GKX

Contents

  • Quickstart
    • Install
    • Executable demo
    • Self-contained VMEC geometry
    • Geometry path overrides
    • Python demo
    • Run from TOML
    • Figure generation
  • Input Files and Executable
    • Unified Runtime Schema
      • Minimal runtime TOML example
      • Quasilinear diagnostics
    • Minimal TOML example
      • Executable path overrides
    • Solver and fit-signal keys
    • Executable usage
    • Python driver
    • TOML sections
      • Runtime sections
      • Runtime parallelization controls
      • Runtime output and restart controls
  • Saved Outputs and Restart Files
    • Lightweight saved outputs
    • Nonlinear NetCDF bundle
      • *.out.nc
      • *.big.nc
      • *.restart.nc
    • Restart workflow
    • Plotting diagnostics
  • Theory
    • Gyrokinetic ordering
    • Flux-tube model
    • Hermite-Laguerre velocity space
    • Field solve and gyrokinetic variable
    • Linear gyrokinetic operator
      • Field-aligned streaming representation
    • Nonlinear E×B and flutter terms
  • Linear Model And Derivations
    • Scope
    • Normalized equation
    • Hermite-Laguerre projection
    • Gyroaverage and \(k_\perp\)
    • Field equations
    • Growth-rate/frequency extraction
    • Numerical realization
    • Benchmark contract
  • Operators And Terms
    • State And Coupled Variable
    • Implemented Linear Operator
    • Gyroaverage And Bessel Factors
    • Streaming
    • Mirror
    • Curvature And Grad-B
    • Diamagnetic Drive
    • Collisions
      • Claim boundary and extension plan
      • Reduced drift-kinetic Sugama equation gate
      • Lowest-order improved-Sugama correction
      • Driven parallel-current response
    • Hypercollisions
    • Hyperdiffusion And End Damping
    • Nonlinear \(E \\times B\) And Flutter
    • Source Mapping
    • Parameter Surface
  • Numerics
    • Spectral discretization
    • Algorithm mapping (numerics → code)
    • JAX execution model
    • Structured solver dependency contract
    • Time integration algorithms
    • Diffrax integration
    • Nonlinear FFT bracket
    • Equilibrium-flow shearing coordinates
    • De-aliasing and hyperdiffusion
    • Performance tuning
    • Automatic solver + fit-signal selection
    • Custom collision operators
    • Gyroaverage and polarization
    • Parallel streaming
    • Curvature, grad-B, and mirror couplings
    • Field solve and electromagnetic coupling
    • Normalization control
    • Diamagnetic drive
    • Time integration
    • Boundary damping
    • Dealiasing
    • Nonlinear Electromagnetic Terms
  • Parallelization policy
    • Strategy registry
    • Production path: independent work
    • Production closure status
    • Diagnostic path: whole-state nonlinear sharding
    • Velocity-space communication gates
    • Claim rules
    • Large-run scaling acceptance checklist
    • Fast artifact contract check
    • Release artifact policy
  • Normalization
    • Canonical normalization contract
    • Dimensionless units
    • Kinetic species conventions
    • Field-aligned grid parameters
    • Spectral grids
    • Perpendicular normalization
    • Sign conventions
    • Normalization parameters
    • Diagnostic normalization mode
    • Diagnostic scaling
    • Programmatic usage
  • Quasilinear Transport
    • Current validated scope
    • Literature anchors and claim policy
    • Scoped core and universal-stress verdict
    • Executable usage
    • Model details
      • Linear eigenproblem
      • Field solve and linear weights
      • Amplitude normalization and effective scale
    • Implementation map
    • Algorithmic workflow
    • Numerics and differentiability
    • Validation gates
      • Implicit sensitivity example
    • Calibration reports
    • Train/holdout transfer
    • Non-axisymmetric HSX holdout
    • W7-X NetCDF nonlinear-window path
    • Saturation-rule sweep
    • Shape-aware saturation diagnostic
    • Candidate uncertainty gate
    • Residual-anatomy gate
    • Regularization sensitivity audit
    • Stellarator usefulness summary
    • Screening and rank-correlation gate
    • Dataset-sufficiency gate
    • Model-selection status
    • Holdout-gap report
    • External-VMEC holdout results
    • VMEC equilibrium portfolio for future holdouts
    • Axisymmetric spectrum-shape gates
  • Differentiable Stellarator Optimization
    • Purpose
    • Source Map
    • VMEC-JAX-Style QA Transport Scripts
    • Optimizer Strategy and Literature Anchor
      • Current optimizer evidence
    • Broad nonlinear matrix outcome
    • Optimizer-Comparison Manifest
    • Full Max-Mode-5 Optimizer Sweeps
    • Development-Only Reduced Diagnostics
    • Solved QA Transport Optimization
    • Historical Projected-Gradient Evidence
      • Boundary-Coefficient Objective Landscapes
      • Implementation Map
    • VMEC-JAX Geometry Examples
    • Production VMEC-JAX Optimization Plan
    • Development Portfolio Gate
    • Objective
    • Numerics and Differentiation
    • Objective-portfolio artifact guard
    • Development Diagnostic Results
    • Zonal-flow Objective Contract
    • Connection to Literature
    • Solver-objective Geometry Gradients
    • Promotion Gates for Full VMEC/Boozer/GK Optimization
  • Geometry
    • S-alpha flux-tube model
    • Parameters
    • Field-aligned grid parameters
    • Curvature and grad-B drift
    • Slab Model
    • Geometry Data Contract
      • Multi-Equilibrium Boozer Parity Matrix
    • In-memory differentiable geometry API
    • VMEC and Miller runtime examples
  • Algorithms
    • Linear operator workflow
    • Linear operator decomposition
    • Operator splitting summary
    • Data layout and memory
  • Solvers
    • Time integration
    • Optional damping
    • Performance caching
    • Growth rate extraction
  • Architecture
    • Core modules
    • Term-level source mapping
    • Data flow
  • Benchmarks
    • Figure generation
    • Capability and matched-comparison contract
    • Tracked results index
    • Tracked benchmark metrics
    • Primary publication set
    • Interpretation of validation
    • Benchmark runner internals
    • README summary panel
    • Supplementary closure figures
    • Extended stress matrix
    • Case groups
      • Tokamak core cases
      • Stellarator core cases
      • Reduced and stress cases
    • Notes on interpretation
  • Examples
    • Config-backed runtime cases
      • Tokamak cases
      • VMEC-backed tokamak and stellarator cases
    • Runtime TOML entry points
    • Scaling utilities
    • Plotting outputs
    • Geometry examples
    • Nonlinear restart and continuation
    • Geometry generation workflows
    • Benchmark and scan helpers
    • Foundational demos
    • Differentiable optimization examples
    • Secondary slab workflow
    • Full-GK ETG nonlinear pilot
  • Related Codes
    • Comparison-code roles
    • How references are used
    • Current benchmarking policy
    • Implementation lessons carried forward
  • Performance
    • JAX performance model
      • Current-branch representative refresh
    • Cache profiling
    • Fixed-step linear integrator profiling
    • Nonlinear profiling
    • JAX/XProf operational notes
    • Recent nonlinear profiling (Cyclone, benchmark-locked config)
    • Nonlinear benchmark harness
    • RHS kernel profile (nonlinear Cyclone)
    • Benchmark-size Cyclone Miller RHS profile
    • Runtime-mode stellarator RHS smoke profile
    • Linear RHS term profile
    • Full fused linear RHS trace
    • Parallelization scaling guardrail
    • Fixed-step nonlinear state sharding
    • Spectral nonlinear mode (gated fast toggle)
    • Runtime and memory comparison workflow
    • Final runtime/memory figure
    • Interpretation of short nonlinear GPU rows
    • Startup phase profiler
    • Cached basis indices
    • GMRES preconditioner policy
    • JIT considerations
    • Planned optimizations
    • Linear-to-nonlinear optimization roadmap
  • Testing
    • Testing philosophy
    • Current testing target
    • Nonlinear matrix release gates
    • Test categories
    • Unit tests (numerical invariants)
    • Physics regression tests
    • Benchmark regression tests
    • Literature-anchored response and spectrum tests
    • Diffrax and nonlinear smoke tests
    • Parallelization identity gates
    • Nonlinear parity snapshots
    • Linear physics checks
    • Running tests
    • Benchmark reproducibility stack
    • Stress-matrix parity gates
    • CI split: fast PR vs manual full
    • Core modular coverage gate
    • Core solver coverage gates
  • Validation And Coverage Strategy
    • Purpose
    • Claim-scope synchronization
    • How to check the manifest
    • Finalization sequence
    • Release readiness criteria
  • Verification Matrix
    • Purpose
    • Literature Baselines Reviewed
    • Status Legend
    • Tokamak Linear
    • Stellarator Linear
    • Nonlinear Validation
    • Equilibrium Flow Shear
    • Quasilinear Diagnostics and Model Selection
    • Autodiff Validation
    • Differentiable Geometry and Stellarator Objectives
    • Parallelization Validation
    • Notes
  • Release Scope and Claim Boundaries
    • Current scoped claims
    • Explicitly unpromoted claims
    • Release figure and artifact inventory
    • Artifact-backed details
    • Deferred manuscript lanes
    • Pre-release checklist
  • Code Structure
    • Purpose
    • Repository Roles
    • Public API vs Internal Modules
    • Runtime Flow
    • Physics / Numerics / IO Map
    • Refactor Mapping
    • Traceability For Refactors
    • Testing Taxonomy
    • Repository Artifact Hygiene
  • Manuscript Figures
    • Purpose
    • Current Readiness Snapshot
    • Current Vs Deferred Figure Inventory
    • Core Validation Figures
    • Differentiable-Physics Figures
    • Quasilinear Model-Selection Figures
    • Caption Policy
    • Open Issues Before Drafting
  • References
  • API Reference
    • Public API Registry
    • Collision Operator Interface
      • CollisionContext
      • CollisionOperator
      • SplitCollisionOperator
    • Velocity-Space Core
      • J_l_all()
      • associated_bessel_laguerre_coefficients()
      • bessel_j0()
      • bessel_j1()
      • bessel_laguerre_kernels()
      • gamma0()
      • hermite_ladder_coeffs()
      • hermite_normed()
      • hermite_physicists()
      • laguerre()
      • laguerre_gyroaverage_neighbors()
      • laguerre_quadrature_count()
      • laguerre_transform()
      • single_precision_factorial()
      • sum_Jl2()
    • Geometry
    • Geometry Core
      • FluxTubeGeometryData
      • GeometryConfig
      • GridConfig
      • SAlphaGeometry
      • SlabGeometry
      • _bgrad_from_bmag()
      • _periodic_spectral_derivative()
      • apply_geometry_grid_defaults()
      • apply_imported_geometry_grid_defaults()
      • build_flux_tube_geometry()
      • effective_boundary()
      • ensure_flux_tube_geometry_data()
      • load_imported_geometry_netcdf()
      • sample_flux_tube_geometry()
      • twist_shift_params()
      • zero_shear_enabled()
    • Analytic Geometry
      • MillerCoreParams
      • SAlphaGeometry
      • SlabGeometry
      • build_collocation_surfaces()
      • effective_boundary()
      • zero_shear_enabled()
    • Flux-Tube Geometry
      • FluxTubeGeometryData
      • _ImportedGeometrySelection
      • _bgrad_from_bmag()
      • _infer_root_theta_closed_interval()
      • _periodic_spectral_derivative()
      • _select_imported_geometry_variables()
      • load_imported_geometry_netcdf()
      • sample_flux_tube_geometry()
    • Miller EIK Generation
      • MillerGeometryRequest
      • build_miller_geometry_request()
      • default_miller_eik_output_path()
      • generate_runtime_miller_eik()
    • VMEC EIK Generation
      • VmecGeometryRequest
      • _resolve_runtime_vmec_file()
      • build_vmec_geometry_request()
      • default_vmec_eik_output_path()
      • generate_runtime_vmec_eik()
    • Differentiable Geometry
      • booz_xform_flux_tube_mapping_from_inputs()
      • booz_xform_flux_tube_sensitivity_report()
      • booz_xform_spectral_sensitivity_report()
      • discover_differentiable_geometry_backends()
      • evaluate_boozer_bmag_on_field_line()
      • finite_difference_jacobian()
      • flux_tube_geometry_from_mapping()
      • flux_tube_geometry_from_vmec_boozer_state()
      • flux_tube_geometry_observables()
      • geometry_inverse_design_report()
      • geometry_observable_names()
      • geometry_sensitivity_report()
      • observable_gradient_validation_report()
      • vmec_boundary_aspect_sensitivity_report()
      • vmec_field_line_tensor_observable_names()
      • vmec_metric_tensor_observable_names()
      • vmex_boozer_equal_arc_core_profiles_from_state()
      • vmex_boozer_flux_tube_sensitivity_report()
      • vmex_field_line_tensor_sensitivity_report()
      • vmex_flux_tube_array_parity_report()
      • vmex_flux_tube_mapping_from_state()
      • vmex_flux_tube_sensitivity_report()
      • vmex_metric_tensor_sensitivity_report()
    • Differentiable Geometry Backend Discovery
      • _candidate_paths()
      • _find_importable_module()
      • _is_traced()
      • _jax_float_dtype()
      • discover_differentiable_geometry_backends()
      • internal_vmec_backend_available()
    • Differentiable Flux-Tube Contract
      • flux_tube_geometry_from_mapping()
      • flux_tube_geometry_observables()
      • geometry_observable_names()
      • vmec_field_line_tensor_observable_names()
      • vmec_metric_tensor_observable_names()
    • Differentiable Geometry AD Checks
      • _json_ready()
      • _sensitivity_conditioning_metadata()
      • finite_difference_jacobian()
      • observable_gradient_validation_report()
    • Differentiable Geometry Sensitivity
      • geometry_inverse_design_report()
      • geometry_sensitivity_report()
    • Differentiable Boozer Bridge
      • booz_xform_flux_tube_mapping_from_inputs()
      • booz_xform_flux_tube_sensitivity_report()
      • booz_xform_spectral_sensitivity_report()
      • evaluate_boozer_bmag_on_field_line()
      • vmec_boundary_aspect_sensitivity_report()
    • Differentiable VMEC-State Sensitivity
      • vmex_boozer_flux_tube_sensitivity_report()
      • vmex_field_line_tensor_sensitivity_report()
      • vmex_metric_tensor_sensitivity_report()
    • Differentiable VMEC Boozer Core
      • flux_tube_geometry_from_vmec_boozer_state()
      • load_solved_vmex_case()
      • prewarm_vmec_boozer_equal_arc_cache()
      • resolve_vmex_case_input_path()
      • vmex_boozer_equal_arc_core_profiles_from_state()
    • Differentiable VMEC Boozer Constants
      • _cached_booz_xform_constants()
      • prewarm_vmec_boozer_equal_arc_cache()
    • Differentiable VMEC Flux-Tube Reports
      • vmex_flux_tube_array_parity_report()
      • vmex_flux_tube_sensitivity_report()
    • Differentiable VMEC Tensor Mapping
      • vmex_flux_tube_mapping_from_state()
    • Differentiable Geometry Numerics
      • _boozer_half_mesh_s_grid()
      • _interp_equal_arc_profile()
      • _periodic_bilinear_sample_2d()
    • Grids
      • SpectralGrid
      • real_fft_mesh()
      • real_fft_ordered_kx()
      • real_fft_unique_ky()
      • select_ky_grid()
      • select_real_fft_ky_grid()
      • twothirds_mask()
    • Species and Linear Parameters
      • Species
      • build_linear_params()
    • Operators
      • hermite_streaming()
    • Linear Operators
    • Linear Linked Boundaries
      • _build_linked_end_damping_profile()
      • _build_linked_fft_maps()
    • Linear Cache
    • Linear Collisions
    • Linear Moments
      • apply_hermite_v()
      • apply_hermite_v2()
      • apply_laguerre_x()
      • build_H()
      • compute_b()
      • diamagnetic_drive_coeffs()
      • energy_operator()
      • grad_z_periodic()
      • hermite_streaming()
      • lenard_bernstein_eigenvalues()
      • quasineutrality_phi()
      • shift_axis()
      • streaming_term()
    • Linear Parameters
    • Linear RHS
      • linear_rhs()
      • linear_rhs_cached()
    • Linear Dissipation
      • CollisionInvariantRates
      • collision_invariant_rates()
      • collision_quadratic_rate()
      • drift_kinetic_coulomb_six_moment_contribution()
      • drift_kinetic_dougherty_contribution()
      • drift_kinetic_sugama_six_moment_contribution()
      • hyperdiffusion_contribution()
    • Linear Implicit Solvers
      • _integrate_linear_implicit_cached()
    • Linear Integrators
      • _integrate_linear_cached_impl()
      • integrate_linear()
      • integrate_linear_diagnostics()
    • Linear Diagnostic Integration
      • integrate_linear_diagnostics()
    • Linear Parallel RHS
      • _electrostatic_streaming_field_rhs()
      • _linear_rhs_electrostatic_slices_velocity_sharded_fused()
      • _resolve_parallel_devices()
      • _streaming_electrostatic_from_phi_velocity_sharded()
      • linear_rhs_electrostatic_slices_velocity_sharded()
      • linear_rhs_electrostatic_species_hermite_sharded()
      • linear_rhs_electrostatic_species_sharded()
      • linear_rhs_parallel_cached()
      • linear_rhs_streaming_electrostatic_velocity_sharded()
      • linear_rhs_streaming_velocity_sharded()
      • prepare_electrostatic_species_hermite_state()
      • prepare_electrostatic_species_inputs()
    • Linear Parallel Policy
      • _resolve_parallel_devices()
    • Linear Parallel Streaming
      • _electrostatic_streaming_field_rhs()
      • _streaming_electrostatic_from_phi_velocity_sharded()
      • linear_rhs_electrostatic_species_hermite_sharded()
      • linear_rhs_streaming_electrostatic_velocity_sharded()
      • linear_rhs_streaming_velocity_sharded()
      • prepare_electrostatic_species_hermite_state()
    • Linear Parallel Electrostatic Slices
      • _linear_rhs_electrostatic_slices_velocity_sharded_fused()
      • linear_rhs_electrostatic_slices_velocity_sharded()
      • linear_rhs_electrostatic_species_sharded()
      • prepare_electrostatic_species_inputs()
    • Linear Krylov Solvers
      • KrylovConfig
      • _build_shift_invert_precond()
      • _mode_family_sign()
      • _omega_scale()
      • _physical_omega()
      • _select_by_overlap()
      • _select_by_target()
      • dominant_eigenpair()
      • dominant_eigenpair_cached()
      • dominant_eigenpair_power()
      • dominant_eigenpair_propagator_cached()
      • dominant_eigenpair_shift_invert_cached()
    • Linear Eigenmode Solver Internals
    • Nonlinear Diagnostics
    • Nonlinear Diagnostic State
      • NonlinearDiagnosticKernels
      • compute_nonlinear_diagnostic_tuple()
      • make_nonlinear_diagnostic_tuple_fn()
    • Nonlinear Collision Split Helpers
      • NonlinearCollisionSplitPolicy
      • _apply_collision_split()
      • _collision_damping()
      • build_nonlinear_collision_split_policy()
    • Nonlinear Helpers
    • Nonlinear Projection Helpers
      • ShearingCoordinateUpdate
      • _make_fixed_mode_projector()
      • _make_hermitian_projector()
      • _make_nonlinear_state_projector()
      • advance_shearing_coordinates()
    • Nonlinear RHS
      • linear_rhs_jit_for_terms_impl()
      • nonlinear_em_term_cached_impl()
      • nonlinear_rhs_cached_impl()
    • Nonlinear Bracket Kernels
      • _fft2_xy_remove_radial_phase()
      • _ifft2_xy_with_radial_phase()
    • Nonlinear Term Assembly
      • _LaguerreGridContext
      • _NonlinearBracketContext
      • _PreparedNonlinearInputs
      • _PreparedNonlinearPath
      • _prepare_nonlinear_path()
      • exb_nonlinear_contribution()
      • nonlinear_em_components()
      • nonlinear_em_contribution()
      • placeholder_nonlinear_contribution()
    • Nonlinear Explicit Step
      • advance_explicit_nonlinear_state()
      • checkpoint_explicit_step()
      • integrate_cached_explicit_scan()
      • integrate_nonlinear_scan()
      • make_explicit_diagnostic_step()
      • run_explicit_diagnostic_scan()
    • Nonlinear State Integration
    • Nonlinear Diagnostic Drivers
      • ExplicitNonlinearDiagnosticsDeps
      • IMEXNonlinearDiagnosticsDeps
      • PreparedExplicitNonlinearDiagnostics
      • integrate_explicit_nonlinear_diagnostics_impl()
      • integrate_imex_nonlinear_diagnostics_impl()
      • prepare_explicit_nonlinear_diagnostics_impl()
    • Nonlinear Diagnostic Integration
    • Nonlinear IMEX
      • advance_imex_nonlinear_state()
      • imex_fixed_point_guess()
      • integrate_cached_imex_scan()
      • make_imex_diagnostic_step()
      • make_imex_nonlinear_term()
      • make_imex_solve_step()
      • run_imex_diagnostic_scan()
      • solve_imex_step()
    • Explicit Time Integrators
      • ExplicitTimeConfig
      • _apply_completed_step_state_mask()
      • _completed_step_state_mask()
      • _growth_rate_mode_mask()
      • _instantaneous_growth_rate_step()
      • _linear_explicit_step()
      • _rk3_heun_step()
      • _rk4_step()
      • integrate_linear_explicit()
      • integrate_linear_explicit_diagnostics()
      • integrate_linear_explicit_from_config()
    • Explicit Step Kernels
      • _apply_completed_step_state_mask()
      • _completed_step_state_mask()
      • _growth_rate_mode_mask()
      • _instantaneous_growth_rate_step()
      • _linear_explicit_step()
      • _rk3_heun_step()
      • _rk4_step()
    • Explicit Diagnostic Integrators
      • ExplicitTimeConfigLike
      • integrate_linear_explicit_diagnostics()
    • Explicit CFL Policy
    • Diffrax Time Integrators
      • integrate_linear_diffrax()
      • integrate_linear_diffrax_streaming()
      • integrate_nonlinear_diffrax()
    • Config-Driven Time Runners
      • _validate_nonlinear_config_state_sharding()
      • integrate_linear_from_config()
      • integrate_nonlinear_from_config()
    • Runtime Execution Dispatch
      • RuntimeLinearDispatchDeps
      • RuntimeNonlinearDispatchDeps
      • _RuntimeLinearRequest
      • build_runtime_linear_dispatch_deps()
      • build_runtime_nonlinear_dispatch_deps()
      • run_runtime_linear_impl()
      • run_runtime_nonlinear_impl()
    • Nonlinear Replicate Diagnostics
      • NonlinearReplicateSpreadConfig
      • NonlinearWindowEnsembleManifestConfig
      • nonlinear_replicate_spread_report()
      • nonlinear_window_ensemble_artifact_manifest()
      • summarize_window_evidence()
    • Nonlinear Transport Optimization Diagnostics
      • ProductionNonlinearOptimizationGuardConfig
      • matched_optimized_transport_report()
      • optimization_artifact_reduction_scope()
      • optimized_equilibrium_transport_report()
      • production_nonlinear_optimization_guard_report()
      • reduced_artifact_scope_report()
      • replicated_transport_ensemble_report()
    • Nonlinear Gradient Evidence Diagnostics
      • NonlinearTurbulenceGradientBracketSweepConfig
      • NonlinearTurbulenceGradientCandidateRankingConfig
      • NonlinearTurbulenceGradientEvidenceConfig
      • NonlinearTurbulenceGradientFiniteDifferenceConfig
      • NonlinearTurbulenceGradientGapConfig
      • classify_gradient_artifact()
      • load_json_artifact()
      • nonlinear_turbulence_gradient_bracket_sweep_report()
      • nonlinear_turbulence_gradient_candidate_ranking_report()
      • nonlinear_turbulence_gradient_evidence_gap_report()
      • nonlinear_turbulence_gradient_evidence_report()
      • nonlinear_turbulence_gradient_finite_difference_report()
      • summarize_window_evidence()
    • Nonlinear Gradient Statistics
      • NonlinearGradientControlMeanGateConfig
      • NonlinearGradientVarianceReductionConfig
      • nonlinear_gradient_control_mean_gate()
      • nonlinear_gradient_variance_reduction_plan()
    • Benchmarks
    • Validation Gates
      • GateReport
      • ScalarGateResult
      • ZonalFlowResponseMetrics
      • branch_continuity_gate_report()
      • eigenfunction_gate_report()
      • evaluate_scalar_gate()
      • gate_report()
      • gate_report_to_dict()
      • linear_metrics_gate_report()
      • matched_nonlinear_transport_report()
      • nonlinear_heat_flux_convergence_gate_report()
      • nonlinear_window_gate_report()
      • observed_order_gate_report()
      • zonal_response_gate_report()
    • Autodiff Validation
      • autodiff_finite_difference_report()
      • central_finite_difference_jacobian()
      • covariance_diagnostics()
      • explicit_complex_operator_matrix()
      • implicit_eigenpair_observable_sensitivity_report()
      • isolated_eigenpair_observable_sensitivity_report()
      • isolated_eigenvalue_sensitivity_report()
    • Parallelization
      • DecompositionContract
      • IndependentEnsembleProvenanceReport
      • IndependentMapExecutionError
      • IndependentWorkerMetadata
      • ParallelIdentityReport
      • ReconstructionIdentityReport
      • ShardAssignment
      • VelocityShardingPlan
      • batch_map()
      • batch_map_identity_report()
      • build_diagnostic_nonlinear_domain_decomposition()
      • build_independent_portfolio_decomposition()
      • build_velocity_sharding_plan()
      • curvature_gradb_drift_reference()
      • curvature_gradb_drift_shard_map()
      • diamagnetic_drive_reference()
      • diamagnetic_drive_shard_map()
      • electrostatic_phi_reference()
      • electrostatic_phi_shard_map()
      • hermite_neighbor_reference()
      • hermite_neighbor_shard_map()
      • hermite_shift_reference()
      • hermite_shift_shard_map()
      • hermite_streaming_ladder_reference()
      • hermite_streaming_ladder_shard_map()
      • independent_ensemble_provenance_gate()
      • independent_map()
      • independent_map_identity_report()
      • independent_worker_metadata()
      • integrate_linear_sharded()
      • integrate_nonlinear_sharded()
      • ky_scan_batches()
      • mirror_drift_reference()
      • mirror_drift_shard_map()
      • pad_to_multiple()
      • parallel_identity_report()
      • periodic_streaming_reference()
      • periodic_streaming_shard_map()
      • reconstruct_serial()
      • resolve_state_sharding()
      • serial_reconstruction_identity_report()
      • shard_sequence()
      • split_evenly()
      • velocity_field_reduce_reference()
      • velocity_field_reduce_shard_map()
    • Parallel Identity Reports
      • ParallelIdentityReport
      • parallel_identity_report()
    • Parallel Batch Mapping
      • batch_map()
      • batch_map_identity_report()
      • ky_scan_batches()
      • pad_to_multiple()
      • split_evenly()
    • Parallel Independent Tasks
      • IndependentEnsembleProvenanceReport
      • IndependentMapExecutionError
      • IndependentWorkerMetadata
      • independent_ensemble_provenance_gate()
      • independent_map()
      • independent_map_identity_report()
      • independent_worker_metadata()
    • Nonlinear Parallel Spectral Core
      • _host_max_abs_rel_error()
      • _host_staged_array_for_sharding()
      • _normalize_spectral_tile_bounds()
      • _pencil_fft2()
      • _pencil_ifft2()
      • _pencil_spectral_bracket()
      • _pencil_spectral_bracket_z_chunked()
      • _spectral_layout_round_trip()
      • _spectral_rhs_from_bracket()
      • _within_abs_or_rel_tolerance()
      • deterministic_nonlinear_spectral_state()
      • device_z_pencil_fft_batch_pressure_model()
      • nonlinear_spectral_domain_work_model()
      • nonlinear_spectral_pencil_work_model()
    • Nonlinear Domain Decomposition
      • build_nonlinear_domain_decomposition_plan()
      • deterministic_nonlinear_domain_state()
      • local_stencil_nonlinear_domain_decomposed_step()
      • local_stencil_nonlinear_domain_serial_step()
      • nonlinear_domain_identity_report()
      • nonlinear_domain_parallel_identity_gate()
      • nonlinear_domain_transport_window_identity_gate()
    • Nonlinear Parallel Device-Z Core
      • _append_device_z_transport_observables()
      • _append_spectral_physical_observable_vector()
      • _blocked_device_z_rhs_report()
      • _blocked_device_z_transport_window_report()
      • _device_z_pencil_shard_map_observables_fn()
      • _device_z_pencil_shard_map_rhs_fn()
      • _device_z_rhs_identity_report()
      • _device_z_sharding_for_spectral_state()
      • _device_z_transport_identity_passed()
      • _device_z_transport_window_report()
      • _new_transport_trace_dict()
      • _run_device_z_compute_window_states()
      • _serial_transport_compute_state()
      • _spectral_physical_transport_observable_sums()
      • _spectral_physical_transport_observable_vector_from_sums()
      • _transport_trace_error_pairs()
      • _transport_trace_tuples()
      • device_z_pencil_nonlinear_spectral_rhs()
      • device_z_pencil_nonlinear_spectral_transport_window_identity_gate()
    • Velocity Sharding Plans
      • VelocityShardingPlan
      • build_velocity_sharding_plan()
      • hermite_neighbor_reference()
      • hermite_neighbor_shard_map()
      • hermite_shift_reference()
      • hermite_shift_shard_map()
      • velocity_field_reduce_reference()
      • velocity_field_reduce_shard_map()
      • curvature_gradb_drift_reference()
      • curvature_gradb_drift_shard_map()
      • hermite_streaming_ladder_reference()
      • hermite_streaming_ladder_shard_map()
      • mirror_drift_reference()
      • mirror_drift_shard_map()
      • periodic_streaming_reference()
      • periodic_streaming_shard_map()
      • diamagnetic_drive_reference()
      • diamagnetic_drive_shard_map()
      • electrostatic_phi_reference()
      • electrostatic_phi_shard_map()
    • State Sharding Policy
      • resolve_state_sharding()
    • Sharded Integrators
      • integrate_linear_sharded()
      • integrate_nonlinear_sharded()
    • Zonal Validation
    • Zonal Flow Objectives
      • ZonalFlowObjectiveConfig
      • zonal_flow_objective_artifact_from_records()
      • zonal_flow_objective_rows()
      • zonal_flow_objective_sensitivity_report()
      • zonal_flow_reduced_objective()
    • Analysis
    • Mode Diagnostics
      • EigenfunctionComparisonMetrics
      • EigenfunctionReferenceBundle
      • ModeSelection
      • ModeSelectionBatch
      • compare_eigenfunctions()
      • density_moment()
      • extract_eigenfunction()
      • extract_mode()
      • extract_mode_time_series()
      • load_eigenfunction_reference_bundle()
      • normalize_eigenfunction()
      • phase_align_eigenfunction()
      • save_eigenfunction_reference_bundle()
      • select_ky_index()
    • Growth-Rate Diagnostics
      • _log_amp_phase()
      • fit_growth_rate()
      • fit_growth_rate_auto()
      • fit_growth_rate_auto_with_stats()
      • fit_growth_rate_with_stats()
      • instantaneous_growth_rate_from_phi()
      • select_fit_window()
      • select_fit_window_loglinear()
      • windowed_growth_rate_from_omega_series()
    • Growth-Rate Fit Windows
      • late_time_window()
      • select_fit_window()
      • select_fit_window_loglinear()
    • Zonal Response Plots
      • zonal_flow_response_figure()
    • Publication Plotting
    • Config
      • CycloneBaseCase
      • GeometryConfig
      • GridConfig
      • InitializationConfig
      • KBMBaseCase
      • KineticElectronModelConfig
      • ModelConfig
      • TimeConfig
      • explicit_method_default_cfl_fac()
      • resolve_cfl_fac()
    • Normalization
      • NormalizationContract
      • apply_diagnostic_normalization()
      • get_normalization_contract()
    • Moment And Energy Diagnostics
      • _cached_hermitian_mode_weight()
      • _hermitian_mode_weight()
      • _jl_family()
      • _masked_abs2()
      • _reduce_scalar_kykxz()
      • _reduce_species_kykxz()
      • _transport_mode_weight()
      • distribution_free_energy()
      • distribution_free_energy_resolved()
      • electrostatic_field_energy()
      • electrostatic_field_energy_resolved()
      • fieldline_quadrature_weights()
      • heat_flux_channel_resolved_species()
      • heat_flux_resolved_species()
      • magnetic_vector_potential_energy()
      • magnetic_vector_potential_energy_resolved()
      • particle_flux_channel_resolved_species()
      • particle_flux_resolved_species()
      • phi2_resolved()
      • turbulent_heating_resolved_species()
      • zonal_phi_line_kxt()
      • zonal_phi_mode_kxt()
    • Transport Diagnostics
      • heat_flux_channel_species()
      • heat_flux_species()
      • heat_flux_total()
      • nonlinear_turbulence_gradient_finite_difference_report()
      • particle_flux_channel_species()
      • particle_flux_species()
      • particle_flux_total()
      • turbulent_heating_species()
      • turbulent_heating_total()
    • Runtime Config
      • RuntimeCollisionConfig
      • RuntimeConfig
      • RuntimeExpertConfig
      • RuntimeNormalizationConfig
      • RuntimeOutputConfig
      • RuntimeParallelConfig
      • RuntimePhysicsConfig
      • RuntimeQuasilinearConfig
      • RuntimeSpeciesConfig
      • RuntimeTermsConfig
    • Runtime Startup
      • _as_runtime_species_array()
      • _build_initial_condition()
      • _build_single_phi_gaussian_profile()
      • _centered_glibc_random_pairs()
      • _dealiased_initial_mode_pairs()
      • _density_moments_for_target_phi()
      • _enforce_full_ky_hermitian()
      • _periodic_zp_from_grid()
      • build_runtime_geometry()
      • build_runtime_linear_params()
      • build_runtime_linear_terms()
      • build_runtime_term_config()
      • load_netcdf_restart_state()
      • runtime_geometry_config_for_builder()
    • Runtime Policies
      • RuntimeIndependentParallelPlan
      • _infer_runtime_nonlinear_steps()
      • _parallel_requests_combined_ky_scan()
      • _runtime_external_phi()
      • _runtime_independent_parallel_plan()
      • build_runtime_nonlinear_diagnostics_kwargs()
    • Runtime Diagnostics
      • RuntimeLinearFitResult
      • RuntimeQuasilinearFinalizationDeps
      • finalize_runtime_linear_quasilinear()
      • fit_runtime_linear_diagnostics()
      • refit_runtime_linear_trajectory()
    • Runtime Diagnostic Arrays
      • concat_runtime_diagnostics()
      • slice_runtime_diagnostics()
      • stride_runtime_diagnostics()
      • truncate_runtime_diagnostics()
      • validate_finite_runtime_diagnostics()
    • Runtime Initial Conditions
      • _InitialConditionBuilder
      • _build_single_phi_gaussian_profile()
      • _centered_glibc_random_pairs()
      • _dealiased_initial_mode_pairs()
      • _enforce_full_ky_hermitian()
      • _periodic_zp_from_grid()
    • Runtime Phi Initializer
      • _PhiMomentAlgebra
      • _as_runtime_species_array()
      • _density_moments_for_target_phi()
    • Runtime Chunks
      • AdaptiveChunkResult
      • RuntimeProgressSnapshot
      • _chunk_end_time()
      • _effective_diagnostics_stride()
      • _next_elapsed_time()
      • _offset_chunk_diagnostics_time()
      • build_runtime_progress_message()
      • format_duration()
      • run_adaptive_runtime_chunk_loop()
    • Runtime Results
      • RuntimeLinearResult
      • RuntimeLinearScanResult
      • RuntimeNonlinearResult
      • RuntimeParameterScanResult
      • build_runtime_nonlinear_result()
      • nonlinear_field_phi2()
    • Runtime Orchestration
      • RuntimeScanBatchDeps
      • RuntimeScanDeps
      • build_runtime_scan_batch_deps()
      • build_runtime_scan_orchestration_deps()
      • run_runtime_parameter_scan()
      • run_runtime_scan_batch()
      • run_runtime_scan_ky_task()
      • run_runtime_scan_orchestration()
      • NonlinearArtifactPolicy
      • RuntimeArtifactHandoffDeps
      • print_nonlinear_command_outputs()
      • print_saved_paths()
      • resolve_nonlinear_artifact_policy()
      • run_runtime_nonlinear_artifact_handoff()
      • write_command_outputs()
      • write_linear_runtime_command_outputs()
      • write_scan_runtime_command_outputs()
    • Runtime Commands
      • RuntimeCaseDeps
      • RuntimeCommandDeps
      • RuntimeLinearCommandOptions
      • RuntimeNonlinearCommandOptions
      • RuntimeScanCommandOptions
      • _arg_or_section()
      • _parse_ky_values()
      • _prepare_runtime_command_config()
      • _resolve_grid_time_options()
      • _resolve_linear_command_options()
      • _resolve_linear_fit_options()
      • _resolve_nonlinear_command_options()
      • _resolve_scan_command_options()
      • _runtime_fit_config()
      • apply_quasilinear_overrides()
      • apply_runtime_path_overrides()
      • attach_preloaded_runtime_config()
      • build_runtime_command_deps()
      • load_runtime_command_config()
      • plot_saved_output_command()
      • print_linear_run_header()
      • print_nonlinear_run_header()
      • print_nonlinear_run_summary()
      • run_linear_case()
      • run_nonlinear_case()
      • run_runtime_linear_command()
      • run_runtime_nonlinear_command()
      • runtime_output_path()
      • scan_runtime_linear_command()
      • should_show_progress()
    • Runtime TOML Inputs
      • _apply_runtime_section_overrides()
      • _merge_dataclass()
      • _normalize_geometry_overrides()
      • _replace_runtime_section()
      • _resolve_runtime_config_paths()
      • _runtime_base_config()
      • _runtime_species_from_toml()
      • direct_config_shorthand_args()
      • is_runtime_toml()
      • load_runtime_from_toml()
      • load_toml()
      • resolve_runtime_path()
      • toml_shorthand_command()
    • Runtime Artifact Package
      • validate_finite_array()
      • validate_finite_runtime_result()
      • write_quasilinear_artifacts()
      • write_runtime_linear_artifacts()
      • write_runtime_linear_scan_artifacts()
      • write_runtime_nonlinear_table_artifacts()
    • Runtime Artifact IO
      • DiagnosticTimeSeries
      • load_diagnostic_time_series()
      • load_netcdf_restart_state()
      • validate_finite_array()
      • validate_finite_runtime_result()
      • write_netcdf_restart_state()
      • write_quasilinear_artifacts()
      • write_runtime_linear_artifacts()
      • write_runtime_linear_scan_artifacts()
      • write_runtime_nonlinear_table_artifacts()
    • NetCDF Spectral Layout
      • _condense_kx_for_output()
      • _condense_ky_for_output()
      • _condense_kykx_for_output()
      • infer_triple_dealiased_ny()
    • Nonlinear Output NetCDF
      • _build_output_grid_and_geometry()
      • _write_diagnostics_group()
    • Quasilinear Transport Diagnostics
      • QuasilinearTransportResult
      • compute_quasilinear_from_linear_state()
      • effective_kperp2()
      • mixing_length_amplitude2_jax()
      • normalize_quasilinear_channels()
      • phi_norm2()
      • quasilinear_feature_objective()
      • saturated_flux_from_linear_weight()
      • saturation_amplitude2()
      • shape_aware_power_law_objective()
      • spectral_phi_weights()
    • Quasilinear Calibration
      • QuasilinearCalibrationPoint
      • apply_heat_flux_scale()
      • calibration_point_from_nonlinear_window_summary()
      • calibration_point_from_spectrum_and_nonlinear_window()
      • fit_train_heat_flux_scale()
      • integrated_quasilinear_flux_from_spectrum()
      • quasilinear_calibration_report()
      • write_quasilinear_calibration_report()
    • Quasilinear Nonlinear-Window Gates
      • NonlinearWindowConvergenceConfig
      • NonlinearWindowEnsembleConfig
      • nonlinear_window_convergence_from_csv()
      • nonlinear_window_convergence_from_summary()
      • nonlinear_window_convergence_report()
      • nonlinear_window_ensemble_report()
      • nonlinear_window_stats_promotion_ready()
    • Quasilinear Model Selection
      • build_quasilinear_model_selection_status()
      • build_quasilinear_model_selection_status_from_paths()
    • Solver Eigen Objectives
      • dominant_eigenvalue_branch_locality_report()
      • dominant_real_eigenvalue()
    • Solver Objective Core
      • solver_growth_rate_from_geometry()
      • solver_linear_operator_matrix_from_geometry()
      • solver_objective_vector_from_geometry()
      • solver_scalar_objective_from_vector()
    • Solver Objective Sampling
      • solver_grid_options_from_ky_values()
    • Solver Geometry Objectives
      • default_solver_geometry_design_params()
      • solver_ready_geometry_mapping()
      • tiny_differentiable_objective_gradient_report()
    • Solver-Ready Gradient Gates
      • linear_solver_geometry_gradient_report()
      • solver_objective_branch_gradient_report()
    • Solver VMEC/Boozer Gradient Gates
      • _mode21_vmec_boozer_linear_context()
      • _mode21_vmec_boozer_quasilinear_features()
      • mode21_vmec_boozer_linear_frequency_gradient_report()
      • mode21_vmec_boozer_nonlinear_window_gradient_report()
      • mode21_vmec_boozer_quasilinear_gradient_report()
    • Solver VMEC/Boozer Objectives
      • _split_vmec_boozer_objective_kwargs()
      • vmec_boozer_aggregate_scalar_objective_from_state()
      • vmec_boozer_scalar_objective_from_state()
      • vmec_boozer_solver_objective_table_from_state()
      • vmec_boozer_solver_objective_table_with_metadata_from_state()
      • vmec_boozer_solver_objective_vector_from_state()
    • Solver VMEC/Boozer Finite-Difference Gates
      • _load_vmex_example_state_bundle()
      • _report_float()
      • vmec_boozer_aggregate_scalar_objective_finite_difference_report()
      • vmec_boozer_scalar_objective_finite_difference_report()
    • Solver VMEC/Boozer Line-Search Gates
      • vmec_boozer_aggregate_line_search_holdout_report()
      • vmec_boozer_aggregate_scalar_objective_line_search_report()
      • vmec_boozer_scalar_objective_line_search_report()
    • Parallel Decomposition Contracts
      • DecompositionContract
      • ReconstructionIdentityReport
      • ShardAssignment
      • build_diagnostic_nonlinear_domain_decomposition()
      • build_independent_portfolio_decomposition()
      • reconstruct_serial()
      • serial_reconstruction_identity_report()
      • shard_sequence()
    • VMEC-JAX Transport Objective
      • VMEXGKXTransportObjective
      • VMEXTransportObjectiveConfig
      • vmex_transport_objective_from_state()
    • VMEC-JAX Transport Branch Gates
      • vmex_transport_growth_branch_locality_report_from_states()
    • VMEC-JAX Transport Admission
      • VMEXNonlinearAuditPolicy
      • VMEXNonlinearCampaignPolicy
      • VMEXReducedPrelaunchPolicy
      • VMEXTransportAdmissionPolicy
      • build_transport_admission_report()
      • candidate_transport_metric()
      • select_admitted_transport_candidate()
      • transport_objective_sample_summary()
    • Stellarator Transport Reports
      • build_nonlinear_audit_redesign_report()
      • build_nonlinear_campaign_admission_report()
      • build_nonlinear_landscape_admission_report()
      • build_reduced_nonlinear_audit_prelaunch_report()
    • VMEC-JAX Transport Optimization
      • ProjectedLineSearchPolicy
      • boundary_chain_accepted_parameter_indices()
      • boundary_spec_record()
      • build_boundary_transport_gradient_report()
      • projected_line_search_input_manifest()
      • select_projected_line_search_candidate()
      • sparse_descent_direction_from_gradient_report()
      • write_boundary_transport_gradient_report()
    • VMEC-JAX Boundary Chain
      • boundary_chain_summary_from_probe()
      • build_boundary_chain_collection_summary()
      • build_boundary_chain_summary()
    • VMEC-JAX Candidate Gates
      • build_authoritative_wout_candidate_gate()
      • build_solved_vmec_candidate_gate()
      • build_wout_reproducibility_gate()
      • final_iota_profiles_from_vmec_result()
    • Stellarator ITG Objectives
    • Stellarator ITG Objective Tables
      • stellarator_itg_density_gradient_scan()
      • stellarator_itg_portfolio_gate_payload()
      • stellarator_itg_portfolio_sensitivity_report()
      • stellarator_itg_reduced_portfolio_objective()
      • stellarator_itg_sample_objective_table()
      • stellarator_itg_vmec_boozer_portfolio_objective_from_state()
      • stellarator_itg_vmec_boozer_sample_objective_table_from_state()
    • Stellarator ITG Contracts
      • StellaratorITGOptimizationConfig
      • StellaratorITGOptimizationResult
      • StellaratorITGSampleSet
    • Stellarator Reduced ITG Model And Gates
      • _conditioning_gate_from_covariance()
      • _precision_gate_tolerances()
      • _qa_core_features()
      • _qa_geometry_features()
      • _qa_gradient_drives()
      • _qa_linear_itg_features()
      • _qa_quasilinear_heat_flux()
      • _residual_precision_gate_tolerances()
      • _sampled_qa_itg_fields()
      • default_stellarator_initial_params()
      • nonlinear_heat_flux_trace()
      • nonlinear_heat_flux_window_metrics()
      • qa_max_mode1_observables()
      • qa_observable_vector()
      • smooth_positive()
      • stellarator_itg_objective()
      • stellarator_itg_objective_residual_names()
      • stellarator_itg_objective_residual_vector()
      • stellarator_itg_residual_sensitivity_report()
    • Stellarator Objective Portfolios
      • StellaratorObjectivePortfolioContract
      • aggregate_objective_portfolio()
      • objective_portfolio_sensitivity_report()
      • portfolio_objective_weight_vector()
      • portfolio_sample_weight_tensor()
      • validate_objective_portfolio_contract()
    • Stellarator Objective Portfolio Guard
      • ReducedPortfolioArtifactGuardConfig
      • reduced_portfolio_artifact_guard_report()
    • Runtime Runner
      • RuntimeIndependentParallelPlan
      • RuntimeLinearResult
      • RuntimeLinearScanResult
      • RuntimeNonlinearResult
      • build_runtime_geometry()
      • build_runtime_linear_params()
      • build_runtime_linear_terms()
      • build_runtime_term_config()
      • run_runtime_linear()
      • run_runtime_nonlinear()
      • run_runtime_scan()
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