Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | X | Z A ABP abs() (SFI.statefunc.structexpr.StructuredExpr method) add() (in module SFI.integrate) (in module SFI.integrate.timeops) advection_by() (SFI.statefunc.layout.GridLayout method) AdvectionBy() (in module SFI.bases.spde) AIC alias (SFI.integrate.ConstOperand attribute) (SFI.integrate.ExprOperand attribute) (SFI.integrate.integrand.ConstOperand attribute) (SFI.integrate.integrand.ExprOperand attribute) (SFI.integrate.integrand.TimeOperand attribute) (SFI.integrate.TimeOperand attribute) all_ic() (SFI.inference.sparse.result.SparsityResult method) (SFI.inference.sparse.SparsityResult method) (SFI.inference.sparsity.SparsityResult method) (SFI.inference.SparsityResult method) angle_coupling() (in module SFI.bases.pairs) angular_pair_basis() (in module SFI.bases.pairs) animate_particles() (in module SFI.utils.plotting) animate_spde_comparison() (in module SFI.utils.plotting) as_default_float() (in module SFI.utils) (in module SFI.utils.maths) assess() (in module SFI.diagnostics) autocorrelation_tests() (in module SFI.diagnostics.residual_tests) axisvector() (in module SFI.utils.plotting) B backend (SFI.diagnostics.residuals.ResidualBundle attribute) BaseLangevinInference (class in SFI.inference.base) Basis (class in SFI.statefunc) (class in SFI.statefunc.basis) batch_call() (SFI.integrate.Integrand method) (SFI.integrate.integrand.Integrand method) batch_producers (SFI.integrate.api.IntegrationPlan attribute) bc (SFI.statefunc.layout.GridLayout property) beam search BeamSearchStrategy (class in SFI.inference) (class in SFI.inference.sparse) (class in SFI.inference.sparse.beam) (class in SFI.inference.sparsity) best_coeffs_by_k (SFI.inference.sparse.result.SparsityResult attribute) (SFI.inference.sparse.SparsityResult attribute) (SFI.inference.sparsity.SparsityResult attribute) (SFI.inference.SparsityResult attribute) best_info_by_k (SFI.inference.sparse.result.SparsityResult attribute) (SFI.inference.sparse.SparsityResult attribute) (SFI.inference.sparsity.SparsityResult attribute) (SFI.inference.SparsityResult attribute) best_support_by_k (SFI.inference.sparse.result.SparsityResult attribute) (SFI.inference.sparse.SparsityResult attribute) (SFI.inference.sparsity.SparsityResult attribute) (SFI.inference.SparsityResult attribute) BIC Biharmonic (class in SFI.bases.spde) biharmonic() (SFI.statefunc.layout.GridLayout method) bind() (SFI.statefunc.PSF method) (SFI.statefunc.psf.PSF method) bootstrapped trajectory broadcast_extra_bytes_for_children() (in module SFI.statefunc.memhint) build_extras() (SFI.trajectory.dataset.TrajectoryDataset method) (SFI.trajectory.TrajectoryDataset method) build_neighbor_csr() (in module SFI.utils.neighbors) build_overdamped_residuals() (in module SFI.diagnostics.residuals) build_residuals() (in module SFI.diagnostics.residuals) build_underdamped_residuals() (in module SFI.diagnostics.residuals) bytes_hint (SFI.integrate.api.IntegrationPlan attribute) C chunks (SFI.integrate.api.IntegrationPlan attribute) ChunkSpec (class in SFI.integrate.api) classify_dynamics() (in module SFI.diagnostics) (in module SFI.diagnostics.dynamics_order) coeff_block() (SFI.inference.base.BaseLangevinInference method) (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) coerce() (SFI.statefunc.params.ParamSuite method) (SFI.statefunc.ParamSuite method) columns_and_extras_to_dataset() (in module SFI.trajectory.io) compact_kernels() (in module SFI.bases.pairs) compare_params_to_exact() (SFI.inference.base.BaseLangevinInference method) (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) compare_to_exact() (SFI.inference.base.BaseLangevinInference method) (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) comparison_scatter() (in module SFI.utils.plotting) (SFI.inference.base.BaseLangevinInference method) (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) compatible_with() (SFI.statefunc.params.ParamSpec method) (SFI.statefunc.ParamSpec method) CompositeNoise (class in SFI.langevin) (class in SFI.langevin.noise) compute_diffusion_constant() (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) compute_diffusion_error() (SFI.inference.base.BaseLangevinInference method) (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) compute_force_error() (SFI.inference.base.BaseLangevinInference method) (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) concat() (SFI.trajectory.collection.TrajectoryCollection method) (SFI.trajectory.TrajectoryCollection method) conditional NLL conserved_noise_pbc() (in module SFI.bases.spde) ConservedNoise (class in SFI.langevin) (class in SFI.langevin.noise) const() (SFI.statefunc.layout.GridLayout method) (SFI.statefunc.layout.IdentityLayout method) constant_array() (in module SFI.bases) (in module SFI.bases.constants) ConstOperand (class in SFI.integrate) (class in SFI.integrate.integrand) context (SFI.integrate.api.IntegrationPlan attribute) cos() (SFI.statefunc.structexpr.StructuredExpr method) cross_check (SFI.diagnostics.dynamics_order.DynamicsOrderReport attribute) (SFI.diagnostics.DynamicsOrderReport attribute) Curl (class in SFI.bases.spde) D d (SFI.diagnostics.residuals.ResidualBundle attribute) D (SFI.langevin.overdamped.OverdampedProcess attribute) (SFI.langevin.OverdampedProcess attribute) (SFI.langevin.underdamped.UnderdampedProcess attribute) (SFI.langevin.UnderdampedProcess attribute) d (SFI.trajectory.dataset.TrajectoryDataset property) (SFI.trajectory.TrajectoryDataset property) d_theta() (SFI.statefunc.PSF method) (SFI.statefunc.psf.PSF method) d_v() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) (SFI.statefunc.Basis method) (SFI.statefunc.basis.Basis method) (SFI.statefunc.Interactor method) (SFI.statefunc.interactor.Interactor method) (SFI.statefunc.PSF method) (SFI.statefunc.psf.PSF method) (SFI.statefunc.SF method) (SFI.statefunc.sf.SF method) (SFI.statefunc.StateExpr method) (SFI.statefunc.stateexpr.StateExpr method) d_x() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) (SFI.statefunc.Basis method) (SFI.statefunc.basis.Basis method) (SFI.statefunc.Interactor method) (SFI.statefunc.interactor.Interactor method) (SFI.statefunc.PSF method) (SFI.statefunc.psf.PSF method) (SFI.statefunc.SF method) (SFI.statefunc.sf.SF method) (SFI.statefunc.StateExpr method) (SFI.statefunc.stateexpr.StateExpr method) dark_ax() (in module SFI.utils.plotting) dark_fig() (in module SFI.utils.plotting) data (SFI.trajectory.dataset.TimeSeriesExtra attribute) (SFI.trajectory.TimeSeriesExtra attribute) dataset_index (SFI.integrate.api.ChunkSpec attribute) (SFI.trajectory.reserved_extras.ExtrasContext attribute) dataset_index() (SFI.trajectory.collection.TrajectoryCollection method) (SFI.trajectory.TrajectoryCollection method) dataset_indicator() (in module SFI.bases) (in module SFI.bases.constants) datasets (SFI.trajectory.collection.TrajectoryCollection attribute) (SFI.trajectory.TrajectoryCollection attribute) default (SFI.statefunc.params.ParamSpec attribute) (SFI.statefunc.ParamSpec attribute) default_float_dtype() (in module SFI.utils) (in module SFI.utils.maths) default_leaf_hint() (in module SFI.statefunc.memhint) default_op_hint() (in module SFI.statefunc.memhint) defaults() (SFI.statefunc.params.ParamSuite method) (SFI.statefunc.ParamSuite method) degradation degrade() (SFI.trajectory.collection.TrajectoryCollection method) (SFI.trajectory.TrajectoryCollection method) degrade_collection() (in module SFI.trajectory.degrade) degrade_dataset() (in module SFI.trajectory.degrade) degrade_spatial_data() (in module SFI.trajectory.degrade) degrade_spatial_dataset() (in module SFI.trajectory.degrade) dense() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) (SFI.statefunc.Basis method) (SFI.statefunc.basis.Basis method) (SFI.statefunc.Interactor method) (SFI.statefunc.interactor.Interactor method) (SFI.statefunc.PSF method) (SFI.statefunc.psf.PSF method) (SFI.statefunc.SF method) (SFI.statefunc.sf.SF method) (SFI.statefunc.StateExpr method) (SFI.statefunc.stateexpr.StateExpr method) (SFI.statefunc.structexpr.StructuredExpr method) diagnose() (SFI.inference.base.BaseLangevinInference method) (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) DiagnosticsReport (class in SFI.diagnostics) (class in SFI.diagnostics.report) diffusion_comparison_arrays() (SFI.inference.base.BaseLangevinInference method) (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) diffusion_sf (SFI.langevin.overdamped.OverdampedProcess property) (SFI.langevin.OverdampedProcess property) (SFI.langevin.underdamped.UnderdampedProcess property) (SFI.langevin.UnderdampedProcess property) dim (SFI.inference.InferenceResultSF property) (SFI.inference.result.InferenceResultSF property) (SFI.langevin.CompositeNoise property) (SFI.langevin.ConservedNoise property) (SFI.langevin.noise.CompositeNoise property) (SFI.langevin.noise.ConservedNoise property) (SFI.langevin.noise.NoiseModel property) (SFI.langevin.noise.WhiteNoise property) (SFI.langevin.NoiseModel property) (SFI.langevin.WhiteNoise property) (SFI.statefunc.Basis property) (SFI.statefunc.basis.Basis property) (SFI.statefunc.Interactor property) (SFI.statefunc.interactor.Interactor property) (SFI.statefunc.layout.GridLayout property) (SFI.statefunc.layout.IdentityLayout property) (SFI.statefunc.layout.StateLayout property) (SFI.statefunc.PSF property) (SFI.statefunc.psf.PSF property) (SFI.statefunc.SF property) (SFI.statefunc.sf.SF property) (SFI.statefunc.StateExpr property) (SFI.statefunc.stateexpr.StateExpr property) dispatch() (SFI.statefunc.Interactor method) (SFI.statefunc.interactor.Interactor method) dispatch_pairs() (SFI.statefunc.Interactor method) (SFI.statefunc.interactor.Interactor method) dispatch_pairs_from_extras() (SFI.statefunc.Interactor method) (SFI.statefunc.interactor.Interactor method) div() (SFI.statefunc.layout.GridLayout method) Divergence (class in SFI.bases.spde) dot() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) (SFI.statefunc.Basis method) (SFI.statefunc.basis.Basis method) (SFI.statefunc.Interactor method) (SFI.statefunc.interactor.Interactor method) (SFI.statefunc.PSF method) (SFI.statefunc.psf.PSF method) (SFI.statefunc.SF method) (SFI.statefunc.sf.SF method) (SFI.statefunc.StateExpr method) (SFI.statefunc.stateexpr.StateExpr method) (SFI.statefunc.structexpr.StructuredExpr method) drop_features (SFI.inference.InferenceResultSF attribute) (SFI.inference.result.InferenceResultSF attribute) (SFI.statefunc.PSF attribute) (SFI.statefunc.psf.PSF attribute) (SFI.statefunc.SF attribute) (SFI.statefunc.sf.SF attribute) dt (SFI.trajectory.dataset.TrajectoryDataset attribute) (SFI.trajectory.TrajectoryDataset attribute) dtype (SFI.statefunc.params.ParamSpec attribute) (SFI.statefunc.ParamSpec attribute) duration (SFI.trajectory.reserved_extras.ExtrasContext attribute) dyadic_pair_basis() (in module SFI.bases.pairs) dynamic_mask (SFI.trajectory.dataset.TrajectoryDataset attribute) (SFI.trajectory.TrajectoryDataset attribute) DynamicsOrderReport (class in SFI.diagnostics) (class in SFI.diagnostics.dynamics_order) E effective_D_per_site() (SFI.langevin.CompositeNoise method) (SFI.langevin.ConservedNoise method) (SFI.langevin.noise.CompositeNoise method) (SFI.langevin.noise.ConservedNoise method) (SFI.langevin.noise.NoiseModel method) (SFI.langevin.noise.WhiteNoise method) (SFI.langevin.NoiseModel method) (SFI.langevin.WhiteNoise method) einsum() (SFI.inference.InferenceResultSF class method) (SFI.inference.result.InferenceResultSF class method) (SFI.statefunc.Basis class method) (SFI.statefunc.basis.Basis class method) (SFI.statefunc.Interactor class method) (SFI.statefunc.interactor.Interactor class method) (SFI.statefunc.PSF class method) (SFI.statefunc.psf.PSF class method) (SFI.statefunc.SF class method) (SFI.statefunc.sf.SF class method) (SFI.statefunc.StateExpr class method) (SFI.statefunc.stateexpr.StateExpr class method) (SFI.statefunc.structexpr.StructuredExpr static method) elementwisemap() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) (SFI.statefunc.Basis method) (SFI.statefunc.basis.Basis method) (SFI.statefunc.Interactor method) (SFI.statefunc.interactor.Interactor method) (SFI.statefunc.PSF method) (SFI.statefunc.psf.PSF method) (SFI.statefunc.SF method) (SFI.statefunc.sf.SF method) (SFI.statefunc.StateExpr method) (SFI.statefunc.stateexpr.StateExpr method) (SFI.statefunc.structexpr.StructuredExpr method) embed() (SFI.statefunc.layout.GridLayout method) (SFI.statefunc.layout.IdentityLayout method) (SFI.statefunc.layout.StateLayout method) enable_logging() (in module SFI) eq (SFI.integrate.integrand.Term attribute) (SFI.integrate.Term attribute) errors-in-variables estimate_bytes_per_sample() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) (SFI.integrate.Integrand method) (SFI.integrate.integrand.Integrand method) (SFI.statefunc.Basis method) (SFI.statefunc.basis.Basis method) (SFI.statefunc.Interactor method) (SFI.statefunc.interactor.Interactor method) (SFI.statefunc.PSF method) (SFI.statefunc.psf.PSF method) (SFI.statefunc.SF method) (SFI.statefunc.sf.SF method) (SFI.statefunc.StateExpr method) (SFI.statefunc.stateexpr.StateExpr method) euler_flow() (in module SFI.integrate.rk4) euler_step() (in module SFI.integrate.rk4) exp() (SFI.statefunc.structexpr.StructuredExpr method) exp_poly_kernels() (in module SFI.bases.pairs) expr (SFI.integrate.ExprOperand attribute) (SFI.integrate.integrand.ExprOperand attribute) ExprOperand (class in SFI.integrate) (class in SFI.integrate.integrand) extra_scalar() (in module SFI.bases) (in module SFI.bases.constants) Extras extras_global (SFI.langevin.overdamped.OverdampedProcess attribute) (SFI.langevin.OverdampedProcess attribute) (SFI.langevin.underdamped.UnderdampedProcess attribute) (SFI.langevin.UnderdampedProcess attribute) (SFI.trajectory.dataset.TrajectoryDataset attribute) (SFI.trajectory.TrajectoryDataset attribute) extras_local (SFI.langevin.overdamped.OverdampedProcess attribute) (SFI.langevin.OverdampedProcess attribute) (SFI.langevin.underdamped.UnderdampedProcess attribute) (SFI.langevin.UnderdampedProcess attribute) (SFI.trajectory.dataset.TrajectoryDataset attribute) (SFI.trajectory.TrajectoryDataset attribute) ExtrasContext (class in SFI.trajectory.reserved_extras) eye() (SFI.statefunc.structexpr.StructuredExpr class method) F F (SFI.langevin.overdamped.OverdampedProcess attribute) (SFI.langevin.OverdampedProcess attribute) (SFI.langevin.underdamped.UnderdampedProcess attribute) (SFI.langevin.UnderdampedProcess attribute) fd_velocity() (in module SFI.utils) (in module SFI.utils.maths) features_to_rank() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) (SFI.statefunc.Basis method) (SFI.statefunc.basis.Basis method) (SFI.statefunc.Interactor method) (SFI.statefunc.interactor.Interactor method) (SFI.statefunc.PSF method) (SFI.statefunc.psf.PSF method) (SFI.statefunc.SF method) (SFI.statefunc.sf.SF method) (SFI.statefunc.StateExpr method) (SFI.statefunc.stateexpr.StateExpr method) (SFI.statefunc.structexpr.StructuredExpr method) field_component() (in module SFI.bases) fit (SFI.diagnostics.dynamics_order.DynamicsOrderReport attribute) (SFI.diagnostics.DynamicsOrderReport attribute) flag_issues() (SFI.diagnostics.DiagnosticsReport method) (SFI.diagnostics.report.DiagnosticsReport method) flatten_params() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) (SFI.statefunc.PSF method) (SFI.statefunc.psf.PSF method) force_comparison_arrays() (SFI.inference.base.BaseLangevinInference method) (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) force_quadratic_form (SFI.diagnostics.residuals.ResidualBundle attribute) force_sf (SFI.langevin.overdamped.OverdampedProcess property) (SFI.langevin.OverdampedProcess property) (SFI.langevin.underdamped.UnderdampedProcess property) (SFI.langevin.UnderdampedProcess property) frame() (in module SFI.bases) (in module SFI.bases.linear) frame_times (SFI.trajectory.reserved_extras.ExtrasContext attribute) from_arrays() (SFI.statefunc.memhint.SampleMeta static method) (SFI.trajectory.collection.TrajectoryCollection class method) (SFI.trajectory.dataset.TrajectoryDataset class method) (SFI.trajectory.TrajectoryCollection class method) (SFI.trajectory.TrajectoryDataset class method) from_columns() (SFI.trajectory.collection.TrajectoryCollection class method) (SFI.trajectory.TrajectoryCollection class method) from_dataframe() (SFI.trajectory.collection.TrajectoryCollection class method) (SFI.trajectory.TrajectoryCollection class method) from_dataset() (SFI.trajectory.collection.TrajectoryCollection class method) (SFI.trajectory.TrajectoryCollection class method) from_specs() (SFI.statefunc.params.ParamSuite class method) (SFI.statefunc.ParamSuite class method) func (SFI.trajectory.dataset.FunctionExtra attribute) (SFI.trajectory.FunctionExtra attribute) function_extra() (in module SFI.trajectory) (in module SFI.trajectory.dataset) FunctionExtra (class in SFI.trajectory) (class in SFI.trajectory.dataset) G G_mode gaussian_kernels() (in module SFI.bases.pairs) Gauss–Newton get_diffusion_timeop() (SFI.inference.base.BaseLangevinInference method) (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) grad() (SFI.statefunc.layout.GridLayout method) Gradient (class in SFI.bases.spde) Gram matrix GreedyStepwiseStrategy (class in SFI.inference) (class in SFI.inference.sparse) (class in SFI.inference.sparse.greedy) (class in SFI.inference.sparsity) grid_shape (SFI.langevin.ConservedNoise property) (SFI.langevin.noise.ConservedNoise property) GridLayout (class in SFI.statefunc.layout) H has_defaults (SFI.statefunc.params.ParamSuite property) (SFI.statefunc.ParamSuite property) has_mask (SFI.statefunc.memhint.SampleMeta attribute) has_v (SFI.statefunc.memhint.SampleMeta attribute) heading_vector() (in module SFI.bases.pairs) held-out NMSE Heun HillClimbStrategy (class in SFI.inference) (class in SFI.inference.sparse) (class in SFI.inference.sparse.hillclimb) holdout_score() (SFI.inference.base.BaseLangevinInference method) (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) I identity_matrix_basis() (in module SFI.bases) (in module SFI.bases.constants) IdentityLayout (class in SFI.statefunc.layout) indices (SFI.statefunc.layout.ScalarSector attribute) (SFI.statefunc.layout.SymTensorSector attribute) (SFI.statefunc.layout.TensorSector attribute) (SFI.statefunc.layout.VectorSector attribute) infer_diffusion() (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) infer_diffusion_linear() (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) infer_force() (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) infer_force_linear() (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) InferenceResultSF (class in SFI.inference) (class in SFI.inference.result) inflate_for_grad() (in module SFI.statefunc.memhint) info_and_coeffs() (SFI.inference.sparse.scorer.SparseScorer method) (SFI.inference.sparse.SparseScorer method) (SFI.inference.SparseScorer method) (SFI.inference.sparsity.SparseScorer method) information criterion init (SFI.statefunc.params.ParamSpec attribute) (SFI.statefunc.ParamSpec attribute) initialize() (SFI.langevin.overdamped.OverdampedProcess method) (SFI.langevin.OverdampedProcess method) (SFI.langevin.underdamped.UnderdampedProcess method) (SFI.langevin.UnderdampedProcess method) instrument Integrand (class in SFI.integrate) (class in SFI.integrate.integrand) integrate() (in module SFI.integrate) (in module SFI.integrate.api) IntegrationPlan (class in SFI.integrate.api) Interactor (class in SFI.statefunc) (class in SFI.statefunc.interactor) is_reserved() (in module SFI.trajectory.reserved_extras) itemsize_of() (in module SFI.statefunc.memhint) iter_slices() (SFI.trajectory.collection.TrajectoryCollection method) (SFI.trajectory.TrajectoryCollection method) Itô convention J JAX persistent cache K K (SFI.statefunc.memhint.SampleMeta attribute) K_fixed (SFI.integrate.api.IntegrationPlan attribute) kernel_predict_ci() (in module SFI.inference.result) L L-BFGS labels (SFI.inference.InferenceResultSF property) (SFI.inference.result.InferenceResultSF property) (SFI.statefunc.Basis property) (SFI.statefunc.basis.Basis property) (SFI.statefunc.PSF property) (SFI.statefunc.psf.PSF property) (SFI.statefunc.SF property) (SFI.statefunc.sf.SF property) (SFI.statefunc.structexpr.StructuredExpr attribute) lap() (SFI.statefunc.layout.GridLayout method) lap_of_grad_sq() (SFI.statefunc.layout.GridLayout method) Laplacian (class in SFI.bases.spde) LaplacianOfGradientSquared (class in SFI.bases.spde) LASSO LassoStrategy (class in SFI.inference) (class in SFI.inference.sparse) (class in SFI.inference.sparse.lasso) (class in SFI.inference.sparsity) Layout linear estimators linear_basis() (in module SFI.bases) (in module SFI.bases.linear) load() (SFI.inference.InferenceResultSF class method) (SFI.inference.result.InferenceResultSF class method) (SFI.trajectory.collection.TrajectoryCollection class method) (SFI.trajectory.TrajectoryCollection class method) load_model() (in module SFI.inference) (in module SFI.inference.serialization) load_results() (in module SFI.inference) (in module SFI.inference.serialization) (SFI.inference.base.BaseLangevinInference static method) (SFI.inference.overdamped.OverdampedLangevinInference static method) (SFI.inference.OverdampedLangevinInference static method) (SFI.inference.underdamped.UnderdampedLangevinInference static method) (SFI.inference.UnderdampedLangevinInference static method) load_trajectory() (in module SFI.trajectory.io) local-precision NLL log() (SFI.statefunc.structexpr.StructuredExpr method) M M_mode make_basis() (in module SFI.statefunc) (in module SFI.statefunc.factory) make_batch_producer() (SFI.trajectory.dataset.TrajectoryDataset method) (SFI.trajectory.TrajectoryDataset method) make_interactor() (in module SFI.statefunc) (in module SFI.statefunc.factory) make_minibatch_parametric_integrator() (in module SFI.integrate) (in module SFI.integrate.api) make_neighbor_extras() (in module SFI.utils.neighbors) make_parametric_integrator() (in module SFI.integrate) (in module SFI.integrate.api) make_producer() (SFI.trajectory.dataset.TrajectoryDataset method) (SFI.trajectory.TrajectoryDataset method) make_psf() (in module SFI.statefunc) (in module SFI.statefunc.factory) make_sf() (in module SFI.statefunc) (in module SFI.statefunc.factory) mask (SFI.trajectory.dataset.TrajectoryDataset attribute) (SFI.trajectory.TrajectoryDataset attribute) materialize() (SFI.statefunc.params.ParamSuite method) (SFI.statefunc.ParamSuite method) materialize_params() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) materialize_time() (SFI.trajectory.dataset.TrajectoryDataset method) (SFI.trajectory.TrajectoryDataset method) MATRIX (SFI.statefunc.Rank attribute) mean_dt (SFI.diagnostics.residuals.ResidualBundle attribute) measurement-noise covariance MemHint (class in SFI.statefunc.memhint) memory_hint() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) (SFI.statefunc.Basis method) (SFI.statefunc.basis.Basis method) (SFI.statefunc.Interactor method) (SFI.statefunc.interactor.Interactor method) (SFI.statefunc.PSF method) (SFI.statefunc.psf.PSF method) (SFI.statefunc.SF method) (SFI.statefunc.sf.SF method) (SFI.statefunc.StateExpr method) (SFI.statefunc.stateexpr.StateExpr method) merge() (SFI.statefunc.params.ParamSuite method) (SFI.statefunc.ParamSuite method) (SFI.trajectory.collection.TrajectoryCollection method) (SFI.trajectory.TrajectoryCollection method) merge_many() (SFI.statefunc.params.ParamSuite class method) (SFI.statefunc.ParamSuite class method) merged_with() (SFI.statefunc.params.ParamSpec method) (SFI.statefunc.ParamSpec method) meta (SFI.diagnostics.DiagnosticsReport attribute) (SFI.diagnostics.dynamics_order.DynamicsOrderReport attribute) (SFI.diagnostics.DynamicsOrderReport attribute) (SFI.diagnostics.report.DiagnosticsReport attribute) (SFI.inference.InferenceResultSF attribute) (SFI.inference.result.InferenceResultSF attribute) (SFI.trajectory.dataset.TrajectoryDataset attribute) (SFI.trajectory.TrajectoryDataset attribute) metadata (SFI.langevin.overdamped.OverdampedProcess attribute) (SFI.langevin.OverdampedProcess attribute) (SFI.langevin.underdamped.UnderdampedProcess attribute) (SFI.langevin.UnderdampedProcess attribute) method (SFI.inference.sparse.result.SparsityResult attribute) (SFI.inference.sparse.SparsityResult attribute) (SFI.inference.sparsity.SparsityResult attribute) (SFI.inference.SparsityResult attribute) minkowski_sum_offsets() (in module SFI.bases.spde) model_summary() (in module SFI.utils) (in module SFI.utils.formatting) module SFI SFI.bases SFI.bases.constants SFI.bases.linear SFI.bases.monomials SFI.bases.pairs SFI.bases.spde SFI.diagnostics SFI.diagnostics.dynamics_order SFI.diagnostics.plotting SFI.diagnostics.report SFI.diagnostics.residual_tests SFI.diagnostics.residuals SFI.inference SFI.inference.base SFI.inference.optimizers SFI.inference.overdamped SFI.inference.result SFI.inference.serialization SFI.inference.sparse SFI.inference.sparse.base SFI.inference.sparse.beam SFI.inference.sparse.greedy SFI.inference.sparse.hillclimb SFI.inference.sparse.lasso SFI.inference.sparse.metrics SFI.inference.sparse.result SFI.inference.sparse.scorer SFI.inference.sparse.stlsq SFI.inference.sparsity SFI.inference.underdamped SFI.integrate SFI.integrate.api SFI.integrate.integrand SFI.integrate.rk4 SFI.integrate.timeops SFI.langevin SFI.langevin.chunked SFI.langevin.noise SFI.langevin.overdamped SFI.langevin.underdamped SFI.statefunc SFI.statefunc.basis SFI.statefunc.factory SFI.statefunc.interactor SFI.statefunc.layout SFI.statefunc.memhint SFI.statefunc.params SFI.statefunc.psf SFI.statefunc.sf SFI.statefunc.stateexpr SFI.statefunc.structexpr SFI.trajectory SFI.trajectory.collection SFI.trajectory.dataset SFI.trajectory.degrade SFI.trajectory.io SFI.trajectory.reserved_extras SFI.utils SFI.utils.formatting SFI.utils.maths SFI.utils.neighbors SFI.utils.plotting moment estimator monomials_degree() (in module SFI.bases) (in module SFI.bases.monomials) monomials_up_to() (in module SFI.bases) (in module SFI.bases.monomials) mse_consistency() (in module SFI.diagnostics.residual_tests) N N (SFI.trajectory.dataset.TrajectoryDataset property) (SFI.trajectory.TrajectoryDataset property) n_data (SFI.statefunc.layout.ScalarSector property) (SFI.statefunc.layout.SymTensorSector property) (SFI.statefunc.layout.TensorSector property) (SFI.statefunc.layout.VectorSector property) n_features (SFI.inference.InferenceResultSF property) (SFI.inference.result.InferenceResultSF property) (SFI.statefunc.Basis property) (SFI.statefunc.basis.Basis property) (SFI.statefunc.Interactor property) (SFI.statefunc.interactor.Interactor property) (SFI.statefunc.PSF property) (SFI.statefunc.psf.PSF property) (SFI.statefunc.SF property) (SFI.statefunc.sf.SF property) (SFI.statefunc.StateExpr property) (SFI.statefunc.stateexpr.StateExpr property) (SFI.statefunc.structexpr.StructuredExpr attribute) n_fields (SFI.langevin.CompositeNoise property) (SFI.langevin.ConservedNoise property) (SFI.langevin.noise.CompositeNoise property) (SFI.langevin.noise.ConservedNoise property) (SFI.langevin.noise.NoiseModel property) (SFI.langevin.noise.WhiteNoise property) (SFI.langevin.NoiseModel property) (SFI.langevin.WhiteNoise property) n_obs (SFI.diagnostics.residuals.ResidualBundle attribute) n_particles (SFI.diagnostics.residuals.ResidualBundle attribute) (SFI.trajectory.reserved_extras.ExtrasContext attribute) name (SFI.inference.BeamSearchStrategy attribute) (SFI.inference.GreedyStepwiseStrategy attribute) (SFI.inference.HillClimbStrategy attribute) (SFI.inference.LassoStrategy attribute) (SFI.inference.sparse.base.SparsityStrategy attribute) (SFI.inference.sparse.beam.BeamSearchStrategy attribute) (SFI.inference.sparse.BeamSearchStrategy attribute) (SFI.inference.sparse.greedy.GreedyStepwiseStrategy attribute) (SFI.inference.sparse.GreedyStepwiseStrategy attribute) (SFI.inference.sparse.hillclimb.HillClimbStrategy attribute) (SFI.inference.sparse.HillClimbStrategy attribute) (SFI.inference.sparse.lasso.LassoStrategy attribute) (SFI.inference.sparse.LassoStrategy attribute) (SFI.inference.sparse.SparsityStrategy attribute) (SFI.inference.sparse.stlsq.STLSQStrategy attribute) (SFI.inference.sparse.STLSQStrategy attribute) (SFI.inference.sparsity.BeamSearchStrategy attribute) (SFI.inference.sparsity.GreedyStepwiseStrategy attribute) (SFI.inference.sparsity.LassoStrategy attribute) (SFI.inference.sparsity.SparsityStrategy attribute) (SFI.inference.sparsity.STLSQStrategy attribute) (SFI.inference.SparsityStrategy attribute) (SFI.inference.STLSQStrategy attribute) (SFI.integrate.timeops.TimeOp property) (SFI.statefunc.params.ParamSpec attribute) (SFI.statefunc.ParamSpec attribute) (SFI.trajectory.reserved_extras.ReservedKey attribute) named_scalar() (in module SFI.bases) (in module SFI.bases.constants) named_scalars() (in module SFI.bases) (in module SFI.bases.constants) ndim (SFI.statefunc.layout.GridLayout property) needs_v (SFI.inference.InferenceResultSF property) (SFI.inference.result.InferenceResultSF property) (SFI.statefunc.Basis property) (SFI.statefunc.basis.Basis property) (SFI.statefunc.Interactor property) (SFI.statefunc.interactor.Interactor property) (SFI.statefunc.PSF property) (SFI.statefunc.psf.PSF property) (SFI.statefunc.SF property) (SFI.statefunc.sf.SF property) (SFI.statefunc.StateExpr property) (SFI.statefunc.stateexpr.StateExpr property) neighbour list NMSE nmse_excess_factor (SFI.diagnostics.residuals.ResidualBundle attribute) noise_kind (SFI.langevin.CompositeNoise property) (SFI.langevin.ConservedNoise property) (SFI.langevin.noise.CompositeNoise property) (SFI.langevin.noise.ConservedNoise property) (SFI.langevin.noise.NoiseModel property) (SFI.langevin.noise.WhiteNoise property) (SFI.langevin.NoiseModel property) (SFI.langevin.WhiteNoise property) NoiseModel (class in SFI.langevin) (class in SFI.langevin.noise) normality_test() (in module SFI.diagnostics.residual_tests) O ode_flow() (in module SFI.integrate.rk4) ones_basis() (in module SFI.bases) (in module SFI.bases.constants) op (SFI.integrate.integrand.TimeOperand attribute) (SFI.integrate.TimeOperand attribute) ops (SFI.integrate.integrand.Term attribute) (SFI.integrate.Term attribute) optimize_adam() (in module SFI.inference.optimizers) optimize_lbfgsb() (in module SFI.inference.optimizers) output_bytes_per_sample() (in module SFI.statefunc.memhint) output_elems_per_sample() (in module SFI.statefunc.memhint) OverdampedLangevinInference (class in SFI.inference) (class in SFI.inference.overdamped) OverdampedProcess (class in SFI.langevin) (class in SFI.langevin.overdamped) overlap_metrics() (in module SFI.inference) (in module SFI.inference.sparse) (in module SFI.inference.sparse.metrics) (in module SFI.inference.sparsity) P p (SFI.inference.sparse.result.SparsityResult attribute) (SFI.inference.sparse.SparsityResult attribute) (SFI.inference.sparsity.SparsityResult attribute) (SFI.inference.SparsityResult attribute) P (SFI.statefunc.memhint.SampleMeta attribute) pad_neighbor_csr() (in module SFI.utils.neighbors) pair_direction() (in module SFI.bases.pairs) pair_velocity_difference() (in module SFI.bases.pairs) param_cov (SFI.inference.InferenceResultSF attribute) (SFI.inference.result.InferenceResultSF attribute) param_suite (SFI.statefunc.structexpr.StructuredExpr attribute) parametric estimators parametric_four_point_diagnostic() (in module SFI.diagnostics) (in module SFI.diagnostics.residual_tests) parametric_radial_kernel() (in module SFI.bases.pairs) params (SFI.inference.InferenceResultSF attribute) (SFI.inference.result.InferenceResultSF attribute) (SFI.statefunc.SF attribute) (SFI.statefunc.sf.SF attribute) params_template (SFI.integrate.ExprOperand attribute) (SFI.integrate.integrand.ExprOperand attribute) ParamSpec (class in SFI.statefunc) (class in SFI.statefunc.params) ParamSuite (class in SFI.statefunc) (class in SFI.statefunc.params) Pareto front parse() (SFI.statefunc.params.ParamSuite class method) (SFI.statefunc.ParamSuite class method) particle_extras (SFI.inference.InferenceResultSF property) (SFI.inference.result.InferenceResultSF property) (SFI.statefunc.Basis property) (SFI.statefunc.basis.Basis property) (SFI.statefunc.Interactor property) (SFI.statefunc.interactor.Interactor property) (SFI.statefunc.PSF property) (SFI.statefunc.psf.PSF property) (SFI.statefunc.SF property) (SFI.statefunc.sf.SF property) (SFI.statefunc.StateExpr property) (SFI.statefunc.stateexpr.StateExpr property) particle_heading() (in module SFI.bases.pairs) particle_velocity() (in module SFI.bases.pairs) particles particles_input (SFI.inference.InferenceResultSF property) (SFI.inference.result.InferenceResultSF property) (SFI.statefunc.Basis property) (SFI.statefunc.basis.Basis property) (SFI.statefunc.Interactor property) (SFI.statefunc.interactor.Interactor property) (SFI.statefunc.PSF property) (SFI.statefunc.psf.PSF property) (SFI.statefunc.SF property) (SFI.statefunc.sf.SF property) (SFI.statefunc.StateExpr property) (SFI.statefunc.stateexpr.StateExpr property) PASTIS PBC pbc_displacement() (in module SFI.bases.pairs) pdepth (SFI.inference.InferenceResultSF property) (SFI.inference.result.InferenceResultSF property) (SFI.statefunc.Basis property) (SFI.statefunc.basis.Basis property) (SFI.statefunc.Interactor property) (SFI.statefunc.interactor.Interactor property) (SFI.statefunc.PSF property) (SFI.statefunc.psf.PSF property) (SFI.statefunc.SF property) (SFI.statefunc.sf.SF property) (SFI.statefunc.StateExpr property) (SFI.statefunc.stateexpr.StateExpr property) peek_dt() (SFI.trajectory.collection.TrajectoryCollection method) (SFI.trajectory.TrajectoryCollection method) peek_dX() (SFI.trajectory.collection.TrajectoryCollection method) (SFI.trajectory.TrajectoryCollection method) peek_mask() (SFI.trajectory.collection.TrajectoryCollection method) (SFI.trajectory.TrajectoryCollection method) peek_row() (SFI.trajectory.collection.TrajectoryCollection method) (SFI.trajectory.TrajectoryCollection method) peek_X() (SFI.trajectory.collection.TrajectoryCollection method) (SFI.trajectory.TrajectoryCollection method) per-dataset parameter per_dataset_scalar() (in module SFI.bases) (in module SFI.bases.constants) per_sample_bytes (SFI.statefunc.memhint.MemHint attribute) persistent_bytes (SFI.statefunc.memhint.MemHint attribute) phase2d() (in module SFI.utils.plotting) phase2d_scalar() (in module SFI.utils.plotting) phase3d() (in module SFI.utils.plotting) plot_dynamics_order() (in module SFI.diagnostics) (in module SFI.diagnostics.plotting) plot_field() (in module SFI.utils.plotting) plot_field_error() (in module SFI.utils.plotting) plot_nematic_director() (in module SFI.utils.plotting) plot_pareto_front() (in module SFI.utils.plotting) plot_particles() (in module SFI.utils.plotting) plot_particles_field() (in module SFI.utils.plotting) plot_profile_1d() (in module SFI.utils.plotting) plot_qq() (in module SFI.diagnostics) (in module SFI.diagnostics.plotting) plot_recovery_bar() (in module SFI.utils.plotting) plot_recovery_bar_multi() (in module SFI.utils.plotting) plot_recovery_matrix() (in module SFI.utils.plotting) plot_residual_acf() (in module SFI.diagnostics) (in module SFI.diagnostics.plotting) plot_residual_histogram() (in module SFI.diagnostics) (in module SFI.diagnostics.plotting) plot_rods() (in module SFI.utils.plotting) plot_spde_snapshot() (in module SFI.utils.plotting) plot_summary() (in module SFI.diagnostics) (in module SFI.diagnostics.plotting) plot_tensor_field() (in module SFI.utils.plotting) plot_time_profile_comparison() (in module SFI.utils.plotting) power_kernels() (in module SFI.bases.pairs) predict_ci() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) predict_cov() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) predict_time_profile() (SFI.inference.base.BaseLangevinInference method) (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) predict_var() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) predictive_nmse() (in module SFI.inference) (in module SFI.inference.sparse) (in module SFI.inference.sparse.metrics) (in module SFI.inference.sparsity) print_model_comparison() (in module SFI.utils) (in module SFI.utils.formatting) print_report() (SFI.inference.base.BaseLangevinInference method) (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) print_summary() (SFI.diagnostics.DiagnosticsReport method) (SFI.diagnostics.dynamics_order.DynamicsOrderReport method) (SFI.diagnostics.DynamicsOrderReport method) (SFI.diagnostics.report.DiagnosticsReport method) producers (SFI.integrate.api.IntegrationPlan attribute) profiling PSF (class in SFI.statefunc) (class in SFI.statefunc.psf) R radial_pair_basis() (in module SFI.bases.pairs) rank Rank (class in SFI.statefunc) rank (SFI.inference.InferenceResultSF property) (SFI.inference.result.InferenceResultSF property) (SFI.statefunc.Basis property) (SFI.statefunc.basis.Basis property) (SFI.statefunc.Interactor property) (SFI.statefunc.interactor.Interactor property) (SFI.statefunc.PSF property) (SFI.statefunc.psf.PSF property) (SFI.statefunc.SF property) (SFI.statefunc.sf.SF property) (SFI.statefunc.StateExpr property) (SFI.statefunc.stateexpr.StateExpr property) rank_to_features() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) (SFI.statefunc.Basis method) (SFI.statefunc.basis.Basis method) (SFI.statefunc.Interactor method) (SFI.statefunc.interactor.Interactor method) (SFI.statefunc.PSF method) (SFI.statefunc.psf.PSF method) (SFI.statefunc.SF method) (SFI.statefunc.sf.SF method) (SFI.statefunc.StateExpr method) (SFI.statefunc.stateexpr.StateExpr method) (SFI.statefunc.structexpr.StructuredExpr method) reduce (SFI.integrate.api.IntegrationPlan attribute) reduce_over_particles (SFI.integrate.api.IntegrationPlan attribute) regime (SFI.diagnostics.residuals.ResidualBundle attribute) register() (in module SFI.trajectory.reserved_extras) report_dict() (SFI.inference.base.BaseLangevinInference method) (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) require() (SFI.integrate.Integrand method) (SFI.integrate.integrand.Integrand method) required_extras (SFI.inference.InferenceResultSF property) (SFI.inference.result.InferenceResultSF property) (SFI.integrate.ExprOperand property) (SFI.integrate.integrand.ExprOperand property) (SFI.statefunc.Basis property) (SFI.statefunc.basis.Basis property) (SFI.statefunc.Interactor property) (SFI.statefunc.interactor.Interactor property) (SFI.statefunc.PSF property) (SFI.statefunc.psf.PSF property) (SFI.statefunc.SF property) (SFI.statefunc.sf.SF property) (SFI.statefunc.StateExpr property) (SFI.statefunc.stateexpr.StateExpr property) required_extras() (SFI.integrate.Integrand method) (SFI.integrate.integrand.Integrand method) requires (SFI.integrate.ExprOperand property) (SFI.integrate.integrand.ExprOperand property) (SFI.integrate.integrand.TimeOperand property) (SFI.integrate.TimeOperand property) (SFI.integrate.timeops.TimeOp property) RESERVED_NAMES (in module SFI.trajectory.reserved_extras) ReservedKey (class in SFI.trajectory.reserved_extras) residual_moments() (in module SFI.diagnostics.residual_tests) ResidualBundle (class in SFI.diagnostics.residuals) residuals (SFI.diagnostics.DiagnosticsReport attribute) (SFI.diagnostics.report.DiagnosticsReport attribute) resolve (SFI.trajectory.reserved_extras.ReservedKey attribute) resolve_extras() (in module SFI.trajectory.reserved_extras) resolve_P() (in module SFI.statefunc.memhint) resolve_reserved() (in module SFI.trajectory.reserved_extras) RK4 rk4_step() (in module SFI.integrate.rk4) root (SFI.inference.InferenceResultSF attribute) (SFI.inference.result.InferenceResultSF attribute) (SFI.statefunc.Basis attribute) (SFI.statefunc.basis.Basis attribute) (SFI.statefunc.Interactor attribute) (SFI.statefunc.interactor.Interactor attribute) (SFI.statefunc.PSF attribute) (SFI.statefunc.psf.PSF attribute) (SFI.statefunc.SF attribute) (SFI.statefunc.sf.SF attribute) (SFI.statefunc.StateExpr attribute) (SFI.statefunc.stateexpr.StateExpr attribute) run() (SFI.inference.BeamSearchStrategy method) (SFI.inference.GreedyStepwiseStrategy method) (SFI.inference.HillClimbStrategy method) (SFI.inference.LassoStrategy method) (SFI.inference.sparse.base.SparsityStrategy method) (SFI.inference.sparse.beam.BeamSearchStrategy method) (SFI.inference.sparse.BeamSearchStrategy method) (SFI.inference.sparse.greedy.GreedyStepwiseStrategy method) (SFI.inference.sparse.GreedyStepwiseStrategy method) (SFI.inference.sparse.hillclimb.HillClimbStrategy method) (SFI.inference.sparse.HillClimbStrategy method) (SFI.inference.sparse.lasso.LassoStrategy method) (SFI.inference.sparse.LassoStrategy method) (SFI.inference.sparse.SparsityStrategy method) (SFI.inference.sparse.stlsq.STLSQStrategy method) (SFI.inference.sparse.STLSQStrategy method) (SFI.inference.sparsity.BeamSearchStrategy method) (SFI.inference.sparsity.GreedyStepwiseStrategy method) (SFI.inference.sparsity.LassoStrategy method) (SFI.inference.sparsity.SparsityStrategy method) (SFI.inference.sparsity.STLSQStrategy method) (SFI.inference.SparsityStrategy method) (SFI.inference.STLSQStrategy method) S sample() (SFI.langevin.CompositeNoise method) (SFI.langevin.ConservedNoise method) (SFI.langevin.noise.CompositeNoise method) (SFI.langevin.noise.ConservedNoise method) (SFI.langevin.noise.NoiseModel method) (SFI.langevin.noise.WhiteNoise method) (SFI.langevin.NoiseModel method) (SFI.langevin.WhiteNoise method) SampleMeta (class in SFI.statefunc.memhint) save() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) (SFI.trajectory.collection.TrajectoryCollection method) (SFI.trajectory.TrajectoryCollection method) save_model() (in module SFI.inference) (in module SFI.inference.serialization) save_results() (in module SFI.inference) (in module SFI.inference.serialization) (SFI.inference.base.BaseLangevinInference method) (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) save_trajectory() (in module SFI.trajectory.io) SCALAR (SFI.statefunc.Rank attribute) scalar_pair_basis() (in module SFI.bases.pairs) ScalarSector (class in SFI.statefunc.layout) scale (SFI.integrate.integrand.Term attribute) (SFI.integrate.Term attribute) scale() (in module SFI.integrate) (in module SFI.integrate.timeops) scaled() (SFI.statefunc.memhint.MemHint method) scaling (SFI.diagnostics.dynamics_order.DynamicsOrderReport attribute) (SFI.diagnostics.DynamicsOrderReport attribute) scan (SFI.diagnostics.dynamics_order.DynamicsOrderReport attribute) (SFI.diagnostics.DynamicsOrderReport attribute) sdim (SFI.statefunc.layout.SymTensorSector attribute) (SFI.statefunc.layout.VectorSector attribute) sdims (SFI.inference.InferenceResultSF property) (SFI.inference.result.InferenceResultSF property) (SFI.statefunc.Basis property) (SFI.statefunc.basis.Basis property) (SFI.statefunc.Interactor property) (SFI.statefunc.interactor.Interactor property) (SFI.statefunc.layout.ScalarSector property) (SFI.statefunc.layout.SymTensorSector property) (SFI.statefunc.layout.TensorSector attribute) (SFI.statefunc.layout.VectorSector property) (SFI.statefunc.PSF property) (SFI.statefunc.psf.PSF property) (SFI.statefunc.SF property) (SFI.statefunc.sf.SF property) (SFI.statefunc.StateExpr property) (SFI.statefunc.stateexpr.StateExpr property) (SFI.statefunc.structexpr.StructuredExpr attribute) secant velocity second_info_by_k (SFI.inference.sparse.result.SparsityResult attribute) (SFI.inference.sparse.SparsityResult attribute) (SFI.inference.sparsity.SparsityResult attribute) (SFI.inference.SparsityResult attribute) second_support_by_k (SFI.inference.sparse.result.SparsityResult attribute) (SFI.inference.sparse.SparsityResult attribute) (SFI.inference.sparsity.SparsityResult attribute) (SFI.inference.SparsityResult attribute) Sector sectors (SFI.statefunc.layout.GridLayout property) (SFI.statefunc.layout.IdentityLayout property) select_by_ic() (SFI.inference.sparse.result.SparsityResult method) (SFI.inference.sparse.SparsityResult method) (SFI.inference.sparsity.SparsityResult method) (SFI.inference.SparsityResult method) select_flow() (in module SFI.integrate.rk4) set_extras() (SFI.langevin.overdamped.OverdampedProcess method) (SFI.langevin.OverdampedProcess method) (SFI.langevin.underdamped.UnderdampedProcess method) (SFI.langevin.UnderdampedProcess method) set_jit() (in module SFI.statefunc) set_params() (SFI.langevin.overdamped.OverdampedProcess method) (SFI.langevin.OverdampedProcess method) (SFI.langevin.underdamped.UnderdampedProcess method) (SFI.langevin.UnderdampedProcess method) SF (class in SFI.statefunc) (class in SFI.statefunc.sf) SFI module SFI.bases module SFI.bases.constants module SFI.bases.linear module SFI.bases.monomials module SFI.bases.pairs module SFI.bases.spde module SFI.diagnostics module SFI.diagnostics.dynamics_order module SFI.diagnostics.plotting module SFI.diagnostics.report module SFI.diagnostics.residual_tests module SFI.diagnostics.residuals module SFI.inference module SFI.inference.base module SFI.inference.optimizers module SFI.inference.overdamped module SFI.inference.result module SFI.inference.serialization module SFI.inference.sparse module SFI.inference.sparse.base module SFI.inference.sparse.beam module SFI.inference.sparse.greedy module SFI.inference.sparse.hillclimb module SFI.inference.sparse.lasso module SFI.inference.sparse.metrics module SFI.inference.sparse.result module SFI.inference.sparse.scorer module SFI.inference.sparse.stlsq module SFI.inference.sparsity module SFI.inference.underdamped module SFI.integrate module SFI.integrate.api module SFI.integrate.integrand module SFI.integrate.rk4 module SFI.integrate.timeops module SFI.langevin module SFI.langevin.chunked module SFI.langevin.noise module SFI.langevin.overdamped module SFI.langevin.underdamped module SFI.statefunc module SFI.statefunc.basis module SFI.statefunc.factory module SFI.statefunc.interactor module SFI.statefunc.layout module SFI.statefunc.memhint module SFI.statefunc.params module SFI.statefunc.psf module SFI.statefunc.sf module SFI.statefunc.stateexpr module SFI.statefunc.structexpr module SFI.trajectory module SFI.trajectory.collection module SFI.trajectory.dataset module SFI.trajectory.degrade module SFI.trajectory.io module SFI.trajectory.reserved_extras module SFI.utils module SFI.utils.formatting module SFI.utils.maths module SFI.utils.neighbors module SFI.utils.plotting module SFI_COLORS (in module SFI.utils.plotting) shape (SFI.statefunc.params.ParamSpec attribute) (SFI.statefunc.ParamSpec attribute) sigma (SFI.langevin.ConservedNoise property) (SFI.langevin.noise.ConservedNoise property) (SFI.langevin.noise.WhiteNoise property) (SFI.langevin.WhiteNoise property) simulate() (SFI.langevin.overdamped.OverdampedProcess method) (SFI.langevin.OverdampedProcess method) (SFI.langevin.underdamped.UnderdampedProcess method) (SFI.langevin.UnderdampedProcess method) simulate_bootstrapped_trajectory() (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) simulate_chunked() (in module SFI.langevin.chunked) sin() (SFI.statefunc.structexpr.StructuredExpr method) size (SFI.statefunc.params.ParamSpec property) (SFI.statefunc.params.ParamSuite property) (SFI.statefunc.ParamSpec property) (SFI.statefunc.ParamSuite property) SkewGrad (class in SFI.bases.spde) skip-trick slice_frame_extras() (in module SFI.trajectory.reserved_extras) solve_or_pinv() (in module SFI.utils) (in module SFI.utils.maths) SparseScorer (class in SFI.inference) (class in SFI.inference.sparse) (class in SFI.inference.sparse.scorer) (class in SFI.inference.sparsity) sparsify_force() (SFI.inference.base.BaseLangevinInference method) (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) SparsityResult (class in SFI.inference) (class in SFI.inference.sparse) (class in SFI.inference.sparse.result) (class in SFI.inference.sparsity) SparsityStrategy (class in SFI.inference) (class in SFI.inference.sparse) (class in SFI.inference.sparse.base) (class in SFI.inference.sparsity) spatial (SFI.statefunc.layout.VectorSector attribute) spatial_acorr2d() (in module SFI.utils.plotting) SPDE specialize specialize() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) (SFI.statefunc.Basis method) (SFI.statefunc.basis.Basis method) (SFI.statefunc.Interactor method) (SFI.statefunc.interactor.Interactor method) (SFI.statefunc.PSF method) (SFI.statefunc.psf.PSF method) (SFI.statefunc.SF method) (SFI.statefunc.sf.SF method) (SFI.statefunc.StateExpr method) (SFI.statefunc.stateexpr.StateExpr method) specs (SFI.statefunc.params.ParamSuite attribute) (SFI.statefunc.ParamSuite attribute) split_time() (SFI.trajectory.collection.TrajectoryCollection method) (SFI.trajectory.dataset.TrajectoryDataset method) (SFI.trajectory.TrajectoryCollection method) (SFI.trajectory.TrajectoryDataset method) sqrt() (SFI.statefunc.structexpr.StructuredExpr method) sqrtm() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) (SFI.statefunc.Basis method) (SFI.statefunc.basis.Basis method) (SFI.statefunc.Interactor method) (SFI.statefunc.interactor.Interactor method) (SFI.statefunc.PSF method) (SFI.statefunc.psf.PSF method) (SFI.statefunc.SF method) (SFI.statefunc.sf.SF method) (SFI.statefunc.StateExpr method) (SFI.statefunc.stateexpr.StateExpr method) sqrtm_psd() (in module SFI.utils) (in module SFI.utils.maths) square_grid_extras() (in module SFI.bases.spde) srank (SFI.statefunc.structexpr.StructuredExpr property) stable_pinv() (in module SFI.utils) (in module SFI.utils.maths) stack() (SFI.inference.InferenceResultSF class method) (SFI.inference.result.InferenceResultSF class method) (SFI.statefunc.Basis class method) (SFI.statefunc.basis.Basis class method) (SFI.statefunc.Interactor class method) (SFI.statefunc.interactor.Interactor class method) (SFI.statefunc.PSF class method) (SFI.statefunc.psf.PSF class method) (SFI.statefunc.SF class method) (SFI.statefunc.sf.SF class method) (SFI.statefunc.StateExpr class method) (SFI.statefunc.stateexpr.StateExpr class method) (SFI.statefunc.structexpr.StructuredExpr class method) stamp() (SFI.statefunc.params.ParamSuite method) (SFI.statefunc.ParamSuite method) stamp_fig() (in module SFI.utils.plotting) stamp_output() (in module SFI.utils.plotting) StateExpr (class in SFI.statefunc) (class in SFI.statefunc.stateexpr) StateLayout (class in SFI.statefunc.layout) StencilOp (class in SFI.bases.spde) STLSQ STLSQStrategy (class in SFI.inference) (class in SFI.inference.sparse) (class in SFI.inference.sparse.stlsq) (class in SFI.inference.sparsity) strain_rate() (SFI.statefunc.layout.GridLayout method) Stratonovich convention stream() (in module SFI.integrate) (in module SFI.integrate.timeops) stream_field() (in module SFI.utils.plotting) StructuredExpr (class in SFI.statefunc.structexpr) summary() (SFI.inference.base.BaseLangevinInference method) (SFI.inference.InferenceResultSF method) (SFI.inference.overdamped.OverdampedLangevinInference method) (SFI.inference.OverdampedLangevinInference method) (SFI.inference.result.InferenceResultSF method) (SFI.inference.underdamped.UnderdampedLangevinInference method) (SFI.inference.UnderdampedLangevinInference method) SymGrad (class in SFI.bases.spde) symmetric_matrix_basis() (in module SFI.bases) (in module SFI.bases.constants) SymTensorSector (class in SFI.statefunc.layout) T T (SFI.statefunc.structexpr.StructuredExpr property) t (SFI.trajectory.dataset.TrajectoryDataset attribute) T (SFI.trajectory.dataset.TrajectoryDataset property) t (SFI.trajectory.TrajectoryDataset attribute) T (SFI.trajectory.TrajectoryDataset property) t_block (SFI.integrate.api.ChunkSpec attribute) tanh() (SFI.statefunc.structexpr.StructuredExpr method) Teff() (SFI.trajectory.collection.TrajectoryCollection method) (SFI.trajectory.dataset.TrajectoryDataset method) (SFI.trajectory.TrajectoryCollection method) (SFI.trajectory.TrajectoryDataset method) template (SFI.statefunc.PSF attribute) (SFI.statefunc.psf.PSF attribute) TENSOR3 (SFI.statefunc.Rank attribute) TENSOR4 (SFI.statefunc.Rank attribute) tensordot() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) (SFI.statefunc.Basis method) (SFI.statefunc.basis.Basis method) (SFI.statefunc.Interactor method) (SFI.statefunc.interactor.Interactor method) (SFI.statefunc.PSF method) (SFI.statefunc.psf.PSF method) (SFI.statefunc.SF method) (SFI.statefunc.sf.SF method) (SFI.statefunc.StateExpr method) (SFI.statefunc.stateexpr.StateExpr method) tensorize() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) (SFI.statefunc.Basis method) (SFI.statefunc.basis.Basis method) (SFI.statefunc.Interactor method) (SFI.statefunc.interactor.Interactor method) (SFI.statefunc.PSF method) (SFI.statefunc.psf.PSF method) (SFI.statefunc.SF method) (SFI.statefunc.sf.SF method) (SFI.statefunc.StateExpr method) (SFI.statefunc.stateexpr.StateExpr method) TensorSector (class in SFI.statefunc.layout) Term (class in SFI.integrate) (class in SFI.integrate.integrand) theta_D (SFI.langevin.overdamped.OverdampedProcess attribute) (SFI.langevin.OverdampedProcess attribute) (SFI.langevin.underdamped.UnderdampedProcess attribute) (SFI.langevin.UnderdampedProcess attribute) theta_F (SFI.langevin.overdamped.OverdampedProcess attribute) (SFI.langevin.OverdampedProcess attribute) (SFI.langevin.underdamped.UnderdampedProcess attribute) (SFI.langevin.UnderdampedProcess attribute) time_fourier() (in module SFI.bases) (in module SFI.bases.constants) time_series_extra() (in module SFI.trajectory) (in module SFI.trajectory.dataset) TimeOp (class in SFI.integrate.timeops) timeop() (in module SFI.integrate) (in module SFI.integrate.timeops) TimeOperand (class in SFI.integrate) (class in SFI.integrate.integrand) timeseries() (in module SFI.utils.plotting) timeseries_colored() (in module SFI.utils.plotting) TimeSeriesExtra (class in SFI.trajectory) (class in SFI.trajectory.dataset) to_array() (SFI.trajectory.collection.TrajectoryCollection method) (SFI.trajectory.TrajectoryCollection method) to_arrays() (SFI.trajectory.collection.TrajectoryCollection method) (SFI.trajectory.dataset.TrajectoryDataset method) (SFI.trajectory.TrajectoryCollection method) (SFI.trajectory.TrajectoryDataset method) to_dict() (SFI.diagnostics.DiagnosticsReport method) (SFI.diagnostics.dynamics_order.DynamicsOrderReport method) (SFI.diagnostics.DynamicsOrderReport method) (SFI.diagnostics.report.DiagnosticsReport method) to_json() (SFI.diagnostics.DiagnosticsReport method) (SFI.diagnostics.dynamics_order.DynamicsOrderReport method) (SFI.diagnostics.DynamicsOrderReport method) (SFI.diagnostics.report.DiagnosticsReport method) to_psf() (SFI.statefunc.Basis method) (SFI.statefunc.basis.Basis method) total_info (SFI.inference.sparse.result.SparsityResult attribute) (SFI.inference.sparse.SparsityResult attribute) (SFI.inference.sparsity.SparsityResult attribute) (SFI.inference.SparsityResult attribute) traceless (SFI.statefunc.layout.SymTensorSector attribute) trajectory_scatter() (in module SFI.utils.plotting) TrajectoryCollection (class in SFI.trajectory) (class in SFI.trajectory.collection) TrajectoryDataset (class in SFI.trajectory) (class in SFI.trajectory.dataset) trapeze tree_flatten() (SFI.statefunc.params.ParamSuite method) (SFI.statefunc.ParamSuite method) tree_unflatten() (SFI.statefunc.params.ParamSuite class method) (SFI.statefunc.ParamSuite class method) U ULI UnderdampedLangevinInference (class in SFI.inference) (class in SFI.inference.underdamped) UnderdampedProcess (class in SFI.langevin) (class in SFI.langevin.underdamped) unflatten_params() (SFI.statefunc.PSF method) (SFI.statefunc.psf.PSF method) unit_axes() (in module SFI.bases) (in module SFI.bases.linear) unit_vector_basis() (in module SFI.bases) (in module SFI.bases.constants) unpack() (SFI.statefunc.layout.GridLayout method) (SFI.statefunc.layout.IdentityLayout method) (SFI.statefunc.layout.StateLayout method) uuid (SFI.trajectory.dataset.TrajectoryDataset property) (SFI.trajectory.TrajectoryDataset property) V v (SFI.integrate.ExprOperand attribute) (SFI.integrate.integrand.ExprOperand attribute) V() (in module SFI.bases) (in module SFI.bases.linear) v_components() (in module SFI.bases) (in module SFI.bases.linear) v_coordinate() (in module SFI.bases) (in module SFI.bases.linear) v_coordinates() (in module SFI.bases) (in module SFI.bases.linear) valid_block (SFI.integrate.api.ChunkSpec attribute) valid_indices() (SFI.trajectory.dataset.TrajectoryDataset method) (SFI.trajectory.TrajectoryDataset method) value (SFI.integrate.ConstOperand attribute) (SFI.integrate.integrand.ConstOperand attribute) VECTOR (SFI.statefunc.Rank attribute) vector_field() (in module SFI.bases.spde) vectorize() (SFI.inference.InferenceResultSF method) (SFI.inference.result.InferenceResultSF method) (SFI.statefunc.Basis method) (SFI.statefunc.basis.Basis method) (SFI.statefunc.Interactor method) (SFI.statefunc.interactor.Interactor method) (SFI.statefunc.params.ParamSuite method) (SFI.statefunc.ParamSuite method) (SFI.statefunc.PSF method) (SFI.statefunc.psf.PSF method) (SFI.statefunc.SF method) (SFI.statefunc.sf.SF method) (SFI.statefunc.StateExpr method) (SFI.statefunc.stateexpr.StateExpr method) VectorSector (class in SFI.statefunc.layout) velocity reconstruction velocity() (in module SFI.integrate) (in module SFI.integrate.timeops) velocity_array() (SFI.trajectory.collection.TrajectoryCollection method) (SFI.trajectory.TrajectoryCollection method) verdict (SFI.diagnostics.dynamics_order.DynamicsOrderReport attribute) (SFI.diagnostics.DynamicsOrderReport attribute) Vestergaard vision_gate() (in module SFI.bases.pairs) visualize_stencil() (SFI.bases.spde.Biharmonic method) (SFI.bases.spde.Curl method) (SFI.bases.spde.Divergence method) (SFI.bases.spde.Gradient method) (SFI.bases.spde.Laplacian method) (SFI.bases.spde.LaplacianOfGradientSquared method) (SFI.bases.spde.SkewGrad method) (SFI.bases.spde.StencilOp method) (SFI.bases.spde.SymGrad method) vmap_info() (SFI.inference.sparse.scorer.SparseScorer method) (SFI.inference.sparse.SparseScorer method) (SFI.inference.SparseScorer method) (SFI.inference.sparsity.SparseScorer method) voigt_pairs (SFI.statefunc.layout.SymTensorSector property) vorticity() (SFI.statefunc.layout.GridLayout method) W WeakNoise weight (SFI.integrate.api.ChunkSpec attribute) weight_by_dt (SFI.integrate.api.IntegrationPlan attribute) weights (multi-experiment) (SFI.trajectory.collection.TrajectoryCollection attribute) (SFI.trajectory.TrajectoryCollection attribute) whitened (SFI.diagnostics.residuals.ResidualBundle attribute) WhiteNoise (class in SFI.langevin) (class in SFI.langevin.noise) windowed precision with_label() (SFI.statefunc.structexpr.StructuredExpr method) with_weights() (SFI.trajectory.collection.TrajectoryCollection method) (SFI.trajectory.TrajectoryCollection method) wrap_angle() (in module SFI.bases.pairs) wrap_positions() (in module SFI.utils.plotting) X x (SFI.integrate.ExprOperand attribute) (SFI.integrate.integrand.ExprOperand attribute) X (SFI.trajectory.dataset.TrajectoryDataset attribute) (SFI.trajectory.TrajectoryDataset attribute) X() (in module SFI.bases) (in module SFI.bases.linear) x_components() (in module SFI.bases) (in module SFI.bases.linear) x_coordinate() (in module SFI.bases) (in module SFI.bases.linear) x_coordinates() (in module SFI.bases) (in module SFI.bases.linear) Z z (SFI.diagnostics.residuals.ResidualBundle attribute) z_components (SFI.diagnostics.residuals.ResidualBundle attribute) z_squared_norms (SFI.diagnostics.residuals.ResidualBundle attribute) zeros() (SFI.statefunc.params.ParamSuite method) (SFI.statefunc.ParamSuite method)