Index

A

abc (ipsuite.models.TorchDFTD3 attribute) (ipsuite.TorchDFTD3 attribute) accuracy (ipsuite.calculators.xtb.xTBSinglePoint attribute) (ipsuite.calculators.xTBSinglePoint attribute) (ipsuite.xTBSinglePoint attribute) AddData (class in ipsuite) (class in ipsuite.data_loading) (class in ipsuite.data_loading.add_data_ase) AddDataH5MD (class in ipsuite) (class in ipsuite.data_loading) (class in ipsuite.data_loading.add_data_h5md) additive (ipsuite.ApplyCalculator attribute) AllowedStructuresFilter (class in ipsuite) (class in ipsuite.analysis) alpha (ipsuite.AnalyseSingleForceSensitivity attribute) (ipsuite.analysis.AnalyseSingleForceSensitivity attribute) (ipsuite.analysis.sensitivity.AnalyseSingleForceSensitivity attribute) AnalyseAtoms (class in ipsuite.base) (class in ipsuite.base.base) AnalyseDensity (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.md) AnalyseGlobalForceSensitivity (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.sensitivity) AnalyseSingleForceSensitivity (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.sensitivity) AnalyseStructureMeanForce (class in ipsuite) (class in ipsuite.analysis) angles (ipsuite.analysis.ForceAngles attribute) (ipsuite.analysis.model.ForceAngles attribute) (ipsuite.analysis.model.predict.ForceAngles attribute) (ipsuite.ForceAngles attribute) apply_modifiers() (ipsuite.ASEMD method)

ApplyCalculator (class in ipsuite) ase_calculator (ipsuite.analysis.bond_stretch.BondStretchAnalyses attribute) (ipsuite.analysis.BondStretchAnalyses attribute) ASEGeoOpt (class in ipsuite) (class in ipsuite.calculators) (class in ipsuite.calculators.ase_geoopt) ASEMD (class in ipsuite) ASEMDSafeSampling (class in ipsuite) atom_id (ipsuite.analysis.MoveSingleParticle attribute) (ipsuite.analysis.sensitivity.MoveSingleParticle attribute) (ipsuite.FixedSphereConstraint attribute) (ipsuite.MoveSingleParticle attribute) atom_id_1 (ipsuite.FixedBondLengthConstraint attribute) atom_id_2 (ipsuite.FixedBondLengthConstraint attribute) atom_ids (ipsuite.HookeanConstraint attribute) atom_type (ipsuite.FixedSphereConstraint attribute) atoms (ipsuite.analysis.MoveSingleParticle attribute) (ipsuite.analysis.sensitivity.MoveSingleParticle attribute) (ipsuite.MoveSingleParticle attribute) Atoms() (in module ipsuite.fields) (in module ipsuite.fields.atoms) atoms_list (ipsuite.AnalyseGlobalForceSensitivity attribute) (ipsuite.analysis.AnalyseGlobalForceSensitivity attribute) (ipsuite.analysis.MoveSingleParticle attribute) (ipsuite.analysis.sensitivity.AnalyseGlobalForceSensitivity attribute) (ipsuite.analysis.sensitivity.MoveSingleParticle attribute) (ipsuite.MoveSingleParticle attribute) atoms_list_id (ipsuite.analysis.MoveSingleParticle attribute) (ipsuite.analysis.sensitivity.MoveSingleParticle attribute) (ipsuite.MoveSingleParticle attribute) atoms_path (ipsuite.analysis.MoveSingleParticle attribute) (ipsuite.analysis.sensitivity.MoveSingleParticle attribute) (ipsuite.MoveSingleParticle attribute) atoms_to_graph() (in module ipsuite.geometry.graphs) available (ipsuite.GenericASEModel property) (ipsuite.models.GenericASEModel property)

B

backward_mapping() (ipsuite.BarycenterMapping method) (ipsuite.geometry.BarycenterMapping method) (ipsuite.geometry.mapping.BarycenterMapping method) barycenter_backmapping() (in module ipsuite.geometry.barycenter_coarse_grain) BarycenterMapping (class in ipsuite) (class in ipsuite.geometry) (class in ipsuite.geometry.mapping) BatchConfigurationSelection (class in ipsuite.configuration_selection.base) Berendsen (class in ipsuite) betaT (ipsuite.SVCRBarostat attribute) bins (ipsuite.analysis.bin_property.LabelHistogram attribute) (ipsuite.analysis.bin_property.StressHistogram attribute) (ipsuite.analysis.MDStability attribute) (ipsuite.analysis.model.dynamics.MDStability attribute) (ipsuite.analysis.model.MDStability attribute) (ipsuite.analysis.StressHistogram attribute) (ipsuite.MDStability attribute) (ipsuite.StressHistogram attribute) blocks (ipsuite.models.ORCAModel attribute) (ipsuite.ORCAModel attribute) bonded_max_dist (ipsuite.ConnectivityCheck attribute) bonded_min_dist (ipsuite.ConnectivityCheck attribute)

BondStretchAnalyses (class in ipsuite.analysis) (class in ipsuite.analysis.bond_stretch) Bootstrap (class in ipsuite.bootstrap.random_displacements) bootstrap_configs() (ipsuite.bootstrap.random_displacements.Bootstrap method) (ipsuite.bootstrap.random_displacements.RattleAtoms method) (ipsuite.bootstrap.random_displacements.RotateMolecules method) (ipsuite.bootstrap.random_displacements.TranslateMolecules method) (ipsuite.bootstrap.RattleAtoms method) (ipsuite.bootstrap.RotateMolecules method) (ipsuite.bootstrap.TranslateMolecules method) (ipsuite.RattleAtoms method) (ipsuite.RotateMolecules method) (ipsuite.TranslateMolecules method) BoxHeatUp (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.model) (class in ipsuite.analysis.model.dynamics) BoxOscillatingRampModifier (class in ipsuite) BoxScale (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.model) (class in ipsuite.analysis.model.dynamics)

C

calculate() (ipsuite.calculators.ase_standard.EMTCalculator method) (ipsuite.models.ensemble.EnsembleCalculator method) calculate_l_p_norm() (in module ipsuite.utils.metrics) calculators (ipsuite.calculators.MixCalculator attribute) (ipsuite.MixCalculator attribute) CalibrationMetrics (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.model) (class in ipsuite.analysis.model.predict) cell (ipsuite.RescaleBoxModifier attribute) cell_amplitude (ipsuite.BoxOscillatingRampModifier attribute) cell_fraction (ipsuite.bootstrap.surface_mods.SurfaceRasterScan attribute) (ipsuite.bootstrap.SurfaceRasterScan attribute) (ipsuite.SurfaceRasterScan attribute) charge (ipsuite.calculators.xtb.xTBSinglePoint attribute) (ipsuite.calculators.xTBSinglePoint attribute) (ipsuite.models.TBLiteModel attribute) (ipsuite.TBLiteModel attribute) (ipsuite.xTBSinglePoint attribute) Check (class in ipsuite.base) (class in ipsuite.base.base) check() (ipsuite.base.base.Check method) (ipsuite.base.Check method) (ipsuite.ConnectivityCheck method) (ipsuite.DebugCheck method) (ipsuite.DensityCheck method) (ipsuite.EnergySpikeCheck method) (ipsuite.NaNCheck method) (ipsuite.TemperatureCheck method) (ipsuite.ThresholdCheck method) check_dimension() (in module ipsuite.configuration_selection.threshold) check_duplicate_keys() (in module ipsuite.utils.helpers) checks (ipsuite.analysis.MDStability attribute) (ipsuite.analysis.model.dynamics.MDStability attribute) (ipsuite.analysis.model.MDStability attribute) (ipsuite.ASEGeoOpt attribute) (ipsuite.ASEMD attribute) (ipsuite.calculators.ase_geoopt.ASEGeoOpt attribute) (ipsuite.calculators.ASEGeoOpt attribute) (ipsuite.MDStability attribute) class_name (ipsuite.GenericASEModel attribute) (ipsuite.models.GenericASEModel attribute) cleanup (ipsuite.configuration_generation.Smiles2Gromacs attribute) (ipsuite.Smiles2Gromacs attribute) closest_atom_to_center() (in module ipsuite.geometry.unwrap) cmd (ipsuite.CP2KModel attribute) (ipsuite.models.CP2KModel attribute) (ipsuite.models.ORCAModel attribute) (ipsuite.ORCAModel attribute) cnthr (ipsuite.models.TorchDFTD3 attribute) (ipsuite.TorchDFTD3 attribute) coarse_grain_to_barycenter() (in module ipsuite.geometry.barycenter_coarse_grain) CollectMDSteps (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.md)

ComparePredictions (class in ipsuite.base) (class in ipsuite.base.base) comptue_rll() (in module ipsuite.analysis.model.math) compute_intertia_tensor() (in module ipsuite.analysis.model.math) compute_rmse() (in module ipsuite.analysis.model.math) compute_rot_forces() (in module ipsuite.analysis.model.math) compute_trans_forces() (in module ipsuite.analysis.model.math) compute_uncertainty_metrics() (in module ipsuite.analysis.model.math) config (ipsuite.calculators.PlumedModel attribute) (ipsuite.CP2KModel attribute) (ipsuite.models.CP2KModel attribute) (ipsuite.PlumedModel attribute) config_files (ipsuite.configuration_generation.Smiles2Gromacs attribute) (ipsuite.Smiles2Gromacs attribute) ConfigurationSelection (class in ipsuite.configuration_selection) (class in ipsuite.configuration_selection.base) ConnectivityCheck (class in ipsuite) constraints (ipsuite.ASEGeoOpt attribute) (ipsuite.ASEMD attribute) (ipsuite.calculators.ase_geoopt.ASEGeoOpt attribute) (ipsuite.calculators.ASEGeoOpt attribute) count (ipsuite.configuration_generation.MultiPackmol attribute) (ipsuite.configuration_generation.Packmol attribute) (ipsuite.configuration_generation.packmol.MultiPackmol attribute) (ipsuite.configuration_generation.packmol.Packmol attribute) (ipsuite.configuration_generation.Smiles2Gromacs attribute) (ipsuite.Packmol attribute) (ipsuite.Smiles2Gromacs attribute) cp2k_directory (ipsuite.calculators.cp2k.CP2KSinglePoint attribute) (ipsuite.calculators.CP2KSinglePoint attribute) (ipsuite.CP2KSinglePoint attribute) cp2k_files (ipsuite.calculators.cp2k.CP2KSinglePoint attribute) (ipsuite.calculators.CP2KSinglePoint attribute) (ipsuite.CP2KSinglePoint attribute) cp2k_params (ipsuite.calculators.cp2k.CP2KSinglePoint attribute) (ipsuite.calculators.CP2KSinglePoint attribute) (ipsuite.CP2KSinglePoint attribute) cp2k_shell (ipsuite.calculators.cp2k.CP2KSinglePoint attribute) (ipsuite.calculators.CP2KSinglePoint attribute) (ipsuite.CP2KSinglePoint attribute) CP2KModel (class in ipsuite) (class in ipsuite.models) CP2KSinglePoint (class in ipsuite) (class in ipsuite.calculators) (class in ipsuite.calculators.cp2k) create_input_script() (ipsuite.calculators.lammps.LammpsSimulator method) (ipsuite.calculators.LammpsSimulator method) (ipsuite.LammpsSimulator method) cutoff (ipsuite.models.TorchDFTD3 attribute) (ipsuite.TorchDFTD3 attribute) cutoffs (ipsuite.AllowedStructuresFilter attribute) (ipsuite.analysis.AllowedStructuresFilter attribute) (ipsuite.BarycenterMapping attribute) (ipsuite.geometry.BarycenterMapping attribute) (ipsuite.geometry.mapping.BarycenterMapping attribute)

D

damping (ipsuite.MACEMPModel attribute) (ipsuite.models.MACEMPModel attribute) (ipsuite.models.TorchDFTD3 attribute) (ipsuite.TorchDFTD3 attribute) data (ipsuite.AllowedStructuresFilter attribute) (ipsuite.AnalyseSingleForceSensitivity attribute) (ipsuite.AnalyseStructureMeanForce attribute) (ipsuite.analysis.AllowedStructuresFilter attribute) (ipsuite.analysis.AnalyseDensity attribute) (ipsuite.analysis.AnalyseSingleForceSensitivity attribute) (ipsuite.analysis.AnalyseStructureMeanForce attribute) (ipsuite.analysis.bin_property.DipoleHistogram attribute) (ipsuite.analysis.bin_property.EnergyHistogram attribute) (ipsuite.analysis.bin_property.EnergyUncertaintyHistogram attribute) (ipsuite.analysis.bin_property.ForcesHistogram attribute) (ipsuite.analysis.bin_property.ForcesUncertaintyHistogram attribute) (ipsuite.analysis.bin_property.StressHistogram attribute) (ipsuite.analysis.BondStretchAnalyses attribute) (ipsuite.analysis.BoxHeatUp attribute) (ipsuite.analysis.BoxScale attribute) (ipsuite.analysis.DipoleHistogram attribute) (ipsuite.analysis.EnergyHistogram attribute) (ipsuite.analysis.EnergyUncertaintyHistogram attribute) (ipsuite.analysis.ForcesHistogram attribute) (ipsuite.analysis.ForcesUncertaintyHistogram attribute) (ipsuite.analysis.md.AnalyseDensity attribute) (ipsuite.analysis.MDStability attribute) (ipsuite.analysis.model.BoxHeatUp attribute) (ipsuite.analysis.model.BoxScale attribute) (ipsuite.analysis.model.dynamics.BoxHeatUp attribute) (ipsuite.analysis.model.dynamics.BoxScale attribute) (ipsuite.analysis.model.dynamics.MDStability attribute) (ipsuite.analysis.model.dynamics.RattleAnalysis attribute) (ipsuite.analysis.model.MDStability attribute) (ipsuite.analysis.model.predict.Prediction attribute) (ipsuite.analysis.model.Prediction attribute) (ipsuite.analysis.model.RattleAnalysis attribute) (ipsuite.analysis.Prediction attribute) (ipsuite.analysis.RattleAnalysis attribute) (ipsuite.analysis.sensitivity.AnalyseSingleForceSensitivity attribute) (ipsuite.analysis.StressHistogram attribute) (ipsuite.ApplyCalculator attribute) (ipsuite.ASEGeoOpt attribute) (ipsuite.ASEMD attribute) (ipsuite.base.AnalyseAtoms attribute) (ipsuite.base.base.AnalyseAtoms attribute) (ipsuite.base.base.Flatten attribute) (ipsuite.base.base.ProcessAtoms attribute) (ipsuite.base.base.ProcessSingleAtom attribute) (ipsuite.base.Flatten attribute) (ipsuite.base.ProcessAtoms attribute) (ipsuite.base.ProcessSingleAtom attribute) (ipsuite.bootstrap.random_displacements.Bootstrap attribute) (ipsuite.bootstrap.surface_mods.SurfaceRasterScan attribute) (ipsuite.bootstrap.SurfaceRasterScan attribute) (ipsuite.calculators.ase_geoopt.ASEGeoOpt attribute) (ipsuite.calculators.ASEGeoOpt attribute) (ipsuite.calculators.cp2k.CP2KSinglePoint attribute) (ipsuite.calculators.CP2KSinglePoint attribute) (ipsuite.calculators.lammps.LammpsSimulator attribute) (ipsuite.calculators.LammpsSimulator attribute) (ipsuite.calculators.orca.OrcaSinglePoint attribute) (ipsuite.calculators.OrcaSinglePoint attribute) (ipsuite.calculators.PlumedModel attribute) (ipsuite.calculators.xtb.xTBSinglePoint attribute) (ipsuite.calculators.xTBSinglePoint attribute) (ipsuite.configuration_generation.MultiPackmol attribute) (ipsuite.configuration_generation.Packmol attribute) (ipsuite.configuration_generation.packmol.MultiPackmol attribute) (ipsuite.configuration_generation.packmol.Packmol attribute) (ipsuite.configuration_selection.base.ConfigurationSelection attribute) (ipsuite.configuration_selection.ConfigurationSelection attribute) (ipsuite.configuration_selection.filter.FilterOutlier attribute) (ipsuite.configuration_selection.FilterOutlier attribute) (ipsuite.configuration_selection.index.IndexSelection attribute) (ipsuite.configuration_selection.IndexSelection attribute) (ipsuite.configuration_selection.random.RandomSelection attribute) (ipsuite.configuration_selection.RandomSelection attribute) (ipsuite.configuration_selection.split.SplitSelection attribute) (ipsuite.configuration_selection.SplitSelection attribute) (ipsuite.configuration_selection.threshold.ThresholdSelection attribute) (ipsuite.configuration_selection.ThresholdSelection attribute) (ipsuite.configuration_selection.uniform_arange.UniformArangeSelection attribute) (ipsuite.configuration_selection.uniform_energetic.UniformEnergeticSelection attribute) (ipsuite.configuration_selection.uniform_temporal.UniformTemporalSelection attribute) (ipsuite.configuration_selection.UniformArangeSelection attribute) (ipsuite.configuration_selection.UniformEnergeticSelection attribute) (ipsuite.configuration_selection.UniformTemporalSelection attribute) (ipsuite.CP2KSinglePoint attribute) (ipsuite.FilterOutlier attribute) (ipsuite.Flatten attribute) (ipsuite.MDStability attribute) (ipsuite.models.MLModel attribute) (ipsuite.OrcaSinglePoint attribute) (ipsuite.Packmol attribute) (ipsuite.PlumedModel attribute) (ipsuite.utils.combine.ExcludeIds attribute)

data_file (ipsuite.analysis.CalibrationMetrics attribute) (ipsuite.analysis.model.CalibrationMetrics attribute) (ipsuite.analysis.model.predict.CalibrationMetrics attribute) (ipsuite.analysis.model.predict.PredictionMetrics attribute) (ipsuite.analysis.model.PredictionMetrics attribute) (ipsuite.analysis.PredictionMetrics attribute) (ipsuite.CalibrationMetrics attribute) (ipsuite.PredictionMetrics attribute) data_id (ipsuite.analysis.bond_stretch.BondStretchAnalyses attribute) (ipsuite.analysis.BondStretchAnalyses attribute) (ipsuite.ASEGeoOpt attribute) (ipsuite.base.base.ProcessSingleAtom attribute) (ipsuite.base.ProcessSingleAtom attribute) (ipsuite.bootstrap.random_displacements.Bootstrap attribute) (ipsuite.calculators.ase_geoopt.ASEGeoOpt attribute) (ipsuite.calculators.ASEGeoOpt attribute) (ipsuite.calculators.PlumedModel attribute) (ipsuite.PlumedModel attribute) data_ids (ipsuite.ASEMD attribute) (ipsuite.configuration_generation.Packmol attribute) (ipsuite.configuration_generation.packmol.Packmol attribute) (ipsuite.Packmol attribute) datalabel (ipsuite.analysis.bin_property.DipoleHistogram attribute) (ipsuite.analysis.bin_property.EnergyHistogram attribute) (ipsuite.analysis.bin_property.EnergyUncertaintyHistogram attribute) (ipsuite.analysis.bin_property.ForcesHistogram attribute) (ipsuite.analysis.bin_property.ForcesUncertaintyHistogram attribute) (ipsuite.analysis.DipoleHistogram attribute) (ipsuite.analysis.EnergyHistogram attribute) (ipsuite.analysis.EnergyUncertaintyHistogram attribute) (ipsuite.analysis.ForcesHistogram attribute) (ipsuite.analysis.ForcesUncertaintyHistogram attribute) (ipsuite.DipoleHistogram attribute) (ipsuite.EnergyHistogram attribute) (ipsuite.EnergyUncertaintyHistogram attribute) (ipsuite.ForcesHistogram attribute) (ipsuite.ForcesUncertaintyHistogram attribute) dataset (ipsuite.MD22Dataset attribute) datasets (ipsuite.MD22Dataset attribute) DebugCheck (class in ipsuite) decompose_force_uncertainty() (in module ipsuite.analysis.model.predict) decompose_stress_tensor() (in module ipsuite.analysis.model.math) default_dtype (ipsuite.MACEMPModel attribute) (ipsuite.models.MACEMPModel attribute) density (ipsuite.AnalyseDensity attribute) (ipsuite.analysis.AnalyseDensity attribute) (ipsuite.analysis.md.AnalyseDensity attribute) (ipsuite.configuration_generation.MultiPackmol attribute) (ipsuite.configuration_generation.Packmol attribute) (ipsuite.configuration_generation.packmol.MultiPackmol attribute) (ipsuite.configuration_generation.packmol.Packmol attribute) (ipsuite.configuration_generation.Smiles2Gromacs attribute) (ipsuite.Packmol attribute) (ipsuite.RescaleBoxModifier attribute) (ipsuite.Smiles2Gromacs attribute) density_scatter() (in module ipsuite.analysis.model.plots) DensityCheck (class in ipsuite) device (ipsuite.MACEMPModel attribute) (ipsuite.models.MACEMPModel attribute) (ipsuite.models.TorchDFTD3 attribute) (ipsuite.TorchDFTD3 attribute) dim_reduction (ipsuite.configuration_selection.threshold.ThresholdSelection attribute) (ipsuite.configuration_selection.ThresholdSelection attribute) (ipsuite.ThresholdSelection attribute) DipoleHistogram (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.bin_property) direction (ipsuite.configuration_selection.filter.FilterOutlier attribute) (ipsuite.configuration_selection.FilterOutlier attribute) (ipsuite.FilterOutlier attribute) dispersion (ipsuite.MACEMPModel attribute) (ipsuite.models.MACEMPModel attribute) dispersion_cutoff (ipsuite.MACEMPModel attribute) (ipsuite.models.MACEMPModel attribute) dispersion_xc (ipsuite.MACEMPModel attribute) (ipsuite.models.MACEMPModel attribute) displace_neighbors() (in module ipsuite.geometry.unwrap) dtype (ipsuite.models.TorchDFTD3 attribute) (ipsuite.TorchDFTD3 attribute) dump_file (ipsuite.calculators.lammps.LammpsSimulator attribute) (ipsuite.calculators.LammpsSimulator attribute) (ipsuite.LammpsSimulator attribute) dump_rate (ipsuite.ApplyCalculator attribute) (ipsuite.ASEGeoOpt attribute) (ipsuite.ASEMD attribute) (ipsuite.calculators.ase_geoopt.ASEGeoOpt attribute) (ipsuite.calculators.ASEGeoOpt attribute)

E

edges_from_atoms() (in module ipsuite.geometry.graphs) electronic_temperature (ipsuite.calculators.xtb.xTBSinglePoint attribute) (ipsuite.calculators.xTBSinglePoint attribute) (ipsuite.xTBSinglePoint attribute) EMTCalculator (class in ipsuite.calculators.ase_standard) EMTSinglePoint (class in ipsuite) (class in ipsuite.calculators) (class in ipsuite.calculators.ase_standard) end (ipsuite.AnalyseDensity attribute) (ipsuite.analysis.AnalyseDensity attribute) (ipsuite.analysis.md.AnalyseDensity attribute) end_cell (ipsuite.BoxOscillatingRampModifier attribute) end_pressure_au (ipsuite.PressureRampModifier attribute) end_temperature (ipsuite.TemperatureOscillatingRampModifier attribute) energies (ipsuite.analysis.BoxScale attribute) (ipsuite.analysis.model.BoxScale attribute) (ipsuite.analysis.model.dynamics.BoxScale attribute) (ipsuite.analysis.model.dynamics.RattleAnalysis attribute) (ipsuite.analysis.model.RattleAnalysis attribute) (ipsuite.analysis.RattleAnalysis attribute) (ipsuite.BoxScale attribute) (ipsuite.RattleAnalysis attribute) energy (ipsuite.analysis.CalibrationMetrics attribute) (ipsuite.analysis.model.CalibrationMetrics attribute) (ipsuite.analysis.model.predict.CalibrationMetrics attribute) (ipsuite.analysis.model.predict.PredictionMetrics attribute) (ipsuite.analysis.model.PredictionMetrics attribute) (ipsuite.analysis.PredictionMetrics attribute) (ipsuite.CalibrationMetrics attribute) (ipsuite.PredictionMetrics attribute)

EnergyHistogram (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.bin_property) EnergySpikeCheck (class in ipsuite) EnergyUncertaintyHistogram (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.bin_property) EnsembleCalculator (class in ipsuite.models.ensemble) EnsembleModel (class in ipsuite) (class in ipsuite.models) (class in ipsuite.models.ensemble) epsilon (ipsuite.calculators.ase_standard.LJSinglePoint attribute) (ipsuite.calculators.LJSinglePoint attribute) (ipsuite.LJSinglePoint attribute) excluded_frames (ipsuite.AllowedStructuresFilter property) (ipsuite.analysis.AllowedStructuresFilter property) (ipsuite.configuration_selection.base.ConfigurationSelection property) (ipsuite.configuration_selection.ConfigurationSelection property) (ipsuite.configuration_selection.filter.FilterOutlier property) (ipsuite.configuration_selection.FilterOutlier property) (ipsuite.FilterOutlier property) ExcludeIds (class in ipsuite.utils.combine)

F

factor (ipsuite.analysis.model.dynamics.RattleAnalysis attribute) (ipsuite.analysis.model.RattleAnalysis attribute) (ipsuite.analysis.RattleAnalysis attribute) (ipsuite.RattleAnalysis attribute) fail (ipsuite.AllowedStructuresFilter attribute) (ipsuite.analysis.AllowedStructuresFilter attribute) failed_configs (ipsuite.calculators.cp2k.CP2KSinglePoint attribute) (ipsuite.calculators.CP2KSinglePoint attribute) (ipsuite.CP2KSinglePoint attribute) failure_policy (ipsuite.calculators.cp2k.CP2KSinglePoint attribute) (ipsuite.calculators.CP2KSinglePoint attribute) (ipsuite.CP2KSinglePoint attribute) fig_size (ipsuite.analysis.bond_stretch.BondStretchAnalyses attribute) (ipsuite.analysis.BondStretchAnalyses attribute) figure (ipsuite.AnalyseDensity attribute) (ipsuite.analysis.AnalyseDensity attribute) (ipsuite.analysis.md.AnalyseDensity attribute) figure_path (ipsuite.AnalyseStructureMeanForce attribute) (ipsuite.analysis.AnalyseStructureMeanForce attribute) figure_ymax (ipsuite.analysis.model.predict.PredictionMetrics attribute) (ipsuite.analysis.model.PredictionMetrics attribute) (ipsuite.analysis.PredictionMetrics attribute) (ipsuite.bootstrap.surface_mods.SurfaceRasterMetrics attribute) (ipsuite.bootstrap.SurfaceRasterMetrics attribute) (ipsuite.PredictionMetrics attribute) file (ipsuite.AddData attribute) (ipsuite.AddDataH5MD attribute) (ipsuite.data_loading.add_data_ase.AddData attribute) (ipsuite.data_loading.add_data_h5md.AddDataH5MD attribute) (ipsuite.data_loading.AddData attribute) (ipsuite.data_loading.AddDataH5MD attribute) file_paths (ipsuite.GenericASEModel attribute) (ipsuite.models.GenericASEModel attribute) files (ipsuite.CP2KModel attribute) (ipsuite.models.CP2KModel attribute) fill_atoms_with_life() (ipsuite.calculators.lammps.LammpsSimulator method) (ipsuite.calculators.LammpsSimulator method) (ipsuite.LammpsSimulator method) filtered_indices (ipsuite.configuration_selection.filter.FilterOutlier attribute) (ipsuite.configuration_selection.FilterOutlier attribute) (ipsuite.FilterOutlier attribute) FilterOutlier (class in ipsuite) (class in ipsuite.configuration_selection) (class in ipsuite.configuration_selection.filter) FixedBondLengthConstraint (class in ipsuite) FixedLayerConstraint (class in ipsuite) FixedSphereConstraint (class in ipsuite) Flatten (class in ipsuite) (class in ipsuite.base) (class in ipsuite.base.base) flux_data (ipsuite.analysis.BoxHeatUp attribute) (ipsuite.analysis.model.BoxHeatUp attribute) (ipsuite.analysis.model.dynamics.BoxHeatUp attribute) (ipsuite.BoxHeatUp attribute) force_decomposition() (in module ipsuite.analysis.model.math) force_dist_slices (ipsuite.analysis.CalibrationMetrics attribute) (ipsuite.analysis.model.CalibrationMetrics attribute) (ipsuite.analysis.model.predict.CalibrationMetrics attribute) (ipsuite.CalibrationMetrics attribute) ForceAngles (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.model) (class in ipsuite.analysis.model.predict) ForceDecomposition (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.model) (class in ipsuite.analysis.model.predict) forces (ipsuite.AnalyseStructureMeanForce attribute) (ipsuite.analysis.AnalyseStructureMeanForce attribute) (ipsuite.analysis.CalibrationMetrics attribute) (ipsuite.analysis.model.CalibrationMetrics attribute) (ipsuite.analysis.model.predict.CalibrationMetrics attribute) (ipsuite.analysis.model.predict.PredictionMetrics attribute) (ipsuite.analysis.model.PredictionMetrics attribute) (ipsuite.analysis.PredictionMetrics attribute) (ipsuite.CalibrationMetrics attribute) (ipsuite.PredictionMetrics attribute) ForcesHistogram (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.bin_property) ForcesUncertaintyHistogram (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.bin_property)

ForceUncertaintyDecomposition (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.model) (class in ipsuite.analysis.model.predict) forward_mapping() (ipsuite.BarycenterMapping method) (ipsuite.geometry.BarycenterMapping method) (ipsuite.geometry.mapping.BarycenterMapping method) fraction_traceless (ipsuite.NPTThermostat attribute) frames (ipsuite.AddData property) (ipsuite.AddDataH5MD property) (ipsuite.AllowedStructuresFilter property) (ipsuite.analysis.AllowedStructuresFilter property) (ipsuite.analysis.MDStability property) (ipsuite.analysis.model.dynamics.MDStability property) (ipsuite.analysis.model.MDStability property) (ipsuite.ApplyCalculator property) (ipsuite.ASEGeoOpt property) (ipsuite.ASEMD property) (ipsuite.base.base.ProcessAtoms attribute) (ipsuite.base.base.ProcessSingleAtom attribute) (ipsuite.base.ProcessAtoms attribute) (ipsuite.base.ProcessSingleAtom attribute) (ipsuite.bootstrap.random_displacements.Bootstrap property) (ipsuite.calculators.ase_geoopt.ASEGeoOpt property) (ipsuite.calculators.ASEGeoOpt property) (ipsuite.calculators.cp2k.CP2KSinglePoint property) (ipsuite.calculators.CP2KSinglePoint property) (ipsuite.calculators.lammps.LammpsSimulator property) (ipsuite.calculators.LammpsSimulator property) (ipsuite.calculators.orca.OrcaSinglePoint property) (ipsuite.calculators.OrcaSinglePoint property) (ipsuite.configuration_generation.Packmol property) (ipsuite.configuration_generation.packmol.Packmol property) (ipsuite.configuration_generation.Smiles2Atoms property) (ipsuite.configuration_generation.Smiles2Conformers property) (ipsuite.configuration_generation.Smiles2Gromacs property) (ipsuite.configuration_generation.smiles_to_atoms.Smiles2Atoms property) (ipsuite.configuration_generation.smiles_to_atoms.Smiles2Conformers property) (ipsuite.configuration_selection.base.ConfigurationSelection property) (ipsuite.configuration_selection.ConfigurationSelection property) (ipsuite.configuration_selection.filter.FilterOutlier property) (ipsuite.configuration_selection.FilterOutlier property) (ipsuite.CP2KSinglePoint property) (ipsuite.data_loading.add_data_ase.AddData property) (ipsuite.data_loading.add_data_h5md.AddDataH5MD property) (ipsuite.data_loading.AddData property) (ipsuite.data_loading.AddDataH5MD property) (ipsuite.FilterOutlier property) (ipsuite.LammpsSimulator property) (ipsuite.MD22Dataset attribute) (ipsuite.MDStability property) (ipsuite.OrcaSinglePoint property) (ipsuite.Packmol property) (ipsuite.Smiles2Atoms property) (ipsuite.Smiles2Conformers property) (ipsuite.Smiles2Gromacs property) frames_path (ipsuite.AddData attribute) (ipsuite.ApplyCalculator attribute) (ipsuite.ASEMD attribute) (ipsuite.bootstrap.random_displacements.Bootstrap attribute) (ipsuite.configuration_generation.Packmol attribute) (ipsuite.configuration_generation.packmol.Packmol attribute) (ipsuite.configuration_generation.Smiles2Atoms attribute) (ipsuite.configuration_generation.Smiles2Conformers attribute) (ipsuite.configuration_generation.smiles_to_atoms.Smiles2Atoms attribute) (ipsuite.configuration_generation.smiles_to_atoms.Smiles2Conformers attribute) (ipsuite.data_loading.add_data_ase.AddData attribute) (ipsuite.data_loading.AddData attribute) (ipsuite.Packmol attribute) (ipsuite.Smiles2Atoms attribute) (ipsuite.Smiles2Conformers attribute) freeze_copy_atoms() (in module ipsuite.utils.ase_sim) friction (ipsuite.analysis.BoxHeatUp attribute) (ipsuite.analysis.model.BoxHeatUp attribute) (ipsuite.analysis.model.dynamics.BoxHeatUp attribute) (ipsuite.BoxHeatUp attribute) (ipsuite.LangevinThermostat attribute) frozen (ipsuite.BarycenterMapping attribute) (ipsuite.geometry.BarycenterMapping attribute) (ipsuite.geometry.mapping.BarycenterMapping attribute) fudgeLJ (ipsuite.configuration_generation.Smiles2Gromacs attribute) (ipsuite.Smiles2Gromacs attribute) fudgeQQ (ipsuite.configuration_generation.Smiles2Gromacs attribute) (ipsuite.Smiles2Gromacs attribute)

G

gauss() (in module ipsuite.analysis.model.plots) GenericASEModel (class in ipsuite) (class in ipsuite.models) get_angles() (in module ipsuite.utils.metrics) get_atom_filenames() (ipsuite.analysis.MoveSingleParticle method) (ipsuite.analysis.sensitivity.MoveSingleParticle method) (ipsuite.MoveSingleParticle method) get_atoms() (ipsuite.analysis.BoxHeatUp method) (ipsuite.analysis.model.BoxHeatUp method) (ipsuite.analysis.model.dynamics.BoxHeatUp method) (ipsuite.ASEGeoOpt method) (ipsuite.BoxHeatUp method) (ipsuite.calculators.ase_geoopt.ASEGeoOpt method) (ipsuite.calculators.ASEGeoOpt method) (ipsuite.calculators.lammps.LammpsSimulator method) (ipsuite.calculators.LammpsSimulator method) (ipsuite.LammpsSimulator method) get_box_from_density() (in module ipsuite.utils.ase_sim) get_calculator() (ipsuite.calculators.ase_standard.EMTSinglePoint method) (ipsuite.calculators.ase_standard.LJSinglePoint method) (ipsuite.calculators.cp2k.CP2KSinglePoint method) (ipsuite.calculators.CP2KSinglePoint method) (ipsuite.calculators.EMTSinglePoint method) (ipsuite.calculators.LJSinglePoint method) (ipsuite.calculators.MixCalculator method) (ipsuite.calculators.orca.OrcaSinglePoint method) (ipsuite.calculators.OrcaSinglePoint method) (ipsuite.calculators.PlumedModel method) (ipsuite.calculators.xtb.xTBSinglePoint method) (ipsuite.calculators.xTBSinglePoint method) (ipsuite.CP2KModel method) (ipsuite.CP2KSinglePoint method) (ipsuite.EMTSinglePoint method) (ipsuite.EnsembleModel method) (ipsuite.GenericASEModel method) (ipsuite.LJSinglePoint method) (ipsuite.MACEMPModel method) (ipsuite.MixCalculator method) (ipsuite.models.base.MLModel method) (ipsuite.models.CP2KModel method) (ipsuite.models.ensemble.EnsembleModel method) (ipsuite.models.EnsembleModel method) (ipsuite.models.GenericASEModel method) (ipsuite.models.MACEMPModel method) (ipsuite.models.MLModel method) (ipsuite.models.ORCAModel method) (ipsuite.models.TBLiteModel method) (ipsuite.models.TorchDFTD3 method) (ipsuite.ORCAModel method) (ipsuite.OrcaSinglePoint method) (ipsuite.PlumedModel method) (ipsuite.TBLiteModel method) (ipsuite.TorchDFTD3 method) (ipsuite.xTBSinglePoint method) get_calibration_figure() (in module ipsuite.analysis.model.plots) get_clean_data() (ipsuite.utils.combine.ExcludeIds method) get_constraint() (ipsuite.FixedBondLengthConstraint method) (ipsuite.FixedLayerConstraint method) (ipsuite.FixedSphereConstraint method) (ipsuite.HookeanConstraint method) get_content() (ipsuite.analysis.model.predict.PredictionMetrics method) (ipsuite.analysis.model.PredictionMetrics method) (ipsuite.analysis.PredictionMetrics method) (ipsuite.PredictionMetrics method) get_data() (ipsuite.analysis.CalibrationMetrics method) (ipsuite.analysis.model.CalibrationMetrics method) (ipsuite.analysis.model.predict.CalibrationMetrics method) (ipsuite.analysis.model.predict.PredictionMetrics method) (ipsuite.analysis.model.PredictionMetrics method) (ipsuite.analysis.PredictionMetrics method) (ipsuite.base.base.ProcessAtoms method) (ipsuite.base.base.ProcessSingleAtom method) (ipsuite.base.ProcessAtoms method) (ipsuite.base.ProcessSingleAtom method) (ipsuite.CalibrationMetrics method) (ipsuite.configuration_selection.base.ConfigurationSelection method) (ipsuite.configuration_selection.ConfigurationSelection method) (ipsuite.PredictionMetrics method) get_density_from_atoms() (in module ipsuite.utils.ase_sim) get_deps_if_node() (in module ipsuite.utils.helpers) get_desc() (in module ipsuite.utils.ase_sim) get_energy() (in module ipsuite.utils.ase_sim) get_energy_terms() (in module ipsuite.utils.md) get_figure() (in module ipsuite.analysis.model.plots) get_flat_data_from_dict() (in module ipsuite.utils.combine) get_full_metrics() (in module ipsuite.utils.metrics) get_gaussianicity_figure() (in module ipsuite.analysis.model.plots) get_hist() (in module ipsuite.analysis.model.plots) (ipsuite.analysis.bin_property.LabelHistogram method) (ipsuite.analysis.bin_property.StressHistogram method) (ipsuite.analysis.StressHistogram method) (ipsuite.StressHistogram method) get_histogram() (ipsuite.analysis.ForceDecomposition method) (ipsuite.analysis.model.ForceDecomposition method) (ipsuite.analysis.model.predict.ForceDecomposition method) (ipsuite.ForceDecomposition method)

get_histogram_figure() (in module ipsuite.analysis.model.plots) get_ids_per_key() (in module ipsuite.utils.combine) get_input_script() (ipsuite.calculators.cp2k.CP2KSinglePoint method) (ipsuite.calculators.CP2KSinglePoint method) (ipsuite.CP2KModel method) (ipsuite.CP2KSinglePoint method) (ipsuite.models.CP2KModel method) get_labels() (ipsuite.analysis.bin_property.DipoleHistogram method) (ipsuite.analysis.bin_property.EnergyHistogram method) (ipsuite.analysis.bin_property.EnergyUncertaintyHistogram method) (ipsuite.analysis.bin_property.ForcesHistogram method) (ipsuite.analysis.bin_property.ForcesUncertaintyHistogram method) (ipsuite.analysis.bin_property.LabelHistogram method) (ipsuite.analysis.bin_property.StressHistogram method) (ipsuite.analysis.DipoleHistogram method) (ipsuite.analysis.EnergyHistogram method) (ipsuite.analysis.EnergyUncertaintyHistogram method) (ipsuite.analysis.ForcesHistogram method) (ipsuite.analysis.ForcesUncertaintyHistogram method) (ipsuite.analysis.StressHistogram method) (ipsuite.DipoleHistogram method) (ipsuite.EnergyHistogram method) (ipsuite.EnergyUncertaintyHistogram method) (ipsuite.ForcesHistogram method) (ipsuite.ForcesUncertaintyHistogram method) (ipsuite.StressHistogram method) get_metrics() (ipsuite.analysis.CalibrationMetrics method) (ipsuite.analysis.ForceDecomposition method) (ipsuite.analysis.ForceUncertaintyDecomposition method) (ipsuite.analysis.model.CalibrationMetrics method) (ipsuite.analysis.model.ForceDecomposition method) (ipsuite.analysis.model.ForceUncertaintyDecomposition method) (ipsuite.analysis.model.predict.CalibrationMetrics method) (ipsuite.analysis.model.predict.ForceDecomposition method) (ipsuite.analysis.model.predict.ForceUncertaintyDecomposition method) (ipsuite.analysis.model.predict.PredictionMetrics method) (ipsuite.analysis.model.PredictionMetrics method) (ipsuite.analysis.PredictionMetrics method) (ipsuite.CalibrationMetrics method) (ipsuite.ForceDecomposition method) (ipsuite.ForceUncertaintyDecomposition method) (ipsuite.PredictionMetrics method) get_original_ids() (ipsuite.utils.combine.ExcludeIds method) get_pairs() (ipsuite.HookeanConstraint method) get_plots() (ipsuite.analysis.bin_property.LabelHistogram method) (ipsuite.analysis.bin_property.StressHistogram method) (ipsuite.analysis.bond_stretch.BondStretchAnalyses method) (ipsuite.analysis.BondStretchAnalyses method) (ipsuite.analysis.CalibrationMetrics method) (ipsuite.analysis.ForceDecomposition method) (ipsuite.analysis.ForceUncertaintyDecomposition method) (ipsuite.analysis.MDStability method) (ipsuite.analysis.model.CalibrationMetrics method) (ipsuite.analysis.model.dynamics.MDStability method) (ipsuite.analysis.model.ForceDecomposition method) (ipsuite.analysis.model.ForceUncertaintyDecomposition method) (ipsuite.analysis.model.MDStability method) (ipsuite.analysis.model.predict.CalibrationMetrics method) (ipsuite.analysis.model.predict.ForceDecomposition method) (ipsuite.analysis.model.predict.ForceUncertaintyDecomposition method) (ipsuite.analysis.model.predict.PredictionMetrics method) (ipsuite.analysis.model.PredictionMetrics method) (ipsuite.analysis.PredictionMetrics method) (ipsuite.analysis.StressHistogram method) (ipsuite.bootstrap.surface_mods.SurfaceRasterMetrics method) (ipsuite.bootstrap.SurfaceRasterMetrics method) (ipsuite.CalibrationMetrics method) (ipsuite.ForceDecomposition method) (ipsuite.ForceUncertaintyDecomposition method) (ipsuite.MDStability method) (ipsuite.PredictionMetrics method) (ipsuite.StressHistogram method) (ipsuite.SurfaceRasterMetrics method) get_quantity() (ipsuite.base.base.Check method) (ipsuite.base.Check method) (ipsuite.DensityCheck method) (ipsuite.ThresholdCheck method) get_selected_atom_id() (ipsuite.FixedSphereConstraint method) get_template() (ipsuite.calculators.lammps.LammpsSimulator class method) (ipsuite.calculators.LammpsSimulator class method) (ipsuite.LammpsSimulator class method) get_thermostat() (ipsuite.Berendsen method) (ipsuite.LangevinThermostat method) (ipsuite.NPTThermostat method) (ipsuite.SVCRBarostat method) (ipsuite.VelocityVerletDynamic method) get_u_vecs() (in module ipsuite.utils.metrics) get_value() (ipsuite.base.base.Check method) (ipsuite.base.Check method) (ipsuite.DensityCheck method) (ipsuite.ThresholdCheck method) get_values() (ipsuite.AnalyseSingleForceSensitivity method) (ipsuite.analysis.AnalyseSingleForceSensitivity method) (ipsuite.analysis.sensitivity.AnalyseSingleForceSensitivity method)

H

histogram (ipsuite.configuration_selection.filter.FilterOutlier attribute) (ipsuite.configuration_selection.FilterOutlier attribute) (ipsuite.FilterOutlier attribute) histogram_plt (ipsuite.analysis.ForceDecomposition attribute) (ipsuite.analysis.model.ForceDecomposition attribute) (ipsuite.analysis.model.predict.ForceDecomposition attribute) (ipsuite.ForceDecomposition attribute)

HookeanConstraint (class in ipsuite)

I

identify_molecules() (in module ipsuite.geometry.graphs) ids (ipsuite.utils.combine.ExcludeIds attribute) ids_as_list (ipsuite.utils.combine.ExcludeIds property) idxs (ipsuite.analysis.bond_stretch.BondStretchAnalyses attribute) (ipsuite.analysis.BondStretchAnalyses attribute) img_selection (ipsuite.configuration_selection.base.ConfigurationSelection attribute) (ipsuite.configuration_selection.ConfigurationSelection attribute) implemented_properties (ipsuite.ApplyCalculator attribute) include_original (ipsuite.bootstrap.random_displacements.Bootstrap attribute) IndexSelection (class in ipsuite) (class in ipsuite.configuration_selection) (class in ipsuite.configuration_selection.index) indices (ipsuite.configuration_selection.index.IndexSelection attribute) (ipsuite.configuration_selection.IndexSelection attribute) (ipsuite.IndexSelection attribute) init_kwargs (ipsuite.ASEGeoOpt attribute) (ipsuite.calculators.ase_geoopt.ASEGeoOpt attribute) (ipsuite.calculators.ASEGeoOpt attribute) initial_guess (ipsuite.calculators.xtb.xTBSinglePoint attribute) (ipsuite.calculators.xTBSinglePoint attribute) (ipsuite.xTBSinglePoint attribute) initial_temperature (ipsuite.analysis.MDStability attribute) (ipsuite.analysis.model.dynamics.MDStability attribute) (ipsuite.analysis.model.MDStability attribute) (ipsuite.MDStability attribute) initialize() (ipsuite.base.base.Check method) (ipsuite.base.Check method) (ipsuite.ConnectivityCheck method) (ipsuite.DebugCheck method) (ipsuite.EnergySpikeCheck method) (ipsuite.NaNCheck method) (ipsuite.TemperatureCheck method) (ipsuite.ThresholdCheck method) initialize_atoms() (ipsuite.ASEMD method) initialize_checks() (ipsuite.ASEMD method) initialize_md() (ipsuite.ASEMD method) initialize_progress_bar() (ipsuite.ASEMD method) interval (ipsuite.BoxOscillatingRampModifier attribute) (ipsuite.PressureRampModifier attribute) (ipsuite.TemperatureOscillatingRampModifier attribute) (ipsuite.TemperatureRampModifier attribute) IPSNode (class in ipsuite.base) (class in ipsuite.base.base) ipsuite module ipsuite.analysis module ipsuite.analysis.bin_property module ipsuite.analysis.bond_stretch module ipsuite.analysis.ensemble module ipsuite.analysis.md module ipsuite.analysis.model module ipsuite.analysis.model.dynamics module ipsuite.analysis.model.math module ipsuite.analysis.model.plots module ipsuite.analysis.model.predict module ipsuite.analysis.sensitivity module ipsuite.base module ipsuite.base.base module ipsuite.bootstrap module ipsuite.bootstrap.random_displacements module ipsuite.bootstrap.surface_mods module ipsuite.calculators module ipsuite.calculators.ase_geoopt module ipsuite.calculators.ase_standard module

ipsuite.calculators.cp2k module ipsuite.calculators.lammps module ipsuite.calculators.orca module ipsuite.calculators.xtb module ipsuite.configuration_generation module ipsuite.configuration_generation.packmol module ipsuite.configuration_generation.smiles_to_atoms module ipsuite.configuration_selection module ipsuite.configuration_selection.base module ipsuite.configuration_selection.filter module ipsuite.configuration_selection.index module ipsuite.configuration_selection.random module ipsuite.configuration_selection.split module ipsuite.configuration_selection.threshold module ipsuite.configuration_selection.uniform_arange module ipsuite.configuration_selection.uniform_energetic module ipsuite.configuration_selection.uniform_temporal module ipsuite.data_loading module ipsuite.data_loading.add_data_ase module ipsuite.data_loading.add_data_h5md module ipsuite.fields module ipsuite.fields.atoms module ipsuite.geometry module ipsuite.geometry.barycenter_coarse_grain module ipsuite.geometry.graphs module ipsuite.geometry.mapping module ipsuite.geometry.unwrap module ipsuite.models module ipsuite.models.base module ipsuite.models.ensemble module ipsuite.nodes module ipsuite.project module ipsuite.static_data module ipsuite.utils module ipsuite.utils.ase_sim module ipsuite.utils.combine module ipsuite.utils.helpers module ipsuite.utils.logs module ipsuite.utils.md module ipsuite.utils.metrics module IsConstraintMD (class in ipsuite.analysis.sensitivity) itp_files (ipsuite.configuration_generation.Smiles2Gromacs attribute) (ipsuite.Smiles2Gromacs attribute)

K

k (ipsuite.HookeanConstraint attribute) key (ipsuite.configuration_selection.filter.FilterOutlier attribute) (ipsuite.configuration_selection.FilterOutlier attribute) (ipsuite.configuration_selection.threshold.ThresholdSelection attribute) (ipsuite.configuration_selection.ThresholdSelection attribute) (ipsuite.FilterOutlier attribute) (ipsuite.ThresholdCheck attribute) (ipsuite.ThresholdSelection attribute)

kwargs (ipsuite.GenericASEModel attribute) (ipsuite.models.GenericASEModel attribute)

L

LabelHistogram (class in ipsuite.analysis.bin_property) labels (ipsuite.configuration_generation.Smiles2Gromacs attribute) (ipsuite.Smiles2Gromacs attribute) labels_df (ipsuite.analysis.bin_property.LabelHistogram attribute) (ipsuite.analysis.bin_property.StressHistogram attribute) (ipsuite.analysis.StressHistogram attribute) (ipsuite.StressHistogram attribute) lammps_pair_coeff (ipsuite.models.base.MLModel property) (ipsuite.models.MLModel property) lammps_pair_style (ipsuite.models.base.MLModel property) (ipsuite.models.MLModel property) LammpsSimulator (class in ipsuite) (class in ipsuite.calculators) (class in ipsuite.calculators.lammps) LangevinThermostat (class in ipsuite) larger_only (ipsuite.ThresholdCheck attribute) laufband_path (ipsuite.ASEMD attribute) lines_to_read (ipsuite.AddData attribute) (ipsuite.data_loading.add_data_ase.AddData attribute) (ipsuite.data_loading.AddData attribute) LJSinglePoint (class in ipsuite) (class in ipsuite.calculators) (class in ipsuite.calculators.ase_standard) lmp_directory (ipsuite.calculators.lammps.LammpsSimulator attribute) (ipsuite.calculators.LammpsSimulator attribute) (ipsuite.LammpsSimulator attribute) lmp_exe (ipsuite.calculators.lammps.LammpsSimulator attribute) (ipsuite.calculators.LammpsSimulator attribute) (ipsuite.LammpsSimulator attribute)

lmp_params (ipsuite.calculators.lammps.LammpsSimulator attribute) (ipsuite.calculators.LammpsSimulator attribute) (ipsuite.LammpsSimulator attribute) lmp_template (ipsuite.calculators.lammps.LammpsSimulator attribute) (ipsuite.calculators.LammpsSimulator attribute) (ipsuite.LammpsSimulator attribute) load_data() (in module ipsuite.data_loading.add_data_ase) log_file (ipsuite.ASEGeoOpt attribute) (ipsuite.calculators.ase_geoopt.ASEGeoOpt attribute) (ipsuite.calculators.ASEGeoOpt attribute) (ipsuite.calculators.lammps.LammpsSimulator attribute) (ipsuite.calculators.LammpsSimulator attribute) (ipsuite.LammpsSimulator attribute) log_plot (ipsuite.analysis.ForceAngles attribute) (ipsuite.analysis.model.ForceAngles attribute) (ipsuite.analysis.model.predict.ForceAngles attribute) (ipsuite.ForceAngles attribute) logspace (ipsuite.analysis.model.dynamics.RattleAnalysis attribute) (ipsuite.analysis.model.RattleAnalysis attribute) (ipsuite.analysis.RattleAnalysis attribute) (ipsuite.RattleAnalysis attribute) logy_scale (ipsuite.analysis.bin_property.LabelHistogram attribute) (ipsuite.analysis.bin_property.StressHistogram attribute) (ipsuite.analysis.StressHistogram attribute) (ipsuite.StressHistogram attribute) lower_dict() (in module ipsuite.utils.helpers) lower_limit (ipsuite.FixedLayerConstraint attribute)

M

MACEMPModel (class in ipsuite) (class in ipsuite.models) mapping (ipsuite.analysis.BoxScale attribute) (ipsuite.analysis.model.BoxScale attribute) (ipsuite.analysis.model.dynamics.BoxScale attribute) (ipsuite.BoxScale attribute) max_density (ipsuite.DensityCheck attribute) max_energy (ipsuite.EnergySpikeCheck attribute) max_factor (ipsuite.EnergySpikeCheck attribute) max_iterations (ipsuite.calculators.xtb.xTBSinglePoint attribute) (ipsuite.calculators.xTBSinglePoint attribute) (ipsuite.xTBSinglePoint attribute) max_rattel_shift (ipsuite.bootstrap.surface_mods.SurfaceRasterScan attribute) (ipsuite.bootstrap.SurfaceRasterScan attribute) (ipsuite.SurfaceRasterScan attribute) max_reduction() (in module ipsuite.configuration_selection.threshold) max_std (ipsuite.ThresholdCheck attribute) max_steps (ipsuite.analysis.MDStability attribute) (ipsuite.analysis.model.dynamics.MDStability attribute) (ipsuite.analysis.model.MDStability attribute) (ipsuite.MDStability attribute) max_temperature (ipsuite.analysis.BoxHeatUp attribute) (ipsuite.analysis.model.BoxHeatUp attribute) (ipsuite.analysis.model.dynamics.BoxHeatUp attribute) (ipsuite.BoxHeatUp attribute) (ipsuite.TemperatureCheck attribute) max_value (ipsuite.ThresholdCheck attribute) maxAttempts (ipsuite.configuration_generation.Smiles2Conformers attribute) (ipsuite.configuration_generation.smiles_to_atoms.Smiles2Conformers attribute) (ipsuite.Smiles2Conformers attribute) maximum (ipsuite.bootstrap.random_displacements.Bootstrap attribute) maximum_error() (in module ipsuite.utils.metrics) maxstep (ipsuite.ASEGeoOpt attribute) (ipsuite.calculators.ase_geoopt.ASEGeoOpt attribute) (ipsuite.calculators.ASEGeoOpt attribute) maxwarn (ipsuite.configuration_generation.Smiles2Gromacs attribute) (ipsuite.Smiles2Gromacs attribute) MD22Dataset (class in ipsuite) mdp_files (ipsuite.configuration_generation.Smiles2Gromacs attribute) (ipsuite.Smiles2Gromacs attribute) mds (ipsuite.analysis.CollectMDSteps attribute) (ipsuite.analysis.md.CollectMDSteps attribute) (ipsuite.CollectMDSteps attribute) MDStability (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.model) (class in ipsuite.analysis.model.dynamics) mean_absolute_error() (in module ipsuite.utils.metrics) mean_reduction() (in module ipsuite.configuration_selection.threshold) mean_squared_error() (in module ipsuite.utils.metrics) method (ipsuite.calculators.MixCalculator attribute) (ipsuite.calculators.xtb.xTBSinglePoint attribute) (ipsuite.calculators.xTBSinglePoint attribute) (ipsuite.MixCalculator attribute) (ipsuite.models.TBLiteModel attribute) (ipsuite.TBLiteModel attribute) (ipsuite.xTBSinglePoint attribute) metrics (ipsuite.analysis.bin_property.LabelHistogram attribute) (ipsuite.analysis.CollectMDSteps attribute) (ipsuite.analysis.md.CollectMDSteps attribute) (ipsuite.ASEMD attribute) (ipsuite.CollectMDSteps attribute) min_density (ipsuite.DensityCheck attribute) min_distance (ipsuite.configuration_selection.threshold.ThresholdSelection attribute) (ipsuite.configuration_selection.ThresholdSelection attribute) (ipsuite.ThresholdSelection attribute) min_energy (ipsuite.EnergySpikeCheck attribute) min_factor (ipsuite.EnergySpikeCheck attribute) minimum_window_size (ipsuite.ThresholdCheck attribute) MixCalculator (class in ipsuite) (class in ipsuite.calculators) mixer_damping (ipsuite.calculators.xtb.xTBSinglePoint attribute) (ipsuite.calculators.xTBSinglePoint attribute) (ipsuite.xTBSinglePoint attribute) MLModel (class in ipsuite.models) (class in ipsuite.models.base) model (ipsuite.analysis.BoxHeatUp attribute) (ipsuite.analysis.BoxScale attribute) (ipsuite.analysis.MDStability attribute) (ipsuite.analysis.model.BoxHeatUp attribute) (ipsuite.analysis.model.BoxScale attribute) (ipsuite.analysis.model.dynamics.BoxHeatUp attribute) (ipsuite.analysis.model.dynamics.BoxScale attribute) (ipsuite.analysis.model.dynamics.MDStability attribute) (ipsuite.analysis.model.dynamics.RattleAnalysis attribute) (ipsuite.analysis.model.MDStability attribute) (ipsuite.analysis.model.predict.Prediction attribute) (ipsuite.analysis.model.Prediction attribute) (ipsuite.analysis.model.RattleAnalysis attribute) (ipsuite.analysis.Prediction attribute) (ipsuite.analysis.RattleAnalysis attribute) (ipsuite.ApplyCalculator attribute) (ipsuite.ASEGeoOpt attribute) (ipsuite.ASEMD attribute) (ipsuite.BoxHeatUp attribute) (ipsuite.BoxScale attribute) (ipsuite.calculators.ase_geoopt.ASEGeoOpt attribute) (ipsuite.calculators.ASEGeoOpt attribute) (ipsuite.calculators.PlumedModel attribute) (ipsuite.MACEMPModel attribute) (ipsuite.MDStability attribute) (ipsuite.models.MACEMPModel attribute) (ipsuite.PlumedModel attribute) (ipsuite.Prediction attribute) (ipsuite.RattleAnalysis attribute) model_outs (ipsuite.analysis.BoxHeatUp attribute) (ipsuite.analysis.BoxScale attribute) (ipsuite.analysis.MDStability attribute) (ipsuite.analysis.model.BoxHeatUp attribute) (ipsuite.analysis.model.BoxScale attribute) (ipsuite.analysis.model.dynamics.BoxHeatUp attribute) (ipsuite.analysis.model.dynamics.BoxScale attribute) (ipsuite.analysis.model.dynamics.MDStability attribute) (ipsuite.analysis.model.dynamics.RattleAnalysis attribute) (ipsuite.analysis.model.MDStability attribute) (ipsuite.analysis.model.RattleAnalysis attribute) (ipsuite.analysis.RattleAnalysis attribute) (ipsuite.ApplyCalculator attribute) (ipsuite.ASEGeoOpt attribute) (ipsuite.ASEMD attribute) (ipsuite.BoxHeatUp attribute) (ipsuite.BoxScale attribute) (ipsuite.calculators.ase_geoopt.ASEGeoOpt attribute) (ipsuite.calculators.ASEGeoOpt attribute) (ipsuite.MDStability attribute) (ipsuite.RattleAnalysis attribute)

model_path (ipsuite.MACEMPModel attribute) (ipsuite.models.MACEMPModel attribute) models (ipsuite.EnsembleModel attribute) (ipsuite.models.ensemble.EnsembleModel attribute) (ipsuite.models.EnsembleModel attribute) modifiers (ipsuite.ASEMD attribute) modify() (ipsuite.BoxOscillatingRampModifier method) (ipsuite.PressureRampModifier method) (ipsuite.RescaleBoxModifier method) (ipsuite.TemperatureOscillatingRampModifier method) (ipsuite.TemperatureRampModifier method) (ipsuite.WrapModifier method) module ipsuite ipsuite.analysis ipsuite.analysis.bin_property ipsuite.analysis.bond_stretch ipsuite.analysis.ensemble ipsuite.analysis.md ipsuite.analysis.model ipsuite.analysis.model.dynamics ipsuite.analysis.model.math ipsuite.analysis.model.plots ipsuite.analysis.model.predict ipsuite.analysis.sensitivity ipsuite.base ipsuite.base.base ipsuite.bootstrap ipsuite.bootstrap.random_displacements ipsuite.bootstrap.surface_mods ipsuite.calculators ipsuite.calculators.ase_geoopt ipsuite.calculators.ase_standard ipsuite.calculators.cp2k ipsuite.calculators.lammps ipsuite.calculators.orca ipsuite.calculators.xtb ipsuite.configuration_generation ipsuite.configuration_generation.packmol ipsuite.configuration_generation.smiles_to_atoms ipsuite.configuration_selection ipsuite.configuration_selection.base ipsuite.configuration_selection.filter ipsuite.configuration_selection.index ipsuite.configuration_selection.random ipsuite.configuration_selection.split ipsuite.configuration_selection.threshold ipsuite.configuration_selection.uniform_arange ipsuite.configuration_selection.uniform_energetic ipsuite.configuration_selection.uniform_temporal ipsuite.data_loading ipsuite.data_loading.add_data_ase ipsuite.data_loading.add_data_h5md ipsuite.fields ipsuite.fields.atoms ipsuite.geometry ipsuite.geometry.barycenter_coarse_grain ipsuite.geometry.graphs ipsuite.geometry.mapping ipsuite.geometry.unwrap ipsuite.models ipsuite.models.base ipsuite.models.ensemble ipsuite.nodes ipsuite.project ipsuite.static_data ipsuite.utils ipsuite.utils.ase_sim ipsuite.utils.combine ipsuite.utils.helpers ipsuite.utils.logs ipsuite.utils.md ipsuite.utils.metrics module (ipsuite.GenericASEModel attribute) (ipsuite.models.GenericASEModel attribute) molecule_image_path (ipsuite.configuration_generation.Smiles2Atoms attribute) (ipsuite.configuration_generation.Smiles2Conformers attribute) (ipsuite.configuration_generation.smiles_to_atoms.Smiles2Atoms attribute) (ipsuite.configuration_generation.smiles_to_atoms.Smiles2Conformers attribute) (ipsuite.Smiles2Atoms attribute) (ipsuite.Smiles2Conformers attribute) molecules (ipsuite.AllowedStructuresFilter attribute) (ipsuite.analysis.AllowedStructuresFilter attribute) MoveSingleParticle (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.sensitivity) MultiPackmol (class in ipsuite) (class in ipsuite.configuration_generation) (class in ipsuite.configuration_generation.packmol) multiplicity (ipsuite.calculators.xtb.xTBSinglePoint attribute) (ipsuite.calculators.xTBSinglePoint attribute) (ipsuite.models.TBLiteModel attribute) (ipsuite.TBLiteModel attribute) (ipsuite.xTBSinglePoint attribute)

N

n_conf_per_dist (ipsuite.bootstrap.surface_mods.SurfaceRasterScan attribute) (ipsuite.bootstrap.SurfaceRasterScan attribute) (ipsuite.SurfaceRasterScan attribute) n_configurations (ipsuite.bootstrap.random_displacements.Bootstrap attribute) (ipsuite.configuration_generation.MultiPackmol attribute) (ipsuite.configuration_generation.packmol.MultiPackmol attribute) (ipsuite.configuration_selection.random.RandomSelection attribute) (ipsuite.configuration_selection.RandomSelection attribute) (ipsuite.configuration_selection.threshold.ThresholdSelection attribute) (ipsuite.configuration_selection.ThresholdSelection attribute) (ipsuite.configuration_selection.uniform_energetic.UniformEnergeticSelection attribute) (ipsuite.configuration_selection.uniform_temporal.UniformTemporalSelection attribute) (ipsuite.configuration_selection.UniformEnergeticSelection attribute) (ipsuite.configuration_selection.UniformTemporalSelection attribute) (ipsuite.MultiPackmol attribute) (ipsuite.RandomSelection attribute) (ipsuite.ThresholdSelection attribute) (ipsuite.UniformEnergeticSelection attribute) (ipsuite.UniformTemporalSelection attribute) n_iterations (ipsuite.DebugCheck attribute)

n_steps (ipsuite.analysis.bond_stretch.BondStretchAnalyses attribute) (ipsuite.analysis.BondStretchAnalyses attribute) NaNCheck (class in ipsuite) nll() (in module ipsuite.analysis.model.math) nlls() (in module ipsuite.analysis.model.math) nonuniform_imshow() (in module ipsuite.analysis.sensitivity) NPTThermostat (class in ipsuite) num (ipsuite.analysis.BoxScale attribute) (ipsuite.analysis.model.BoxScale attribute) (ipsuite.analysis.model.dynamics.BoxScale attribute) (ipsuite.analysis.model.dynamics.RattleAnalysis attribute) (ipsuite.analysis.model.RattleAnalysis attribute) (ipsuite.analysis.RattleAnalysis attribute) (ipsuite.BoxScale attribute) (ipsuite.RattleAnalysis attribute) num_oscillations (ipsuite.BoxOscillatingRampModifier attribute) (ipsuite.TemperatureOscillatingRampModifier attribute) num_ramp_oscillations (ipsuite.BoxOscillatingRampModifier attribute) numConfs (ipsuite.configuration_generation.Smiles2Conformers attribute) (ipsuite.configuration_generation.smiles_to_atoms.Smiles2Conformers attribute) (ipsuite.Smiles2Conformers attribute)

O

optimizer (ipsuite.ASEGeoOpt attribute) (ipsuite.calculators.ase_geoopt.ASEGeoOpt attribute) (ipsuite.calculators.ASEGeoOpt attribute) orca_directory (ipsuite.calculators.orca.OrcaSinglePoint attribute) (ipsuite.calculators.OrcaSinglePoint attribute) (ipsuite.OrcaSinglePoint attribute) orca_shell (ipsuite.calculators.orca.OrcaSinglePoint attribute) (ipsuite.calculators.OrcaSinglePoint attribute) (ipsuite.OrcaSinglePoint attribute) orcablocks (ipsuite.calculators.orca.OrcaSinglePoint attribute) (ipsuite.calculators.OrcaSinglePoint attribute) (ipsuite.OrcaSinglePoint attribute) ORCAModel (class in ipsuite) (class in ipsuite.models) orcasimpleinput (ipsuite.calculators.orca.OrcaSinglePoint attribute) (ipsuite.calculators.OrcaSinglePoint attribute) (ipsuite.OrcaSinglePoint attribute)

OrcaSinglePoint (class in ipsuite) (class in ipsuite.calculators) (class in ipsuite.calculators.orca) outliers (ipsuite.AllowedStructuresFilter attribute) (ipsuite.analysis.AllowedStructuresFilter attribute) output_dir (ipsuite.configuration_generation.Smiles2Gromacs attribute) (ipsuite.Smiles2Gromacs attribute) output_file (ipsuite.calculators.cp2k.CP2KSinglePoint attribute) (ipsuite.calculators.CP2KSinglePoint attribute) (ipsuite.calculators.orca.OrcaSinglePoint attribute) (ipsuite.calculators.OrcaSinglePoint attribute) (ipsuite.CP2KSinglePoint attribute) (ipsuite.OrcaSinglePoint attribute)

P

Packmol (class in ipsuite) (class in ipsuite.configuration_generation) (class in ipsuite.configuration_generation.packmol) parameter_paths (ipsuite.GenericASEModel attribute) (ipsuite.models.GenericASEModel attribute) pbc (ipsuite.configuration_generation.Packmol attribute) (ipsuite.configuration_generation.packmol.Packmol attribute) (ipsuite.Packmol attribute) pdb_files (ipsuite.configuration_generation.Smiles2Gromacs attribute) (ipsuite.Smiles2Gromacs attribute) pfactor (ipsuite.NPTThermostat attribute) plot (ipsuite.analysis.BoxScale attribute) (ipsuite.analysis.ForceAngles attribute) (ipsuite.analysis.model.BoxScale attribute) (ipsuite.analysis.model.dynamics.BoxScale attribute) (ipsuite.analysis.model.ForceAngles attribute) (ipsuite.analysis.model.predict.ForceAngles attribute) (ipsuite.BoxScale attribute) (ipsuite.ForceAngles attribute) plot_temperature() (ipsuite.analysis.BoxHeatUp method) (ipsuite.analysis.model.BoxHeatUp method) (ipsuite.analysis.model.dynamics.BoxHeatUp method) (ipsuite.BoxHeatUp method) plot_ture_vs_pred() (in module ipsuite.bootstrap.surface_mods) plot_with_uncertainty() (in module ipsuite.analysis.ensemble) plots (ipsuite.AnalyseGlobalForceSensitivity attribute) (ipsuite.analysis.AnalyseGlobalForceSensitivity attribute) (ipsuite.analysis.BoxHeatUp attribute) (ipsuite.analysis.model.BoxHeatUp attribute) (ipsuite.analysis.model.dynamics.BoxHeatUp attribute) (ipsuite.analysis.sensitivity.AnalyseGlobalForceSensitivity attribute) (ipsuite.BoxHeatUp attribute) plots_dir (ipsuite.analysis.bin_property.LabelHistogram attribute) (ipsuite.analysis.bin_property.StressHistogram attribute) (ipsuite.analysis.bond_stretch.BondStretchAnalyses attribute) (ipsuite.analysis.BondStretchAnalyses attribute) (ipsuite.analysis.CalibrationMetrics attribute) (ipsuite.analysis.ForceUncertaintyDecomposition attribute) (ipsuite.analysis.MDStability attribute) (ipsuite.analysis.model.CalibrationMetrics attribute) (ipsuite.analysis.model.dynamics.MDStability attribute) (ipsuite.analysis.model.ForceUncertaintyDecomposition attribute) (ipsuite.analysis.model.MDStability attribute) (ipsuite.analysis.model.predict.CalibrationMetrics attribute) (ipsuite.analysis.model.predict.ForceUncertaintyDecomposition attribute) (ipsuite.analysis.model.predict.PredictionMetrics attribute) (ipsuite.analysis.model.PredictionMetrics attribute) (ipsuite.analysis.PredictionMetrics attribute) (ipsuite.analysis.StressHistogram attribute) (ipsuite.CalibrationMetrics attribute) (ipsuite.ForceUncertaintyDecomposition attribute) (ipsuite.MDStability attribute) (ipsuite.PredictionMetrics attribute) (ipsuite.StressHistogram attribute)

PlumedModel (class in ipsuite) (class in ipsuite.calculators) predict() (ipsuite.EnsembleModel method) (ipsuite.models.base.MLModel method) (ipsuite.models.ensemble.EnsembleModel method) (ipsuite.models.EnsembleModel method) (ipsuite.models.MLModel method) Prediction (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.model) (class in ipsuite.analysis.model.predict) PredictionMetrics (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.model) (class in ipsuite.analysis.model.predict) pressure (ipsuite.NPTThermostat attribute) pressure_au (ipsuite.SVCRBarostat attribute) PressureRampModifier (class in ipsuite) ProcessAtoms (class in ipsuite.base) (class in ipsuite.base.base) ProcessSingleAtom (class in ipsuite.base) (class in ipsuite.base.base) production_indices (ipsuite.configuration_generation.Smiles2Gromacs attribute) (ipsuite.Smiles2Gromacs attribute) Project (class in ipsuite) (class in ipsuite.project)

R

r_max (ipsuite.analysis.bond_stretch.BondStretchAnalyses attribute) (ipsuite.analysis.BondStretchAnalyses attribute) r_min (ipsuite.analysis.bond_stretch.BondStretchAnalyses attribute) (ipsuite.analysis.BondStretchAnalyses attribute) radius (ipsuite.analysis.sensitivity.IsConstraintMD attribute) (ipsuite.FixedSphereConstraint attribute) random (ipsuite.bootstrap.surface_mods.SurfaceRasterScan attribute) (ipsuite.bootstrap.SurfaceRasterScan attribute) (ipsuite.SurfaceRasterScan attribute) RandomSelection (class in ipsuite) (class in ipsuite.configuration_selection) (class in ipsuite.configuration_selection.random) RattleAnalysis (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.model) (class in ipsuite.analysis.model.dynamics) RattleAtoms (class in ipsuite) (class in ipsuite.bootstrap) (class in ipsuite.bootstrap.random_displacements) rc (ipsuite.calculators.ase_standard.LJSinglePoint attribute) (ipsuite.calculators.LJSinglePoint attribute) (ipsuite.LJSinglePoint attribute) reduction_axis (ipsuite.configuration_selection.threshold.ThresholdSelection attribute) (ipsuite.configuration_selection.ThresholdSelection attribute) (ipsuite.ThresholdSelection attribute) reference (ipsuite.configuration_selection.threshold.ThresholdSelection attribute) (ipsuite.configuration_selection.ThresholdSelection attribute) (ipsuite.ThresholdSelection attribute) relative_rmse() (in module ipsuite.utils.metrics) repeat (ipsuite.analysis.BoxHeatUp attribute) (ipsuite.analysis.model.BoxHeatUp attribute) (ipsuite.analysis.model.dynamics.BoxHeatUp attribute) (ipsuite.ASEGeoOpt attribute) (ipsuite.ASEMD attribute) (ipsuite.BoxHeatUp attribute) (ipsuite.calculators.ase_geoopt.ASEGeoOpt attribute) (ipsuite.calculators.ASEGeoOpt attribute) RescaleBoxModifier (class in ipsuite) results (ipsuite.AnalyseDensity attribute) (ipsuite.analysis.AnalyseDensity attribute) (ipsuite.analysis.md.AnalyseDensity attribute) root_mean_squared_error() (in module ipsuite.utils.metrics) rot_force_plt (ipsuite.analysis.ForceDecomposition attribute) (ipsuite.analysis.model.ForceDecomposition attribute) (ipsuite.analysis.model.predict.ForceDecomposition attribute) (ipsuite.ForceDecomposition attribute) rot_forces (ipsuite.analysis.ForceDecomposition attribute) (ipsuite.analysis.ForceUncertaintyDecomposition attribute) (ipsuite.analysis.model.ForceDecomposition attribute) (ipsuite.analysis.model.ForceUncertaintyDecomposition attribute) (ipsuite.analysis.model.predict.ForceDecomposition attribute) (ipsuite.analysis.model.predict.ForceUncertaintyDecomposition attribute) (ipsuite.ForceDecomposition attribute) (ipsuite.ForceUncertaintyDecomposition attribute) RotateMolecules (class in ipsuite) (class in ipsuite.bootstrap) (class in ipsuite.bootstrap.random_displacements) rt (ipsuite.HookeanConstraint attribute) run() (ipsuite.AddData method) (ipsuite.AddDataH5MD method) (ipsuite.AllowedStructuresFilter method) (ipsuite.AnalyseDensity method) (ipsuite.AnalyseGlobalForceSensitivity method) (ipsuite.AnalyseSingleForceSensitivity method) (ipsuite.AnalyseStructureMeanForce method) (ipsuite.analysis.AllowedStructuresFilter method) (ipsuite.analysis.AnalyseDensity method) (ipsuite.analysis.AnalyseGlobalForceSensitivity method) (ipsuite.analysis.AnalyseSingleForceSensitivity method) (ipsuite.analysis.AnalyseStructureMeanForce method) (ipsuite.analysis.bin_property.LabelHistogram method) (ipsuite.analysis.bin_property.StressHistogram method) (ipsuite.analysis.bond_stretch.BondStretchAnalyses method) (ipsuite.analysis.BondStretchAnalyses method) (ipsuite.analysis.BoxHeatUp method) (ipsuite.analysis.BoxScale method) (ipsuite.analysis.CalibrationMetrics method) (ipsuite.analysis.CollectMDSteps method) (ipsuite.analysis.ForceAngles method) (ipsuite.analysis.ForceDecomposition method) (ipsuite.analysis.ForceUncertaintyDecomposition method) (ipsuite.analysis.md.AnalyseDensity method) (ipsuite.analysis.md.CollectMDSteps method) (ipsuite.analysis.MDStability method) (ipsuite.analysis.model.BoxHeatUp method) (ipsuite.analysis.model.BoxScale method) (ipsuite.analysis.model.CalibrationMetrics method) (ipsuite.analysis.model.dynamics.BoxHeatUp method) (ipsuite.analysis.model.dynamics.BoxScale method) (ipsuite.analysis.model.dynamics.MDStability method) (ipsuite.analysis.model.dynamics.RattleAnalysis method) (ipsuite.analysis.model.ForceAngles method) (ipsuite.analysis.model.ForceDecomposition method) (ipsuite.analysis.model.ForceUncertaintyDecomposition method) (ipsuite.analysis.model.MDStability method) (ipsuite.analysis.model.predict.CalibrationMetrics method) (ipsuite.analysis.model.predict.ForceAngles method) (ipsuite.analysis.model.predict.ForceDecomposition method) (ipsuite.analysis.model.predict.ForceUncertaintyDecomposition method) (ipsuite.analysis.model.predict.Prediction method) (ipsuite.analysis.model.predict.PredictionMetrics method) (ipsuite.analysis.model.Prediction method) (ipsuite.analysis.model.PredictionMetrics method) (ipsuite.analysis.model.RattleAnalysis method) (ipsuite.analysis.MoveSingleParticle method) (ipsuite.analysis.Prediction method) (ipsuite.analysis.PredictionMetrics method) (ipsuite.analysis.RattleAnalysis method) (ipsuite.analysis.sensitivity.AnalyseGlobalForceSensitivity method) (ipsuite.analysis.sensitivity.AnalyseSingleForceSensitivity method) (ipsuite.analysis.sensitivity.MoveSingleParticle method) (ipsuite.analysis.StressHistogram method) (ipsuite.ApplyCalculator method) (ipsuite.ASEGeoOpt method) (ipsuite.ASEMD method) (ipsuite.ASEMDSafeSampling method) (ipsuite.base.base.Flatten method) (ipsuite.base.Flatten method) (ipsuite.bootstrap.random_displacements.Bootstrap method) (ipsuite.bootstrap.surface_mods.SurfaceRasterScan method) (ipsuite.bootstrap.SurfaceRasterScan method) (ipsuite.BoxHeatUp method) (ipsuite.BoxScale method) (ipsuite.calculators.ase_geoopt.ASEGeoOpt method) (ipsuite.calculators.ASEGeoOpt method) (ipsuite.calculators.cp2k.CP2KSinglePoint method) (ipsuite.calculators.CP2KSinglePoint method) (ipsuite.calculators.lammps.LammpsSimulator method) (ipsuite.calculators.LammpsSimulator method) (ipsuite.calculators.MixCalculator method) (ipsuite.calculators.orca.OrcaSinglePoint method) (ipsuite.calculators.OrcaSinglePoint method) (ipsuite.calculators.PlumedModel method) (ipsuite.calculators.xtb.xTBSinglePoint method) (ipsuite.calculators.xTBSinglePoint method) (ipsuite.CalibrationMetrics method) (ipsuite.CollectMDSteps method) (ipsuite.configuration_generation.MultiPackmol method) (ipsuite.configuration_generation.Packmol method) (ipsuite.configuration_generation.packmol.MultiPackmol method) (ipsuite.configuration_generation.packmol.Packmol method) (ipsuite.configuration_generation.Smiles2Atoms method) (ipsuite.configuration_generation.Smiles2Conformers method) (ipsuite.configuration_generation.Smiles2Gromacs method) (ipsuite.configuration_generation.smiles_to_atoms.Smiles2Atoms method) (ipsuite.configuration_generation.smiles_to_atoms.Smiles2Conformers method) (ipsuite.configuration_selection.base.ConfigurationSelection method) (ipsuite.configuration_selection.ConfigurationSelection method) (ipsuite.configuration_selection.filter.FilterOutlier method) (ipsuite.configuration_selection.FilterOutlier method) (ipsuite.CP2KSinglePoint method) (ipsuite.data_loading.add_data_ase.AddData method) (ipsuite.data_loading.add_data_h5md.AddDataH5MD method) (ipsuite.data_loading.AddData method) (ipsuite.data_loading.AddDataH5MD method) (ipsuite.EnsembleModel method) (ipsuite.FilterOutlier method) (ipsuite.Flatten method) (ipsuite.ForceAngles method) (ipsuite.ForceDecomposition method) (ipsuite.ForceUncertaintyDecomposition method) (ipsuite.LammpsSimulator method) (ipsuite.MD22Dataset method) (ipsuite.MDStability method) (ipsuite.MixCalculator method) (ipsuite.models.ensemble.EnsembleModel method) (ipsuite.models.EnsembleModel method) (ipsuite.MoveSingleParticle method) (ipsuite.MultiPackmol method) (ipsuite.OrcaSinglePoint method) (ipsuite.Packmol method) (ipsuite.PlumedModel method) (ipsuite.Prediction method) (ipsuite.PredictionMetrics method) (ipsuite.RattleAnalysis method) (ipsuite.Smiles2Atoms method) (ipsuite.Smiles2Conformers method) (ipsuite.Smiles2Gromacs method) (ipsuite.StressHistogram method) (ipsuite.SurfaceRasterScan method) (ipsuite.xTBSinglePoint method)

run_kwargs (ipsuite.ASEGeoOpt attribute) (ipsuite.calculators.ase_geoopt.ASEGeoOpt attribute) (ipsuite.calculators.ASEGeoOpt attribute) run_md() (ipsuite.ASEMD method) run_stability_nve() (in module ipsuite.analysis.model.dynamics)

S

samples (ipsuite.analysis.MoveSingleParticle attribute) (ipsuite.analysis.sensitivity.MoveSingleParticle attribute) (ipsuite.MoveSingleParticle attribute) sampling_rate (ipsuite.ASEGeoOpt attribute) (ipsuite.ASEMD attribute) (ipsuite.calculators.ase_geoopt.ASEGeoOpt attribute) (ipsuite.calculators.ASEGeoOpt attribute) save_atoms_to_file() (ipsuite.AddData class method) (ipsuite.data_loading.add_data_ase.AddData class method) (ipsuite.data_loading.AddData class method) save_last_n (ipsuite.analysis.MDStability attribute) (ipsuite.analysis.model.dynamics.MDStability attribute) (ipsuite.analysis.model.MDStability attribute) (ipsuite.MDStability attribute) save_metrics() (ipsuite.ASEMD method) scale (ipsuite.analysis.MoveSingleParticle attribute) (ipsuite.analysis.sensitivity.MoveSingleParticle attribute) (ipsuite.MoveSingleParticle attribute) scan_node (ipsuite.bootstrap.surface_mods.SurfaceRasterMetrics attribute) (ipsuite.bootstrap.SurfaceRasterMetrics attribute) (ipsuite.SurfaceRasterMetrics attribute) seed (ipsuite.analysis.MDStability attribute) (ipsuite.analysis.model.dynamics.MDStability attribute) (ipsuite.analysis.model.dynamics.RattleAnalysis attribute) (ipsuite.analysis.model.MDStability attribute) (ipsuite.analysis.model.RattleAnalysis attribute) (ipsuite.analysis.MoveSingleParticle attribute) (ipsuite.analysis.RattleAnalysis attribute) (ipsuite.analysis.sensitivity.MoveSingleParticle attribute) (ipsuite.ASEMD attribute) (ipsuite.bootstrap.random_displacements.Bootstrap attribute) (ipsuite.bootstrap.surface_mods.SurfaceRasterScan attribute) (ipsuite.bootstrap.SurfaceRasterScan attribute) (ipsuite.configuration_generation.MultiPackmol attribute) (ipsuite.configuration_generation.packmol.MultiPackmol attribute) (ipsuite.configuration_generation.Smiles2Atoms attribute) (ipsuite.configuration_generation.Smiles2Conformers attribute) (ipsuite.configuration_generation.smiles_to_atoms.Smiles2Atoms attribute) (ipsuite.configuration_generation.smiles_to_atoms.Smiles2Conformers attribute) (ipsuite.configuration_selection.random.RandomSelection attribute) (ipsuite.configuration_selection.RandomSelection attribute) (ipsuite.MDStability attribute) (ipsuite.MoveSingleParticle attribute) (ipsuite.MultiPackmol attribute) (ipsuite.RandomSelection attribute) (ipsuite.RattleAnalysis attribute) (ipsuite.Smiles2Atoms attribute) (ipsuite.Smiles2Conformers attribute) (ipsuite.SurfaceRasterScan attribute) select_atoms() (ipsuite.configuration_selection.base.ConfigurationSelection method) (ipsuite.configuration_selection.ConfigurationSelection method) (ipsuite.configuration_selection.index.IndexSelection method) (ipsuite.configuration_selection.IndexSelection method) (ipsuite.configuration_selection.random.RandomSelection method) (ipsuite.configuration_selection.RandomSelection method) (ipsuite.configuration_selection.split.SplitSelection method) (ipsuite.configuration_selection.SplitSelection method) (ipsuite.configuration_selection.threshold.ThresholdSelection method) (ipsuite.configuration_selection.ThresholdSelection method) (ipsuite.configuration_selection.uniform_arange.UniformArangeSelection method) (ipsuite.configuration_selection.uniform_energetic.UniformEnergeticSelection method) (ipsuite.configuration_selection.uniform_temporal.UniformTemporalSelection method) (ipsuite.configuration_selection.UniformArangeSelection method) (ipsuite.configuration_selection.UniformEnergeticSelection method) (ipsuite.configuration_selection.UniformTemporalSelection method) (ipsuite.IndexSelection method) (ipsuite.RandomSelection method) (ipsuite.SplitSelection method) (ipsuite.ThresholdSelection method) (ipsuite.UniformArangeSelection method) (ipsuite.UniformEnergeticSelection method) (ipsuite.UniformTemporalSelection method) selected_atom_id (ipsuite.analysis.sensitivity.IsConstraintMD attribute) selected_ids (ipsuite.configuration_selection.base.ConfigurationSelection attribute) (ipsuite.configuration_selection.ConfigurationSelection attribute) sensitivity (ipsuite.AnalyseSingleForceSensitivity attribute) (ipsuite.analysis.AnalyseSingleForceSensitivity attribute) (ipsuite.analysis.sensitivity.AnalyseSingleForceSensitivity attribute) sensitivity_plot (ipsuite.AnalyseSingleForceSensitivity attribute) (ipsuite.analysis.AnalyseSingleForceSensitivity attribute) (ipsuite.analysis.sensitivity.AnalyseSingleForceSensitivity attribute) setup_ase() (in module ipsuite.utils.helpers) setup_logging() (in module ipsuite.utils.logs) sigma (ipsuite.calculators.ase_standard.LJSinglePoint attribute) (ipsuite.calculators.LJSinglePoint attribute) (ipsuite.LJSinglePoint attribute) sim_list (ipsuite.AnalyseSingleForceSensitivity attribute) (ipsuite.analysis.AnalyseSingleForceSensitivity attribute) (ipsuite.analysis.sensitivity.AnalyseSingleForceSensitivity attribute) simpleinput (ipsuite.models.ORCAModel attribute) (ipsuite.ORCAModel attribute) skin (ipsuite.models.TorchDFTD3 attribute) (ipsuite.TorchDFTD3 attribute) skiprun (ipsuite.calculators.lammps.LammpsSimulator attribute) (ipsuite.calculators.LammpsSimulator attribute) (ipsuite.LammpsSimulator attribute) slice_ensemble_uncertainty() (in module ipsuite.analysis.model.plots) slice_uncertainty() (in module ipsuite.analysis.model.plots) smiles (ipsuite.AllowedStructuresFilter attribute) (ipsuite.analysis.AllowedStructuresFilter attribute) (ipsuite.configuration_generation.Smiles2Atoms attribute) (ipsuite.configuration_generation.Smiles2Conformers attribute) (ipsuite.configuration_generation.Smiles2Gromacs attribute) (ipsuite.configuration_generation.smiles_to_atoms.Smiles2Atoms attribute) (ipsuite.configuration_generation.smiles_to_atoms.Smiles2Conformers attribute) (ipsuite.Smiles2Atoms attribute) (ipsuite.Smiles2Conformers attribute) (ipsuite.Smiles2Gromacs attribute)

Smiles2Atoms (class in ipsuite) (class in ipsuite.configuration_generation) (class in ipsuite.configuration_generation.smiles_to_atoms) Smiles2Conformers (class in ipsuite) (class in ipsuite.configuration_generation) (class in ipsuite.configuration_generation.smiles_to_atoms) Smiles2Gromacs (class in ipsuite) (class in ipsuite.configuration_generation) sort_atomic_edges() (in module ipsuite.geometry.unwrap) spin_polarization (ipsuite.calculators.xtb.xTBSinglePoint attribute) (ipsuite.calculators.xTBSinglePoint attribute) (ipsuite.xTBSinglePoint attribute) split (ipsuite.configuration_selection.split.SplitSelection attribute) (ipsuite.configuration_selection.SplitSelection attribute) (ipsuite.SplitSelection attribute) split_molecule() (in module ipsuite.geometry.graphs) SplitSelection (class in ipsuite) (class in ipsuite.configuration_selection) (class in ipsuite.configuration_selection.split) stable_steps_df (ipsuite.analysis.MDStability attribute) (ipsuite.analysis.model.dynamics.MDStability attribute) (ipsuite.analysis.model.MDStability attribute) (ipsuite.MDStability attribute) start (ipsuite.AnalyseDensity attribute) (ipsuite.analysis.AnalyseDensity attribute) (ipsuite.analysis.BoxScale attribute) (ipsuite.analysis.md.AnalyseDensity attribute) (ipsuite.analysis.model.BoxScale attribute) (ipsuite.analysis.model.dynamics.BoxScale attribute) (ipsuite.BoxScale attribute) (ipsuite.configuration_selection.index.IndexSelection attribute) (ipsuite.configuration_selection.IndexSelection attribute) (ipsuite.IndexSelection attribute) start_pressure_au (ipsuite.PressureRampModifier attribute) start_temperature (ipsuite.analysis.BoxHeatUp attribute) (ipsuite.analysis.model.BoxHeatUp attribute) (ipsuite.analysis.model.dynamics.BoxHeatUp attribute) (ipsuite.BoxHeatUp attribute) (ipsuite.TemperatureOscillatingRampModifier attribute) (ipsuite.TemperatureRampModifier attribute) status (ipsuite.base.base.Check attribute) (ipsuite.base.Check attribute) (ipsuite.DensityCheck attribute) step (ipsuite.configuration_selection.index.IndexSelection attribute) (ipsuite.configuration_selection.IndexSelection attribute) (ipsuite.configuration_selection.uniform_arange.UniformArangeSelection attribute) (ipsuite.configuration_selection.UniformArangeSelection attribute) (ipsuite.IndexSelection attribute) (ipsuite.UniformArangeSelection attribute) steps (ipsuite.analysis.BoxHeatUp attribute) (ipsuite.analysis.model.BoxHeatUp attribute) (ipsuite.analysis.model.dynamics.BoxHeatUp attribute) (ipsuite.ASEMD attribute) (ipsuite.BoxHeatUp attribute) stop (ipsuite.analysis.BoxScale attribute) (ipsuite.analysis.model.BoxScale attribute) (ipsuite.analysis.model.dynamics.BoxScale attribute) (ipsuite.analysis.model.dynamics.RattleAnalysis attribute) (ipsuite.analysis.model.RattleAnalysis attribute) (ipsuite.analysis.RattleAnalysis attribute) (ipsuite.BoxScale attribute) (ipsuite.configuration_selection.index.IndexSelection attribute) (ipsuite.configuration_selection.IndexSelection attribute) (ipsuite.IndexSelection attribute) (ipsuite.RattleAnalysis attribute) stop_temperature (ipsuite.analysis.BoxHeatUp attribute) (ipsuite.analysis.model.BoxHeatUp attribute) (ipsuite.analysis.model.dynamics.BoxHeatUp attribute) (ipsuite.BoxHeatUp attribute) stress (ipsuite.analysis.model.predict.PredictionMetrics attribute) (ipsuite.analysis.model.PredictionMetrics attribute) (ipsuite.analysis.PredictionMetrics attribute) (ipsuite.PredictionMetrics attribute) stress_deviat (ipsuite.analysis.model.predict.PredictionMetrics attribute) (ipsuite.analysis.model.PredictionMetrics attribute) (ipsuite.analysis.PredictionMetrics attribute) (ipsuite.PredictionMetrics attribute) stress_hydro (ipsuite.analysis.model.predict.PredictionMetrics attribute) (ipsuite.analysis.model.PredictionMetrics attribute) (ipsuite.analysis.PredictionMetrics attribute) (ipsuite.PredictionMetrics attribute) StressHistogram (class in ipsuite) (class in ipsuite.analysis) (class in ipsuite.analysis.bin_property) structures (ipsuite.ASEMD property) SurfaceRasterMetrics (class in ipsuite) (class in ipsuite.bootstrap) (class in ipsuite.bootstrap.surface_mods) SurfaceRasterScan (class in ipsuite) (class in ipsuite.bootstrap) (class in ipsuite.bootstrap.surface_mods) SVCRBarostat (class in ipsuite) symbol (ipsuite.bootstrap.surface_mods.SurfaceRasterScan attribute) (ipsuite.bootstrap.SurfaceRasterScan attribute) (ipsuite.SurfaceRasterScan attribute)

T

t_confidence_interval() (ipsuite.AnalyseSingleForceSensitivity method) (ipsuite.analysis.AnalyseSingleForceSensitivity method) (ipsuite.analysis.sensitivity.AnalyseSingleForceSensitivity method) taup (ipsuite.SVCRBarostat attribute) taut (ipsuite.Berendsen attribute) (ipsuite.SVCRBarostat attribute) TBLiteModel (class in ipsuite) (class in ipsuite.models) temperature (ipsuite.Berendsen attribute) (ipsuite.calculators.PlumedModel attribute) (ipsuite.LangevinThermostat attribute) (ipsuite.NPTThermostat attribute) (ipsuite.PlumedModel attribute) (ipsuite.SVCRBarostat attribute) (ipsuite.TemperatureRampModifier attribute) temperature_amplitude (ipsuite.TemperatureOscillatingRampModifier attribute) temperature_reduction_factor (ipsuite.ASEMDSafeSampling attribute) TemperatureCheck (class in ipsuite) TemperatureOscillatingRampModifier (class in ipsuite) TemperatureRampModifier (class in ipsuite) tetragonal_strain (ipsuite.NPTThermostat attribute) thermostat (ipsuite.ASEMD attribute) threshold (ipsuite.configuration_selection.filter.FilterOutlier attribute) (ipsuite.configuration_selection.FilterOutlier attribute) (ipsuite.configuration_selection.threshold.ThresholdSelection attribute) (ipsuite.configuration_selection.ThresholdSelection attribute) (ipsuite.FilterOutlier attribute) (ipsuite.ThresholdSelection attribute) ThresholdCheck (class in ipsuite) ThresholdSelection (class in ipsuite) (class in ipsuite.configuration_selection) (class in ipsuite.configuration_selection.threshold) time_step (ipsuite.analysis.BoxHeatUp attribute) (ipsuite.analysis.MDStability attribute) (ipsuite.analysis.model.BoxHeatUp attribute) (ipsuite.analysis.model.dynamics.BoxHeatUp attribute) (ipsuite.analysis.model.dynamics.MDStability attribute) (ipsuite.analysis.model.MDStability attribute) (ipsuite.Berendsen attribute) (ipsuite.BoxHeatUp attribute) (ipsuite.LangevinThermostat attribute) (ipsuite.MDStability attribute) (ipsuite.NPTThermostat attribute) (ipsuite.SVCRBarostat attribute) (ipsuite.VelocityVerletDynamic attribute)

timestep (ipsuite.calculators.PlumedModel attribute) (ipsuite.PlumedModel attribute) tolerance (ipsuite.configuration_generation.Packmol attribute) (ipsuite.configuration_generation.packmol.Packmol attribute) (ipsuite.configuration_generation.Smiles2Gromacs attribute) (ipsuite.Packmol attribute) (ipsuite.Smiles2Gromacs attribute) TorchDFTD3 (class in ipsuite) (class in ipsuite.models) train_data (ipsuite.configuration_selection.base.BatchConfigurationSelection attribute) traj_file (ipsuite.analysis.MDStability attribute) (ipsuite.analysis.model.dynamics.MDStability attribute) (ipsuite.analysis.model.MDStability attribute) (ipsuite.ASEGeoOpt attribute) (ipsuite.calculators.ase_geoopt.ASEGeoOpt attribute) (ipsuite.calculators.ASEGeoOpt attribute) (ipsuite.configuration_generation.Smiles2Gromacs attribute) (ipsuite.MDStability attribute) (ipsuite.Smiles2Gromacs attribute) trans_force_plt (ipsuite.analysis.ForceDecomposition attribute) (ipsuite.analysis.model.ForceDecomposition attribute) (ipsuite.analysis.model.predict.ForceDecomposition attribute) (ipsuite.ForceDecomposition attribute) trans_forces (ipsuite.analysis.ForceDecomposition attribute) (ipsuite.analysis.ForceUncertaintyDecomposition attribute) (ipsuite.analysis.model.ForceDecomposition attribute) (ipsuite.analysis.model.ForceUncertaintyDecomposition attribute) (ipsuite.analysis.model.predict.ForceDecomposition attribute) (ipsuite.analysis.model.predict.ForceUncertaintyDecomposition attribute) (ipsuite.ForceDecomposition attribute) (ipsuite.ForceUncertaintyDecomposition attribute) TranslateMolecules (class in ipsuite) (class in ipsuite.bootstrap) (class in ipsuite.bootstrap.random_displacements) ttime (ipsuite.NPTThermostat attribute)

U

UniformArangeSelection (class in ipsuite) (class in ipsuite.configuration_selection) (class in ipsuite.configuration_selection.uniform_arange) UniformEnergeticSelection (class in ipsuite) (class in ipsuite.configuration_selection) (class in ipsuite.configuration_selection.uniform_energetic) UniformTemporalSelection (class in ipsuite) (class in ipsuite.configuration_selection) (class in ipsuite.configuration_selection.uniform_temporal)

unwrap() (in module ipsuite.geometry.unwrap) unwrap_system() (in module ipsuite.geometry.unwrap) upper_limit (ipsuite.FixedLayerConstraint attribute) use_energy (ipsuite.models.base.MLModel attribute) (ipsuite.models.MLModel attribute) use_forces (ipsuite.models.base.MLModel attribute) (ipsuite.models.MLModel attribute) use_momenta (ipsuite.ASEMD attribute) use_stresses (ipsuite.models.base.MLModel attribute) (ipsuite.models.MLModel attribute)

V

VelocityVerletDynamic (class in ipsuite) verbosity (ipsuite.models.TBLiteModel attribute) (ipsuite.TBLiteModel attribute) vib_force_plt (ipsuite.analysis.ForceDecomposition attribute) (ipsuite.analysis.model.ForceDecomposition attribute) (ipsuite.analysis.model.predict.ForceDecomposition attribute) (ipsuite.ForceDecomposition attribute)

vib_forces (ipsuite.analysis.ForceDecomposition attribute) (ipsuite.analysis.ForceUncertaintyDecomposition attribute) (ipsuite.analysis.model.ForceDecomposition attribute) (ipsuite.analysis.model.ForceUncertaintyDecomposition attribute) (ipsuite.analysis.model.predict.ForceDecomposition attribute) (ipsuite.analysis.model.predict.ForceUncertaintyDecomposition attribute) (ipsuite.ForceDecomposition attribute) (ipsuite.ForceUncertaintyDecomposition attribute)

W

wasserstein_distance (ipsuite.analysis.ForceDecomposition attribute) (ipsuite.analysis.model.ForceDecomposition attribute) (ipsuite.analysis.model.predict.ForceDecomposition attribute) (ipsuite.ForceDecomposition attribute) wfn_restart_file (ipsuite.calculators.cp2k.CP2KSinglePoint attribute) (ipsuite.calculators.CP2KSinglePoint attribute) (ipsuite.CP2KSinglePoint attribute) wfn_restart_node (ipsuite.calculators.cp2k.CP2KSinglePoint attribute) (ipsuite.calculators.CP2KSinglePoint attribute) (ipsuite.CP2KSinglePoint attribute)

window (ipsuite.AnalyseDensity attribute) (ipsuite.analysis.AnalyseDensity attribute) (ipsuite.analysis.md.AnalyseDensity attribute) window_size (ipsuite.ThresholdCheck attribute) WrapModifier (class in ipsuite) write_data_to_file() (ipsuite.models.base.MLModel static method) (ipsuite.models.MLModel static method)

X

x (ipsuite.analysis.CalibrationMetrics attribute) (ipsuite.analysis.ForceAngles attribute) (ipsuite.analysis.ForceDecomposition attribute) (ipsuite.analysis.ForceUncertaintyDecomposition attribute) (ipsuite.analysis.model.CalibrationMetrics attribute) (ipsuite.analysis.model.ForceAngles attribute) (ipsuite.analysis.model.ForceDecomposition attribute) (ipsuite.analysis.model.ForceUncertaintyDecomposition attribute) (ipsuite.analysis.model.predict.CalibrationMetrics attribute) (ipsuite.analysis.model.predict.ForceAngles attribute) (ipsuite.analysis.model.predict.ForceDecomposition attribute) (ipsuite.analysis.model.predict.ForceUncertaintyDecomposition attribute) (ipsuite.analysis.model.predict.PredictionMetrics attribute) (ipsuite.analysis.model.PredictionMetrics attribute) (ipsuite.analysis.PredictionMetrics attribute) (ipsuite.base.base.ComparePredictions attribute) (ipsuite.base.ComparePredictions attribute) (ipsuite.bootstrap.surface_mods.SurfaceRasterMetrics attribute) (ipsuite.bootstrap.SurfaceRasterMetrics attribute) x_lim (ipsuite.analysis.bin_property.LabelHistogram attribute)

xc (ipsuite.models.TorchDFTD3 attribute) (ipsuite.TorchDFTD3 attribute) xlabel (ipsuite.analysis.bin_property.DipoleHistogram attribute) (ipsuite.analysis.bin_property.EnergyHistogram attribute) (ipsuite.analysis.bin_property.EnergyUncertaintyHistogram attribute) (ipsuite.analysis.bin_property.ForcesHistogram attribute) (ipsuite.analysis.bin_property.ForcesUncertaintyHistogram attribute) (ipsuite.analysis.DipoleHistogram attribute) (ipsuite.analysis.EnergyHistogram attribute) (ipsuite.analysis.EnergyUncertaintyHistogram attribute) (ipsuite.analysis.ForcesHistogram attribute) (ipsuite.analysis.ForcesUncertaintyHistogram attribute) (ipsuite.DipoleHistogram attribute) (ipsuite.EnergyHistogram attribute) (ipsuite.EnergyUncertaintyHistogram attribute) (ipsuite.ForcesHistogram attribute) (ipsuite.ForcesUncertaintyHistogram attribute) xTBSinglePoint (class in ipsuite) (class in ipsuite.calculators) (class in ipsuite.calculators.xtb)

Y

y (ipsuite.analysis.CalibrationMetrics attribute) (ipsuite.analysis.ForceAngles attribute) (ipsuite.analysis.ForceDecomposition attribute) (ipsuite.analysis.ForceUncertaintyDecomposition attribute) (ipsuite.analysis.model.CalibrationMetrics attribute) (ipsuite.analysis.model.ForceAngles attribute) (ipsuite.analysis.model.ForceDecomposition attribute) (ipsuite.analysis.model.ForceUncertaintyDecomposition attribute) (ipsuite.analysis.model.predict.CalibrationMetrics attribute) (ipsuite.analysis.model.predict.ForceAngles attribute) (ipsuite.analysis.model.predict.ForceDecomposition attribute) (ipsuite.analysis.model.predict.ForceUncertaintyDecomposition attribute) (ipsuite.analysis.model.predict.PredictionMetrics attribute) (ipsuite.analysis.model.PredictionMetrics attribute) (ipsuite.analysis.PredictionMetrics attribute) (ipsuite.base.base.ComparePredictions attribute) (ipsuite.base.ComparePredictions attribute) (ipsuite.bootstrap.surface_mods.SurfaceRasterMetrics attribute) (ipsuite.bootstrap.SurfaceRasterMetrics attribute)

y_lim (ipsuite.analysis.bin_property.LabelHistogram attribute)

Z

z_dist_list (ipsuite.bootstrap.surface_mods.SurfaceRasterScan attribute) (ipsuite.bootstrap.SurfaceRasterScan attribute) (ipsuite.SurfaceRasterScan attribute)