LICENSE
MANIFEST.in
README.md
pyproject.toml
benchmarks/README.md
benchmarks/basis_orthonormality.py
benchmarks/capability_matrix.toml
benchmarks/collisional_zonal_response.toml
benchmarks/cyclone_linear_benchmark.py
benchmarks/etg_linear_benchmark.py
benchmarks/kbm_linear_comparison.py
benchmarks/kinetic_linear_benchmark.py
benchmarks/runtime_miller_zonal_response.toml
benchmarks/runtime_secondary_slab.toml
benchmarks/runtime_w7x_zonal_response_vmec.toml
benchmarks/secondary_slab_workflow.py
benchmarks/tem_linear_benchmark.py
benchmarks/performance/__init__.py
benchmarks/performance/benchmark_integrators.py
benchmarks/performance/benchmark_lineax_linear_solve.py
benchmarks/performance/benchmark_nonlinear_suite.py
benchmarks/performance/benchmark_runtime_memory.py
benchmarks/results/README.md
benchmarks/results/manifest.toml
docs/algorithms.rst
docs/api.rst
docs/architecture.rst
docs/architecture_refactor_plan.rst
docs/benchmarks.rst
docs/code_structure.rst
docs/codes.rst
docs/conf.py
docs/differentiable_refactor_plan.rst
docs/examples.rst
docs/geometry.rst
docs/index.rst
docs/inputs.rst
docs/linear_model.rst
docs/manuscript_figures.rst
docs/normalization.rst
docs/numerics.rst
docs/operators.rst
docs/outputs.rst
docs/parallelization.rst
docs/performance.rst
docs/quasilinear.rst
docs/quickstart.rst
docs/references.rst
docs/release_scope.rst
docs/roadmap.rst
docs/solvers.rst
docs/stellarator_optimization.rst
docs/testing.rst
docs/theory.rst
docs/validation_strategy.rst
docs/verification_matrix.rst
examples/linear/axisymmetric/cyclone.toml
examples/linear/axisymmetric/cyclone_runtime_linear.py
examples/linear/axisymmetric/etg.toml
examples/linear/axisymmetric/etg_runtime_linear.py
examples/linear/axisymmetric/kaw_runtime_linear.py
examples/linear/axisymmetric/kbm_runtime_linear.py
examples/linear/axisymmetric/runtime_circular_vmec_linear.toml
examples/linear/axisymmetric/runtime_cyclone_miller_quasilinear.toml
examples/linear/axisymmetric/runtime_cyclone_quasilinear.toml
examples/linear/axisymmetric/runtime_etg.toml
examples/linear/axisymmetric/runtime_kaw.toml
examples/linear/axisymmetric/runtime_kbm.toml
examples/linear/axisymmetric/runtime_kinetic_electron.toml
examples/linear/axisymmetric/runtime_tem.toml
examples/linear/non-axisymmetric/hsx_linear_imported_geometry.py
examples/linear/non-axisymmetric/runtime_hsx_linear_quasilinear.toml
examples/linear/non-axisymmetric/runtime_w7x_linear_imported_geometry.toml
examples/linear/non-axisymmetric/runtime_w7x_linear_quasilinear_vmec.toml
examples/linear/non-axisymmetric/w7x_linear_imported_geometry.py
examples/nonlinear/axisymmetric/cyclone_runtime_nonlinear.py
examples/nonlinear/axisymmetric/etg_runtime_nonlinear.py
examples/nonlinear/axisymmetric/kbm_runtime_nonlinear.py
examples/nonlinear/axisymmetric/miller_nonlinear_runtime.py
examples/nonlinear/axisymmetric/runtime_circular_vmec_nonlinear.toml
examples/nonlinear/axisymmetric/runtime_cyclone_nonlinear.toml
examples/nonlinear/axisymmetric/runtime_cyclone_nonlinear_miller.toml
examples/nonlinear/axisymmetric/runtime_cyclone_nonlinear_short.toml
examples/nonlinear/axisymmetric/runtime_cyclone_nonlinear_t400.toml
examples/nonlinear/axisymmetric/runtime_etg_nonlinear.toml
examples/nonlinear/axisymmetric/runtime_kbm_nonlinear.toml
examples/nonlinear/axisymmetric/runtime_kbm_nonlinear_seed.toml
examples/nonlinear/axisymmetric/runtime_kbm_nonlinear_short.toml
examples/nonlinear/axisymmetric/runtime_kbm_nonlinear_short_lockin.toml
examples/nonlinear/axisymmetric/runtime_kbm_nonlinear_t100.toml
examples/nonlinear/axisymmetric/runtime_kbm_nonlinear_t100_nx4ny8_dt9e4.toml
examples/nonlinear/non-axisymmetric/hsx_nonlinear_imported_geometry.py
examples/nonlinear/non-axisymmetric/hsx_nonlinear_vmec_geometry.py
examples/nonlinear/non-axisymmetric/reference_hsx_nonlinear_adiabatic_electrons.toml
examples/nonlinear/non-axisymmetric/runtime_hsx_nonlinear_vmec_geometry.toml
examples/nonlinear/non-axisymmetric/runtime_w7x_nonlinear_imported_geometry.toml
examples/nonlinear/non-axisymmetric/runtime_w7x_nonlinear_vmec_geometry.toml
examples/nonlinear/non-axisymmetric/w7x_nonlinear_imported_geometry.py
examples/nonlinear/non-axisymmetric/w7x_nonlinear_vmec_geometry.py
examples/optimization/QA_nonlinear_ITG_matched_audit.py
examples/optimization/QA_nonlinear_ITG_transport_matrix.py
examples/optimization/QA_optimization_linear_ITG.py
examples/optimization/QA_optimization_nonlinear_ITG.py
examples/optimization/QA_optimization_quasilinear_ITG.py
examples/optimization/QA_parameter_scan.py
examples/parallelization/independent_ky_runtime_batch_scan.py
examples/parallelization/runtime_batch_ky_scan.toml
examples/theory_and_demos/autodiff_inverse_growth.py
examples/theory_and_demos/autodiff_inverse_twomode.py
examples/theory_and_demos/cyclone_geometry.py
examples/theory_and_demos/differentiable_geometry_bridge.py
examples/theory_and_demos/diffrax_linear_demo.py
examples/theory_and_demos/example.py
examples/theory_and_demos/gradB_coupling_hl_1d.py
examples/theory_and_demos/linear_rhs_demo.py
examples/theory_and_demos/quasilinear_implicit_sensitivity.py
examples/theory_and_demos/two_stream_hermite_1d.py
examples/theory_and_demos/reduced_stellarator_itg/_stellarator_itg_plotting.py
examples/theory_and_demos/reduced_stellarator_itg/_stellarator_itg_workflow.py
examples/theory_and_demos/reduced_stellarator_itg/compare_stellarator_itg_optimizations.py
examples/theory_and_demos/reduced_stellarator_itg/stellarator_itg_growth_optimization.py
examples/theory_and_demos/reduced_stellarator_itg/stellarator_itg_nonlinear_heat_flux_optimization.py
examples/theory_and_demos/reduced_stellarator_itg/stellarator_itg_portfolio_gate.py
examples/theory_and_demos/reduced_stellarator_itg/stellarator_itg_quasilinear_flux_optimization.py
examples/utilities/plot_runtime_outputs.py
examples/utilities/runtime_from_toml.py
examples/utilities/strong_scaling_sweep.py
src/spectraxgk/__init__.py
src/spectraxgk/_version.py
src/spectraxgk/benchmarks.py
src/spectraxgk/cli.py
src/spectraxgk/config.py
src/spectraxgk/linear.py
src/spectraxgk/nonlinear.py
src/spectraxgk/quasilinear.py
src/spectraxgk/runtime.py
src/spectraxgk.egg-info/PKG-INFO
src/spectraxgk.egg-info/SOURCES.txt
src/spectraxgk.egg-info/dependency_links.txt
src/spectraxgk.egg-info/entry_points.txt
src/spectraxgk.egg-info/requires.txt
src/spectraxgk.egg-info/top_level.txt
src/spectraxgk/api/__init__.py
src/spectraxgk/artifacts/__init__.py
src/spectraxgk/artifacts/benchmark_plots.py
src/spectraxgk/artifacts/diagnostic_plots.py
src/spectraxgk/artifacts/io.py
src/spectraxgk/artifacts/linear.py
src/spectraxgk/artifacts/nonlinear.py
src/spectraxgk/artifacts/nonlinear_diagnostics.py
src/spectraxgk/artifacts/nonlinear_netcdf.py
src/spectraxgk/artifacts/nonlinear_netcdf_diagnostics.py
src/spectraxgk/artifacts/nonlinear_netcdf_fields.py
src/spectraxgk/artifacts/nonlinear_netcdf_geometry.py
src/spectraxgk/artifacts/plotting.py
src/spectraxgk/artifacts/restart.py
src/spectraxgk/artifacts/runtime_plots.py
src/spectraxgk/artifacts/spectral_layout.py
src/spectraxgk/artifacts/zonal_plots.py
src/spectraxgk/benchmarking/__init__.py
src/spectraxgk/benchmarking/shared.py
src/spectraxgk/core/__init__.py
src/spectraxgk/core/contracts.py
src/spectraxgk/core/extension_points.py
src/spectraxgk/core/grid.py
src/spectraxgk/core/species.py
src/spectraxgk/core/velocity.py
src/spectraxgk/data/advanced_collision_six_moment.json
src/spectraxgk/data/advanced_collision_six_moment.npy
src/spectraxgk/data/cyclone_reference_adiabatic.csv
src/spectraxgk/data/cyclone_reference_kinetic.csv
src/spectraxgk/data/etg_reference.csv
src/spectraxgk/data/kbm_reference.csv
src/spectraxgk/data/tem_reference.csv
src/spectraxgk/diagnostics/__init__.py
src/spectraxgk/diagnostics/analysis.py
src/spectraxgk/diagnostics/channels.py
src/spectraxgk/diagnostics/core.py
src/spectraxgk/diagnostics/energy.py
src/spectraxgk/diagnostics/growth_fit.py
src/spectraxgk/diagnostics/growth_rates.py
src/spectraxgk/diagnostics/growth_windows.py
src/spectraxgk/diagnostics/metadata.py
src/spectraxgk/diagnostics/modes.py
src/spectraxgk/diagnostics/nonlinear_gradient_evidence.py
src/spectraxgk/diagnostics/nonlinear_replicates.py
src/spectraxgk/diagnostics/nonlinear_transport_optimization.py
src/spectraxgk/diagnostics/normalization.py
src/spectraxgk/diagnostics/quasilinear_calibration.py
src/spectraxgk/diagnostics/quasilinear_model_selection.py
src/spectraxgk/diagnostics/quasilinear_transport.py
src/spectraxgk/diagnostics/resolved.py
src/spectraxgk/diagnostics/stellarator_transport_reports.py
src/spectraxgk/diagnostics/transport.py
src/spectraxgk/diagnostics/transport_windows.py
src/spectraxgk/diagnostics/validation_gates.py
src/spectraxgk/diagnostics/weights.py
src/spectraxgk/diagnostics/zonal_validation.py
src/spectraxgk/geometry/__init__.py
src/spectraxgk/geometry/analytic.py
src/spectraxgk/geometry/autodiff_checks.py
src/spectraxgk/geometry/backend_discovery.py
src/spectraxgk/geometry/booz_xform_bridge.py
src/spectraxgk/geometry/core.py
src/spectraxgk/geometry/differentiable.py
src/spectraxgk/geometry/flux_tube.py
src/spectraxgk/geometry/flux_tube_contract.py
src/spectraxgk/geometry/imported_miller.py
src/spectraxgk/geometry/imported_vmec.py
src/spectraxgk/geometry/kernels.py
src/spectraxgk/geometry/miller_eik.py
src/spectraxgk/geometry/numerics.py
src/spectraxgk/geometry/sensitivity.py
src/spectraxgk/geometry/vmec_boozer_constants.py
src/spectraxgk/geometry/vmec_boozer_core.py
src/spectraxgk/geometry/vmec_boozer_derivatives.py
src/spectraxgk/geometry/vmec_boundary_chain.py
src/spectraxgk/geometry/vmec_eik.py
src/spectraxgk/geometry/vmec_field_line_sampling.py
src/spectraxgk/geometry/vmec_flux_tube_reports.py
src/spectraxgk/geometry/vmec_state_controls.py
src/spectraxgk/geometry/vmec_state_sensitivity.py
src/spectraxgk/geometry/vmec_tensor_mapping.py
src/spectraxgk/objectives/__init__.py
src/spectraxgk/objectives/autodiff_validation.py
src/spectraxgk/objectives/core.py
src/spectraxgk/objectives/eigen.py
src/spectraxgk/objectives/geometry.py
src/spectraxgk/objectives/gradient_gates.py
src/spectraxgk/objectives/portfolio_artifacts.py
src/spectraxgk/objectives/portfolio_contracts.py
src/spectraxgk/objectives/portfolio_sensitivity.py
src/spectraxgk/objectives/qa_low_turbulence_artifacts.py
src/spectraxgk/objectives/qa_low_turbulence_model.py
src/spectraxgk/objectives/qa_low_turbulence_optimizer.py
src/spectraxgk/objectives/sampling.py
src/spectraxgk/objectives/solver_gradient_reports.py
src/spectraxgk/objectives/solver_vmec.py
src/spectraxgk/objectives/stellarator.py
src/spectraxgk/objectives/stellarator_contracts.py
src/spectraxgk/objectives/stellarator_reduced.py
src/spectraxgk/objectives/stellarator_tables.py
src/spectraxgk/objectives/vmec_boozer.py
src/spectraxgk/objectives/vmec_boozer_context.py
src/spectraxgk/objectives/vmec_boozer_fd.py
src/spectraxgk/objectives/vmec_boozer_gradients.py
src/spectraxgk/objectives/vmec_boozer_line_search.py
src/spectraxgk/objectives/vmec_candidate_admission.py
src/spectraxgk/objectives/vmec_transport.py
src/spectraxgk/objectives/vmec_transport_admission.py
src/spectraxgk/objectives/vmec_transport_branch.py
src/spectraxgk/objectives/vmec_transport_config.py
src/spectraxgk/objectives/vmec_transport_gradient.py
src/spectraxgk/objectives/vmec_transport_line_search.py
src/spectraxgk/objectives/vmec_transport_tables.py
src/spectraxgk/objectives/zonal.py
src/spectraxgk/objectives/zonal_records.py
src/spectraxgk/operators/__init__.py
src/spectraxgk/operators/linear/__init__.py
src/spectraxgk/operators/linear/cache_arrays.py
src/spectraxgk/operators/linear/cache_builder.py
src/spectraxgk/operators/linear/cache_model.py
src/spectraxgk/operators/linear/collision_tables.py
src/spectraxgk/operators/linear/collisions.py
src/spectraxgk/operators/linear/dissipation.py
src/spectraxgk/operators/linear/linked.py
src/spectraxgk/operators/linear/moments.py
src/spectraxgk/operators/linear/params.py
src/spectraxgk/operators/linear/rhs.py
src/spectraxgk/operators/linear/streaming.py
src/spectraxgk/operators/nonlinear/__init__.py
src/spectraxgk/operators/nonlinear/brackets.py
src/spectraxgk/operators/nonlinear/collisions.py
src/spectraxgk/operators/nonlinear/device_z.py
src/spectraxgk/operators/nonlinear/device_z_reports.py
src/spectraxgk/operators/nonlinear/diagnostic_state.py
src/spectraxgk/operators/nonlinear/diagnostics.py
src/spectraxgk/operators/nonlinear/domain_decomposition.py
src/spectraxgk/operators/nonlinear/parallel.py
src/spectraxgk/operators/nonlinear/parallel_contracts_domain.py
src/spectraxgk/operators/nonlinear/parallel_contracts_spectral.py
src/spectraxgk/operators/nonlinear/parallel_contracts_strategy.py
src/spectraxgk/operators/nonlinear/policies.py
src/spectraxgk/operators/nonlinear/projection.py
src/spectraxgk/operators/nonlinear/rhs.py
src/spectraxgk/operators/nonlinear/spectral_core.py
src/spectraxgk/operators/nonlinear/spectral_identity_integrator.py
src/spectraxgk/operators/nonlinear/spectral_identity_reports.py
src/spectraxgk/operators/nonlinear/spectral_identity_rhs.py
src/spectraxgk/operators/nonlinear/spectral_layout.py
src/spectraxgk/parallel/__init__.py
src/spectraxgk/parallel/batch.py
src/spectraxgk/parallel/decomposition.py
src/spectraxgk/parallel/identity.py
src/spectraxgk/parallel/independent.py
src/spectraxgk/parallel/integrators.py
src/spectraxgk/parallel/state.py
src/spectraxgk/parallel/velocity.py
src/spectraxgk/parallel/velocity_drive.py
src/spectraxgk/parallel/velocity_hermite.py
src/spectraxgk/parallel/velocity_plan.py
src/spectraxgk/parallel/velocity_streaming.py
src/spectraxgk/solvers/__init__.py
src/spectraxgk/solvers/linear/__init__.py
src/spectraxgk/solvers/linear/eigen_operator.py
src/spectraxgk/solvers/linear/implicit.py
src/spectraxgk/solvers/linear/integrator_diagnostics.py
src/spectraxgk/solvers/linear/integrators.py
src/spectraxgk/solvers/linear/krylov.py
src/spectraxgk/solvers/linear/krylov_algorithms.py
src/spectraxgk/solvers/linear/parallel.py
src/spectraxgk/solvers/linear/parallel_common.py
src/spectraxgk/solvers/linear/parallel_electrostatic.py
src/spectraxgk/solvers/linear/parallel_streaming.py
src/spectraxgk/solvers/nonlinear/__init__.py
src/spectraxgk/solvers/nonlinear/diagnostic_integration.py
src/spectraxgk/solvers/nonlinear/diagnostics.py
src/spectraxgk/solvers/nonlinear/explicit.py
src/spectraxgk/solvers/nonlinear/imex.py
src/spectraxgk/solvers/nonlinear/imex_diagnostics.py
src/spectraxgk/solvers/nonlinear/state_integration.py
src/spectraxgk/solvers/time/__init__.py
src/spectraxgk/solvers/time/diffrax_core.py
src/spectraxgk/solvers/time/diffrax_linear.py
src/spectraxgk/solvers/time/diffrax_nonlinear.py
src/spectraxgk/solvers/time/diffrax_streaming.py
src/spectraxgk/solvers/time/explicit.py
src/spectraxgk/solvers/time/explicit_cfl.py
src/spectraxgk/solvers/time/explicit_diagnostics.py
src/spectraxgk/solvers/time/explicit_steps.py
src/spectraxgk/solvers/time/runners.py
src/spectraxgk/terms/__init__.py
src/spectraxgk/terms/assembly.py
src/spectraxgk/terms/config.py
src/spectraxgk/terms/fields.py
src/spectraxgk/terms/linear_terms.py
src/spectraxgk/terms/nonlinear.py
src/spectraxgk/utils/__init__.py
src/spectraxgk/utils/callbacks.py
src/spectraxgk/workflows/__init__.py
src/spectraxgk/workflows/cases.py
src/spectraxgk/workflows/demo.py
src/spectraxgk/workflows/linear.py
src/spectraxgk/workflows/nonlinear.py
src/spectraxgk/workflows/runtime/__init__.py
src/spectraxgk/workflows/runtime/artifacts.py
src/spectraxgk/workflows/runtime/chunks.py
src/spectraxgk/workflows/runtime/commands.py
src/spectraxgk/workflows/runtime/config.py
src/spectraxgk/workflows/runtime/diagnostic_arrays.py
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src/spectraxgk/workflows/runtime/execution.py
src/spectraxgk/workflows/runtime/initial_conditions.py
src/spectraxgk/workflows/runtime/initial_phi.py
src/spectraxgk/workflows/runtime/orchestration_artifacts.py
src/spectraxgk/workflows/runtime/orchestration_scan.py
src/spectraxgk/workflows/runtime/policies.py
src/spectraxgk/workflows/runtime/results.py
src/spectraxgk/workflows/runtime/startup.py
src/spectraxgk/workflows/runtime/toml.py