# Manuscript Figures NTX now includes a manuscript-ready figure bundle built directly from repository examples. ## Curated Figure Set ### Main Text 1. `validation_summary.{png,pdf,json}` 2. `closure_validation_report.{png,pdf,json,txt}` 3. `bootstrap_current_reference_audit_w7x.{png,pdf}` 4. `derivative_path_benchmark.{png,pdf,json}` 5. `bootstrap_current_optimization.{png,pdf,json}` 6. `performance_scaling_production.{png,pdf,json}` 7. `primitive_profile_transport.{png,pdf}` ### Supplement 1. `autodiff_inverse_problem.{png,pdf}` 2. `autodiff_neopax_profiles.{png,pdf}` 3. `autodiff_profile_uncertainty.{png,pdf,json}` 4. `geometry_control_derivative_benchmark.{png,pdf,json}` 5. `file_backed_geometry_control_derivative_benchmark.{png,pdf,json}` 6. `boundary_forward_mode_current_derivative_benchmark.{png,pdf,json}` 7. `implicit_equilibrium_forward_mode_derivative_benchmark.{png,pdf,json}` 8. `explicit_relaxed_boundary_current_derivative_benchmark.{png,pdf,json}` 9. `geometry_family_breadth_summary.{png,pdf,json}` 10. `geometry_family_transport_convergence.{png,pdf,json}` 11. `boozmn_finite_beta_wout_roundtrip_audit.{png,pdf,json}` 12. `owned_geometry_neopax_dataset.{png,pdf,json}` 13. `owned_finite_beta_sfincs_jax_inputs.{png,pdf,json}` 14. `owned_finite_beta_sfincs_jax_resolution_audit.{png,pdf,json}` 15. `owned_finite_beta_sfincs_jax_production_ladder_audit.{png,pdf,json}` 16. `owned_finite_beta_sfincs_jax_profile_current_audit.{png,pdf,json}` 17. `owned_finite_beta_bootstrap_comparison.{png,pdf,json}` 18. `owned_finite_beta_closure_localization.{png,pdf,json}` 19. `owned_finite_beta_profile_current_observable_audit.{png,pdf,json}` 20. `owned_finite_beta_current_conditioning_audit.{png,pdf,json}` 21. `owned_finite_beta_closure_quadrature_audit.{png,pdf,json}` 22. `owned_finite_beta_source_channel_audit.{png,pdf,json}` 23. `owned_finite_beta_source_response_profile_audit.{png,pdf,json}` 24. `owned_finite_beta_closure_target_audit.{png,pdf,json}` 25. `owned_finite_beta_radial_interpolation_audit.{png,pdf,json}` 26. `owned_finite_beta_field_radius_matched_closure_quadrature_audit.{png,pdf,json}` 27. `owned_finite_beta_field_radius_matched_source_channel_audit.{png,pdf,json}` 28. `bootstrap_current_from_vmec_or_boozmn.{png,pdf,json}` 29. `bootstrap_current_robust_optimization.{png,pdf,json}` 30. `performance_scaling_smoke.{png,pdf,json}` 31. `performance_scaling_heavy.{png,pdf,json}` 32. `performance_strong_scaling_production.{png,pdf,json}` 33. `prepared_geometry_reuse_profile.{png,pdf,json}` 34. `ambipolar_profile.{png,pdf}` 35. `ambipolar_profile_family.{png,pdf}` 36. `profile_force_reconstruction_audit.{png,pdf,json}` 37. `profile_control_optimization.{png,pdf}` 38. `profile_basis_optimization.{png,pdf,json}` 39. `profile_transport_loop.{png,pdf}` ## Full Figure Inventory 1. `validation_summary.{png,pdf,json}` - transport-curve behavior on the sample DKES-style and VMEC surfaces - Onsager closure - Legendre convergence - machine-readable benchmark metrics for the literature-anchored methods lane 2. `closure_validation_report.{png,pdf,json,txt}` - fixed-field precise-QS Redl gate and scoped NTX+NEOPAX total-current closure stress gate in the same manuscript-facing validation report 3. `autodiff_inverse_problem.{png,pdf}` - inverse recovery of a surface harmonic from synthetic transport data 4. `autodiff_neopax_profiles.{png,pdf}` - autodiff-based profile inversion on NEOPAX-style arrays 5. `autodiff_profile_uncertainty.{png,pdf,json}` - three-term radial-basis uncertainty propagation on the same differentiable profile fit, including Monte Carlo, linearized covariance, and Fisher/Hessian-vector consistency diagnostics 6. `geometry_control_derivative_benchmark.{png,pdf,json}` - three-harmonic geometry-control derivative audit against centered finite differences; tracked as an autodiff stress benchmark 7. `file_backed_geometry_control_derivative_benchmark.{png,pdf,json}` - file-backed Boozer and VMEC geometry-control derivative audit against centered finite differences; stronger than the owned-surface stress test but still below a reusable geometry-family claim 8. `boundary_forward_mode_current_derivative_benchmark.{png,pdf,json}` - low-dimensional boundary controls propagated through boundary-projected `vmec_jax -> booz_xform_jax -> NTX` and an `NTX+NEOPAX` integrated-current objective under forward mode 9. `implicit_equilibrium_forward_mode_derivative_benchmark.{png,pdf,json}` - low-dimensional boundary controls propagated through the implicit fixed-boundary `vmec_jax` residual solve, `booz_xform_jax`, and an NTX monoenergetic transport response under forward mode, with the reverse-mode Boozer failure recorded in the JSON artifact 10. `explicit_relaxed_boundary_current_derivative_benchmark.{png,pdf,json}` - low-dimensional boundary controls propagated through an explicitly relaxed fixed-boundary `vmec_jax -> booz_xform_jax -> NTX` path and an `NTX+NEOPAX` integrated-current objective, with ordinary-versus-explicit primal-volume agreement recorded on committed QA and QH family cases 11. `geometry_family_breadth_summary.{png,pdf,json}` - artifact-backed breadth summary across analytic, file-backed, boundary-projected, explicit-relaxed, and implicit-equilibrium derivative paths; this is a stress summary and not a broad geometry-family validation claim 12. `geometry_family_transport_convergence.{png,pdf,json}` - public VMEC example-family `D11/D31/D33` convergence stress scan across tokamak, precise-QS, QI-style, W7-X, and stellarator-family inputs when the local checkouts are available; this is not an independent-code parity claim 13. `boozmn_finite_beta_wout_roundtrip_audit.{png,pdf,json}` - optimized finite-beta finalized-wout magnetic-channel Boozer transfer audit; validates same-coordinate file-backed `D11/D31/D13/D33` round-trip behavior while leaving fully differentiable finite-beta state sensitivities as a non-shipping lane for unsupported current-profile representations 14. `owned_geometry_neopax_dataset.{png,pdf,json}` - finite-beta owned `input/wout -> NTX -> NEOPAX-style` provenance figure, with the physical VMEC edge-flux scale passed into the Boozer-coordinate path, direct VMEC-harmonic interpolation-path stress diagnostics, and explicit geometry-backend blockers in the JSON sidecar 15. `owned_finite_beta_sfincs_jax_inputs.{png,pdf,json}` - six-point same-grid SFINCS-JAX finite-beta coefficient ladder with completed HDF5 ingestion, the SFINCS-reported `nuPrime -> nu_n` bridge, and a coefficient-level NTX `L13/L31/L33` comparison before profile-current parity promotion 16. `owned_finite_beta_sfincs_jax_resolution_audit.{png,pdf,json}` - production stress-radius rerun of the same finite-beta coefficient point at `35 x 43 x 48`, plus a tighter VMEC harmonic-cutoff probe; the coefficient floor remains near `2.05e-2`, about `15.8x` above the cancellation-conditioned current target 17. `owned_finite_beta_sfincs_jax_production_ladder_audit.{png,pdf,json}` - production six-point finite-beta QA same-grid SFINCS-JAX/NTX ladder across radius and collisionality; all coefficient differences stay below `2.07e-2`, with the current-conditioned precision gap localized to the most cancellation-sensitive radius 18. `owned_finite_beta_sfincs_jax_profile_current_audit.{png,pdf,json}` - bounded RHSMode=1 profile-current diagnostic on the same finite-beta VMEC/profile contract; retained as a convergence and normalization diagnostic, not as a parity claim, because the direct profile-current amplitudes need their own pitch/velocity/radial ladder 19. `owned_finite_beta_sfincs_jax_profile_current_resolution_audit.{png,pdf,json}` - same-contract RHSMode=1 pitch Legendre truncation audit; the sparse-PC solver residual lane is closed, and the high-`Nxi` even/odd terminal-mode gap of about `1.32e-1` is accepted under the `1.5e-1` reduced-closure stress tolerance 20. `owned_finite_beta_bootstrap_comparison.{png,pdf,json}` - same finite-beta QA pressure/current `wout`, Boozer transform, analytic profiles, normalized-radius `B00(rho)` Boozer-field convention, production radial/collisionality ladder, physical `nu/v` support, `D33_spitzer` branch, and current normalization used for Redl and `NTX+NEOPAX`; retained as a reduced-closure stress audit because the corrected-field current residual remains above the `1e-1` target over the profile 20. `owned_finite_beta_closure_localization.{png,pdf,json}` - sidecar figure and JSON that compare the same-grid coefficient ladder with the finite-beta profile-current stress artifact; the coefficient ladder stays below the coefficient gate while the current-profile residual remains above the `1e-1` current gate 21. `owned_finite_beta_profile_current_observable_audit.{png,pdf,json}` - stress-radius decomposition of the profile-current observable into no-momentum current, applied momentum correction, correction needed to match Redl, species-current cancellation scale, local profile/geometry drivers, and Pmax trend 22. `owned_finite_beta_current_conditioning_audit.{png,pdf,json}` - cancellation-conditioned coefficient-precision requirement for the finite-beta net-current observable; this explains why the smoke coefficient ladder is not yet sufficient for a `1e-1` bootstrap-current parity claim 23. `owned_finite_beta_closure_quadrature_audit.{png,pdf,json}` - Sonine-order versus velocity-quadrature stress audit; the accepted quadrature-stable pass count is zero and the best stress value remains above `1e-1`, so no apparent finite-beta current-gate pass is promoted 24. `owned_finite_beta_source_channel_audit.{png,pdf,json}` - frozen stress-radius source-channel decomposition of the same momentum-restoring system; one-channel solves reconstruct the full current to roundoff and localize the high-order response to mixed density/electric and temperature-gradient drives under the current profile contract; Redl density and temperature target terms are stored on the same observable rather than converted into a fitted runtime correction 25. `owned_finite_beta_source_response_profile_audit.{png,pdf,json}` - profile-wide source-response map at `X=18, P=18`; the temperature-channel response multiplier spans `0.765` to `1.349` with median `1.040`, preserves source sign agreement, and keeps the maximum current stress at the inner radius while storing correlations with Redl collisionality and geometry factors 26. `owned_finite_beta_closure_target_audit.{png,pdf,json}` - driver-identification artifact for the profile source-response target; the strongest single local driver is the Redl geometry factor `epsilon` (`|r|=0.970`), the best leave-one-out diagnostic model is epsilon-only with RMSE `5.58e-2`; the JSON also cross-links the field-radius-matched source/quadrature sidecars, confirming the same stress radius, exact source reconstruction, and no quadrature-stable current-gate pass, with no runtime correction applied 27. `owned_finite_beta_radial_interpolation_audit.{png,pdf,json}` - interpolation-contract diagnostic; rebuilding the finite-beta database on the exact field radii changes individual radii but leaves the full-profile maximum near `2.3e-1`, so no runtime interpolation policy is promoted 28. `owned_finite_beta_field_radius_matched_closure_quadrature_audit.{png,pdf,json}` - field-radius-matched Sonine/quadrature rerun; the best apparent stress value remains above `1e-1`, the quadrature-stable pass count is zero, and `X=18, P=18` gives about `1.44e-1`, so the remaining current gap is not closed by interpolation removal or Pmax alone 29. `owned_finite_beta_field_radius_matched_source_channel_audit.{png,pdf,json}` - field-radius-matched source-channel rerun; one-channel solves reconstruct the corrected current to roundoff, and the quadrature-stable `X=18`, `P=18` response remains a reduced-closure stress diagnostic 30. `derivative_path_benchmark.{png,pdf}` - prepared-derivative timing and agreement against direct reverse-mode 31. `bootstrap_current_optimization.{png,pdf}` - science/application figure for differentiable bootstrap-current optimization 32. `bootstrap_current_robust_optimization.{png,pdf,json}` - deterministic versus robust optimization under a prescribed control uncertainty; tracked as an open robust-design lane 33. `bootstrap_current_from_vmec_or_boozmn.{png,pdf}` - NTX-only reduced bootstrap-current response profile from VMEC/Boozer input 34. `bootstrap_current_reference_audit_w7x.{png,pdf}` - W7-X imported-workflow bootstrap-current convergence audit 35. `performance_scaling_smoke.{png,pdf,json}` - CPU/GPU scaling on the repository smoke grid 36. `performance_scaling_heavy.{png,pdf,json}` - heavier-grid scaling where throughput effects are visible 37. `performance_scaling_production.{png,pdf,json}` - production-grid CPU/GPU scaling with serial, device-parallel, multiprocess, memory, and coefficient-agreement metadata 38. `performance_strong_scaling_production.{png,pdf,json}` - fixed-workload CPU/GPU strong scaling with worker/device sweeps, memory, and coefficient-agreement metadata 39. `prepared_geometry_reuse_profile.{png,pdf,json}` - fixed-geometry repeated-solve profile showing the direct, prepared, and compiled prepared solver paths with coefficient agreement recorded in the JSON artifact 40. `ambipolar_profile.{png,pdf}` - profile-grade ambipolar electric-field solve and reduced bootstrap-current response 41. `ambipolar_profile_family.{png,pdf}` - control-parameter family of ambipolar closures and scalar bootstrap-current objective 42. `profile_force_reconstruction_audit.{png,pdf,json}` - archived precise-QS QA/QH primitive-to-force reconstruction audit 43. `profile_control_optimization.{png,pdf}` - differentiable optimization of a scalar profile control on top of the ambipolar closure 44. `profile_basis_optimization.{png,pdf,json}` - low-dimensional radial-basis optimization of the same profile closure 45. `profile_transport_loop.{png,pdf}` - explicit self-consistent transport-relaxation iteration on the same profile closure 46. `primitive_profile_transport.{png,pdf}` - primitive density/temperature transport iteration mapped back to ambipolar-field and bootstrap-current evolution Together these figures cover: - formulation and numerical behavior - validation and convergence - fixed-field Redl validation and reduced-closure total-current stress reporting - differentiable inverse and profile problems - differentiable uncertainty propagation on the same profile map - multi-parameter geometry-control derivative auditing - file-backed Boozer and VMEC geometry-control derivative auditing - boundary-to-output forward-mode auditing on projected `vmec_jax` geometry - implicit-equilibrium derivative diagnostics that isolate where parity is lost: equilibrium volume matches, but Boozer geometry and NTX transport are closed as non-shipping diagnostics - equilibrium-relaxed boundary-to-current forward-mode auditing on committed QA/QH family cases - artifact-backed geometry-breadth status across the committed derivative families, with unresolved implicit objectives kept out of promoted claims - same-grid finite-beta Redl and `NTX+NEOPAX` bootstrap-current stress diagnostics with the physical Boozer flux scale, normalized-radius `B00` evaluation, production radial/collisionality ladder, adaptive `nu/v` support, Sonine-order convergence sidecar, and accepted RHSMode=1 pitch stress gap recorded as a closed reduced-closure stress benchmark - finite-beta source-response and closure-target diagnostics that map the dominant effective-temperature channel over the full profile, rank physical geometry/trapped-particle/collisionality drivers, and keep fitted diagnostic models out of the runtime before any reduced closure change is promoted - production same-grid finite-beta SFINCS-JAX coefficient ladders that close radius/collisionality resolution as the leading explanation for that gap - a deterministic robust-design stress benchmark for differentiable current optimization - derivative cost for prepared optimization workflows - a science-facing bootstrap-current optimization workflow - a pure NTX radial-profile figure - a profile-grade ambipolar and reduced bootstrap-current response workflow - a control-parameter family view of the same profile-grade closure - a literature-anchored primitive-to-force reconstruction audit on the precise-QS profile family - a direct optimization view of the profile-grade closure - a low-dimensional multi-parameter version of that optimization - a self-consistent transport-relaxation view of the same closure - a primitive-profile transport view with positive density and temperature updates - a W7-X imported-workflow convergence figure - practical performance guidance - prepared-geometry and compiled-solver reuse guidance for optimization workloads ## Manuscript Tables And Reproducibility ```bash python scripts/build_manuscript_artifacts.py ``` This writes: ```text docs/_static/manuscript_artifacts.json docs/_static/manuscript_tables.md docs/_static/manuscript_claims.md ``` These artifacts collect the current NTX commit, software environment, the validated W7-X convergence numbers, derivative benchmark summaries, production-grid CPU/GPU performance and strong-scaling tables, geometry-control derivative stress metrics, finite-beta bootstrap-current stress and closure-localization metrics, bootstrap-current optimization summaries, and the exact commands needed to regenerate the figures and validation subset used in the manuscript. ## One-Command Figure Bundle ```bash python examples/make_publication_figures.py ``` This writes the full figure set into `docs/_static/` and also creates: ```text docs/_static/publication_figure_manifest.json ``` Generate the frozen main-text set: ```bash python examples/make_publication_figures.py --figures main_text ``` Generate the supplement set: ```bash python examples/make_publication_figures.py --figures supplement ``` ## Science Figure ```bash python examples/bootstrap_current_optimization.py ``` The science/application figure is written to: ```text docs/_static/bootstrap_current_optimization.png docs/_static/bootstrap_current_optimization.pdf docs/_static/bootstrap_current_optimization.json ``` It uses: - a VMEC-derived radial surface family - a dominant non-axisymmetric harmonic as the control parameter - a weighted bootstrap-current response based on the current-response coefficients - JAX autodiff to optimize that control directly The committed JSON artifact is also a monitored benchmark-matrix and physics-gate entry: the optimized weighted-current response must remain at least as large as the baseline before the manuscript cites the gain. Broader stellarator-design claims still require reusable geometry-family controls and their derivative audits. This is the recommended figure for a paper focused on differentiable bootstrap current analysis and optimization with NTX. ## Prepared-Derivative Efficiency Figure ```bash python examples/derivative_path_benchmark.py ``` This writes: ```text docs/_static/derivative_path_benchmark.png docs/_static/derivative_path_benchmark.pdf docs/_static/derivative_path_benchmark.json ``` Use this figure when the paper needs an explicit statement of how NTX moves from plain reverse-mode to a prepared differentiable workflow that is better suited to repeated optimization scans. ## NTX Reduced Bootstrap-Current Response Figure ```bash python examples/bootstrap_current_from_vmec_or_boozmn.py ``` This writes: ```text docs/_static/bootstrap_current_from_vmec_or_boozmn.png docs/_static/bootstrap_current_from_vmec_or_boozmn.pdf docs/_static/bootstrap_current_from_vmec_or_boozmn.json ``` It is the recommended figure when the paper needs a compact NTX-only radial profile panel without bringing in the external database workflow. The panel stays close to directly interpretable quantities: geometry, profile inputs, parallel-flow drive, and the resulting interior reduced bootstrap-current response built from analytic profile gradients. ![NTX reduced bootstrap-current response profile](_static/bootstrap_current_from_vmec_or_boozmn.png) ## Ambipolar Profile Figure ```bash python examples/ambipolar_profile.py ``` This writes: ```text docs/_static/ambipolar_profile.png docs/_static/ambipolar_profile.pdf ``` Use this figure when the paper needs a profile-grade closure panel built entirely from NTX scan data, including the ambipolar residual landscape over the scanned `E_r` axis and the resulting reduced bootstrap-current response. ![Ambipolar profile](_static/ambipolar_profile.png) ## Ambipolar Profile Family Figure ```bash python examples/ambipolar_profile_family.py ``` This writes: ```text docs/_static/ambipolar_profile_family.png docs/_static/ambipolar_profile_family.pdf ``` Use this figure when the paper needs an optimization-facing profile figure that shows how a scalar control changes the residual landscape and the reduced bootstrap-current response profiles, while also exposing a one-dimensional objective landscape. ![Ambipolar profile family](_static/ambipolar_profile_family.png) ## Profile-Control Optimization Figure ```bash python examples/profile_control_optimization.py ``` This writes: ```text docs/_static/profile_control_optimization.png docs/_static/profile_control_optimization.pdf ``` Use this figure when the paper needs a direct optimization panel on top of the profile closure itself, rather than the separate geometry-control science figure. ![Profile control optimization](_static/profile_control_optimization.png) ## Profile-Basis Optimization Figure ```bash python examples/profile_basis_optimization.py ``` This writes: ```text docs/_static/profile_basis_optimization.png docs/_static/profile_basis_optimization.pdf docs/_static/profile_basis_optimization.json ``` Use this figure when the paper needs a profile-control optimization panel beyond one scalar amplitude while still keeping the optimization space compact and interpretable. ![Profile basis optimization](_static/profile_basis_optimization.png) ## Profile Transport Loop Figure ```bash python examples/profile_transport_loop.py ``` This writes: ```text docs/_static/profile_transport_loop.png docs/_static/profile_transport_loop.pdf ``` Use this figure when the paper needs a self-consistent profile-transport panel instead of a pure control-optimization panel. It shows how the ambipolar residual, reduced bootstrap-current response, and thermodynamic-force profiles evolve under an accepted-step transport-relaxation iteration. ![Profile transport loop](_static/profile_transport_loop.png) ## Primitive Profile Transport Figure ```bash python examples/primitive_profile_transport.py ``` This writes: ```text docs/_static/primitive_profile_transport.png docs/_static/primitive_profile_transport.pdf ``` Use this figure when the paper needs to move beyond direct `A1/A3` channel updates and show a primitive profile workflow in which density and temperature remain positive, respond to explicit source-target closure terms, and feed back into the ambipolar closure through reconstructed thermodynamic forces. The panel is now framed around initial-versus-final closure profiles and the derived monoenergetic forces rather than a noisy iteration trace. ![Primitive profile transport](_static/primitive_profile_transport.png) ## W7-X Bootstrap-Current Convergence Figure ```bash python examples/bootstrap_current_reference_audit_w7x.py ``` This writes: ```text docs/_static/bootstrap_current_reference_audit_w7x.png docs/_static/bootstrap_current_reference_audit_w7x.pdf docs/_static/bootstrap_current_reference_audit_w7x.json ``` Use this figure when the paper needs an explicit W7-X imported-workflow bootstrap-current convergence panel alongside the NTX-only methods figures. ![W7-X bootstrap-current convergence](_static/bootstrap_current_reference_audit_w7x.png)