) inject_dynamic_types() (pyiron_contrib.protocol.utils.types.PyironJobTypeRegistryMetaType static method) Input (class in pyiron_contrib.atomistics.interactive.langevin) (class in pyiron_contrib.atomistics.interactive.mixer) input (pyiron_contrib.atomistics.interactive.langevin.LangevinAse attribute) (pyiron_contrib.atomistics.interactive.mixer.Mixer attribute) (pyiron_contrib.atomistics.interactive.montecarlo.MonteCarloMaster attribute) (pyiron_contrib.protocol.generic.Vertex attribute)

InputDictionary (class in pyiron_contrib.protocol.utils.dictionaries) interactive_add_structure() (pyiron_contrib.atomistics.atomicrex.interactive.AtomicrexInteractive method) interactive_calculate_gradient() (pyiron_contrib.atomistics.atomicrex.interactive.AtomicrexInteractive method) interactive_calculate_hessian() (pyiron_contrib.atomistics.atomicrex.interactive.AtomicrexInteractive method) interactive_calculate_residual() (pyiron_contrib.atomistics.atomicrex.interactive.AtomicrexInteractive method) interactive_close() (pyiron_contrib.atomistics.interactive.mixer.Mixer method) interactive_initialize_interface() (pyiron_contrib.atomistics.interactive.mixer.Mixer method) interactive_prepare_job() (pyiron_contrib.atomistics.atomicrex.interactive.AtomicrexInteractive method) interactive_store_in_cache() (pyiron_contrib.atomistics.interactive.mixer.Mixer method) IODictionary (class in pyiron_contrib.protocol.utils.dictionaries) is_iterable() (in module pyiron_contrib.protocol.utils.misc) IsGEq (class in pyiron_contrib.protocol.primitive.two_state) IsLEq (class in pyiron_contrib.protocol.primitive.two_state) Item (pyiron_contrib.protocol.utils.pointer.CrumbType attribute) item() (pyiron_contrib.protocol.utils.pointer.Crumb static method) items() (pyiron_contrib.protocol.utils.dictionaries.InputDictionary method) (pyiron_contrib.protocol.utils.dictionaries.TimelineDict method) iter() (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingContainer method) (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingStorage method)

J

job_name() (pyiron_contrib.atomistics.dft.parametermaster.ParameterJobGenerator static method) (pyiron_contrib.atomistics.mlip.masters.DisplacementJobGenerator static method) (pyiron_contrib.atomistics.mlip.masters.RandomMDJobGenerator static method)

join() (pyiron_contrib.protocol.utils.pointer.Path class method)

K

keys() (pyiron_contrib.protocol.utils.dictionaries.InputDictionary method) (pyiron_contrib.protocol.utils.dictionaries.TimelineDict method)

L

lammps_potential (pyiron_contrib.atomistics.atomicrex.base.AtomicrexBase property) LammpsMlip (class in pyiron_contrib.atomistics.mlip.lammps) langevin_delta_v() (pyiron_contrib.protocol.primitive.one_state.VerletParent static method) LangevinAse (class in pyiron_contrib.atomistics.interactive.langevin) LangevinThermostat (class in pyiron_contrib.protocol.primitive.one_state) lat (pyiron_contrib.atomistics.mlip.cfgs.Cfg attribute) ld_ccsaq() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) ld_lbfgs() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) ld_mma() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) ld_slsqp() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) ld_var1() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) ld_var2() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) lennard_jones_potential() (pyiron_contrib.atomistics.atomicrex.potential_factory.ARPotFactory static method) list_of_structures (pyiron_contrib.atomistics.randspg.randspg.RandSpg property) list_structures() (pyiron_contrib.atomistics.randspg.randspg.RandSpg method) ListComparer (class in pyiron_contrib.protocol.utils.comparers) ListVertex (class in pyiron_contrib.protocol.list) LJPotential (class in pyiron_contrib.atomistics.atomicrex.potential_factory) ln_bobyqa() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) ln_cobyla() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) ln_neldermead() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method)

ln_newuoa() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) ln_newuoa_bound() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) ln_praxis() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) ln_sbplx() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) load() (pyiron_contrib.atomistics.mlip.potential.MtpPotential method) load_default() (pyiron_contrib.atomistics.interactive.langevin.Input method) (pyiron_contrib.atomistics.interactive.mixer.Input method) (pyiron_contrib.atomistics.interactive.montecarlo.MonteCarloInput method) (pyiron_contrib.atomistics.mlip.lammps.MlipParameter method) (pyiron_contrib.atomistics.mlip.mlip.CommandLine method) (pyiron_contrib.atomistics.mlip.mlip.MlipParameter method) (pyiron_contrib.atomistics.mlip.mlipjob.MlipParameter method) (pyiron_contrib.atomistics.randspg.randspg.ExampleInput method) loadcfgs() (in module pyiron_contrib.atomistics.mlip.cfgs) lock() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionParameter method) lock_parameters() (pyiron_contrib.atomistics.atomicrex.function_factory.BaseFunctionMixin method) (pyiron_contrib.atomistics.atomicrex.function_factory.MetaFunctionMixin method) (pyiron_contrib.atomistics.atomicrex.function_factory.Spline method) (pyiron_contrib.atomistics.atomicrex.potential_factory.EAMlikeMixin method) LockedIfAttributeTrue (class in pyiron_contrib.image.utils) logger (pyiron_contrib.protocol.utils.misc.LoggerMixin property) LoggerMixin (class in pyiron_contrib.protocol.utils.misc)

M

make_edge() (pyiron_contrib.protocol.generic.Graph method) make_pipeline() (pyiron_contrib.protocol.generic.Graph method) Max (class in pyiron_contrib.protocol.primitive.one_state) meam_potential() (pyiron_contrib.atomistics.atomicrex.potential_factory.ARPotFactory static method) MEAMPotential (class in pyiron_contrib.atomistics.atomicrex.potential_factory) Metadata (class in pyiron_contrib.image.image) metadata (pyiron_contrib.image.image.Image attribute) (pyiron_contrib.image.image.Image property) MetaFunctionMixin (class in pyiron_contrib.atomistics.atomicrex.function_factory) Minimize (class in pyiron_contrib.protocol.compound.minimize) MinimizeReferenceJob (class in pyiron_contrib.protocol.primitive.one_state) MishinCuF (class in pyiron_contrib.atomistics.atomicrex.function_factory) MishinCuF() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method) MishinCuRho (class in pyiron_contrib.atomistics.atomicrex.function_factory) MishinCuRho() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method) MishinCuV() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method) Mixer (class in pyiron_contrib.atomistics.interactive.mixer) MixingOutput (class in pyiron_contrib.atomistics.interactive.mixer) Mlip (class in pyiron_contrib.atomistics.mlip.mlip) MlipInput (class in pyiron_contrib.atomistics.mlip.lammps) MlipJob (class in pyiron_contrib.atomistics.mlip.mlipjob) MlipParameter (class in pyiron_contrib.atomistics.mlip.lammps) (class in pyiron_contrib.atomistics.mlip.mlip) (class in pyiron_contrib.atomistics.mlip.mlipjob) MlipSelect (class in pyiron_contrib.atomistics.mlip.mlipselect) modify_job() (pyiron_contrib.atomistics.dft.parametermaster.ParameterJobGenerator method) (pyiron_contrib.atomistics.mlip.masters.DisplacementJobGenerator method) (pyiron_contrib.atomistics.mlip.masters.RandomMDJobGenerator method) ModIsZero (class in pyiron_contrib.protocol.primitive.two_state) module pyiron_contrib pyiron_contrib.atomistics pyiron_contrib.atomistics.atomicrex pyiron_contrib.atomistics.atomicrex.atomicrex_job pyiron_contrib.atomistics.atomicrex.base pyiron_contrib.atomistics.atomicrex.fit_properties pyiron_contrib.atomistics.atomicrex.function_factory pyiron_contrib.atomistics.atomicrex.general_input pyiron_contrib.atomistics.atomicrex.interactive pyiron_contrib.atomistics.atomicrex.output pyiron_contrib.atomistics.atomicrex.parameter_constraints pyiron_contrib.atomistics.atomicrex.potential_factory pyiron_contrib.atomistics.atomicrex.structure_list pyiron_contrib.atomistics.atomicrex.utility_functions pyiron_contrib.atomistics.atomistics pyiron_contrib.atomistics.atomistics.job pyiron_contrib.atomistics.atomistics.job.structurelistmasterinteractive pyiron_contrib.atomistics.atomistics.job.structurestorage pyiron_contrib.atomistics.atomistics.job.trainingcontainer pyiron_contrib.atomistics.dft pyiron_contrib.atomistics.dft.parametermaster pyiron_contrib.atomistics.interactive pyiron_contrib.atomistics.interactive.langevin pyiron_contrib.atomistics.interactive.mixer pyiron_contrib.atomistics.interactive.montecarlo pyiron_contrib.atomistics.ml pyiron_contrib.atomistics.ml.potentialfit pyiron_contrib.atomistics.mlip pyiron_contrib.atomistics.mlip.cfgs pyiron_contrib.atomistics.mlip.lammps pyiron_contrib.atomistics.mlip.masters pyiron_contrib.atomistics.mlip.mlip pyiron_contrib.atomistics.mlip.mlipjob pyiron_contrib.atomistics.mlip.mlipselect pyiron_contrib.atomistics.mlip.parser pyiron_contrib.atomistics.mlip.potential pyiron_contrib.atomistics.pacemaker pyiron_contrib.atomistics.pacemaker.job pyiron_contrib.atomistics.randspg pyiron_contrib.atomistics.randspg.randspg pyiron_contrib.atomistics.runner pyiron_contrib.image pyiron_contrib.image.custom_filters pyiron_contrib.image.image pyiron_contrib.image.job pyiron_contrib.image.utils pyiron_contrib.protocol pyiron_contrib.protocol.compound pyiron_contrib.protocol.compound.finite_temperature_string pyiron_contrib.protocol.compound.minimize pyiron_contrib.protocol.compound.molecular_dynamics pyiron_contrib.protocol.compound.nudged_elastic_band pyiron_contrib.protocol.compound.qmmm pyiron_contrib.protocol.compound.thermodynamic_integration pyiron_contrib.protocol.generic pyiron_contrib.protocol.list pyiron_contrib.protocol.math pyiron_contrib.protocol.primitive pyiron_contrib.protocol.primitive.fts_vertices pyiron_contrib.protocol.primitive.one_state pyiron_contrib.protocol.primitive.two_state pyiron_contrib.protocol.utils pyiron_contrib.protocol.utils.comparers pyiron_contrib.protocol.utils.dictionaries pyiron_contrib.protocol.utils.event pyiron_contrib.protocol.utils.misc pyiron_contrib.protocol.utils.pointer pyiron_contrib.protocol.utils.pptree pyiron_contrib.protocol.utils.types pyiron_contrib.RDM

ModuleScraper (class in pyiron_contrib.image.utils) MolecularDynamics (class in pyiron_contrib.protocol.compound.molecular_dynamics) moment_coefficients (pyiron_contrib.atomistics.mlip.potential.MtpPotential property) MonteCarloInput (class in pyiron_contrib.atomistics.interactive.montecarlo) MonteCarloMaster (class in pyiron_contrib.atomistics.interactive.montecarlo) morse_A() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method) morse_B() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method) morse_C() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method) MorseA (class in pyiron_contrib.atomistics.atomicrex.function_factory) MorseB (class in pyiron_contrib.atomistics.atomicrex.function_factory) MorseC (class in pyiron_contrib.atomistics.atomicrex.function_factory) MtpPotential (class in pyiron_contrib.atomistics.mlip.potential)

N

n_history (pyiron_contrib.protocol.generic.Vertex attribute) (pyiron_contrib.protocol.list.ListVertex property) name (pyiron_contrib.atomistics.atomicrex.general_input.SpaMinimizer property) (pyiron_contrib.image.utils.LockedIfAttributeTrue attribute) (pyiron_contrib.image.utils.ModuleScraper attribute), [1], [2], [3], [4], [5] (pyiron_contrib.protocol.utils.event.EventHandler attribute) (pyiron_contrib.protocol.utils.pointer.Crumb property) named_handlers (pyiron_contrib.protocol.utils.event.Event property) NEB (class in pyiron_contrib.protocol.compound.nudged_elastic_band)

NEBForces (class in pyiron_contrib.protocol.primitive.one_state) NloptAlgorithm (class in pyiron_contrib.atomistics.atomicrex.general_input) NloptGlobalLocal (class in pyiron_contrib.atomistics.atomicrex.general_input) Node (class in pyiron_contrib.atomistics.atomicrex.function_factory) NodeList (class in pyiron_contrib.atomistics.atomicrex.function_factory) Norm (class in pyiron_contrib.protocol.primitive.one_state) normalize() (pyiron_contrib.protocol.primitive.one_state.NEBForces static method) Note (pyiron_contrib.protocol.list.ParallelList attribute) NumpyArrayComparer (class in pyiron_contrib.protocol.utils.comparers)

O

object (pyiron_contrib.protocol.utils.comparers.Comparer property) (pyiron_contrib.protocol.utils.pointer.Crumb property) on (pyiron_contrib.protocol.generic.Vertex attribute) ordered_dict_get_index() (in module pyiron_contrib.protocol.utils.misc)

ordered_dict_get_last() (in module pyiron_contrib.protocol.utils.misc) Output (class in pyiron_contrib.atomistics.atomicrex.output) output (pyiron_contrib.protocol.generic.Vertex attribute) Overwrite (class in pyiron_contrib.protocol.primitive.one_state) overwrite_source() (pyiron_contrib.image.image.Image method)

P

PacemakerJob (class in pyiron_contrib.atomistics.pacemaker.job) parallel_setup() (pyiron_contrib.protocol.generic.Vertex method) ParallelList (class in pyiron_contrib.protocol.list) param_file (pyiron_contrib.atomistics.atomicrex.potential_factory.BOPAbstract property) parameter_list (pyiron_contrib.atomistics.dft.parametermaster.ParameterJobGenerator property) (pyiron_contrib.atomistics.mlip.masters.DisplacementJobGenerator property) (pyiron_contrib.atomistics.mlip.masters.RandomMDJobGenerator property) ParameterConstraints (class in pyiron_contrib.atomistics.atomicrex.parameter_constraints) ParameterJobGenerator (class in pyiron_contrib.atomistics.dft.parametermaster) ParameterMaster (class in pyiron_contrib.atomistics.dft.parametermaster) partition_input() (pyiron_contrib.protocol.compound.qmmm.QMMM method) PartitionStructure (class in pyiron_contrib.protocol.compound.qmmm) pass_and_set_image_data() (in module pyiron_contrib.image.image) pass_image_data() (in module pyiron_contrib.image.image) Path (class in pyiron_contrib.protocol.utils.pointer) path (pyiron_contrib.protocol.utils.pointer.Pointer property) plot (pyiron_contrib.atomistics.atomicrex.structure_list.ARStructureContainer property) (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingContainer property) (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingStorage property) (pyiron_contrib.atomistics.ml.potentialfit.PotentialFit property) plot() (in module pyiron_contrib.atomistics.atomicrex.function_factory) (pyiron_contrib.atomistics.atomicrex.function_factory.SpecialFunction method) (pyiron_contrib.image.image.Image method) (pyiron_contrib.image.job.ImageJob method) plot_elastic_band() (pyiron_contrib.protocol.compound.nudged_elastic_band.NEB method) plot_final_potential() (pyiron_contrib.atomistics.atomicrex.base.AtomicrexBase method) (pyiron_contrib.atomistics.atomicrex.potential_factory.EAMPotential method) plot_string() (pyiron_contrib.protocol.compound.finite_temperature_string.FTSEvolution method) Pointer (class in pyiron_contrib.protocol.utils.pointer) Poly (class in pyiron_contrib.atomistics.atomicrex.function_factory) poly() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method) PolyCoeff (class in pyiron_contrib.atomistics.atomicrex.function_factory) PolyCoeffList (class in pyiron_contrib.atomistics.atomicrex.function_factory) pool (pyiron_contrib.protocol.list.ParallelList attribute) pos (pyiron_contrib.atomistics.mlip.cfgs.Cfg attribute) PositionsRunningAverage (class in pyiron_contrib.protocol.primitive.fts_vertices) possible_vertex_states (pyiron_contrib.protocol.generic.Vertex attribute) potential (pyiron_contrib.atomistics.mlip.mlip.Mlip property) (pyiron_contrib.atomistics.mlip.mlipjob.MlipJob property) potential() (in module pyiron_contrib.atomistics.mlip.parser) potential_as_pd_df() (pyiron_contrib.atomistics.atomicrex.base.AtomicrexBase method) potential_dataframe() (pyiron_contrib.atomistics.mlip.mlip.Mlip method) potential_files (pyiron_contrib.atomistics.mlip.mlip.Mlip property) PotentialFit (class in pyiron_contrib.atomistics.ml.potentialfit) PotentialPlots (class in pyiron_contrib.atomistics.ml.potentialfit) predefined_structure_xml() (in module pyiron_contrib.atomistics.atomicrex.structure_list) predicted_data (pyiron_contrib.atomistics.atomicrex.structure_list.ARStructureContainer property) (pyiron_contrib.atomistics.ml.potentialfit.PotentialFit property) prepare_plotting() (pyiron_contrib.atomistics.atomicrex.structure_list.ARStructureContainer method) pressures (pyiron_contrib.atomistics.interactive.mixer.MixingOutput property) primitives_list (pyiron_contrib.image.utils.ModuleScraper attribute), [1] PrimitiveVertex (class in pyiron_contrib.protocol.generic) print_tree() (in module pyiron_contrib.protocol.utils.pptree) printcfg() (in module pyiron_contrib.atomistics.mlip.cfgs) Product (class in pyiron_contrib.atomistics.atomicrex.function_factory) product() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method) prop (pyiron_contrib.atomistics.atomicrex.fit_properties.ARFitProperty property) Protocol (class in pyiron_contrib.protocol.generic) ProtocolQMMM (class in pyiron_contrib.protocol.compound.qmmm) ProtoConfinedMD (class in pyiron_contrib.protocol.compound.molecular_dynamics) ProtoFTSEvoPar (class in pyiron_contrib.protocol.compound.finite_temperature_string) ProtoFTSEvoSer (class in pyiron_contrib.protocol.compound.finite_temperature_string) ProtoHarmMD (class in pyiron_contrib.protocol.compound.molecular_dynamics) ProtoHarmTILDPar (class in pyiron_contrib.protocol.compound.thermodynamic_integration) ProtoHarmTILDSer (class in pyiron_contrib.protocol.compound.thermodynamic_integration) ProtoMD (class in pyiron_contrib.protocol.compound.molecular_dynamics) ProtoMinimGradDes (class in pyiron_contrib.protocol.compound.minimize) ProtoNEBSer (class in pyiron_contrib.protocol.compound.nudged_elastic_band) ProtoVacForm (class in pyiron_contrib.protocol.compound.thermodynamic_integration) ProtoVacTILDPar (class in pyiron_contrib.protocol.compound.thermodynamic_integration) ProtoVacTILDSer (class in pyiron_contrib.protocol.compound.thermodynamic_integration) publication (pyiron_contrib.atomistics.atomicrex.base.AtomicrexBase property) (pyiron_contrib.atomistics.pacemaker.job.PacemakerJob property) pyiron_contrib module pyiron_contrib.atomistics module pyiron_contrib.atomistics.atomicrex module pyiron_contrib.atomistics.atomicrex.atomicrex_job module pyiron_contrib.atomistics.atomicrex.base module pyiron_contrib.atomistics.atomicrex.fit_properties module pyiron_contrib.atomistics.atomicrex.function_factory module pyiron_contrib.atomistics.atomicrex.general_input module pyiron_contrib.atomistics.atomicrex.interactive module pyiron_contrib.atomistics.atomicrex.output module pyiron_contrib.atomistics.atomicrex.parameter_constraints module pyiron_contrib.atomistics.atomicrex.potential_factory module pyiron_contrib.atomistics.atomicrex.structure_list module pyiron_contrib.atomistics.atomicrex.utility_functions module pyiron_contrib.atomistics.atomistics module pyiron_contrib.atomistics.atomistics.job module pyiron_contrib.atomistics.atomistics.job.structurelistmasterinteractive module

pyiron_contrib.atomistics.atomistics.job.structurestorage module pyiron_contrib.atomistics.atomistics.job.trainingcontainer module pyiron_contrib.atomistics.dft module pyiron_contrib.atomistics.dft.parametermaster module pyiron_contrib.atomistics.interactive module pyiron_contrib.atomistics.interactive.langevin module pyiron_contrib.atomistics.interactive.mixer module pyiron_contrib.atomistics.interactive.montecarlo module pyiron_contrib.atomistics.ml module pyiron_contrib.atomistics.ml.potentialfit module pyiron_contrib.atomistics.mlip module pyiron_contrib.atomistics.mlip.cfgs module pyiron_contrib.atomistics.mlip.lammps module pyiron_contrib.atomistics.mlip.masters module pyiron_contrib.atomistics.mlip.mlip module pyiron_contrib.atomistics.mlip.mlipjob module pyiron_contrib.atomistics.mlip.mlipselect module pyiron_contrib.atomistics.mlip.parser module pyiron_contrib.atomistics.mlip.potential module pyiron_contrib.atomistics.pacemaker module pyiron_contrib.atomistics.pacemaker.job module pyiron_contrib.atomistics.randspg module pyiron_contrib.atomistics.randspg.randspg module pyiron_contrib.atomistics.runner module pyiron_contrib.image module pyiron_contrib.image.custom_filters module pyiron_contrib.image.image module pyiron_contrib.image.job module pyiron_contrib.image.utils module pyiron_contrib.protocol module pyiron_contrib.protocol.compound module pyiron_contrib.protocol.compound.finite_temperature_string module pyiron_contrib.protocol.compound.minimize module pyiron_contrib.protocol.compound.molecular_dynamics module pyiron_contrib.protocol.compound.nudged_elastic_band module pyiron_contrib.protocol.compound.qmmm module pyiron_contrib.protocol.compound.thermodynamic_integration module pyiron_contrib.protocol.generic module pyiron_contrib.protocol.list module pyiron_contrib.protocol.math module pyiron_contrib.protocol.primitive module pyiron_contrib.protocol.primitive.fts_vertices module pyiron_contrib.protocol.primitive.one_state module pyiron_contrib.protocol.primitive.two_state module pyiron_contrib.protocol.utils module pyiron_contrib.protocol.utils.comparers module pyiron_contrib.protocol.utils.dictionaries module pyiron_contrib.protocol.utils.event module pyiron_contrib.protocol.utils.misc module pyiron_contrib.protocol.utils.pointer module pyiron_contrib.protocol.utils.pptree module pyiron_contrib.protocol.utils.types module pyiron_contrib.RDM module PyironJobTypeRegistry (class in pyiron_contrib.protocol.utils.types) PyironJobTypeRegistryMetaType (class in pyiron_contrib.protocol.utils.types)

Q

QMMM (class in pyiron_contrib.protocol.compound.qmmm)

R

radial_basis (pyiron_contrib.atomistics.mlip.potential.MtpPotential property) random_displacement() (in module pyiron_contrib.atomistics.mlip.masters) RandomDisMaster (class in pyiron_contrib.atomistics.mlip.masters) RandomMDJobGenerator (class in pyiron_contrib.atomistics.mlip.masters) RandomMDMaster (class in pyiron_contrib.atomistics.mlip.masters) RandomVelocity (class in pyiron_contrib.protocol.primitive.one_state) RandSpg (class in pyiron_contrib.atomistics.randspg.randspg) read_cgfs() (in module pyiron_contrib.atomistics.mlip.mlip) read_eam_fs_file() (in module pyiron_contrib.atomistics.atomicrex.potential_factory) readcfg() (in module pyiron_contrib.atomistics.mlip.cfgs) recursive (pyiron_contrib.image.utils.ModuleScraper attribute), [1] ref_job (pyiron_contrib.atomistics.interactive.mixer.Mixer property) (pyiron_contrib.atomistics.interactive.montecarlo.MonteCarloMaster attribute) ref_job_0 (pyiron_contrib.atomistics.interactive.mixer.Mixer attribute) (pyiron_contrib.atomistics.interactive.mixer.Mixer property) ref_job_1 (pyiron_contrib.atomistics.interactive.mixer.Mixer attribute) (pyiron_contrib.atomistics.interactive.mixer.Mixer property) Registry (class in pyiron_contrib.protocol.utils.misc) registry (pyiron_contrib.protocol.utils.comparers.AtomsComparer attribute) (pyiron_contrib.protocol.utils.comparers.Comparer attribute) (pyiron_contrib.protocol.utils.comparers.ListComparer attribute) (pyiron_contrib.protocol.utils.comparers.NumpyArrayComparer attribute) relative_weight (pyiron_contrib.atomistics.atomicrex.fit_properties.FlattenedARProperty property) reload_data() (pyiron_contrib.image.image.Image method) remove_event_handler() (pyiron_contrib.protocol.utils.event.Event method) RemoveJob (class in pyiron_contrib.protocol.primitive.one_state)

requires_arguments() (in module pyiron_contrib.protocol.utils.misc) reshape_masses() (pyiron_contrib.protocol.primitive.one_state.VerletParent static method) residual_style (pyiron_contrib.atomistics.atomicrex.fit_properties.ARFitProperty property) (pyiron_contrib.atomistics.atomicrex.fit_properties.FlattenedARProperty property) resolve() (pyiron_contrib.protocol.utils.dictionaries.IODictionary method) (pyiron_contrib.protocol.utils.pointer.Pointer method) restarting_vertex (pyiron_contrib.protocol.generic.Graph attribute) restore_default_whitelist() (pyiron_contrib.protocol.generic.CompoundVertex method) retransform_forces() (pyiron_contrib.protocol.primitive.one_state.HarmonicHamiltonian static method) Root (pyiron_contrib.protocol.utils.pointer.CrumbType attribute) root() (pyiron_contrib.protocol.utils.pointer.Crumb static method) ROOT_EV_PER_ANGSTROM_SQUARE_PER_AMU_IN_S (in module pyiron_contrib.protocol.compound.thermodynamic_integration) RsMinusRPowN (class in pyiron_contrib.atomistics.atomicrex.function_factory) RsMinusRPowN() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method) run() (pyiron_contrib.image.job.ImageJob method) (pyiron_contrib.protocol.generic.Protocol method) (pyiron_contrib.protocol.primitive.two_state.BoolVertex method) run_if_interactive() (pyiron_contrib.atomistics.atomicrex.interactive.AtomicrexInteractive method) (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingContainer method) (pyiron_contrib.atomistics.interactive.mixer.Mixer method) run_static() (pyiron_contrib.atomistics.atomistics.job.structurelistmasterinteractive.StructureMasterInt method) (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingContainer method) (pyiron_contrib.atomistics.interactive.langevin.LangevinAse method) (pyiron_contrib.atomistics.interactive.montecarlo.MonteCarloMaster method) (pyiron_contrib.atomistics.mlip.masters.RandomMDMaster method) (pyiron_contrib.image.job.ImageJob method) (pyiron_contrib.protocol.generic.Protocol method)

S

safe (pyiron_contrib.image.utils.ModuleScraper attribute), [1] sample() (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingContainer method) saturating_angle_control() (pyiron_contrib.protocol.primitive.one_state.NEBForces static method) savecfg() (in module pyiron_contrib.atomistics.mlip.cfgs) savecfgs() (in module pyiron_contrib.atomistics.mlip.cfgs) scipy_algorithm() (pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory static method) ScipyAlgorithm (class in pyiron_contrib.atomistics.atomicrex.general_input) scrape_classes (pyiron_contrib.image.utils.ModuleScraper attribute), [1] scrape_functions (pyiron_contrib.image.utils.ModuleScraper attribute), [1] scrape_primitives (pyiron_contrib.image.utils.ModuleScraper attribute), [1] selected_structures (pyiron_contrib.atomistics.mlip.lammps.LammpsMlip property) SerialList (class in pyiron_contrib.protocol.list) set_archive_period() (pyiron_contrib.protocol.generic.CompoundVertex method) (pyiron_contrib.protocol.generic.Vertex method) set_event_handler() (pyiron_contrib.protocol.utils.event.Event method) set_graph_archive_clock() (pyiron_contrib.protocol.generic.CompoundVertex method) set_image_data() (in module pyiron_contrib.image.image) set_input_archive_period() (pyiron_contrib.protocol.generic.CompoundVertex method) (pyiron_contrib.protocol.generic.Vertex method) set_input_to_read_only() (pyiron_contrib.atomistics.interactive.langevin.LangevinAse method) (pyiron_contrib.atomistics.interactive.mixer.Mixer method) (pyiron_contrib.atomistics.interactive.montecarlo.MonteCarloMaster method) (pyiron_contrib.atomistics.mlip.lammps.LammpsMlip method) (pyiron_contrib.atomistics.mlip.mlip.Mlip method) (pyiron_contrib.atomistics.mlip.mlipjob.MlipJob method) (pyiron_contrib.atomistics.randspg.randspg.RandSpg method) set_input_whitelist() (pyiron_contrib.protocol.generic.CompoundVertex method) (pyiron_contrib.protocol.generic.Vertex method) set_max_val() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionParameter method) set_max_values() (pyiron_contrib.atomistics.atomicrex.function_factory.BaseFunctionMixin method) (pyiron_contrib.atomistics.atomicrex.function_factory.MetaFunctionMixin method) (pyiron_contrib.atomistics.atomicrex.function_factory.Spline method) set_min_val() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionParameter method) set_min_values() (pyiron_contrib.atomistics.atomicrex.function_factory.BaseFunctionMixin method) (pyiron_contrib.atomistics.atomicrex.function_factory.MetaFunctionMixin method) (pyiron_contrib.atomistics.atomicrex.function_factory.Spline method) set_output_archive_period() (pyiron_contrib.protocol.generic.CompoundVertex method) (pyiron_contrib.protocol.generic.Vertex method) set_output_whitelist() (pyiron_contrib.protocol.generic.CompoundVertex method) (pyiron_contrib.protocol.generic.Vertex method)

set_whitelist() (pyiron_contrib.protocol.generic.CompoundVertex method) (pyiron_contrib.protocol.generic.Vertex method) shape (pyiron_contrib.image.image.Image property) shell_distances() (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingPlots method) show_boxes() (pyiron_contrib.protocol.compound.qmmm.QMMM method) show_mm() (pyiron_contrib.protocol.compound.qmmm.QMMM method) show_qm() (pyiron_contrib.protocol.compound.qmmm.QMMM method) Slice (class in pyiron_contrib.protocol.primitive.one_state) sort_structure() (in module pyiron_contrib.atomistics.atomicrex.structure_list) source (pyiron_contrib.image.image.Image attribute) (pyiron_contrib.image.image.Image property) spacegroups() (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingPlots method) SpaMinimizer (class in pyiron_contrib.atomistics.atomicrex.general_input) SpecialFunction (class in pyiron_contrib.atomistics.atomicrex.function_factory) SphereReflection (class in pyiron_contrib.protocol.primitive.one_state) SphereReflectionPerAtom (class in pyiron_contrib.protocol.primitive.one_state) Spline (class in pyiron_contrib.atomistics.atomicrex.function_factory) spline() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method) start_vals_from_file() (pyiron_contrib.atomistics.atomicrex.potential_factory.ABOPParameters method) (pyiron_contrib.atomistics.atomicrex.potential_factory.TersoffParameters method) starting_vertex (pyiron_contrib.protocol.generic.Graph attribute) step() (pyiron_contrib.protocol.generic.Graph method) stress_tensor_components() (pyiron_contrib.atomistics.mlip.mlip.Mlip static method) stresses (pyiron_contrib.atomistics.mlip.cfgs.Cfg attribute) StringRecenter (class in pyiron_contrib.protocol.primitive.fts_vertices) StringReflect (class in pyiron_contrib.protocol.primitive.fts_vertices) structure (pyiron_contrib.atomistics.interactive.mixer.Mixer property) structure_job_id_lst (pyiron_contrib.atomistics.mlip.masters.RandomMDMaster property) structure_lattice (pyiron_contrib.atomistics.interactive.montecarlo.MonteCarloMaster attribute) (pyiron_contrib.atomistics.interactive.montecarlo.MonteCarloMaster property) structure_meta_xml() (in module pyiron_contrib.atomistics.atomicrex.structure_list) structure_sublattice (pyiron_contrib.atomistics.interactive.montecarlo.MonteCarloMaster attribute) (pyiron_contrib.atomistics.interactive.montecarlo.MonteCarloMaster property) StructureMasterInt (class in pyiron_contrib.atomistics.atomistics.job.structurelistmasterinteractive) StructureStorage (class in pyiron_contrib.atomistics.atomistics.job.structurestorage) Sum (class in pyiron_contrib.atomistics.atomicrex.function_factory) sum() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method) suppressed (pyiron_contrib.protocol.utils.event.Event attribute) Synchronization (class in pyiron_contrib.protocol.utils.event) synchronized() (in module pyiron_contrib.protocol.utils.event)

T

tags_from_elements() (pyiron_contrib.atomistics.atomicrex.potential_factory.BOPParameters static method) target_val (pyiron_contrib.atomistics.atomicrex.fit_properties.FlattenedARScalarProperty property) (pyiron_contrib.atomistics.atomicrex.fit_properties.FlattenedARVectorProperty property) temperature (pyiron_contrib.atomistics.interactive.mixer.MixingOutput property) tersoff_potential() (pyiron_contrib.atomistics.atomicrex.potential_factory.ARPotFactory static method) TersoffParameters (class in pyiron_contrib.atomistics.atomicrex.potential_factory) TersoffPotential (class in pyiron_contrib.atomistics.atomicrex.potential_factory) TILDPostProcess (class in pyiron_contrib.protocol.primitive.one_state) timeline (pyiron_contrib.protocol.utils.dictionaries.TimelineDict property) TimelineDict (class in pyiron_contrib.protocol.utils.dictionaries) to_dict() (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingContainer method) (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingStorage method) to_hdf() (pyiron_contrib.atomistics.atomicrex.base.AtomicrexBase method) (pyiron_contrib.atomistics.atomicrex.general_input.ScipyAlgorithm method) (pyiron_contrib.atomistics.atomicrex.structure_list.ARStructureContainer method) (pyiron_contrib.atomistics.atomistics.job.structurelistmasterinteractive.StructureMasterInt method) (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingContainer method) (pyiron_contrib.atomistics.dft.parametermaster.ParameterMaster method) (pyiron_contrib.atomistics.interactive.montecarlo.MonteCarloMaster method) (pyiron_contrib.atomistics.mlip.lammps.MlipInput method) (pyiron_contrib.atomistics.mlip.mlip.Mlip method) (pyiron_contrib.atomistics.mlip.mlipjob.MlipJob method) (pyiron_contrib.atomistics.mlip.potential.MtpPotential method) (pyiron_contrib.atomistics.pacemaker.job.PacemakerJob method) (pyiron_contrib.atomistics.randspg.randspg.RandSpg method) (pyiron_contrib.image.image.Image method) (pyiron_contrib.image.image.Metadata method) (pyiron_contrib.image.job.ImageJob method) (pyiron_contrib.image.utils.ModuleScraper method) (pyiron_contrib.protocol.generic.CompoundVertex method) (pyiron_contrib.protocol.generic.Edges method) (pyiron_contrib.protocol.generic.Graph method) (pyiron_contrib.protocol.generic.Protocol method) (pyiron_contrib.protocol.generic.Vertex method) (pyiron_contrib.protocol.generic.Vertices method) (pyiron_contrib.protocol.list.ListVertex method) (pyiron_contrib.protocol.utils.dictionaries.IODictionary method)

to_list() (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingContainer method) (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingStorage method) to_pandas() (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingContainer method) (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingStorage method) to_xml_element() (pyiron_contrib.atomistics.atomicrex.fit_properties.ARFitProperty method) (pyiron_contrib.atomistics.atomicrex.fit_properties.ARFitPropertyList method) (pyiron_contrib.atomistics.atomicrex.fit_properties.FlattenedARScalarProperty method) (pyiron_contrib.atomistics.atomicrex.fit_properties.FlattenedARVectorProperty method) tolerance (pyiron_contrib.atomistics.atomicrex.fit_properties.FlattenedARProperty property) training_data (pyiron_contrib.atomistics.atomicrex.structure_list.ARStructureContainer property) (pyiron_contrib.atomistics.ml.potentialfit.PotentialFit property) TrainingContainer (class in pyiron_contrib.atomistics.atomistics.job.trainingcontainer) TrainingPlots (class in pyiron_contrib.atomistics.atomistics.job.trainingcontainer) TrainingStorage (class in pyiron_contrib.atomistics.atomistics.job.trainingcontainer) transform_displacements() (pyiron_contrib.protocol.primitive.one_state.HarmonicHamiltonian static method) transform_force_constants() (pyiron_contrib.protocol.primitive.one_state.HarmonicHamiltonian static method) Transpose (class in pyiron_contrib.protocol.primitive.one_state) type (pyiron_contrib.protocol.utils.comparers.AtomsComparer attribute) (pyiron_contrib.protocol.utils.comparers.ListComparer attribute) (pyiron_contrib.protocol.utils.comparers.NumpyArrayComparer attribute) types (pyiron_contrib.atomistics.mlip.cfgs.Cfg attribute)

U

unnamed_handlers (pyiron_contrib.protocol.utils.event.Event property) update_and_archive() (pyiron_contrib.protocol.generic.Vertex method)

user_function() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method) user_structure_to_xml_element() (in module pyiron_contrib.atomistics.atomicrex.structure_list) UserFunction (class in pyiron_contrib.atomistics.atomicrex.function_factory)

V

VacancyFormation (class in pyiron_contrib.protocol.compound.thermodynamic_integration) VacancyTILD (class in pyiron_contrib.protocol.compound.thermodynamic_integration) VacancyTILDParallel (class in pyiron_contrib.protocol.compound.thermodynamic_integration) validate_ready_to_run() (pyiron_contrib.atomistics.atomistics.job.structurelistmasterinteractive.StructureMasterInt method) (pyiron_contrib.atomistics.interactive.montecarlo.MonteCarloMaster method) (pyiron_contrib.atomistics.mlip.mlipselect.MlipSelect method) values() (pyiron_contrib.protocol.utils.dictionaries.InputDictionary method) VerletParent (class in pyiron_contrib.protocol.primitive.one_state) VerletPositionUpdate (class in pyiron_contrib.protocol.primitive.one_state)

VerletVelocityUpdate (class in pyiron_contrib.protocol.primitive.one_state) Vertex (class in pyiron_contrib.protocol.generic) vertex_name (pyiron_contrib.protocol.generic.Vertex attribute) vertex_state (pyiron_contrib.protocol.generic.Vertex attribute) (pyiron_contrib.protocol.generic.Vertex property) Vertices (class in pyiron_contrib.protocol.generic) vertices (pyiron_contrib.protocol.generic.Graph attribute) visualize() (pyiron_contrib.protocol.generic.CompoundVertex method) (pyiron_contrib.protocol.generic.Graph method) VoronoiReflection (class in pyiron_contrib.protocol.primitive.one_state)

W

WeightedSum (class in pyiron_contrib.protocol.primitive.one_state) welford_online() (in module pyiron_contrib.protocol.math) WelfordOnline (class in pyiron_contrib.protocol.primitive.one_state) whitelist (pyiron_contrib.protocol.generic.CompoundVertex property) (pyiron_contrib.protocol.generic.Vertex property) write() (pyiron_contrib.atomistics.mlip.potential.MtpPotential method) write_cfg() (in module pyiron_contrib.atomistics.mlip.mlip) write_file() (pyiron_contrib.atomistics.randspg.randspg.ExampleInput method) write_input() (pyiron_contrib.atomistics.atomicrex.base.AtomicrexBase method) (pyiron_contrib.atomistics.atomistics.job.structurelistmasterinteractive.StructureMasterInt method) (pyiron_contrib.atomistics.atomistics.job.trainingcontainer.TrainingContainer method) (pyiron_contrib.atomistics.interactive.langevin.LangevinAse method) (pyiron_contrib.atomistics.interactive.mixer.Mixer method) (pyiron_contrib.atomistics.interactive.montecarlo.MonteCarloMaster method) (pyiron_contrib.atomistics.mlip.lammps.LammpsMlip method) (pyiron_contrib.atomistics.mlip.mlip.Mlip method) (pyiron_contrib.atomistics.mlip.mlipjob.MlipJob method) (pyiron_contrib.atomistics.mlip.mlipselect.MlipSelect method) (pyiron_contrib.atomistics.pacemaker.job.PacemakerJob method) (pyiron_contrib.atomistics.randspg.randspg.RandSpg method) (pyiron_contrib.image.job.ImageJob method) (pyiron_contrib.protocol.generic.Protocol method)

write_modified_poscar() (in module pyiron_contrib.atomistics.atomicrex.structure_list) write_pretty_xml() (in module pyiron_contrib.atomistics.atomicrex.utility_functions) write_xml_file() (pyiron_contrib.atomistics.atomicrex.potential_factory.AbstractPotential method) (pyiron_contrib.atomistics.atomicrex.potential_factory.ADPotential method) (pyiron_contrib.atomistics.atomicrex.potential_factory.BOPAbstract method) (pyiron_contrib.atomistics.atomicrex.potential_factory.EAMPotential method) (pyiron_contrib.atomistics.atomicrex.potential_factory.LJPotential method) (pyiron_contrib.atomistics.atomicrex.potential_factory.MEAMPotential method) (pyiron_contrib.atomistics.atomicrex.structure_list.ARStructureContainer method)

X

x_pow_n_cutoff() (pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory static method)

XpowNCutoff (class in pyiron_contrib.atomistics.atomicrex.function_factory)

Z

Zeros (class in pyiron_contrib.protocol.primitive.one_state)