Output schema¶

Every active MHX run writes a JSON manifest plus schema-versioned data files. Artifacts also record api_version = "v1" so loaders can enforce the public API contract selected by MHX_API_VERSION.

Run directory¶

mhx run examples/linear_tearing.toml --outdir outputs/smoke writes:

config_effective.json: JSON serialization of the effective config.
diagnostics.json: scalar JSON diagnostics.
trajectory.npz: compressed trajectory arrays using schema mhx.reduced_mhd.trajectory.v1.
manifest.json: file list, SHA-256 hashes, and claim metadata.

Manifest claim levels¶

Every v1 manifest.json contains:

Key	Meaning
`schema`	Manifest schema, currently `mhx.manifest.v1`.
`api_version`	Public API version selected by `MHX_API_VERSION`, currently `v1`.
`created_utc`	ISO-8601 creation timestamp in UTC.
`mhx_version`	Package version that wrote the manifest.
`claim_level`	One of `unspecified`, `smoke`, `validation`, `production_template`, or `production`.
`claim_scope`	Human-readable boundary explaining what the artifact can and cannot support.
`config`	JSON-serializable run or benchmark configuration.
`outputs`	Mapping from stable output names to run-directory-relative file paths.
`hashes`	SHA-256 hashes for output files that existed when the manifest was written.

mhx artifact-manifest also collects nested manifest.json claim levels in a top-level claim_levels mapping. This lets CI and reviewers check whether a figure directory mixes smoke, validation, production-template, or production artifacts.

`trajectory.npz` keys¶

The reduced-MHD v1 trajectory file contains:

Key	Meaning
`schema`	Schema string, currently `mhx.reduced_mhd.trajectory.v1`.
`api_version`	Public API version string, currently `v1`.
`mhx_version`	Package version that wrote the file.
`time`	Saved times.
`psi`	Saved magnetic flux arrays with shape `(n_save, nx, ny)`.
`omega`	Saved vorticity arrays with shape `(n_save, nx, ny)`.
`config_json`	JSON-encoded effective run config.
`diagnostics_json`	JSON-encoded scalar diagnostics.

Important scalar diagnostics include equilibrium, equilibrium_parameters, physics_plugin_modules, physics_plugin_entry_point_groups, physics_terms, diagnostic_plugin_modules, diagnostic_plugin_entry_point_groups, diagnostic_quantities, diagnostic_mode, fit_time_window, fit_sample_count, gamma_fit, and final_magnetic_divergence_linf. These fields are saved so model assembly, extension modules, entry-point plugin discovery, growth-rate plots, divergence checks, and comparisons can be audited.

`diagnostics.json` keys¶

The default reduced-MHD run uses the diagnostic registry entries energy, mode_growth, and divergence_error. The default scalar output includes:

Key	Meaning
`diagnostic_quantities`	Diagnostic registry names evaluated for this run.
`diagnostic_plugin_modules`	Importable modules used to register custom diagnostics.
`diagnostic_plugin_entry_point_groups`	Installed entry-point groups used to register diagnostics.
`physics_plugin_modules`	Importable modules used to register custom RHS physics terms.
`physics_plugin_entry_point_groups`	Installed entry-point groups used to register RHS physics terms.
`initial_total_energy`	Initial reduced-MHD total energy.
`final_total_energy`	Final reduced-MHD total energy.
`final_magnetic_energy`	Final mean magnetic perturbation energy.
`final_kinetic_energy`	Final mean kinetic energy.
`diagnostic_mode`	Fourier mode used by the mode-growth diagnostic.
`fit_time_window`	Inclusive time window used for the exponential fit.
`fit_sample_count`	Number of saved samples used in the fit.
`initial_mode_amplitude`	Initial normalized magnetic-flux Fourier amplitude.
`final_mode_amplitude`	Final normalized magnetic-flux Fourier amplitude.
`gamma_fit`	Least-squares exponential growth/decay rate.
`final_magnetic_divergence_linf`	Final spectral \(\|\nabla\cdot B_\perp\|_\infty\) check.

Figures¶

Figures are regenerated from saved data:

mhx figures outputs/smoke --gif

Expected files:

outputs/smoke/figures/energy_history.png
outputs/smoke/figures/flux_final.png
outputs/smoke/figures/mode_amplitude.png
outputs/smoke/figures/flux_movie.gif

Reports¶

Run summaries are regenerated from saved outputs:

mhx report outputs/smoke

Expected files:

outputs/smoke/report.json
outputs/smoke/report.md

report.json also includes additional_scalar_diagnostics, a dictionary of plugin-provided scalar metrics not part of the core reduced-MHD diagnostic schema. report.md renders the same values in an Additional scalar diagnostics table. Reports also include diagnostic_metadata when MHX can reconstruct the selected diagnostic registry from config_effective.json; any import or registry reconstruction failures are recorded in warnings. Diagnostics may also provide optional figure hooks. mhx figures writes those figures under figures/diagnostics/. mhx report dispatches the same hooks and records a diagnostic_figures list in report.json, with each entry containing a stable figure key and run-relative path.

Artifact manifests¶

For reproducible figure/report diffs, write a recursive checksum manifest:

mhx artifact-manifest outputs/smoke

This writes outputs/smoke/artifact_manifest.json with schema mhx.artifacts.v1, API version, file paths, byte sizes, and SHA-256 hashes.

Paper-pipeline bundle¶

mhx validate paper-pipeline --outdir outputs/paper_pipeline writes the reviewer-facing validation bundle:

File	Schema	Meaning
`paper_pipeline.json`	`mhx.paper_pipeline.v1`	Included validation cases, readiness status, claim boundary, and API metadata.
`validation.json`	`mhx.paper_pipeline.gates.v1`	Gate status for suite pass, readiness generation, and release-ready requirement.
`paper_pipeline.md`	Markdown	Human-readable summary of gates and included cases.
`validation_suite/validation_suite.json`	`mhx.validation.suite.v1`	Full or declared-subset validation-suite summary.
`readiness/readiness.json`	`mhx.readiness_report.v1`	Public-release and publication-claim readiness status.
`artifact_manifest.json`	`mhx.artifacts.v1`	Recursive SHA-256 hashes for the whole bundle.
`manifest.json`	`mhx.manifest.v1`	Top-level claim metadata with `claim_level = "validation"`.

Subsets requested with --cases are command-validation artifacts, not full release evidence unless the readiness gate is also required and passing.

Validation-suite outputs¶

mhx validate all --outdir outputs/validation_suite executes the active FAST validation cases, including double-Harris, turbulence, seed-QI, fitted latent ODE, and restartable Rutherford execution chunks. Important closed-lane schemas include:

Orszag–Tang vortex¶

mhx benchmark orszag-tang --outdir outputs/benchmarks/orszag_tang_vortex --movies writes:

File	Schema / contents
`orszag_tang_vortex.npz`	`mhx.validation.orszag_tang_vortex.v1`; keys `time`, `psi`, `omega`, `current_density`, `magnetic_energy`, `kinetic_energy`, `total_energy`, `current_linf`, `vorticity_linf`, `current_high_k_fraction`, `vorticity_high_k_fraction`, and scalar gate summaries.
`diagnostics.json`	Scalar run controls, energy/drop diagnostics, high-\(k\) growth, and divergence summary.
`validation.json`	`mhx.validation.orszag_tang_vortex.gates.v1`; finite-array, monotone-energy, dissipation, high-\(k\), and divergence gates.
`figures/orszag_tang_summary.png`	Energy, high-\(k\), final-current, and final-vorticity summary.
`figures/orszag_tang_*.gif`	Optional flux, current, and vorticity movies when `--movies` is set.

Decaying turbulence and forced turbulent reconnection¶

mhx benchmark decaying-turbulence --outdir outputs/benchmarks/decaying_mhd_turbulence --movies and mhx benchmark forced-turbulent-reconnection --outdir outputs/benchmarks/forced_turbulent_reconnection --movies write:

File	Schema / contents
`decaying_mhd_turbulence.npz`	`mhx.validation.decaying_mhd_turbulence.v1`; keys `time`, `psi`, `omega`, `current_density`, `magnetic_energy`, `kinetic_energy`, `total_energy`, `current_linf`, `vorticity_linf`, `current_high_k_fraction`, and `magnetic_divergence_linf`.
`forced_turbulent_reconnection.npz`	`mhx.validation.forced_turbulent_reconnection.v1`; same core keys plus `reconnection_proxy` and `reconnection_rate_proxy`.
`diagnostics.json`	Scalar controls, energy/current diagnostics, high-\(k\) summaries, and reconnection-proxy statistics.
`validation.json`	Finite-array, energy, current, high-\(k\), and reconnection-proxy gates.
`figures/*_summary.png`	Energy, current/reconnection, final current, and final flux summary.
`figures/_flux_contours.gif`, `figures/_current.gif`	Optional fixed-scale movies when `--movies` is set.

mhx benchmark forced-turbulent-reconnection-readiness-check <run-dir> writes <run-dir>/readiness/ by default:

File	Schema / contents
`promotion_readiness.json`	`mhx.validation.forced_turbulent_reconnection.readiness.v1`; validation-only claim boundary, terminal time, sample count, reconnecting-flux/rate proxy changes, energy growth, thresholds, and pass/fail checks.
`validation.json`	`mhx.validation.forced_turbulent_reconnection.readiness.gates.v1`; finite-history, schema, duration, reconnection-proxy, energy, summary, and optional movie checks.
`figures/promotion_matrix.png`	Reviewer-readable pass/fail readiness matrix.
`artifact_manifest.json`	Recursive hashes for the readiness bundle.
`manifest.json`	`claim_level = validation`; this command deliberately cannot promote the artifact to 3-D LV99 or production turbulent-reconnection evidence.

The validation suite records this readiness check as its own required public-release case (forced_turbulent_reconnection_readiness) so release readiness cannot pass on the trajectory artifact alone.

Rutherford production execution¶

mhx campaign rutherford-execute <run-dir> writes:

File	Schema / contents
`production_history.npz`	`mhx.campaign.rutherford_history.v1`; keys `step`, `time`, `reconnected_flux`, `rutherford_island_width`, `reconnection_rate_proxy`, `magnetic_energy`, `kinetic_energy`, `total_energy`, `dissipation_budget_residual`, `magnetic_divergence_linf`, `current_density_linf`, `current_sheet_length`, `current_sheet_thickness`, `current_sheet_aspect_ratio`, `x_point_count`, and `o_point_count`.
`checkpoints/state_step_*.npz`	`mhx.campaign.rutherford_state.v1`; keys `step`, `time`, `psi`, `omega`.
`checkpoints/checkpoint_index.json`	Ordered checkpoint metadata for resume and audit.
`resume_plan.json`	Next-step metadata for chunked continuation.
`diagnostics.json`	`mhx.campaign.rutherford_execution.v1`; start/end step, target step, run controls, `allow_production_claim`, `production_promotion_report_ready`, divergence and energy-growth summaries.
`validation.json`	`mhx.campaign.rutherford_execution.gates.v1`; finite-history, checkpoint, energy, divergence, and movie gates.
`figures/*.png`	Island-width, reconnected-flux, energy-budget, and `current_sheet_aspect_ratio.png` quick-look figures.
`figures/*.gif`	Optional fixed-scale flux and current movies.
`artifact_manifest.json`	Recursive hashes for chunk outputs, including the final `manifest.json`. The top-level `manifest.json` records this file as an output but does not rely on mutually recursive hashes.
`manifest.json`	Top-level claim metadata and output hashes.

mhx campaign rutherford-promotion-check <run-dir> writes a separate promotion bundle under <run-dir>/promotion/ by default:

File	Schema / contents
`promotion_readiness.json`	`mhx.campaign.rutherford_promotion.v1`; target-completion, convergence, seed-QI, movie, geometry, X/O count, reconnecting-flux/island-width response, energy, and divergence promotion diagnostics.
`validation.json`	`mhx.campaign.rutherford_promotion.gates.v1`; pass/fail checks for every promotion gate.
`figures/promotion_matrix.png`	Reviewer-readable pass/fail matrix.
`artifact_manifest.json`	Recursive hashes for the promotion bundle.
`manifest.json`	`claim_level = production` only when all promotion checks pass; otherwise `claim_level = validation`.

Fitted neural ODE¶

mhx neural-ode train --outdir outputs/neural_ode/latent_ode_fast writes:

File	Schema / contents
`latent_ode_model.json`	`mhx.neural_ode.latent_model.v1`; random-feature weights, ridge coefficient matrix, target names, and training controls.
`latent_ode_metrics.json`	`mhx.neural_ode.latent_metrics.v1`; train/validation/test MAE/RMSE and ratio to the best baseline.
`latent_ode_predictions.npz`	Prediction tensor, target tensor, times, seeds, and target names.
`failure_modes.json`	`mhx.neural_ode.failure_modes.v1`; seed-extrapolation and late-vs-early forecast-drift probes.
`dataset.npz`	Frozen deterministic FAST dataset when the train command generated it locally.
`splits.json`	Train/validation/test seed split metadata.
`baseline_metrics.json`	Persistence/linear baseline metrics used in comparisons.
`calibration.json`	Calibration and coverage diagnostics for the deterministic fit.
`experiment_spec.json`	Reproducible experiment controls.
`validation.json`	`mhx.neural_ode.training.gates.v1`; finite-model, finite-prediction, split, held-out forecast, and failure-mode reporting gates.
`manifest.json`	Top-level validation manifest.

The suite also writes:

validation_suite.json: schema mhx.validation.suite.v1, aggregate pass/fail status, jax_enable_x64, case list, per-case validation schemas, checks, and relative paths.
validation_suite.md: reviewer-readable pass/fail summary table.
artifact_manifest.json: recursive checksum manifest for every generated validation artifact.
manifest.json: top-level manifest for the suite summary files.
one subdirectory per case, for example resistive_decay/, harris_delta_prime/, linear_tearing_eigenvalue/, linear_tearing_dispersion/, linear_tearing_layer/, linear_tearing_timedomain/, cosine_equilibrium_linearization/, periodic_current_sheet_eigenvalue/, periodic_current_sheet_timedomain/, periodic_current_sheet_nonlinear_bridge/, periodic_double_harris_nonlinear_growth/, periodic_double_harris_convergence/, nonlinear_energy_budget/, orszag_tang_vortex/, decaying_mhd_turbulence/, forced_turbulent_reconnection/, nonlinear_duration_audit/, seed_robust_qi/, seed_robust_qi_sweep/, neural_ode_reproducibility/, neural_ode_latent_fit/, rutherford_production_execution/, duration_policy/, diffusion_eigenvalue/, power_iteration/, and arnoldi/.

Each validation-suite case includes a claim_level copied from its nested manifest. Most cases are validation; the short linear-tearing smoke run is explicitly smoke.

Campaign-template outputs¶

mhx campaign rutherford-template --outdir outputs/campaigns/rutherford_template writes:

campaign.json: schema mhx.campaign.rutherford_template.v1, generated config, duration assessment, required production outputs, and claim boundary.
campaign_config.toml: long-run TOML template with physics.model = "reduced_mhd_nonlinear_tearing_campaign".
duration_assessment.json: serialized duration guard for the chosen \(\gamma\), e-fold count, and safety factor.
validation.json: pass/fail checks for duration, non-FAST resolution, saved-frame count, and required runtime diagnostics.
manifest.json: top-level claim metadata with claim_level = "production_template".

FAST Rutherford runner outputs¶

mhx campaign rutherford-run-fast --outdir outputs/campaigns/rutherford_fast writes validation-grade campaign artifacts:

rutherford_fast_histories.npz: schema mhx.validation.rutherford_campaign_run.v1, with time, seed, reconnected_flux, rutherford_island_width, reconnection_rate_proxy, magnetic_energy, kinetic_energy, total_energy, magnetic_divergence_linf, and current_density_linf.
diagnostics.json: scalar pass/fail diagnostics and run metadata.
validation.json: finite-value, duration, energy-growth, divergence, and claim-level checks.
campaign_template.json: copy of the production-template requirements used to interpret the FAST run.
figures/rutherford_fast_histories.png: quick-look histories.
manifest.json: top-level claim metadata with claim_level = "validation" unless explicitly configured otherwise.

The schema intentionally mirrors the future long Rutherford campaign history keys, but the FAST runner is not a production nonlinear result.

Seed-robust QI outputs¶

mhx benchmark seed-robust-qi --outdir outputs/benchmarks/seed_robust_qi writes:

diagnostics.json: schema mhx.validation.seed_robust_qi.v1, including sample means, standard deviations, CVs, and gate results.
validation.json: schema mhx.validation.seed_robust_qi.gates.v1, including per-metric pass/fail checks.
ensemble.npz: seed list and full metric samples for gamma_fit, final energies, and magnetic-divergence error.
figures/qi_summary.png: compact metric stability summary when plotting dependencies are available.
manifest.json: top-level claim metadata with claim_level = "validation".

Exact-decay validation outputs¶

mhx benchmark decay --outdir outputs/benchmarks/resistive_decay writes:

diagnostics.json: scalar decay-rate and error diagnostics with schema mhx.validation.resistive_decay.v1.
validation.json: pass/fail physics gates and thresholds.
decay_history.npz: time, numerical/exact amplitude, numerical/exact energy, and relative-error arrays.
figures/decay_amplitude.png, figures/decay_energy.png, and figures/decay_relative_error.png.

Reconnection scaling validation outputs¶

mhx benchmark scaling --outdir outputs/benchmarks/reconnection_scaling writes:

diagnostics.json: fitted and expected log-log slopes with schema mhx.validation.reconnection_scaling.v1.
validation.json: pass/fail slope gates and tolerances.
scaling_history.npz: Lundquist samples and analytic scaling arrays.
figures/fkr_scaling.png, figures/plasmoid_scaling.png, and figures/ideal_tearing_scaling.png.

FKR-window validation outputs¶

mhx benchmark fkr-window --outdir outputs/benchmarks/fkr_window writes:

diagnostics.json: fixed-\(S_a\) FKR constant-\(\psi\) regime-window diagnostics with schema mhx.validation.fkr_window.v1.
validation.json: pass/fail gates for positive \(\Delta'a\), thin inner layer, and \(\Delta'\delta\).
fkr_window.npz: sampled ka, gamma_tau_a, inner_width_a, delta_prime_a, and constant_psi_product arrays.
figures/fkr_constant_psi_window.png: publication-style regime-window plot.

FKR growth-rate validation outputs¶

mhx benchmark fkr-growth --outdir outputs/benchmarks/fkr_growth_rate writes:

diagnostics.json: asymptotic FKR growth-rate diagnostics with schema mhx.validation.fkr_growth_rate.v1.
validation.json: pass/fail gates for the \(S_a^{-3/5}\) slope, \((\Delta'a)^{4/5}\) response, numerical-\(\Delta'\) propagation error, and the constant-\(\psi\) window.
fkr_growth_rate.npz: sampled lundquist, gamma_vs_lundquist, ka, numerical_delta_prime_a, gamma_vs_delta_prime, and gamma_relative_error arrays.
figures/fkr_growth_rate.png: growth-rate scaling and error-gate plot.

Harris Delta-prime validation outputs¶

mhx benchmark harris-delta-prime --outdir outputs/benchmarks/harris_delta_prime writes:

diagnostics.json: numerical Harris outer-region matching diagnostics with schema mhx.validation.harris_delta_prime.v1.
validation.json: pass/fail gates for finite positive \(\Delta'a\), monotonicity, and relative error against the analytic Harris formula.
harris_delta_prime.npz: sampled ka, numerical and analytic delta_prime_a, and relative-error arrays.
figures/harris_delta_prime.png: numerical-vs-analytic matching plot and relative-error gate.

Direct Harris-sheet tearing eigenvalue outputs¶

mhx benchmark linear-tearing-eigenvalue --outdir outputs/benchmarks/linear_tearing_eigenvalue writes:

diagnostics.json: direct 1D Harris-sheet finite-difference tearing eigenvalue diagnostics with schema mhx.validation.linear_tearing_eigenvalue.v1.
validation.json: pass/fail gates for selected growth-rate error, extrapolated growth-rate error, real eigenvalue, eigen-residual, grid convergence, and tearing parity.
linear_tearing_eigenvalue.npz: grid counts, dx, finite-grid growth rates, fitted second-order growth rates, extrapolated/reference growth rates, stable-control wavenumber/max-real-part/residual, selected spectrum real/imaginary parts, normalized flux eigenfunction, and normalized imaginary stream-function eigenfunction.
figures/linear_tearing_eigenvalue.png: grid extrapolation, selected spectrum, and tearing-parity plot.

Finite-domain tearing dispersion outputs¶

mhx benchmark linear-tearing-dispersion --outdir outputs/benchmarks/linear_tearing_dispersion writes:

diagnostics.json: finite-domain Harris-sheet tearing dispersion diagnostics with schema mhx.validation.linear_tearing_dispersion.v1.
validation.json: pass/fail gates for finite eigenvalues, positive growth in the sampled unstable band, no positive growth in stable controls, residuals, and the \(ka=0.5\) reference point.
linear_tearing_dispersion.npz: wavenumber, growth_rate, eigenvalue_imag, residual_norm, reference-point metadata, and boolean masks for unstable samples and stable controls.
figures/linear_tearing_dispersion.png: growth branch, oscillatory stable controls, and residual gate.

Harris tearing eigenfunction-layer outputs¶

mhx benchmark linear-tearing-layer --outdir outputs/benchmarks/linear_tearing_layer writes:

diagnostics.json: FAST Harris eigenfunction-shape diagnostics with schema mhx.validation.linear_tearing_layer.v1.
validation.json: pass/fail gates for positive growth, monotonic flow-layer narrowing with \(S\), outer-flux width stability, broad fitted-slope ranges, and dense eigen-residuals.
linear_tearing_layer.npz: sampled lundquist, growth_rate, stream_half_width, current_half_width, flux_half_width, residual_norm, fitted slopes, flux-width spread, and normalized reference eigenfunction profiles.
figures/linear_tearing_layer.png: growth trend, layer-width trend, reference eigenfunction localization, and residual gate.

Harris tearing time-domain replay outputs¶

mhx benchmark linear-tearing-timedomain --outdir outputs/benchmarks/linear_tearing_timedomain writes:

diagnostics.json: linear time-domain replay diagnostics with schema mhx.validation.linear_tearing_timedomain.v1.
validation.json: pass/fail gates for fitted growth-rate error, RK4 amplitude error against \(\exp(\gamma t)\), final eigenmode alignment, and the selected dense-eigenpair residual.
linear_tearing_timedomain.npz: time, amplitude, exact_amplitude, relative_amplitude_error, fitted_growth_rate, expected_growth_rate, relative_growth_error, final_mode_alignment, selected eigenvalue parts, and selected residual.
figures/linear_tearing_timedomain.png: semilog amplitude replay, fitted-growth plot, and relative-amplitude-error gate.

Linearized-RHS validation outputs¶

mhx benchmark linearized-rhs --outdir outputs/benchmarks/linearized_rhs writes:

diagnostics.json: JVP/finite-difference linearized-RHS consistency metrics with schema mhx.validation.linearized_rhs.v1.
validation.json: pass/fail gates for relative JVP consistency errors.
linearized_rhs.npz: saved JVP and finite-difference psi/omega arrays.
figures/linearized_rhs_errors.png: relative-error plot with the configured gate.

Reduced-MHD linear eigenmode outputs¶

mhx benchmark reduced-mhd-eigenmode --outdir outputs/benchmarks/reduced_mhd_eigenmode writes:

diagnostics.json: zero-state linear eigenmode diagnostics with schema mhx.validation.reduced_mhd_linear_eigenmode.v1.
validation.json: pass/fail gates for resistive \(\psi\) and viscous \(\omega\) Fourier diffusion eigenvalues and residuals.
reduced_mhd_linear_eigenmode.npz: saved eigenfunctions, flattened operator actions, expected eigenvalues, and measured Rayleigh quotients.
figures/reduced_mhd_linear_eigenmode_errors.png: eigenvalue/residual error plot.

Cosine-equilibrium linearization outputs¶

mhx benchmark cosine-equilibrium-linearization --outdir outputs/benchmarks/cosine_equilibrium_linearization writes:

diagnostics.json: analytic nonzero-equilibrium linearized-RHS diagnostics with schema mhx.validation.cosine_equilibrium_linearization.v1.
validation.json: pass/fail gates for flow-to-flux and magnetic-tension coupling errors around \(\psi_0=A\cos y\).
cosine_equilibrium_linearization.npz: numerical and analytic JVP arrays for the selected flow and flux perturbations.
figures/cosine_equilibrium_linearization_errors.png: relative-error plot.

Periodic current-sheet eigenvalue outputs¶

mhx benchmark current-sheet-eigenvalue --outdir outputs/benchmarks/periodic_current_sheet_eigenvalue writes:

diagnostics.json: tiny dense-spectrum diagnostics with schema mhx.validation.periodic_current_sheet_eigenvalue.v1.
validation.json: pass/fail gates for gauge residuals, non-gauge damping, spurious positive growth, and selected dense-eigenpair residual.
periodic_current_sheet_eigenvalue.npz: dense operator matrix, eigenvalue real/imaginary parts, selected eigenvector real/imaginary parts, residual, and leading-real-part diagnostics.
figures/periodic_current_sheet_spectrum.png: complex spectrum and selected-eigenpair residual plot.

Periodic current-sheet time-domain outputs¶

mhx benchmark current-sheet-timedomain --outdir outputs/benchmarks/periodic_current_sheet_timedomain writes:

diagnostics.json: RK4 eigenmode replay diagnostics with schema mhx.validation.periodic_current_sheet_timedomain.v1.
validation.json: pass/fail gates for spectrum consistency, real decaying mode selection, dense-eigenpair residual, full-state replay error, and fitted decay-rate error.
periodic_current_sheet_timedomain.npz: saved time, numerical and exact amplitudes, relative state errors, selected/fitted decay rates, residuals, and initial/final psi and omega fields.
figures/periodic_current_sheet_timedomain.png: semilog amplitude replay and relative full-state error against the configured gate.

Nonlinear current-sheet bridge outputs¶

mhx benchmark current-sheet-nonlinear-bridge --outdir outputs/benchmarks/periodic_current_sheet_nonlinear_bridge writes:

diagnostics.json: nonlinear trajectory-map differentiability diagnostics with schema mhx.validation.periodic_current_sheet_nonlinear_bridge.v1.
validation.json: pass/fail gates for finite positive errors, monotonic centered-difference convergence, second-order slope, finest-error tolerance, and nonzero tangent norm.
periodic_current_sheet_nonlinear_bridge.npz: saved epsilon, relative_error, fitted convergence_order, tangent norm, perturbation fields, and final tangent fields.
figures/periodic_current_sheet_nonlinear_bridge.png: log-log convergence plot against an \(O(\epsilon^2)\) guide and the configured slope/error gates.

Periodic double-Harris nonlinear-growth outputs¶

mhx benchmark double-harris-growth --outdir outputs/benchmarks/periodic_double_harris_nonlinear_growth writes:

diagnostics.json: nonlinear growth diagnostics with schema mhx.validation.periodic_double_harris_nonlinear_growth.v1.
validation.json: pass/fail gates for a finite dense spectrum/history, positive unstable eigenvalue, small eigen-residual, nonlinear perturbation growth factor, positive fitted growth, and fitted-vs-eigenvalue error.
periodic_double_harris_nonlinear_growth.npz: saved dense eigenvalue spectrum, selected eigenvector/eigenvalue, time, perturbation norm, expected frozen-linear norm, fitted growth rate, growth factor, and base/perturbed final fields.
figures/periodic_double_harris_nonlinear_growth.png: semilog nonlinear growth history with fitted and frozen-linear references plus initial/final flux panels.

Periodic double-Harris seeded long-run outputs¶

mhx benchmark double-harris-long-run --outdir outputs/benchmarks/periodic_double_harris_seeded_long_run writes:

diagnostics.json: scalable seeded nonlinear replay diagnostics with schema mhx.validation.periodic_double_harris_seeded_long_run.v1.
validation.json: pass/fail gates for finite histories, full-duration completion, sample count, early growth, visible amplification, dominant reconnecting-flux response, Rutherford-width response, and dissipative total-energy behavior.
periodic_double_harris_seeded_long_run.npz: saved time, normalized perturbed-minus-base norm, dominant reconnecting-flux proxy reconnected_flux, configured-mode proxy seed_mode_reconnected_flux, Rutherford-width proxy rutherford_island_width, dominant Fourier-mode indices, X/O critical-point counts, magnetic/kinetic/total energy, peak current density, fitted early growth rate, base/perturbed trajectories, and initial states.
figures/periodic_double_harris_seeded_long_run.png: early-growth, energy, current-density, reconnection-proxy, flux, and perturbed-minus-base morphology panels.
Optional figures/periodic_double_harris_flux.gif and figures/periodic_double_harris_current.gif when --movies is supplied.

Periodic double-Harris convergence outputs¶

mhx benchmark double-harris-convergence --outdir outputs/benchmarks/periodic_double_harris_convergence writes:

diagnostics.json: convergence scaffold diagnostics with schema mhx.validation.periodic_double_harris_convergence.v1, including resolutions, dt_values, thresholds, per-case metrics, and spread statistics.
validation.json: pass/fail gates for finite case metrics, successful subcases, positive early growth, dissipative energy, and bounded resolution/time-step spread in growth rate, maximum amplification, reconnecting-flux amplification, and Rutherford-width amplification.
periodic_double_harris_convergence.npz: stable keys schema, case_kind, resolution, dt, samples, fitted_early_growth_rate, early_growth_factor, max_growth_factor, reconnected_flux_amplification, island_width_amplification, relative_energy_increase, max_current_density_linf, and max_kinetic_energy.
figures/periodic_double_harris_convergence.png: resolution/time-step gamma_fit, nonlinear amplification, energy, and peak-current panels.

Periodic double-Harris parameter-sweep outputs¶

mhx benchmark double-harris-parameter-sweep --outdir outputs/benchmarks/periodic_double_harris_parameter_sweep writes:

diagnostics.json: parameter-sweep diagnostics with schema mhx.validation.periodic_double_harris_parameter_sweep.v1, including sweep_axis, case labels, fixed baseline parameters, per-case response metrics, and anomaly-scale spread statistics.
validation.json: pass/fail gates for finite case metrics, at least three cases, successful subcase gates, positive early growth, visible nonlinear response, reconnecting-flux amplification, island-width amplification, dissipative energy, and bounded anomaly spreads.
periodic_double_harris_parameter_sweep.npz: stable keys schema, sweep_axis, case_index, case_label, mode_x, mode_y, width, resistivity, viscosity, dt, t_end, save_every, samples, passed, fitted_early_growth_rate, early_growth_factor, max_growth_factor, reconnected_flux_amplification, seed_mode_reconnected_flux_amplification, island_width_amplification, relative_energy_increase, max_current_density_linf, max_kinetic_energy, max_x_point_count, max_o_point_count, growth_rate_spread, and max_growth_spread.
figures/periodic_double_harris_parameter_sweep.png: fitted-growth, amplification, energy, current-density, and X/O-count panels.

Periodic double-Harris promotion report¶

mhx benchmark double-harris-promotion-check <run-dir> --convergence-dir <dir> writes <run-dir>/promotion/ by default:

promotion_readiness.json: schema mhx.validation.periodic_double_harris_promotion.v1; includes the long-run history schema, terminal time, response amplifications, X/O counts, convergence-evidence status, thresholds, and pass/fail checks.
validation.json: schema mhx.validation.periodic_double_harris_promotion.gates.v1; this is a promotion-to-validation gate, not a production Rutherford/plasmoid gate.
figures/promotion_matrix.png: reviewer-readable matrix of every promotion check.
manifest.json and artifact_manifest.json: checksummed report metadata.

Nonlinear energy-budget outputs¶

mhx benchmark nonlinear-energy-budget --outdir outputs/benchmarks/nonlinear_energy_budget writes:

diagnostics.json: nonlinear reduced-MHD budget diagnostics with schema mhx.validation.nonlinear_energy_budget.v1.
validation.json: pass/fail gates for finite arrays, nontrivial nonlinear RHS activity, nonincreasing total energy, integrated budget residual, net dissipation, and positive dissipation.
nonlinear_energy_budget.npz: saved time, magnetic/kinetic/total energy, resistive and viscous dissipation channels, cumulative dissipation, budget_residual, relative_budget_residual, nonlinear-RHS ratio, initial fields, and final fields.
figures/nonlinear_energy_budget.png: energy-vs-integrated-dissipation, relative budget residual, dissipation channels, and initial/final flux contours.

Nonlinear duration-audit outputs¶

mhx benchmark nonlinear-duration-audit --outdir outputs/benchmarks/nonlinear_duration_audit writes:

diagnostics.json: runtime-window audit diagnostics with schema mhx.validation.nonlinear_duration_audit.v1.
validation.json: pass/fail gates confirming that current FAST nonlinear runs are explicitly flagged as too short for nonlinear island/plasmoid claims and that production target windows are recorded.
nonlinear_duration_audit.npz: saved current_case_names, current_end_times, target_names, target_end_times, plasmoid_lundquist, plasmoid_efold_times, harris_growth_rate, and requested_linear_efolds.
figures/nonlinear_duration_audit.png: log-time comparison of current FAST run durations, target nonlinear windows, and plasmoid linear e-fold estimates.

Duration-policy outputs¶

mhx benchmark duration-policy --outdir outputs/benchmarks/duration_policy writes:

duration_policy.json: schema mhx.duration_policy.v1, current and future duration assessments, growth rates, required e-folds, required final times, observed e-folds, sufficient_for_intended_scope, sufficient_for_production_claim, sufficient_for_nonlinear_claim, and claim-boundary actions.
duration_policy.md: reviewer-readable table generated from the same JSON.
validation.json: pass/fail gates confirming that current short runs are validation-only and future production templates are long enough for their declared e-fold targets.
manifest.json: hashes for all duration-policy artifacts.

Diffusion eigenvalue validation outputs¶

mhx benchmark diffusion-eigenvalue --outdir outputs/benchmarks/diffusion_eigenvalue writes:

diagnostics.json: Rayleigh-quotient and eigen-residual diagnostics with schema mhx.validation.diffusion_eigenvalue.v1.
validation.json: pass/fail gates for eigenvalue and residual errors.
diffusion_eigenvalue.npz: saved eigenfunction, operator action, expected eigenvalue, and measured Rayleigh quotient.
figures/diffusion_eigenvalue_errors.png: eigenvalue/residual error plot.

Power-iteration validation outputs¶

mhx benchmark power-iteration --outdir outputs/benchmarks/power_iteration writes:

diagnostics.json: dominant-eigenpair diagnostics with schema mhx.validation.power_iteration.v1.
validation.json: pass/fail gates for dominant eigenvalue and residual errors.
power_iteration_history.npz: saved iteration index, Rayleigh-quotient history, residual history, and expected dominant eigenvalue.
figures/power_iteration_history.png: convergence history plot.

Arnoldi validation outputs¶

mhx benchmark arnoldi --outdir outputs/benchmarks/arnoldi writes:

diagnostics.json: Krylov Ritz-spectrum diagnostics with schema mhx.validation.arnoldi.v1.
validation.json: pass/fail gates for fixture Ritz-value, imaginary-part, and residual-estimate errors.
arnoldi_spectrum.npz: expected eigenvalues, measured Ritz values, Arnoldi residual estimates, and the projected Hessenberg matrix.
figures/arnoldi_ritz_values.png: complex-plane Ritz spectrum and residual estimate plot.

Timing benchmark outputs¶

mhx benchmark timing --outdir outputs/benchmarks/timing writes:

timing.json: schema mhx.benchmark.timing.v1, raw repeat durations, median/min/max summaries, Python tracemalloc peaks, case details, and environment metadata.
timing.md: reviewer-readable Markdown timing table.
figures/timing_summary.png: wall-clock and Python-allocation summary plot.
manifest.json: schema mhx.manifest.v1, output paths, and SHA-256 hashes.

Absolute timings are machine-dependent. The schema is meant for artifact comparison across commits on the same runner class, not as a universal performance guarantee.

Neural-ODE reproducibility outputs¶

mhx neural-ode dataset --outdir outputs/neural_ode/seed_qi_fast writes a deterministic no-training bundle for future neural-ODE work:

File	Schema	Meaning
`dataset.npz`	`mhx.neural_ode.dataset.v1`	Seed-QI trajectory tensor, target tensor, times, seeds, and feature names.
`splits.json`	`mhx.neural_ode.splits.v1`	Disjoint train/validation/test seed IDs and split checks.
`baseline_metrics.json`	`mhx.neural_ode.baselines.v1`	Persistence, linear-prefix, and train-mean MAE/RMSE scores.
`calibration.json`	`mhx.neural_ode.calibration.v1`	Empirical 1-sigma and 2-sigma residual coverage.
`experiment_spec.json`	`mhx.neural_ode.experiment_spec.v1`	Reviewer-facing experiment contract and future neural-ODE requirements.
`validation.json`	`mhx.neural_ode.reproducibility.gates.v1`	Gate summary tying seed-QI validation, splits, baselines, and calibration together.
`manifest.json`	`mhx.manifest.v1`	Hashes and `claim_level = "validation"`.

dataset.npz keys are schema, seeds, times, features, targets, feature_names, target_names, diagnostics_json, and source_diagnostics_json. The v1 array convention is features[n_seed, n_time, n_feature] and targets[n_seed, n_time, n_target].

Benchmark catalog outputs¶

mhx benchmark catalog --outdir outputs/benchmarks/catalog writes:

benchmark_catalog.json: schema mhx.benchmark_catalog.v1, active FAST validation entries, commands, output schemas, expected files, and literature anchors.
benchmark_catalog.md: reviewer-readable table generated from the same catalog entries.
manifest.json: hashes for the generated catalog files.