Implement Bernstein's breakdown for the perturbed potential energy

.gitignore

@@ -31,6 +31,7 @@ docs/_build/
 docs/examples/*/gal_solution.dat
 docs/examples/*/delta_gw.dat
 docs/examples/*/gal_solution_cut.dat
+docs/examples/DIIID_ideal_example/*.py
 
 deps/bin/*
 deps/hdf5
@@ -53,3 +54,16 @@ sum/sum
 xdraw/pspack
 xdraw/xdraw
 slayer/slayer
+
+*.aux
+*.blg
+*.bbl
+*.fdb_latexmk
+*.fls
+*.log
+*.synctex.gz
+*.pdf
+*.png
+
+# keep the figure included by docs/tex/recon/main.tex
+!docs/tex/recon/QvsC_quant_n1.png

docs/examples/DIIID_ideal_example/gpec.in

@@ -87,4 +87,4 @@
 &GPEC_DIAGNOSE
    timeit=t                 ! Print timer splits for major subroutines
    radvar_flag=f            ! Map various radial variables (rho,psi_tor) on psi_n grid
-/
+/

docs/examples/solovev_ideal_example/gpec.in

@@ -1,13 +1,13 @@
 &GPEC_INPUT
-   dcon_dir   = './'                 ! Path to DCON outputs. Individual file paths are appended to this
+   dcon_dir   = ''                   ! Path to DCON outputs. Individual file paths are appended to this
    idconfile  = 'euler.bin'          ! Eigenfunctions output by DCON run
    ieqfile    = 'psi_in.bin'         ! Flux surfaces output by DCON run
    rdconfile  = 'globalsol.bin'      ! Galerkin eigenfunctions output by resistive DCON run
 
    gal_flag = f             ! Use the Galerkin eigenfunctions from resistive DCON instead of the ideal DCON shooting method solutions
 
-   jac_in="pest"            ! Coordinate system of external perturbation (affects data_flag and harmonic_flag). Options include: pest,boozer,hamada
-   jsurf_in=0               ! True(1) if external perturbation is area weighted (i.e. flux)
+   jac_in="hamada"            ! Coordinate system of external perturbation (affects data_flag and harmonic_flag). Options include: pest,boozer,hamada
+   jsurf_in=1               ! True(1) if external perturbation is area weighted (i.e. flux)
    tmag_in =0               ! True(1) if external perturbation has toroidal angle defined by jac_in. False(0) if machine angle.
    mthsurf =0               ! Number of poloidal angle gridpoints. Minimum of twice the Nyquist condition from DCON m limits is enforced.
 
@@ -28,7 +28,7 @@
    displacement_flag=f      ! Perturbations are displacement (m). Default is field (T).
    fixed_boundary_flag=f    ! Total perturbation = external perturbation
 
-   mode_flag = t          ! Return only a single DCON eigenfunction defined by mode (ignores external pert.)
+   mode_flag = .T.          ! Return only a single DCON eigenfunction defined by mode (ignores external pert.)
    mode  = 1                ! DCON eigen function index (1 is least stable)
    filter_types = 'w'       ! Isolate the filter_modes of energy (w), reluctance (r), permiability (p) or singular coupling (s) eigenvectors/singular-vectors
    filter_modes = 0         ! Number of modes isolated, negative values isolate backwards from the last mode
@@ -47,28 +47,29 @@
    use_classic_splines = f  ! Use a classical cubic spline instead of tri-diagonal solution for splines with extrapolation boundary conditions
 /
 &GPEC_OUTPUT
-   jac_out="pest"           ! Coordinate system of outputs
+   jac_out="hamada"         ! Coordinate system of outputs
    jsurf_out=0              ! True(1) for area weighted outputs (only appends standard gpec_control output)
    tmag_out=1               ! True(1) for magnetic toroidal angle outputs (affects singcoup and singfld, appends gpec_control)
    mlim_out=64              ! If positive, Fourier decomposed outputs will span -mlim_out<=m<=mlim_out. Default (<=0) outputs on internal m range.
 
-   resp_flag=t              ! Output energy, reluctance, inductance, and permeability eigenvalues, eigenvectors, and matrices
-   filter_flag=t            ! Outputs energy, reluctance, permeability, and (optionally) the singular-coupling eigenmodes on the control surface
+   resp_flag=f              ! Output energy, reluctance, inductance, and permeability eigenvalues, eigenvectors, and matrices
+   filter_flag=f            ! Outputs energy, reluctance, pereability, and (optionally) the singular-coupling eigenmodes on the control surface
    singcoup_flag=f          ! Calculate coupling of each m to resonant surfaces
-   singfld_flag=t           ! Output of resonant surface quantities (flux,current,etc.)
+   singfld_flag=f           ! Output of resonant surface quantities (flux,current,etc.)
    vsingfld_flag=f          ! Output of vacuum resonant surface quantities
+   singthresh_flag=f        ! Calculate Callen resonant field penetration threshold (requires kinetic profiles from pentrc.in)
 
    pmodb_flag=f             ! Outputs delta-B_Lagrangian
-   xbnormal_flag=t          ! Outputs normal displacement and field in plasma
+   xbnormal_flag=f          ! Outputs normal displacement and field in plasma
    vbnormal_flag=f          ! Outputs vacuum normal displacement and field in plasma
-   xclebsch_flag=t          ! Outputs clebsch coordinate displacement for PENT
+   xclebsch_flag=f          ! Outputs clebsch coordinate displacement for PENT
    dw_flag=f                ! Outputs self-consistent energy and torque profiles (when kin_flag=t from DCON)
 
    eqbrzphi_flag=f          ! Outputs equilibrium field on regular (r,z) grid
-   brzphi_flag=t            ! Outputs perturbed field on regular (r,z) grid
+   brzphi_flag=f            ! Outputs perturbed field on regular (r,z) grid
    xrzphi_flag=f            ! Outputs displacement on regular (r,z) grid
    vbrzphi_flag=f           ! Outputs field on regular (r,z) grid due to total boundary surface current (not a real field)
-   vvbrzphi_flag=f          ! Outputs field on regular (r,z) grid due to external perturbation surface current (not a real field)
+   vvbrzphi_flag=f          ! Outputs field on regular (r,z) grid due to exeternal perturbation surface current (not a real field)
    vsbrzphi_flag=f          ! Outputs the field on regular (r,z) grid due to singular surface currents
    ss_flag(3)=f             ! Outputs the field on regular (r,z) grid due to the 3rd singular surface current, etc.
    xbrzphifun_flag=f        ! Outputs r,z, and perturbation vectors on psi,theta grid
@@ -82,8 +83,11 @@
    bin_2d_flag=f            ! Write 2D binary outputs for use with xdraw
    max_linesout=0           ! Maximum length of ascii data tables enforced by increasing radial step size (iff .gt. 0).
    verbose=t                ! Print run log to terminal
+
+   recon_flag=t
+   netcdf_flag=t
 /
 &GPEC_DIAGNOSE
-   timeit=f                 ! Print timer splits for major subroutines
+   timeit=t                 ! Print timer splits for major subroutines
    radvar_flag=f            ! Map various radial variables (rho,psi_tor) on psi_n grid
 /