ANALYSIS - Add equilibrium, stability, and PE visualization toolkit#198
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…tion toolkit New component and summary plot functions across three Analysis submodules: ForceFreeStates (src/Analysis/ForceFreeStates.jl): - plot_energy_eigenvectors: heatmap of |Wt| eigenvectors vs (m, mode index) - plot_eigenvalue_spectrum: eigenvalue scatter colored by stability (red/green) - plot_delta_prime: |Δ'| bar chart from FFS asymptotic coefficients (ca_left/ca_right) - plot_dcon_summary: 4-panel composer (eigenvectors, criterion, spectrum, Δ') - plot_singular_surfaces: 2-panel composer (q-profile with surface markers, Δ') Equilibrium (src/Analysis/Equilibrium.jl): - plot_qprofile: q(ψ) with rational surface overlays - plot_pressure_profile: μ₀p(ψ) - plot_f_profile: 2πF(ψ) - plot_equilibrium_summary: 3-panel composer (q, pressure, F profiles) PerturbedEquilibrium (src/Analysis/PerturbedEquilibrium.jl, new file): - plot_resonant_flux, plot_island_widths, plot_chirikov_parameter, plot_pe_delta_prime - plot_resonant_field: 5-panel composer of resonant coupling quantities - plot_mode_spectrogram: 2-panel line+heatmap spectrogram (xi_psi/b_psi/b_theta/b_zeta) - plot_perturbed_equilibrium_summary: 3-panel composer (islands, energies, spectrogram) PE HDF5 output (src/PerturbedEquilibrium/Utils.jl): - Write resonant_flux, resonant_current, island_width_sq, penetrated_field, delta_prime (ComplexF64), island_half_width and chirikov_parameter (Float64) to singular_coupling group Updated all analyze_example.jl scripts to demonstrate the new functions. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…x, response shape - ForceFreeStates: Replace hline! with vline! in plot_eigenvalue_spectrum (stability boundary is Re(eigenvalue)=0, a vertical line, not horizontal) - ForceFreeStates: Replace invalid annotate!(p, :center, :top, ...) with title! in plot_dcon_summary (no-vacuum-data branch); :center/:top are not data coords - ForceFreeStates: Add inline note explaining imag(xi_psi) phase convention - PerturbedEquilibrium: Fix plot_resonant_flux, plot_pe_delta_prime, _plot_resonant_current to read PE forcing mode n from perturbed_equilibrium/forcing_modes/n instead of info/mn_index (FFS). PE coupling matrices are (num_forcing_modes, msing), not (numpert_total_FFS, msing) - PerturbedEquilibrium: Fix plot_mode_spectrogram data layout and psi axis. Response data is (npsi, numpert_total) not (numpert_total, npsi); psi axis is integration/psi (737 pts), not splines/profiles/xs (183 pts) - PerturbedEquilibrium: Fix plot_perturbed_equilibrium_summary docstring to match implementation (no Chirikov overlay on island-width panel) - Add examples/DIIID-like_ideal_example/make_plots.jl: saves all 20 plots to examples/DIIID-like_ideal_example/plots/ using GR backend Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…, and spacing fixes - plot_mode_spectrogram: flip heatmap to (m, ψ_N) with psi on vertical axis (conventional spectrogram orientation); rational surface overlays use hline! - plot_mode_spectrogram: trim line plot legend to m ∈ [0, nhigh·q95) to avoid unwieldy legend from negative/high-m modes outside the resonant range - All plots: add left_margin, bottom_margin, right_margin (Plots.mm) throughout to prevent axis labels, rotated xtick text, and colorbar titles from clipping - plot_equilibrium_summary: increase size to (1300, 450), add top_margin for plot_title clearance; reduce plot_titlefontsize to avoid overlap - Summary plots: adjust sizes to give subpanels more breathing room Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…coloring - plot_eigenmode_summary: align top eigenvector bar with heatmap x-axis using @layout [a{0.25h} _{0.25w}; b c{0.25w}] (blank cell preserves column widths) - plot_eigenmode_summary: color scatter by sign (red=negative, blue=positive) and add markerstrokewidth=0 to remove black rings from dots - plot_eigenvalue_spectrum: apply same color convention (red=negative/unstable, blue=positive/stable) instead of previous red/green Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…onversions, new equilibrium panels - Eigenmode summary (ffs_eigenmode_summary): removed from make_plots (redundant with ffs_summary) - ffs_dcon_summary → ffs_summary; eigenvalue plot replaced with mode displacement (|ξ_ψ| vs ψ_N) - All bar charts (Δ', resonant flux/current, island widths, Chirikov) converted to scatter plots on ψ_N axis with integer-q annotations - plot_delta_prime: shows Re(Δ') with sign coloring and zero reference line - Equilibrium summary: tall RZ panel (left column), profiles stacked right; x-axes share [0,1] range; upper panels suppress redundant x-axis labels - plot_flux_surfaces_h5: rational surfaces drawn as red closed contours with q labels - plot_f_profile: rational surface vlines added (consistent with q and P plots) - GSE panels: log-scale y-axis; integrated error overplotted on theta-slice panel; single legend entry - All ψ_N labels use LaTeXStrings (L"\psi_N"); |ξ_ψ| and |D_c| similarly subscripted - Profile plot titles removed (y-axis labels carry the information) - Stability criterion: ylabel/title updated to |D_c|, zero reference line added - PlotlyJS and LaTeXStrings added to Project.toml - CLAUDE.md: note added to never remove packages from Project.toml Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…nd alignment Remove titles from all 5 subplots in plot_resonant_field (ylabels carry the same information). Move outertopright legends inside (:topright) for the top 3 panels so all 5 panels share the same right margin and x-axes align. Suppress x-axis labels and ticks on the top 4 panels; only the bottom (Chirikov) panel shows the x-axis. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…reason and fixes some labels, xlims, etc.
…o analyze scripts, increase margins and fix colorbar overlap Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Documenter was failing with missing_docs error because all PerturbedEquilibrium analysis functions had docstrings but no @autodocs block in analysis.md. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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No main src changes here - anything is an improvement over what we had before and everyone should feel empowered to improve any/all plots as we go. API is bound to change for PE stuff, so I am not going to waste anyone's time asking for reviews now. |
logan-nc
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Apr 2, 2026
Incorporates: - PR #207: FastInterpolations v0.4 API (Series() wrappers, ZeroCurvBC, remove explicit defaults) - PR #208: Separatrix finder Brent method fix - PR #198: Analysis module improvements (plot_eigenvalues, plot_delta_prime, plot_ffs_summary) - AdaptiveArrayPools v0.3.5, FastInterpolations v0.4.7 Conflict resolved in src/Analysis/ForceFreeStates.jl: retained our plot_edge_stability_scan alongside develop's new plot_eigenvalues, plot_delta_prime, and plot_ffs_summary functions. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
Analysissubmodules, each implemented as a standalone component callable independently or composed into summary plotsAnalysis.PerturbedEquilibriumsubmodule for resonant coupling and island visualizationPerturbedEquilibrium/Utils.jlto write full singular coupling matrices to HDF5 (previously only scalars were written)analyze_example.jlscripts to demonstrate the new functionsNew functions
Analysis.ForceFreeStates(component → summary pattern):plot_energy_eigenvectors(h5path; matrix_type=:total)— heatmap of |Wₜ| eigenvectorsplot_eigenvalue_spectrum(h5path; matrix_type=:total/:plasma/:vacuum)— eigenvalue scatter colored by stabilityplot_delta_prime(h5path)— |Δ'| bar chart from FFS asymptotic coefficientsplot_dcon_summary(h5path)— 4-panel composer (eigenvectors, criterion, spectrum, Δ')plot_singular_surfaces(h5path)— 2-panel composer (q-profile with surface markers, Δ')Analysis.Equilibrium:plot_qprofile(h5path; show_singular=true)— q(ψ) with optional rational surface overlaysplot_pressure_profile(h5path)— μ₀p(ψ)plot_f_profile(h5path)— 2πF(ψ)plot_equilibrium_summary(h5path)— 3-panel composerAnalysis.PerturbedEquilibrium(new submodule):plot_resonant_flux,plot_island_widths,plot_chirikov_parameter,plot_pe_delta_primeplot_resonant_field(h5path)— 5-panel composer of resonant coupling quantitiesplot_mode_spectrogram(h5path; component=:xi_psi/:b_psi/:b_theta/:b_zeta)— line + heatmap spectrogramplot_perturbed_equilibrium_summary(h5path)— 3-panel composer (islands, energies, spectrogram)OMFIT plots ported and not ported
Ported
plot_dcon_summary.pyplot_dcon_summary+ component functionsAnalysis.ForceFreeStatesplot_equil_summary.py(profiles)plot_equilibrium_summary+ component functionsAnalysis.Equilibriumplot_resonant_field.pyplot_resonant_field+ component functionsAnalysis.PerturbedEquilibriumplot_spectrograms.pyplot_mode_spectrogramAnalysis.PerturbedEquilibriumplot_singular_surfaces,plot_perturbed_equilibrium_summaryNot ported
PENTRC/NTV not implemented in Julia:
plot_torque.py,plot_torque_summary.py,plot_torque_matrices.py,plot_torque_by_coil.py— require NTV torque output (T_xe,T_coil) not computed in Julia GPECRequires outputs not yet in Julia:
plot_resonant_coupling.py,plot_resonant_coupling_matrix.py— require control surface coupling matrixC_xeplot_control_1d/2d.py,plot_control_mode_coil_summary.py— require coil decomposition matricesplot_field_at_wall.py— requires cylindrical (wall-projected) outputplot_reluctance_matrix.py— requires reluctance matrixR_xeplot_stride_summary.py— requires full STRIDE Δ' matrix (available inedge_jacobianbranch, not yet merged)3D visualization (Mayavi-based, no Plots.jl equivalent):
plot_3d_basics.py,plot_gpec_wall.py,plot_gpec_coils.py,plot_control_modes_3d.py,plot_control_3d.pyInput profiles (not GPEC output):
plot_profiles.py— kinetic input profiles (n_e, T_i, T_e, ω_E), not from gpec.h5Already covered:
plot_equilibrium.py— flux surfaces covered by existingAnalysis.Equilibrium.plot_flux_surfacesTest plan
julia --project=. examples/Solovev_ideal_example/analyze_example.jl— verify all new plot calls execute without errorjulia --project=. examples/DIIID-like_ideal_example/analyze_example.jl— verify FFS summary plots render; PE plots should gracefully return "no data" plots if PE not enabledjulia --project=. -e 'using Test; using GeneralizedPerturbedEquilibrium; include("test/runtests_fullruns.jl")'🤖 Generated with Claude Code